0s autopkgtest [03:40:25]: starting date and time: 2025-05-04 03:40:25+0000 0s autopkgtest [03:40:25]: git checkout: 9986aa8c Merge branch 'skia/fix_network_interface' into 'ubuntu/production' 0s autopkgtest [03:40:25]: host juju-7f2275-prod-proposed-migration-environment-21; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.4m0zqsy4/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:joblib,src:sphinx --apt-upgrade spades --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=joblib/1.4.2-4 sphinx/8.2.3-1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-cpu2-ram4-disk20-amd64 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-21@sto01-2.secgroup --name adt-questing-amd64-spades-20250504-034025-juju-7f2275-prod-proposed-migration-environment-21-a59e9744-b842-404b-b37a-ee2f7455a8a1 --image adt/ubuntu-questing-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-21 --net-id=net_prod-autopkgtest-workers-amd64 -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 54s autopkgtest [03:41:19]: testbed dpkg architecture: amd64 54s autopkgtest [03:41:19]: testbed apt version: 3.0.0 54s autopkgtest [03:41:19]: @@@@@@@@@@@@@@@@@@@@ test bed setup 54s autopkgtest [03:41:19]: testbed release detected to be: None 55s autopkgtest [03:41:20]: updating testbed package index (apt update) 55s Get:1 http://ftpmaster.internal/ubuntu questing-proposed InRelease [110 kB] 55s Hit:2 http://ftpmaster.internal/ubuntu questing InRelease 55s Hit:3 http://ftpmaster.internal/ubuntu questing-updates InRelease 55s Hit:4 http://ftpmaster.internal/ubuntu questing-security InRelease 55s Get:5 http://ftpmaster.internal/ubuntu questing-proposed/multiverse Sources [33.2 kB] 55s Get:6 http://ftpmaster.internal/ubuntu questing-proposed/universe Sources [1375 kB] 56s Get:7 http://ftpmaster.internal/ubuntu questing-proposed/main Sources [141 kB] 56s Get:8 http://ftpmaster.internal/ubuntu questing-proposed/main amd64 Packages [193 kB] 56s Get:9 http://ftpmaster.internal/ubuntu questing-proposed/main i386 Packages [137 kB] 56s Get:10 http://ftpmaster.internal/ubuntu questing-proposed/universe i386 Packages [567 kB] 56s Get:11 http://ftpmaster.internal/ubuntu questing-proposed/universe amd64 Packages [1419 kB] 56s Get:12 http://ftpmaster.internal/ubuntu questing-proposed/multiverse amd64 Packages [51.1 kB] 56s Get:13 http://ftpmaster.internal/ubuntu questing-proposed/multiverse i386 Packages [26.8 kB] 56s Fetched 4055 kB in 1s (4286 kB/s) 57s Reading package lists... 57s autopkgtest [03:41:22]: upgrading testbed (apt dist-upgrade and autopurge) 57s Reading package lists... 58s Building dependency tree... 58s Reading state information... 58s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 58s Starting 2 pkgProblemResolver with broken count: 0 58s Done 58s Entering ResolveByKeep 58s 58s Calculating upgrade... 58s The following packages will be upgraded: 58s libperl5.40 perl perl-base perl-modules-5.40 58s 4 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 58s Need to get 10.2 MB of archives. 58s After this operation, 0 B of additional disk space will be used. 58s Get:1 http://ftpmaster.internal/ubuntu questing-proposed/main amd64 libperl5.40 amd64 5.40.1-3 [4877 kB] 59s Get:2 http://ftpmaster.internal/ubuntu questing-proposed/main amd64 perl amd64 5.40.1-3 [262 kB] 59s Get:3 http://ftpmaster.internal/ubuntu questing-proposed/main amd64 perl-base amd64 5.40.1-3 [1840 kB] 59s Get:4 http://ftpmaster.internal/ubuntu questing-proposed/main amd64 perl-modules-5.40 all 5.40.1-3 [3217 kB] 59s Fetched 10.2 MB in 1s (14.6 MB/s) 59s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 80517 files and directories currently installed.) 59s Preparing to unpack .../libperl5.40_5.40.1-3_amd64.deb ... 59s Unpacking libperl5.40:amd64 (5.40.1-3) over (5.40.1-2ubuntu0.1) ... 60s Preparing to unpack .../perl_5.40.1-3_amd64.deb ... 60s Unpacking perl (5.40.1-3) over (5.40.1-2ubuntu0.1) ... 60s Preparing to unpack .../perl-base_5.40.1-3_amd64.deb ... 60s Unpacking perl-base (5.40.1-3) over (5.40.1-2ubuntu0.1) ... 60s Setting up perl-base (5.40.1-3) ... 60s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 80517 files and directories currently installed.) 60s Preparing to unpack .../perl-modules-5.40_5.40.1-3_all.deb ... 60s Unpacking perl-modules-5.40 (5.40.1-3) over (5.40.1-2ubuntu0.1) ... 60s Setting up perl-modules-5.40 (5.40.1-3) ... 60s Setting up libperl5.40:amd64 (5.40.1-3) ... 60s Setting up perl (5.40.1-3) ... 60s Processing triggers for man-db (2.13.0-1) ... 60s Processing triggers for libc-bin (2.41-6ubuntu1) ... 61s Reading package lists... 61s Building dependency tree... 61s Reading state information... 61s Starting pkgProblemResolver with broken count: 0 61s Starting 2 pkgProblemResolver with broken count: 0 61s Done 61s Solving dependencies... 61s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 63s autopkgtest [03:41:28]: testbed running kernel: Linux 6.14.0-15-generic #15-Ubuntu SMP PREEMPT_DYNAMIC Sun Apr 6 15:05:05 UTC 2025 63s autopkgtest [03:41:28]: @@@@@@@@@@@@@@@@@@@@ apt-source spades 65s Get:1 http://ftpmaster.internal/ubuntu questing/universe spades 3.15.5+dfsg-8 (dsc) [2439 B] 65s Get:2 http://ftpmaster.internal/ubuntu questing/universe spades 3.15.5+dfsg-8 (tar) [9903 kB] 65s Get:3 http://ftpmaster.internal/ubuntu questing/universe spades 3.15.5+dfsg-8 (diff) [32.4 kB] 65s gpgv: Signature made Fri Dec 13 23:10:06 2024 UTC 65s gpgv: using RSA key 33CB284313E90BD27DCB4523600316A6DC277476 65s gpgv: Can't check signature: No public key 65s dpkg-source: warning: cannot verify inline signature for ./spades_3.15.5+dfsg-8.dsc: no acceptable signature found 66s autopkgtest [03:41:31]: testing package spades version 3.15.5+dfsg-8 66s autopkgtest [03:41:31]: build not needed 70s autopkgtest [03:41:35]: test run-upstreams-tests: preparing testbed 70s Reading package lists... 70s Building dependency tree... 70s Reading state information... 70s Starting pkgProblemResolver with broken count: 0 70s Starting 2 pkgProblemResolver with broken count: 0 70s Done 70s The following NEW packages will be installed: 70s bamtools bwa libbamtools2.5.2 libdeflate0 libgomp1 libhts3t64 libhtscodecs2 70s libjsoncpp26 libnlopt0 libssw0 python3-joblib samtools spades 70s 0 upgraded, 13 newly installed, 0 to remove and 0 not upgraded. 70s Need to get 12.0 MB of archives. 70s After this operation, 47.7 MB of additional disk space will be used. 70s Get:1 http://ftpmaster.internal/ubuntu questing/universe amd64 libbamtools2.5.2 amd64 2.5.2+dfsg-6build1 [144 kB] 70s Get:2 http://ftpmaster.internal/ubuntu questing/main amd64 libjsoncpp26 amd64 1.9.6-3 [90.0 kB] 70s Get:3 http://ftpmaster.internal/ubuntu questing/universe amd64 bamtools amd64 2.5.2+dfsg-6build1 [178 kB] 70s Get:4 http://ftpmaster.internal/ubuntu questing/universe amd64 bwa amd64 0.7.18-1 [204 kB] 70s Get:5 http://ftpmaster.internal/ubuntu questing/main amd64 libdeflate0 amd64 1.23-2 [49.9 kB] 70s Get:6 http://ftpmaster.internal/ubuntu questing/main amd64 libgomp1 amd64 15-20250404-0ubuntu1 [151 kB] 70s Get:7 http://ftpmaster.internal/ubuntu questing/universe amd64 libhtscodecs2 amd64 1.6.1-2 [132 kB] 70s Get:8 http://ftpmaster.internal/ubuntu questing/universe amd64 libhts3t64 amd64 1.21+ds-1 [514 kB] 70s Get:9 http://ftpmaster.internal/ubuntu questing/universe amd64 libssw0 amd64 1.1-15 [22.5 kB] 70s Get:10 http://ftpmaster.internal/ubuntu questing-proposed/universe amd64 python3-joblib all 1.4.2-4 [205 kB] 70s Get:11 http://ftpmaster.internal/ubuntu questing/universe amd64 samtools amd64 1.21-1 [655 kB] 71s Get:12 http://ftpmaster.internal/ubuntu questing/universe amd64 libnlopt0 amd64 2.7.1-6ubuntu3 [251 kB] 71s Get:13 http://ftpmaster.internal/ubuntu questing/universe amd64 spades amd64 3.15.5+dfsg-8 [9374 kB] 71s Fetched 12.0 MB in 1s (23.0 MB/s) 71s Selecting previously unselected package libbamtools2.5.2:amd64. 71s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 80517 files and directories currently installed.) 71s Preparing to unpack .../00-libbamtools2.5.2_2.5.2+dfsg-6build1_amd64.deb ... 71s Unpacking libbamtools2.5.2:amd64 (2.5.2+dfsg-6build1) ... 71s Selecting previously unselected package libjsoncpp26:amd64. 71s Preparing to unpack .../01-libjsoncpp26_1.9.6-3_amd64.deb ... 71s Unpacking libjsoncpp26:amd64 (1.9.6-3) ... 71s Selecting previously unselected package bamtools. 71s Preparing to unpack .../02-bamtools_2.5.2+dfsg-6build1_amd64.deb ... 71s Unpacking bamtools (2.5.2+dfsg-6build1) ... 71s Selecting previously unselected package bwa. 71s Preparing to unpack .../03-bwa_0.7.18-1_amd64.deb ... 71s Unpacking bwa (0.7.18-1) ... 71s Selecting previously unselected package libdeflate0:amd64. 71s Preparing to unpack .../04-libdeflate0_1.23-2_amd64.deb ... 71s Unpacking libdeflate0:amd64 (1.23-2) ... 71s Selecting previously unselected package libgomp1:amd64. 71s Preparing to unpack .../05-libgomp1_15-20250404-0ubuntu1_amd64.deb ... 71s Unpacking libgomp1:amd64 (15-20250404-0ubuntu1) ... 71s Selecting previously unselected package libhtscodecs2:amd64. 71s Preparing to unpack .../06-libhtscodecs2_1.6.1-2_amd64.deb ... 71s Unpacking libhtscodecs2:amd64 (1.6.1-2) ... 71s Selecting previously unselected package libhts3t64:amd64. 71s Preparing to unpack .../07-libhts3t64_1.21+ds-1_amd64.deb ... 71s Unpacking libhts3t64:amd64 (1.21+ds-1) ... 71s Selecting previously unselected package libssw0:amd64. 71s Preparing to unpack .../08-libssw0_1.1-15_amd64.deb ... 71s Unpacking libssw0:amd64 (1.1-15) ... 71s Selecting previously unselected package python3-joblib. 71s Preparing to unpack .../09-python3-joblib_1.4.2-4_all.deb ... 71s Unpacking python3-joblib (1.4.2-4) ... 71s Selecting previously unselected package samtools. 71s Preparing to unpack .../10-samtools_1.21-1_amd64.deb ... 71s Unpacking samtools (1.21-1) ... 71s Selecting previously unselected package libnlopt0:amd64. 71s Preparing to unpack .../11-libnlopt0_2.7.1-6ubuntu3_amd64.deb ... 71s Unpacking libnlopt0:amd64 (2.7.1-6ubuntu3) ... 71s Selecting previously unselected package spades. 71s Preparing to unpack .../12-spades_3.15.5+dfsg-8_amd64.deb ... 71s Unpacking spades (3.15.5+dfsg-8) ... 71s Setting up libhtscodecs2:amd64 (1.6.1-2) ... 71s Setting up python3-joblib (1.4.2-4) ... 72s Setting up bwa (0.7.18-1) ... 72s Setting up libdeflate0:amd64 (1.23-2) ... 72s Setting up libnlopt0:amd64 (2.7.1-6ubuntu3) ... 72s Setting up libgomp1:amd64 (15-20250404-0ubuntu1) ... 72s Setting up libjsoncpp26:amd64 (1.9.6-3) ... 72s Setting up libbamtools2.5.2:amd64 (2.5.2+dfsg-6build1) ... 72s Setting up bamtools (2.5.2+dfsg-6build1) ... 72s Setting up libhts3t64:amd64 (1.21+ds-1) ... 72s Setting up libssw0:amd64 (1.1-15) ... 72s Setting up samtools (1.21-1) ... 72s Setting up spades (3.15.5+dfsg-8) ... 72s Processing triggers for man-db (2.13.0-1) ... 72s Processing triggers for libc-bin (2.41-6ubuntu1) ... 73s autopkgtest [03:41:38]: test run-upstreams-tests: [----------------------- 73s + mktemp -d 73s + WORKDIR=/tmp/tmp.cMLX1ajB23 73s + trap rm -rf /tmp/tmp.cMLX1ajB23 0 INT QUIT ABRT PIPE TERM 73s + cd /tmp/tmp.cMLX1ajB23 73s + spades --test 73s 73s 73s == Warning == No assembly mode was specified! If you intend to assemble high-coverage multi-cell/isolate data, use '--isolate' option. 73s 73s 73s Command line: /usr/libexec/spades/spades.py --test 73s 73s System information: 73s SPAdes version: 3.15.5 73s Python version: 3.13.3 73s OS: Linux-6.14.0-15-generic-x86_64-with-glibc2.41 73s 73s Output dir: /tmp/tmp.cMLX1ajB23/spades_test 73s Mode: read error correction and assembling 73s Debug mode is turned OFF 73s 73s Dataset parameters: 73s Standard mode 73s For multi-cell/isolate data we recommend to use '--isolate' option; for single-cell MDA data use '--sc'; for metagenomic data use '--meta'; for RNA-Seq use '--rna'. 73s Reads: 73s Library number: 1, library type: paired-end 73s orientation: fr 73s left reads: ['/usr/share/spades/test_dataset/ecoli_1K_1.fq.gz'] 73s right reads: ['/usr/share/spades/test_dataset/ecoli_1K_2.fq.gz'] 73s interlaced reads: not specified 73s single reads: not specified 73s merged reads: not specified 73s Read error correction parameters: 73s Iterations: 1 73s PHRED offset will be auto-detected 73s Corrected reads will be compressed 73s Assembly parameters: 73s k: automatic selection based on read length 73s Repeat resolution is enabled 73s Mismatch careful mode is turned OFF 73s MismatchCorrector will be SKIPPED 73s Coverage cutoff is turned OFF 73s Other parameters: 73s Dir for temp files: /tmp/tmp.cMLX1ajB23/spades_test/tmp 73s Threads: 16 73s Memory limit (in Gb): 3 73s 73s 73s ======= SPAdes pipeline started. Log can be found here: /tmp/tmp.cMLX1ajB23/spades_test/spades.log 73s 73s /usr/share/spades/test_dataset/ecoli_1K_1.fq.gz: max reads length: 100 73s /usr/share/spades/test_dataset/ecoli_1K_2.fq.gz: max reads length: 100 73s 73s Reads length: 100 73s 73s 73s ===== Before start started. 73s 73s 73s ===== Read error correction started. 73s 73s 73s ===== Read error correction started. 73s 73s 73s == Running: /usr/libexec/spades/spades-hammer /tmp/tmp.cMLX1ajB23/spades_test/corrected/configs/config.info 73s 73s 0:00:00.000 1M / 19M INFO General (main.cpp : 75) Starting BayesHammer, built from N/A, git revision N/A 73s 0:00:00.000 1M / 19M INFO General (main.cpp : 76) Loading config from /tmp/tmp.cMLX1ajB23/spades_test/corrected/configs/config.info 73s 0:00:00.000 1M / 19M INFO General (main.cpp : 78) Maximum # of threads to use (adjusted due to OMP capabilities): 2 73s 0:00:00.000 1M / 19M INFO General (memory_limit.cpp : 54) Memory limit set to 3 Gb 73s 0:00:00.000 1M / 19M INFO General (main.cpp : 86) Trying to determine PHRED offset 73s 0:00:00.000 1M / 19M INFO General (main.cpp : 92) Determined value is 33 73s 0:00:00.000 1M / 19M INFO General (hammer_tools.cpp : 38) Hamming graph threshold tau=1, k=21, subkmer positions = [ 0 10 ] 73s 0:00:00.000 1M / 19M INFO General (main.cpp : 113) Size of aux. kmer data 24 bytes 73s === ITERATION 0 begins === 73s 0:00:00.000 1M / 19M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 16 files using 2 threads. This might take a while. 73s 0:00:00.000 1M / 19M INFO General (file_limit.hpp : 42) Open file limit set to 1024 73s 0:00:00.000 1M / 19M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 0.499985 Gb 73s 0:00:00.000 1M / 19M INFO General (kmer_splitter.hpp : 101) Using cell size of 4194180 73s 0:00:00.000 1153M / 1153M INFO K-mer Splitting (kmer_data.cpp : 97) Processing /usr/share/spades/test_dataset/ecoli_1K_1.fq.gz 73s 0:00:00.016 1153M / 1153M INFO K-mer Splitting (kmer_data.cpp : 97) Processing /usr/share/spades/test_dataset/ecoli_1K_2.fq.gz 73s 0:00:00.032 1153M / 1153M INFO K-mer Splitting (kmer_data.cpp : 112) Total 4108 reads processed 73s 0:00:00.032 1M / 19M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. 73s 0:00:00.034 1M / 19M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 1974 kmers in total. 73s 0:00:00.034 1M / 19M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices 73s 0:00:00.035 1M / 19M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 1974 kmers, 13944 bytes occupied (56.5106 bits per kmer). 73s 0:00:00.035 1M / 19M INFO K-mer Counting (kmer_data.cpp : 354) Arranging kmers in hash map order 73s 0:00:00.036 1M / 19M INFO General (main.cpp : 148) Clustering Hamming graph. 73s 0:00:00.038 1M / 19M INFO General (main.cpp : 155) Extracting clusters: 73s 0:00:00.038 1M / 19M INFO General (concurrent_dsu.cpp : 18) Connecting to root 73s 0:00:00.038 1M / 19M INFO General (concurrent_dsu.cpp : 34) Calculating counts 73s 0:00:00.038 1M / 19M INFO General (concurrent_dsu.cpp : 63) Writing down entries 73s 0:00:00.039 1M / 19M INFO General (main.cpp : 167) Clustering done. Total clusters: 1960 73s 0:00:00.039 1M / 19M INFO K-mer Counting (kmer_data.cpp : 371) Collecting K-mer information, this takes a while. 73s 0:00:00.039 1M / 19M INFO K-mer Counting (kmer_data.cpp : 377) Processing /usr/share/spades/test_dataset/ecoli_1K_1.fq.gz 73s 0:00:00.070 1M / 19M INFO K-mer Counting (kmer_data.cpp : 377) Processing /usr/share/spades/test_dataset/ecoli_1K_2.fq.gz 73s 0:00:00.101 1M / 19M INFO K-mer Counting (kmer_data.cpp : 384) Collection done, postprocessing. 73s 0:00:00.101 1M / 19M INFO K-mer Counting (kmer_data.cpp : 397) There are 1974 kmers in total. Among them 0 (0%) are singletons. 73s 0:00:00.102 1M / 19M INFO General (main.cpp : 173) Subclustering Hamming graph 73s 0:00:00.102 1M / 19M INFO Hamming Subclustering (kmer_cluster.cpp : 650) Subclustering done. Total 0 non-read kmers were generated. 73s 0:00:00.102 1M / 19M INFO Hamming Subclustering (kmer_cluster.cpp : 651) Subclustering statistics: 73s 0:00:00.102 1M / 19M INFO Hamming Subclustering (kmer_cluster.cpp : 652) Total singleton hamming clusters: 1946. Among them 1946 (100%) are good 73s 0:00:00.102 1M / 19M INFO Hamming Subclustering (kmer_cluster.cpp : 653) Total singleton subclusters: 8. Among them 8 (100%) are good 73s 0:00:00.102 1M / 19M INFO Hamming Subclustering (kmer_cluster.cpp : 654) Total non-singleton subcluster centers: 10. Among them 10 (100%) are good 73s 0:00:00.102 1M / 19M INFO Hamming Subclustering (kmer_cluster.cpp : 655) Average size of non-trivial subcluster: 2.8 kmers 73s 0:00:00.102 1M / 19M INFO Hamming Subclustering (kmer_cluster.cpp : 656) Average number of sub-clusters per non-singleton cluster: 1.28571 73s 0:00:00.102 1M / 19M INFO Hamming Subclustering (kmer_cluster.cpp : 657) Total solid k-mers: 1964 73s 0:00:00.102 1M / 19M INFO Hamming Subclustering (kmer_cluster.cpp : 658) Substitution probabilities: [4,4]((0.875,0.125,0,0),(0,1,0,0),(0,0,1,0),(0,0,0.125,0.875)) 73s 0:00:00.102 1M / 19M INFO General (main.cpp : 178) Finished clustering. 73s 0:00:00.102 1M / 19M INFO General (main.cpp : 197) Starting solid k-mers expansion in 2 threads. 73s 0:00:00.120 1M / 19M INFO General (main.cpp : 218) Solid k-mers iteration 0 produced 0 new k-mers. 73s 0:00:00.120 1M / 19M INFO General (main.cpp : 222) Solid k-mers finalized 73s 0:00:00.120 1M / 19M INFO General (hammer_tools.cpp : 222) Starting read correction in 2 threads. 73s 0:00:00.120 1M / 19M INFO General (hammer_tools.cpp : 235) Correcting pair of reads: /usr/share/spades/test_dataset/ecoli_1K_1.fq.gz and /usr/share/spades/test_dataset/ecoli_1K_2.fq.gz 73s 0:00:00.142 46M / 51M INFO General (hammer_tools.cpp : 170) Prepared batch 0 of 2054 reads. 73s 0:00:00.146 46M / 51M INFO General (hammer_tools.cpp : 177) Processed batch 0 73s 0:00:00.148 46M / 51M INFO General (hammer_tools.cpp : 187) Written batch 0 73s 0:00:00.150 1M / 51M INFO General (hammer_tools.cpp : 276) Correction done. Changed 4 bases in 4 reads. 73s 0:00:00.150 1M / 51M INFO General (hammer_tools.cpp : 277) Failed to correct 0 bases out of 353915. 73s 0:00:00.150 1M / 51M INFO General (main.cpp : 255) Saving corrected dataset description to /tmp/tmp.cMLX1ajB23/spades_test/corrected/corrected.yaml 73s 0:00:00.150 1M / 51M INFO General (main.cpp : 262) All done. Exiting. 73s 73s ===== Read error correction finished. 73s 73s 73s ===== corrected reads compression started. 73s 73s 73s == Running: /usr/bin/python3 /usr/share/spades/spades_pipeline/scripts/compress_all.py --input_file /tmp/tmp.cMLX1ajB23/spades_test/corrected/corrected.yaml --ext_python_modules_home /usr/share/spades --max_threads 16 --output_dir /tmp/tmp.cMLX1ajB23/spades_test/corrected --gzip_output 73s 73s == Compressing corrected reads (with gzip) 73s == Files to compress: ['/tmp/tmp.cMLX1ajB23/spades_test/corrected/ecoli_1K_1.fq.00.0_0.cor.fastq', '/tmp/tmp.cMLX1ajB23/spades_test/corrected/ecoli_1K_2.fq.00.0_0.cor.fastq', '/tmp/tmp.cMLX1ajB23/spades_test/corrected/ecoli_1K__unpaired.00.0_0.cor.fastq'] 74s == Files compression is finished 74s == Dataset yaml file is updated 74s 74s ===== corrected reads compression finished. 74s 74s 74s ===== Read error correction finished. 74s 74s 74s ===== Assembling started. 74s 74s 74s ===== K21 started. 74s 74s 74s == Running: /usr/libexec/spades/spades-core /tmp/tmp.cMLX1ajB23/spades_test/K21/configs/config.info 74s 74s 0:00:00.000 1M / 19M INFO General (main.cpp : 99) Loaded config from /tmp/tmp.cMLX1ajB23/spades_test/K21/configs/config.info 74s 0:00:00.000 1M / 19M INFO General (memory_limit.cpp : 54) Memory limit set to 3 Gb 74s 0:00:00.000 1M / 19M INFO General (main.cpp : 107) Starting SPAdes, built from N/A, git revision N/A 74s 0:00:00.000 1M / 19M INFO General (main.cpp : 108) Maximum k-mer length: 128 74s 0:00:00.000 1M / 19M INFO General (main.cpp : 109) Assembling dataset (/tmp/tmp.cMLX1ajB23/spades_test/dataset.info) with K=21 74s 0:00:00.000 1M / 19M INFO General (main.cpp : 110) Maximum # of threads to use (adjusted due to OMP capabilities): 2 74s 0:00:00.000 1M / 19M INFO General (pipeline.cpp : 212) SPAdes started 74s 0:00:00.000 1M / 19M INFO General (pipeline.cpp : 225) Starting from stage: read_conversion 74s 0:00:00.000 1M / 19M INFO General (pipeline.cpp : 231) Two-step repeat resolution disabled 74s 0:00:00.000 1M / 19M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 74s 0:00:00.000 1M / 19M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 74s 0:00:00.000 1M / 19M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 74s 0:00:00.000 1M / 19M INFO StageManager (stage.cpp : 185) STAGE == Binary Read Conversion (id: read_conversion) 74s 0:00:00.000 1M / 19M INFO General (read_converter.cpp : 72) Converting reads to binary format for library #0 (takes a while) 74s 0:00:00.000 1M / 19M INFO General (read_converter.cpp : 73) Converting paired reads 74s 0:00:00.009 63M / 63M INFO General (binary_converter.cpp : 111) 2054 reads written 74s 0:00:00.009 41M / 41M INFO General (read_converter.cpp : 86) Converting single reads 74s 0:00:00.009 71M / 71M INFO General (binary_converter.cpp : 111) 0 reads written 74s 0:00:00.009 61M / 61M INFO General (read_converter.cpp : 92) Converting merged reads 74s 0:00:00.009 71M / 71M INFO General (binary_converter.cpp : 111) 0 reads written 74s 0:00:00.009 1M / 19M INFO StageManager (stage.cpp : 185) STAGE == de Bruijn graph construction (id: construction) 74s 0:00:00.009 1M / 19M INFO General (construction.cpp : 153) Max read length 100 74s 0:00:00.009 1M / 19M INFO General (construction.cpp : 159) Average read length 86.1526 74s 0:00:00.009 1M / 19M INFO General (stage.cpp : 117) PROCEDURE == k+1-mer counting (id: construction:kpomer_counting) 74s 0:00:00.010 1M / 19M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 20 files using 2 threads. This might take a while. 74s 0:00:00.010 1M / 19M INFO General (file_limit.hpp : 42) Open file limit set to 1024 74s 0:00:00.010 1M / 19M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 0.499973 Gb 74s 0:00:00.010 1M / 19M INFO General (kmer_splitter.hpp : 101) Using cell size of 3355264 74s 0:00:00.020 1M / 19M INFO General (kmer_splitters.hpp : 131) Used 8216 reads 74s 0:00:00.020 1M / 19M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. 74s 0:00:00.021 1M / 19M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 984 kmers in total. 74s 0:00:00.021 1M / 19M INFO General (stage.cpp : 117) PROCEDURE == Extension index construction (id: construction:extension_index_construction) 74s 0:00:00.021 1M / 19M INFO K-mer Index Building (kmer_index_builder.hpp : 438) Building kmer index 74s 0:00:00.022 1M / 19M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 20 files using 2 threads. This might take a while. 74s 0:00:00.022 1M / 19M INFO General (file_limit.hpp : 42) Open file limit set to 1024 74s 0:00:00.022 1M / 19M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 0.499971 Gb 74s 0:00:00.022 1M / 19M INFO General (kmer_splitter.hpp : 101) Using cell size of 3355245 74s 0:00:00.023 1161M / 1161M INFO General (kmer_splitters.hpp : 199) Used 984 kmers. 74s 0:00:00.023 1M / 19M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. 74s 0:00:00.024 1M / 19M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 985 kmers in total. 74s 0:00:00.024 1M / 19M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices 74s 0:00:00.026 1M / 19M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 985 kmers, 16424 bytes occupied (133.393 bits per kmer). 74s 0:00:00.026 1M / 19M INFO General (kmer_index_builder.hpp : 169) Merging final buckets. 74s 0:00:00.027 1M / 19M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 100) Building k-mer extensions from k+1-mers 74s 0:00:00.027 1M / 19M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 105) Building k-mer extensions from k+1-mers finished. 74s 0:00:00.027 1M / 19M INFO General (stage.cpp : 117) PROCEDURE == Early tip clipping (id: construction:early_tip_clipper) 74s 0:00:00.027 1M / 19M INFO General (construction.cpp : 301) Early tip clipper length bound set as (RL - K) 74s 0:00:00.027 1M / 19M INFO Early tip clipping (early_simplification.hpp : 47) Early tip clipping 74s 0:00:00.028 1M / 19M INFO Early tip clipping (early_simplification.hpp : 82) #tipped junctions: 2 74s 0:00:00.028 1M / 19M INFO Early tip clipping (early_simplification.hpp : 93) Clipped tips: 2 74s 0:00:00.028 1M / 19M INFO Early tip clipping (early_simplification.hpp : 49) 5 22-mers were removed by early tip clipper 74s 0:00:00.028 1M / 19M INFO General (stage.cpp : 117) PROCEDURE == Condensing graph (id: construction:graph_condensing) 74s 0:00:00.028 1M / 19M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths 74s 0:00:00.028 1M / 19M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 1 sequences extracted 74s 0:00:00.028 1M / 19M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops 74s 0:00:00.028 1M / 19M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 0 loops collected 74s 0:00:00.028 1M / 19M INFO General (debruijn_graph_constructor: 487) Total 2 edges to create 74s 0:00:00.028 1M / 19M INFO General (debruijn_graph_constructor: 489) Collecting link records 74s 0:00:00.028 1M / 19M INFO General (debruijn_graph_constructor: 491) Ordering link records 74s 0:00:00.028 1M / 19M INFO General (debruijn_graph_constructor: 493) Sorting done 74s 0:00:00.028 1M / 19M INFO General (debruijn_graph_constructor: 503) Total 2 vertices to create 74s 0:00:00.028 1M / 19M INFO General (debruijn_graph_constructor: 506) Connecting the graph 74s 0:00:00.028 1M / 19M INFO General (stage.cpp : 117) PROCEDURE == Filling coverage indices (PHM) (id: construction:coverage_filling_phm) 74s 0:00:00.028 1M / 19M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices 74s 0:00:00.030 1M / 19M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 984 kmers, 16392 bytes occupied (133.268 bits per kmer). 74s 0:00:00.030 1M / 19M INFO General (coverage_hash_map_builder.: 47) Collecting k-mer coverage information from reads, this takes a while. 74s 0:00:00.044 1M / 19M INFO General (construction.cpp : 430) Filling coverage and flanking coverage from PHM 74s 0:00:00.044 1M / 19M INFO StageManager (stage.cpp : 185) STAGE == EC Threshold Finding (id: ec_threshold_finder) 74s 0:00:00.044 1M / 19M INFO General (kmer_coverage_model.cpp : 181) Kmer coverage valley at: 0 74s 0:00:00.044 1M / 19M INFO General (kmer_coverage_model.cpp : 201) K-mer histogram maximum: 348 74s 0:00:00.044 1M / 19M INFO General (kmer_coverage_model.cpp : 237) Estimated median coverage: 348. Coverage mad: 62.2692 74s 0:00:00.044 1M / 19M INFO General (kmer_coverage_model.cpp : 259) Fitting coverage model 74s 0:00:00.076 1M / 19M INFO General (kmer_coverage_model.cpp : 295) ... iteration 2 74s 0:00:00.142 1M / 19M INFO General (kmer_coverage_model.cpp : 295) ... iteration 4 74s 0:00:00.272 1M / 19M INFO General (kmer_coverage_model.cpp : 295) ... iteration 8 74s 0:00:00.463 1M / 19M INFO General (kmer_coverage_model.cpp : 295) ... iteration 16 74s 0:00:00.805 1M / 19M INFO General (kmer_coverage_model.cpp : 295) ... iteration 32 75s 0:00:01.649 1M / 19M INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 342.845. Fitted coverage std. dev: 68.3997 75s 0:00:01.649 1M / 19M INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 0.999994 75s 0:00:01.649 1M / 19M INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 355 75s 0:00:01.650 1M / 19M INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 171 75s 0:00:01.650 1M / 19M INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 749 75s 0:00:01.650 1M / 19M INFO General (genomic_info_filler.cpp : 55) Mean coverage was calculated as 342.845 75s 0:00:01.650 1M / 19M INFO General (genomic_info_filler.cpp : 70) EC coverage threshold value was calculated as 171 75s 0:00:01.650 1M / 19M INFO General (genomic_info_filler.cpp : 71) Trusted kmer low bound: 0 75s 0:00:01.650 1M / 19M INFO StageManager (stage.cpp : 185) STAGE == Raw Simplification (id: raw_simplification) 75s 0:00:01.650 1M / 19M INFO General (simplification.cpp : 127) PROCEDURE == Initial cleaning 75s 0:00:01.650 1M / 19M INFO General (graph_simplification.hpp : 662) Flanking coverage based disconnection disabled 75s 0:00:01.650 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Self conjugate edge remover 75s 0:00:01.650 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Self conjugate edge remover triggered 0 times 75s 0:00:01.650 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Initial tip clipper 75s 0:00:01.650 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Initial tip clipper triggered 0 times 75s 0:00:01.650 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Initial ec remover 75s 0:00:01.650 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Initial ec remover triggered 0 times 75s 0:00:01.650 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Initial isolated edge remover 75s 0:00:01.650 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Initial isolated edge remover triggered 0 times 75s 0:00:01.650 1M / 19M INFO StageManager (stage.cpp : 185) STAGE == Simplification (id: simplification) 75s 0:00:01.650 1M / 19M INFO General (simplification.cpp : 368) Graph simplification started 75s 0:00:01.650 1M / 19M INFO General (graph_simplification.hpp : 634) Creating parallel br instance 75s 0:00:01.650 1M / 19M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 1 75s 0:00:01.650 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 75s 0:00:01.650 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 75s 0:00:01.650 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 75s 0:00:01.650 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 75s 0:00:01.650 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 75s 0:00:01.650 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 0 times 75s 0:00:01.650 1M / 19M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 2 75s 0:00:01.650 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 75s 0:00:01.650 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 75s 0:00:01.650 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 75s 0:00:01.650 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 75s 0:00:01.650 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 75s 0:00:01.650 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 0 times 75s 0:00:01.650 1M / 19M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 3 75s 0:00:01.650 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 75s 0:00:01.650 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 75s 0:00:01.650 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 75s 0:00:01.650 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 75s 0:00:01.650 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 75s 0:00:01.650 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 0 times 75s 0:00:01.650 1M / 19M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 4 75s 0:00:01.650 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 75s 0:00:01.650 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 75s 0:00:01.650 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 75s 0:00:01.650 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 75s 0:00:01.650 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 75s 0:00:01.650 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 0 times 75s 0:00:01.650 1M / 19M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 5 75s 0:00:01.650 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 75s 0:00:01.650 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 75s 0:00:01.650 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 75s 0:00:01.650 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 75s 0:00:01.650 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 75s 0:00:01.650 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 0 times 75s 0:00:01.650 1M / 19M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 6 75s 0:00:01.650 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 75s 0:00:01.650 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 75s 0:00:01.650 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 75s 0:00:01.650 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 75s 0:00:01.650 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 75s 0:00:01.650 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 0 times 75s 0:00:01.650 1M / 19M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 7 75s 0:00:01.650 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 75s 0:00:01.650 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 75s 0:00:01.650 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 75s 0:00:01.650 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 75s 0:00:01.650 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 75s 0:00:01.650 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 0 times 75s 0:00:01.650 1M / 19M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 8 75s 0:00:01.650 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 75s 0:00:01.650 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 75s 0:00:01.650 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 75s 0:00:01.650 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 75s 0:00:01.650 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 75s 0:00:01.650 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 0 times 75s 0:00:01.650 1M / 19M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 9 75s 0:00:01.650 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 75s 0:00:01.650 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 75s 0:00:01.650 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 75s 0:00:01.650 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 75s 0:00:01.650 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 75s 0:00:01.651 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 0 times 75s 0:00:01.651 1M / 19M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 10 75s 0:00:01.651 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 75s 0:00:01.651 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 75s 0:00:01.651 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 75s 0:00:01.651 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 75s 0:00:01.651 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 75s 0:00:01.651 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 0 times 75s 0:00:01.651 1M / 19M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 11 75s 0:00:01.651 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 75s 0:00:01.651 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 75s 0:00:01.651 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 75s 0:00:01.651 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 75s 0:00:01.651 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 75s 0:00:01.651 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 0 times 75s 0:00:01.651 1M / 19M INFO StageManager (stage.cpp : 185) STAGE == Simplification Cleanup (id: simplification_cleanup) 75s 0:00:01.651 1M / 19M INFO General (simplification.cpp : 176) PROCEDURE == Post simplification 75s 0:00:01.651 1M / 19M INFO General (graph_simplification.hpp : 448) Disconnection of relatively low covered edges disabled 75s 0:00:01.651 1M / 19M INFO General (graph_simplification.hpp : 485) Complex tip clipping disabled 75s 0:00:01.651 1M / 19M INFO General (graph_simplification.hpp : 634) Creating parallel br instance 75s 0:00:01.651 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 75s 0:00:01.651 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 75s 0:00:01.651 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 75s 0:00:01.651 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 75s 0:00:01.651 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 75s 0:00:01.651 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 75s 0:00:01.651 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 75s 0:00:01.651 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 75s 0:00:01.651 1M / 19M INFO General (simplification.cpp : 327) Disrupting self-conjugate edges 75s 0:00:01.651 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Removing isolated edges 75s 0:00:01.651 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Removing isolated edges triggered 0 times 75s 0:00:01.651 1M / 19M INFO General (simplification.cpp : 495) After simplification: 75s 0:00:01.651 1M / 19M INFO General (simplification.cpp : 496) Average coverage = 273.35 75s 0:00:01.651 1M / 19M INFO General (simplification.cpp : 497) Total length = 979 75s 0:00:01.651 1M / 19M INFO General (simplification.cpp : 498) Median edge length: 979 75s 0:00:01.651 1M / 19M INFO General (simplification.cpp : 499) Edges: 2 75s 0:00:01.651 1M / 19M INFO General (simplification.cpp : 500) Vertices: 4 75s 0:00:01.651 1M / 19M INFO StageManager (stage.cpp : 185) STAGE == Contig Output (id: contig_output) 75s 0:00:01.651 1M / 19M INFO General (read_converter.cpp : 107) Outputting contigs to /tmp/tmp.cMLX1ajB23/spades_test/K21/simplified_contigs 75s 0:00:01.653 3M / 19M INFO General (binary_converter.cpp : 111) 1 reads written 75s 0:00:01.654 1M / 19M INFO General (pipeline.cpp : 287) SPAdes finished 75s 0:00:01.654 1M / 19M INFO General (main.cpp : 136) Assembling time: 0 hours 0 minutes 1 seconds 75s 75s ===== K21 finished. 75s 75s 75s ===== K33 started. 75s 75s 75s == Running: /usr/libexec/spades/spades-core /tmp/tmp.cMLX1ajB23/spades_test/K33/configs/config.info 75s 75s 0:00:00.000 1M / 19M INFO General (main.cpp : 99) Loaded config from /tmp/tmp.cMLX1ajB23/spades_test/K33/configs/config.info 75s 0:00:00.000 1M / 19M INFO General (memory_limit.cpp : 54) Memory limit set to 3 Gb 75s 0:00:00.000 1M / 19M INFO General (main.cpp : 107) Starting SPAdes, built from N/A, git revision N/A 75s 0:00:00.000 1M / 19M INFO General (main.cpp : 108) Maximum k-mer length: 128 75s 0:00:00.000 1M / 19M INFO General (main.cpp : 109) Assembling dataset (/tmp/tmp.cMLX1ajB23/spades_test/dataset.info) with K=33 75s 0:00:00.000 1M / 19M INFO General (main.cpp : 110) Maximum # of threads to use (adjusted due to OMP capabilities): 2 75s 0:00:00.000 1M / 19M INFO General (pipeline.cpp : 212) SPAdes started 75s 0:00:00.000 1M / 19M INFO General (pipeline.cpp : 225) Starting from stage: read_conversion 75s 0:00:00.000 1M / 19M INFO General (pipeline.cpp : 231) Two-step repeat resolution disabled 75s 0:00:00.000 1M / 19M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 75s 0:00:00.000 1M / 19M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 75s 0:00:00.000 1M / 19M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 75s 0:00:00.000 1M / 19M INFO StageManager (stage.cpp : 185) STAGE == Binary Read Conversion (id: read_conversion) 75s 0:00:00.000 1M / 19M INFO General (read_converter.cpp : 53) Binary reads detected 75s 0:00:00.000 1M / 19M INFO StageManager (stage.cpp : 185) STAGE == de Bruijn graph construction (id: construction) 75s 0:00:00.000 1M / 19M INFO General (construction.cpp : 118) Contigs from previous K will be used: /tmp/tmp.cMLX1ajB23/spades_test/K21/simplified_contigs 75s 0:00:00.000 1M / 19M INFO General (construction.cpp : 153) Max read length 100 75s 0:00:00.000 1M / 19M INFO General (construction.cpp : 159) Average read length 86.1526 75s 0:00:00.000 1M / 19M INFO General (stage.cpp : 117) PROCEDURE == k+1-mer counting (id: construction:kpomer_counting) 75s 0:00:00.000 1M / 19M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 20 files using 2 threads. This might take a while. 75s 0:00:00.000 1M / 19M INFO General (file_limit.hpp : 42) Open file limit set to 1024 75s 0:00:00.000 1M / 19M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 0.49997 Gb 75s 0:00:00.000 1M / 19M INFO General (kmer_splitter.hpp : 101) Using cell size of 1677622 75s 0:00:00.009 1M / 19M INFO General (kmer_splitters.hpp : 131) Used 8218 reads 75s 0:00:00.009 1M / 19M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. 75s 0:00:00.011 1M / 19M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 972 kmers in total. 75s 0:00:00.011 1M / 19M INFO General (stage.cpp : 117) PROCEDURE == Extension index construction (id: construction:extension_index_construction) 75s 0:00:00.011 1M / 19M INFO K-mer Index Building (kmer_index_builder.hpp : 438) Building kmer index 75s 0:00:00.011 1M / 19M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 20 files using 2 threads. This might take a while. 75s 0:00:00.011 1M / 19M INFO General (file_limit.hpp : 42) Open file limit set to 1024 75s 0:00:00.011 1M / 19M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 0.499968 Gb 75s 0:00:00.011 1M / 19M INFO General (kmer_splitter.hpp : 101) Using cell size of 1677612 75s 0:00:00.013 1161M / 1161M INFO General (kmer_splitters.hpp : 199) Used 972 kmers. 75s 0:00:00.013 1M / 19M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. 75s 0:00:00.014 1M / 19M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 973 kmers in total. 75s 0:00:00.014 1M / 19M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices 75s 0:00:00.016 1M / 19M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 973 kmers, 16392 bytes occupied (134.775 bits per kmer). 75s 0:00:00.016 1M / 19M INFO General (kmer_index_builder.hpp : 169) Merging final buckets. 75s 0:00:00.016 1M / 19M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 100) Building k-mer extensions from k+1-mers 75s 0:00:00.017 1M / 19M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 105) Building k-mer extensions from k+1-mers finished. 75s 0:00:00.017 1M / 19M INFO General (stage.cpp : 117) PROCEDURE == Early tip clipping (id: construction:early_tip_clipper) 75s 0:00:00.017 1M / 19M INFO General (construction.cpp : 301) Early tip clipper length bound set as (RL - K) 75s 0:00:00.017 1M / 19M INFO Early tip clipping (early_simplification.hpp : 47) Early tip clipping 75s 0:00:00.017 1M / 19M INFO Early tip clipping (early_simplification.hpp : 82) #tipped junctions: 2 75s 0:00:00.018 1M / 19M INFO Early tip clipping (early_simplification.hpp : 93) Clipped tips: 2 75s 0:00:00.018 1M / 19M INFO Early tip clipping (early_simplification.hpp : 49) 5 34-mers were removed by early tip clipper 75s 0:00:00.018 1M / 19M INFO General (stage.cpp : 117) PROCEDURE == Condensing graph (id: construction:graph_condensing) 75s 0:00:00.018 1M / 19M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths 75s 0:00:00.018 1M / 19M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 1 sequences extracted 75s 0:00:00.018 1M / 19M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops 75s 0:00:00.018 1M / 19M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 0 loops collected 75s 0:00:00.018 1M / 19M INFO General (debruijn_graph_constructor: 487) Total 2 edges to create 75s 0:00:00.018 1M / 19M INFO General (debruijn_graph_constructor: 489) Collecting link records 75s 0:00:00.019 1M / 19M INFO General (debruijn_graph_constructor: 491) Ordering link records 75s 0:00:00.019 1M / 19M INFO General (debruijn_graph_constructor: 493) Sorting done 75s 0:00:00.019 1M / 19M INFO General (debruijn_graph_constructor: 503) Total 2 vertices to create 75s 0:00:00.019 1M / 19M INFO General (debruijn_graph_constructor: 506) Connecting the graph 75s 0:00:00.019 1M / 19M INFO General (stage.cpp : 117) PROCEDURE == Filling coverage indices (PHM) (id: construction:coverage_filling_phm) 75s 0:00:00.019 1M / 19M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices 75s 0:00:00.020 1M / 19M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 972 kmers, 16392 bytes occupied (134.914 bits per kmer). 75s 0:00:00.020 1M / 19M INFO General (coverage_hash_map_builder.: 47) Collecting k-mer coverage information from reads, this takes a while. 75s 0:00:00.030 1M / 19M INFO General (construction.cpp : 430) Filling coverage and flanking coverage from PHM 75s 0:00:00.031 1M / 19M INFO StageManager (stage.cpp : 185) STAGE == EC Threshold Finding (id: ec_threshold_finder) 75s 0:00:00.031 1M / 19M INFO General (kmer_coverage_model.cpp : 181) Kmer coverage valley at: 0 75s 0:00:00.031 1M / 19M INFO General (kmer_coverage_model.cpp : 201) K-mer histogram maximum: 17 75s 0:00:00.031 1M / 19M INFO General (kmer_coverage_model.cpp : 237) Estimated median coverage: 17. Coverage mad: 11.8608 75s 0:00:00.031 1M / 19M INFO General (kmer_coverage_model.cpp : 259) Fitting coverage model 75s 0:00:00.045 1M / 19M INFO General (kmer_coverage_model.cpp : 295) ... iteration 2 75s 0:00:00.075 1M / 19M INFO General (kmer_coverage_model.cpp : 295) ... iteration 4 75s 0:00:00.121 1M / 19M INFO General (kmer_coverage_model.cpp : 295) ... iteration 8 75s 0:00:00.174 1M / 19M INFO General (kmer_coverage_model.cpp : 295) ... iteration 16 76s 0:00:00.276 1M / 19M INFO General (kmer_coverage_model.cpp : 295) ... iteration 32 76s 0:00:00.484 1M / 19M INFO General (kmer_coverage_model.cpp : 295) ... iteration 64 76s 0:00:00.898 1M / 19M INFO General (kmer_coverage_model.cpp : 295) ... iteration 128 77s 0:00:01.424 1M / 19M INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 108.181. Fitted coverage std. dev: 65.0594 77s 0:00:01.424 1M / 19M INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 0.0555142 77s 0:00:01.424 1M / 19M INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 3 77s 0:00:01.425 1M / 19M INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 3 77s 0:00:01.425 1M / 19M INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 400 77s 0:00:01.425 1M / 19M INFO General (genomic_info_filler.cpp : 55) Mean coverage was calculated as 108.181 77s 0:00:01.425 1M / 19M INFO General (genomic_info_filler.cpp : 70) EC coverage threshold value was calculated as 3 77s 0:00:01.425 1M / 19M INFO General (genomic_info_filler.cpp : 71) Trusted kmer low bound: 0 77s 0:00:01.425 1M / 19M INFO StageManager (stage.cpp : 185) STAGE == Raw Simplification (id: raw_simplification) 77s 0:00:01.425 1M / 19M INFO General (simplification.cpp : 127) PROCEDURE == Initial cleaning 77s 0:00:01.425 1M / 19M INFO General (graph_simplification.hpp : 662) Flanking coverage based disconnection disabled 77s 0:00:01.425 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Self conjugate edge remover 77s 0:00:01.425 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Self conjugate edge remover triggered 0 times 77s 0:00:01.425 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Initial tip clipper 77s 0:00:01.425 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Initial tip clipper triggered 0 times 77s 0:00:01.425 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Initial ec remover 77s 0:00:01.425 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Initial ec remover triggered 0 times 77s 0:00:01.425 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Initial isolated edge remover 77s 0:00:01.425 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Initial isolated edge remover triggered 0 times 77s 0:00:01.425 1M / 19M INFO StageManager (stage.cpp : 185) STAGE == Simplification (id: simplification) 77s 0:00:01.425 1M / 19M INFO General (simplification.cpp : 368) Graph simplification started 77s 0:00:01.425 1M / 19M INFO General (graph_simplification.hpp : 634) Creating parallel br instance 77s 0:00:01.425 1M / 19M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 1 77s 0:00:01.425 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 77s 0:00:01.425 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 77s 0:00:01.425 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 77s 0:00:01.425 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 77s 0:00:01.425 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 77s 0:00:01.425 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 0 times 77s 0:00:01.426 1M / 19M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 2 77s 0:00:01.426 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 77s 0:00:01.426 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 77s 0:00:01.426 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 77s 0:00:01.426 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 77s 0:00:01.426 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 77s 0:00:01.426 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 0 times 77s 0:00:01.426 1M / 19M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 3 77s 0:00:01.426 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 77s 0:00:01.426 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 77s 0:00:01.426 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 77s 0:00:01.426 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 77s 0:00:01.426 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 77s 0:00:01.426 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 0 times 77s 0:00:01.426 1M / 19M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 4 77s 0:00:01.426 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 77s 0:00:01.426 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 77s 0:00:01.426 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 77s 0:00:01.426 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 77s 0:00:01.426 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 77s 0:00:01.426 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 0 times 77s 0:00:01.427 1M / 19M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 5 77s 0:00:01.427 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 77s 0:00:01.427 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 77s 0:00:01.427 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 77s 0:00:01.427 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 77s 0:00:01.427 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 77s 0:00:01.427 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 0 times 77s 0:00:01.427 1M / 19M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 6 77s 0:00:01.427 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 77s 0:00:01.427 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 77s 0:00:01.427 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 77s 0:00:01.427 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 77s 0:00:01.427 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 77s 0:00:01.427 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 0 times 77s 0:00:01.427 1M / 19M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 7 77s 0:00:01.428 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 77s 0:00:01.428 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 77s 0:00:01.428 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 77s 0:00:01.428 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 77s 0:00:01.428 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 77s 0:00:01.428 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 0 times 77s 0:00:01.428 1M / 19M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 8 77s 0:00:01.428 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 77s 0:00:01.428 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 77s 0:00:01.428 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 77s 0:00:01.428 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 77s 0:00:01.428 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 77s 0:00:01.428 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 0 times 77s 0:00:01.428 1M / 19M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 9 77s 0:00:01.428 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 77s 0:00:01.428 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 77s 0:00:01.428 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 77s 0:00:01.428 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 77s 0:00:01.428 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 77s 0:00:01.428 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 0 times 77s 0:00:01.428 1M / 19M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 10 77s 0:00:01.428 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 77s 0:00:01.428 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 77s 0:00:01.428 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 77s 0:00:01.428 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 77s 0:00:01.428 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 77s 0:00:01.428 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 0 times 77s 0:00:01.428 1M / 19M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 11 77s 0:00:01.428 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 77s 0:00:01.428 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 77s 0:00:01.428 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 77s 0:00:01.428 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 77s 0:00:01.428 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 77s 0:00:01.428 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 0 times 77s 0:00:01.428 1M / 19M INFO StageManager (stage.cpp : 185) STAGE == Simplification Cleanup (id: simplification_cleanup) 77s 0:00:01.428 1M / 19M INFO General (simplification.cpp : 176) PROCEDURE == Post simplification 77s 0:00:01.428 1M / 19M INFO General (graph_simplification.hpp : 448) Disconnection of relatively low covered edges disabled 77s 0:00:01.428 1M / 19M INFO General (graph_simplification.hpp : 485) Complex tip clipping disabled 77s 0:00:01.428 1M / 19M INFO General (graph_simplification.hpp : 634) Creating parallel br instance 77s 0:00:01.428 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 77s 0:00:01.428 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 77s 0:00:01.428 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 77s 0:00:01.428 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 77s 0:00:01.428 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 77s 0:00:01.428 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 77s 0:00:01.428 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 77s 0:00:01.428 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 77s 0:00:01.428 1M / 19M INFO General (simplification.cpp : 327) Disrupting self-conjugate edges 77s 0:00:01.428 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Removing isolated edges 77s 0:00:01.428 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Removing isolated edges triggered 0 times 77s 0:00:01.428 1M / 19M INFO General (simplification.cpp : 495) After simplification: 77s 0:00:01.428 1M / 19M INFO General (simplification.cpp : 496) Average coverage = 225.839 77s 0:00:01.428 1M / 19M INFO General (simplification.cpp : 497) Total length = 967 77s 0:00:01.428 1M / 19M INFO General (simplification.cpp : 498) Median edge length: 967 77s 0:00:01.428 1M / 19M INFO General (simplification.cpp : 499) Edges: 2 77s 0:00:01.428 1M / 19M INFO General (simplification.cpp : 500) Vertices: 4 77s 0:00:01.428 1M / 19M INFO StageManager (stage.cpp : 185) STAGE == Contig Output (id: contig_output) 77s 0:00:01.428 1M / 19M INFO General (read_converter.cpp : 107) Outputting contigs to /tmp/tmp.cMLX1ajB23/spades_test/K33/simplified_contigs 77s 0:00:01.429 3M / 19M INFO General (binary_converter.cpp : 111) 1 reads written 77s 0:00:01.429 1M / 19M INFO General (pipeline.cpp : 287) SPAdes finished 77s 0:00:01.429 1M / 19M INFO General (main.cpp : 136) Assembling time: 0 hours 0 minutes 1 seconds 77s 77s ===== K33 finished. 77s 77s 77s ===== K55 started. 77s 77s 77s == Running: /usr/libexec/spades/spades-core /tmp/tmp.cMLX1ajB23/spades_test/K55/configs/config.info 77s 77s 0:00:00.000 1M / 19M INFO General (main.cpp : 99) Loaded config from /tmp/tmp.cMLX1ajB23/spades_test/K55/configs/config.info 77s 0:00:00.000 1M / 19M INFO General (memory_limit.cpp : 54) Memory limit set to 3 Gb 77s 0:00:00.000 1M / 19M INFO General (main.cpp : 107) Starting SPAdes, built from N/A, git revision N/A 77s 0:00:00.000 1M / 19M INFO General (main.cpp : 108) Maximum k-mer length: 128 77s 0:00:00.000 1M / 19M INFO General (main.cpp : 109) Assembling dataset (/tmp/tmp.cMLX1ajB23/spades_test/dataset.info) with K=55 77s 0:00:00.000 1M / 19M INFO General (main.cpp : 110) Maximum # of threads to use (adjusted due to OMP capabilities): 2 77s 0:00:00.000 1M / 19M INFO General (pipeline.cpp : 212) SPAdes started 77s 0:00:00.000 1M / 19M INFO General (pipeline.cpp : 225) Starting from stage: read_conversion 77s 0:00:00.000 1M / 19M INFO General (pipeline.cpp : 231) Two-step repeat resolution disabled 77s 0:00:00.000 1M / 19M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 77s 0:00:00.000 1M / 19M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 77s 0:00:00.000 1M / 19M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 77s 0:00:00.000 1M / 19M INFO General (pipeline.cpp : 242) Will need read mapping, kmer mapper will be attached 77s 0:00:00.000 1M / 19M INFO StageManager (stage.cpp : 185) STAGE == Binary Read Conversion (id: read_conversion) 77s 0:00:00.000 1M / 19M INFO General (read_converter.cpp : 53) Binary reads detected 77s 0:00:00.000 1M / 19M INFO StageManager (stage.cpp : 185) STAGE == de Bruijn graph construction (id: construction) 77s 0:00:00.000 1M / 19M INFO General (construction.cpp : 118) Contigs from previous K will be used: /tmp/tmp.cMLX1ajB23/spades_test/K33/simplified_contigs 77s 0:00:00.000 1M / 19M INFO General (construction.cpp : 153) Max read length 100 77s 0:00:00.000 1M / 19M INFO General (construction.cpp : 159) Average read length 86.1526 77s 0:00:00.000 1M / 19M INFO General (stage.cpp : 117) PROCEDURE == k+1-mer counting (id: construction:kpomer_counting) 77s 0:00:00.000 1M / 19M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 20 files using 2 threads. This might take a while. 77s 0:00:00.000 1M / 19M INFO General (file_limit.hpp : 42) Open file limit set to 1024 77s 0:00:00.000 1M / 19M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 0.49997 Gb 77s 0:00:00.000 1M / 19M INFO General (kmer_splitter.hpp : 101) Using cell size of 1677621 77s 0:00:00.007 1M / 19M INFO General (kmer_splitters.hpp : 131) Used 8218 reads 77s 0:00:00.007 1M / 19M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. 77s 0:00:00.009 1M / 19M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 949 kmers in total. 77s 0:00:00.009 1M / 19M INFO General (stage.cpp : 117) PROCEDURE == Extension index construction (id: construction:extension_index_construction) 77s 0:00:00.009 1M / 19M INFO K-mer Index Building (kmer_index_builder.hpp : 438) Building kmer index 77s 0:00:00.009 1M / 19M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 20 files using 2 threads. This might take a while. 77s 0:00:00.009 1M / 19M INFO General (file_limit.hpp : 42) Open file limit set to 1024 77s 0:00:00.009 1M / 19M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 0.499967 Gb 77s 0:00:00.009 1M / 19M INFO General (kmer_splitter.hpp : 101) Using cell size of 1677612 77s 0:00:00.010 1161M / 1161M INFO General (kmer_splitters.hpp : 199) Used 949 kmers. 77s 0:00:00.010 1M / 19M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. 77s 0:00:00.012 1M / 19M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 951 kmers in total. 77s 0:00:00.012 1M / 19M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices 77s 0:00:00.013 1M / 19M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 951 kmers, 16384 bytes occupied (137.825 bits per kmer). 77s 0:00:00.013 1M / 19M INFO General (kmer_index_builder.hpp : 169) Merging final buckets. 77s 0:00:00.014 1M / 19M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 100) Building k-mer extensions from k+1-mers 77s 0:00:00.015 1M / 19M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 105) Building k-mer extensions from k+1-mers finished. 77s 0:00:00.015 1M / 19M INFO General (stage.cpp : 117) PROCEDURE == Condensing graph (id: construction:graph_condensing) 77s 0:00:00.015 1M / 19M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths 77s 0:00:00.015 1M / 19M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 4 sequences extracted 77s 0:00:00.015 1M / 19M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops 77s 0:00:00.015 1M / 19M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 0 loops collected 77s 0:00:00.015 1M / 19M INFO General (debruijn_graph_constructor: 487) Total 8 edges to create 77s 0:00:00.016 1M / 19M INFO General (debruijn_graph_constructor: 489) Collecting link records 77s 0:00:00.016 1M / 19M INFO General (debruijn_graph_constructor: 491) Ordering link records 77s 0:00:00.016 1M / 19M INFO General (debruijn_graph_constructor: 493) Sorting done 77s 0:00:00.016 1M / 19M INFO General (debruijn_graph_constructor: 503) Total 6 vertices to create 77s 0:00:00.016 1M / 19M INFO General (debruijn_graph_constructor: 506) Connecting the graph 77s 0:00:00.016 1M / 19M INFO General (stage.cpp : 117) PROCEDURE == Filling coverage indices (PHM) (id: construction:coverage_filling_phm) 77s 0:00:00.016 1M / 19M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices 77s 0:00:00.017 1M / 19M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 949 kmers, 16392 bytes occupied (138.183 bits per kmer). 77s 0:00:00.018 1M / 19M INFO General (coverage_hash_map_builder.: 47) Collecting k-mer coverage information from reads, this takes a while. 77s 0:00:00.025 1M / 19M INFO General (construction.cpp : 430) Filling coverage and flanking coverage from PHM 77s 0:00:00.025 1M / 19M INFO StageManager (stage.cpp : 185) STAGE == EC Threshold Finding (id: ec_threshold_finder) 77s 0:00:00.025 1M / 19M INFO General (kmer_coverage_model.cpp : 181) Kmer coverage valley at: 0 77s 0:00:00.025 1M / 19M INFO General (kmer_coverage_model.cpp : 201) K-mer histogram maximum: 6 77s 0:00:00.025 1M / 19M INFO General (kmer_coverage_model.cpp : 237) Estimated median coverage: 6. Coverage mad: 4.4478 77s 0:00:00.025 1M / 19M INFO General (kmer_coverage_model.cpp : 259) Fitting coverage model 77s 0:00:00.029 1M / 19M INFO General (kmer_coverage_model.cpp : 295) ... iteration 2 77s 0:00:00.041 1M / 19M INFO General (kmer_coverage_model.cpp : 295) ... iteration 4 77s 0:00:00.079 1M / 19M INFO General (kmer_coverage_model.cpp : 295) ... iteration 8 77s 0:00:00.132 1M / 19M INFO General (kmer_coverage_model.cpp : 295) ... iteration 16 77s 0:00:00.180 1M / 19M INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 13.7375. Fitted coverage std. dev: 9.60863 77s 0:00:00.180 1M / 19M INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 2.02732e-07 77s 0:00:00.180 1M / 19M INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 1 77s 0:00:00.180 1M / 19M INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 1 77s 0:00:00.180 1M / 19M INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 238 77s 0:00:00.180 1M / 19M INFO General (genomic_info_filler.cpp : 55) Mean coverage was calculated as 13.7375 77s 0:00:00.180 1M / 19M INFO General (genomic_info_filler.cpp : 70) EC coverage threshold value was calculated as 1 77s 0:00:00.180 1M / 19M INFO General (genomic_info_filler.cpp : 71) Trusted kmer low bound: 0 77s 0:00:00.180 1M / 19M INFO StageManager (stage.cpp : 185) STAGE == Gap Closer (id: early_gapcloser) 77s 0:00:00.185 10M / 20M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 77s 0:00:00.185 10M / 20M INFO General (gap_closer.cpp : 101) Total edges in tip neighborhood: 7 out of 8, length: 1520 77s 0:00:00.185 10M / 20M INFO General (edge_index.hpp : 167) Using small index (max_id = 11) 77s 0:00:00.185 10M / 20M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices 77s 0:00:00.185 10M / 20M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 949 kmers, 1456 bytes occupied (12.274 bits per kmer). 77s 0:00:00.185 10M / 20M INFO General (edge_index_builders.hpp : 265) Collecting edge information from graph, this takes a while. 77s 0:00:00.187 10M / 20M INFO General (sequence_mapper_notifier.h: 95) Total 2054 reads processed 77s 0:00:00.188 10M / 20M INFO General (gap_closer.cpp : 452) Initializing gap closer 77s 0:00:00.188 10M / 20M INFO GapCloser (gap_closer.cpp : 359) Closing short gaps 77s 0:00:00.188 10M / 20M INFO GapCloser (gap_closer.cpp : 391) Closing short gaps complete: filled 0 gaps after checking 4 candidates 77s 0:00:00.188 10M / 20M INFO General (gap_closer.cpp : 456) Gap closer done 77s 0:00:00.189 1M / 20M INFO StageManager (stage.cpp : 185) STAGE == Raw Simplification (id: raw_simplification) 77s 0:00:00.189 1M / 20M INFO General (simplification.cpp : 127) PROCEDURE == Initial cleaning 77s 0:00:00.189 1M / 20M INFO General (graph_simplification.hpp : 662) Flanking coverage based disconnection disabled 77s 0:00:00.189 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Self conjugate edge remover 77s 0:00:00.189 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Self conjugate edge remover triggered 0 times 77s 0:00:00.189 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Initial tip clipper 77s 0:00:00.189 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Initial tip clipper triggered 0 times 77s 0:00:00.189 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Initial ec remover 77s 0:00:00.189 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Initial ec remover triggered 0 times 77s 0:00:00.189 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Initial isolated edge remover 77s 0:00:00.189 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Initial isolated edge remover triggered 1 times 77s 0:00:00.189 1M / 20M INFO StageManager (stage.cpp : 185) STAGE == Simplification (id: simplification) 77s 0:00:00.189 1M / 20M INFO General (simplification.cpp : 368) Graph simplification started 77s 0:00:00.189 1M / 20M INFO General (graph_simplification.hpp : 634) Creating parallel br instance 77s 0:00:00.189 1M / 20M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 1 77s 0:00:00.189 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 77s 0:00:00.190 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 1 times 77s 0:00:00.190 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 77s 0:00:00.190 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 77s 0:00:00.190 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 77s 0:00:00.190 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 0 times 77s 0:00:00.190 1M / 20M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 2 77s 0:00:00.190 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 77s 0:00:00.190 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 77s 0:00:00.190 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 77s 0:00:00.190 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 77s 0:00:00.190 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 77s 0:00:00.190 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 0 times 77s 0:00:00.190 1M / 20M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 3 77s 0:00:00.190 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 77s 0:00:00.190 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 77s 0:00:00.190 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 77s 0:00:00.190 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 77s 0:00:00.191 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 77s 0:00:00.191 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 0 times 77s 0:00:00.191 1M / 20M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 4 77s 0:00:00.191 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 77s 0:00:00.191 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 77s 0:00:00.191 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 77s 0:00:00.191 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 77s 0:00:00.191 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 77s 0:00:00.191 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 0 times 77s 0:00:00.191 1M / 20M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 5 77s 0:00:00.191 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 77s 0:00:00.191 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 77s 0:00:00.191 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 77s 0:00:00.191 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 77s 0:00:00.191 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 77s 0:00:00.191 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 0 times 77s 0:00:00.191 1M / 20M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 6 77s 0:00:00.191 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 77s 0:00:00.191 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 77s 0:00:00.191 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 77s 0:00:00.191 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 77s 0:00:00.192 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 77s 0:00:00.192 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 0 times 77s 0:00:00.192 1M / 20M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 7 77s 0:00:00.192 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 77s 0:00:00.192 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 77s 0:00:00.192 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 77s 0:00:00.192 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 77s 0:00:00.192 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 77s 0:00:00.192 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 0 times 77s 0:00:00.192 1M / 20M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 8 77s 0:00:00.192 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 77s 0:00:00.192 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 77s 0:00:00.192 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 77s 0:00:00.192 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 77s 0:00:00.192 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 77s 0:00:00.192 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 0 times 77s 0:00:00.192 1M / 20M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 9 77s 0:00:00.192 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 77s 0:00:00.192 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 77s 0:00:00.192 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 77s 0:00:00.192 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 77s 0:00:00.192 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 77s 0:00:00.192 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 0 times 77s 0:00:00.192 1M / 20M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 10 77s 0:00:00.192 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 77s 0:00:00.192 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 77s 0:00:00.192 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 77s 0:00:00.192 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 77s 0:00:00.192 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 77s 0:00:00.192 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 0 times 77s 0:00:00.192 1M / 20M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 11 77s 0:00:00.192 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 77s 0:00:00.192 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 77s 0:00:00.192 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 77s 0:00:00.192 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 77s 0:00:00.192 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 77s 0:00:00.192 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 0 times 77s 0:00:00.192 1M / 20M INFO StageManager (stage.cpp : 185) STAGE == Gap Closer (id: late_gapcloser) 77s 0:00:00.193 10M / 20M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 77s 0:00:00.193 10M / 20M INFO General (gap_closer.cpp : 101) Total edges in tip neighborhood: 2 out of 2, length: 1890 77s 0:00:00.193 10M / 20M INFO General (edge_index.hpp : 167) Using small index (max_id = 11) 77s 0:00:00.193 10M / 20M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices 77s 0:00:00.193 10M / 20M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 945 kmers, 1456 bytes occupied (12.3259 bits per kmer). 77s 0:00:00.193 10M / 20M INFO General (edge_index_builders.hpp : 265) Collecting edge information from graph, this takes a while. 77s 0:00:00.196 10M / 20M INFO General (sequence_mapper_notifier.h: 95) Total 2054 reads processed 77s 0:00:00.197 10M / 20M INFO General (gap_closer.cpp : 452) Initializing gap closer 77s 0:00:00.197 10M / 20M INFO GapCloser (gap_closer.cpp : 359) Closing short gaps 77s 0:00:00.197 10M / 20M INFO GapCloser (gap_closer.cpp : 391) Closing short gaps complete: filled 0 gaps after checking 0 candidates 77s 0:00:00.197 10M / 20M INFO General (gap_closer.cpp : 456) Gap closer done 77s 0:00:00.197 1M / 20M INFO StageManager (stage.cpp : 185) STAGE == Simplification Cleanup (id: simplification_cleanup) 77s 0:00:00.197 1M / 20M INFO General (simplification.cpp : 176) PROCEDURE == Post simplification 77s 0:00:00.197 1M / 20M INFO General (graph_simplification.hpp : 448) Disconnection of relatively low covered edges disabled 77s 0:00:00.197 1M / 20M INFO General (graph_simplification.hpp : 485) Complex tip clipping disabled 77s 0:00:00.197 1M / 20M INFO General (graph_simplification.hpp : 634) Creating parallel br instance 77s 0:00:00.197 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 77s 0:00:00.197 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 77s 0:00:00.197 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 77s 0:00:00.198 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 77s 0:00:00.198 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 77s 0:00:00.198 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 77s 0:00:00.198 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 77s 0:00:00.198 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 77s 0:00:00.198 1M / 20M INFO General (simplification.cpp : 327) Disrupting self-conjugate edges 77s 0:00:00.198 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Removing isolated edges 77s 0:00:00.198 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Removing isolated edges triggered 0 times 77s 0:00:00.198 1M / 20M INFO General (simplification.cpp : 495) After simplification: 77s 0:00:00.198 1M / 20M INFO General (simplification.cpp : 496) Average coverage = 140.62 77s 0:00:00.198 1M / 20M INFO General (simplification.cpp : 497) Total length = 945 77s 0:00:00.198 1M / 21M INFO General (simplification.cpp : 498) Median edge length: 945 77s 0:00:00.198 1M / 21M INFO General (simplification.cpp : 499) Edges: 2 77s 0:00:00.198 1M / 21M INFO General (simplification.cpp : 500) Vertices: 4 77s 0:00:00.198 1M / 21M INFO StageManager (stage.cpp : 185) STAGE == Mismatch Correction (id: mismatch_correction) 77s 0:00:00.198 1M / 21M INFO General (graph_pack.cpp : 67) Index refill 77s 0:00:00.198 1M / 21M INFO General (edge_index.hpp : 156) Using small index (max_id = 11) 77s 0:00:00.199 1M / 21M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices 77s 0:00:00.199 1M / 21M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 945 kmers, 1456 bytes occupied (12.3259 bits per kmer). 77s 0:00:00.199 1M / 21M INFO General (edge_index_builders.hpp : 252) Collecting edge information from graph, this takes a while. 77s 0:00:00.199 1M / 21M INFO General (graph_pack.cpp : 77) Normalizing k-mer map. Total 0 kmers to process 77s 0:00:00.199 1M / 21M INFO General (graph_pack.cpp : 79) Normalizing done 77s 0:00:00.199 1M / 21M INFO General (mismatch_correction.cpp : 400) Collect potential mismatches 77s 0:00:00.199 1M / 21M INFO General (mismatch_correction.cpp : 192) Total 0 edges (out of 2) with 0 potential mismatch positions (-nan positions per edge) 77s 0:00:00.199 1M / 21M INFO General (mismatch_correction.cpp : 402) Potential mismatches collected 77s 0:00:00.203 1M / 21M INFO General (sequence_mapper_notifier.h: 95) Total 8216 reads processed 77s 0:00:00.203 1M / 21M INFO General (mismatch_correction.cpp : 395) All edges processed 77s 0:00:00.203 1M / 21M INFO General (mismatch_correction.cpp : 450) Corrected 0 nucleotides 77s 0:00:00.203 1M / 21M INFO StageManager (stage.cpp : 185) STAGE == Contig Output (id: contig_output) 77s 0:00:00.203 1M / 21M INFO General (contig_output.hpp : 16) Outputting contigs to /tmp/tmp.cMLX1ajB23/spades_test/K55/before_rr.fasta 77s 0:00:00.203 1M / 21M INFO General (contig_output_stage.cpp : 151) Writing GFA graph to /tmp/tmp.cMLX1ajB23/spades_test/K55/assembly_graph_after_simplification.gfa 77s 0:00:00.203 1M / 21M INFO StageManager (stage.cpp : 185) STAGE == Paired Information Counting (id: late_pair_info_count) 77s 0:00:00.203 1M / 21M INFO General (graph_pack.cpp : 77) Normalizing k-mer map. Total 0 kmers to process 77s 0:00:00.203 1M / 21M INFO General (graph_pack.cpp : 79) Normalizing done 77s 0:00:00.203 1M / 21M INFO General (pair_info_count.cpp : 339) Min edge length for estimation: 945 77s 0:00:00.203 1M / 21M INFO General (pair_info_count.cpp : 350) Estimating insert size for library #0 77s 0:00:00.204 1M / 21M INFO General (pair_info_count.cpp : 202) Estimating insert size (takes a while) 77s 0:00:00.221 49M / 60M INFO General (pair_info_count.cpp : 48) Selecting usual mapper 77s 0:00:00.244 49M / 60M INFO General (sequence_mapper_notifier.h: 95) Total 2054 reads processed 77s 0:00:00.309 49M / 60M INFO General (pair_info_count.cpp : 220) Edge pairs: 2 77s 0:00:00.309 49M / 60M INFO General (pair_info_count.cpp : 222) 1636 paired reads (79.6495% of all) aligned to long edges 77s 0:00:00.309 1M / 60M INFO General (pair_info_count.cpp : 369) Insert size = 214.696, deviation = 10.4821, left quantile = 201, right quantile = 228, read length = 100 77s 0:00:00.309 1M / 60M INFO General (pair_info_count.cpp : 390) Filtering data for library #0 77s 0:00:00.310 1M / 60M INFO General (pair_info_count.cpp : 48) Selecting usual mapper 77s 0:00:00.311 1M / 60M INFO General (sequence_mapper_notifier.h: 95) Total 2054 reads processed 77s 0:00:00.311 1M / 60M INFO General (pair_info_count.cpp : 402) Mapping library #0 77s 0:00:00.312 1M / 60M INFO General (pair_info_count.cpp : 404) Mapping paired reads (takes a while) 77s 0:00:00.312 1M / 60M INFO General (pair_info_count.cpp : 299) Left insert size quantile 201, right insert size quantile 228, filtering threshold 2, rounding threshold 0 77s 0:00:00.313 10M / 60M INFO General (pair_info_count.cpp : 48) Selecting usual mapper 77s 0:00:00.315 10M / 60M INFO General (sequence_mapper_notifier.h: 95) Total 2054 reads processed 77s 0:00:00.316 1M / 60M INFO StageManager (stage.cpp : 185) STAGE == Distance Estimation (id: distance_estimation) 77s 0:00:00.316 1M / 60M INFO General (distance_estimation.cpp : 179) Processing library #0 77s 0:00:00.317 1M / 60M INFO General (distance_estimation.cpp : 150) Weight Filter Done 77s 0:00:00.317 1M / 60M INFO DistanceEstimator (distance_estimation.hpp : 116) Using SIMPLE distance estimator 77s 0:00:00.317 1M / 60M INFO General (distance_estimation.cpp : 37) Filtering info 77s 0:00:00.317 1M / 60M INFO General (pair_info_filters.hpp : 242) Start filtering; library index size: 2 77s 0:00:00.317 1M / 60M INFO General (pair_info_filters.hpp : 263) Done filtering; library index size: 2 77s 0:00:00.317 1M / 60M INFO General (distance_estimation.cpp : 156) Refining clustered pair information 77s 0:00:00.317 1M / 60M INFO General (distance_estimation.cpp : 158) The refining of clustered pair information has been finished 77s 0:00:00.317 1M / 60M INFO General (distance_estimation.cpp : 160) Improving paired information 77s 0:00:00.317 1M / 60M INFO PairInfoImprover (pair_info_improver.hpp : 104) Paired info stats: missing = 0; contradictional = 0 77s 0:00:00.317 1M / 60M INFO PairInfoImprover (pair_info_improver.hpp : 104) Paired info stats: missing = 0; contradictional = 0 77s 0:00:00.317 1M / 60M INFO General (distance_estimation.cpp : 104) Filling scaffolding index 77s 0:00:00.317 1M / 60M INFO DistanceEstimator (distance_estimation.hpp : 116) Using SMOOTHING distance estimator 77s 0:00:00.317 1M / 60M INFO General (distance_estimation.cpp : 37) Filtering info 77s 0:00:00.317 1M / 60M INFO General (pair_info_filters.hpp : 242) Start filtering; library index size: 2 77s 0:00:00.317 1M / 60M INFO General (pair_info_filters.hpp : 263) Done filtering; library index size: 2 77s 0:00:00.318 1M / 60M INFO General (distance_estimation.cpp : 186) Clearing raw paired index 77s 0:00:00.318 1M / 60M INFO StageManager (stage.cpp : 185) STAGE == Repeat Resolving (id: repeat_resolving) 77s 0:00:00.318 1M / 60M INFO General (repeat_resolving.cpp : 87) Using Path-Extend repeat resolving 77s 0:00:00.318 1M / 60M INFO General (launcher.cpp : 600) ExSPAnder repeat resolving tool started 77s 0:00:00.318 1M / 60M INFO General (coverage_uniformity_analyz: 25) genomic coverage is 140.62 calculated of length 945 77s 0:00:00.318 1M / 60M WARN General (launcher.cpp : 178) Your data seems to have high uniform coverage depth. It is strongly recommended to use --isolate option. 77s 0:00:00.318 1M / 60M INFO General (launcher.cpp : 418) Creating main extenders, unique edge length = 2000 77s 0:00:00.318 1M / 60M INFO General (extenders_logic.cpp : 334) Estimated coverage of library #0 is 140.62 77s 0:00:00.318 1M / 60M INFO General (extenders_logic.cpp : 345) Creating extender; library index size: 2 77s 0:00:00.318 1M / 60M INFO General (extenders_logic.cpp : 334) Estimated coverage of library #0 is 140.62 77s 0:00:00.318 1M / 60M INFO General (extenders_logic.cpp : 345) Creating extender; library index size: 2 77s 0:00:00.318 1M / 60M INFO General (extenders_logic.cpp : 543) Using 1 paired-end library 77s 0:00:00.318 1M / 60M INFO General (extenders_logic.cpp : 544) Using 1 paired-end scaffolding library 77s 0:00:00.318 1M / 60M INFO General (extenders_logic.cpp : 545) Using 0 single read libraries 77s 0:00:00.318 1M / 60M INFO General (launcher.cpp : 447) Total number of extenders is 3 77s 0:00:00.318 1M / 60M INFO General (launcher.cpp : 250) Finalizing paths 77s 0:00:00.318 1M / 60M INFO General (launcher.cpp : 252) Deduplicating paths 77s 0:00:00.318 1M / 60M INFO General (launcher.cpp : 256) Paths deduplicated 77s 0:00:00.318 1M / 60M INFO PEResolver (pe_resolver.cpp : 60) Removing overlaps 77s 0:00:00.318 1M / 60M INFO PEResolver (pe_resolver.cpp : 63) Sorting paths 77s 0:00:00.318 1M / 60M INFO PEResolver (pe_resolver.cpp : 70) Marking overlaps 77s 0:00:00.318 1M / 60M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps 77s 0:00:00.318 1M / 60M INFO OverlapRemover (overlap_remover.hpp : 119) Marking remaining overlaps 77s 0:00:00.318 1M / 60M INFO PEResolver (pe_resolver.cpp : 73) Splitting paths 77s 0:00:00.318 1M / 60M INFO PEResolver (pe_resolver.cpp : 78) Deduplicating paths 77s 0:00:00.318 1M / 60M INFO PEResolver (pe_resolver.cpp : 80) Overlaps removed 77s 0:00:00.318 1M / 60M INFO General (launcher.cpp : 273) Paths finalized 77s 0:00:00.318 1M / 60M INFO General (launcher.cpp : 454) Closing gaps in paths 77s 0:00:00.318 1M / 60M INFO General (launcher.cpp : 484) Gap closing completed 77s 0:00:00.318 1M / 60M INFO General (launcher.cpp : 302) Traversing tandem repeats 77s 0:00:00.318 1M / 60M INFO General (launcher.cpp : 312) Traversed 0 loops 77s 0:00:00.318 1M / 60M INFO General (launcher.cpp : 250) Finalizing paths 77s 0:00:00.319 1M / 60M INFO General (launcher.cpp : 252) Deduplicating paths 77s 0:00:00.319 1M / 60M INFO General (launcher.cpp : 256) Paths deduplicated 77s 0:00:00.319 1M / 60M INFO PEResolver (pe_resolver.cpp : 60) Removing overlaps 77s 0:00:00.319 1M / 60M INFO PEResolver (pe_resolver.cpp : 63) Sorting paths 77s 0:00:00.319 1M / 60M INFO PEResolver (pe_resolver.cpp : 70) Marking overlaps 77s 0:00:00.319 1M / 60M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps 77s 0:00:00.319 1M / 60M INFO OverlapRemover (overlap_remover.hpp : 119) Marking remaining overlaps 77s 0:00:00.319 1M / 60M INFO PEResolver (pe_resolver.cpp : 73) Splitting paths 77s 0:00:00.319 1M / 60M INFO PEResolver (pe_resolver.cpp : 78) Deduplicating paths 77s 0:00:00.319 1M / 60M INFO PEResolver (pe_resolver.cpp : 80) Overlaps removed 77s 0:00:00.319 1M / 60M INFO General (launcher.cpp : 273) Paths finalized 77s 0:00:00.319 1M / 60M INFO General (launcher.cpp : 664) ExSPAnder repeat resolving tool finished 77s 0:00:00.319 1M / 60M INFO StageManager (stage.cpp : 185) STAGE == Contig Output (id: contig_output) 77s 0:00:00.319 1M / 60M INFO General (contig_output.hpp : 16) Outputting contigs to /tmp/tmp.cMLX1ajB23/spades_test/K55/before_rr.fasta 77s 0:00:00.319 1M / 60M INFO General (contig_output_stage.cpp : 151) Writing GFA graph to /tmp/tmp.cMLX1ajB23/spades_test/K55/assembly_graph_with_scaffolds.gfa 77s 0:00:00.319 1M / 60M INFO General (contig_output_stage.cpp : 165) Outputting FastG graph to /tmp/tmp.cMLX1ajB23/spades_test/K55/assembly_graph.fastg 77s 0:00:00.319 1M / 60M INFO General (contig_output_stage.cpp : 196) Breaking scaffolds 77s 0:00:00.320 1M / 60M INFO General (contig_output_stage.cpp : 98) Outputting contigs to /tmp/tmp.cMLX1ajB23/spades_test/K55/final_contigs.fasta 77s 0:00:00.320 1M / 60M INFO General (contig_output_stage.cpp : 104) Outputting FastG paths to /tmp/tmp.cMLX1ajB23/spades_test/K55/final_contigs.paths 77s 0:00:00.320 1M / 60M INFO General (contig_output_stage.cpp : 98) Outputting contigs to /tmp/tmp.cMLX1ajB23/spades_test/K55/scaffolds.fasta 77s 0:00:00.320 1M / 60M INFO General (contig_output_stage.cpp : 104) Outputting FastG paths to /tmp/tmp.cMLX1ajB23/spades_test/K55/scaffolds.paths 77s 0:00:00.320 1M / 60M INFO General (contig_output_stage.cpp : 111) Populating GFA with scaffold paths 77s 0:00:00.320 1M / 60M INFO General (pipeline.cpp : 287) SPAdes finished 77s 0:00:00.320 1M / 60M INFO General (main.cpp : 136) Assembling time: 0 hours 0 minutes 0 seconds 77s 77s ===== K55 finished. 77s 77s 77s ===== Copy files started. 77s 77s 77s == Running: /usr/bin/python3 /usr/share/spades/spades_pipeline/scripts/copy_files.py /tmp/tmp.cMLX1ajB23/spades_test/K55/before_rr.fasta /tmp/tmp.cMLX1ajB23/spades_test/before_rr.fasta /tmp/tmp.cMLX1ajB23/spades_test/K55/assembly_graph_after_simplification.gfa /tmp/tmp.cMLX1ajB23/spades_test/assembly_graph_after_simplification.gfa /tmp/tmp.cMLX1ajB23/spades_test/K55/final_contigs.fasta /tmp/tmp.cMLX1ajB23/spades_test/contigs.fasta /tmp/tmp.cMLX1ajB23/spades_test/K55/first_pe_contigs.fasta /tmp/tmp.cMLX1ajB23/spades_test/first_pe_contigs.fasta /tmp/tmp.cMLX1ajB23/spades_test/K55/strain_graph.gfa /tmp/tmp.cMLX1ajB23/spades_test/strain_graph.gfa /tmp/tmp.cMLX1ajB23/spades_test/K55/scaffolds.fasta /tmp/tmp.cMLX1ajB23/spades_test/scaffolds.fasta /tmp/tmp.cMLX1ajB23/spades_test/K55/scaffolds.paths /tmp/tmp.cMLX1ajB23/spades_test/scaffolds.paths /tmp/tmp.cMLX1ajB23/spades_test/K55/assembly_graph_with_scaffolds.gfa /tmp/tmp.cMLX1ajB23/spades_test/assembly_graph_with_scaffolds.gfa /tmp/tmp.cMLX1ajB23/spades_test/K55/assembly_graph.fastg /tmp/tmp.cMLX1ajB23/spades_test/assembly_graph.fastg /tmp/tmp.cMLX1ajB23/spades_test/K55/final_contigs.paths /tmp/tmp.cMLX1ajB23/spades_test/contigs.paths 77s 77s 77s ===== Copy files finished. 77s 77s 77s ===== Assembling finished. 77s 77s 77s ===== Check test started. 77s 77s 77s == Running: /usr/bin/python3 /usr/share/spades/spades_pipeline/scripts/check_test_script.py --mode common --result_contigs_filename /tmp/tmp.cMLX1ajB23/spades_test/contigs.fasta --result_scaffolds_filename /tmp/tmp.cMLX1ajB23/spades_test/scaffolds.fasta 77s 77s ========= TEST PASSED CORRECTLY. 77s 77s ===== Check test finished. 77s 77s 77s ===== Breaking scaffolds started. 77s 77s 77s == Running: /usr/bin/python3 /usr/share/spades/spades_pipeline/scripts/breaking_scaffolds_script.py --result_scaffolds_filename /tmp/tmp.cMLX1ajB23/spades_test/scaffolds.fasta --misc_dir /tmp/tmp.cMLX1ajB23/spades_test/misc --threshold_for_breaking_scaffolds 3 77s 77s 77s ===== Breaking scaffolds finished. 77s 77s 77s ===== Terminate started. 77s 77s 77s ===== Terminate finished. 77s 77s * Corrected reads are in /tmp/tmp.cMLX1ajB23/spades_test/corrected/ 77s * Assembled contigs are in /tmp/tmp.cMLX1ajB23/spades_test/contigs.fasta 77s * Assembled scaffolds are in /tmp/tmp.cMLX1ajB23/spades_test/scaffolds.fasta 77s * Paths in the assembly graph corresponding to the contigs are in /tmp/tmp.cMLX1ajB23/spades_test/contigs.paths 77s * Paths in the assembly graph corresponding to the scaffolds are in /tmp/tmp.cMLX1ajB23/spades_test/scaffolds.paths 77s * Assembly graph is in /tmp/tmp.cMLX1ajB23/spades_test/assembly_graph.fastg 77s * Assembly graph in GFA format is in /tmp/tmp.cMLX1ajB23/spades_test/assembly_graph_with_scaffolds.gfa 77s 77s ======= SPAdes pipeline finished WITH WARNINGS! 77s 77s === Error correction and assembling warnings: 77s * 0:00:00.318 1M / 60M WARN General (launcher.cpp : 178) Your data seems to have high uniform coverage depth. It is strongly recommended to use --isolate option. 77s ======= Warnings saved to /tmp/tmp.cMLX1ajB23/spades_test/warnings.log 77s 77s SPAdes log can be found here: /tmp/tmp.cMLX1ajB23/spades_test/spades.log 77s 77s Thank you for using SPAdes! 77s + coronaspades --test 77s Command line: /usr/libexec/spades/coronaspades.py --test 77s 77s System information: 77s SPAdes version: 3.15.5 77s Python version: 3.13.3 77s OS: Linux-6.14.0-15-generic-x86_64-with-glibc2.41 77s 77s Output dir: /tmp/tmp.cMLX1ajB23/spades_test 77s Mode: ONLY assembling (without read error correction) 77s Debug mode is turned OFF 77s 77s Dataset parameters: 77s RNA virus assembly mode 77s Metagenomic mode 77s Reads: 77s Library number: 1, library type: paired-end 77s orientation: fr 77s left reads: ['/usr/share/spades/test_dataset/ecoli_1K_1.fq.gz'] 77s right reads: ['/usr/share/spades/test_dataset/ecoli_1K_2.fq.gz'] 77s interlaced reads: not specified 77s single reads: not specified 77s merged reads: not specified 77s Assembly parameters: 77s k: auto 77s Repeat resolution is enabled 77s Mismatch careful mode is turned OFF 77s MismatchCorrector will be SKIPPED 77s Coverage cutoff is turned OFF 77s Other parameters: 77s Dir for temp files: /tmp/tmp.cMLX1ajB23/spades_test/tmp 77s Threads: 16 77s Memory limit (in Gb): 3 77s 77s 77s ======= SPAdes pipeline started. Log can be found here: /tmp/tmp.cMLX1ajB23/spades_test/spades.log 77s 77s /usr/share/spades/test_dataset/ecoli_1K_1.fq.gz: max reads length: 100 77s /usr/share/spades/test_dataset/ecoli_1K_2.fq.gz: max reads length: 100 77s 77s Reads length: 100 77s 77s K values to be used: [21, 33, 49] 77s 77s ===== Before start started. 77s 77s 77s ===== Assembling started. 77s 77s 77s ===== K21 started. 77s 77s 77s == Running: /usr/libexec/spades/spades-core /tmp/tmp.cMLX1ajB23/spades_test/K21/configs/config.info /tmp/tmp.cMLX1ajB23/spades_test/K21/configs/mda_mode.info /tmp/tmp.cMLX1ajB23/spades_test/K21/configs/meta_mode.info /tmp/tmp.cMLX1ajB23/spades_test/K21/configs/rnaviral_mode.info /tmp/tmp.cMLX1ajB23/spades_test/K21/configs/hmm_mode.info 77s 77s 0:00:00.000 1M / 19M INFO General (main.cpp : 99) Loaded config from /tmp/tmp.cMLX1ajB23/spades_test/K21/configs/config.info 77s 0:00:00.000 1M / 19M INFO General (main.cpp : 99) Loaded config from /tmp/tmp.cMLX1ajB23/spades_test/K21/configs/mda_mode.info 77s 0:00:00.000 1M / 19M INFO General (main.cpp : 99) Loaded config from /tmp/tmp.cMLX1ajB23/spades_test/K21/configs/meta_mode.info 77s 0:00:00.000 1M / 19M INFO General (main.cpp : 99) Loaded config from /tmp/tmp.cMLX1ajB23/spades_test/K21/configs/rnaviral_mode.info 77s 0:00:00.000 1M / 19M INFO General (main.cpp : 99) Loaded config from /tmp/tmp.cMLX1ajB23/spades_test/K21/configs/hmm_mode.info 77s 0:00:00.000 1M / 19M INFO General (memory_limit.cpp : 54) Memory limit set to 3 Gb 77s 0:00:00.000 1M / 19M INFO General (main.cpp : 107) Starting SPAdes, built from N/A, git revision N/A 77s 0:00:00.000 1M / 19M INFO General (main.cpp : 108) Maximum k-mer length: 128 77s 0:00:00.000 1M / 19M INFO General (main.cpp : 109) Assembling dataset (/tmp/tmp.cMLX1ajB23/spades_test/dataset.info) with K=21 77s 0:00:00.000 1M / 19M INFO General (main.cpp : 110) Maximum # of threads to use (adjusted due to OMP capabilities): 2 77s 0:00:00.000 1M / 19M INFO General (pipeline.cpp : 212) SPAdes started 77s 0:00:00.000 1M / 19M INFO General (pipeline.cpp : 225) Starting from stage: read_conversion 77s 0:00:00.000 1M / 19M INFO General (pipeline.cpp : 231) Two-step repeat resolution disabled 77s 0:00:00.000 1M / 19M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 77s 0:00:00.000 1M / 19M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 77s 0:00:00.000 1M / 19M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 77s 0:00:00.000 1M / 19M INFO StageManager (stage.cpp : 185) STAGE == Binary Read Conversion (id: read_conversion) 77s 0:00:00.000 1M / 19M INFO General (read_converter.cpp : 72) Converting reads to binary format for library #0 (takes a while) 77s 0:00:00.000 1M / 19M INFO General (read_converter.cpp : 73) Converting paired reads 77s 0:00:00.008 63M / 63M INFO General (binary_converter.cpp : 111) 2054 reads written 77s 0:00:00.008 41M / 41M INFO General (read_converter.cpp : 86) Converting single reads 77s 0:00:00.008 51M / 51M INFO General (binary_converter.cpp : 111) 0 reads written 77s 0:00:00.008 41M / 41M INFO General (read_converter.cpp : 92) Converting merged reads 77s 0:00:00.008 51M / 51M INFO General (binary_converter.cpp : 111) 0 reads written 77s 0:00:00.009 1M / 19M INFO StageManager (stage.cpp : 185) STAGE == de Bruijn graph construction (id: construction) 77s 0:00:00.009 1M / 19M INFO General (construction.cpp : 153) Max read length 100 77s 0:00:00.009 1M / 19M INFO General (construction.cpp : 159) Average read length 86.1611 77s 0:00:00.009 1M / 19M INFO General (stage.cpp : 117) PROCEDURE == k+1-mer counting (id: construction:kpomer_counting) 77s 0:00:00.009 1M / 19M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 20 files using 2 threads. This might take a while. 77s 0:00:00.009 1M / 19M INFO General (file_limit.hpp : 42) Open file limit set to 1024 77s 0:00:00.009 1M / 19M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 0.499973 Gb 77s 0:00:00.009 1M / 19M INFO General (kmer_splitter.hpp : 101) Using cell size of 3355263 77s 0:00:00.018 1M / 19M INFO General (kmer_splitters.hpp : 131) Used 8216 reads 77s 0:00:00.019 1M / 19M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. 77s 0:00:00.020 1M / 19M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 986 kmers in total. 77s 0:00:00.020 1M / 19M INFO General (stage.cpp : 117) PROCEDURE == Extension index construction (id: construction:extension_index_construction) 77s 0:00:00.020 1M / 19M INFO K-mer Index Building (kmer_index_builder.hpp : 438) Building kmer index 77s 0:00:00.020 1M / 19M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 20 files using 2 threads. This might take a while. 77s 0:00:00.020 1M / 19M INFO General (file_limit.hpp : 42) Open file limit set to 1024 77s 0:00:00.021 1M / 19M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 0.49997 Gb 77s 0:00:00.021 1M / 19M INFO General (kmer_splitter.hpp : 101) Using cell size of 3355244 77s 0:00:00.022 1161M / 1161M INFO General (kmer_splitters.hpp : 199) Used 986 kmers. 77s 0:00:00.022 1M / 19M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. 77s 0:00:00.023 1M / 19M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 987 kmers in total. 77s 0:00:00.023 1M / 19M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices 77s 0:00:00.025 1M / 19M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 987 kmers, 16424 bytes occupied (133.123 bits per kmer). 77s 0:00:00.025 1M / 19M INFO General (kmer_index_builder.hpp : 169) Merging final buckets. 77s 0:00:00.026 1M / 19M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 100) Building k-mer extensions from k+1-mers 77s 0:00:00.026 1M / 19M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 105) Building k-mer extensions from k+1-mers finished. 77s 0:00:00.026 1M / 19M INFO General (stage.cpp : 117) PROCEDURE == Early A/T remover (id: construction:early_at_remover) 77s 0:00:00.026 1M / 19M INFO Early A/T remover (early_simplification.hpp : 176) Remove short poly A/T edges 77s 0:00:00.027 1M / 19M INFO Early A/T remover (early_simplification.hpp : 254) Links removed: 0 77s 0:00:00.027 1M / 19M INFO Early A/T remover (early_simplification.hpp : 179) 0 22-mers were removed by early poly A/T remover 77s 0:00:00.027 1M / 19M INFO Early A/T remover (early_simplification.hpp : 262) Remove poly A/T tips 77s 0:00:00.027 1M / 19M INFO Early A/T remover (early_simplification.hpp : 331) Clipped tips: 0 77s 0:00:00.027 1M / 19M INFO Early A/T remover (early_simplification.hpp : 265) 0 22-mers were removed by early poly A/T tip clipper 77s 0:00:00.027 1M / 19M INFO General (stage.cpp : 117) PROCEDURE == Early tip clipping (id: construction:early_tip_clipper) 77s 0:00:00.027 1M / 19M INFO General (construction.cpp : 301) Early tip clipper length bound set as (RL - K) 77s 0:00:00.027 1M / 19M INFO Early tip clipping (early_simplification.hpp : 47) Early tip clipping 77s 0:00:00.027 1M / 19M INFO Early tip clipping (early_simplification.hpp : 82) #tipped junctions: 2 77s 0:00:00.027 1M / 19M INFO Early tip clipping (early_simplification.hpp : 93) Clipped tips: 2 77s 0:00:00.027 1M / 19M INFO Early tip clipping (early_simplification.hpp : 49) 7 22-mers were removed by early tip clipper 77s 0:00:00.028 1M / 19M INFO General (stage.cpp : 117) PROCEDURE == Condensing graph (id: construction:graph_condensing) 77s 0:00:00.028 1M / 19M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths 77s 0:00:00.028 1M / 19M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 1 sequences extracted 77s 0:00:00.028 1M / 19M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops 77s 0:00:00.028 1M / 19M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 0 loops collected 77s 0:00:00.028 1M / 19M INFO General (debruijn_graph_constructor: 487) Total 2 edges to create 77s 0:00:00.028 1M / 19M INFO General (debruijn_graph_constructor: 489) Collecting link records 77s 0:00:00.028 1M / 19M INFO General (debruijn_graph_constructor: 491) Ordering link records 77s 0:00:00.028 1M / 19M INFO General (debruijn_graph_constructor: 493) Sorting done 77s 0:00:00.029 1M / 19M INFO General (debruijn_graph_constructor: 503) Total 2 vertices to create 77s 0:00:00.029 1M / 19M INFO General (debruijn_graph_constructor: 506) Connecting the graph 77s 0:00:00.029 1M / 19M INFO General (stage.cpp : 117) PROCEDURE == Filling coverage indices (PHM) (id: construction:coverage_filling_phm) 77s 0:00:00.029 1M / 19M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices 77s 0:00:00.030 1M / 19M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 986 kmers, 16392 bytes occupied (132.998 bits per kmer). 77s 0:00:00.030 1M / 19M INFO General (coverage_hash_map_builder.: 47) Collecting k-mer coverage information from reads, this takes a while. 77s 0:00:00.043 1M / 19M INFO General (construction.cpp : 430) Filling coverage and flanking coverage from PHM 77s 0:00:00.044 1M / 19M INFO StageManager (stage.cpp : 185) STAGE == Raw Simplification (id: raw_simplification) 77s 0:00:00.044 1M / 19M INFO General (simplification.cpp : 106) PROCEDURE == Initial cleaning 77s 0:00:00.044 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running poly A/T short edge remover 77s 0:00:00.044 1M / 19M INFO Simplification (parallel_processing.hpp : 170) poly A/T short edge remover triggered 0 times 77s 0:00:00.044 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running poly A/T tip clipper 77s 0:00:00.044 1M / 19M INFO Simplification (parallel_processing.hpp : 170) poly A/T tip clipper triggered 0 times 77s 0:00:00.044 1M / 19M INFO General (graph_simplification.hpp : 703) Removing loops and rc loops with erroneous connections 77s 0:00:00.044 1M / 19M INFO ECLoopRemover (erroneous_connection_remov: 406) Loops: accurately removed/deadend removed/other: 0/0/0 77s 0:00:00.044 1M / 19M INFO ECLoopRemover (erroneous_connection_remov: 407) RC loops: accurately removed/deadend removed/other: 0/0/0 77s 0:00:00.044 1M / 19M INFO General (simplification.cpp : 127) PROCEDURE == Initial cleaning 77s 0:00:00.045 1M / 19M INFO General (graph_simplification.hpp : 662) Flanking coverage based disconnection disabled 77s 0:00:00.045 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Self conjugate edge remover 77s 0:00:00.045 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Self conjugate edge remover triggered 0 times 77s 0:00:00.045 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Initial tip clipper 77s 0:00:00.045 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Initial tip clipper triggered 0 times 77s 0:00:00.045 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Initial ec remover 77s 0:00:00.045 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Initial ec remover triggered 0 times 77s 0:00:00.045 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Initial isolated edge remover 77s 0:00:00.045 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Initial isolated edge remover triggered 0 times 77s 0:00:00.045 1M / 19M INFO StageManager (stage.cpp : 185) STAGE == Simplification (id: simplification) 77s 0:00:00.045 1M / 19M INFO General (simplification.cpp : 368) Graph simplification started 77s 0:00:00.045 1M / 19M INFO General (graph_simplification.hpp : 634) Creating parallel br instance 77s 0:00:00.045 1M / 19M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 1 77s 0:00:00.045 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 77s 0:00:00.045 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 77s 0:00:00.045 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 77s 0:00:00.045 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 77s 0:00:00.045 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 77s 0:00:00.045 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 0 times 77s 0:00:00.045 1M / 19M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 2 77s 0:00:00.045 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 77s 0:00:00.045 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 77s 0:00:00.045 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 77s 0:00:00.045 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 77s 0:00:00.045 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 77s 0:00:00.045 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 0 times 77s 0:00:00.045 1M / 19M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 3 77s 0:00:00.045 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 77s 0:00:00.045 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 77s 0:00:00.045 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 77s 0:00:00.045 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 77s 0:00:00.046 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 77s 0:00:00.046 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 0 times 77s 0:00:00.046 1M / 19M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 4 77s 0:00:00.046 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 77s 0:00:00.046 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 77s 0:00:00.046 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 77s 0:00:00.046 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 77s 0:00:00.046 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 77s 0:00:00.046 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 0 times 77s 0:00:00.046 1M / 19M INFO StageManager (stage.cpp : 185) STAGE == Simplification Cleanup (id: simplification_cleanup) 77s 0:00:00.046 1M / 19M INFO General (simplification.cpp : 176) PROCEDURE == Post simplification 77s 0:00:00.046 1M / 19M INFO General (graph_simplification.hpp : 634) Creating parallel br instance 77s 0:00:00.046 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Relative coverage component remover 77s 0:00:00.046 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Relative coverage component remover triggered 0 times 77s 0:00:00.046 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Disconnecting edges with relatively low coverage 77s 0:00:00.046 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Disconnecting edges with relatively low coverage triggered 0 times 77s 0:00:00.046 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Complex tip clipper 77s 0:00:00.046 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Complex tip clipper triggered 0 times 77s 0:00:00.046 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Complex bulge remover 77s 0:00:00.047 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Complex bulge remover triggered 0 times 77s 0:00:00.047 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 77s 0:00:00.047 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 77s 0:00:00.047 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Final tip clipper 77s 0:00:00.047 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Final tip clipper triggered 0 times 77s 0:00:00.047 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 77s 0:00:00.047 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 77s 0:00:00.047 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Thorn remover (meta) 77s 0:00:00.047 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Thorn remover (meta) triggered 0 times 77s 0:00:00.047 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Relative coverage component remover 77s 0:00:00.047 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Relative coverage component remover triggered 0 times 77s 0:00:00.047 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Disconnecting edges with relatively low coverage 77s 0:00:00.047 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Disconnecting edges with relatively low coverage triggered 0 times 77s 0:00:00.047 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Complex tip clipper 77s 0:00:00.047 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Complex tip clipper triggered 0 times 77s 0:00:00.047 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Complex bulge remover 77s 0:00:00.047 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Complex bulge remover triggered 0 times 77s 0:00:00.047 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 77s 0:00:00.047 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 77s 0:00:00.047 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Final tip clipper 77s 0:00:00.047 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Final tip clipper triggered 0 times 77s 0:00:00.047 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 77s 0:00:00.047 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 77s 0:00:00.047 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Thorn remover (meta) 77s 0:00:00.047 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Thorn remover (meta) triggered 0 times 77s 0:00:00.047 1M / 19M INFO General (simplification.cpp : 323) Running Hidden EC remover (meta) 77s 0:00:00.047 1M / 19M INFO General (simplification.cpp : 327) Disrupting self-conjugate edges 77s 0:00:00.047 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Removing isolated edges 77s 0:00:00.047 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Removing isolated edges triggered 0 times 77s 0:00:00.047 1M / 19M INFO General (simplification.cpp : 495) After simplification: 77s 0:00:00.047 1M / 19M INFO General (simplification.cpp : 496) Average coverage = 273.372 77s 0:00:00.048 1M / 19M INFO General (simplification.cpp : 497) Total length = 979 77s 0:00:00.048 1M / 19M INFO General (simplification.cpp : 498) Median edge length: 979 77s 0:00:00.048 1M / 19M INFO General (simplification.cpp : 499) Edges: 2 77s 0:00:00.048 1M / 19M INFO General (simplification.cpp : 500) Vertices: 4 77s 0:00:00.048 1M / 19M INFO StageManager (stage.cpp : 185) STAGE == Contig Output (id: contig_output) 77s 0:00:00.048 1M / 19M INFO General (read_converter.cpp : 107) Outputting contigs to /tmp/tmp.cMLX1ajB23/spades_test/K21/simplified_contigs 77s 0:00:00.048 3M / 19M INFO General (binary_converter.cpp : 111) 1 reads written 77s 0:00:00.048 1M / 19M INFO General (pipeline.cpp : 287) SPAdes finished 77s 0:00:00.048 1M / 19M INFO General (main.cpp : 136) Assembling time: 0 hours 0 minutes 0 seconds 77s 77s ===== K21 finished. 77s 77s 77s ===== K33 started. 77s 77s 77s == Running: /usr/libexec/spades/spades-core /tmp/tmp.cMLX1ajB23/spades_test/K33/configs/config.info /tmp/tmp.cMLX1ajB23/spades_test/K33/configs/mda_mode.info /tmp/tmp.cMLX1ajB23/spades_test/K33/configs/meta_mode.info /tmp/tmp.cMLX1ajB23/spades_test/K33/configs/rnaviral_mode.info /tmp/tmp.cMLX1ajB23/spades_test/K33/configs/hmm_mode.info 77s 77s 0:00:00.000 1M / 19M INFO General (main.cpp : 99) Loaded config from /tmp/tmp.cMLX1ajB23/spades_test/K33/configs/config.info 77s 0:00:00.000 1M / 19M INFO General (main.cpp : 99) Loaded config from /tmp/tmp.cMLX1ajB23/spades_test/K33/configs/mda_mode.info 77s 0:00:00.000 1M / 19M INFO General (main.cpp : 99) Loaded config from /tmp/tmp.cMLX1ajB23/spades_test/K33/configs/meta_mode.info 77s 0:00:00.000 1M / 19M INFO General (main.cpp : 99) Loaded config from /tmp/tmp.cMLX1ajB23/spades_test/K33/configs/rnaviral_mode.info 77s 0:00:00.000 1M / 19M INFO General (main.cpp : 99) Loaded config from /tmp/tmp.cMLX1ajB23/spades_test/K33/configs/hmm_mode.info 77s 0:00:00.000 1M / 19M INFO General (memory_limit.cpp : 54) Memory limit set to 3 Gb 77s 0:00:00.000 1M / 19M INFO General (main.cpp : 107) Starting SPAdes, built from N/A, git revision N/A 77s 0:00:00.000 1M / 19M INFO General (main.cpp : 108) Maximum k-mer length: 128 77s 0:00:00.000 1M / 19M INFO General (main.cpp : 109) Assembling dataset (/tmp/tmp.cMLX1ajB23/spades_test/dataset.info) with K=33 77s 0:00:00.000 1M / 19M INFO General (main.cpp : 110) Maximum # of threads to use (adjusted due to OMP capabilities): 2 77s 0:00:00.000 1M / 19M INFO General (pipeline.cpp : 212) SPAdes started 77s 0:00:00.000 1M / 19M INFO General (pipeline.cpp : 225) Starting from stage: read_conversion 77s 0:00:00.000 1M / 19M INFO General (pipeline.cpp : 231) Two-step repeat resolution disabled 77s 0:00:00.000 1M / 19M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 77s 0:00:00.000 1M / 19M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 77s 0:00:00.000 1M / 19M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 77s 0:00:00.000 1M / 19M INFO StageManager (stage.cpp : 185) STAGE == Binary Read Conversion (id: read_conversion) 77s 0:00:00.000 1M / 19M INFO General (read_converter.cpp : 53) Binary reads detected 77s 0:00:00.000 1M / 19M INFO StageManager (stage.cpp : 185) STAGE == de Bruijn graph construction (id: construction) 77s 0:00:00.000 1M / 19M INFO General (construction.cpp : 118) Contigs from previous K will be used: /tmp/tmp.cMLX1ajB23/spades_test/K21/simplified_contigs 77s 0:00:00.000 1M / 19M INFO General (construction.cpp : 153) Max read length 100 77s 0:00:00.000 1M / 19M INFO General (construction.cpp : 159) Average read length 86.1611 77s 0:00:00.000 1M / 19M INFO General (stage.cpp : 117) PROCEDURE == k+1-mer counting (id: construction:kpomer_counting) 77s 0:00:00.000 1M / 19M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 20 files using 2 threads. This might take a while. 77s 0:00:00.000 1M / 19M INFO General (file_limit.hpp : 42) Open file limit set to 1024 77s 0:00:00.000 1M / 19M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 0.49997 Gb 77s 0:00:00.000 1M / 19M INFO General (kmer_splitter.hpp : 101) Using cell size of 1677621 77s 0:00:00.009 1M / 19M INFO General (kmer_splitters.hpp : 131) Used 8218 reads 77s 0:00:00.009 1M / 19M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. 77s 0:00:00.011 1M / 19M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 974 kmers in total. 77s 0:00:00.011 1M / 19M INFO General (stage.cpp : 117) PROCEDURE == Extension index construction (id: construction:extension_index_construction) 77s 0:00:00.011 1M / 19M INFO K-mer Index Building (kmer_index_builder.hpp : 438) Building kmer index 77s 0:00:00.011 1M / 19M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 20 files using 2 threads. This might take a while. 77s 0:00:00.011 1M / 19M INFO General (file_limit.hpp : 42) Open file limit set to 1024 77s 0:00:00.011 1M / 19M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 0.499967 Gb 77s 0:00:00.011 1M / 19M INFO General (kmer_splitter.hpp : 101) Using cell size of 1677612 77s 0:00:00.012 1161M / 1161M INFO General (kmer_splitters.hpp : 199) Used 974 kmers. 77s 0:00:00.012 1M / 19M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. 77s 0:00:00.014 1M / 19M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 975 kmers in total. 77s 0:00:00.014 1M / 19M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices 77s 0:00:00.015 1M / 19M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 975 kmers, 16392 bytes occupied (134.498 bits per kmer). 77s 0:00:00.015 1M / 19M INFO General (kmer_index_builder.hpp : 169) Merging final buckets. 77s 0:00:00.016 1M / 19M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 100) Building k-mer extensions from k+1-mers 77s 0:00:00.017 1M / 19M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 105) Building k-mer extensions from k+1-mers finished. 77s 0:00:00.017 1M / 19M INFO General (stage.cpp : 117) PROCEDURE == Early A/T remover (id: construction:early_at_remover) 77s 0:00:00.017 1M / 19M INFO Early A/T remover (early_simplification.hpp : 176) Remove short poly A/T edges 77s 0:00:00.017 1M / 19M INFO Early A/T remover (early_simplification.hpp : 254) Links removed: 0 77s 0:00:00.017 1M / 19M INFO Early A/T remover (early_simplification.hpp : 179) 0 34-mers were removed by early poly A/T remover 77s 0:00:00.017 1M / 19M INFO Early A/T remover (early_simplification.hpp : 262) Remove poly A/T tips 77s 0:00:00.017 1M / 19M INFO Early A/T remover (early_simplification.hpp : 331) Clipped tips: 0 77s 0:00:00.017 1M / 19M INFO Early A/T remover (early_simplification.hpp : 265) 0 34-mers were removed by early poly A/T tip clipper 77s 0:00:00.017 1M / 19M INFO General (stage.cpp : 117) PROCEDURE == Early tip clipping (id: construction:early_tip_clipper) 77s 0:00:00.017 1M / 19M INFO General (construction.cpp : 301) Early tip clipper length bound set as (RL - K) 77s 0:00:00.017 1M / 19M INFO Early tip clipping (early_simplification.hpp : 47) Early tip clipping 77s 0:00:00.017 1M / 19M INFO Early tip clipping (early_simplification.hpp : 82) #tipped junctions: 2 77s 0:00:00.017 1M / 19M INFO Early tip clipping (early_simplification.hpp : 93) Clipped tips: 2 77s 0:00:00.017 1M / 19M INFO Early tip clipping (early_simplification.hpp : 49) 7 34-mers were removed by early tip clipper 77s 0:00:00.017 1M / 19M INFO General (stage.cpp : 117) PROCEDURE == Condensing graph (id: construction:graph_condensing) 77s 0:00:00.017 1M / 19M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths 77s 0:00:00.018 1M / 19M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 1 sequences extracted 77s 0:00:00.018 1M / 19M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops 77s 0:00:00.018 1M / 19M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 0 loops collected 77s 0:00:00.018 1M / 19M INFO General (debruijn_graph_constructor: 487) Total 2 edges to create 77s 0:00:00.018 1M / 19M INFO General (debruijn_graph_constructor: 489) Collecting link records 77s 0:00:00.018 1M / 19M INFO General (debruijn_graph_constructor: 491) Ordering link records 77s 0:00:00.018 1M / 19M INFO General (debruijn_graph_constructor: 493) Sorting done 77s 0:00:00.018 1M / 19M INFO General (debruijn_graph_constructor: 503) Total 2 vertices to create 77s 0:00:00.018 1M / 19M INFO General (debruijn_graph_constructor: 506) Connecting the graph 77s 0:00:00.018 1M / 19M INFO General (stage.cpp : 117) PROCEDURE == Filling coverage indices (PHM) (id: construction:coverage_filling_phm) 77s 0:00:00.018 1M / 19M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices 77s 0:00:00.019 1M / 19M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 974 kmers, 16392 bytes occupied (134.637 bits per kmer). 77s 0:00:00.019 1M / 19M INFO General (coverage_hash_map_builder.: 47) Collecting k-mer coverage information from reads, this takes a while. 77s 0:00:00.030 1M / 19M INFO General (construction.cpp : 430) Filling coverage and flanking coverage from PHM 77s 0:00:00.031 1M / 19M INFO StageManager (stage.cpp : 185) STAGE == Raw Simplification (id: raw_simplification) 77s 0:00:00.031 1M / 19M INFO General (simplification.cpp : 106) PROCEDURE == Initial cleaning 77s 0:00:00.031 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running poly A/T short edge remover 77s 0:00:00.031 1M / 19M INFO Simplification (parallel_processing.hpp : 170) poly A/T short edge remover triggered 0 times 77s 0:00:00.031 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running poly A/T tip clipper 77s 0:00:00.031 1M / 19M INFO Simplification (parallel_processing.hpp : 170) poly A/T tip clipper triggered 0 times 77s 0:00:00.031 1M / 19M INFO General (graph_simplification.hpp : 703) Removing loops and rc loops with erroneous connections 77s 0:00:00.031 1M / 19M INFO ECLoopRemover (erroneous_connection_remov: 406) Loops: accurately removed/deadend removed/other: 0/0/0 77s 0:00:00.031 1M / 19M INFO ECLoopRemover (erroneous_connection_remov: 407) RC loops: accurately removed/deadend removed/other: 0/0/0 77s 0:00:00.031 1M / 19M INFO General (simplification.cpp : 127) PROCEDURE == Initial cleaning 77s 0:00:00.031 1M / 19M INFO General (graph_simplification.hpp : 662) Flanking coverage based disconnection disabled 77s 0:00:00.031 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Self conjugate edge remover 77s 0:00:00.031 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Self conjugate edge remover triggered 0 times 77s 0:00:00.031 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Initial tip clipper 77s 0:00:00.031 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Initial tip clipper triggered 0 times 77s 0:00:00.031 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Initial ec remover 77s 0:00:00.031 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Initial ec remover triggered 0 times 77s 0:00:00.031 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Initial isolated edge remover 77s 0:00:00.031 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Initial isolated edge remover triggered 0 times 77s 0:00:00.031 1M / 19M INFO StageManager (stage.cpp : 185) STAGE == Simplification (id: simplification) 77s 0:00:00.031 1M / 19M INFO General (simplification.cpp : 368) Graph simplification started 77s 0:00:00.031 1M / 19M INFO General (graph_simplification.hpp : 634) Creating parallel br instance 77s 0:00:00.031 1M / 19M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 1 77s 0:00:00.031 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 77s 0:00:00.031 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 77s 0:00:00.031 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 77s 0:00:00.031 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 77s 0:00:00.031 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 77s 0:00:00.031 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 0 times 77s 0:00:00.031 1M / 19M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 2 77s 0:00:00.031 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 77s 0:00:00.031 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 77s 0:00:00.031 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 77s 0:00:00.031 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 77s 0:00:00.031 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 77s 0:00:00.031 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 0 times 77s 0:00:00.031 1M / 19M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 3 77s 0:00:00.031 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 77s 0:00:00.031 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 77s 0:00:00.031 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 77s 0:00:00.031 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 77s 0:00:00.031 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 77s 0:00:00.031 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 0 times 77s 0:00:00.031 1M / 19M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 4 77s 0:00:00.031 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 77s 0:00:00.031 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 77s 0:00:00.031 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 77s 0:00:00.031 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 77s 0:00:00.031 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 77s 0:00:00.031 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 0 times 77s 0:00:00.031 1M / 19M INFO StageManager (stage.cpp : 185) STAGE == Simplification Cleanup (id: simplification_cleanup) 77s 0:00:00.031 1M / 19M INFO General (simplification.cpp : 176) PROCEDURE == Post simplification 77s 0:00:00.032 1M / 19M INFO General (graph_simplification.hpp : 634) Creating parallel br instance 77s 0:00:00.032 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Relative coverage component remover 77s 0:00:00.032 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Relative coverage component remover triggered 0 times 77s 0:00:00.032 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Disconnecting edges with relatively low coverage 77s 0:00:00.032 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Disconnecting edges with relatively low coverage triggered 0 times 77s 0:00:00.032 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Complex tip clipper 77s 0:00:00.032 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Complex tip clipper triggered 0 times 77s 0:00:00.032 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Complex bulge remover 77s 0:00:00.032 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Complex bulge remover triggered 0 times 77s 0:00:00.032 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 77s 0:00:00.032 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 77s 0:00:00.032 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Final tip clipper 77s 0:00:00.032 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Final tip clipper triggered 0 times 77s 0:00:00.032 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 77s 0:00:00.032 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 77s 0:00:00.032 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Thorn remover (meta) 77s 0:00:00.032 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Thorn remover (meta) triggered 0 times 77s 0:00:00.032 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Relative coverage component remover 77s 0:00:00.032 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Relative coverage component remover triggered 0 times 77s 0:00:00.032 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Disconnecting edges with relatively low coverage 77s 0:00:00.032 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Disconnecting edges with relatively low coverage triggered 0 times 77s 0:00:00.032 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Complex tip clipper 77s 0:00:00.032 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Complex tip clipper triggered 0 times 77s 0:00:00.032 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Complex bulge remover 77s 0:00:00.032 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Complex bulge remover triggered 0 times 77s 0:00:00.032 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 77s 0:00:00.032 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 77s 0:00:00.032 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Final tip clipper 77s 0:00:00.032 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Final tip clipper triggered 0 times 77s 0:00:00.032 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 77s 0:00:00.032 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 77s 0:00:00.032 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Thorn remover (meta) 77s 0:00:00.032 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Thorn remover (meta) triggered 0 times 77s 0:00:00.032 1M / 19M INFO General (simplification.cpp : 323) Running Hidden EC remover (meta) 77s 0:00:00.032 1M / 19M INFO General (simplification.cpp : 327) Disrupting self-conjugate edges 77s 0:00:00.032 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Removing isolated edges 77s 0:00:00.032 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Removing isolated edges triggered 0 times 77s 0:00:00.032 1M / 19M INFO General (simplification.cpp : 495) After simplification: 77s 0:00:00.032 1M / 19M INFO General (simplification.cpp : 496) Average coverage = 225.865 77s 0:00:00.032 1M / 19M INFO General (simplification.cpp : 497) Total length = 967 77s 0:00:00.032 1M / 19M INFO General (simplification.cpp : 498) Median edge length: 967 77s 0:00:00.032 1M / 19M INFO General (simplification.cpp : 499) Edges: 2 77s 0:00:00.032 1M / 19M INFO General (simplification.cpp : 500) Vertices: 4 77s 0:00:00.032 1M / 19M INFO StageManager (stage.cpp : 185) STAGE == Contig Output (id: contig_output) 77s 0:00:00.032 1M / 19M INFO General (read_converter.cpp : 107) Outputting contigs to /tmp/tmp.cMLX1ajB23/spades_test/K33/simplified_contigs 77s 0:00:00.032 3M / 19M INFO General (binary_converter.cpp : 111) 1 reads written 77s 0:00:00.032 1M / 19M INFO General (pipeline.cpp : 287) SPAdes finished 77s 0:00:00.032 1M / 19M INFO General (main.cpp : 136) Assembling time: 0 hours 0 minutes 0 seconds 77s 77s ===== K33 finished. 77s 77s 77s ===== K49 started. 77s 77s 77s == Running: /usr/libexec/spades/spades-core /tmp/tmp.cMLX1ajB23/spades_test/K49/configs/config.info /tmp/tmp.cMLX1ajB23/spades_test/K49/configs/mda_mode.info /tmp/tmp.cMLX1ajB23/spades_test/K49/configs/meta_mode.info /tmp/tmp.cMLX1ajB23/spades_test/K49/configs/rnaviral_mode.info /tmp/tmp.cMLX1ajB23/spades_test/K49/configs/hmm_mode.info 77s 77s 0:00:00.000 1M / 19M INFO General (main.cpp : 99) Loaded config from /tmp/tmp.cMLX1ajB23/spades_test/K49/configs/config.info 77s 0:00:00.000 1M / 19M INFO General (main.cpp : 99) Loaded config from /tmp/tmp.cMLX1ajB23/spades_test/K49/configs/mda_mode.info 77s 0:00:00.000 1M / 19M INFO General (main.cpp : 99) Loaded config from /tmp/tmp.cMLX1ajB23/spades_test/K49/configs/meta_mode.info 77s 0:00:00.000 1M / 19M INFO General (main.cpp : 99) Loaded config from /tmp/tmp.cMLX1ajB23/spades_test/K49/configs/rnaviral_mode.info 77s 0:00:00.000 1M / 19M INFO General (main.cpp : 99) Loaded config from /tmp/tmp.cMLX1ajB23/spades_test/K49/configs/hmm_mode.info 77s 0:00:00.000 1M / 19M INFO General (memory_limit.cpp : 54) Memory limit set to 3 Gb 77s 0:00:00.000 1M / 19M INFO General (main.cpp : 107) Starting SPAdes, built from N/A, git revision N/A 77s 0:00:00.000 1M / 19M INFO General (main.cpp : 108) Maximum k-mer length: 128 77s 0:00:00.000 1M / 19M INFO General (main.cpp : 109) Assembling dataset (/tmp/tmp.cMLX1ajB23/spades_test/dataset.info) with K=49 77s 0:00:00.000 1M / 19M INFO General (main.cpp : 110) Maximum # of threads to use (adjusted due to OMP capabilities): 2 77s 0:00:00.000 1M / 19M INFO General (pipeline.cpp : 212) SPAdes started 77s 0:00:00.000 1M / 19M INFO General (pipeline.cpp : 225) Starting from stage: read_conversion 77s 0:00:00.000 1M / 19M INFO General (pipeline.cpp : 231) Two-step repeat resolution disabled 77s 0:00:00.000 1M / 19M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 77s 0:00:00.000 1M / 19M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 77s 0:00:00.000 1M / 19M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 77s 0:00:00.000 1M / 19M INFO General (pipeline.cpp : 242) Will need read mapping, kmer mapper will be attached 77s 0:00:00.000 1M / 19M INFO StageManager (stage.cpp : 185) STAGE == Binary Read Conversion (id: read_conversion) 77s 0:00:00.000 1M / 19M INFO General (read_converter.cpp : 53) Binary reads detected 77s 0:00:00.000 1M / 19M INFO StageManager (stage.cpp : 185) STAGE == de Bruijn graph construction (id: construction) 77s 0:00:00.000 1M / 19M INFO General (construction.cpp : 118) Contigs from previous K will be used: /tmp/tmp.cMLX1ajB23/spades_test/K33/simplified_contigs 77s 0:00:00.000 1M / 19M INFO General (construction.cpp : 153) Max read length 100 77s 0:00:00.000 1M / 19M INFO General (construction.cpp : 159) Average read length 86.1611 77s 0:00:00.000 1M / 19M INFO General (stage.cpp : 117) PROCEDURE == k+1-mer counting (id: construction:kpomer_counting) 77s 0:00:00.000 1M / 19M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 20 files using 2 threads. This might take a while. 77s 0:00:00.000 1M / 19M INFO General (file_limit.hpp : 42) Open file limit set to 1024 77s 0:00:00.000 1M / 19M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 0.49997 Gb 77s 0:00:00.000 1M / 19M INFO General (kmer_splitter.hpp : 101) Using cell size of 1677621 77s 0:00:00.007 1M / 19M INFO General (kmer_splitters.hpp : 131) Used 8218 reads 77s 0:00:00.008 1M / 19M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. 77s 0:00:00.009 1M / 19M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 958 kmers in total. 77s 0:00:00.009 1M / 19M INFO General (stage.cpp : 117) PROCEDURE == Extension index construction (id: construction:extension_index_construction) 77s 0:00:00.009 1M / 19M INFO K-mer Index Building (kmer_index_builder.hpp : 438) Building kmer index 77s 0:00:00.009 1M / 19M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 20 files using 2 threads. This might take a while. 77s 0:00:00.009 1M / 19M INFO General (file_limit.hpp : 42) Open file limit set to 1024 77s 0:00:00.009 1M / 19M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 0.499967 Gb 77s 0:00:00.009 1M / 19M INFO General (kmer_splitter.hpp : 101) Using cell size of 1677611 77s 0:00:00.011 1161M / 1161M INFO General (kmer_splitters.hpp : 199) Used 958 kmers. 77s 0:00:00.011 1M / 19M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. 77s 0:00:00.012 1M / 19M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 959 kmers in total. 77s 0:00:00.012 1M / 19M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices 77s 0:00:00.013 1M / 19M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 959 kmers, 16392 bytes occupied (136.742 bits per kmer). 77s 0:00:00.014 1M / 19M INFO General (kmer_index_builder.hpp : 169) Merging final buckets. 77s 0:00:00.014 1M / 19M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 100) Building k-mer extensions from k+1-mers 77s 0:00:00.015 1M / 19M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 105) Building k-mer extensions from k+1-mers finished. 77s 0:00:00.015 1M / 19M INFO General (stage.cpp : 117) PROCEDURE == Early A/T remover (id: construction:early_at_remover) 77s 0:00:00.015 1M / 19M INFO Early A/T remover (early_simplification.hpp : 176) Remove short poly A/T edges 77s 0:00:00.015 1M / 19M INFO Early A/T remover (early_simplification.hpp : 254) Links removed: 0 77s 0:00:00.015 1M / 19M INFO Early A/T remover (early_simplification.hpp : 179) 0 50-mers were removed by early poly A/T remover 77s 0:00:00.015 1M / 19M INFO Early A/T remover (early_simplification.hpp : 262) Remove poly A/T tips 77s 0:00:00.016 1M / 19M INFO Early A/T remover (early_simplification.hpp : 331) Clipped tips: 0 77s 0:00:00.016 1M / 19M INFO Early A/T remover (early_simplification.hpp : 265) 0 50-mers were removed by early poly A/T tip clipper 77s 0:00:00.016 1M / 19M INFO General (stage.cpp : 117) PROCEDURE == Condensing graph (id: construction:graph_condensing) 77s 0:00:00.016 1M / 19M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths 77s 0:00:00.016 1M / 19M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 5 sequences extracted 77s 0:00:00.016 1M / 19M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops 77s 0:00:00.016 1M / 19M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 0 loops collected 77s 0:00:00.016 1M / 19M INFO General (debruijn_graph_constructor: 487) Total 10 edges to create 77s 0:00:00.016 1M / 19M INFO General (debruijn_graph_constructor: 489) Collecting link records 77s 0:00:00.016 1M / 19M INFO General (debruijn_graph_constructor: 491) Ordering link records 77s 0:00:00.016 1M / 19M INFO General (debruijn_graph_constructor: 493) Sorting done 77s 0:00:00.016 1M / 19M INFO General (debruijn_graph_constructor: 503) Total 6 vertices to create 77s 0:00:00.016 1M / 19M INFO General (debruijn_graph_constructor: 506) Connecting the graph 77s 0:00:00.016 1M / 19M INFO General (stage.cpp : 117) PROCEDURE == Filling coverage indices (PHM) (id: construction:coverage_filling_phm) 77s 0:00:00.016 1M / 19M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices 77s 0:00:00.018 1M / 19M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 958 kmers, 16384 bytes occupied (136.818 bits per kmer). 77s 0:00:00.018 1M / 19M INFO General (coverage_hash_map_builder.: 47) Collecting k-mer coverage information from reads, this takes a while. 77s 0:00:00.026 1M / 19M INFO General (construction.cpp : 430) Filling coverage and flanking coverage from PHM 77s 0:00:00.027 1M / 19M INFO StageManager (stage.cpp : 185) STAGE == Gap Closer (id: early_gapcloser) 77s 0:00:00.031 10M / 19M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 77s 0:00:00.031 10M / 19M INFO General (gap_closer.cpp : 101) Total edges in tip neighborhood: 4 out of 10, length: 860 77s 0:00:00.031 10M / 19M INFO General (edge_index.hpp : 167) Using small index (max_id = 13) 77s 0:00:00.032 10M / 19M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices 77s 0:00:00.032 10M / 19M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 860 kmers, 1384 bytes occupied (12.8744 bits per kmer). 77s 0:00:00.032 10M / 19M INFO General (edge_index_builders.hpp : 265) Collecting edge information from graph, this takes a while. 77s 0:00:00.034 10M / 19M INFO General (sequence_mapper_notifier.h: 95) Total 2054 reads processed 77s 0:00:00.035 10M / 19M INFO General (gap_closer.cpp : 452) Initializing gap closer 77s 0:00:00.035 10M / 19M INFO GapCloser (gap_closer.cpp : 359) Closing short gaps 77s 0:00:00.035 10M / 19M INFO GapCloser (gap_closer.cpp : 391) Closing short gaps complete: filled 0 gaps after checking 0 candidates 77s 0:00:00.035 10M / 19M INFO General (gap_closer.cpp : 456) Gap closer done 77s 0:00:00.035 1M / 19M INFO StageManager (stage.cpp : 185) STAGE == Raw Simplification (id: raw_simplification) 77s 0:00:00.035 1M / 19M INFO General (simplification.cpp : 106) PROCEDURE == Initial cleaning 77s 0:00:00.035 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running poly A/T short edge remover 77s 0:00:00.036 1M / 20M INFO Simplification (parallel_processing.hpp : 170) poly A/T short edge remover triggered 0 times 77s 0:00:00.036 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running poly A/T tip clipper 77s 0:00:00.036 1M / 20M INFO Simplification (parallel_processing.hpp : 170) poly A/T tip clipper triggered 1 times 77s 0:00:00.036 1M / 20M INFO General (graph_simplification.hpp : 703) Removing loops and rc loops with erroneous connections 77s 0:00:00.036 1M / 20M INFO ECLoopRemover (erroneous_connection_remov: 406) Loops: accurately removed/deadend removed/other: 0/0/0 77s 0:00:00.036 1M / 20M INFO ECLoopRemover (erroneous_connection_remov: 407) RC loops: accurately removed/deadend removed/other: 0/0/0 77s 0:00:00.036 1M / 20M INFO General (simplification.cpp : 127) PROCEDURE == Initial cleaning 77s 0:00:00.036 1M / 20M INFO General (graph_simplification.hpp : 662) Flanking coverage based disconnection disabled 77s 0:00:00.036 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Self conjugate edge remover 77s 0:00:00.036 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Self conjugate edge remover triggered 0 times 77s 0:00:00.036 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Initial tip clipper 77s 0:00:00.036 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Initial tip clipper triggered 0 times 77s 0:00:00.036 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Initial ec remover 77s 0:00:00.036 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Initial ec remover triggered 0 times 77s 0:00:00.036 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Initial isolated edge remover 77s 0:00:00.036 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Initial isolated edge remover triggered 0 times 77s 0:00:00.036 1M / 20M INFO StageManager (stage.cpp : 185) STAGE == Simplification (id: simplification) 77s 0:00:00.036 1M / 20M INFO General (simplification.cpp : 368) Graph simplification started 77s 0:00:00.036 1M / 20M INFO General (graph_simplification.hpp : 634) Creating parallel br instance 77s 0:00:00.036 1M / 20M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 1 77s 0:00:00.036 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 77s 0:00:00.036 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 1 times 77s 0:00:00.036 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 77s 0:00:00.036 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 77s 0:00:00.036 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 77s 0:00:00.036 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 0 times 77s 0:00:00.036 1M / 20M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 2 77s 0:00:00.036 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 77s 0:00:00.036 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 77s 0:00:00.036 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 77s 0:00:00.036 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 77s 0:00:00.036 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 77s 0:00:00.036 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 0 times 77s 0:00:00.036 1M / 20M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 3 77s 0:00:00.036 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 77s 0:00:00.036 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 77s 0:00:00.036 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 77s 0:00:00.036 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 77s 0:00:00.036 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 77s 0:00:00.036 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 0 times 77s 0:00:00.036 1M / 20M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 4 77s 0:00:00.036 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 77s 0:00:00.036 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 77s 0:00:00.036 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 77s 0:00:00.036 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 77s 0:00:00.036 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 77s 0:00:00.036 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 0 times 77s 0:00:00.036 1M / 20M INFO StageManager (stage.cpp : 185) STAGE == Gap Closer (id: late_gapcloser) 77s 0:00:00.037 10M / 20M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 77s 0:00:00.037 10M / 20M INFO General (gap_closer.cpp : 101) Total edges in tip neighborhood: 2 out of 2, length: 1902 77s 0:00:00.037 10M / 20M INFO General (edge_index.hpp : 167) Using small index (max_id = 13) 77s 0:00:00.038 10M / 20M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices 77s 0:00:00.038 10M / 20M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 951 kmers, 1456 bytes occupied (12.2482 bits per kmer). 77s 0:00:00.038 10M / 20M INFO General (edge_index_builders.hpp : 265) Collecting edge information from graph, this takes a while. 77s 0:00:00.040 10M / 20M INFO General (sequence_mapper_notifier.h: 95) Total 2054 reads processed 77s 0:00:00.041 10M / 20M INFO General (gap_closer.cpp : 452) Initializing gap closer 77s 0:00:00.041 10M / 20M INFO GapCloser (gap_closer.cpp : 359) Closing short gaps 77s 0:00:00.041 10M / 20M INFO GapCloser (gap_closer.cpp : 391) Closing short gaps complete: filled 0 gaps after checking 0 candidates 77s 0:00:00.041 10M / 20M INFO General (gap_closer.cpp : 456) Gap closer done 77s 0:00:00.041 1M / 20M INFO StageManager (stage.cpp : 185) STAGE == Simplification Cleanup (id: simplification_cleanup) 77s 0:00:00.041 1M / 20M INFO General (simplification.cpp : 176) PROCEDURE == Post simplification 77s 0:00:00.041 1M / 20M INFO General (graph_simplification.hpp : 634) Creating parallel br instance 77s 0:00:00.041 1M / 20M INFO General (graph_simplification.hpp : 634) Creating parallel br instance 77s 0:00:00.042 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Relative coverage component remover 77s 0:00:00.042 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Relative coverage component remover triggered 0 times 77s 0:00:00.042 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Disconnecting edges with relatively low coverage 77s 0:00:00.042 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Disconnecting edges with relatively low coverage triggered 0 times 77s 0:00:00.042 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Complex tip clipper 77s 0:00:00.042 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Complex tip clipper triggered 0 times 77s 0:00:00.042 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Complex bulge remover 77s 0:00:00.042 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Complex bulge remover triggered 0 times 77s 0:00:00.042 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 77s 0:00:00.042 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 77s 0:00:00.042 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Final tip clipper 77s 0:00:00.042 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Final tip clipper triggered 0 times 77s 0:00:00.042 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 77s 0:00:00.042 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 77s 0:00:00.042 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Subspecies bulge remover 77s 0:00:00.043 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Subspecies bulge remover triggered 0 times 77s 0:00:00.043 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Thorn remover (meta) 77s 0:00:00.043 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Thorn remover (meta) triggered 0 times 77s 0:00:00.043 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Relative coverage component remover 77s 0:00:00.043 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Relative coverage component remover triggered 0 times 77s 0:00:00.043 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Disconnecting edges with relatively low coverage 77s 0:00:00.043 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Disconnecting edges with relatively low coverage triggered 0 times 77s 0:00:00.043 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Complex tip clipper 77s 0:00:00.043 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Complex tip clipper triggered 0 times 77s 0:00:00.043 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Complex bulge remover 77s 0:00:00.043 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Complex bulge remover triggered 0 times 77s 0:00:00.043 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 77s 0:00:00.043 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 77s 0:00:00.043 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Final tip clipper 77s 0:00:00.043 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Final tip clipper triggered 0 times 77s 0:00:00.043 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 77s 0:00:00.043 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 77s 0:00:00.043 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Subspecies bulge remover 77s 0:00:00.043 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Subspecies bulge remover triggered 0 times 77s 0:00:00.043 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Thorn remover (meta) 77s 0:00:00.043 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Thorn remover (meta) triggered 0 times 77s 0:00:00.043 1M / 20M INFO General (simplification.cpp : 323) Running Hidden EC remover (meta) 77s 0:00:00.043 1M / 20M INFO General (simplification.cpp : 327) Disrupting self-conjugate edges 77s 0:00:00.043 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Removing isolated edges 77s 0:00:00.043 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Removing isolated edges triggered 0 times 77s 0:00:00.043 1M / 20M INFO General (simplification.cpp : 495) After simplification: 77s 0:00:00.043 1M / 20M INFO General (simplification.cpp : 496) Average coverage = 163.37 77s 0:00:00.043 1M / 20M INFO General (simplification.cpp : 497) Total length = 951 77s 0:00:00.043 1M / 20M INFO General (simplification.cpp : 498) Median edge length: 951 77s 0:00:00.043 1M / 20M INFO General (simplification.cpp : 499) Edges: 2 77s 0:00:00.043 1M / 20M INFO General (simplification.cpp : 500) Vertices: 4 77s 0:00:00.043 1M / 20M INFO StageManager (stage.cpp : 185) STAGE == Mismatch Correction (id: mismatch_correction) 77s 0:00:00.043 1M / 20M INFO General (graph_pack.cpp : 67) Index refill 77s 0:00:00.043 1M / 20M INFO General (edge_index.hpp : 156) Using small index (max_id = 13) 77s 0:00:00.043 1M / 20M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices 77s 0:00:00.043 1M / 20M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 951 kmers, 1456 bytes occupied (12.2482 bits per kmer). 77s 0:00:00.043 1M / 20M INFO General (edge_index_builders.hpp : 252) Collecting edge information from graph, this takes a while. 77s 0:00:00.043 1M / 20M INFO General (graph_pack.cpp : 77) Normalizing k-mer map. Total 0 kmers to process 77s 0:00:00.043 1M / 20M INFO General (graph_pack.cpp : 79) Normalizing done 77s 0:00:00.043 1M / 20M INFO General (mismatch_correction.cpp : 400) Collect potential mismatches 77s 0:00:00.043 1M / 20M INFO General (mismatch_correction.cpp : 192) Total 0 edges (out of 2) with 0 potential mismatch positions (-nan positions per edge) 77s 0:00:00.043 1M / 20M INFO General (mismatch_correction.cpp : 402) Potential mismatches collected 77s 0:00:00.048 1M / 20M INFO General (sequence_mapper_notifier.h: 95) Total 8216 reads processed 77s 0:00:00.048 1M / 20M INFO General (mismatch_correction.cpp : 395) All edges processed 77s 0:00:00.048 1M / 20M INFO General (mismatch_correction.cpp : 450) Corrected 0 nucleotides 77s 0:00:00.048 1M / 20M INFO StageManager (stage.cpp : 185) STAGE == Contig Output (id: contig_output) 77s 0:00:00.048 1M / 20M INFO General (contig_output.hpp : 16) Outputting contigs to /tmp/tmp.cMLX1ajB23/spades_test/K49/before_rr.fasta 77s 0:00:00.048 1M / 20M INFO General (contig_output_stage.cpp : 151) Writing GFA graph to /tmp/tmp.cMLX1ajB23/spades_test/K49/assembly_graph_after_simplification.gfa 77s 0:00:00.048 1M / 20M INFO StageManager (stage.cpp : 185) STAGE == Paired Information Counting (id: late_pair_info_count) 77s 0:00:00.048 1M / 20M INFO General (graph_pack.cpp : 77) Normalizing k-mer map. Total 0 kmers to process 77s 0:00:00.048 1M / 20M INFO General (graph_pack.cpp : 79) Normalizing done 77s 0:00:00.048 1M / 20M INFO General (pair_info_count.cpp : 339) Min edge length for estimation: 900 77s 0:00:00.048 1M / 20M INFO General (pair_info_count.cpp : 350) Estimating insert size for library #0 77s 0:00:00.048 1M / 20M INFO General (pair_info_count.cpp : 202) Estimating insert size (takes a while) 77s 0:00:00.066 49M / 59M INFO General (pair_info_count.cpp : 48) Selecting usual mapper 77s 0:00:00.088 49M / 59M INFO General (sequence_mapper_notifier.h: 95) Total 2054 reads processed 77s 0:00:00.153 49M / 59M INFO General (pair_info_count.cpp : 220) Edge pairs: 2 77s 0:00:00.153 49M / 59M INFO General (pair_info_count.cpp : 222) 1751 paired reads (85.2483% of all) aligned to long edges 77s 0:00:00.153 1M / 59M INFO General (pair_info_count.cpp : 369) Insert size = 214.709, deviation = 10.4946, left quantile = 201, right quantile = 228, read length = 100 77s 0:00:00.153 1M / 59M INFO General (pair_info_count.cpp : 390) Filtering data for library #0 77s 0:00:00.153 1M / 59M INFO General (pair_info_count.cpp : 48) Selecting usual mapper 77s 0:00:00.155 1M / 59M INFO General (sequence_mapper_notifier.h: 95) Total 2054 reads processed 77s 0:00:00.155 1M / 59M INFO General (pair_info_count.cpp : 402) Mapping library #0 77s 0:00:00.155 1M / 59M INFO General (pair_info_count.cpp : 404) Mapping paired reads (takes a while) 77s 0:00:00.155 1M / 59M INFO General (pair_info_count.cpp : 299) Left insert size quantile 201, right insert size quantile 228, filtering threshold 1, rounding threshold 0 77s 0:00:00.157 10M / 59M INFO General (pair_info_count.cpp : 48) Selecting usual mapper 77s 0:00:00.160 10M / 59M INFO General (sequence_mapper_notifier.h: 95) Total 2054 reads processed 77s 0:00:00.161 1M / 59M INFO StageManager (stage.cpp : 185) STAGE == Distance Estimation (id: distance_estimation) 77s 0:00:00.161 1M / 59M INFO General (distance_estimation.cpp : 179) Processing library #0 77s 0:00:00.161 1M / 59M INFO General (distance_estimation.cpp : 150) Weight Filter Done 77s 0:00:00.161 1M / 59M INFO DistanceEstimator (distance_estimation.hpp : 116) Using SIMPLE distance estimator 77s 0:00:00.161 1M / 59M INFO General (distance_estimation.cpp : 37) Filtering info 77s 0:00:00.161 1M / 59M INFO General (pair_info_filters.hpp : 242) Start filtering; library index size: 2 77s 0:00:00.161 1M / 59M INFO General (pair_info_filters.hpp : 263) Done filtering; library index size: 2 77s 0:00:00.161 1M / 59M INFO General (distance_estimation.cpp : 156) Refining clustered pair information 77s 0:00:00.161 1M / 59M INFO General (distance_estimation.cpp : 158) The refining of clustered pair information has been finished 77s 0:00:00.161 1M / 59M INFO General (distance_estimation.cpp : 160) Improving paired information 77s 0:00:00.162 1M / 59M INFO PairInfoImprover (pair_info_improver.hpp : 104) Paired info stats: missing = 0; contradictional = 0 77s 0:00:00.162 1M / 59M INFO PairInfoImprover (pair_info_improver.hpp : 104) Paired info stats: missing = 0; contradictional = 0 77s 0:00:00.162 1M / 59M INFO General (distance_estimation.cpp : 104) Filling scaffolding index 77s 0:00:00.162 1M / 59M INFO DistanceEstimator (distance_estimation.hpp : 116) Using SMOOTHING distance estimator 77s 0:00:00.162 1M / 59M INFO General (distance_estimation.cpp : 37) Filtering info 77s 0:00:00.162 1M / 59M INFO General (pair_info_filters.hpp : 242) Start filtering; library index size: 2 77s 0:00:00.162 1M / 59M INFO General (pair_info_filters.hpp : 263) Done filtering; library index size: 2 77s 0:00:00.162 1M / 59M INFO General (distance_estimation.cpp : 186) Clearing raw paired index 77s 0:00:00.162 1M / 59M INFO StageManager (stage.cpp : 185) STAGE == Repeat Resolving (id: repeat_resolving) 77s 0:00:00.162 1M / 59M INFO General (repeat_resolving.cpp : 87) Using Path-Extend repeat resolving 77s 0:00:00.162 1M / 59M INFO General (launcher.cpp : 600) ExSPAnder repeat resolving tool started 77s 0:00:00.162 1M / 59M INFO General (launcher.cpp : 418) Creating main extenders, unique edge length = 2000 77s 0:00:00.162 1M / 60M INFO General (extenders_logic.cpp : 345) Creating extender; library index size: 2 77s 0:00:00.162 1M / 60M INFO General (extenders_logic.cpp : 345) Creating extender; library index size: 2 77s 0:00:00.162 1M / 60M INFO General (extenders_logic.cpp : 543) Using 1 paired-end library 77s 0:00:00.162 1M / 60M INFO General (extenders_logic.cpp : 544) Using 1 paired-end scaffolding library 77s 0:00:00.162 1M / 60M INFO General (extenders_logic.cpp : 545) Using 0 single read libraries 77s 0:00:00.162 1M / 60M INFO General (extenders_logic.cpp : 456) Using additional coordinated coverage extender 77s 0:00:00.162 1M / 60M INFO General (launcher.cpp : 447) Total number of extenders is 4 77s 0:00:00.162 1M / 60M INFO General (launcher.cpp : 250) Finalizing paths 77s 0:00:00.162 1M / 60M INFO General (launcher.cpp : 252) Deduplicating paths 77s 0:00:00.162 1M / 60M INFO General (launcher.cpp : 256) Paths deduplicated 77s 0:00:00.162 1M / 60M INFO PEResolver (pe_resolver.cpp : 60) Removing overlaps 77s 0:00:00.162 1M / 60M INFO PEResolver (pe_resolver.cpp : 70) Marking overlaps 77s 0:00:00.162 1M / 60M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps 77s 0:00:00.162 1M / 60M INFO OverlapRemover (overlap_remover.hpp : 119) Marking remaining overlaps 77s 0:00:00.162 1M / 60M INFO PEResolver (pe_resolver.cpp : 73) Splitting paths 77s 0:00:00.162 1M / 60M INFO PEResolver (pe_resolver.cpp : 78) Deduplicating paths 77s 0:00:00.162 1M / 60M INFO PEResolver (pe_resolver.cpp : 80) Overlaps removed 77s 0:00:00.162 1M / 60M INFO General (launcher.cpp : 273) Paths finalized 77s 0:00:00.162 1M / 60M INFO General (launcher.cpp : 454) Closing gaps in paths 77s 0:00:00.162 1M / 60M INFO General (launcher.cpp : 484) Gap closing completed 77s 0:00:00.162 1M / 60M INFO General (launcher.cpp : 302) Traversing tandem repeats 77s 0:00:00.162 1M / 60M INFO General (launcher.cpp : 312) Traversed 0 loops 77s 0:00:00.162 1M / 60M INFO General (launcher.cpp : 250) Finalizing paths 77s 0:00:00.162 1M / 60M INFO General (launcher.cpp : 252) Deduplicating paths 77s 0:00:00.162 1M / 60M INFO General (launcher.cpp : 256) Paths deduplicated 77s 0:00:00.162 1M / 60M INFO PEResolver (pe_resolver.cpp : 60) Removing overlaps 77s 0:00:00.162 1M / 60M INFO PEResolver (pe_resolver.cpp : 70) Marking overlaps 77s 0:00:00.162 1M / 60M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps 77s 0:00:00.162 1M / 60M INFO OverlapRemover (overlap_remover.hpp : 119) Marking remaining overlaps 77s 0:00:00.162 1M / 60M INFO PEResolver (pe_resolver.cpp : 73) Splitting paths 77s 0:00:00.162 1M / 60M INFO PEResolver (pe_resolver.cpp : 78) Deduplicating paths 77s 0:00:00.162 1M / 60M INFO PEResolver (pe_resolver.cpp : 80) Overlaps removed 77s 0:00:00.162 1M / 60M INFO General (launcher.cpp : 273) Paths finalized 77s 0:00:00.162 1M / 60M INFO General (launcher.cpp : 664) ExSPAnder repeat resolving tool finished 77s 0:00:00.162 1M / 60M INFO StageManager (stage.cpp : 185) STAGE == Contig Output (id: contig_output) 77s 0:00:00.162 1M / 60M INFO General (contig_output.hpp : 16) Outputting contigs to /tmp/tmp.cMLX1ajB23/spades_test/K49/before_rr.fasta 77s 0:00:00.162 1M / 60M INFO General (contig_output_stage.cpp : 151) Writing GFA graph to /tmp/tmp.cMLX1ajB23/spades_test/K49/assembly_graph_with_scaffolds.gfa 77s 0:00:00.162 1M / 60M INFO General (contig_output_stage.cpp : 165) Outputting FastG graph to /tmp/tmp.cMLX1ajB23/spades_test/K49/assembly_graph.fastg 77s 0:00:00.162 1M / 60M INFO General (contig_output_stage.cpp : 196) Breaking scaffolds 77s 0:00:00.162 1M / 60M INFO General (contig_output_stage.cpp : 98) Outputting contigs to /tmp/tmp.cMLX1ajB23/spades_test/K49/final_contigs.fasta 77s 0:00:00.162 1M / 60M INFO General (contig_output_stage.cpp : 104) Outputting FastG paths to /tmp/tmp.cMLX1ajB23/spades_test/K49/final_contigs.paths 77s 0:00:00.162 1M / 60M INFO General (contig_output_stage.cpp : 98) Outputting contigs to /tmp/tmp.cMLX1ajB23/spades_test/K49/scaffolds.fasta 77s 0:00:00.163 1M / 60M INFO General (contig_output_stage.cpp : 104) Outputting FastG paths to /tmp/tmp.cMLX1ajB23/spades_test/K49/scaffolds.paths 77s 0:00:00.163 1M / 60M INFO General (contig_output_stage.cpp : 111) Populating GFA with scaffold paths 77s 0:00:00.163 1M / 60M INFO StageManager (stage.cpp : 185) STAGE == Domain Graph Construction (id: domain_graph_construction) 78s 0:00:00.226 4M / 63M INFO General (domain_matcher.cpp : 207) Matching contigs with bCoV_lipid_BD 78s 0:00:00.227 4M / 64M INFO General (domain_matcher.cpp : 216) Matches for 'bCoV_lipid_BD': 0 78s 0:00:00.227 4M / 64M INFO General (domain_matcher.cpp : 207) Matching contigs with bCoV_NAR 78s 0:00:00.227 4M / 64M INFO General (domain_matcher.cpp : 207) Matching contigs with CoV_RPol_N 78s 0:00:00.227 4M / 64M INFO General (domain_matcher.cpp : 216) Matches for 'bCoV_NAR': 0 78s 0:00:00.227 4M / 64M INFO General (domain_matcher.cpp : 207) Matching contigs with bCoV_NS6 78s 0:00:00.227 4M / 64M INFO General (domain_matcher.cpp : 216) Matches for 'bCoV_NS6': 0 78s 0:00:00.227 4M / 64M INFO General (domain_matcher.cpp : 207) Matching contigs with bCoV_NS7A 78s 0:00:00.227 4M / 64M INFO General (domain_matcher.cpp : 216) Matches for 'bCoV_NS7A': 0 78s 0:00:00.227 4M / 64M INFO General (domain_matcher.cpp : 207) Matching contigs with bCoV_NS7B 78s 0:00:00.227 4M / 64M INFO General (domain_matcher.cpp : 216) Matches for 'bCoV_NS7B': 0 78s 0:00:00.227 4M / 64M INFO General (domain_matcher.cpp : 207) Matching contigs with bCoV_NS8 78s 0:00:00.227 4M / 64M INFO General (domain_matcher.cpp : 216) Matches for 'bCoV_NS8': 0 78s 0:00:00.227 4M / 64M INFO General (domain_matcher.cpp : 207) Matching contigs with bCoV_NSP1 78s 0:00:00.227 4M / 64M INFO General (domain_matcher.cpp : 216) Matches for 'CoV_RPol_N': 0 78s 0:00:00.227 4M / 64M INFO General (domain_matcher.cpp : 207) Matching contigs with CoV_S1_C 78s 0:00:00.228 4M / 64M INFO General (domain_matcher.cpp : 216) Matches for 'CoV_S1_C': 0 78s 0:00:00.228 4M / 64M INFO General (domain_matcher.cpp : 207) Matching contigs with CoV_S2 78s 0:00:00.228 4M / 64M INFO General (domain_matcher.cpp : 216) Matches for 'bCoV_NSP1': 0 78s 0:00:00.228 4M / 64M INFO General (domain_matcher.cpp : 207) Matching contigs with bCoV_NSP3_N 78s 0:00:00.228 4M / 64M INFO General (domain_matcher.cpp : 216) Matches for 'bCoV_NSP3_N': 0 78s 0:00:00.228 4M / 64M INFO General (domain_matcher.cpp : 207) Matching contigs with bCoV_Orf14 78s 0:00:00.228 4M / 64M INFO General (domain_matcher.cpp : 216) Matches for 'bCoV_Orf14': 0 78s 0:00:00.228 4M / 64M INFO General (domain_matcher.cpp : 207) Matching contigs with bCoV_S1_N 78s 0:00:00.228 4M / 64M INFO General (domain_matcher.cpp : 216) Matches for 'CoV_S2': 0 78s 0:00:00.228 4M / 64M INFO General (domain_matcher.cpp : 207) Matching contigs with Macro 78s 0:00:00.228 4M / 64M INFO General (domain_matcher.cpp : 216) Matches for 'bCoV_S1_N': 0 78s 0:00:00.228 4M / 64M INFO General (domain_matcher.cpp : 207) Matching contigs with bCoV_S1_RBD 78s 0:00:00.228 4M / 64M INFO General (domain_matcher.cpp : 216) Matches for 'Macro': 0 78s 0:00:00.228 4M / 64M INFO General (domain_matcher.cpp : 207) Matching contigs with Peptidase_C30 78s 0:00:00.228 4M / 64M INFO General (domain_matcher.cpp : 216) Matches for 'bCoV_S1_RBD': 0 78s 0:00:00.228 4M / 64M INFO General (domain_matcher.cpp : 207) Matching contigs with bCoV_SUD_C 78s 0:00:00.228 4M / 64M INFO General (domain_matcher.cpp : 216) Matches for 'bCoV_SUD_C': 0 78s 0:00:00.228 4M / 64M INFO General (domain_matcher.cpp : 207) Matching contigs with bCoV_SUD_M 78s 0:00:00.229 4M / 64M INFO General (domain_matcher.cpp : 216) Matches for 'Peptidase_C30': 0 78s 0:00:00.229 4M / 64M INFO General (domain_matcher.cpp : 216) Matches for 'bCoV_SUD_M': 0 78s 0:00:00.229 4M / 64M INFO General (domain_matcher.cpp : 207) Matching contigs with bCoV_viroporin 78s 0:00:00.229 4M / 64M INFO General (domain_matcher.cpp : 207) Matching contigs with RdRP_1 78s 0:00:00.229 4M / 64M INFO General (domain_matcher.cpp : 216) Matches for 'bCoV_viroporin': 0 78s 0:00:00.229 4M / 64M INFO General (domain_matcher.cpp : 207) Matching contigs with CoV_E 78s 0:00:00.230 4M / 64M INFO General (domain_matcher.cpp : 216) Matches for 'CoV_E': 0 78s 0:00:00.230 4M / 64M INFO General (domain_matcher.cpp : 207) Matching contigs with CoV_M 78s 0:00:00.230 4M / 64M INFO General (domain_matcher.cpp : 216) Matches for 'CoV_M': 0 78s 0:00:00.230 4M / 64M INFO General (domain_matcher.cpp : 207) Matching contigs with CoV_Methyltr_1 78s 0:00:00.230 4M / 64M INFO General (domain_matcher.cpp : 216) Matches for 'RdRP_1': 0 78s 0:00:00.230 4M / 64M INFO General (domain_matcher.cpp : 207) Matching contigs with Viral_helicase1 78s 0:00:00.230 4M / 64M INFO General (domain_matcher.cpp : 216) Matches for 'CoV_Methyltr_1': 0 78s 0:00:00.230 4M / 64M INFO General (domain_matcher.cpp : 207) Matching contigs with CoV_Methyltr_2 78s 0:00:00.230 4M / 64M INFO General (domain_matcher.cpp : 216) Matches for 'Viral_helicase1': 0 78s 0:00:00.231 4M / 64M INFO General (domain_matcher.cpp : 207) Matching contigs with AAA_11 78s 0:00:00.231 4M / 64M INFO General (domain_matcher.cpp : 216) Matches for 'CoV_Methyltr_2': 0 78s 0:00:00.231 4M / 64M INFO General (domain_matcher.cpp : 207) Matching contigs with CoV_NSP10 78s 0:00:00.231 4M / 64M INFO General (domain_matcher.cpp : 216) Matches for 'AAA_11': 0 78s 0:00:00.231 4M / 64M INFO General (domain_matcher.cpp : 207) Matching contigs with AAA_12 78s 0:00:00.231 4M / 64M INFO General (domain_matcher.cpp : 216) Matches for 'CoV_NSP10': 0 78s 0:00:00.231 4M / 64M INFO General (domain_matcher.cpp : 207) Matching contigs with CoV_NSP15_C 78s 0:00:00.231 4M / 64M INFO General (domain_matcher.cpp : 216) Matches for 'CoV_NSP15_C': 0 78s 0:00:00.231 4M / 64M INFO General (domain_matcher.cpp : 207) Matching contigs with CoV_NSP15_M 78s 0:00:00.231 4M / 64M INFO General (domain_matcher.cpp : 216) Matches for 'CoV_NSP15_M': 0 78s 0:00:00.231 4M / 64M INFO General (domain_matcher.cpp : 207) Matching contigs with CoV_NSP15_N 78s 0:00:00.231 4M / 64M INFO General (domain_matcher.cpp : 216) Matches for 'CoV_NSP15_N': 0 78s 0:00:00.231 4M / 64M INFO General (domain_matcher.cpp : 207) Matching contigs with CoV_NSP2_C 78s 0:00:00.231 4M / 64M INFO General (domain_matcher.cpp : 216) Matches for 'AAA_12': 0 78s 0:00:00.231 4M / 64M INFO General (domain_matcher.cpp : 207) Matching contigs with AAA_19 78s 0:00:00.231 4M / 64M INFO General (domain_matcher.cpp : 216) Matches for 'CoV_NSP2_C': 0 78s 0:00:00.231 4M / 64M INFO General (domain_matcher.cpp : 207) Matching contigs with CoV_NSP2_N 78s 0:00:00.232 4M / 64M INFO General (domain_matcher.cpp : 216) Matches for 'AAA_19': 0 78s 0:00:00.232 4M / 64M INFO General (domain_matcher.cpp : 216) Matches for 'CoV_NSP2_N': 0 78s 0:00:00.232 4M / 64M INFO General (domain_matcher.cpp : 207) Matching contigs with CoV_NSP3_C 78s 0:00:00.232 4M / 64M INFO General (domain_matcher.cpp : 207) Matching contigs with AAA_30 78s 0:00:00.232 4M / 64M INFO General (domain_matcher.cpp : 216) Matches for 'AAA_30': 0 78s 0:00:00.232 4M / 64M INFO General (domain_matcher.cpp : 207) Matching contigs with CNV-Replicase_N 78s 0:00:00.232 4M / 64M INFO General (domain_matcher.cpp : 216) Matches for 'CNV-Replicase_N': 0 78s 0:00:00.232 4M / 64M INFO General (domain_matcher.cpp : 207) Matching contigs with Corona_3 78s 0:00:00.233 4M / 64M INFO General (domain_matcher.cpp : 216) Matches for 'Corona_3': 0 78s 0:00:00.233 4M / 64M INFO General (domain_matcher.cpp : 207) Matching contigs with Corona_5a 78s 0:00:00.233 4M / 64M INFO General (domain_matcher.cpp : 216) Matches for 'CoV_NSP3_C': 0 78s 0:00:00.233 4M / 64M INFO General (domain_matcher.cpp : 207) Matching contigs with CoV_NSP4_C 78s 0:00:00.233 4M / 64M INFO General (domain_matcher.cpp : 216) Matches for 'Corona_5a': 0 78s 0:00:00.233 4M / 64M INFO General (domain_matcher.cpp : 207) Matching contigs with Corona_6B_7B 78s 0:00:00.233 4M / 64M INFO General (domain_matcher.cpp : 216) Matches for 'CoV_NSP4_C': 0 78s 0:00:00.233 4M / 64M INFO General (domain_matcher.cpp : 207) Matching contigs with CoV_NSP4_N 78s 0:00:00.233 4M / 64M INFO General (domain_matcher.cpp : 216) Matches for 'Corona_6B_7B': 0 78s 0:00:00.233 4M / 64M INFO General (domain_matcher.cpp : 207) Matching contigs with Corona_7 78s 0:00:00.233 4M / 64M INFO General (domain_matcher.cpp : 216) Matches for 'Corona_7': 0 78s 0:00:00.233 4M / 64M INFO General (domain_matcher.cpp : 207) Matching contigs with Corona_I 78s 0:00:00.233 4M / 64M INFO General (domain_matcher.cpp : 216) Matches for 'CoV_NSP4_N': 0 78s 0:00:00.233 4M / 64M INFO General (domain_matcher.cpp : 207) Matching contigs with CoV_NSP6 78s 0:00:00.233 4M / 64M INFO General (domain_matcher.cpp : 216) Matches for 'Corona_I': 0 78s 0:00:00.233 4M / 64M INFO General (domain_matcher.cpp : 207) Matching contigs with Corona_NS2A 78s 0:00:00.233 4M / 64M INFO General (domain_matcher.cpp : 216) Matches for 'CoV_NSP6': 0 78s 0:00:00.233 4M / 64M INFO General (domain_matcher.cpp : 207) Matching contigs with CoV_NSP7 78s 0:00:00.233 4M / 64M INFO General (domain_matcher.cpp : 216) Matches for 'CoV_NSP7': 0 78s 0:00:00.233 4M / 64M INFO General (domain_matcher.cpp : 207) Matching contigs with CoV_NSP8 78s 0:00:00.233 4M / 64M INFO General (domain_matcher.cpp : 216) Matches for 'Corona_NS2A': 0 78s 0:00:00.233 4M / 64M INFO General (domain_matcher.cpp : 207) Matching contigs with Corona_NS4 78s 0:00:00.234 4M / 64M INFO General (domain_matcher.cpp : 216) Matches for 'Corona_NS4': 0 78s 0:00:00.234 4M / 64M INFO General (domain_matcher.cpp : 207) Matching contigs with Corona_NS12-7 78s 0:00:00.234 4M / 64M INFO General (domain_matcher.cpp : 216) Matches for 'Corona_NS12-7': 0 78s 0:00:00.234 4M / 64M INFO General (domain_matcher.cpp : 216) Matches for 'CoV_NSP8': 0 78s 0:00:00.234 4M / 64M INFO General (domain_matcher.cpp : 207) Matching contigs with CoV_NSP9 78s 0:00:00.234 4M / 64M INFO General (domain_matcher.cpp : 207) Matching contigs with Coronavirus_5 78s 0:00:00.234 4M / 64M INFO General (domain_matcher.cpp : 216) Matches for 'CoV_NSP9': 0 78s 0:00:00.234 4M / 64M INFO General (domain_matcher.cpp : 207) Matching contigs with CoV_nucleocap 78s 0:00:00.235 4M / 64M INFO General (domain_matcher.cpp : 216) Matches for 'Coronavirus_5': 0 78s 0:00:00.235 4M / 64M INFO General (domain_matcher.cpp : 207) Matching contigs with CoV_S1 78s 0:00:00.235 4M / 64M INFO General (domain_matcher.cpp : 216) Matches for 'CoV_nucleocap': 0 78s 0:00:00.235 4M / 64M INFO General (domain_matcher.cpp : 207) Matching contigs with CoV_peptidase 78s 0:00:00.235 4M / 64M INFO General (domain_matcher.cpp : 216) Matches for 'CoV_S1': 0 78s 0:00:00.235 4M / 64M INFO General (domain_matcher.cpp : 207) Matching contigs with DUF2632 78s 0:00:00.235 4M / 64M INFO General (domain_matcher.cpp : 216) Matches for 'CoV_peptidase': 0 78s 0:00:00.235 4M / 64M INFO General (domain_matcher.cpp : 216) Matches for 'DUF2632': 0 78s 0:00:00.235 4M / 64M INFO General (domain_matcher.cpp : 207) Matching contigs with DUF3477 78s 0:00:00.236 4M / 64M INFO General (domain_matcher.cpp : 216) Matches for 'DUF3477': 0 78s 0:00:00.236 4M / 64M INFO General (domain_matcher.cpp : 207) Matching contigs with Hema_esterase 78s 0:00:00.236 4M / 64M INFO General (domain_matcher.cpp : 216) Matches for 'Hema_esterase': 0 78s 0:00:00.236 4M / 64M INFO General (domain_matcher.cpp : 207) Matching contigs with Hema_HEFG 78s 0:00:00.236 4M / 64M INFO General (domain_matcher.cpp : 216) Matches for 'Hema_HEFG': 0 78s 0:00:00.236 4M / 64M INFO General (domain_matcher.cpp : 207) Matching contigs with IBV_3A 78s 0:00:00.236 4M / 64M INFO General (domain_matcher.cpp : 216) Matches for 'IBV_3A': 0 78s 0:00:00.236 4M / 64M INFO General (domain_matcher.cpp : 207) Matching contigs with IBV_3B 78s 0:00:00.237 4M / 64M INFO General (domain_matcher.cpp : 216) Matches for 'IBV_3B': 0 78s 0:00:00.237 4M / 64M INFO General (domain_matcher.cpp : 207) Matching contigs with IBV_3C 78s 0:00:00.237 4M / 64M INFO General (domain_matcher.cpp : 216) Matches for 'IBV_3C': 0 78s 0:00:00.237 4M / 64M INFO General (domain_matcher.cpp : 207) Matching contigs with Peptidase_C16 78s 0:00:00.237 4M / 64M INFO General (domain_matcher.cpp : 216) Matches for 'Peptidase_C16': 0 78s 0:00:00.237 4M / 64M INFO General (domain_matcher.cpp : 207) Matching contigs with SARS_3b 78s 0:00:00.238 4M / 64M INFO General (domain_matcher.cpp : 216) Matches for 'SARS_3b': 0 78s 0:00:00.238 4M / 64M INFO General (domain_matcher.cpp : 207) Matching contigs with Spike_torovirin 78s 0:00:00.239 4M / 64M INFO General (domain_matcher.cpp : 216) Matches for 'Spike_torovirin': 0 78s 0:00:00.239 4M / 64M INFO General (domain_matcher.cpp : 207) Matching contigs with UvrD_C_2 78s 0:00:00.239 4M / 64M INFO General (domain_matcher.cpp : 216) Matches for 'UvrD_C_2': 0 78s 0:00:00.239 4M / 64M INFO General (domain_matcher.cpp : 221) Total domain matches: 0 78s 0:00:00.239 1M / 64M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 78s 0:00:00.239 1M / 64M INFO GraphCore (graph_core.hpp : 673) Vertex size: 192, edge size: 56 78s 0:00:00.239 1M / 64M INFO DomainGraphConstruction (domain_graph_construction.: 96) Domain graph construction started 78s 0:00:00.239 1M / 64M INFO DomainGraphConstruction (domain_graph_construction.: 97) Constructing nodes... 78s 0:00:00.239 1M / 64M INFO DomainGraphConstruction (domain_graph_construction.: 386) Reconstructing alignment paths 78s 0:00:00.240 1M / 64M INFO DomainGraphConstruction (domain_graph_construction.: 394) Creating vertices 78s 0:00:00.240 1M / 64M INFO DomainGraphConstruction (domain_graph_construction.: 99) Constructing strong edges... 78s 0:00:00.240 1M / 64M INFO DomainGraphConstruction (domain_graph_construction.: 101) Constructing weak edges... 78s 0:00:00.240 1M / 64M INFO DomainGraphConstruction (domain_graph_construction.: 103) Domain graph construction constructed, total vertices: 0, edges: 0 78s 0:00:00.240 1M / 64M INFO DomainGraph (domain_graph.cpp : 501) Total start vertices: 0 78s 0:00:00.240 1M / 64M INFO General (pipeline.cpp : 287) SPAdes finished 78s 0:00:00.240 1M / 64M INFO General (main.cpp : 136) Assembling time: 0 hours 0 minutes 0 seconds 78s 78s ===== K49 finished. 78s 78s 78s ===== Copy files started. 78s 78s 78s == Running: /usr/bin/python3 /usr/share/spades/spades_pipeline/scripts/copy_files.py /tmp/tmp.cMLX1ajB23/spades_test/K49/before_rr.fasta /tmp/tmp.cMLX1ajB23/spades_test/before_rr.fasta /tmp/tmp.cMLX1ajB23/spades_test/K49/assembly_graph_after_simplification.gfa /tmp/tmp.cMLX1ajB23/spades_test/assembly_graph_after_simplification.gfa /tmp/tmp.cMLX1ajB23/spades_test/K49/final_contigs.fasta /tmp/tmp.cMLX1ajB23/spades_test/raw_contigs.fasta /tmp/tmp.cMLX1ajB23/spades_test/K49/first_pe_contigs.fasta /tmp/tmp.cMLX1ajB23/spades_test/first_pe_contigs.fasta /tmp/tmp.cMLX1ajB23/spades_test/K49/strain_graph.gfa /tmp/tmp.cMLX1ajB23/spades_test/strain_graph.gfa /tmp/tmp.cMLX1ajB23/spades_test/K49/scaffolds.fasta /tmp/tmp.cMLX1ajB23/spades_test/raw_scaffolds.fasta /tmp/tmp.cMLX1ajB23/spades_test/K49/scaffolds.paths /tmp/tmp.cMLX1ajB23/spades_test/raw_scaffolds.paths /tmp/tmp.cMLX1ajB23/spades_test/K49/assembly_graph_with_scaffolds.gfa /tmp/tmp.cMLX1ajB23/spades_test/assembly_graph_with_scaffolds.gfa /tmp/tmp.cMLX1ajB23/spades_test/K49/assembly_graph.fastg /tmp/tmp.cMLX1ajB23/spades_test/assembly_graph.fastg /tmp/tmp.cMLX1ajB23/spades_test/K49/final_contigs.paths /tmp/tmp.cMLX1ajB23/spades_test/contigs.paths /tmp/tmp.cMLX1ajB23/spades_test/K49/gene_clusters.fasta /tmp/tmp.cMLX1ajB23/spades_test/scaffolds.fasta /tmp/tmp.cMLX1ajB23/spades_test/K49/hmm_statistics.txt /tmp/tmp.cMLX1ajB23/spades_test/hmm_statistics.txt /tmp/tmp.cMLX1ajB23/spades_test/K49/domain_graph.dot /tmp/tmp.cMLX1ajB23/spades_test/domain_graph.dot 78s 78s 78s ===== Copy files finished. 78s 78s 78s ===== Assembling finished. 78s 78s 78s ===== Check test started. 78s 78s 78s == Running: /usr/bin/python3 /usr/share/spades/spades_pipeline/scripts/check_test_script.py --mode common --result_contigs_filename /tmp/tmp.cMLX1ajB23/spades_test/raw_contigs.fasta --result_scaffolds_filename /tmp/tmp.cMLX1ajB23/spades_test/raw_scaffolds.fasta 78s 78s ========= TEST PASSED CORRECTLY. 78s 78s ===== Check test finished. 78s 78s 78s ===== Breaking scaffolds started. 78s 78s 78s == Running: /usr/bin/python3 /usr/share/spades/spades_pipeline/scripts/breaking_scaffolds_script.py --result_scaffolds_filename /tmp/tmp.cMLX1ajB23/spades_test/raw_scaffolds.fasta --misc_dir /tmp/tmp.cMLX1ajB23/spades_test/misc --threshold_for_breaking_scaffolds 3 78s 78s 78s ===== Breaking scaffolds finished. 78s 78s 78s ===== Terminate started. 78s 78s 78s ===== Terminate finished. 78s 78s * Assembled contigs are in /tmp/tmp.cMLX1ajB23/spades_test/raw_contigs.fasta 78s * Domain graph is in /tmp/tmp.cMLX1ajB23/spades_test/domain_graph.dot 78s * Gene cluster sequences are in /tmp/tmp.cMLX1ajB23/spades_test/scaffolds.fasta 78s * BGC cluster statistics /tmp/tmp.cMLX1ajB23/spades_test/hmm_statistics.txt 78s * Assembled scaffolds are in /tmp/tmp.cMLX1ajB23/spades_test/raw_scaffolds.fasta 78s * Paths in the assembly graph corresponding to the contigs are in /tmp/tmp.cMLX1ajB23/spades_test/contigs.paths 78s * Paths in the assembly graph corresponding to the scaffolds are in /tmp/tmp.cMLX1ajB23/spades_test/raw_scaffolds.paths 78s * Assembly graph is in /tmp/tmp.cMLX1ajB23/spades_test/assembly_graph.fastg 78s * Assembly graph in GFA format is in /tmp/tmp.cMLX1ajB23/spades_test/assembly_graph_with_scaffolds.gfa 78s 78s ======= SPAdes pipeline finished. 78s 78s SPAdes log can be found here: /tmp/tmp.cMLX1ajB23/spades_test/spades.log 78s 78s Thank you for using SPAdes! 78s + metaspades --test 78s Command line: /usr/libexec/spades/metaspades.py --test 78s 78s System information: 78s SPAdes version: 3.15.5 78s Python version: 3.13.3 78s OS: Linux-6.14.0-15-generic-x86_64-with-glibc2.41 78s 78s Output dir: /tmp/tmp.cMLX1ajB23/spades_test 78s Mode: read error correction and assembling 78s Debug mode is turned OFF 78s 78s Dataset parameters: 78s Metagenomic mode 78s Reads: 78s Library number: 1, library type: paired-end 78s orientation: fr 78s left reads: ['/usr/share/spades/test_dataset/ecoli_1K_1.fq.gz'] 78s right reads: ['/usr/share/spades/test_dataset/ecoli_1K_2.fq.gz'] 78s interlaced reads: not specified 78s single reads: not specified 78s merged reads: not specified 78s Read error correction parameters: 78s Iterations: 1 78s PHRED offset will be auto-detected 78s Corrected reads will be compressed 78s Assembly parameters: 78s k: [21, 33, 55] 78s Repeat resolution is enabled 78s Mismatch careful mode is turned OFF 78s MismatchCorrector will be SKIPPED 78s Coverage cutoff is turned OFF 78s Other parameters: 78s Dir for temp files: /tmp/tmp.cMLX1ajB23/spades_test/tmp 78s Threads: 16 78s Memory limit (in Gb): 3 78s 78s 78s ======= SPAdes pipeline started. Log can be found here: /tmp/tmp.cMLX1ajB23/spades_test/spades.log 78s 78s /usr/share/spades/test_dataset/ecoli_1K_1.fq.gz: max reads length: 100 78s /usr/share/spades/test_dataset/ecoli_1K_2.fq.gz: max reads length: 100 78s 78s Reads length: 100 78s 78s 78s ===== Before start started. 78s 78s 78s ===== Read error correction started. 78s 78s 78s ===== Read error correction started. 78s 78s 78s == Running: /usr/libexec/spades/spades-hammer /tmp/tmp.cMLX1ajB23/spades_test/corrected/configs/config.info 78s 78s 0:00:00.000 1M / 19M INFO General (main.cpp : 75) Starting BayesHammer, built from N/A, git revision N/A 78s 0:00:00.000 1M / 19M INFO General (main.cpp : 76) Loading config from /tmp/tmp.cMLX1ajB23/spades_test/corrected/configs/config.info 78s 0:00:00.000 1M / 19M INFO General (main.cpp : 78) Maximum # of threads to use (adjusted due to OMP capabilities): 2 78s 0:00:00.000 1M / 19M INFO General (memory_limit.cpp : 54) Memory limit set to 3 Gb 78s 0:00:00.000 1M / 19M INFO General (main.cpp : 86) Trying to determine PHRED offset 78s 0:00:00.000 1M / 19M INFO General (main.cpp : 92) Determined value is 33 78s 0:00:00.000 1M / 19M INFO General (hammer_tools.cpp : 38) Hamming graph threshold tau=1, k=21, subkmer positions = [ 0 10 ] 78s 0:00:00.000 1M / 19M INFO General (main.cpp : 113) Size of aux. kmer data 24 bytes 78s === ITERATION 0 begins === 78s 0:00:00.000 1M / 19M INFO K-mer Counting (kmer_data.cpp : 283) Estimating k-mer count 78s 0:00:00.015 33M / 38M INFO K-mer Counting (kmer_data.cpp : 288) Processing /usr/share/spades/test_dataset/ecoli_1K_1.fq.gz 78s 0:00:00.024 33M / 38M INFO K-mer Counting (kmer_data.cpp : 288) Processing /usr/share/spades/test_dataset/ecoli_1K_2.fq.gz 78s 0:00:00.033 33M / 38M INFO K-mer Counting (kmer_data.cpp : 302) Total 4108 reads processed 78s 0:00:00.108 33M / 38M INFO K-mer Counting (kmer_data.cpp : 305) Estimated 2171 distinct kmers 78s 0:00:00.108 1M / 38M INFO K-mer Counting (kmer_data.cpp : 309) Filtering singleton k-mers 78s 0:00:00.108 1M / 38M INFO K-mer Counting (kmer_data.cpp : 315) Processing /usr/share/spades/test_dataset/ecoli_1K_1.fq.gz 78s 0:00:00.130 1M / 38M INFO K-mer Counting (kmer_data.cpp : 315) Processing /usr/share/spades/test_dataset/ecoli_1K_2.fq.gz 78s 0:00:00.152 1M / 38M INFO K-mer Counting (kmer_data.cpp : 329) Total 4108 reads processed 78s 0:00:00.153 1M / 38M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 16 files using 2 threads. This might take a while. 78s 0:00:00.153 1M / 38M INFO General (file_limit.hpp : 42) Open file limit set to 1024 78s 0:00:00.153 1M / 38M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 0.499983 Gb 78s 0:00:00.153 1M / 38M INFO General (kmer_splitter.hpp : 101) Using cell size of 4194164 78s 0:00:00.153 1153M / 1153M INFO K-mer Splitting (kmer_data.cpp : 97) Processing /usr/share/spades/test_dataset/ecoli_1K_1.fq.gz 78s 0:00:00.174 1153M / 1153M INFO K-mer Splitting (kmer_data.cpp : 97) Processing /usr/share/spades/test_dataset/ecoli_1K_2.fq.gz 78s 0:00:00.195 1153M / 1153M INFO K-mer Splitting (kmer_data.cpp : 112) Total 4108 reads processed 78s 0:00:00.195 1M / 42M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. 78s 0:00:00.197 1M / 42M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 1974 kmers in total. 78s 0:00:00.197 1M / 42M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices 78s 0:00:00.198 1M / 42M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 1974 kmers, 13944 bytes occupied (56.5106 bits per kmer). 78s 0:00:00.198 1M / 42M INFO K-mer Counting (kmer_data.cpp : 354) Arranging kmers in hash map order 78s 0:00:00.199 1M / 42M INFO General (main.cpp : 148) Clustering Hamming graph. 78s 0:00:00.201 1M / 42M INFO General (main.cpp : 155) Extracting clusters: 78s 0:00:00.201 1M / 42M INFO General (concurrent_dsu.cpp : 18) Connecting to root 78s 0:00:00.201 1M / 42M INFO General (concurrent_dsu.cpp : 34) Calculating counts 78s 0:00:00.202 1M / 42M INFO General (concurrent_dsu.cpp : 63) Writing down entries 78s 0:00:00.202 1M / 42M INFO General (main.cpp : 167) Clustering done. Total clusters: 1960 78s 0:00:00.202 1M / 42M INFO K-mer Counting (kmer_data.cpp : 371) Collecting K-mer information, this takes a while. 78s 0:00:00.202 1M / 42M INFO K-mer Counting (kmer_data.cpp : 377) Processing /usr/share/spades/test_dataset/ecoli_1K_1.fq.gz 78s 0:00:00.233 1M / 42M INFO K-mer Counting (kmer_data.cpp : 377) Processing /usr/share/spades/test_dataset/ecoli_1K_2.fq.gz 78s 0:00:00.265 1M / 42M INFO K-mer Counting (kmer_data.cpp : 384) Collection done, postprocessing. 78s 0:00:00.265 1M / 42M INFO K-mer Counting (kmer_data.cpp : 397) There are 1974 kmers in total. Among them 0 (0%) are singletons. 78s 0:00:00.265 1M / 42M INFO General (main.cpp : 173) Subclustering Hamming graph 78s 0:00:00.265 1M / 42M INFO Hamming Subclustering (kmer_cluster.cpp : 650) Subclustering done. Total 0 non-read kmers were generated. 78s 0:00:00.265 1M / 42M INFO Hamming Subclustering (kmer_cluster.cpp : 651) Subclustering statistics: 78s 0:00:00.265 1M / 42M INFO Hamming Subclustering (kmer_cluster.cpp : 652) Total singleton hamming clusters: 1946. Among them 1946 (100%) are good 78s 0:00:00.265 1M / 42M INFO Hamming Subclustering (kmer_cluster.cpp : 653) Total singleton subclusters: 8. Among them 8 (100%) are good 78s 0:00:00.265 1M / 42M INFO Hamming Subclustering (kmer_cluster.cpp : 654) Total non-singleton subcluster centers: 10. Among them 10 (100%) are good 78s 0:00:00.265 1M / 42M INFO Hamming Subclustering (kmer_cluster.cpp : 655) Average size of non-trivial subcluster: 2.8 kmers 78s 0:00:00.265 1M / 42M INFO Hamming Subclustering (kmer_cluster.cpp : 656) Average number of sub-clusters per non-singleton cluster: 1.28571 78s 0:00:00.266 1M / 42M INFO Hamming Subclustering (kmer_cluster.cpp : 657) Total solid k-mers: 1964 78s 0:00:00.266 1M / 42M INFO Hamming Subclustering (kmer_cluster.cpp : 658) Substitution probabilities: [4,4]((0.875,0.125,0,0),(0,1,0,0),(0,0,1,0),(0,0,0.125,0.875)) 78s 0:00:00.266 1M / 42M INFO General (main.cpp : 178) Finished clustering. 78s 0:00:00.266 1M / 42M INFO General (main.cpp : 197) Starting solid k-mers expansion in 2 threads. 78s 0:00:00.283 1M / 42M INFO General (main.cpp : 218) Solid k-mers iteration 0 produced 0 new k-mers. 78s 0:00:00.283 1M / 42M INFO General (main.cpp : 222) Solid k-mers finalized 78s 0:00:00.284 1M / 42M INFO General (hammer_tools.cpp : 222) Starting read correction in 2 threads. 78s 0:00:00.284 1M / 42M INFO General (hammer_tools.cpp : 235) Correcting pair of reads: /usr/share/spades/test_dataset/ecoli_1K_1.fq.gz and /usr/share/spades/test_dataset/ecoli_1K_2.fq.gz 78s 0:00:00.297 46M / 57M INFO General (hammer_tools.cpp : 170) Prepared batch 0 of 2054 reads. 78s 0:00:00.301 46M / 57M INFO General (hammer_tools.cpp : 177) Processed batch 0 78s 0:00:00.303 46M / 57M INFO General (hammer_tools.cpp : 187) Written batch 0 78s 0:00:00.305 1M / 57M INFO General (hammer_tools.cpp : 276) Correction done. Changed 4 bases in 4 reads. 78s 0:00:00.305 1M / 57M INFO General (hammer_tools.cpp : 277) Failed to correct 0 bases out of 353915. 78s 0:00:00.305 1M / 57M INFO General (main.cpp : 255) Saving corrected dataset description to /tmp/tmp.cMLX1ajB23/spades_test/corrected/corrected.yaml 78s 0:00:00.305 1M / 57M INFO General (main.cpp : 262) All done. Exiting. 78s 78s ===== Read error correction finished. 78s 78s 78s ===== corrected reads compression started. 78s 78s 78s == Running: /usr/bin/python3 /usr/share/spades/spades_pipeline/scripts/compress_all.py --input_file /tmp/tmp.cMLX1ajB23/spades_test/corrected/corrected.yaml --ext_python_modules_home /usr/share/spades --max_threads 16 --output_dir /tmp/tmp.cMLX1ajB23/spades_test/corrected --gzip_output 78s 78s == Compressing corrected reads (with gzip) 78s == Files to compress: ['/tmp/tmp.cMLX1ajB23/spades_test/corrected/ecoli_1K_1.fq.00.0_0.cor.fastq', '/tmp/tmp.cMLX1ajB23/spades_test/corrected/ecoli_1K_2.fq.00.0_0.cor.fastq', '/tmp/tmp.cMLX1ajB23/spades_test/corrected/ecoli_1K__unpaired.00.0_0.cor.fastq'] 78s == Files compression is finished 78s == Dataset yaml file is updated 78s 78s ===== corrected reads compression finished. 78s 78s 78s ===== Read error correction finished. 78s 78s 78s ===== Assembling started. 78s 78s 78s ===== K21 started. 78s 78s 78s == Running: /usr/libexec/spades/spades-core /tmp/tmp.cMLX1ajB23/spades_test/K21/configs/config.info /tmp/tmp.cMLX1ajB23/spades_test/K21/configs/mda_mode.info /tmp/tmp.cMLX1ajB23/spades_test/K21/configs/meta_mode.info 78s 78s 0:00:00.000 1M / 19M INFO General (main.cpp : 99) Loaded config from /tmp/tmp.cMLX1ajB23/spades_test/K21/configs/config.info 78s 0:00:00.000 1M / 19M INFO General (main.cpp : 99) Loaded config from /tmp/tmp.cMLX1ajB23/spades_test/K21/configs/mda_mode.info 78s 0:00:00.001 1M / 19M INFO General (main.cpp : 99) Loaded config from /tmp/tmp.cMLX1ajB23/spades_test/K21/configs/meta_mode.info 78s 0:00:00.001 1M / 19M INFO General (memory_limit.cpp : 54) Memory limit set to 3 Gb 78s 0:00:00.001 1M / 19M INFO General (main.cpp : 107) Starting SPAdes, built from N/A, git revision N/A 78s 0:00:00.001 1M / 19M INFO General (main.cpp : 108) Maximum k-mer length: 128 78s 0:00:00.001 1M / 19M INFO General (main.cpp : 109) Assembling dataset (/tmp/tmp.cMLX1ajB23/spades_test/dataset.info) with K=21 78s 0:00:00.001 1M / 19M INFO General (main.cpp : 110) Maximum # of threads to use (adjusted due to OMP capabilities): 2 78s 0:00:00.001 1M / 19M INFO General (pipeline.cpp : 212) SPAdes started 78s 0:00:00.001 1M / 19M INFO General (pipeline.cpp : 225) Starting from stage: read_conversion 78s 0:00:00.001 1M / 19M INFO General (pipeline.cpp : 231) Two-step repeat resolution disabled 78s 0:00:00.001 1M / 19M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 78s 0:00:00.001 1M / 19M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 78s 0:00:00.001 1M / 19M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 78s 0:00:00.001 1M / 19M INFO StageManager (stage.cpp : 185) STAGE == Binary Read Conversion (id: read_conversion) 78s 0:00:00.001 1M / 19M INFO General (read_converter.cpp : 72) Converting reads to binary format for library #0 (takes a while) 78s 0:00:00.001 1M / 19M INFO General (read_converter.cpp : 73) Converting paired reads 78s 0:00:00.014 63M / 63M INFO General (binary_converter.cpp : 111) 2054 reads written 78s 0:00:00.014 41M / 41M INFO General (read_converter.cpp : 86) Converting single reads 78s 0:00:00.015 71M / 71M INFO General (binary_converter.cpp : 111) 0 reads written 78s 0:00:00.015 61M / 61M INFO General (read_converter.cpp : 92) Converting merged reads 78s 0:00:00.015 71M / 71M INFO General (binary_converter.cpp : 111) 0 reads written 78s 0:00:00.015 1M / 19M INFO StageManager (stage.cpp : 185) STAGE == de Bruijn graph construction (id: construction) 78s 0:00:00.016 1M / 19M INFO General (construction.cpp : 153) Max read length 100 78s 0:00:00.016 1M / 19M INFO General (construction.cpp : 159) Average read length 86.1526 78s 0:00:00.016 1M / 19M INFO General (stage.cpp : 117) PROCEDURE == k+1-mer counting (id: construction:kpomer_counting) 78s 0:00:00.016 1M / 19M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 20 files using 2 threads. This might take a while. 78s 0:00:00.016 1M / 19M INFO General (file_limit.hpp : 42) Open file limit set to 1024 78s 0:00:00.016 1M / 19M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 0.499973 Gb 78s 0:00:00.016 1M / 19M INFO General (kmer_splitter.hpp : 101) Using cell size of 3355263 78s 0:00:00.025 1M / 19M INFO General (kmer_splitters.hpp : 131) Used 8216 reads 78s 0:00:00.026 1M / 19M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. 78s 0:00:00.027 1M / 19M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 984 kmers in total. 78s 0:00:00.027 1M / 19M INFO General (stage.cpp : 117) PROCEDURE == Extension index construction (id: construction:extension_index_construction) 78s 0:00:00.027 1M / 19M INFO K-mer Index Building (kmer_index_builder.hpp : 438) Building kmer index 78s 0:00:00.028 1M / 19M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 20 files using 2 threads. This might take a while. 78s 0:00:00.028 1M / 19M INFO General (file_limit.hpp : 42) Open file limit set to 1024 78s 0:00:00.028 1M / 19M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 0.49997 Gb 78s 0:00:00.028 1M / 19M INFO General (kmer_splitter.hpp : 101) Using cell size of 3355245 78s 0:00:00.029 1161M / 1161M INFO General (kmer_splitters.hpp : 199) Used 984 kmers. 78s 0:00:00.029 1M / 19M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. 78s 0:00:00.031 1M / 19M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 985 kmers in total. 78s 0:00:00.031 1M / 19M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices 78s 0:00:00.032 1M / 19M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 985 kmers, 16424 bytes occupied (133.393 bits per kmer). 78s 0:00:00.032 1M / 19M INFO General (kmer_index_builder.hpp : 169) Merging final buckets. 78s 0:00:00.033 1M / 19M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 100) Building k-mer extensions from k+1-mers 78s 0:00:00.033 1M / 19M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 105) Building k-mer extensions from k+1-mers finished. 78s 0:00:00.034 1M / 19M INFO General (stage.cpp : 117) PROCEDURE == Early tip clipping (id: construction:early_tip_clipper) 78s 0:00:00.034 1M / 19M INFO General (construction.cpp : 301) Early tip clipper length bound set as (RL - K) 78s 0:00:00.034 1M / 19M INFO Early tip clipping (early_simplification.hpp : 47) Early tip clipping 78s 0:00:00.034 1M / 19M INFO Early tip clipping (early_simplification.hpp : 82) #tipped junctions: 2 78s 0:00:00.034 1M / 19M INFO Early tip clipping (early_simplification.hpp : 93) Clipped tips: 2 78s 0:00:00.034 1M / 19M INFO Early tip clipping (early_simplification.hpp : 49) 5 22-mers were removed by early tip clipper 78s 0:00:00.034 1M / 19M INFO General (stage.cpp : 117) PROCEDURE == Condensing graph (id: construction:graph_condensing) 78s 0:00:00.034 1M / 19M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths 78s 0:00:00.035 1M / 19M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 1 sequences extracted 78s 0:00:00.035 1M / 19M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops 78s 0:00:00.035 1M / 19M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 0 loops collected 78s 0:00:00.035 1M / 19M INFO General (debruijn_graph_constructor: 487) Total 2 edges to create 78s 0:00:00.035 1M / 19M INFO General (debruijn_graph_constructor: 489) Collecting link records 78s 0:00:00.035 1M / 19M INFO General (debruijn_graph_constructor: 491) Ordering link records 78s 0:00:00.035 1M / 19M INFO General (debruijn_graph_constructor: 493) Sorting done 78s 0:00:00.035 1M / 19M INFO General (debruijn_graph_constructor: 503) Total 2 vertices to create 78s 0:00:00.035 1M / 19M INFO General (debruijn_graph_constructor: 506) Connecting the graph 78s 0:00:00.036 1M / 19M INFO General (stage.cpp : 117) PROCEDURE == Filling coverage indices (PHM) (id: construction:coverage_filling_phm) 78s 0:00:00.036 1M / 19M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices 78s 0:00:00.037 1M / 19M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 984 kmers, 16392 bytes occupied (133.268 bits per kmer). 78s 0:00:00.037 1M / 19M INFO General (coverage_hash_map_builder.: 47) Collecting k-mer coverage information from reads, this takes a while. 78s 0:00:00.050 1M / 19M INFO General (construction.cpp : 430) Filling coverage and flanking coverage from PHM 78s 0:00:00.051 1M / 19M INFO StageManager (stage.cpp : 185) STAGE == Raw Simplification (id: raw_simplification) 78s 0:00:00.051 1M / 19M INFO General (simplification.cpp : 127) PROCEDURE == Initial cleaning 78s 0:00:00.051 1M / 19M INFO General (graph_simplification.hpp : 662) Flanking coverage based disconnection disabled 78s 0:00:00.051 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Self conjugate edge remover 78s 0:00:00.051 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Self conjugate edge remover triggered 0 times 78s 0:00:00.051 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Initial tip clipper 78s 0:00:00.051 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Initial tip clipper triggered 0 times 78s 0:00:00.051 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Initial ec remover 78s 0:00:00.051 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Initial ec remover triggered 0 times 78s 0:00:00.051 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Initial isolated edge remover 78s 0:00:00.051 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Initial isolated edge remover triggered 0 times 78s 0:00:00.051 1M / 19M INFO StageManager (stage.cpp : 185) STAGE == Simplification (id: simplification) 78s 0:00:00.051 1M / 19M INFO General (simplification.cpp : 368) Graph simplification started 78s 0:00:00.051 1M / 19M INFO General (graph_simplification.hpp : 634) Creating parallel br instance 78s 0:00:00.051 1M / 19M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 1 78s 0:00:00.051 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 78s 0:00:00.051 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 78s 0:00:00.051 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 78s 0:00:00.051 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 78s 0:00:00.051 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 78s 0:00:00.051 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 0 times 78s 0:00:00.051 1M / 19M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 2 78s 0:00:00.051 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 78s 0:00:00.051 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 78s 0:00:00.051 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 78s 0:00:00.051 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 78s 0:00:00.051 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 78s 0:00:00.051 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 0 times 78s 0:00:00.051 1M / 19M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 3 78s 0:00:00.051 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 78s 0:00:00.051 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 78s 0:00:00.051 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 78s 0:00:00.051 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 78s 0:00:00.051 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 78s 0:00:00.051 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 0 times 78s 0:00:00.051 1M / 19M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 4 78s 0:00:00.051 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 78s 0:00:00.051 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 78s 0:00:00.051 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 78s 0:00:00.051 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 78s 0:00:00.051 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 78s 0:00:00.051 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 0 times 78s 0:00:00.051 1M / 19M INFO StageManager (stage.cpp : 185) STAGE == Simplification Cleanup (id: simplification_cleanup) 78s 0:00:00.051 1M / 19M INFO General (simplification.cpp : 176) PROCEDURE == Post simplification 78s 0:00:00.051 1M / 19M INFO General (graph_simplification.hpp : 634) Creating parallel br instance 78s 0:00:00.052 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Relative coverage component remover 78s 0:00:00.052 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Relative coverage component remover triggered 0 times 78s 0:00:00.052 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Disconnecting edges with relatively low coverage 78s 0:00:00.052 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Disconnecting edges with relatively low coverage triggered 0 times 78s 0:00:00.052 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Complex tip clipper 78s 0:00:00.052 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Complex tip clipper triggered 0 times 78s 0:00:00.052 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Complex bulge remover 78s 0:00:00.052 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Complex bulge remover triggered 0 times 78s 0:00:00.052 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 78s 0:00:00.052 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 78s 0:00:00.052 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Final tip clipper 78s 0:00:00.052 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Final tip clipper triggered 0 times 78s 0:00:00.052 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 78s 0:00:00.052 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 78s 0:00:00.052 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Thorn remover (meta) 78s 0:00:00.052 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Thorn remover (meta) triggered 0 times 78s 0:00:00.052 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Relative coverage component remover 78s 0:00:00.052 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Relative coverage component remover triggered 0 times 78s 0:00:00.052 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Disconnecting edges with relatively low coverage 78s 0:00:00.052 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Disconnecting edges with relatively low coverage triggered 0 times 78s 0:00:00.052 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Complex tip clipper 78s 0:00:00.052 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Complex tip clipper triggered 0 times 78s 0:00:00.052 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Complex bulge remover 78s 0:00:00.052 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Complex bulge remover triggered 0 times 78s 0:00:00.052 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 78s 0:00:00.052 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 78s 0:00:00.052 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Final tip clipper 78s 0:00:00.052 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Final tip clipper triggered 0 times 78s 0:00:00.052 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 78s 0:00:00.052 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 78s 0:00:00.052 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Thorn remover (meta) 78s 0:00:00.052 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Thorn remover (meta) triggered 0 times 78s 0:00:00.052 1M / 19M INFO General (simplification.cpp : 323) Running Hidden EC remover (meta) 78s 0:00:00.052 1M / 19M INFO General (simplification.cpp : 327) Disrupting self-conjugate edges 78s 0:00:00.052 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Removing isolated edges 78s 0:00:00.052 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Removing isolated edges triggered 0 times 78s 0:00:00.052 1M / 19M INFO General (simplification.cpp : 495) After simplification: 78s 0:00:00.052 1M / 19M INFO General (simplification.cpp : 496) Average coverage = 273.35 78s 0:00:00.052 1M / 19M INFO General (simplification.cpp : 497) Total length = 979 78s 0:00:00.052 1M / 19M INFO General (simplification.cpp : 498) Median edge length: 979 78s 0:00:00.052 1M / 19M INFO General (simplification.cpp : 499) Edges: 2 78s 0:00:00.052 1M / 19M INFO General (simplification.cpp : 500) Vertices: 4 78s 0:00:00.052 1M / 19M INFO StageManager (stage.cpp : 185) STAGE == Contig Output (id: contig_output) 78s 0:00:00.052 1M / 19M INFO General (read_converter.cpp : 107) Outputting contigs to /tmp/tmp.cMLX1ajB23/spades_test/K21/simplified_contigs 78s 0:00:00.053 3M / 19M INFO General (binary_converter.cpp : 111) 1 reads written 78s 0:00:00.053 1M / 19M INFO General (pipeline.cpp : 287) SPAdes finished 78s 0:00:00.053 1M / 19M INFO General (main.cpp : 136) Assembling time: 0 hours 0 minutes 0 seconds 78s 78s ===== K21 finished. 78s 78s 78s ===== K33 started. 78s 78s 78s == Running: /usr/libexec/spades/spades-core /tmp/tmp.cMLX1ajB23/spades_test/K33/configs/config.info /tmp/tmp.cMLX1ajB23/spades_test/K33/configs/mda_mode.info /tmp/tmp.cMLX1ajB23/spades_test/K33/configs/meta_mode.info 78s 78s 0:00:00.000 1M / 19M INFO General (main.cpp : 99) Loaded config from /tmp/tmp.cMLX1ajB23/spades_test/K33/configs/config.info 78s 0:00:00.000 1M / 19M INFO General (main.cpp : 99) Loaded config from /tmp/tmp.cMLX1ajB23/spades_test/K33/configs/mda_mode.info 78s 0:00:00.000 1M / 19M INFO General (main.cpp : 99) Loaded config from /tmp/tmp.cMLX1ajB23/spades_test/K33/configs/meta_mode.info 78s 0:00:00.000 1M / 19M INFO General (memory_limit.cpp : 54) Memory limit set to 3 Gb 78s 0:00:00.000 1M / 19M INFO General (main.cpp : 107) Starting SPAdes, built from N/A, git revision N/A 78s 0:00:00.000 1M / 19M INFO General (main.cpp : 108) Maximum k-mer length: 128 78s 0:00:00.000 1M / 19M INFO General (main.cpp : 109) Assembling dataset (/tmp/tmp.cMLX1ajB23/spades_test/dataset.info) with K=33 78s 0:00:00.000 1M / 19M INFO General (main.cpp : 110) Maximum # of threads to use (adjusted due to OMP capabilities): 2 78s 0:00:00.000 1M / 19M INFO General (pipeline.cpp : 212) SPAdes started 78s 0:00:00.000 1M / 19M INFO General (pipeline.cpp : 225) Starting from stage: read_conversion 78s 0:00:00.000 1M / 19M INFO General (pipeline.cpp : 231) Two-step repeat resolution disabled 78s 0:00:00.000 1M / 19M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 78s 0:00:00.000 1M / 19M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 78s 0:00:00.000 1M / 19M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 78s 0:00:00.000 1M / 19M INFO StageManager (stage.cpp : 185) STAGE == Binary Read Conversion (id: read_conversion) 78s 0:00:00.000 1M / 19M INFO General (read_converter.cpp : 53) Binary reads detected 78s 0:00:00.000 1M / 19M INFO StageManager (stage.cpp : 185) STAGE == de Bruijn graph construction (id: construction) 78s 0:00:00.000 1M / 19M INFO General (construction.cpp : 118) Contigs from previous K will be used: /tmp/tmp.cMLX1ajB23/spades_test/K21/simplified_contigs 78s 0:00:00.000 1M / 19M INFO General (construction.cpp : 153) Max read length 100 78s 0:00:00.000 1M / 19M INFO General (construction.cpp : 159) Average read length 86.1526 78s 0:00:00.000 1M / 19M INFO General (stage.cpp : 117) PROCEDURE == k+1-mer counting (id: construction:kpomer_counting) 78s 0:00:00.000 1M / 19M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 20 files using 2 threads. This might take a while. 78s 0:00:00.000 1M / 19M INFO General (file_limit.hpp : 42) Open file limit set to 1024 78s 0:00:00.000 1M / 19M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 0.49997 Gb 78s 0:00:00.000 1M / 19M INFO General (kmer_splitter.hpp : 101) Using cell size of 1677621 79s 0:00:00.009 1M / 19M INFO General (kmer_splitters.hpp : 131) Used 8218 reads 79s 0:00:00.009 1M / 19M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. 79s 0:00:00.010 1M / 19M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 972 kmers in total. 79s 0:00:00.010 1M / 19M INFO General (stage.cpp : 117) PROCEDURE == Extension index construction (id: construction:extension_index_construction) 79s 0:00:00.011 1M / 19M INFO K-mer Index Building (kmer_index_builder.hpp : 438) Building kmer index 79s 0:00:00.011 1M / 19M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 20 files using 2 threads. This might take a while. 79s 0:00:00.011 1M / 19M INFO General (file_limit.hpp : 42) Open file limit set to 1024 79s 0:00:00.011 1M / 19M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 0.499968 Gb 79s 0:00:00.011 1M / 19M INFO General (kmer_splitter.hpp : 101) Using cell size of 1677612 79s 0:00:00.012 1161M / 1161M INFO General (kmer_splitters.hpp : 199) Used 972 kmers. 79s 0:00:00.012 1M / 19M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. 79s 0:00:00.014 1M / 19M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 973 kmers in total. 79s 0:00:00.014 1M / 19M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices 79s 0:00:00.015 1M / 19M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 973 kmers, 16392 bytes occupied (134.775 bits per kmer). 79s 0:00:00.015 1M / 19M INFO General (kmer_index_builder.hpp : 169) Merging final buckets. 79s 0:00:00.016 1M / 19M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 100) Building k-mer extensions from k+1-mers 79s 0:00:00.016 1M / 19M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 105) Building k-mer extensions from k+1-mers finished. 79s 0:00:00.017 1M / 19M INFO General (stage.cpp : 117) PROCEDURE == Early tip clipping (id: construction:early_tip_clipper) 79s 0:00:00.017 1M / 19M INFO General (construction.cpp : 301) Early tip clipper length bound set as (RL - K) 79s 0:00:00.017 1M / 19M INFO Early tip clipping (early_simplification.hpp : 47) Early tip clipping 79s 0:00:00.017 1M / 19M INFO Early tip clipping (early_simplification.hpp : 82) #tipped junctions: 2 79s 0:00:00.017 1M / 19M INFO Early tip clipping (early_simplification.hpp : 93) Clipped tips: 2 79s 0:00:00.017 1M / 19M INFO Early tip clipping (early_simplification.hpp : 49) 5 34-mers were removed by early tip clipper 79s 0:00:00.017 1M / 19M INFO General (stage.cpp : 117) PROCEDURE == Condensing graph (id: construction:graph_condensing) 79s 0:00:00.017 1M / 19M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths 79s 0:00:00.017 1M / 19M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 1 sequences extracted 79s 0:00:00.018 1M / 19M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops 79s 0:00:00.018 1M / 19M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 0 loops collected 79s 0:00:00.018 1M / 19M INFO General (debruijn_graph_constructor: 487) Total 2 edges to create 79s 0:00:00.018 1M / 19M INFO General (debruijn_graph_constructor: 489) Collecting link records 79s 0:00:00.018 1M / 19M INFO General (debruijn_graph_constructor: 491) Ordering link records 79s 0:00:00.018 1M / 19M INFO General (debruijn_graph_constructor: 493) Sorting done 79s 0:00:00.018 1M / 19M INFO General (debruijn_graph_constructor: 503) Total 2 vertices to create 79s 0:00:00.018 1M / 19M INFO General (debruijn_graph_constructor: 506) Connecting the graph 79s 0:00:00.018 1M / 19M INFO General (stage.cpp : 117) PROCEDURE == Filling coverage indices (PHM) (id: construction:coverage_filling_phm) 79s 0:00:00.018 1M / 19M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices 79s 0:00:00.020 1M / 19M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 972 kmers, 16392 bytes occupied (134.914 bits per kmer). 79s 0:00:00.020 1M / 19M INFO General (coverage_hash_map_builder.: 47) Collecting k-mer coverage information from reads, this takes a while. 79s 0:00:00.031 1M / 19M INFO General (construction.cpp : 430) Filling coverage and flanking coverage from PHM 79s 0:00:00.031 1M / 19M INFO StageManager (stage.cpp : 185) STAGE == Raw Simplification (id: raw_simplification) 79s 0:00:00.031 1M / 19M INFO General (simplification.cpp : 127) PROCEDURE == Initial cleaning 79s 0:00:00.031 1M / 19M INFO General (graph_simplification.hpp : 662) Flanking coverage based disconnection disabled 79s 0:00:00.031 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Self conjugate edge remover 79s 0:00:00.031 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Self conjugate edge remover triggered 0 times 79s 0:00:00.031 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Initial tip clipper 79s 0:00:00.031 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Initial tip clipper triggered 0 times 79s 0:00:00.031 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Initial ec remover 79s 0:00:00.031 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Initial ec remover triggered 0 times 79s 0:00:00.031 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Initial isolated edge remover 79s 0:00:00.031 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Initial isolated edge remover triggered 0 times 79s 0:00:00.031 1M / 19M INFO StageManager (stage.cpp : 185) STAGE == Simplification (id: simplification) 79s 0:00:00.031 1M / 19M INFO General (simplification.cpp : 368) Graph simplification started 79s 0:00:00.031 1M / 19M INFO General (graph_simplification.hpp : 634) Creating parallel br instance 79s 0:00:00.031 1M / 19M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 1 79s 0:00:00.031 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 79s 0:00:00.031 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 79s 0:00:00.031 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 79s 0:00:00.031 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 79s 0:00:00.031 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 79s 0:00:00.032 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 0 times 79s 0:00:00.032 1M / 19M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 2 79s 0:00:00.032 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 79s 0:00:00.032 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 79s 0:00:00.032 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 79s 0:00:00.032 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 79s 0:00:00.032 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 79s 0:00:00.032 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 0 times 79s 0:00:00.032 1M / 19M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 3 79s 0:00:00.032 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 79s 0:00:00.032 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 79s 0:00:00.032 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 79s 0:00:00.032 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 79s 0:00:00.032 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 79s 0:00:00.032 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 0 times 79s 0:00:00.032 1M / 19M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 4 79s 0:00:00.032 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 79s 0:00:00.032 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 79s 0:00:00.032 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 79s 0:00:00.032 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 79s 0:00:00.032 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 79s 0:00:00.032 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 0 times 79s 0:00:00.032 1M / 19M INFO StageManager (stage.cpp : 185) STAGE == Simplification Cleanup (id: simplification_cleanup) 79s 0:00:00.032 1M / 19M INFO General (simplification.cpp : 176) PROCEDURE == Post simplification 79s 0:00:00.032 1M / 19M INFO General (graph_simplification.hpp : 634) Creating parallel br instance 79s 0:00:00.032 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Relative coverage component remover 79s 0:00:00.032 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Relative coverage component remover triggered 0 times 79s 0:00:00.032 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Disconnecting edges with relatively low coverage 79s 0:00:00.032 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Disconnecting edges with relatively low coverage triggered 0 times 79s 0:00:00.032 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Complex tip clipper 79s 0:00:00.032 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Complex tip clipper triggered 0 times 79s 0:00:00.032 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Complex bulge remover 79s 0:00:00.032 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Complex bulge remover triggered 0 times 79s 0:00:00.032 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 79s 0:00:00.032 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 79s 0:00:00.032 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Final tip clipper 79s 0:00:00.032 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Final tip clipper triggered 0 times 79s 0:00:00.032 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 79s 0:00:00.032 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 79s 0:00:00.032 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Thorn remover (meta) 79s 0:00:00.032 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Thorn remover (meta) triggered 0 times 79s 0:00:00.032 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Relative coverage component remover 79s 0:00:00.032 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Relative coverage component remover triggered 0 times 79s 0:00:00.032 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Disconnecting edges with relatively low coverage 79s 0:00:00.032 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Disconnecting edges with relatively low coverage triggered 0 times 79s 0:00:00.032 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Complex tip clipper 79s 0:00:00.032 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Complex tip clipper triggered 0 times 79s 0:00:00.032 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Complex bulge remover 79s 0:00:00.032 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Complex bulge remover triggered 0 times 79s 0:00:00.032 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 79s 0:00:00.032 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 79s 0:00:00.032 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Final tip clipper 79s 0:00:00.032 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Final tip clipper triggered 0 times 79s 0:00:00.032 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 79s 0:00:00.032 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 79s 0:00:00.032 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Thorn remover (meta) 79s 0:00:00.032 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Thorn remover (meta) triggered 0 times 79s 0:00:00.032 1M / 19M INFO General (simplification.cpp : 323) Running Hidden EC remover (meta) 79s 0:00:00.032 1M / 19M INFO General (simplification.cpp : 327) Disrupting self-conjugate edges 79s 0:00:00.032 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Removing isolated edges 79s 0:00:00.032 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Removing isolated edges triggered 0 times 79s 0:00:00.032 1M / 19M INFO General (simplification.cpp : 495) After simplification: 79s 0:00:00.032 1M / 19M INFO General (simplification.cpp : 496) Average coverage = 225.839 79s 0:00:00.032 1M / 19M INFO General (simplification.cpp : 497) Total length = 967 79s 0:00:00.032 1M / 19M INFO General (simplification.cpp : 498) Median edge length: 967 79s 0:00:00.032 1M / 19M INFO General (simplification.cpp : 499) Edges: 2 79s 0:00:00.032 1M / 19M INFO General (simplification.cpp : 500) Vertices: 4 79s 0:00:00.032 1M / 19M INFO StageManager (stage.cpp : 185) STAGE == Contig Output (id: contig_output) 79s 0:00:00.032 1M / 19M INFO General (read_converter.cpp : 107) Outputting contigs to /tmp/tmp.cMLX1ajB23/spades_test/K33/simplified_contigs 79s 0:00:00.032 3M / 19M INFO General (binary_converter.cpp : 111) 1 reads written 79s 0:00:00.033 1M / 19M INFO General (pipeline.cpp : 287) SPAdes finished 79s 0:00:00.033 1M / 19M INFO General (main.cpp : 136) Assembling time: 0 hours 0 minutes 0 seconds 79s 79s ===== K33 finished. 79s 79s 79s ===== K55 started. 79s 79s 79s == Running: /usr/libexec/spades/spades-core /tmp/tmp.cMLX1ajB23/spades_test/K55/configs/config.info /tmp/tmp.cMLX1ajB23/spades_test/K55/configs/mda_mode.info /tmp/tmp.cMLX1ajB23/spades_test/K55/configs/meta_mode.info 79s 79s 0:00:00.000 1M / 19M INFO General (main.cpp : 99) Loaded config from /tmp/tmp.cMLX1ajB23/spades_test/K55/configs/config.info 79s 0:00:00.000 1M / 19M INFO General (main.cpp : 99) Loaded config from /tmp/tmp.cMLX1ajB23/spades_test/K55/configs/mda_mode.info 79s 0:00:00.000 1M / 19M INFO General (main.cpp : 99) Loaded config from /tmp/tmp.cMLX1ajB23/spades_test/K55/configs/meta_mode.info 79s 0:00:00.000 1M / 19M INFO General (memory_limit.cpp : 54) Memory limit set to 3 Gb 79s 0:00:00.000 1M / 19M INFO General (main.cpp : 107) Starting SPAdes, built from N/A, git revision N/A 79s 0:00:00.000 1M / 19M INFO General (main.cpp : 108) Maximum k-mer length: 128 79s 0:00:00.000 1M / 19M INFO General (main.cpp : 109) Assembling dataset (/tmp/tmp.cMLX1ajB23/spades_test/dataset.info) with K=55 79s 0:00:00.000 1M / 19M INFO General (main.cpp : 110) Maximum # of threads to use (adjusted due to OMP capabilities): 2 79s 0:00:00.000 1M / 19M INFO General (pipeline.cpp : 212) SPAdes started 79s 0:00:00.000 1M / 19M INFO General (pipeline.cpp : 225) Starting from stage: read_conversion 79s 0:00:00.000 1M / 19M INFO General (pipeline.cpp : 231) Two-step repeat resolution enabled 79s 0:00:00.000 1M / 19M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 79s 0:00:00.000 1M / 19M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 79s 0:00:00.000 1M / 19M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 79s 0:00:00.000 1M / 19M INFO General (pipeline.cpp : 242) Will need read mapping, kmer mapper will be attached 79s 0:00:00.000 1M / 19M INFO StageManager (stage.cpp : 185) STAGE == Binary Read Conversion (id: read_conversion) 79s 0:00:00.000 1M / 19M INFO General (read_converter.cpp : 53) Binary reads detected 79s 0:00:00.000 1M / 19M INFO StageManager (stage.cpp : 185) STAGE == de Bruijn graph construction (id: construction) 79s 0:00:00.000 1M / 19M INFO General (construction.cpp : 118) Contigs from previous K will be used: /tmp/tmp.cMLX1ajB23/spades_test/K33/simplified_contigs 79s 0:00:00.000 1M / 19M INFO General (construction.cpp : 153) Max read length 100 79s 0:00:00.000 1M / 19M INFO General (construction.cpp : 159) Average read length 86.1526 79s 0:00:00.000 1M / 19M INFO General (stage.cpp : 117) PROCEDURE == k+1-mer counting (id: construction:kpomer_counting) 79s 0:00:00.000 1M / 19M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 20 files using 2 threads. This might take a while. 79s 0:00:00.000 1M / 19M INFO General (file_limit.hpp : 42) Open file limit set to 1024 79s 0:00:00.000 1M / 19M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 0.49997 Gb 79s 0:00:00.000 1M / 19M INFO General (kmer_splitter.hpp : 101) Using cell size of 1677621 79s 0:00:00.007 1M / 19M INFO General (kmer_splitters.hpp : 131) Used 8218 reads 79s 0:00:00.007 1M / 19M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. 79s 0:00:00.009 1M / 19M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 949 kmers in total. 79s 0:00:00.009 1M / 19M INFO General (stage.cpp : 117) PROCEDURE == Extension index construction (id: construction:extension_index_construction) 79s 0:00:00.009 1M / 19M INFO K-mer Index Building (kmer_index_builder.hpp : 438) Building kmer index 79s 0:00:00.009 1M / 19M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 20 files using 2 threads. This might take a while. 79s 0:00:00.009 1M / 19M INFO General (file_limit.hpp : 42) Open file limit set to 1024 79s 0:00:00.009 1M / 19M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 0.499967 Gb 79s 0:00:00.009 1M / 19M INFO General (kmer_splitter.hpp : 101) Using cell size of 1677611 79s 0:00:00.011 1161M / 1161M INFO General (kmer_splitters.hpp : 199) Used 949 kmers. 79s 0:00:00.011 1M / 19M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. 79s 0:00:00.012 1M / 19M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 951 kmers in total. 79s 0:00:00.012 1M / 19M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices 79s 0:00:00.013 1M / 19M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 951 kmers, 16384 bytes occupied (137.825 bits per kmer). 79s 0:00:00.013 1M / 19M INFO General (kmer_index_builder.hpp : 169) Merging final buckets. 79s 0:00:00.014 1M / 19M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 100) Building k-mer extensions from k+1-mers 79s 0:00:00.015 1M / 19M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 105) Building k-mer extensions from k+1-mers finished. 79s 0:00:00.015 1M / 19M INFO General (stage.cpp : 117) PROCEDURE == Condensing graph (id: construction:graph_condensing) 79s 0:00:00.015 1M / 19M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths 79s 0:00:00.015 1M / 19M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 4 sequences extracted 79s 0:00:00.015 1M / 19M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops 79s 0:00:00.015 1M / 19M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 0 loops collected 79s 0:00:00.015 1M / 19M INFO General (debruijn_graph_constructor: 487) Total 8 edges to create 79s 0:00:00.015 1M / 19M INFO General (debruijn_graph_constructor: 489) Collecting link records 79s 0:00:00.015 1M / 19M INFO General (debruijn_graph_constructor: 491) Ordering link records 79s 0:00:00.015 1M / 19M INFO General (debruijn_graph_constructor: 493) Sorting done 79s 0:00:00.015 1M / 19M INFO General (debruijn_graph_constructor: 503) Total 6 vertices to create 79s 0:00:00.015 1M / 19M INFO General (debruijn_graph_constructor: 506) Connecting the graph 79s 0:00:00.015 1M / 19M INFO General (stage.cpp : 117) PROCEDURE == Filling coverage indices (PHM) (id: construction:coverage_filling_phm) 79s 0:00:00.016 1M / 19M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices 79s 0:00:00.017 1M / 19M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 949 kmers, 16392 bytes occupied (138.183 bits per kmer). 79s 0:00:00.017 1M / 19M INFO General (coverage_hash_map_builder.: 47) Collecting k-mer coverage information from reads, this takes a while. 79s 0:00:00.024 1M / 19M INFO General (construction.cpp : 430) Filling coverage and flanking coverage from PHM 79s 0:00:00.025 1M / 19M INFO StageManager (stage.cpp : 185) STAGE == Gap Closer (id: early_gapcloser) 79s 0:00:00.029 10M / 19M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 79s 0:00:00.029 10M / 19M INFO General (gap_closer.cpp : 101) Total edges in tip neighborhood: 7 out of 8, length: 1520 79s 0:00:00.029 10M / 19M INFO General (edge_index.hpp : 167) Using small index (max_id = 11) 79s 0:00:00.029 10M / 19M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices 79s 0:00:00.030 10M / 19M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 949 kmers, 1456 bytes occupied (12.274 bits per kmer). 79s 0:00:00.030 10M / 19M INFO General (edge_index_builders.hpp : 265) Collecting edge information from graph, this takes a while. 79s 0:00:00.032 10M / 20M INFO General (sequence_mapper_notifier.h: 95) Total 2054 reads processed 79s 0:00:00.033 10M / 20M INFO General (gap_closer.cpp : 452) Initializing gap closer 79s 0:00:00.033 10M / 20M INFO GapCloser (gap_closer.cpp : 359) Closing short gaps 79s 0:00:00.033 10M / 20M INFO GapCloser (gap_closer.cpp : 391) Closing short gaps complete: filled 0 gaps after checking 4 candidates 79s 0:00:00.033 10M / 20M INFO General (gap_closer.cpp : 456) Gap closer done 79s 0:00:00.033 1M / 20M INFO StageManager (stage.cpp : 185) STAGE == Raw Simplification (id: raw_simplification) 79s 0:00:00.033 1M / 20M INFO General (simplification.cpp : 127) PROCEDURE == Initial cleaning 79s 0:00:00.033 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Self conjugate edge remover 79s 0:00:00.033 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Self conjugate edge remover triggered 0 times 79s 0:00:00.033 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Initial tip clipper 79s 0:00:00.033 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Initial tip clipper triggered 0 times 79s 0:00:00.033 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Initial ec remover 79s 0:00:00.033 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Initial ec remover triggered 0 times 79s 0:00:00.033 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Disconnecting edges with low flanking coverage 79s 0:00:00.033 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Disconnecting edges with low flanking coverage triggered 0 times 79s 0:00:00.033 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Initial isolated edge remover 79s 0:00:00.033 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Initial isolated edge remover triggered 1 times 79s 0:00:00.033 1M / 20M INFO StageManager (stage.cpp : 185) STAGE == Preliminary Simplification (id: simplification_preliminary) 79s 0:00:00.033 1M / 20M INFO General (simplification.cpp : 368) Graph simplification started 79s 0:00:00.033 1M / 20M INFO General (graph_simplification.hpp : 634) Creating parallel br instance 79s 0:00:00.033 1M / 20M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 1 79s 0:00:00.033 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 79s 0:00:00.033 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 1 times 79s 0:00:00.033 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 79s 0:00:00.033 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 79s 0:00:00.033 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 79s 0:00:00.033 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 0 times 79s 0:00:00.033 1M / 20M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 2 79s 0:00:00.033 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 79s 0:00:00.033 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 79s 0:00:00.033 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 79s 0:00:00.033 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 79s 0:00:00.033 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 79s 0:00:00.033 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 0 times 79s 0:00:00.033 1M / 20M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 3 79s 0:00:00.033 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 79s 0:00:00.033 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 79s 0:00:00.033 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 79s 0:00:00.033 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 79s 0:00:00.033 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 79s 0:00:00.033 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 0 times 79s 0:00:00.033 1M / 20M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 4 79s 0:00:00.033 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 79s 0:00:00.033 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 79s 0:00:00.033 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 79s 0:00:00.033 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 79s 0:00:00.033 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 79s 0:00:00.033 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 0 times 79s 0:00:00.033 1M / 20M INFO StageManager (stage.cpp : 185) STAGE == Gap Closer (id: prelim_gapcloser) 79s 0:00:00.034 10M / 20M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 79s 0:00:00.034 10M / 20M INFO General (gap_closer.cpp : 101) Total edges in tip neighborhood: 2 out of 2, length: 1890 79s 0:00:00.034 10M / 20M INFO General (edge_index.hpp : 167) Using small index (max_id = 11) 79s 0:00:00.034 10M / 20M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices 79s 0:00:00.034 10M / 20M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 945 kmers, 1456 bytes occupied (12.3259 bits per kmer). 79s 0:00:00.034 10M / 20M INFO General (edge_index_builders.hpp : 265) Collecting edge information from graph, this takes a while. 79s 0:00:00.037 10M / 20M INFO General (sequence_mapper_notifier.h: 95) Total 2054 reads processed 79s 0:00:00.038 10M / 20M INFO General (gap_closer.cpp : 452) Initializing gap closer 79s 0:00:00.038 10M / 20M INFO GapCloser (gap_closer.cpp : 359) Closing short gaps 79s 0:00:00.038 10M / 20M INFO GapCloser (gap_closer.cpp : 391) Closing short gaps complete: filled 0 gaps after checking 0 candidates 79s 0:00:00.038 10M / 20M INFO General (gap_closer.cpp : 456) Gap closer done 79s 0:00:00.038 1M / 20M INFO StageManager (stage.cpp : 185) STAGE == Preliminary Paired Information Counting (id: late_pair_info_count_preliminary) 79s 0:00:00.038 1M / 20M INFO General (graph_pack.cpp : 67) Index refill 79s 0:00:00.038 1M / 20M INFO General (edge_index.hpp : 156) Using small index (max_id = 11) 79s 0:00:00.038 1M / 20M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices 79s 0:00:00.039 1M / 20M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 945 kmers, 1456 bytes occupied (12.3259 bits per kmer). 79s 0:00:00.039 1M / 20M INFO General (edge_index_builders.hpp : 252) Collecting edge information from graph, this takes a while. 79s 0:00:00.039 1M / 20M INFO General (graph_pack.cpp : 77) Normalizing k-mer map. Total 0 kmers to process 79s 0:00:00.039 1M / 20M INFO General (graph_pack.cpp : 79) Normalizing done 79s 0:00:00.039 1M / 20M INFO General (pair_info_count.cpp : 339) Min edge length for estimation: 900 79s 0:00:00.039 1M / 20M INFO General (pair_info_count.cpp : 350) Estimating insert size for library #0 79s 0:00:00.039 1M / 20M INFO General (pair_info_count.cpp : 202) Estimating insert size (takes a while) 79s 0:00:00.060 49M / 59M INFO General (pair_info_count.cpp : 48) Selecting usual mapper 79s 0:00:00.082 49M / 59M INFO General (sequence_mapper_notifier.h: 95) Total 2054 reads processed 79s 0:00:00.147 49M / 59M INFO General (pair_info_count.cpp : 220) Edge pairs: 2 79s 0:00:00.147 49M / 59M INFO General (pair_info_count.cpp : 222) 1636 paired reads (79.6495% of all) aligned to long edges 79s 0:00:00.147 1M / 59M INFO General (pair_info_count.cpp : 369) Insert size = 214.696, deviation = 10.4821, left quantile = 201, right quantile = 228, read length = 100 79s 0:00:00.147 1M / 59M INFO General (pair_info_count.cpp : 390) Filtering data for library #0 79s 0:00:00.148 1M / 59M INFO General (pair_info_count.cpp : 48) Selecting usual mapper 79s 0:00:00.149 1M / 59M INFO General (sequence_mapper_notifier.h: 95) Total 2054 reads processed 79s 0:00:00.149 1M / 59M INFO General (pair_info_count.cpp : 402) Mapping library #0 79s 0:00:00.149 1M / 59M INFO General (pair_info_count.cpp : 404) Mapping paired reads (takes a while) 79s 0:00:00.149 1M / 59M INFO General (pair_info_count.cpp : 299) Left insert size quantile 201, right insert size quantile 228, filtering threshold 1, rounding threshold 0 79s 0:00:00.150 10M / 59M INFO General (pair_info_count.cpp : 48) Selecting usual mapper 79s 0:00:00.153 10M / 59M INFO General (sequence_mapper_notifier.h: 95) Total 2054 reads processed 79s 0:00:00.154 1M / 59M INFO StageManager (stage.cpp : 185) STAGE == Preliminary Distance Estimation (id: distance_estimation_preliminary) 79s 0:00:00.154 1M / 59M INFO General (distance_estimation.cpp : 179) Processing library #0 79s 0:00:00.154 1M / 59M INFO General (distance_estimation.cpp : 150) Weight Filter Done 79s 0:00:00.154 1M / 59M INFO DistanceEstimator (distance_estimation.hpp : 116) Using SIMPLE distance estimator 79s 0:00:00.155 1M / 60M INFO General (distance_estimation.cpp : 37) Filtering info 79s 0:00:00.155 1M / 60M INFO General (pair_info_filters.hpp : 242) Start filtering; library index size: 2 79s 0:00:00.155 1M / 60M INFO General (pair_info_filters.hpp : 263) Done filtering; library index size: 2 79s 0:00:00.155 1M / 60M INFO General (distance_estimation.cpp : 156) Refining clustered pair information 79s 0:00:00.155 1M / 60M INFO General (distance_estimation.cpp : 158) The refining of clustered pair information has been finished 79s 0:00:00.155 1M / 60M INFO General (distance_estimation.cpp : 160) Improving paired information 79s 0:00:00.155 1M / 60M INFO PairInfoImprover (pair_info_improver.hpp : 104) Paired info stats: missing = 0; contradictional = 0 79s 0:00:00.155 1M / 60M INFO PairInfoImprover (pair_info_improver.hpp : 104) Paired info stats: missing = 0; contradictional = 0 79s 0:00:00.155 1M / 60M INFO General (distance_estimation.cpp : 104) Filling scaffolding index 79s 0:00:00.155 1M / 60M INFO DistanceEstimator (distance_estimation.hpp : 116) Using SMOOTHING distance estimator 79s 0:00:00.155 1M / 60M INFO General (distance_estimation.cpp : 37) Filtering info 79s 0:00:00.155 1M / 60M INFO General (pair_info_filters.hpp : 242) Start filtering; library index size: 2 79s 0:00:00.155 1M / 60M INFO General (pair_info_filters.hpp : 263) Done filtering; library index size: 2 79s 0:00:00.155 1M / 60M INFO General (distance_estimation.cpp : 186) Clearing raw paired index 79s 0:00:00.155 1M / 60M INFO StageManager (stage.cpp : 185) STAGE == Preliminary Repeat Resolving (id: repeat_resolving_preliminary) 79s 0:00:00.155 1M / 60M INFO General (repeat_resolving.cpp : 74) Setting up preliminary path extend settings 79s 0:00:00.155 1M / 60M INFO General (repeat_resolving.cpp : 87) Using Path-Extend repeat resolving 79s 0:00:00.155 1M / 60M INFO General (launcher.cpp : 600) ExSPAnder repeat resolving tool started 79s 0:00:00.155 1M / 60M INFO General (launcher.cpp : 418) Creating main extenders, unique edge length = 2000 79s 0:00:00.155 1M / 60M INFO General (extenders_logic.cpp : 345) Creating extender; library index size: 2 79s 0:00:00.155 1M / 60M INFO General (extenders_logic.cpp : 345) Creating extender; library index size: 2 79s 0:00:00.155 1M / 60M INFO General (extenders_logic.cpp : 543) Using 1 paired-end library 79s 0:00:00.155 1M / 60M INFO General (extenders_logic.cpp : 544) Using 1 paired-end scaffolding library 79s 0:00:00.155 1M / 60M INFO General (extenders_logic.cpp : 545) Using 0 single read libraries 79s 0:00:00.155 1M / 60M INFO General (launcher.cpp : 447) Total number of extenders is 3 79s 0:00:00.155 1M / 60M INFO General (launcher.cpp : 250) Finalizing paths 79s 0:00:00.155 1M / 60M INFO General (launcher.cpp : 252) Deduplicating paths 79s 0:00:00.155 1M / 60M INFO General (launcher.cpp : 256) Paths deduplicated 79s 0:00:00.155 1M / 60M INFO General (launcher.cpp : 263) Overlaps will not be removed 79s 0:00:00.155 1M / 60M INFO General (launcher.cpp : 273) Paths finalized 79s 0:00:00.155 1M / 60M INFO General (launcher.cpp : 454) Closing gaps in paths 79s 0:00:00.155 1M / 60M INFO General (launcher.cpp : 484) Gap closing completed 79s 0:00:00.155 1M / 60M INFO General (launcher.cpp : 302) Traversing tandem repeats 79s 0:00:00.155 1M / 60M INFO General (launcher.cpp : 312) Traversed 0 loops 79s 0:00:00.155 1M / 60M INFO General (launcher.cpp : 250) Finalizing paths 79s 0:00:00.155 1M / 60M INFO General (launcher.cpp : 252) Deduplicating paths 79s 0:00:00.155 1M / 60M INFO General (launcher.cpp : 256) Paths deduplicated 79s 0:00:00.155 1M / 60M INFO General (launcher.cpp : 263) Overlaps will not be removed 79s 0:00:00.155 1M / 60M INFO General (launcher.cpp : 273) Paths finalized 79s 0:00:00.155 1M / 60M INFO General (launcher.cpp : 664) ExSPAnder repeat resolving tool finished 79s 0:00:00.155 1M / 60M INFO General (repeat_resolving.cpp : 93) Restoring initial path extend settings 79s 0:00:00.155 1M / 60M INFO StageManager (stage.cpp : 185) STAGE == Contig Output (id: contig_output) 79s 0:00:00.155 1M / 60M INFO General (contig_output_stage.cpp : 151) Writing GFA graph to /tmp/tmp.cMLX1ajB23/spades_test/K55/strain_graph.gfa 79s 0:00:00.155 1M / 60M INFO General (contig_output_stage.cpp : 196) Breaking scaffolds 79s 0:00:00.155 1M / 60M INFO General (contig_output_stage.cpp : 98) Outputting contigs to /tmp/tmp.cMLX1ajB23/spades_test/K55/final_contigs.fasta 79s 0:00:00.155 1M / 60M INFO StageManager (stage.cpp : 185) STAGE == Second Phase Setup (id: second_phase_setup) 79s 0:00:00.155 1M / 60M INFO General (second_phase_setup.cpp : 18) Preparing second phase 79s 0:00:00.155 1M / 60M INFO General (second_phase_setup.cpp : 26) Moving preliminary contigs from /tmp/tmp.cMLX1ajB23/spades_test/K55/final_contigs.fasta to /tmp/tmp.cMLX1ajB23/spades_test/K55/first_pe_contigs.fasta 79s 0:00:00.156 1M / 60M INFO General (second_phase_setup.cpp : 38) Ready to run second phase 79s 0:00:00.156 1M / 60M INFO StageManager (stage.cpp : 185) STAGE == Simplification (id: simplification) 79s 0:00:00.156 1M / 60M INFO General (simplification.cpp : 368) Graph simplification started 79s 0:00:00.156 1M / 60M INFO General (graph_simplification.hpp : 634) Creating parallel br instance 79s 0:00:00.156 1M / 60M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 1 79s 0:00:00.156 1M / 60M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 79s 0:00:00.156 1M / 60M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 79s 0:00:00.156 1M / 60M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 79s 0:00:00.156 1M / 60M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 79s 0:00:00.156 1M / 60M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 79s 0:00:00.156 1M / 60M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 0 times 79s 0:00:00.156 1M / 60M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 2 79s 0:00:00.157 1M / 60M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 79s 0:00:00.157 1M / 60M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 79s 0:00:00.157 1M / 60M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 79s 0:00:00.157 1M / 60M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 79s 0:00:00.157 1M / 60M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 79s 0:00:00.157 1M / 60M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 0 times 79s 0:00:00.157 1M / 60M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 3 79s 0:00:00.157 1M / 60M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 79s 0:00:00.157 1M / 60M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 79s 0:00:00.157 1M / 60M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 79s 0:00:00.157 1M / 60M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 79s 0:00:00.157 1M / 60M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 79s 0:00:00.157 1M / 60M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 0 times 79s 0:00:00.157 1M / 60M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 4 79s 0:00:00.157 1M / 60M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 79s 0:00:00.157 1M / 60M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 79s 0:00:00.157 1M / 60M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 79s 0:00:00.157 1M / 60M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 79s 0:00:00.157 1M / 60M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 79s 0:00:00.157 1M / 60M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 0 times 79s 0:00:00.157 1M / 60M INFO StageManager (stage.cpp : 185) STAGE == Gap Closer (id: late_gapcloser) 79s 0:00:00.157 10M / 60M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 79s 0:00:00.157 10M / 60M INFO General (gap_closer.cpp : 101) Total edges in tip neighborhood: 2 out of 2, length: 1890 79s 0:00:00.157 10M / 60M INFO General (edge_index.hpp : 167) Using small index (max_id = 11) 79s 0:00:00.157 10M / 60M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices 79s 0:00:00.158 10M / 60M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 945 kmers, 1456 bytes occupied (12.3259 bits per kmer). 79s 0:00:00.158 10M / 60M INFO General (edge_index_builders.hpp : 265) Collecting edge information from graph, this takes a while. 79s 0:00:00.160 10M / 60M INFO General (sequence_mapper_notifier.h: 95) Total 2054 reads processed 79s 0:00:00.161 10M / 60M INFO General (gap_closer.cpp : 452) Initializing gap closer 79s 0:00:00.161 10M / 60M INFO GapCloser (gap_closer.cpp : 359) Closing short gaps 79s 0:00:00.161 10M / 60M INFO GapCloser (gap_closer.cpp : 391) Closing short gaps complete: filled 0 gaps after checking 0 candidates 79s 0:00:00.161 10M / 60M INFO General (gap_closer.cpp : 456) Gap closer done 79s 0:00:00.161 1M / 60M INFO StageManager (stage.cpp : 185) STAGE == Simplification Cleanup (id: simplification_cleanup) 79s 0:00:00.161 1M / 60M INFO General (simplification.cpp : 176) PROCEDURE == Post simplification 79s 0:00:00.161 1M / 60M INFO General (graph_simplification.hpp : 634) Creating parallel br instance 79s 0:00:00.162 1M / 60M INFO General (graph_simplification.hpp : 634) Creating parallel br instance 79s 0:00:00.162 1M / 60M INFO Simplification (parallel_processing.hpp : 167) Running Relative coverage component remover 79s 0:00:00.162 1M / 60M INFO Simplification (parallel_processing.hpp : 170) Relative coverage component remover triggered 0 times 79s 0:00:00.162 1M / 60M INFO Simplification (parallel_processing.hpp : 167) Running Disconnecting edges with relatively low coverage 79s 0:00:00.162 1M / 60M INFO Simplification (parallel_processing.hpp : 170) Disconnecting edges with relatively low coverage triggered 0 times 79s 0:00:00.162 1M / 60M INFO Simplification (parallel_processing.hpp : 167) Running Complex tip clipper 79s 0:00:00.162 1M / 60M INFO Simplification (parallel_processing.hpp : 170) Complex tip clipper triggered 0 times 79s 0:00:00.162 1M / 60M INFO Simplification (parallel_processing.hpp : 167) Running Complex bulge remover 79s 0:00:00.162 1M / 60M INFO Simplification (parallel_processing.hpp : 170) Complex bulge remover triggered 0 times 79s 0:00:00.162 1M / 60M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 79s 0:00:00.162 1M / 60M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 79s 0:00:00.162 1M / 60M INFO Simplification (parallel_processing.hpp : 167) Running Final tip clipper 79s 0:00:00.162 1M / 60M INFO Simplification (parallel_processing.hpp : 170) Final tip clipper triggered 0 times 79s 0:00:00.162 1M / 60M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 79s 0:00:00.162 1M / 60M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 79s 0:00:00.162 1M / 60M INFO Simplification (parallel_processing.hpp : 167) Running Final bulge remover 79s 0:00:00.163 1M / 60M INFO Simplification (parallel_processing.hpp : 170) Final bulge remover triggered 0 times 79s 0:00:00.163 1M / 60M INFO Simplification (parallel_processing.hpp : 167) Running Thorn remover (meta) 79s 0:00:00.163 1M / 60M INFO Simplification (parallel_processing.hpp : 170) Thorn remover (meta) triggered 0 times 79s 0:00:00.163 1M / 60M INFO Simplification (parallel_processing.hpp : 167) Running Relative coverage component remover 79s 0:00:00.163 1M / 60M INFO Simplification (parallel_processing.hpp : 170) Relative coverage component remover triggered 0 times 79s 0:00:00.163 1M / 60M INFO Simplification (parallel_processing.hpp : 167) Running Disconnecting edges with relatively low coverage 79s 0:00:00.163 1M / 60M INFO Simplification (parallel_processing.hpp : 170) Disconnecting edges with relatively low coverage triggered 0 times 79s 0:00:00.163 1M / 60M INFO Simplification (parallel_processing.hpp : 167) Running Complex tip clipper 79s 0:00:00.163 1M / 60M INFO Simplification (parallel_processing.hpp : 170) Complex tip clipper triggered 0 times 79s 0:00:00.163 1M / 60M INFO Simplification (parallel_processing.hpp : 167) Running Complex bulge remover 79s 0:00:00.163 1M / 60M INFO Simplification (parallel_processing.hpp : 170) Complex bulge remover triggered 0 times 79s 0:00:00.163 1M / 60M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 79s 0:00:00.163 1M / 60M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 79s 0:00:00.163 1M / 60M INFO Simplification (parallel_processing.hpp : 167) Running Final tip clipper 79s 0:00:00.163 1M / 60M INFO Simplification (parallel_processing.hpp : 170) Final tip clipper triggered 0 times 79s 0:00:00.163 1M / 60M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 79s 0:00:00.163 1M / 60M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 79s 0:00:00.163 1M / 60M INFO Simplification (parallel_processing.hpp : 167) Running Final bulge remover 79s 0:00:00.163 1M / 60M INFO Simplification (parallel_processing.hpp : 170) Final bulge remover triggered 0 times 79s 0:00:00.163 1M / 60M INFO Simplification (parallel_processing.hpp : 167) Running Thorn remover (meta) 79s 0:00:00.163 1M / 60M INFO Simplification (parallel_processing.hpp : 170) Thorn remover (meta) triggered 0 times 79s 0:00:00.163 1M / 60M INFO General (simplification.cpp : 323) Running Hidden EC remover (meta) 79s 0:00:00.163 1M / 60M INFO General (simplification.cpp : 327) Disrupting self-conjugate edges 79s 0:00:00.163 1M / 60M INFO Simplification (parallel_processing.hpp : 167) Running Removing isolated edges 79s 0:00:00.163 1M / 60M INFO Simplification (parallel_processing.hpp : 170) Removing isolated edges triggered 0 times 79s 0:00:00.163 1M / 60M INFO General (simplification.cpp : 495) After simplification: 79s 0:00:00.163 1M / 60M INFO General (simplification.cpp : 496) Average coverage = 140.62 79s 0:00:00.163 1M / 60M INFO General (simplification.cpp : 497) Total length = 945 79s 0:00:00.163 1M / 60M INFO General (simplification.cpp : 498) Median edge length: 945 79s 0:00:00.163 1M / 60M INFO General (simplification.cpp : 499) Edges: 2 79s 0:00:00.163 1M / 60M INFO General (simplification.cpp : 500) Vertices: 4 79s 0:00:00.163 1M / 60M INFO StageManager (stage.cpp : 185) STAGE == Mismatch Correction (id: mismatch_correction) 79s 0:00:00.163 1M / 60M INFO General (graph_pack.cpp : 67) Index refill 79s 0:00:00.163 1M / 60M INFO General (edge_index.hpp : 156) Using small index (max_id = 11) 79s 0:00:00.163 1M / 60M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices 79s 0:00:00.163 1M / 60M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 945 kmers, 1456 bytes occupied (12.3259 bits per kmer). 79s 0:00:00.163 1M / 60M INFO General (edge_index_builders.hpp : 252) Collecting edge information from graph, this takes a while. 79s 0:00:00.163 1M / 60M INFO General (graph_pack.cpp : 77) Normalizing k-mer map. Total 0 kmers to process 79s 0:00:00.163 1M / 60M INFO General (graph_pack.cpp : 79) Normalizing done 79s 0:00:00.163 1M / 60M INFO General (mismatch_correction.cpp : 400) Collect potential mismatches 79s 0:00:00.163 1M / 60M INFO General (mismatch_correction.cpp : 192) Total 0 edges (out of 2) with 0 potential mismatch positions (-nan positions per edge) 79s 0:00:00.163 1M / 60M INFO General (mismatch_correction.cpp : 402) Potential mismatches collected 79s 0:00:00.167 1M / 60M INFO General (sequence_mapper_notifier.h: 95) Total 8216 reads processed 79s 0:00:00.167 1M / 60M INFO General (mismatch_correction.cpp : 395) All edges processed 79s 0:00:00.168 1M / 60M INFO General (mismatch_correction.cpp : 450) Corrected 0 nucleotides 79s 0:00:00.168 1M / 60M INFO StageManager (stage.cpp : 185) STAGE == Contig Output (id: contig_output) 79s 0:00:00.168 1M / 60M INFO General (contig_output.hpp : 16) Outputting contigs to /tmp/tmp.cMLX1ajB23/spades_test/K55/before_rr.fasta 79s 0:00:00.168 1M / 60M INFO General (contig_output_stage.cpp : 151) Writing GFA graph to /tmp/tmp.cMLX1ajB23/spades_test/K55/assembly_graph_after_simplification.gfa 79s 0:00:00.168 1M / 60M INFO StageManager (stage.cpp : 185) STAGE == Paired Information Counting (id: late_pair_info_count) 79s 0:00:00.168 1M / 60M INFO General (graph_pack.cpp : 77) Normalizing k-mer map. Total 0 kmers to process 79s 0:00:00.168 1M / 60M INFO General (graph_pack.cpp : 79) Normalizing done 79s 0:00:00.168 1M / 60M INFO General (pair_info_count.cpp : 339) Min edge length for estimation: 900 79s 0:00:00.168 1M / 60M INFO General (pair_info_count.cpp : 350) Estimating insert size for library #0 79s 0:00:00.168 1M / 60M INFO General (pair_info_count.cpp : 202) Estimating insert size (takes a while) 79s 0:00:00.169 49M / 60M INFO General (pair_info_count.cpp : 48) Selecting usual mapper 79s 0:00:00.191 49M / 60M INFO General (sequence_mapper_notifier.h: 95) Total 2054 reads processed 79s 0:00:00.256 49M / 60M INFO General (pair_info_count.cpp : 220) Edge pairs: 2 79s 0:00:00.256 49M / 60M INFO General (pair_info_count.cpp : 222) 1636 paired reads (79.6495% of all) aligned to long edges 79s 0:00:00.256 1M / 60M INFO General (pair_info_count.cpp : 369) Insert size = 214.696, deviation = 10.4821, left quantile = 201, right quantile = 228, read length = 100 79s 0:00:00.256 1M / 60M INFO General (pair_info_count.cpp : 390) Filtering data for library #0 79s 0:00:00.256 1M / 60M INFO General (pair_info_count.cpp : 48) Selecting usual mapper 79s 0:00:00.258 1M / 60M INFO General (sequence_mapper_notifier.h: 95) Total 2054 reads processed 79s 0:00:00.258 1M / 60M INFO General (pair_info_count.cpp : 402) Mapping library #0 79s 0:00:00.258 1M / 60M INFO General (pair_info_count.cpp : 404) Mapping paired reads (takes a while) 79s 0:00:00.258 1M / 60M INFO General (pair_info_count.cpp : 299) Left insert size quantile 201, right insert size quantile 228, filtering threshold 1, rounding threshold 0 79s 0:00:00.259 10M / 60M INFO General (pair_info_count.cpp : 48) Selecting usual mapper 79s 0:00:00.262 10M / 60M INFO General (sequence_mapper_notifier.h: 95) Total 2054 reads processed 79s 0:00:00.263 1M / 60M INFO General (pair_info_count.cpp : 346) Mapping contigs library #1 79s 0:00:00.263 1M / 60M INFO General (pair_info_count.cpp : 48) Selecting usual mapper 79s 0:00:00.263 1M / 61M INFO General (sequence_mapper_notifier.h: 95) Total 1 reads processed 79s 0:00:00.263 1M / 61M INFO StageManager (stage.cpp : 185) STAGE == Distance Estimation (id: distance_estimation) 79s 0:00:00.263 1M / 61M INFO General (distance_estimation.cpp : 179) Processing library #0 79s 0:00:00.263 1M / 61M INFO General (distance_estimation.cpp : 150) Weight Filter Done 79s 0:00:00.263 1M / 61M INFO DistanceEstimator (distance_estimation.hpp : 116) Using SIMPLE distance estimator 79s 0:00:00.264 1M / 61M INFO General (distance_estimation.cpp : 37) Filtering info 79s 0:00:00.264 1M / 61M INFO General (pair_info_filters.hpp : 242) Start filtering; library index size: 2 79s 0:00:00.264 1M / 61M INFO General (pair_info_filters.hpp : 263) Done filtering; library index size: 2 79s 0:00:00.264 1M / 61M INFO General (distance_estimation.cpp : 156) Refining clustered pair information 79s 0:00:00.264 1M / 61M INFO General (distance_estimation.cpp : 158) The refining of clustered pair information has been finished 79s 0:00:00.264 1M / 61M INFO General (distance_estimation.cpp : 160) Improving paired information 79s 0:00:00.264 1M / 61M INFO PairInfoImprover (pair_info_improver.hpp : 104) Paired info stats: missing = 0; contradictional = 0 79s 0:00:00.264 1M / 61M INFO PairInfoImprover (pair_info_improver.hpp : 104) Paired info stats: missing = 0; contradictional = 0 79s 0:00:00.264 1M / 61M INFO General (distance_estimation.cpp : 104) Filling scaffolding index 79s 0:00:00.264 1M / 61M INFO DistanceEstimator (distance_estimation.hpp : 116) Using SMOOTHING distance estimator 79s 0:00:00.264 1M / 61M INFO General (distance_estimation.cpp : 37) Filtering info 79s 0:00:00.264 1M / 61M INFO General (pair_info_filters.hpp : 242) Start filtering; library index size: 2 79s 0:00:00.264 1M / 61M INFO General (pair_info_filters.hpp : 263) Done filtering; library index size: 2 79s 0:00:00.264 1M / 61M INFO General (distance_estimation.cpp : 186) Clearing raw paired index 79s 0:00:00.265 1M / 61M INFO StageManager (stage.cpp : 185) STAGE == Repeat Resolving (id: repeat_resolving) 79s 0:00:00.265 1M / 61M INFO General (repeat_resolving.cpp : 87) Using Path-Extend repeat resolving 79s 0:00:00.265 1M / 61M INFO General (launcher.cpp : 600) ExSPAnder repeat resolving tool started 79s 0:00:00.265 1M / 61M INFO General (launcher.cpp : 418) Creating main extenders, unique edge length = 2000 79s 0:00:00.265 1M / 61M INFO General (launcher.cpp : 342) filling path container 79s 0:00:00.265 1M / 61M INFO General (extenders_logic.cpp : 345) Creating extender; library index size: 2 79s 0:00:00.265 1M / 61M INFO General (extenders_logic.cpp : 345) Creating extender; library index size: 2 79s 0:00:00.265 1M / 61M INFO General (extenders_logic.cpp : 47) resolvable_repeat_length_bound set to 10000 79s 0:00:00.265 1M / 61M INFO General (extenders_logic.cpp : 543) Using 1 paired-end library 79s 0:00:00.265 1M / 61M INFO General (extenders_logic.cpp : 544) Using 1 paired-end scaffolding library 79s 0:00:00.265 1M / 61M INFO General (extenders_logic.cpp : 545) Using 1 single read library 79s 0:00:00.265 1M / 61M INFO General (launcher.cpp : 385) Filling backbone edges for long reads scaffolding... 79s 0:00:00.265 1M / 61M INFO General (launcher.cpp : 387) with long reads paths 79s 0:00:00.265 1M / 61M INFO General (launcher.cpp : 396) Removing fake unique with paired-end libs 79s 0:00:00.265 1M / 61M INFO General (launcher.cpp : 407) 0 unique edges 79s 0:00:00.265 1M / 61M INFO General (extenders_logic.cpp : 446) Using 0 long reads scaffolding libraries 79s 0:00:00.265 1M / 61M INFO General (extenders_logic.cpp : 456) Using additional coordinated coverage extender 79s 0:00:00.265 1M / 61M INFO General (launcher.cpp : 447) Total number of extenders is 5 79s 0:00:00.265 1M / 61M INFO General (launcher.cpp : 250) Finalizing paths 79s 0:00:00.265 1M / 61M INFO General (launcher.cpp : 252) Deduplicating paths 79s 0:00:00.265 1M / 61M INFO General (launcher.cpp : 256) Paths deduplicated 79s 0:00:00.265 1M / 61M INFO PEResolver (pe_resolver.cpp : 60) Removing overlaps 79s 0:00:00.265 1M / 61M INFO PEResolver (pe_resolver.cpp : 70) Marking overlaps 79s 0:00:00.265 1M / 61M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps 79s 0:00:00.265 1M / 61M INFO OverlapRemover (overlap_remover.hpp : 119) Marking remaining overlaps 79s 0:00:00.265 1M / 61M INFO PEResolver (pe_resolver.cpp : 73) Splitting paths 79s 0:00:00.265 1M / 61M INFO PEResolver (pe_resolver.cpp : 78) Deduplicating paths 79s 0:00:00.265 1M / 61M INFO PEResolver (pe_resolver.cpp : 80) Overlaps removed 79s 0:00:00.265 1M / 61M INFO General (launcher.cpp : 273) Paths finalized 79s 0:00:00.265 1M / 61M INFO General (launcher.cpp : 454) Closing gaps in paths 79s 0:00:00.265 1M / 61M INFO General (launcher.cpp : 484) Gap closing completed 79s 0:00:00.265 1M / 61M INFO General (launcher.cpp : 302) Traversing tandem repeats 79s 0:00:00.265 1M / 61M INFO General (launcher.cpp : 312) Traversed 0 loops 79s 0:00:00.265 1M / 61M INFO General (launcher.cpp : 250) Finalizing paths 79s 0:00:00.265 1M / 61M INFO General (launcher.cpp : 252) Deduplicating paths 79s 0:00:00.265 1M / 61M INFO General (launcher.cpp : 256) Paths deduplicated 79s 0:00:00.265 1M / 61M INFO PEResolver (pe_resolver.cpp : 60) Removing overlaps 79s 0:00:00.265 1M / 61M INFO PEResolver (pe_resolver.cpp : 70) Marking overlaps 79s 0:00:00.265 1M / 61M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps 79s 0:00:00.265 1M / 61M INFO OverlapRemover (overlap_remover.hpp : 119) Marking remaining overlaps 79s 0:00:00.265 1M / 61M INFO PEResolver (pe_resolver.cpp : 73) Splitting paths 79s 0:00:00.265 1M / 61M INFO PEResolver (pe_resolver.cpp : 78) Deduplicating paths 79s 0:00:00.265 1M / 61M INFO PEResolver (pe_resolver.cpp : 80) Overlaps removed 79s 0:00:00.265 1M / 61M INFO General (launcher.cpp : 273) Paths finalized 79s 0:00:00.265 1M / 61M INFO General (launcher.cpp : 664) ExSPAnder repeat resolving tool finished 79s 0:00:00.265 1M / 61M INFO StageManager (stage.cpp : 185) STAGE == Contig Output (id: contig_output) 79s 0:00:00.265 1M / 61M INFO General (contig_output.hpp : 16) Outputting contigs to /tmp/tmp.cMLX1ajB23/spades_test/K55/before_rr.fasta 79s 0:00:00.265 1M / 61M INFO General (contig_output_stage.cpp : 151) Writing GFA graph to /tmp/tmp.cMLX1ajB23/spades_test/K55/assembly_graph_with_scaffolds.gfa 79s 0:00:00.265 1M / 61M INFO General (contig_output_stage.cpp : 165) Outputting FastG graph to /tmp/tmp.cMLX1ajB23/spades_test/K55/assembly_graph.fastg 79s 0:00:00.265 1M / 61M INFO General (contig_output_stage.cpp : 196) Breaking scaffolds 79s 0:00:00.265 1M / 61M INFO General (contig_output_stage.cpp : 98) Outputting contigs to /tmp/tmp.cMLX1ajB23/spades_test/K55/final_contigs.fasta 79s 0:00:00.265 1M / 61M INFO General (contig_output_stage.cpp : 104) Outputting FastG paths to /tmp/tmp.cMLX1ajB23/spades_test/K55/final_contigs.paths 79s 0:00:00.265 1M / 61M INFO General (contig_output_stage.cpp : 98) Outputting contigs to /tmp/tmp.cMLX1ajB23/spades_test/K55/scaffolds.fasta 79s 0:00:00.265 1M / 61M INFO General (contig_output_stage.cpp : 104) Outputting FastG paths to /tmp/tmp.cMLX1ajB23/spades_test/K55/scaffolds.paths 79s 0:00:00.266 1M / 61M INFO General (contig_output_stage.cpp : 111) Populating GFA with scaffold paths 79s 0:00:00.266 1M / 61M INFO General (pipeline.cpp : 287) SPAdes finished 79s 0:00:00.266 1M / 61M INFO General (main.cpp : 136) Assembling time: 0 hours 0 minutes 0 seconds 79s 79s ===== K55 finished. 79s 79s 79s ===== Copy files started. 79s 79s 79s == Running: /usr/bin/python3 /usr/share/spades/spades_pipeline/scripts/copy_files.py /tmp/tmp.cMLX1ajB23/spades_test/K55/before_rr.fasta /tmp/tmp.cMLX1ajB23/spades_test/before_rr.fasta /tmp/tmp.cMLX1ajB23/spades_test/K55/assembly_graph_after_simplification.gfa /tmp/tmp.cMLX1ajB23/spades_test/assembly_graph_after_simplification.gfa /tmp/tmp.cMLX1ajB23/spades_test/K55/final_contigs.fasta /tmp/tmp.cMLX1ajB23/spades_test/contigs.fasta /tmp/tmp.cMLX1ajB23/spades_test/K55/first_pe_contigs.fasta /tmp/tmp.cMLX1ajB23/spades_test/first_pe_contigs.fasta /tmp/tmp.cMLX1ajB23/spades_test/K55/strain_graph.gfa /tmp/tmp.cMLX1ajB23/spades_test/strain_graph.gfa /tmp/tmp.cMLX1ajB23/spades_test/K55/scaffolds.fasta /tmp/tmp.cMLX1ajB23/spades_test/scaffolds.fasta /tmp/tmp.cMLX1ajB23/spades_test/K55/scaffolds.paths /tmp/tmp.cMLX1ajB23/spades_test/scaffolds.paths /tmp/tmp.cMLX1ajB23/spades_test/K55/assembly_graph_with_scaffolds.gfa /tmp/tmp.cMLX1ajB23/spades_test/assembly_graph_with_scaffolds.gfa /tmp/tmp.cMLX1ajB23/spades_test/K55/assembly_graph.fastg /tmp/tmp.cMLX1ajB23/spades_test/assembly_graph.fastg /tmp/tmp.cMLX1ajB23/spades_test/K55/final_contigs.paths /tmp/tmp.cMLX1ajB23/spades_test/contigs.paths 79s 79s 79s ===== Copy files finished. 79s 79s 79s ===== Assembling finished. 79s 79s 79s ===== Check test started. 79s 79s 79s == Running: /usr/bin/python3 /usr/share/spades/spades_pipeline/scripts/check_test_script.py --mode common --result_contigs_filename /tmp/tmp.cMLX1ajB23/spades_test/contigs.fasta --result_scaffolds_filename /tmp/tmp.cMLX1ajB23/spades_test/scaffolds.fasta 79s 79s ========= TEST PASSED CORRECTLY. 79s 79s ===== Check test finished. 79s 79s 79s ===== Breaking scaffolds started. 79s 79s 79s == Running: /usr/bin/python3 /usr/share/spades/spades_pipeline/scripts/breaking_scaffolds_script.py --result_scaffolds_filename /tmp/tmp.cMLX1ajB23/spades_test/scaffolds.fasta --misc_dir /tmp/tmp.cMLX1ajB23/spades_test/misc --threshold_for_breaking_scaffolds 3 79s 79s 79s ===== Breaking scaffolds finished. 79s 79s 79s ===== Terminate started. 79s 79s 79s ===== Terminate finished. 79s 79s * Corrected reads are in /tmp/tmp.cMLX1ajB23/spades_test/corrected/ 79s * Assembled contigs are in /tmp/tmp.cMLX1ajB23/spades_test/contigs.fasta 79s * Assembled scaffolds are in /tmp/tmp.cMLX1ajB23/spades_test/scaffolds.fasta 79s * Paths in the assembly graph corresponding to the contigs are in /tmp/tmp.cMLX1ajB23/spades_test/contigs.paths 79s * Paths in the assembly graph corresponding to the scaffolds are in /tmp/tmp.cMLX1ajB23/spades_test/scaffolds.paths 79s * Assembly graph is in /tmp/tmp.cMLX1ajB23/spades_test/assembly_graph.fastg 79s * Assembly graph in GFA format is in /tmp/tmp.cMLX1ajB23/spades_test/assembly_graph_with_scaffolds.gfa 79s 79s ======= SPAdes pipeline finished. 79s 79s SPAdes log can be found here: /tmp/tmp.cMLX1ajB23/spades_test/spades.log 79s 79s Thank you for using SPAdes! 79s + plasmidspades --test 79s Command line: /usr/libexec/spades/plasmidspades.py --test 79s 79s System information: 79s SPAdes version: 3.15.5 79s Python version: 3.13.3 79s OS: Linux-6.14.0-15-generic-x86_64-with-glibc2.41 79s 79s Output dir: /tmp/tmp.cMLX1ajB23/spades_test 79s Mode: read error correction and assembling 79s Debug mode is turned OFF 79s 79s Dataset parameters: 79s Standard mode 79s For multi-cell/isolate data we recommend to use '--isolate' option; for single-cell MDA data use '--sc'; for metagenomic data use '--meta'; for RNA-Seq use '--rna'. 79s Reads: 79s Library number: 1, library type: paired-end 79s orientation: fr 79s left reads: ['/usr/share/spades/test_dataset_plasmid/pl1.fq.gz'] 79s right reads: ['/usr/share/spades/test_dataset_plasmid/pl2.fq.gz'] 79s interlaced reads: not specified 79s single reads: not specified 79s merged reads: not specified 79s Read error correction parameters: 79s Iterations: 1 79s PHRED offset will be auto-detected 79s Corrected reads will be compressed 79s Assembly parameters: 79s k: automatic selection based on read length 79s Extrachromosomal mode is turned ON 79s Repeat resolution is enabled 79s Mismatch careful mode is turned OFF 79s MismatchCorrector will be SKIPPED 79s Coverage cutoff is turned OFF 79s Other parameters: 79s Dir for temp files: /tmp/tmp.cMLX1ajB23/spades_test/tmp 79s Threads: 16 79s Memory limit (in Gb): 3 79s 79s 79s ======= SPAdes pipeline started. Log can be found here: /tmp/tmp.cMLX1ajB23/spades_test/spades.log 79s 79s /usr/share/spades/test_dataset_plasmid/pl1.fq.gz: max reads length: 100 79s /usr/share/spades/test_dataset_plasmid/pl2.fq.gz: max reads length: 100 79s 79s Reads length: 100 79s 79s Default k-mer sizes were set to [21, 33, 55, 77] because estimated read length (100) is less than 150 79s 79s ===== Before start started. 79s 79s 79s ===== Read error correction started. 79s 79s 79s ===== Read error correction started. 79s 79s 79s == Running: /usr/libexec/spades/spades-hammer /tmp/tmp.cMLX1ajB23/spades_test/corrected/configs/config.info 79s 79s 0:00:00.000 1M / 19M INFO General (main.cpp : 75) Starting BayesHammer, built from N/A, git revision N/A 79s 0:00:00.000 1M / 19M INFO General (main.cpp : 76) Loading config from /tmp/tmp.cMLX1ajB23/spades_test/corrected/configs/config.info 79s 0:00:00.000 1M / 19M INFO General (main.cpp : 78) Maximum # of threads to use (adjusted due to OMP capabilities): 2 79s 0:00:00.000 1M / 19M INFO General (memory_limit.cpp : 54) Memory limit set to 3 Gb 79s 0:00:00.000 1M / 19M INFO General (main.cpp : 86) Trying to determine PHRED offset 79s 0:00:00.000 1M / 19M INFO General (main.cpp : 92) Determined value is 33 79s 0:00:00.000 1M / 19M INFO General (hammer_tools.cpp : 38) Hamming graph threshold tau=1, k=21, subkmer positions = [ 0 10 ] 79s 0:00:00.000 1M / 19M INFO General (main.cpp : 113) Size of aux. kmer data 24 bytes 79s === ITERATION 0 begins === 79s 0:00:00.000 1M / 19M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 16 files using 2 threads. This might take a while. 79s 0:00:00.000 1M / 19M INFO General (file_limit.hpp : 42) Open file limit set to 1024 79s 0:00:00.000 1M / 19M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 0.499985 Gb 79s 0:00:00.000 1M / 19M INFO General (kmer_splitter.hpp : 101) Using cell size of 4194180 79s 0:00:00.000 1153M / 1153M INFO K-mer Splitting (kmer_data.cpp : 97) Processing /usr/share/spades/test_dataset_plasmid/pl1.fq.gz 79s 0:00:00.024 1153M / 1153M INFO K-mer Splitting (kmer_data.cpp : 97) Processing /usr/share/spades/test_dataset_plasmid/pl2.fq.gz 79s 0:00:00.046 1153M / 1153M INFO K-mer Splitting (kmer_data.cpp : 112) Total 4000 reads processed 79s 0:00:00.046 1M / 19M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. 79s 0:00:00.050 1M / 19M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 200430 kmers in total. 79s 0:00:00.050 1M / 19M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices 79s 0:00:00.055 1M / 19M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 200430 kmers, 156872 bytes occupied (6.26142 bits per kmer). 79s 0:00:00.055 1M / 19M INFO K-mer Counting (kmer_data.cpp : 354) Arranging kmers in hash map order 79s 0:00:00.061 4M / 19M INFO General (main.cpp : 148) Clustering Hamming graph. 79s 0:00:00.271 4M / 19M INFO General (main.cpp : 155) Extracting clusters: 79s 0:00:00.271 4M / 19M INFO General (concurrent_dsu.cpp : 18) Connecting to root 79s 0:00:00.272 4M / 19M INFO General (concurrent_dsu.cpp : 34) Calculating counts 79s 0:00:00.276 6M / 19M INFO General (concurrent_dsu.cpp : 63) Writing down entries 79s 0:00:00.280 4M / 19M INFO General (main.cpp : 167) Clustering done. Total clusters: 42542 79s 0:00:00.280 3M / 19M INFO K-mer Counting (kmer_data.cpp : 371) Collecting K-mer information, this takes a while. 79s 0:00:00.281 7M / 19M INFO K-mer Counting (kmer_data.cpp : 377) Processing /usr/share/spades/test_dataset_plasmid/pl1.fq.gz 79s 0:00:00.330 7M / 19M INFO K-mer Counting (kmer_data.cpp : 377) Processing /usr/share/spades/test_dataset_plasmid/pl2.fq.gz 79s 0:00:00.376 7M / 19M INFO K-mer Counting (kmer_data.cpp : 384) Collection done, postprocessing. 79s 0:00:00.377 7M / 19M INFO K-mer Counting (kmer_data.cpp : 397) There are 200430 kmers in total. Among them 148866 (74.2733%) are singletons. 79s 0:00:00.377 7M / 19M INFO General (main.cpp : 173) Subclustering Hamming graph 79s 0:00:00.434 7M / 19M INFO Hamming Subclustering (kmer_cluster.cpp : 650) Subclustering done. Total 0 non-read kmers were generated. 79s 0:00:00.434 7M / 19M INFO Hamming Subclustering (kmer_cluster.cpp : 651) Subclustering statistics: 79s 0:00:00.435 7M / 19M INFO Hamming Subclustering (kmer_cluster.cpp : 652) Total singleton hamming clusters: 21328. Among them 140 (0.656414%) are good 79s 0:00:00.435 7M / 19M INFO Hamming Subclustering (kmer_cluster.cpp : 653) Total singleton subclusters: 0. Among them 0 (-nan%) are good 79s 0:00:00.435 7M / 19M INFO Hamming Subclustering (kmer_cluster.cpp : 654) Total non-singleton subcluster centers: 21300. Among them 18380 (86.2911%) are good 79s 0:00:00.435 7M / 19M INFO Hamming Subclustering (kmer_cluster.cpp : 655) Average size of non-trivial subcluster: 8.40854 kmers 79s 0:00:00.435 7M / 19M INFO Hamming Subclustering (kmer_cluster.cpp : 656) Average number of sub-clusters per non-singleton cluster: 1.00405 79s 0:00:00.435 7M / 19M INFO Hamming Subclustering (kmer_cluster.cpp : 657) Total solid k-mers: 18520 79s 0:00:00.435 7M / 19M INFO Hamming Subclustering (kmer_cluster.cpp : 658) Substitution probabilities: [4,4]((0.946946,0.0263331,0.000309174,0.0264118),(0.0270576,0.94529,0.0274231,0.000229408),(0.000229396,0.027409,0.94524,0.0271217),(0.0263886,0.000309201,0.0262751,0.947027)) 79s 0:00:00.435 7M / 19M INFO General (main.cpp : 178) Finished clustering. 79s 0:00:00.435 7M / 19M INFO General (main.cpp : 197) Starting solid k-mers expansion in 2 threads. 79s 0:00:00.457 7M / 19M INFO General (main.cpp : 218) Solid k-mers iteration 0 produced 98 new k-mers. 79s 0:00:00.478 7M / 19M INFO General (main.cpp : 218) Solid k-mers iteration 1 produced 0 new k-mers. 79s 0:00:00.478 7M / 19M INFO General (main.cpp : 222) Solid k-mers finalized 79s 0:00:00.478 7M / 19M INFO General (hammer_tools.cpp : 222) Starting read correction in 2 threads. 79s 0:00:00.478 7M / 19M INFO General (hammer_tools.cpp : 235) Correcting pair of reads: /usr/share/spades/test_dataset_plasmid/pl1.fq.gz and /usr/share/spades/test_dataset_plasmid/pl2.fq.gz 80s 0:00:00.501 53M / 60M INFO General (hammer_tools.cpp : 170) Prepared batch 0 of 2000 reads. 80s 0:00:00.545 53M / 60M INFO General (hammer_tools.cpp : 177) Processed batch 0 80s 0:00:00.547 53M / 60M INFO General (hammer_tools.cpp : 187) Written batch 0 80s 0:00:00.549 7M / 60M INFO General (hammer_tools.cpp : 276) Correction done. Changed 7938 bases in 3451 reads. 80s 0:00:00.549 7M / 60M INFO General (hammer_tools.cpp : 277) Failed to correct 0 bases out of 400000. 80s 0:00:00.549 1M / 60M INFO General (main.cpp : 255) Saving corrected dataset description to /tmp/tmp.cMLX1ajB23/spades_test/corrected/corrected.yaml 80s 0:00:00.549 1M / 60M INFO General (main.cpp : 262) All done. Exiting. 80s 80s ===== Read error correction finished. 80s 80s 80s ===== corrected reads compression started. 80s 80s 80s == Running: /usr/bin/python3 /usr/share/spades/spades_pipeline/scripts/compress_all.py --input_file /tmp/tmp.cMLX1ajB23/spades_test/corrected/corrected.yaml --ext_python_modules_home /usr/share/spades --max_threads 16 --output_dir /tmp/tmp.cMLX1ajB23/spades_test/corrected --gzip_output 80s 80s == Compressing corrected reads (with gzip) 80s == Files to compress: ['/tmp/tmp.cMLX1ajB23/spades_test/corrected/pl1.fq.00.0_0.cor.fastq', '/tmp/tmp.cMLX1ajB23/spades_test/corrected/pl2.fq.00.0_0.cor.fastq', '/tmp/tmp.cMLX1ajB23/spades_test/corrected/pl_unpaired.00.0_0.cor.fastq'] 80s == Files compression is finished 80s == Dataset yaml file is updated 80s 80s ===== corrected reads compression finished. 80s 80s 80s ===== Read error correction finished. 80s 80s 80s ===== Assembling started. 80s 80s 80s ===== K21 started. 80s 80s 80s == Running: /usr/libexec/spades/spades-core /tmp/tmp.cMLX1ajB23/spades_test/K21/configs/config.info /tmp/tmp.cMLX1ajB23/spades_test/K21/configs/plasmid_mode.info 80s 80s 0:00:00.000 1M / 19M INFO General (main.cpp : 99) Loaded config from /tmp/tmp.cMLX1ajB23/spades_test/K21/configs/config.info 80s 0:00:00.000 1M / 19M INFO General (main.cpp : 99) Loaded config from /tmp/tmp.cMLX1ajB23/spades_test/K21/configs/plasmid_mode.info 80s 0:00:00.000 1M / 19M INFO General (memory_limit.cpp : 54) Memory limit set to 3 Gb 80s 0:00:00.000 1M / 19M INFO General (main.cpp : 107) Starting SPAdes, built from N/A, git revision N/A 80s 0:00:00.000 1M / 19M INFO General (main.cpp : 108) Maximum k-mer length: 128 80s 0:00:00.000 1M / 19M INFO General (main.cpp : 109) Assembling dataset (/tmp/tmp.cMLX1ajB23/spades_test/dataset.info) with K=21 80s 0:00:00.000 1M / 19M INFO General (main.cpp : 110) Maximum # of threads to use (adjusted due to OMP capabilities): 2 80s 0:00:00.000 1M / 19M INFO General (pipeline.cpp : 212) SPAdes started 80s 0:00:00.000 1M / 19M INFO General (pipeline.cpp : 225) Starting from stage: read_conversion 80s 0:00:00.000 1M / 19M INFO General (pipeline.cpp : 231) Two-step repeat resolution disabled 80s 0:00:00.000 1M / 19M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 80s 0:00:00.000 1M / 19M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 80s 0:00:00.000 1M / 19M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 80s 0:00:00.000 1M / 19M INFO StageManager (stage.cpp : 185) STAGE == Binary Read Conversion (id: read_conversion) 80s 0:00:00.000 1M / 19M INFO General (read_converter.cpp : 72) Converting reads to binary format for library #0 (takes a while) 80s 0:00:00.000 1M / 19M INFO General (read_converter.cpp : 73) Converting paired reads 80s 0:00:00.009 63M / 63M INFO General (binary_converter.cpp : 111) 1997 reads written 80s 0:00:00.009 41M / 41M INFO General (read_converter.cpp : 86) Converting single reads 80s 0:00:00.009 71M / 71M INFO General (binary_converter.cpp : 111) 3 reads written 80s 0:00:00.009 61M / 61M INFO General (read_converter.cpp : 92) Converting merged reads 80s 0:00:00.009 71M / 71M INFO General (binary_converter.cpp : 111) 0 reads written 80s 0:00:00.009 1M / 19M INFO StageManager (stage.cpp : 185) STAGE == de Bruijn graph construction (id: construction) 80s 0:00:00.010 1M / 19M INFO General (construction.cpp : 153) Max read length 100 80s 0:00:00.010 1M / 19M INFO General (construction.cpp : 159) Average read length 100 80s 0:00:00.010 1M / 19M INFO General (stage.cpp : 117) PROCEDURE == k+1-mer counting (id: construction:kpomer_counting) 80s 0:00:00.010 1M / 19M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 20 files using 2 threads. This might take a while. 80s 0:00:00.010 1M / 19M INFO General (file_limit.hpp : 42) Open file limit set to 1024 80s 0:00:00.010 1M / 19M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 0.499973 Gb 80s 0:00:00.010 1M / 19M INFO General (kmer_splitter.hpp : 101) Using cell size of 3355263 80s 0:00:00.024 1M / 19M INFO General (kmer_splitters.hpp : 131) Used 7994 reads 80s 0:00:00.024 1M / 19M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. 80s 0:00:00.026 1M / 19M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 11924 kmers in total. 80s 0:00:00.026 1M / 19M INFO General (stage.cpp : 117) PROCEDURE == Extension index construction (id: construction:extension_index_construction) 80s 0:00:00.026 1M / 19M INFO K-mer Index Building (kmer_index_builder.hpp : 438) Building kmer index 80s 0:00:00.026 1M / 19M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 20 files using 2 threads. This might take a while. 80s 0:00:00.026 1M / 19M INFO General (file_limit.hpp : 42) Open file limit set to 1024 80s 0:00:00.026 1M / 19M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 0.499971 Gb 80s 0:00:00.026 1M / 19M INFO General (kmer_splitter.hpp : 101) Using cell size of 3355245 80s 0:00:00.028 1161M / 1161M INFO General (kmer_splitters.hpp : 194) Processed 11924 kmers 80s 0:00:00.028 1161M / 1161M INFO General (kmer_splitters.hpp : 199) Used 11924 kmers. 80s 0:00:00.028 1M / 19M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. 80s 0:00:00.030 1M / 19M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 11894 kmers in total. 80s 0:00:00.030 1M / 19M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices 80s 0:00:00.031 1M / 19M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 11894 kmers, 24064 bytes occupied (16.1856 bits per kmer). 80s 0:00:00.032 1M / 19M INFO General (kmer_index_builder.hpp : 169) Merging final buckets. 80s 0:00:00.032 1M / 19M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 100) Building k-mer extensions from k+1-mers 80s 0:00:00.034 1M / 19M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 105) Building k-mer extensions from k+1-mers finished. 80s 0:00:00.034 1M / 19M INFO General (stage.cpp : 117) PROCEDURE == Early tip clipping (id: construction:early_tip_clipper) 80s 0:00:00.035 1M / 19M INFO General (construction.cpp : 301) Early tip clipper length bound set as (RL - K) 80s 0:00:00.035 1M / 19M INFO Early tip clipping (early_simplification.hpp : 47) Early tip clipping 80s 0:00:00.036 1M / 19M INFO Early tip clipping (early_simplification.hpp : 82) #tipped junctions: 58 80s 0:00:00.036 1M / 19M INFO Early tip clipping (early_simplification.hpp : 93) Clipped tips: 58 80s 0:00:00.036 1M / 19M INFO Early tip clipping (early_simplification.hpp : 49) 572 22-mers were removed by early tip clipper 80s 0:00:00.036 1M / 19M INFO General (stage.cpp : 117) PROCEDURE == Condensing graph (id: construction:graph_condensing) 80s 0:00:00.036 1M / 19M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths 80s 0:00:00.038 1M / 19M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 92 sequences extracted 80s 0:00:00.039 1M / 19M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops 80s 0:00:00.040 1M / 19M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 0 loops collected 80s 0:00:00.040 1M / 19M INFO General (debruijn_graph_constructor: 487) Total 184 edges to create 80s 0:00:00.040 1M / 19M INFO General (debruijn_graph_constructor: 489) Collecting link records 80s 0:00:00.040 1M / 19M INFO General (debruijn_graph_constructor: 491) Ordering link records 80s 0:00:00.040 1M / 19M INFO General (debruijn_graph_constructor: 493) Sorting done 80s 0:00:00.040 1M / 19M INFO General (debruijn_graph_constructor: 503) Total 62 vertices to create 80s 0:00:00.040 1M / 19M INFO General (debruijn_graph_constructor: 506) Connecting the graph 80s 0:00:00.040 1M / 19M INFO General (stage.cpp : 117) PROCEDURE == Filling coverage indices (PHM) (id: construction:coverage_filling_phm) 80s 0:00:00.040 1M / 19M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices 80s 0:00:00.042 1M / 19M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 11924 kmers, 24088 bytes occupied (16.161 bits per kmer). 80s 0:00:00.042 1M / 19M INFO General (coverage_hash_map_builder.: 47) Collecting k-mer coverage information from reads, this takes a while. 80s 0:00:00.057 1M / 19M INFO General (construction.cpp : 430) Filling coverage and flanking coverage from PHM 80s 0:00:00.058 1M / 19M INFO StageManager (stage.cpp : 185) STAGE == EC Threshold Finding (id: ec_threshold_finder) 80s 0:00:00.058 1M / 19M INFO General (kmer_coverage_model.cpp : 181) Kmer coverage valley at: 0 80s 0:00:00.058 1M / 19M INFO General (kmer_coverage_model.cpp : 201) K-mer histogram maximum: 14 80s 0:00:00.058 1M / 19M INFO General (kmer_coverage_model.cpp : 237) Estimated median coverage: 16. Coverage mad: 5.9304 80s 0:00:00.058 1M / 19M INFO General (kmer_coverage_model.cpp : 259) Fitting coverage model 80s 0:00:00.070 1M / 19M INFO General (kmer_coverage_model.cpp : 295) ... iteration 2 80s 0:00:00.098 1M / 19M INFO General (kmer_coverage_model.cpp : 295) ... iteration 4 80s 0:00:00.221 1M / 19M INFO General (kmer_coverage_model.cpp : 295) ... iteration 8 80s 0:00:00.430 1M / 19M INFO General (kmer_coverage_model.cpp : 295) ... iteration 16 80s 0:00:00.528 1M / 19M INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 16.4297. Fitted coverage std. dev: 4.18797 80s 0:00:00.529 1M / 19M INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 0.999845 80s 0:00:00.529 1M / 19M INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 11 80s 0:00:00.529 1M / 19M INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 8 80s 0:00:00.529 1M / 19M INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 10217 80s 0:00:00.529 1M / 19M INFO General (genomic_info_filler.cpp : 55) Mean coverage was calculated as 16.4297 80s 0:00:00.529 1M / 19M INFO General (genomic_info_filler.cpp : 70) EC coverage threshold value was calculated as 8 80s 0:00:00.529 1M / 19M INFO General (genomic_info_filler.cpp : 71) Trusted kmer low bound: 0 80s 0:00:00.529 1M / 19M INFO StageManager (stage.cpp : 185) STAGE == Raw Simplification (id: raw_simplification) 80s 0:00:00.529 1M / 19M INFO General (simplification.cpp : 127) PROCEDURE == Initial cleaning 80s 0:00:00.529 1M / 19M INFO General (graph_simplification.hpp : 662) Flanking coverage based disconnection disabled 80s 0:00:00.529 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Self conjugate edge remover 80s 0:00:00.529 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Self conjugate edge remover triggered 0 times 80s 0:00:00.529 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Initial tip clipper 80s 0:00:00.529 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Initial tip clipper triggered 0 times 80s 0:00:00.529 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Initial ec remover 80s 0:00:00.530 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Initial ec remover triggered 24 times 80s 0:00:00.530 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Initial isolated edge remover 80s 0:00:00.530 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Initial isolated edge remover triggered 0 times 80s 0:00:00.530 1M / 19M INFO StageManager (stage.cpp : 185) STAGE == Simplification (id: simplification) 80s 0:00:00.530 1M / 19M INFO General (simplification.cpp : 368) Graph simplification started 80s 0:00:00.530 1M / 19M INFO General (graph_simplification.hpp : 634) Creating parallel br instance 80s 0:00:00.530 1M / 19M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 1 80s 0:00:00.530 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 80s 0:00:00.530 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 80s 0:00:00.530 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 80s 0:00:00.530 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 7 times 80s 0:00:00.530 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 80s 0:00:00.530 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 0 times 80s 0:00:00.530 1M / 19M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 2 80s 0:00:00.530 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 80s 0:00:00.530 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 80s 0:00:00.530 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 80s 0:00:00.530 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 80s 0:00:00.530 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 80s 0:00:00.530 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 0 times 80s 0:00:00.530 1M / 19M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 3 80s 0:00:00.530 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 80s 0:00:00.530 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 80s 0:00:00.530 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 80s 0:00:00.530 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 80s 0:00:00.530 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 80s 0:00:00.530 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 0 times 80s 0:00:00.530 1M / 19M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 4 80s 0:00:00.530 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 80s 0:00:00.530 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 80s 0:00:00.530 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 80s 0:00:00.530 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 80s 0:00:00.530 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 80s 0:00:00.530 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 0 times 80s 0:00:00.530 1M / 19M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 5 80s 0:00:00.530 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 80s 0:00:00.530 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 80s 0:00:00.530 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 80s 0:00:00.530 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 80s 0:00:00.530 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 80s 0:00:00.530 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 0 times 80s 0:00:00.530 1M / 19M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 6 80s 0:00:00.530 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 80s 0:00:00.530 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 80s 0:00:00.530 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 80s 0:00:00.530 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 80s 0:00:00.530 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 80s 0:00:00.530 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 0 times 80s 0:00:00.530 1M / 19M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 7 80s 0:00:00.530 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 80s 0:00:00.530 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 80s 0:00:00.530 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 80s 0:00:00.530 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 80s 0:00:00.530 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 80s 0:00:00.530 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 0 times 80s 0:00:00.530 1M / 19M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 8 80s 0:00:00.530 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 80s 0:00:00.530 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 80s 0:00:00.530 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 80s 0:00:00.530 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 80s 0:00:00.530 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 80s 0:00:00.530 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 0 times 80s 0:00:00.530 1M / 19M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 9 80s 0:00:00.530 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 80s 0:00:00.530 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 80s 0:00:00.530 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 80s 0:00:00.530 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 80s 0:00:00.530 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 80s 0:00:00.530 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 0 times 80s 0:00:00.530 1M / 19M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 10 80s 0:00:00.530 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 80s 0:00:00.530 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 80s 0:00:00.530 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 80s 0:00:00.530 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 80s 0:00:00.530 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 80s 0:00:00.530 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 0 times 80s 0:00:00.530 1M / 19M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 11 80s 0:00:00.530 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 80s 0:00:00.530 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 80s 0:00:00.530 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 80s 0:00:00.530 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 80s 0:00:00.530 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 80s 0:00:00.530 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 0 times 80s 0:00:00.530 1M / 19M INFO StageManager (stage.cpp : 185) STAGE == Simplification Cleanup (id: simplification_cleanup) 80s 0:00:00.530 1M / 19M INFO General (simplification.cpp : 176) PROCEDURE == Post simplification 80s 0:00:00.530 1M / 19M INFO General (graph_simplification.hpp : 448) Disconnection of relatively low covered edges disabled 80s 0:00:00.530 1M / 19M INFO General (graph_simplification.hpp : 485) Complex tip clipping disabled 80s 0:00:00.530 1M / 19M INFO General (graph_simplification.hpp : 634) Creating parallel br instance 80s 0:00:00.530 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 80s 0:00:00.530 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 80s 0:00:00.530 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 80s 0:00:00.530 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 80s 0:00:00.530 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 80s 0:00:00.530 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 80s 0:00:00.530 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 80s 0:00:00.530 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 80s 0:00:00.530 1M / 19M INFO General (simplification.cpp : 327) Disrupting self-conjugate edges 80s 0:00:00.530 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Removing isolated edges 80s 0:00:00.530 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Removing isolated edges triggered 0 times 80s 0:00:00.530 1M / 19M INFO General (simplification.cpp : 495) After simplification: 80s 0:00:00.530 1M / 19M INFO General (simplification.cpp : 496) Average coverage = 29.7009 80s 0:00:00.530 1M / 19M INFO General (simplification.cpp : 497) Total length = 10591 80s 0:00:00.530 1M / 19M INFO General (simplification.cpp : 498) Median edge length: 9612 80s 0:00:00.530 1M / 19M INFO General (simplification.cpp : 499) Edges: 4 80s 0:00:00.530 1M / 19M INFO General (simplification.cpp : 500) Vertices: 6 80s 0:00:00.530 1M / 19M INFO StageManager (stage.cpp : 185) STAGE == Contig Output (id: contig_output) 80s 0:00:00.530 1M / 19M INFO General (read_converter.cpp : 107) Outputting contigs to /tmp/tmp.cMLX1ajB23/spades_test/K21/simplified_contigs 80s 0:00:00.532 3M / 19M INFO General (binary_converter.cpp : 111) 2 reads written 80s 0:00:00.533 1M / 19M INFO General (pipeline.cpp : 287) SPAdes finished 80s 0:00:00.533 1M / 19M INFO General (main.cpp : 136) Assembling time: 0 hours 0 minutes 0 seconds 80s 80s ===== K21 finished. 80s 80s 80s ===== K33 started. 80s 80s 80s == Running: /usr/libexec/spades/spades-core /tmp/tmp.cMLX1ajB23/spades_test/K33/configs/config.info /tmp/tmp.cMLX1ajB23/spades_test/K33/configs/plasmid_mode.info 80s 80s 0:00:00.000 1M / 19M INFO General (main.cpp : 99) Loaded config from /tmp/tmp.cMLX1ajB23/spades_test/K33/configs/config.info 80s 0:00:00.000 1M / 19M INFO General (main.cpp : 99) Loaded config from /tmp/tmp.cMLX1ajB23/spades_test/K33/configs/plasmid_mode.info 80s 0:00:00.000 1M / 19M INFO General (memory_limit.cpp : 54) Memory limit set to 3 Gb 80s 0:00:00.000 1M / 19M INFO General (main.cpp : 107) Starting SPAdes, built from N/A, git revision N/A 80s 0:00:00.000 1M / 19M INFO General (main.cpp : 108) Maximum k-mer length: 128 80s 0:00:00.000 1M / 19M INFO General (main.cpp : 109) Assembling dataset (/tmp/tmp.cMLX1ajB23/spades_test/dataset.info) with K=33 80s 0:00:00.000 1M / 19M INFO General (main.cpp : 110) Maximum # of threads to use (adjusted due to OMP capabilities): 2 80s 0:00:00.000 1M / 19M INFO General (pipeline.cpp : 212) SPAdes started 80s 0:00:00.000 1M / 19M INFO General (pipeline.cpp : 225) Starting from stage: read_conversion 80s 0:00:00.000 1M / 19M INFO General (pipeline.cpp : 231) Two-step repeat resolution disabled 80s 0:00:00.000 1M / 19M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 80s 0:00:00.000 1M / 19M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 80s 0:00:00.000 1M / 19M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 80s 0:00:00.000 1M / 19M INFO StageManager (stage.cpp : 185) STAGE == Binary Read Conversion (id: read_conversion) 80s 0:00:00.000 1M / 19M INFO General (read_converter.cpp : 53) Binary reads detected 80s 0:00:00.000 1M / 19M INFO StageManager (stage.cpp : 185) STAGE == de Bruijn graph construction (id: construction) 80s 0:00:00.000 1M / 19M INFO General (construction.cpp : 118) Contigs from previous K will be used: /tmp/tmp.cMLX1ajB23/spades_test/K21/simplified_contigs 80s 0:00:00.000 1M / 19M INFO General (construction.cpp : 153) Max read length 100 80s 0:00:00.000 1M / 19M INFO General (construction.cpp : 159) Average read length 100 80s 0:00:00.000 1M / 19M INFO General (stage.cpp : 117) PROCEDURE == k+1-mer counting (id: construction:kpomer_counting) 80s 0:00:00.000 1M / 19M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 20 files using 2 threads. This might take a while. 80s 0:00:00.000 1M / 19M INFO General (file_limit.hpp : 42) Open file limit set to 1024 80s 0:00:00.000 1M / 19M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 0.49997 Gb 80s 0:00:00.000 1M / 19M INFO General (kmer_splitter.hpp : 101) Using cell size of 1677622 80s 0:00:00.014 1M / 19M INFO General (kmer_splitters.hpp : 131) Used 7998 reads 80s 0:00:00.014 1M / 19M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. 80s 0:00:00.016 1M / 19M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 12143 kmers in total. 80s 0:00:00.016 1M / 19M INFO General (stage.cpp : 117) PROCEDURE == Extension index construction (id: construction:extension_index_construction) 80s 0:00:00.016 1M / 19M INFO K-mer Index Building (kmer_index_builder.hpp : 438) Building kmer index 80s 0:00:00.016 1M / 19M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 20 files using 2 threads. This might take a while. 80s 0:00:00.016 1M / 19M INFO General (file_limit.hpp : 42) Open file limit set to 1024 80s 0:00:00.016 1M / 19M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 0.499968 Gb 80s 0:00:00.016 1M / 19M INFO General (kmer_splitter.hpp : 101) Using cell size of 1677612 80s 0:00:00.018 1161M / 1161M INFO General (kmer_splitters.hpp : 194) Processed 12143 kmers 80s 0:00:00.018 1161M / 1161M INFO General (kmer_splitters.hpp : 199) Used 12143 kmers. 80s 0:00:00.018 1M / 19M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. 80s 0:00:00.020 1M / 19M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 12133 kmers in total. 80s 0:00:00.020 1M / 19M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices 80s 0:00:00.022 1M / 19M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 12133 kmers, 24248 bytes occupied (15.9881 bits per kmer). 80s 0:00:00.022 1M / 19M INFO General (kmer_index_builder.hpp : 169) Merging final buckets. 80s 0:00:00.023 1M / 19M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 100) Building k-mer extensions from k+1-mers 80s 0:00:00.025 1M / 19M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 105) Building k-mer extensions from k+1-mers finished. 80s 0:00:00.025 1M / 19M INFO General (stage.cpp : 117) PROCEDURE == Early tip clipping (id: construction:early_tip_clipper) 80s 0:00:00.025 1M / 19M INFO General (construction.cpp : 301) Early tip clipper length bound set as (RL - K) 80s 0:00:00.025 1M / 19M INFO Early tip clipping (early_simplification.hpp : 47) Early tip clipping 81s 0:00:00.026 1M / 19M INFO Early tip clipping (early_simplification.hpp : 82) #tipped junctions: 67 81s 0:00:00.026 1M / 19M INFO Early tip clipping (early_simplification.hpp : 93) Clipped tips: 67 81s 0:00:00.027 1M / 19M INFO Early tip clipping (early_simplification.hpp : 49) 1006 34-mers were removed by early tip clipper 81s 0:00:00.027 1M / 19M INFO General (stage.cpp : 117) PROCEDURE == Condensing graph (id: construction:graph_condensing) 81s 0:00:00.027 1M / 19M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths 81s 0:00:00.029 1M / 19M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 42 sequences extracted 81s 0:00:00.030 1M / 19M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops 81s 0:00:00.031 1M / 19M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 0 loops collected 81s 0:00:00.031 1M / 19M INFO General (debruijn_graph_constructor: 487) Total 84 edges to create 81s 0:00:00.031 1M / 19M INFO General (debruijn_graph_constructor: 489) Collecting link records 81s 0:00:00.031 1M / 19M INFO General (debruijn_graph_constructor: 491) Ordering link records 81s 0:00:00.031 1M / 19M INFO General (debruijn_graph_constructor: 493) Sorting done 81s 0:00:00.031 1M / 19M INFO General (debruijn_graph_constructor: 503) Total 32 vertices to create 81s 0:00:00.031 1M / 19M INFO General (debruijn_graph_constructor: 506) Connecting the graph 81s 0:00:00.031 1M / 19M INFO General (stage.cpp : 117) PROCEDURE == Filling coverage indices (PHM) (id: construction:coverage_filling_phm) 81s 0:00:00.031 1M / 19M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices 81s 0:00:00.033 1M / 19M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 12143 kmers, 24224 bytes occupied (15.9592 bits per kmer). 81s 0:00:00.033 1M / 19M INFO General (coverage_hash_map_builder.: 47) Collecting k-mer coverage information from reads, this takes a while. 81s 0:00:00.046 1M / 19M INFO General (construction.cpp : 430) Filling coverage and flanking coverage from PHM 81s 0:00:00.047 1M / 19M INFO StageManager (stage.cpp : 185) STAGE == EC Threshold Finding (id: ec_threshold_finder) 81s 0:00:00.047 1M / 19M INFO General (kmer_coverage_model.cpp : 181) Kmer coverage valley at: 0 81s 0:00:00.047 1M / 19M INFO General (kmer_coverage_model.cpp : 201) K-mer histogram maximum: 12 81s 0:00:00.047 1M / 19M INFO General (kmer_coverage_model.cpp : 237) Estimated median coverage: 13. Coverage mad: 5.9304 81s 0:00:00.047 1M / 19M INFO General (kmer_coverage_model.cpp : 259) Fitting coverage model 81s 0:00:00.058 1M / 19M INFO General (kmer_coverage_model.cpp : 295) ... iteration 2 81s 0:00:00.088 1M / 19M INFO General (kmer_coverage_model.cpp : 295) ... iteration 4 81s 0:00:00.162 1M / 19M INFO General (kmer_coverage_model.cpp : 295) ... iteration 8 81s 0:00:00.229 1M / 19M INFO General (kmer_coverage_model.cpp : 295) ... iteration 16 81s 0:00:00.246 1M / 19M INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 13.8661. Fitted coverage std. dev: 3.9411 81s 0:00:00.246 1M / 19M INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 0.996476 81s 0:00:00.246 1M / 19M INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 9 81s 0:00:00.246 1M / 19M INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 6 81s 0:00:00.246 1M / 19M INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 10118 81s 0:00:00.246 1M / 19M INFO General (genomic_info_filler.cpp : 55) Mean coverage was calculated as 13.8661 81s 0:00:00.246 1M / 19M INFO General (genomic_info_filler.cpp : 70) EC coverage threshold value was calculated as 6 81s 0:00:00.246 1M / 19M INFO General (genomic_info_filler.cpp : 71) Trusted kmer low bound: 0 81s 0:00:00.246 1M / 19M INFO StageManager (stage.cpp : 185) STAGE == Raw Simplification (id: raw_simplification) 81s 0:00:00.246 1M / 19M INFO General (simplification.cpp : 127) PROCEDURE == Initial cleaning 81s 0:00:00.246 1M / 19M INFO General (graph_simplification.hpp : 662) Flanking coverage based disconnection disabled 81s 0:00:00.246 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Self conjugate edge remover 81s 0:00:00.246 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Self conjugate edge remover triggered 0 times 81s 0:00:00.246 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Initial tip clipper 81s 0:00:00.246 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Initial tip clipper triggered 3 times 81s 0:00:00.246 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Initial ec remover 81s 0:00:00.247 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Initial ec remover triggered 7 times 81s 0:00:00.247 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Initial isolated edge remover 81s 0:00:00.247 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Initial isolated edge remover triggered 0 times 81s 0:00:00.247 1M / 19M INFO StageManager (stage.cpp : 185) STAGE == Simplification (id: simplification) 81s 0:00:00.247 1M / 19M INFO General (simplification.cpp : 368) Graph simplification started 81s 0:00:00.247 1M / 19M INFO General (graph_simplification.hpp : 634) Creating parallel br instance 81s 0:00:00.247 1M / 19M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 1 81s 0:00:00.247 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 81s 0:00:00.247 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 1 times 81s 0:00:00.247 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 81s 0:00:00.247 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 4 times 81s 0:00:00.247 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 81s 0:00:00.247 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 0 times 81s 0:00:00.247 1M / 19M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 2 81s 0:00:00.247 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 81s 0:00:00.247 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 81s 0:00:00.247 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 81s 0:00:00.247 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 81s 0:00:00.247 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 81s 0:00:00.247 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 0 times 81s 0:00:00.247 1M / 19M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 3 81s 0:00:00.247 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 81s 0:00:00.247 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 81s 0:00:00.247 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 81s 0:00:00.247 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 81s 0:00:00.247 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 81s 0:00:00.247 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 0 times 81s 0:00:00.247 1M / 19M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 4 81s 0:00:00.247 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 81s 0:00:00.247 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 81s 0:00:00.247 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 81s 0:00:00.247 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 81s 0:00:00.247 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 81s 0:00:00.247 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 0 times 81s 0:00:00.247 1M / 19M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 5 81s 0:00:00.247 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 81s 0:00:00.247 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 81s 0:00:00.247 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 81s 0:00:00.247 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 81s 0:00:00.247 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 81s 0:00:00.247 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 0 times 81s 0:00:00.247 1M / 19M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 6 81s 0:00:00.247 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 81s 0:00:00.247 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 81s 0:00:00.247 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 81s 0:00:00.247 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 81s 0:00:00.247 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 81s 0:00:00.247 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 0 times 81s 0:00:00.247 1M / 19M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 7 81s 0:00:00.247 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 81s 0:00:00.247 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 81s 0:00:00.247 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 81s 0:00:00.247 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 81s 0:00:00.247 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 81s 0:00:00.247 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 0 times 81s 0:00:00.247 1M / 19M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 8 81s 0:00:00.247 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 81s 0:00:00.247 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 81s 0:00:00.247 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 81s 0:00:00.247 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 81s 0:00:00.247 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 81s 0:00:00.247 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 0 times 81s 0:00:00.247 1M / 19M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 9 81s 0:00:00.247 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 81s 0:00:00.247 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 81s 0:00:00.247 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 81s 0:00:00.247 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 81s 0:00:00.247 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 81s 0:00:00.247 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 0 times 81s 0:00:00.247 1M / 19M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 10 81s 0:00:00.247 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 81s 0:00:00.247 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 81s 0:00:00.247 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 81s 0:00:00.247 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 81s 0:00:00.247 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 81s 0:00:00.247 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 0 times 81s 0:00:00.247 1M / 19M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 11 81s 0:00:00.247 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 81s 0:00:00.247 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 81s 0:00:00.247 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 81s 0:00:00.247 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 81s 0:00:00.247 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 81s 0:00:00.247 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 0 times 81s 0:00:00.247 1M / 19M INFO StageManager (stage.cpp : 185) STAGE == Simplification Cleanup (id: simplification_cleanup) 81s 0:00:00.247 1M / 19M INFO General (simplification.cpp : 176) PROCEDURE == Post simplification 81s 0:00:00.247 1M / 19M INFO General (graph_simplification.hpp : 448) Disconnection of relatively low covered edges disabled 81s 0:00:00.247 1M / 19M INFO General (graph_simplification.hpp : 485) Complex tip clipping disabled 81s 0:00:00.247 1M / 19M INFO General (graph_simplification.hpp : 634) Creating parallel br instance 81s 0:00:00.247 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 81s 0:00:00.247 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 81s 0:00:00.247 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 81s 0:00:00.247 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 81s 0:00:00.247 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 81s 0:00:00.247 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 81s 0:00:00.247 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 81s 0:00:00.247 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 81s 0:00:00.247 1M / 19M INFO General (simplification.cpp : 327) Disrupting self-conjugate edges 81s 0:00:00.247 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Removing isolated edges 81s 0:00:00.247 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Removing isolated edges triggered 0 times 81s 0:00:00.247 1M / 19M INFO General (simplification.cpp : 495) After simplification: 81s 0:00:00.247 1M / 19M INFO General (simplification.cpp : 496) Average coverage = 25.1685 81s 0:00:00.247 1M / 19M INFO General (simplification.cpp : 497) Total length = 10579 81s 0:00:00.247 1M / 19M INFO General (simplification.cpp : 498) Median edge length: 9612 81s 0:00:00.247 1M / 19M INFO General (simplification.cpp : 499) Edges: 4 81s 0:00:00.247 1M / 19M INFO General (simplification.cpp : 500) Vertices: 6 81s 0:00:00.247 1M / 19M INFO StageManager (stage.cpp : 185) STAGE == Contig Output (id: contig_output) 81s 0:00:00.247 1M / 19M INFO General (read_converter.cpp : 107) Outputting contigs to /tmp/tmp.cMLX1ajB23/spades_test/K33/simplified_contigs 81s 0:00:00.249 3M / 19M INFO General (binary_converter.cpp : 111) 2 reads written 81s 0:00:00.250 1M / 19M INFO General (pipeline.cpp : 287) SPAdes finished 81s 0:00:00.250 1M / 19M INFO General (main.cpp : 136) Assembling time: 0 hours 0 minutes 0 seconds 81s 81s ===== K33 finished. 81s 81s 81s ===== K55 started. 81s 81s 81s == Running: /usr/libexec/spades/spades-core /tmp/tmp.cMLX1ajB23/spades_test/K55/configs/config.info /tmp/tmp.cMLX1ajB23/spades_test/K55/configs/plasmid_mode.info 81s 81s 0:00:00.000 1M / 19M INFO General (main.cpp : 99) Loaded config from /tmp/tmp.cMLX1ajB23/spades_test/K55/configs/config.info 81s 0:00:00.000 1M / 19M INFO General (main.cpp : 99) Loaded config from /tmp/tmp.cMLX1ajB23/spades_test/K55/configs/plasmid_mode.info 81s 0:00:00.000 1M / 19M INFO General (memory_limit.cpp : 54) Memory limit set to 3 Gb 81s 0:00:00.000 1M / 19M INFO General (main.cpp : 107) Starting SPAdes, built from N/A, git revision N/A 81s 0:00:00.000 1M / 19M INFO General (main.cpp : 108) Maximum k-mer length: 128 81s 0:00:00.000 1M / 19M INFO General (main.cpp : 109) Assembling dataset (/tmp/tmp.cMLX1ajB23/spades_test/dataset.info) with K=55 81s 0:00:00.000 1M / 19M INFO General (main.cpp : 110) Maximum # of threads to use (adjusted due to OMP capabilities): 2 81s 0:00:00.000 1M / 19M INFO General (pipeline.cpp : 212) SPAdes started 81s 0:00:00.000 1M / 19M INFO General (pipeline.cpp : 225) Starting from stage: read_conversion 81s 0:00:00.000 1M / 19M INFO General (pipeline.cpp : 231) Two-step repeat resolution disabled 81s 0:00:00.000 1M / 19M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 81s 0:00:00.000 1M / 19M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 81s 0:00:00.000 1M / 19M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 81s 0:00:00.000 1M / 19M INFO General (pipeline.cpp : 242) Will need read mapping, kmer mapper will be attached 81s 0:00:00.000 1M / 19M INFO StageManager (stage.cpp : 185) STAGE == Binary Read Conversion (id: read_conversion) 81s 0:00:00.000 1M / 19M INFO General (read_converter.cpp : 53) Binary reads detected 81s 0:00:00.000 1M / 19M INFO StageManager (stage.cpp : 185) STAGE == de Bruijn graph construction (id: construction) 81s 0:00:00.000 1M / 19M INFO General (construction.cpp : 118) Contigs from previous K will be used: /tmp/tmp.cMLX1ajB23/spades_test/K33/simplified_contigs 81s 0:00:00.000 1M / 19M INFO General (construction.cpp : 153) Max read length 100 81s 0:00:00.000 1M / 19M INFO General (construction.cpp : 159) Average read length 100 81s 0:00:00.000 1M / 19M INFO General (stage.cpp : 117) PROCEDURE == k+1-mer counting (id: construction:kpomer_counting) 81s 0:00:00.000 1M / 19M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 20 files using 2 threads. This might take a while. 81s 0:00:00.000 1M / 19M INFO General (file_limit.hpp : 42) Open file limit set to 1024 81s 0:00:00.000 1M / 19M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 0.49997 Gb 81s 0:00:00.000 1M / 19M INFO General (kmer_splitter.hpp : 101) Using cell size of 1677622 81s 0:00:00.010 1M / 19M INFO General (kmer_splitters.hpp : 131) Used 7998 reads 81s 0:00:00.011 1M / 19M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. 81s 0:00:00.012 1M / 19M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 12113 kmers in total. 81s 0:00:00.012 1M / 19M INFO General (stage.cpp : 117) PROCEDURE == Extension index construction (id: construction:extension_index_construction) 81s 0:00:00.012 1M / 19M INFO K-mer Index Building (kmer_index_builder.hpp : 438) Building kmer index 81s 0:00:00.012 1M / 19M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 20 files using 2 threads. This might take a while. 81s 0:00:00.012 1M / 19M INFO General (file_limit.hpp : 42) Open file limit set to 1024 81s 0:00:00.012 1M / 19M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 0.499968 Gb 81s 0:00:00.013 1M / 19M INFO General (kmer_splitter.hpp : 101) Using cell size of 1677612 81s 0:00:00.015 1161M / 1161M INFO General (kmer_splitters.hpp : 194) Processed 12113 kmers 81s 0:00:00.015 1161M / 1161M INFO General (kmer_splitters.hpp : 199) Used 12113 kmers. 81s 0:00:00.015 1M / 19M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. 81s 0:00:00.016 1M / 19M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 12121 kmers in total. 81s 0:00:00.016 1M / 19M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices 81s 0:00:00.018 1M / 19M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 12121 kmers, 24248 bytes occupied (16.004 bits per kmer). 81s 0:00:00.018 1M / 19M INFO General (kmer_index_builder.hpp : 169) Merging final buckets. 81s 0:00:00.019 1M / 19M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 100) Building k-mer extensions from k+1-mers 81s 0:00:00.021 1M / 19M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 105) Building k-mer extensions from k+1-mers finished. 81s 0:00:00.021 1M / 19M INFO General (stage.cpp : 117) PROCEDURE == Condensing graph (id: construction:graph_condensing) 81s 0:00:00.021 1M / 19M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths 81s 0:00:00.023 1M / 19M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 151 sequences extracted 81s 0:00:00.025 1M / 19M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops 81s 0:00:00.025 1M / 19M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 0 loops collected 81s 0:00:00.025 1M / 19M INFO General (debruijn_graph_constructor: 487) Total 302 edges to create 81s 0:00:00.025 1M / 19M INFO General (debruijn_graph_constructor: 489) Collecting link records 81s 0:00:00.026 1M / 19M INFO General (debruijn_graph_constructor: 491) Ordering link records 81s 0:00:00.026 1M / 19M INFO General (debruijn_graph_constructor: 493) Sorting done 81s 0:00:00.026 1M / 19M INFO General (debruijn_graph_constructor: 503) Total 159 vertices to create 81s 0:00:00.026 1M / 19M INFO General (debruijn_graph_constructor: 506) Connecting the graph 81s 0:00:00.026 1M / 19M INFO General (stage.cpp : 117) PROCEDURE == Filling coverage indices (PHM) (id: construction:coverage_filling_phm) 81s 0:00:00.026 1M / 19M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices 81s 0:00:00.028 1M / 19M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 12113 kmers, 24224 bytes occupied (15.9987 bits per kmer). 81s 0:00:00.028 1M / 19M INFO General (coverage_hash_map_builder.: 47) Collecting k-mer coverage information from reads, this takes a while. 81s 0:00:00.037 1M / 19M INFO General (construction.cpp : 430) Filling coverage and flanking coverage from PHM 81s 0:00:00.038 1M / 19M INFO StageManager (stage.cpp : 185) STAGE == EC Threshold Finding (id: ec_threshold_finder) 81s 0:00:00.038 1M / 19M INFO General (kmer_coverage_model.cpp : 181) Kmer coverage valley at: 0 81s 0:00:00.039 1M / 19M INFO General (kmer_coverage_model.cpp : 201) K-mer histogram maximum: 7 81s 0:00:00.039 1M / 19M INFO General (kmer_coverage_model.cpp : 237) Estimated median coverage: 9. Coverage mad: 4.4478 81s 0:00:00.039 1M / 19M INFO General (kmer_coverage_model.cpp : 259) Fitting coverage model 81s 0:00:00.046 1M / 19M INFO General (kmer_coverage_model.cpp : 295) ... iteration 2 81s 0:00:00.065 1M / 19M INFO General (kmer_coverage_model.cpp : 295) ... iteration 4 81s 0:00:00.137 1M / 19M INFO General (kmer_coverage_model.cpp : 295) ... iteration 8 81s 0:00:00.276 1M / 19M INFO General (kmer_coverage_model.cpp : 295) ... iteration 16 81s 0:00:00.527 1M / 19M INFO General (kmer_coverage_model.cpp : 295) ... iteration 32 81s 0:00:00.658 1M / 19M INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 9.54532. Fitted coverage std. dev: 3.07466 81s 0:00:00.658 1M / 19M INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 0.997919 81s 0:00:00.658 1M / 19M INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 8 81s 0:00:00.658 1M / 19M INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 4 81s 0:00:00.658 1M / 19M INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 10027 81s 0:00:00.658 1M / 19M INFO General (genomic_info_filler.cpp : 55) Mean coverage was calculated as 9.54532 81s 0:00:00.658 1M / 19M INFO General (genomic_info_filler.cpp : 70) EC coverage threshold value was calculated as 4 81s 0:00:00.659 1M / 19M INFO General (genomic_info_filler.cpp : 71) Trusted kmer low bound: 0 81s 0:00:00.659 1M / 19M INFO StageManager (stage.cpp : 185) STAGE == Gap Closer (id: early_gapcloser) 81s 0:00:00.663 10M / 20M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 81s 0:00:00.663 10M / 20M INFO General (gap_closer.cpp : 101) Total edges in tip neighborhood: 88 out of 302, length: 2079 81s 0:00:00.663 10M / 20M INFO General (edge_index.hpp : 167) Using small index (max_id = 306) 81s 0:00:00.663 10M / 20M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices 81s 0:00:00.664 10M / 20M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 1674 kmers, 1992 bytes occupied (9.51971 bits per kmer). 81s 0:00:00.664 10M / 20M INFO General (edge_index_builders.hpp : 265) Collecting edge information from graph, this takes a while. 81s 0:00:00.671 10M / 20M INFO General (sequence_mapper_notifier.h: 95) Total 1997 reads processed 81s 0:00:00.672 10M / 20M INFO General (gap_closer.cpp : 452) Initializing gap closer 81s 0:00:00.672 10M / 20M INFO GapCloser (gap_closer.cpp : 359) Closing short gaps 81s 0:00:00.672 10M / 20M INFO GapCloser (gap_closer.cpp : 391) Closing short gaps complete: filled 0 gaps after checking 0 candidates 81s 0:00:00.672 10M / 20M INFO General (gap_closer.cpp : 456) Gap closer done 81s 0:00:00.672 1M / 20M INFO StageManager (stage.cpp : 185) STAGE == Raw Simplification (id: raw_simplification) 81s 0:00:00.672 1M / 20M INFO General (simplification.cpp : 127) PROCEDURE == Initial cleaning 81s 0:00:00.673 1M / 20M INFO General (simplification.cpp : 66) Most init cleaning disabled since detected mean 9.54532 was less than activation coverage 10 81s 0:00:00.673 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Self conjugate edge remover 81s 0:00:00.673 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Self conjugate edge remover triggered 0 times 81s 0:00:00.673 1M / 20M INFO StageManager (stage.cpp : 185) STAGE == Simplification (id: simplification) 81s 0:00:00.673 1M / 20M INFO General (simplification.cpp : 368) Graph simplification started 81s 0:00:00.673 1M / 20M INFO General (graph_simplification.hpp : 634) Creating parallel br instance 81s 0:00:00.673 1M / 20M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 1 81s 0:00:00.673 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 81s 0:00:00.673 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 68 times 81s 0:00:00.673 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 81s 0:00:00.673 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 2 times 81s 0:00:00.673 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 81s 0:00:00.673 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 0 times 81s 0:00:00.673 1M / 20M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 2 81s 0:00:00.673 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 81s 0:00:00.673 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 81s 0:00:00.673 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 81s 0:00:00.673 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 81s 0:00:00.673 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 81s 0:00:00.673 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 0 times 81s 0:00:00.673 1M / 20M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 3 81s 0:00:00.673 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 81s 0:00:00.673 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 81s 0:00:00.673 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 81s 0:00:00.673 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 81s 0:00:00.673 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 81s 0:00:00.673 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 0 times 81s 0:00:00.673 1M / 20M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 4 81s 0:00:00.673 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 81s 0:00:00.673 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 81s 0:00:00.673 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 81s 0:00:00.673 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 81s 0:00:00.673 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 81s 0:00:00.673 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 0 times 81s 0:00:00.673 1M / 20M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 5 81s 0:00:00.673 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 81s 0:00:00.673 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 81s 0:00:00.673 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 81s 0:00:00.673 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 81s 0:00:00.673 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 81s 0:00:00.673 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 0 times 81s 0:00:00.673 1M / 20M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 6 81s 0:00:00.673 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 81s 0:00:00.673 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 81s 0:00:00.673 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 81s 0:00:00.673 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 81s 0:00:00.673 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 81s 0:00:00.673 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 0 times 81s 0:00:00.673 1M / 20M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 7 81s 0:00:00.673 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 81s 0:00:00.673 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 81s 0:00:00.673 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 81s 0:00:00.673 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 81s 0:00:00.673 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 81s 0:00:00.673 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 0 times 81s 0:00:00.673 1M / 20M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 8 81s 0:00:00.673 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 81s 0:00:00.673 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 81s 0:00:00.673 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 81s 0:00:00.673 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 81s 0:00:00.673 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 81s 0:00:00.673 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 0 times 81s 0:00:00.673 1M / 20M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 9 81s 0:00:00.673 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 81s 0:00:00.673 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 81s 0:00:00.673 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 81s 0:00:00.673 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 81s 0:00:00.673 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 81s 0:00:00.673 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 0 times 81s 0:00:00.673 1M / 20M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 10 81s 0:00:00.673 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 81s 0:00:00.673 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 81s 0:00:00.673 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 81s 0:00:00.673 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 81s 0:00:00.673 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 81s 0:00:00.673 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 0 times 81s 0:00:00.673 1M / 20M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 11 81s 0:00:00.673 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 81s 0:00:00.673 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 81s 0:00:00.673 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 81s 0:00:00.673 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 81s 0:00:00.673 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 81s 0:00:00.673 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 0 times 81s 0:00:00.673 1M / 20M INFO StageManager (stage.cpp : 185) STAGE == Gap Closer (id: late_gapcloser) 81s 0:00:00.674 10M / 20M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 81s 0:00:00.674 10M / 20M INFO General (gap_closer.cpp : 101) Total edges in tip neighborhood: 20 out of 22, length: 2700 81s 0:00:00.674 10M / 20M INFO General (edge_index.hpp : 167) Using small index (max_id = 306) 81s 0:00:00.674 10M / 20M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices 81s 0:00:00.676 10M / 20M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 1350 kmers, 1744 bytes occupied (10.3348 bits per kmer). 81s 0:00:00.676 10M / 20M INFO General (edge_index_builders.hpp : 265) Collecting edge information from graph, this takes a while. 81s 0:00:00.686 10M / 20M INFO General (sequence_mapper_notifier.h: 95) Total 1997 reads processed 81s 0:00:00.687 10M / 20M INFO General (gap_closer.cpp : 452) Initializing gap closer 81s 0:00:00.687 10M / 20M INFO GapCloser (gap_closer.cpp : 359) Closing short gaps 81s 0:00:00.687 10M / 20M INFO GapCloser (gap_closer.cpp : 391) Closing short gaps complete: filled 0 gaps after checking 0 candidates 81s 0:00:00.687 10M / 20M INFO General (gap_closer.cpp : 456) Gap closer done 81s 0:00:00.687 1M / 20M INFO StageManager (stage.cpp : 185) STAGE == Simplification Cleanup (id: simplification_cleanup) 81s 0:00:00.687 1M / 20M INFO General (simplification.cpp : 176) PROCEDURE == Post simplification 81s 0:00:00.687 1M / 20M INFO General (graph_simplification.hpp : 448) Disconnection of relatively low covered edges disabled 81s 0:00:00.687 1M / 20M INFO General (graph_simplification.hpp : 485) Complex tip clipping disabled 81s 0:00:00.687 1M / 20M INFO General (graph_simplification.hpp : 634) Creating parallel br instance 81s 0:00:00.687 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 81s 0:00:00.687 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 81s 0:00:00.687 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 81s 0:00:00.687 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 81s 0:00:00.687 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 81s 0:00:00.687 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 81s 0:00:00.687 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 81s 0:00:00.687 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 81s 0:00:00.687 1M / 20M INFO General (simplification.cpp : 327) Disrupting self-conjugate edges 81s 0:00:00.687 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Removing isolated edges 81s 0:00:00.687 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Removing isolated edges triggered 9 times 81s 0:00:00.687 1M / 20M INFO General (simplification.cpp : 495) After simplification: 81s 0:00:00.687 1M / 20M INFO General (simplification.cpp : 496) Average coverage = 16.8919 81s 0:00:00.687 1M / 20M INFO General (simplification.cpp : 497) Total length = 10557 81s 0:00:00.687 1M / 20M INFO General (simplification.cpp : 498) Median edge length: 9612 81s 0:00:00.687 1M / 20M INFO General (simplification.cpp : 499) Edges: 4 81s 0:00:00.687 1M / 20M INFO General (simplification.cpp : 500) Vertices: 6 81s 0:00:00.687 1M / 20M INFO StageManager (stage.cpp : 185) STAGE == Contig Output (id: contig_output) 81s 0:00:00.687 1M / 20M INFO General (read_converter.cpp : 107) Outputting contigs to /tmp/tmp.cMLX1ajB23/spades_test/K55/simplified_contigs 81s 0:00:00.688 3M / 20M INFO General (binary_converter.cpp : 111) 2 reads written 81s 0:00:00.688 1M / 20M INFO General (pipeline.cpp : 287) SPAdes finished 81s 0:00:00.688 1M / 20M INFO General (main.cpp : 136) Assembling time: 0 hours 0 minutes 0 seconds 81s 81s ===== K55 finished. 81s 81s 81s ===== K77 started. 81s 81s 81s == Running: /usr/libexec/spades/spades-core /tmp/tmp.cMLX1ajB23/spades_test/K77/configs/config.info /tmp/tmp.cMLX1ajB23/spades_test/K77/configs/plasmid_mode.info 81s 81s 0:00:00.000 1M / 19M INFO General (main.cpp : 99) Loaded config from /tmp/tmp.cMLX1ajB23/spades_test/K77/configs/config.info 81s 0:00:00.000 1M / 19M INFO General (main.cpp : 99) Loaded config from /tmp/tmp.cMLX1ajB23/spades_test/K77/configs/plasmid_mode.info 81s 0:00:00.000 1M / 19M INFO General (memory_limit.cpp : 54) Memory limit set to 3 Gb 81s 0:00:00.000 1M / 19M INFO General (main.cpp : 107) Starting SPAdes, built from N/A, git revision N/A 81s 0:00:00.000 1M / 19M INFO General (main.cpp : 108) Maximum k-mer length: 128 81s 0:00:00.000 1M / 19M INFO General (main.cpp : 109) Assembling dataset (/tmp/tmp.cMLX1ajB23/spades_test/dataset.info) with K=77 81s 0:00:00.000 1M / 19M INFO General (main.cpp : 110) Maximum # of threads to use (adjusted due to OMP capabilities): 2 81s 0:00:00.000 1M / 19M INFO General (pipeline.cpp : 212) SPAdes started 81s 0:00:00.000 1M / 19M INFO General (pipeline.cpp : 225) Starting from stage: read_conversion 81s 0:00:00.000 1M / 19M INFO General (pipeline.cpp : 231) Two-step repeat resolution disabled 81s 0:00:00.000 1M / 19M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 81s 0:00:00.000 1M / 19M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 81s 0:00:00.000 1M / 19M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 81s 0:00:00.000 1M / 19M INFO General (pipeline.cpp : 242) Will need read mapping, kmer mapper will be attached 81s 0:00:00.000 1M / 19M INFO StageManager (stage.cpp : 185) STAGE == Binary Read Conversion (id: read_conversion) 81s 0:00:00.000 1M / 19M INFO General (read_converter.cpp : 53) Binary reads detected 81s 0:00:00.000 1M / 19M INFO StageManager (stage.cpp : 185) STAGE == de Bruijn graph construction (id: construction) 81s 0:00:00.000 1M / 19M INFO General (construction.cpp : 118) Contigs from previous K will be used: /tmp/tmp.cMLX1ajB23/spades_test/K55/simplified_contigs 81s 0:00:00.000 1M / 19M INFO General (construction.cpp : 153) Max read length 100 81s 0:00:00.000 1M / 19M INFO General (construction.cpp : 159) Average read length 100 81s 0:00:00.000 1M / 19M INFO General (stage.cpp : 117) PROCEDURE == k+1-mer counting (id: construction:kpomer_counting) 81s 0:00:00.000 1M / 19M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 20 files using 2 threads. This might take a while. 81s 0:00:00.000 1M / 19M INFO General (file_limit.hpp : 42) Open file limit set to 1024 81s 0:00:00.000 1M / 19M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 0.49997 Gb 81s 0:00:00.000 1M / 19M INFO General (kmer_splitter.hpp : 101) Using cell size of 1118414 81s 0:00:00.007 1M / 19M INFO General (kmer_splitters.hpp : 131) Used 7998 reads 81s 0:00:00.008 1M / 19M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. 81s 0:00:00.009 1M / 19M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 11764 kmers in total. 81s 0:00:00.009 1M / 19M INFO General (stage.cpp : 117) PROCEDURE == Extension index construction (id: construction:extension_index_construction) 81s 0:00:00.010 1M / 19M INFO K-mer Index Building (kmer_index_builder.hpp : 438) Building kmer index 81s 0:00:00.010 1M / 19M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 20 files using 2 threads. This might take a while. 81s 0:00:00.010 1M / 19M INFO General (file_limit.hpp : 42) Open file limit set to 1024 81s 0:00:00.010 1M / 19M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 0.499967 Gb 81s 0:00:00.010 1M / 19M INFO General (kmer_splitter.hpp : 101) Using cell size of 1118408 81s 0:00:00.012 1161M / 1161M INFO General (kmer_splitters.hpp : 194) Processed 11764 kmers 81s 0:00:00.012 1161M / 1161M INFO General (kmer_splitters.hpp : 199) Used 11764 kmers. 81s 0:00:00.012 1M / 19M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. 81s 0:00:00.014 1M / 19M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 11791 kmers in total. 81s 0:00:00.014 1M / 19M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices 81s 0:00:00.016 1M / 19M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 11791 kmers, 24024 bytes occupied (16.2999 bits per kmer). 81s 0:00:00.016 1M / 19M INFO General (kmer_index_builder.hpp : 169) Merging final buckets. 81s 0:00:00.017 1M / 19M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 100) Building k-mer extensions from k+1-mers 81s 0:00:00.019 1M / 19M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 105) Building k-mer extensions from k+1-mers finished. 81s 0:00:00.019 1M / 19M INFO General (stage.cpp : 117) PROCEDURE == Condensing graph (id: construction:graph_condensing) 81s 0:00:00.019 1M / 19M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths 81s 0:00:00.021 1M / 19M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 135 sequences extracted 81s 0:00:00.023 1M / 19M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops 81s 0:00:00.023 1M / 19M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 0 loops collected 81s 0:00:00.023 1M / 19M INFO General (debruijn_graph_constructor: 487) Total 270 edges to create 81s 0:00:00.023 1M / 19M INFO General (debruijn_graph_constructor: 489) Collecting link records 81s 0:00:00.023 1M / 19M INFO General (debruijn_graph_constructor: 491) Ordering link records 81s 0:00:00.023 1M / 19M INFO General (debruijn_graph_constructor: 493) Sorting done 81s 0:00:00.024 1M / 19M INFO General (debruijn_graph_constructor: 503) Total 162 vertices to create 81s 0:00:00.024 1M / 19M INFO General (debruijn_graph_constructor: 506) Connecting the graph 81s 0:00:00.024 1M / 19M INFO General (stage.cpp : 117) PROCEDURE == Filling coverage indices (PHM) (id: construction:coverage_filling_phm) 81s 0:00:00.024 1M / 19M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices 81s 0:00:00.025 1M / 19M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 11764 kmers, 24008 bytes occupied (16.3264 bits per kmer). 81s 0:00:00.025 1M / 19M INFO General (coverage_hash_map_builder.: 47) Collecting k-mer coverage information from reads, this takes a while. 81s 0:00:00.031 1M / 19M INFO General (construction.cpp : 430) Filling coverage and flanking coverage from PHM 81s 0:00:00.032 1M / 19M INFO StageManager (stage.cpp : 185) STAGE == EC Threshold Finding (id: ec_threshold_finder) 81s 0:00:00.032 1M / 19M INFO General (kmer_coverage_model.cpp : 181) Kmer coverage valley at: 0 81s 0:00:00.032 1M / 19M INFO General (kmer_coverage_model.cpp : 201) K-mer histogram maximum: 3 81s 0:00:00.033 1M / 19M INFO General (kmer_coverage_model.cpp : 237) Estimated median coverage: 4. Coverage mad: 2.9652 81s 0:00:00.033 1M / 19M INFO General (kmer_coverage_model.cpp : 259) Fitting coverage model 81s 0:00:00.037 1M / 19M INFO General (kmer_coverage_model.cpp : 295) ... iteration 2 81s 0:00:00.046 1M / 19M INFO General (kmer_coverage_model.cpp : 295) ... iteration 4 82s 0:00:00.084 1M / 19M INFO General (kmer_coverage_model.cpp : 295) ... iteration 8 82s 0:00:00.154 1M / 19M INFO General (kmer_coverage_model.cpp : 295) ... iteration 16 82s 0:00:00.275 1M / 19M INFO General (kmer_coverage_model.cpp : 295) ... iteration 32 82s 0:00:00.510 1M / 19M INFO General (kmer_coverage_model.cpp : 295) ... iteration 64 82s 0:00:00.546 1M / 19M INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 5.11178. Fitted coverage std. dev: 2.00854 82s 0:00:00.546 1M / 19M INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 0.952181 82s 0:00:00.547 1M / 19M WARN General (kmer_coverage_model.cpp : 366) Failed to determine erroneous kmer threshold. Threshold set to: 0 82s 0:00:00.547 1M / 19M INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 0 82s 0:00:00.547 1M / 19M INFO General (genomic_info_filler.cpp : 57) Failed to estimate mean coverage 82s 0:00:00.547 1M / 19M INFO General (genomic_info_filler.cpp : 70) EC coverage threshold value was calculated as 0 82s 0:00:00.547 1M / 19M INFO General (genomic_info_filler.cpp : 71) Trusted kmer low bound: 0 82s 0:00:00.547 1M / 19M INFO StageManager (stage.cpp : 185) STAGE == Gap Closer (id: early_gapcloser) 82s 0:00:00.551 10M / 20M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 82s 0:00:00.551 10M / 20M INFO General (gap_closer.cpp : 101) Total edges in tip neighborhood: 110 out of 270, length: 1983 82s 0:00:00.552 10M / 20M INFO General (edge_index.hpp : 167) Using small index (max_id = 274) 82s 0:00:00.552 10M / 20M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices 82s 0:00:00.552 10M / 20M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 1335 kmers, 1736 bytes occupied (10.403 bits per kmer). 82s 0:00:00.552 10M / 20M INFO General (edge_index_builders.hpp : 265) Collecting edge information from graph, this takes a while. 82s 0:00:00.556 10M / 20M INFO General (sequence_mapper_notifier.h: 95) Total 1997 reads processed 82s 0:00:00.557 10M / 20M INFO General (gap_closer.cpp : 452) Initializing gap closer 82s 0:00:00.557 10M / 20M INFO GapCloser (gap_closer.cpp : 359) Closing short gaps 82s 0:00:00.557 10M / 20M INFO GapCloser (gap_closer.cpp : 391) Closing short gaps complete: filled 0 gaps after checking 0 candidates 82s 0:00:00.557 10M / 20M INFO General (gap_closer.cpp : 456) Gap closer done 82s 0:00:00.558 1M / 20M INFO StageManager (stage.cpp : 185) STAGE == Raw Simplification (id: raw_simplification) 82s 0:00:00.558 1M / 20M INFO General (simplification.cpp : 127) PROCEDURE == Initial cleaning 82s 0:00:00.558 1M / 20M INFO General (simplification.cpp : 66) Most init cleaning disabled since detected mean 0 was less than activation coverage 10 82s 0:00:00.558 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Self conjugate edge remover 82s 0:00:00.558 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Self conjugate edge remover triggered 0 times 82s 0:00:00.558 1M / 20M INFO StageManager (stage.cpp : 185) STAGE == Simplification (id: simplification) 82s 0:00:00.558 1M / 20M INFO General (simplification.cpp : 368) Graph simplification started 82s 0:00:00.558 1M / 20M INFO General (graph_simplification.hpp : 634) Creating parallel br instance 82s 0:00:00.558 1M / 20M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 1 82s 0:00:00.558 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 82s 0:00:00.558 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 50 times 82s 0:00:00.558 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 82s 0:00:00.558 1M / 21M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 2 times 82s 0:00:00.558 1M / 21M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 82s 0:00:00.558 1M / 21M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 0 times 82s 0:00:00.558 1M / 21M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 2 82s 0:00:00.558 1M / 21M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 82s 0:00:00.558 1M / 21M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 82s 0:00:00.558 1M / 21M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 82s 0:00:00.558 1M / 21M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 82s 0:00:00.558 1M / 21M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 82s 0:00:00.558 1M / 21M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 0 times 82s 0:00:00.558 1M / 21M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 3 82s 0:00:00.558 1M / 21M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 82s 0:00:00.558 1M / 21M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 82s 0:00:00.558 1M / 21M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 82s 0:00:00.558 1M / 21M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 82s 0:00:00.558 1M / 21M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 82s 0:00:00.558 1M / 21M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 0 times 82s 0:00:00.558 1M / 21M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 4 82s 0:00:00.558 1M / 21M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 82s 0:00:00.558 1M / 21M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 82s 0:00:00.558 1M / 21M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 82s 0:00:00.558 1M / 21M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 82s 0:00:00.558 1M / 21M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 82s 0:00:00.558 1M / 21M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 0 times 82s 0:00:00.558 1M / 21M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 5 82s 0:00:00.558 1M / 21M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 82s 0:00:00.558 1M / 21M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 82s 0:00:00.558 1M / 21M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 82s 0:00:00.558 1M / 21M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 82s 0:00:00.558 1M / 21M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 82s 0:00:00.558 1M / 21M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 0 times 82s 0:00:00.558 1M / 21M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 6 82s 0:00:00.558 1M / 21M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 82s 0:00:00.558 1M / 21M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 82s 0:00:00.558 1M / 21M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 82s 0:00:00.558 1M / 21M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 82s 0:00:00.558 1M / 21M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 82s 0:00:00.558 1M / 21M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 0 times 82s 0:00:00.558 1M / 21M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 7 82s 0:00:00.558 1M / 21M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 82s 0:00:00.558 1M / 21M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 82s 0:00:00.558 1M / 21M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 82s 0:00:00.558 1M / 21M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 82s 0:00:00.558 1M / 21M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 82s 0:00:00.558 1M / 21M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 0 times 82s 0:00:00.558 1M / 21M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 8 82s 0:00:00.558 1M / 21M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 82s 0:00:00.558 1M / 21M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 82s 0:00:00.558 1M / 21M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 82s 0:00:00.558 1M / 21M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 82s 0:00:00.558 1M / 21M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 82s 0:00:00.558 1M / 21M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 0 times 82s 0:00:00.558 1M / 21M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 9 82s 0:00:00.558 1M / 21M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 82s 0:00:00.558 1M / 21M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 82s 0:00:00.558 1M / 21M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 82s 0:00:00.559 1M / 21M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 82s 0:00:00.559 1M / 21M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 82s 0:00:00.559 1M / 21M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 0 times 82s 0:00:00.559 1M / 21M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 10 82s 0:00:00.559 1M / 21M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 82s 0:00:00.559 1M / 21M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 82s 0:00:00.559 1M / 21M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 82s 0:00:00.559 1M / 21M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 82s 0:00:00.559 1M / 21M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 82s 0:00:00.559 1M / 21M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 0 times 82s 0:00:00.559 1M / 21M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 11 82s 0:00:00.559 1M / 21M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 82s 0:00:00.559 1M / 21M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 82s 0:00:00.559 1M / 21M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 82s 0:00:00.559 1M / 21M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 82s 0:00:00.559 1M / 21M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 82s 0:00:00.559 1M / 21M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 0 times 82s 0:00:00.559 1M / 21M INFO StageManager (stage.cpp : 185) STAGE == Gap Closer (id: late_gapcloser) 82s 0:00:00.559 10M / 21M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 82s 0:00:00.560 10M / 21M INFO General (gap_closer.cpp : 101) Total edges in tip neighborhood: 58 out of 60, length: 3188 82s 0:00:00.560 10M / 21M INFO General (edge_index.hpp : 167) Using small index (max_id = 274) 82s 0:00:00.561 10M / 21M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices 82s 0:00:00.561 10M / 21M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 1594 kmers, 1920 bytes occupied (9.63614 bits per kmer). 82s 0:00:00.561 10M / 21M INFO General (edge_index_builders.hpp : 265) Collecting edge information from graph, this takes a while. 82s 0:00:00.566 10M / 21M INFO General (sequence_mapper_notifier.h: 95) Total 1997 reads processed 82s 0:00:00.567 10M / 21M INFO General (gap_closer.cpp : 452) Initializing gap closer 82s 0:00:00.567 10M / 21M INFO GapCloser (gap_closer.cpp : 359) Closing short gaps 82s 0:00:00.567 10M / 21M INFO GapCloser (gap_closer.cpp : 391) Closing short gaps complete: filled 0 gaps after checking 0 candidates 82s 0:00:00.568 10M / 21M INFO General (gap_closer.cpp : 456) Gap closer done 82s 0:00:00.568 1M / 21M INFO StageManager (stage.cpp : 185) STAGE == Simplification Cleanup (id: simplification_cleanup) 82s 0:00:00.568 1M / 21M INFO General (simplification.cpp : 176) PROCEDURE == Post simplification 82s 0:00:00.568 1M / 21M INFO General (graph_simplification.hpp : 448) Disconnection of relatively low covered edges disabled 82s 0:00:00.568 1M / 21M INFO General (graph_simplification.hpp : 485) Complex tip clipping disabled 82s 0:00:00.568 1M / 21M INFO General (graph_simplification.hpp : 634) Creating parallel br instance 82s 0:00:00.568 1M / 21M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 82s 0:00:00.568 1M / 21M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 82s 0:00:00.568 1M / 21M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 82s 0:00:00.568 1M / 21M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 82s 0:00:00.568 1M / 21M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 82s 0:00:00.568 1M / 21M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 82s 0:00:00.568 1M / 21M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 82s 0:00:00.568 1M / 21M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 82s 0:00:00.568 1M / 21M INFO General (simplification.cpp : 327) Disrupting self-conjugate edges 82s 0:00:00.568 1M / 21M INFO Simplification (parallel_processing.hpp : 167) Running Removing isolated edges 82s 0:00:00.568 1M / 21M INFO Simplification (parallel_processing.hpp : 170) Removing isolated edges triggered 28 times 82s 0:00:00.568 1M / 21M INFO General (simplification.cpp : 495) After simplification: 82s 0:00:00.568 1M / 21M INFO General (simplification.cpp : 496) Average coverage = 8.62012 82s 0:00:00.568 1M / 21M INFO General (simplification.cpp : 497) Total length = 10535 82s 0:00:00.568 1M / 21M INFO General (simplification.cpp : 498) Median edge length: 9612 82s 0:00:00.568 1M / 21M INFO General (simplification.cpp : 499) Edges: 4 82s 0:00:00.568 1M / 21M INFO General (simplification.cpp : 500) Vertices: 6 82s 0:00:00.568 1M / 21M INFO StageManager (stage.cpp : 185) STAGE == Mismatch Correction (id: mismatch_correction) 82s 0:00:00.568 1M / 21M INFO General (graph_pack.cpp : 67) Index refill 82s 0:00:00.568 1M / 21M INFO General (edge_index.hpp : 156) Using small index (max_id = 274) 82s 0:00:00.569 1M / 21M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices 82s 0:00:00.571 1M / 21M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 10535 kmers, 8384 bytes occupied (6.36659 bits per kmer). 82s 0:00:00.571 1M / 21M INFO General (edge_index_builders.hpp : 252) Collecting edge information from graph, this takes a while. 82s 0:00:00.572 1M / 21M INFO General (graph_pack.cpp : 77) Normalizing k-mer map. Total 312 kmers to process 82s 0:00:00.572 1M / 21M INFO General (graph_pack.cpp : 79) Normalizing done 82s 0:00:00.572 1M / 21M INFO General (mismatch_correction.cpp : 400) Collect potential mismatches 82s 0:00:00.572 1M / 21M INFO General (mismatch_correction.cpp : 192) Total 2 edges (out of 4) with 4 potential mismatch positions (2 positions per edge) 82s 0:00:00.572 1M / 21M INFO General (mismatch_correction.cpp : 402) Potential mismatches collected 82s 0:00:00.580 1M / 21M INFO General (sequence_mapper_notifier.h: 95) Total 7994 reads processed 82s 0:00:00.580 1M / 21M INFO General (mismatch_correction.cpp : 395) All edges processed 82s 0:00:00.580 1M / 21M INFO General (mismatch_correction.cpp : 450) Corrected 0 nucleotides 82s 0:00:00.580 1M / 21M INFO StageManager (stage.cpp : 185) STAGE == Contig Output (id: contig_output) 82s 0:00:00.580 1M / 21M INFO General (contig_output.hpp : 16) Outputting contigs to /tmp/tmp.cMLX1ajB23/spades_test/K77/before_rr.fasta 82s 0:00:00.580 1M / 21M INFO General (contig_output_stage.cpp : 151) Writing GFA graph to /tmp/tmp.cMLX1ajB23/spades_test/K77/assembly_graph_after_simplification.gfa 82s 0:00:00.580 1M / 21M INFO StageManager (stage.cpp : 185) STAGE == Chromosome Removal (id: chromosome_removal) 82s 0:00:00.580 1M / 21M INFO ChromosomeRemoval (chromosome_removal.cpp : 18) Starting chromosomal removal procedure, external coverage limit set to 0, there are 6 vertices in graph 82s 0:00:00.580 1M / 21M INFO ChromosomeRemover (chromosome_remover.cpp : 96) Removing of long chromosomal edges started 82s 0:00:00.581 1M / 21M INFO General (coverage_uniformity_analyz: 25) genomic coverage is 4.66833 calculated of length 9612 82s 0:00:00.581 1M / 21M INFO ChromosomeRemover (chromosome_remover.cpp : 118) 0% of bases from long edges have coverage significantly different from median 82s 0:00:00.581 1M / 21M INFO ChromosomeRemover (chromosome_remover.cpp : 125) Connected components calculated 82s 0:00:00.581 1M / 21M INFO ChromosomeRemover (chromosome_remover.cpp : 149) Deleted 0 long edges 82s 0:00:00.581 1M / 21M INFO ChromosomeRemover (chromosome_remover.cpp : 183) Blocked vertices: 0 82s 0:00:00.581 1M / 21M INFO ChromosomeRemover (chromosome_remover.cpp : 96) Removing of long chromosomal edges started 82s 0:00:00.581 1M / 21M INFO ChromosomeRemover (chromosome_remover.cpp : 149) Deleted 0 long edges 82s 0:00:00.581 1M / 21M INFO ChromosomeRemover (chromosome_remover.cpp : 422) Before dead_end simplification 0 6 vertices in graph 82s 0:00:00.581 1M / 21M INFO ChromosomeRemover (chromosome_remover.cpp : 183) Blocked vertices: 0 82s 0:00:00.581 1M / 21M INFO ChromosomeRemover (chromosome_remover.cpp : 426) At iteration 0 graph was not changed 82s 0:00:00.581 1M / 21M INFO ChromosomeRemover (chromosome_remover.cpp : 427) 6 vertices left 82s 0:00:00.581 1M / 21M INFO ChromosomeRemover (chromosome_remover.cpp : 183) Blocked vertices: 0 82s 0:00:00.581 1M / 21M INFO ChromosomeRemover (chromosome_remover.cpp : 183) Blocked vertices: 0 82s 0:00:00.581 1M / 21M INFO ChromosomeRemover (chromosome_remover.cpp : 498) At iteration 1 of small components additional filtering graph was not changed 82s 0:00:00.581 1M / 21M INFO ChromosomeRemover (chromosome_remover.cpp : 502) After chromosome removal subroutine 2 vertices left 82s 0:00:00.581 1M / 21M INFO ChromosomeRemoval (chromosome_removal.cpp : 26) After chromosome removal: 82s 0:00:00.581 1M / 21M INFO ChromosomeRemoval (chromosome_removal.cpp : 27) Average coverage = 4.66833 82s 0:00:00.581 1M / 21M INFO ChromosomeRemoval (chromosome_removal.cpp : 28) Total length = 9612 82s 0:00:00.581 1M / 21M INFO ChromosomeRemoval (chromosome_removal.cpp : 29) Median edge length: 9612 82s 0:00:00.581 1M / 21M INFO ChromosomeRemoval (chromosome_removal.cpp : 30) Edges: 2 82s 0:00:00.581 1M / 21M INFO ChromosomeRemoval (chromosome_removal.cpp : 31) Vertices: 2 82s 0:00:00.581 1M / 21M INFO StageManager (stage.cpp : 185) STAGE == Paired Information Counting (id: late_pair_info_count) 82s 0:00:00.581 1M / 21M INFO General (graph_pack.cpp : 77) Normalizing k-mer map. Total 312 kmers to process 82s 0:00:00.581 1M / 21M INFO General (graph_pack.cpp : 79) Normalizing done 82s 0:00:00.581 1M / 21M INFO General (pair_info_count.cpp : 339) Min edge length for estimation: 9612 82s 0:00:00.581 1M / 21M INFO General (pair_info_count.cpp : 350) Estimating insert size for library #0 82s 0:00:00.581 1M / 21M INFO General (pair_info_count.cpp : 202) Estimating insert size (takes a while) 82s 0:00:00.601 49M / 60M INFO General (pair_info_count.cpp : 48) Selecting usual mapper 82s 0:00:00.626 49M / 60M INFO General (sequence_mapper_notifier.h: 95) Total 1997 reads processed 82s 0:00:00.691 49M / 60M INFO General (pair_info_count.cpp : 220) Edge pairs: 2 82s 0:00:00.691 49M / 60M INFO General (pair_info_count.cpp : 222) 953 paired reads (47.7216% of all) aligned to long edges 82s 0:00:00.691 1M / 60M INFO General (pair_info_count.cpp : 369) Insert size = 222.153, deviation = 49.6879, left quantile = 161, right quantile = 288, read length = 100 82s 0:00:00.691 1M / 60M INFO General (pair_info_count.cpp : 390) Filtering data for library #0 82s 0:00:00.691 1M / 60M INFO General (pair_info_count.cpp : 48) Selecting usual mapper 82s 0:00:00.695 1M / 60M INFO General (sequence_mapper_notifier.h: 95) Total 1997 reads processed 82s 0:00:00.695 1M / 60M INFO General (pair_info_count.cpp : 402) Mapping library #0 82s 0:00:00.695 1M / 60M INFO General (pair_info_count.cpp : 404) Mapping paired reads (takes a while) 82s 0:00:00.695 1M / 60M INFO General (pair_info_count.cpp : 299) Left insert size quantile 161, right insert size quantile 288, filtering threshold 2, rounding threshold 0 82s 0:00:00.696 10M / 60M INFO General (pair_info_count.cpp : 48) Selecting usual mapper 82s 0:00:00.700 10M / 60M INFO General (sequence_mapper_notifier.h: 95) Total 1997 reads processed 82s 0:00:00.701 1M / 60M INFO StageManager (stage.cpp : 185) STAGE == Distance Estimation (id: distance_estimation) 82s 0:00:00.701 1M / 60M INFO General (distance_estimation.cpp : 179) Processing library #0 82s 0:00:00.702 1M / 60M INFO General (distance_estimation.cpp : 150) Weight Filter Done 82s 0:00:00.702 1M / 60M INFO DistanceEstimator (distance_estimation.hpp : 116) Using SIMPLE distance estimator 82s 0:00:00.702 1M / 60M INFO General (distance_estimation.cpp : 37) Filtering info 82s 0:00:00.702 1M / 60M INFO General (pair_info_filters.hpp : 242) Start filtering; library index size: 4 82s 0:00:00.702 1M / 60M INFO General (pair_info_filters.hpp : 263) Done filtering; library index size: 4 82s 0:00:00.702 1M / 60M INFO General (distance_estimation.cpp : 156) Refining clustered pair information 82s 0:00:00.702 1M / 60M INFO General (distance_estimation.cpp : 158) The refining of clustered pair information has been finished 82s 0:00:00.702 1M / 60M INFO General (distance_estimation.cpp : 160) Improving paired information 82s 0:00:00.702 1M / 60M INFO PairInfoImprover (pair_info_improver.hpp : 104) Paired info stats: missing = 0; contradictional = 0 82s 0:00:00.702 1M / 60M INFO PairInfoImprover (pair_info_improver.hpp : 104) Paired info stats: missing = 0; contradictional = 0 82s 0:00:00.702 1M / 60M INFO General (distance_estimation.cpp : 104) Filling scaffolding index 82s 0:00:00.702 1M / 60M INFO DistanceEstimator (distance_estimation.hpp : 116) Using SMOOTHING distance estimator 82s 0:00:00.702 1M / 60M INFO General (distance_estimation.cpp : 37) Filtering info 82s 0:00:00.702 1M / 60M INFO General (pair_info_filters.hpp : 242) Start filtering; library index size: 2 82s 0:00:00.702 1M / 60M INFO General (pair_info_filters.hpp : 263) Done filtering; library index size: 2 82s 0:00:00.702 1M / 60M INFO General (distance_estimation.cpp : 186) Clearing raw paired index 82s 0:00:00.702 1M / 60M INFO StageManager (stage.cpp : 185) STAGE == Repeat Resolving (id: repeat_resolving) 82s 0:00:00.702 1M / 60M INFO General (repeat_resolving.cpp : 87) Using Path-Extend repeat resolving 82s 0:00:00.702 1M / 60M INFO General (launcher.cpp : 600) ExSPAnder repeat resolving tool started 82s 0:00:00.702 1M / 60M INFO General (launcher.cpp : 418) Creating main extenders, unique edge length = 2000 82s 0:00:00.703 1M / 60M INFO General (extenders_logic.cpp : 334) Estimated coverage of library #0 is 4.66833 82s 0:00:00.703 1M / 60M INFO General (extenders_logic.cpp : 345) Creating extender; library index size: 4 82s 0:00:00.703 1M / 60M INFO General (extenders_logic.cpp : 334) Estimated coverage of library #0 is 4.66833 82s 0:00:00.703 1M / 60M INFO General (extenders_logic.cpp : 345) Creating extender; library index size: 4 82s 0:00:00.703 1M / 61M INFO General (extenders_logic.cpp : 543) Using 1 paired-end library 82s 0:00:00.703 1M / 61M INFO General (extenders_logic.cpp : 544) Using 1 paired-end scaffolding library 82s 0:00:00.703 1M / 61M INFO General (extenders_logic.cpp : 545) Using 0 single read libraries 82s 0:00:00.703 1M / 61M INFO General (launcher.cpp : 447) Total number of extenders is 3 82s 0:00:00.703 1M / 61M INFO General (launcher.cpp : 250) Finalizing paths 82s 0:00:00.703 1M / 61M INFO General (launcher.cpp : 252) Deduplicating paths 82s 0:00:00.703 1M / 61M INFO General (launcher.cpp : 256) Paths deduplicated 82s 0:00:00.703 1M / 61M INFO PEResolver (pe_resolver.cpp : 60) Removing overlaps 82s 0:00:00.703 1M / 61M INFO PEResolver (pe_resolver.cpp : 63) Sorting paths 82s 0:00:00.703 1M / 61M INFO PEResolver (pe_resolver.cpp : 70) Marking overlaps 82s 0:00:00.703 1M / 61M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps 82s 0:00:00.703 1M / 61M INFO OverlapRemover (overlap_remover.hpp : 119) Marking remaining overlaps 82s 0:00:00.703 1M / 61M INFO PEResolver (pe_resolver.cpp : 73) Splitting paths 82s 0:00:00.703 1M / 61M INFO PEResolver (pe_resolver.cpp : 78) Deduplicating paths 82s 0:00:00.703 1M / 61M INFO PEResolver (pe_resolver.cpp : 80) Overlaps removed 82s 0:00:00.703 1M / 61M INFO General (launcher.cpp : 273) Paths finalized 82s 0:00:00.703 1M / 61M INFO General (launcher.cpp : 454) Closing gaps in paths 82s 0:00:00.703 1M / 61M INFO General (launcher.cpp : 484) Gap closing completed 82s 0:00:00.703 1M / 61M INFO General (launcher.cpp : 302) Traversing tandem repeats 82s 0:00:00.703 1M / 61M INFO General (launcher.cpp : 312) Traversed 0 loops 82s 0:00:00.703 1M / 61M INFO General (launcher.cpp : 250) Finalizing paths 82s 0:00:00.703 1M / 61M INFO General (launcher.cpp : 252) Deduplicating paths 82s 0:00:00.703 1M / 61M INFO General (launcher.cpp : 256) Paths deduplicated 82s 0:00:00.703 1M / 61M INFO PEResolver (pe_resolver.cpp : 60) Removing overlaps 82s 0:00:00.703 1M / 61M INFO PEResolver (pe_resolver.cpp : 63) Sorting paths 82s 0:00:00.703 1M / 61M INFO PEResolver (pe_resolver.cpp : 70) Marking overlaps 82s 0:00:00.703 1M / 61M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps 82s 0:00:00.703 1M / 61M INFO OverlapRemover (overlap_remover.hpp : 119) Marking remaining overlaps 82s 0:00:00.703 1M / 61M INFO PEResolver (pe_resolver.cpp : 73) Splitting paths 82s 0:00:00.703 1M / 61M INFO PEResolver (pe_resolver.cpp : 78) Deduplicating paths 82s 0:00:00.703 1M / 61M INFO PEResolver (pe_resolver.cpp : 80) Overlaps removed 82s 0:00:00.703 1M / 61M INFO General (launcher.cpp : 273) Paths finalized 82s 0:00:00.703 1M / 61M INFO General (launcher.cpp : 664) ExSPAnder repeat resolving tool finished 82s 0:00:00.703 1M / 61M INFO StageManager (stage.cpp : 185) STAGE == Contig Output (id: contig_output) 82s 0:00:00.703 1M / 61M INFO General (contig_output.hpp : 16) Outputting contigs to /tmp/tmp.cMLX1ajB23/spades_test/K77/before_rr.fasta 82s 0:00:00.703 1M / 61M INFO General (contig_output_stage.cpp : 151) Writing GFA graph to /tmp/tmp.cMLX1ajB23/spades_test/K77/assembly_graph_with_scaffolds.gfa 82s 0:00:00.703 1M / 61M INFO General (contig_output_stage.cpp : 165) Outputting FastG graph to /tmp/tmp.cMLX1ajB23/spades_test/K77/assembly_graph.fastg 82s 0:00:00.703 1M / 61M INFO General (contig_output_stage.cpp : 196) Breaking scaffolds 82s 0:00:00.703 1M / 61M INFO General (contig_output_stage.cpp : 98) Outputting contigs to /tmp/tmp.cMLX1ajB23/spades_test/K77/final_contigs.fasta 82s 0:00:00.703 1M / 61M INFO General (contig_output_stage.cpp : 104) Outputting FastG paths to /tmp/tmp.cMLX1ajB23/spades_test/K77/final_contigs.paths 82s 0:00:00.703 1M / 61M INFO General (contig_output_stage.cpp : 98) Outputting contigs to /tmp/tmp.cMLX1ajB23/spades_test/K77/scaffolds.fasta 82s 0:00:00.704 1M / 61M INFO General (contig_output_stage.cpp : 104) Outputting FastG paths to /tmp/tmp.cMLX1ajB23/spades_test/K77/scaffolds.paths 82s 0:00:00.704 1M / 61M INFO General (contig_output_stage.cpp : 111) Populating GFA with scaffold paths 82s 0:00:00.704 1M / 61M INFO General (pipeline.cpp : 287) SPAdes finished 82s 0:00:00.704 1M / 61M INFO General (main.cpp : 136) Assembling time: 0 hours 0 minutes 0 seconds 82s 82s ===== K77 finished. 82s 82s 82s ===== Copy files started. 82s 82s 82s == Running: /usr/bin/python3 /usr/share/spades/spades_pipeline/scripts/copy_files.py /tmp/tmp.cMLX1ajB23/spades_test/K77/before_rr.fasta /tmp/tmp.cMLX1ajB23/spades_test/before_rr.fasta /tmp/tmp.cMLX1ajB23/spades_test/K77/assembly_graph_after_simplification.gfa /tmp/tmp.cMLX1ajB23/spades_test/assembly_graph_after_simplification.gfa /tmp/tmp.cMLX1ajB23/spades_test/K77/final_contigs.fasta /tmp/tmp.cMLX1ajB23/spades_test/contigs.fasta /tmp/tmp.cMLX1ajB23/spades_test/K77/first_pe_contigs.fasta /tmp/tmp.cMLX1ajB23/spades_test/first_pe_contigs.fasta /tmp/tmp.cMLX1ajB23/spades_test/K77/strain_graph.gfa /tmp/tmp.cMLX1ajB23/spades_test/strain_graph.gfa /tmp/tmp.cMLX1ajB23/spades_test/K77/scaffolds.fasta /tmp/tmp.cMLX1ajB23/spades_test/scaffolds.fasta /tmp/tmp.cMLX1ajB23/spades_test/K77/scaffolds.paths /tmp/tmp.cMLX1ajB23/spades_test/scaffolds.paths /tmp/tmp.cMLX1ajB23/spades_test/K77/assembly_graph_with_scaffolds.gfa /tmp/tmp.cMLX1ajB23/spades_test/assembly_graph_with_scaffolds.gfa /tmp/tmp.cMLX1ajB23/spades_test/K77/assembly_graph.fastg /tmp/tmp.cMLX1ajB23/spades_test/assembly_graph.fastg /tmp/tmp.cMLX1ajB23/spades_test/K77/final_contigs.paths /tmp/tmp.cMLX1ajB23/spades_test/contigs.paths 82s 82s 82s ===== Copy files finished. 82s 82s 82s ===== Assembling finished. 82s 82s 82s ===== Check test started. 82s 82s 82s == Running: /usr/bin/python3 /usr/share/spades/spades_pipeline/scripts/check_test_script.py --mode plasmid --result_contigs_filename /tmp/tmp.cMLX1ajB23/spades_test/contigs.fasta --result_scaffolds_filename /tmp/tmp.cMLX1ajB23/spades_test/scaffolds.fasta 82s 82s ========= TEST PASSED CORRECTLY. 82s 82s ===== Check test finished. 82s 82s 82s ===== Breaking scaffolds started. 82s 82s 82s == Running: /usr/bin/python3 /usr/share/spades/spades_pipeline/scripts/breaking_scaffolds_script.py --result_scaffolds_filename /tmp/tmp.cMLX1ajB23/spades_test/scaffolds.fasta --misc_dir /tmp/tmp.cMLX1ajB23/spades_test/misc --threshold_for_breaking_scaffolds 3 82s 82s 82s ===== Breaking scaffolds finished. 82s 82s 82s ===== Terminate started. 82s 82s 82s ===== Terminate finished. 82s 82s * Corrected reads are in /tmp/tmp.cMLX1ajB23/spades_test/corrected/ 82s * Assembled contigs are in /tmp/tmp.cMLX1ajB23/spades_test/contigs.fasta 82s * Assembled scaffolds are in /tmp/tmp.cMLX1ajB23/spades_test/scaffolds.fasta 82s * Paths in the assembly graph corresponding to the contigs are in /tmp/tmp.cMLX1ajB23/spades_test/contigs.paths 82s * Paths in the assembly graph corresponding to the scaffolds are in /tmp/tmp.cMLX1ajB23/spades_test/scaffolds.paths 82s * Assembly graph is in /tmp/tmp.cMLX1ajB23/spades_test/assembly_graph.fastg 82s * Assembly graph in GFA format is in /tmp/tmp.cMLX1ajB23/spades_test/assembly_graph_with_scaffolds.gfa 82s 82s ======= SPAdes pipeline finished WITH WARNINGS! 82s 82s === Error correction and assembling warnings: 82s * 0:00:00.547 1M / 19M WARN General (kmer_coverage_model.cpp : 366) Failed to determine erroneous kmer threshold. Threshold set to: 0 82s ======= Warnings saved to /tmp/tmp.cMLX1ajB23/spades_test/warnings.log 82s 82s SPAdes log can be found here: /tmp/tmp.cMLX1ajB23/spades_test/spades.log 82s 82s Thank you for using SPAdes! 82s + rnaspades --test 82s Command line: /usr/libexec/spades/rnaspades.py --test 82s 82s System information: 82s SPAdes version: 3.15.5 82s Python version: 3.13.3 82s OS: Linux-6.14.0-15-generic-x86_64-with-glibc2.41 82s 82s Output dir: /tmp/tmp.cMLX1ajB23/spades_test 82s Debug mode is turned OFF 82s 82s Dataset parameters: 82s RNA-seq mode 82s Reads: 82s Library number: 1, library type: paired-end 82s orientation: fr 82s left reads: ['/usr/share/spades/test_dataset/ecoli_1K_1.fq.gz'] 82s right reads: ['/usr/share/spades/test_dataset/ecoli_1K_2.fq.gz'] 82s interlaced reads: not specified 82s single reads: not specified 82s merged reads: not specified 82s Assembly parameters: 82s k: automatic selection based on read length 82s Repeat resolution is enabled 82s Mismatch careful mode is turned OFF 82s MismatchCorrector will be SKIPPED 82s Coverage cutoff is turned OFF 82s Other parameters: 82s Dir for temp files: /tmp/tmp.cMLX1ajB23/spades_test/tmp 82s Threads: 16 82s Memory limit (in Gb): 3 82s 82s 82s ======= SPAdes pipeline started. Log can be found here: /tmp/tmp.cMLX1ajB23/spades_test/spades.log 82s 82s /usr/share/spades/test_dataset/ecoli_1K_1.fq.gz: max reads length: 100 82s /usr/share/spades/test_dataset/ecoli_1K_2.fq.gz: max reads length: 100 82s 82s Reads length: 100 82s 82s K values to be used: [33, 49] 82s 82s ===== Before start started. 82s 82s 82s ===== Assembling started. 82s 82s 82s ===== K33 started. 82s 82s 82s == Running: /usr/libexec/spades/spades-core /tmp/tmp.cMLX1ajB23/spades_test/K33/configs/config.info /tmp/tmp.cMLX1ajB23/spades_test/K33/configs/mda_mode.info /tmp/tmp.cMLX1ajB23/spades_test/K33/configs/rna_mode.info 82s 82s 0:00:00.000 1M / 19M INFO General (main.cpp : 99) Loaded config from /tmp/tmp.cMLX1ajB23/spades_test/K33/configs/config.info 82s 0:00:00.000 1M / 19M INFO General (main.cpp : 99) Loaded config from /tmp/tmp.cMLX1ajB23/spades_test/K33/configs/mda_mode.info 82s 0:00:00.000 1M / 19M INFO General (main.cpp : 99) Loaded config from /tmp/tmp.cMLX1ajB23/spades_test/K33/configs/rna_mode.info 82s 0:00:00.000 1M / 19M INFO General (memory_limit.cpp : 54) Memory limit set to 3 Gb 82s 0:00:00.000 1M / 19M INFO General (main.cpp : 107) Starting SPAdes, built from N/A, git revision N/A 82s 0:00:00.000 1M / 19M INFO General (main.cpp : 108) Maximum k-mer length: 128 82s 0:00:00.000 1M / 19M INFO General (main.cpp : 109) Assembling dataset (/tmp/tmp.cMLX1ajB23/spades_test/dataset.info) with K=33 82s 0:00:00.000 1M / 19M INFO General (main.cpp : 110) Maximum # of threads to use (adjusted due to OMP capabilities): 2 82s 0:00:00.000 1M / 19M INFO General (pipeline.cpp : 212) SPAdes started 82s 0:00:00.000 1M / 19M INFO General (pipeline.cpp : 225) Starting from stage: read_conversion 82s 0:00:00.000 1M / 19M INFO General (pipeline.cpp : 231) Two-step repeat resolution disabled 82s 0:00:00.000 1M / 19M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 82s 0:00:00.000 1M / 19M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 82s 0:00:00.000 1M / 19M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 82s 0:00:00.000 1M / 19M INFO StageManager (stage.cpp : 185) STAGE == Binary Read Conversion (id: read_conversion) 82s 0:00:00.000 1M / 19M INFO General (read_converter.cpp : 72) Converting reads to binary format for library #0 (takes a while) 82s 0:00:00.000 1M / 19M INFO General (read_converter.cpp : 73) Converting paired reads 82s 0:00:00.008 63M / 63M INFO General (binary_converter.cpp : 111) 2054 reads written 82s 0:00:00.008 41M / 41M INFO General (read_converter.cpp : 86) Converting single reads 82s 0:00:00.008 51M / 51M INFO General (binary_converter.cpp : 111) 0 reads written 82s 0:00:00.008 41M / 41M INFO General (read_converter.cpp : 92) Converting merged reads 82s 0:00:00.008 51M / 51M INFO General (binary_converter.cpp : 111) 0 reads written 82s 0:00:00.008 1M / 19M INFO StageManager (stage.cpp : 185) STAGE == de Bruijn graph construction (id: construction) 82s 0:00:00.008 1M / 19M INFO General (construction.cpp : 153) Max read length 100 82s 0:00:00.008 1M / 19M INFO General (construction.cpp : 159) Average read length 86.1611 82s 0:00:00.008 1M / 19M INFO General (stage.cpp : 117) PROCEDURE == k+1-mer counting (id: construction:kpomer_counting) 82s 0:00:00.008 1M / 19M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 20 files using 2 threads. This might take a while. 82s 0:00:00.009 1M / 19M INFO General (file_limit.hpp : 42) Open file limit set to 1024 82s 0:00:00.009 1M / 19M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 0.499973 Gb 82s 0:00:00.009 1M / 19M INFO General (kmer_splitter.hpp : 101) Using cell size of 1677631 82s 0:00:00.017 1M / 19M INFO General (kmer_splitters.hpp : 131) Used 8216 reads 82s 0:00:00.017 1M / 19M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. 82s 0:00:00.018 1M / 19M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 974 kmers in total. 82s 0:00:00.018 1M / 19M INFO General (stage.cpp : 117) PROCEDURE == Extension index construction (id: construction:extension_index_construction) 82s 0:00:00.019 1M / 19M INFO K-mer Index Building (kmer_index_builder.hpp : 438) Building kmer index 82s 0:00:00.019 1M / 19M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 20 files using 2 threads. This might take a while. 82s 0:00:00.019 1M / 19M INFO General (file_limit.hpp : 42) Open file limit set to 1024 82s 0:00:00.019 1M / 19M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 0.49997 Gb 82s 0:00:00.019 1M / 19M INFO General (kmer_splitter.hpp : 101) Using cell size of 1677622 82s 0:00:00.020 1161M / 1161M INFO General (kmer_splitters.hpp : 199) Used 974 kmers. 82s 0:00:00.020 1M / 19M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. 82s 0:00:00.022 1M / 19M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 975 kmers in total. 82s 0:00:00.022 1M / 19M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices 82s 0:00:00.023 1M / 19M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 975 kmers, 16392 bytes occupied (134.498 bits per kmer). 82s 0:00:00.023 1M / 19M INFO General (kmer_index_builder.hpp : 169) Merging final buckets. 82s 0:00:00.024 1M / 19M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 100) Building k-mer extensions from k+1-mers 82s 0:00:00.024 1M / 19M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 105) Building k-mer extensions from k+1-mers finished. 82s 0:00:00.025 1M / 19M INFO General (stage.cpp : 117) PROCEDURE == Early A/T remover (id: construction:early_at_remover) 82s 0:00:00.025 1M / 19M INFO Early A/T remover (early_simplification.hpp : 176) Remove short poly A/T edges 82s 0:00:00.025 1M / 19M INFO Early A/T remover (early_simplification.hpp : 254) Links removed: 0 82s 0:00:00.025 1M / 19M INFO Early A/T remover (early_simplification.hpp : 179) 0 34-mers were removed by early poly A/T remover 82s 0:00:00.025 1M / 19M INFO Early A/T remover (early_simplification.hpp : 262) Remove poly A/T tips 82s 0:00:00.025 1M / 19M INFO Early A/T remover (early_simplification.hpp : 331) Clipped tips: 0 82s 0:00:00.025 1M / 19M INFO Early A/T remover (early_simplification.hpp : 265) 0 34-mers were removed by early poly A/T tip clipper 82s 0:00:00.025 1M / 19M INFO General (stage.cpp : 117) PROCEDURE == Early tip clipping (id: construction:early_tip_clipper) 82s 0:00:00.025 1M / 19M INFO General (construction.cpp : 301) Early tip clipper length bound set as (RL - K) 82s 0:00:00.025 1M / 19M INFO Early tip clipping (early_simplification.hpp : 47) Early tip clipping 82s 0:00:00.025 1M / 19M INFO Early tip clipping (early_simplification.hpp : 82) #tipped junctions: 2 82s 0:00:00.025 1M / 19M INFO Early tip clipping (early_simplification.hpp : 93) Clipped tips: 2 82s 0:00:00.025 1M / 19M INFO Early tip clipping (early_simplification.hpp : 49) 7 34-mers were removed by early tip clipper 82s 0:00:00.025 1M / 19M INFO General (stage.cpp : 117) PROCEDURE == Condensing graph (id: construction:graph_condensing) 82s 0:00:00.025 1M / 19M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths 82s 0:00:00.025 1M / 19M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 1 sequences extracted 82s 0:00:00.025 1M / 19M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops 82s 0:00:00.026 1M / 19M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 0 loops collected 82s 0:00:00.026 1M / 19M INFO General (debruijn_graph_constructor: 487) Total 2 edges to create 82s 0:00:00.026 1M / 19M INFO General (debruijn_graph_constructor: 489) Collecting link records 82s 0:00:00.026 1M / 19M INFO General (debruijn_graph_constructor: 491) Ordering link records 82s 0:00:00.026 1M / 19M INFO General (debruijn_graph_constructor: 493) Sorting done 82s 0:00:00.026 1M / 19M INFO General (debruijn_graph_constructor: 503) Total 2 vertices to create 82s 0:00:00.026 1M / 19M INFO General (debruijn_graph_constructor: 506) Connecting the graph 82s 0:00:00.026 1M / 19M INFO General (stage.cpp : 117) PROCEDURE == Filling coverage indices (PHM) (id: construction:coverage_filling_phm) 82s 0:00:00.026 1M / 19M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices 82s 0:00:00.027 1M / 19M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 974 kmers, 16392 bytes occupied (134.637 bits per kmer). 82s 0:00:00.027 1M / 19M INFO General (coverage_hash_map_builder.: 47) Collecting k-mer coverage information from reads, this takes a while. 82s 0:00:00.037 1M / 19M INFO General (construction.cpp : 430) Filling coverage and flanking coverage from PHM 82s 0:00:00.038 1M / 19M INFO StageManager (stage.cpp : 185) STAGE == EC Threshold Finding (id: ec_threshold_finder) 82s 0:00:00.038 1M / 19M INFO ThresholdFinder (ec_threshold_finder.hpp : 119) Bucket size: 72 82s 0:00:00.038 1M / 19M INFO ThresholdFinder (ec_threshold_finder.hpp : 134) Proper threshold was not found. Threshold set to 0.1 of average coverage 82s 0:00:00.038 1M / 19M INFO General (genomic_info_filler.cpp : 39) Average edge coverage: 225.865 82s 0:00:00.038 1M / 19M INFO General (genomic_info_filler.cpp : 40) Graph threshold: 22.5865 82s 0:00:00.038 1M / 19M INFO General (genomic_info_filler.cpp : 70) EC coverage threshold value was calculated as 22.5865 82s 0:00:00.038 1M / 19M INFO General (genomic_info_filler.cpp : 71) Trusted kmer low bound: 0 82s 0:00:00.038 1M / 19M INFO StageManager (stage.cpp : 185) STAGE == Raw Simplification (id: raw_simplification) 82s 0:00:00.038 1M / 19M INFO General (simplification.cpp : 106) PROCEDURE == Initial cleaning 82s 0:00:00.038 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running poly A/T short edge remover 82s 0:00:00.038 1M / 19M INFO Simplification (parallel_processing.hpp : 170) poly A/T short edge remover triggered 0 times 82s 0:00:00.038 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running poly A/T tip clipper 82s 0:00:00.038 1M / 19M INFO Simplification (parallel_processing.hpp : 170) poly A/T tip clipper triggered 0 times 82s 0:00:00.038 1M / 19M INFO General (graph_simplification.hpp : 703) Removing loops and rc loops with erroneous connections 82s 0:00:00.038 1M / 19M INFO ECLoopRemover (erroneous_connection_remov: 406) Loops: accurately removed/deadend removed/other: 0/0/0 82s 0:00:00.038 1M / 19M INFO ECLoopRemover (erroneous_connection_remov: 407) RC loops: accurately removed/deadend removed/other: 0/0/0 82s 0:00:00.038 1M / 19M INFO StageManager (stage.cpp : 185) STAGE == Simplification (id: simplification) 82s 0:00:00.038 1M / 19M INFO General (simplification.cpp : 368) Graph simplification started 82s 0:00:00.038 1M / 19M INFO General (graph_simplification.hpp : 634) Creating parallel br instance 82s 0:00:00.038 1M / 19M INFO ConditionParser (graph_simplification.hpp : 179) Creating relative coverage EC condition with threshold 1 82s 0:00:00.038 1M / 19M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 1 82s 0:00:00.038 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 82s 0:00:00.038 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 82s 0:00:00.038 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 82s 0:00:00.038 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 0 times 82s 0:00:00.038 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 82s 0:00:00.038 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 82s 0:00:00.038 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 82s 0:00:00.038 1M / 19M INFO ConditionParser (graph_simplification.hpp : 179) Creating relative coverage EC condition with threshold 1 82s 0:00:00.039 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 0 times 82s 0:00:00.039 1M / 19M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 2 82s 0:00:00.039 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 82s 0:00:00.039 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 82s 0:00:00.039 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 82s 0:00:00.039 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 0 times 82s 0:00:00.039 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 82s 0:00:00.039 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 82s 0:00:00.039 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 82s 0:00:00.039 1M / 19M INFO ConditionParser (graph_simplification.hpp : 179) Creating relative coverage EC condition with threshold 1 82s 0:00:00.039 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 0 times 82s 0:00:00.039 1M / 19M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 3 82s 0:00:00.039 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 82s 0:00:00.039 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 82s 0:00:00.039 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 82s 0:00:00.039 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 0 times 82s 0:00:00.039 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 82s 0:00:00.039 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 82s 0:00:00.039 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 82s 0:00:00.039 1M / 19M INFO ConditionParser (graph_simplification.hpp : 179) Creating relative coverage EC condition with threshold 1 82s 0:00:00.039 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 0 times 82s 0:00:00.039 1M / 19M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 4 82s 0:00:00.039 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 82s 0:00:00.039 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 82s 0:00:00.039 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 82s 0:00:00.039 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 0 times 82s 0:00:00.039 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 82s 0:00:00.039 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 82s 0:00:00.039 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 82s 0:00:00.039 1M / 19M INFO ConditionParser (graph_simplification.hpp : 179) Creating relative coverage EC condition with threshold 1 82s 0:00:00.039 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 0 times 82s 0:00:00.039 1M / 19M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 5 82s 0:00:00.039 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 82s 0:00:00.039 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 82s 0:00:00.039 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 82s 0:00:00.039 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 0 times 82s 0:00:00.039 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 82s 0:00:00.039 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 82s 0:00:00.039 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 82s 0:00:00.039 1M / 19M INFO ConditionParser (graph_simplification.hpp : 179) Creating relative coverage EC condition with threshold 1 82s 0:00:00.039 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 0 times 82s 0:00:00.039 1M / 19M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 6 82s 0:00:00.039 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 82s 0:00:00.039 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 82s 0:00:00.039 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 82s 0:00:00.039 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 0 times 82s 0:00:00.039 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 82s 0:00:00.039 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 82s 0:00:00.039 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 82s 0:00:00.039 1M / 19M INFO ConditionParser (graph_simplification.hpp : 179) Creating relative coverage EC condition with threshold 1 82s 0:00:00.039 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 0 times 82s 0:00:00.039 1M / 19M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 7 82s 0:00:00.039 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 82s 0:00:00.039 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 82s 0:00:00.039 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 82s 0:00:00.039 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 0 times 82s 0:00:00.039 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 82s 0:00:00.039 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 82s 0:00:00.039 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 82s 0:00:00.039 1M / 19M INFO ConditionParser (graph_simplification.hpp : 179) Creating relative coverage EC condition with threshold 1 82s 0:00:00.039 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 0 times 82s 0:00:00.039 1M / 19M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 8 82s 0:00:00.039 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 82s 0:00:00.039 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 82s 0:00:00.039 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 82s 0:00:00.039 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 0 times 82s 0:00:00.039 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 82s 0:00:00.039 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 82s 0:00:00.039 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 82s 0:00:00.039 1M / 19M INFO ConditionParser (graph_simplification.hpp : 179) Creating relative coverage EC condition with threshold 1 82s 0:00:00.039 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 0 times 82s 0:00:00.039 1M / 19M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 9 82s 0:00:00.039 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 82s 0:00:00.039 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 82s 0:00:00.039 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 82s 0:00:00.039 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 0 times 82s 0:00:00.039 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 82s 0:00:00.039 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 82s 0:00:00.039 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 82s 0:00:00.039 1M / 19M INFO ConditionParser (graph_simplification.hpp : 179) Creating relative coverage EC condition with threshold 1 82s 0:00:00.039 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 0 times 82s 0:00:00.039 1M / 19M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 10 82s 0:00:00.039 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 82s 0:00:00.040 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 82s 0:00:00.040 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 82s 0:00:00.040 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 0 times 82s 0:00:00.040 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 82s 0:00:00.040 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 82s 0:00:00.040 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 82s 0:00:00.040 1M / 19M INFO ConditionParser (graph_simplification.hpp : 179) Creating relative coverage EC condition with threshold 1 82s 0:00:00.040 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 0 times 82s 0:00:00.040 1M / 19M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 11 82s 0:00:00.040 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 82s 0:00:00.040 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 82s 0:00:00.040 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 82s 0:00:00.040 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 0 times 82s 0:00:00.040 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 82s 0:00:00.040 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 82s 0:00:00.040 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 82s 0:00:00.040 1M / 19M INFO ConditionParser (graph_simplification.hpp : 179) Creating relative coverage EC condition with threshold 1 82s 0:00:00.040 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 0 times 82s 0:00:00.040 1M / 19M INFO StageManager (stage.cpp : 185) STAGE == Simplification Cleanup (id: simplification_cleanup) 82s 0:00:00.040 1M / 19M INFO General (simplification.cpp : 176) PROCEDURE == Post simplification 82s 0:00:00.040 1M / 19M INFO General (graph_simplification.hpp : 448) Disconnection of relatively low covered edges disabled 82s 0:00:00.040 1M / 19M INFO General (graph_simplification.hpp : 485) Complex tip clipping disabled 82s 0:00:00.040 1M / 19M INFO General (graph_simplification.hpp : 634) Creating parallel br instance 82s 0:00:00.040 1M / 19M INFO General (graph_simplification.hpp : 634) Creating parallel br instance 82s 0:00:00.040 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Relative coverage erroneous connection remover 82s 0:00:00.040 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Relative coverage erroneous connection remover triggered 0 times 82s 0:00:00.040 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Relative coverage component remover 82s 0:00:00.040 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Relative coverage component remover triggered 0 times 82s 0:00:00.040 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Complex bulge remover 82s 0:00:00.040 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Complex bulge remover triggered 0 times 82s 0:00:00.040 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 82s 0:00:00.040 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 82s 0:00:00.040 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Final tip clipper 82s 0:00:00.040 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Final tip clipper triggered 0 times 82s 0:00:00.040 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 82s 0:00:00.040 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 82s 0:00:00.041 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Final bulge remover 82s 0:00:00.041 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Final bulge remover triggered 0 times 82s 0:00:00.041 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running AT Tips 82s 0:00:00.041 1M / 19M INFO Simplification (parallel_processing.hpp : 170) AT Tips triggered 0 times 82s 0:00:00.041 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Relative coverage erroneous connection remover 82s 0:00:00.041 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Relative coverage erroneous connection remover triggered 0 times 82s 0:00:00.041 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Relative coverage component remover 82s 0:00:00.041 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Relative coverage component remover triggered 0 times 82s 0:00:00.041 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Complex bulge remover 82s 0:00:00.041 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Complex bulge remover triggered 0 times 82s 0:00:00.041 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 82s 0:00:00.041 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 82s 0:00:00.041 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Final tip clipper 82s 0:00:00.041 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Final tip clipper triggered 0 times 82s 0:00:00.041 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 82s 0:00:00.041 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 82s 0:00:00.041 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Final bulge remover 82s 0:00:00.041 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Final bulge remover triggered 0 times 82s 0:00:00.041 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running AT Tips 82s 0:00:00.041 1M / 19M INFO Simplification (parallel_processing.hpp : 170) AT Tips triggered 0 times 82s 0:00:00.041 1M / 19M INFO General (simplification.cpp : 327) Disrupting self-conjugate edges 82s 0:00:00.041 1M / 19M INFO Simplification (parallel_processing.hpp : 167) Running Removing isolated edges 82s 0:00:00.041 1M / 19M INFO Simplification (parallel_processing.hpp : 170) Removing isolated edges triggered 0 times 82s 0:00:00.041 1M / 19M INFO General (simplification.cpp : 495) After simplification: 82s 0:00:00.041 1M / 19M INFO General (simplification.cpp : 496) Average coverage = 225.865 82s 0:00:00.041 1M / 19M INFO General (simplification.cpp : 497) Total length = 967 82s 0:00:00.041 1M / 19M INFO General (simplification.cpp : 498) Median edge length: 967 82s 0:00:00.041 1M / 19M INFO General (simplification.cpp : 499) Edges: 2 82s 0:00:00.041 1M / 19M INFO General (simplification.cpp : 500) Vertices: 4 82s 0:00:00.041 1M / 19M INFO StageManager (stage.cpp : 185) STAGE == Contig Output (id: contig_output) 82s 0:00:00.041 1M / 19M INFO General (read_converter.cpp : 107) Outputting contigs to /tmp/tmp.cMLX1ajB23/spades_test/K33/simplified_contigs 82s 0:00:00.041 3M / 19M INFO General (binary_converter.cpp : 111) 1 reads written 82s 0:00:00.041 1M / 19M INFO General (pipeline.cpp : 287) SPAdes finished 82s 0:00:00.041 1M / 19M INFO General (main.cpp : 136) Assembling time: 0 hours 0 minutes 0 seconds 82s 82s ===== K33 finished. 82s 82s 82s ===== K49 started. 82s 82s 82s == Running: /usr/libexec/spades/spades-core /tmp/tmp.cMLX1ajB23/spades_test/K49/configs/config.info /tmp/tmp.cMLX1ajB23/spades_test/K49/configs/mda_mode.info /tmp/tmp.cMLX1ajB23/spades_test/K49/configs/rna_mode.info 82s 82s 0:00:00.000 1M / 19M INFO General (main.cpp : 99) Loaded config from /tmp/tmp.cMLX1ajB23/spades_test/K49/configs/config.info 82s 0:00:00.000 1M / 19M INFO General (main.cpp : 99) Loaded config from /tmp/tmp.cMLX1ajB23/spades_test/K49/configs/mda_mode.info 82s 0:00:00.000 1M / 19M INFO General (main.cpp : 99) Loaded config from /tmp/tmp.cMLX1ajB23/spades_test/K49/configs/rna_mode.info 82s 0:00:00.000 1M / 19M INFO General (memory_limit.cpp : 54) Memory limit set to 3 Gb 82s 0:00:00.000 1M / 19M INFO General (main.cpp : 107) Starting SPAdes, built from N/A, git revision N/A 82s 0:00:00.000 1M / 19M INFO General (main.cpp : 108) Maximum k-mer length: 128 82s 0:00:00.000 1M / 19M INFO General (main.cpp : 109) Assembling dataset (/tmp/tmp.cMLX1ajB23/spades_test/dataset.info) with K=49 82s 0:00:00.000 1M / 19M INFO General (main.cpp : 110) Maximum # of threads to use (adjusted due to OMP capabilities): 2 82s 0:00:00.000 1M / 19M INFO General (pipeline.cpp : 212) SPAdes started 82s 0:00:00.000 1M / 19M INFO General (pipeline.cpp : 225) Starting from stage: read_conversion 82s 0:00:00.000 1M / 19M INFO General (pipeline.cpp : 231) Two-step repeat resolution disabled 82s 0:00:00.000 1M / 19M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 82s 0:00:00.000 1M / 19M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 82s 0:00:00.000 1M / 19M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 82s 0:00:00.000 1M / 19M INFO General (pipeline.cpp : 242) Will need read mapping, kmer mapper will be attached 82s 0:00:00.000 1M / 19M INFO StageManager (stage.cpp : 185) STAGE == Binary Read Conversion (id: read_conversion) 82s 0:00:00.000 1M / 19M INFO General (read_converter.cpp : 53) Binary reads detected 82s 0:00:00.000 1M / 19M INFO StageManager (stage.cpp : 185) STAGE == de Bruijn graph construction (id: construction) 82s 0:00:00.000 1M / 19M INFO General (construction.cpp : 118) Contigs from previous K will be used: /tmp/tmp.cMLX1ajB23/spades_test/K33/simplified_contigs 82s 0:00:00.000 1M / 19M INFO General (construction.cpp : 153) Max read length 100 82s 0:00:00.000 1M / 19M INFO General (construction.cpp : 159) Average read length 86.1611 82s 0:00:00.000 1M / 19M INFO General (stage.cpp : 117) PROCEDURE == k+1-mer counting (id: construction:kpomer_counting) 82s 0:00:00.000 1M / 19M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 20 files using 2 threads. This might take a while. 82s 0:00:00.000 1M / 19M INFO General (file_limit.hpp : 42) Open file limit set to 1024 82s 0:00:00.000 1M / 19M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 0.49997 Gb 82s 0:00:00.000 1M / 19M INFO General (kmer_splitter.hpp : 101) Using cell size of 1677621 82s 0:00:00.007 1M / 19M INFO General (kmer_splitters.hpp : 131) Used 8218 reads 82s 0:00:00.007 1M / 19M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. 82s 0:00:00.009 1M / 19M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 958 kmers in total. 82s 0:00:00.009 1M / 19M INFO General (stage.cpp : 117) PROCEDURE == Extension index construction (id: construction:extension_index_construction) 82s 0:00:00.009 1M / 19M INFO K-mer Index Building (kmer_index_builder.hpp : 438) Building kmer index 82s 0:00:00.009 1M / 19M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 20 files using 2 threads. This might take a while. 82s 0:00:00.009 1M / 19M INFO General (file_limit.hpp : 42) Open file limit set to 1024 82s 0:00:00.009 1M / 19M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 0.499967 Gb 82s 0:00:00.009 1M / 19M INFO General (kmer_splitter.hpp : 101) Using cell size of 1677612 82s 0:00:00.010 1161M / 1161M INFO General (kmer_splitters.hpp : 199) Used 958 kmers. 82s 0:00:00.010 1M / 19M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. 82s 0:00:00.012 1M / 19M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 959 kmers in total. 82s 0:00:00.012 1M / 19M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices 82s 0:00:00.013 1M / 19M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 959 kmers, 16392 bytes occupied (136.742 bits per kmer). 82s 0:00:00.013 1M / 19M INFO General (kmer_index_builder.hpp : 169) Merging final buckets. 82s 0:00:00.014 1M / 19M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 100) Building k-mer extensions from k+1-mers 82s 0:00:00.015 1M / 19M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 105) Building k-mer extensions from k+1-mers finished. 82s 0:00:00.015 1M / 19M INFO General (stage.cpp : 117) PROCEDURE == Early A/T remover (id: construction:early_at_remover) 82s 0:00:00.015 1M / 19M INFO Early A/T remover (early_simplification.hpp : 176) Remove short poly A/T edges 82s 0:00:00.015 1M / 19M INFO Early A/T remover (early_simplification.hpp : 254) Links removed: 0 82s 0:00:00.015 1M / 19M INFO Early A/T remover (early_simplification.hpp : 179) 0 50-mers were removed by early poly A/T remover 82s 0:00:00.015 1M / 19M INFO Early A/T remover (early_simplification.hpp : 262) Remove poly A/T tips 82s 0:00:00.015 1M / 19M INFO Early A/T remover (early_simplification.hpp : 331) Clipped tips: 0 82s 0:00:00.015 1M / 19M INFO Early A/T remover (early_simplification.hpp : 265) 0 50-mers were removed by early poly A/T tip clipper 82s 0:00:00.015 1M / 19M INFO General (stage.cpp : 117) PROCEDURE == Condensing graph (id: construction:graph_condensing) 82s 0:00:00.015 1M / 19M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths 82s 0:00:00.015 1M / 19M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 5 sequences extracted 82s 0:00:00.015 1M / 19M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops 82s 0:00:00.016 1M / 19M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 0 loops collected 82s 0:00:00.016 1M / 19M INFO General (debruijn_graph_constructor: 487) Total 10 edges to create 82s 0:00:00.016 1M / 19M INFO General (debruijn_graph_constructor: 489) Collecting link records 82s 0:00:00.016 1M / 19M INFO General (debruijn_graph_constructor: 491) Ordering link records 82s 0:00:00.016 1M / 19M INFO General (debruijn_graph_constructor: 493) Sorting done 82s 0:00:00.016 1M / 19M INFO General (debruijn_graph_constructor: 503) Total 6 vertices to create 82s 0:00:00.016 1M / 19M INFO General (debruijn_graph_constructor: 506) Connecting the graph 82s 0:00:00.016 1M / 19M INFO General (stage.cpp : 117) PROCEDURE == Filling coverage indices (PHM) (id: construction:coverage_filling_phm) 82s 0:00:00.016 1M / 19M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices 82s 0:00:00.017 1M / 19M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 958 kmers, 16384 bytes occupied (136.818 bits per kmer). 82s 0:00:00.017 1M / 19M INFO General (coverage_hash_map_builder.: 47) Collecting k-mer coverage information from reads, this takes a while. 82s 0:00:00.025 1M / 19M INFO General (construction.cpp : 430) Filling coverage and flanking coverage from PHM 82s 0:00:00.026 1M / 19M INFO StageManager (stage.cpp : 185) STAGE == EC Threshold Finding (id: ec_threshold_finder) 82s 0:00:00.026 1M / 19M INFO ThresholdFinder (ec_threshold_finder.hpp : 119) Bucket size: 53 82s 0:00:00.026 1M / 19M INFO ThresholdFinder (ec_threshold_finder.hpp : 134) Proper threshold was not found. Threshold set to 0.1 of average coverage 82s 0:00:00.026 1M / 19M INFO General (genomic_info_filler.cpp : 39) Average edge coverage: 162.219 82s 0:00:00.026 1M / 19M INFO General (genomic_info_filler.cpp : 40) Graph threshold: 16.2219 82s 0:00:00.026 1M / 19M INFO General (genomic_info_filler.cpp : 70) EC coverage threshold value was calculated as 16.2219 82s 0:00:00.026 1M / 19M INFO General (genomic_info_filler.cpp : 71) Trusted kmer low bound: 0 82s 0:00:00.026 1M / 19M INFO StageManager (stage.cpp : 185) STAGE == Gap Closer (id: early_gapcloser) 82s 0:00:00.031 10M / 19M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 82s 0:00:00.031 10M / 19M INFO General (gap_closer.cpp : 101) Total edges in tip neighborhood: 4 out of 10, length: 860 82s 0:00:00.031 10M / 19M INFO General (edge_index.hpp : 167) Using small index (max_id = 13) 82s 0:00:00.031 10M / 19M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices 82s 0:00:00.032 10M / 19M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 860 kmers, 1384 bytes occupied (12.8744 bits per kmer). 82s 0:00:00.032 10M / 19M INFO General (edge_index_builders.hpp : 265) Collecting edge information from graph, this takes a while. 82s 0:00:00.034 10M / 19M INFO General (sequence_mapper_notifier.h: 95) Total 2054 reads processed 82s 0:00:00.035 10M / 19M INFO General (gap_closer.cpp : 452) Initializing gap closer 82s 0:00:00.035 10M / 19M INFO GapCloser (gap_closer.cpp : 359) Closing short gaps 82s 0:00:00.035 10M / 19M INFO GapCloser (gap_closer.cpp : 391) Closing short gaps complete: filled 0 gaps after checking 0 candidates 82s 0:00:00.035 10M / 19M INFO General (gap_closer.cpp : 456) Gap closer done 82s 0:00:00.035 1M / 19M INFO StageManager (stage.cpp : 185) STAGE == Raw Simplification (id: raw_simplification) 82s 0:00:00.035 1M / 19M INFO General (simplification.cpp : 106) PROCEDURE == Initial cleaning 82s 0:00:00.035 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running poly A/T short edge remover 82s 0:00:00.035 1M / 20M INFO Simplification (parallel_processing.hpp : 170) poly A/T short edge remover triggered 0 times 82s 0:00:00.035 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running poly A/T tip clipper 82s 0:00:00.035 1M / 20M INFO Simplification (parallel_processing.hpp : 170) poly A/T tip clipper triggered 1 times 82s 0:00:00.035 1M / 20M INFO General (graph_simplification.hpp : 703) Removing loops and rc loops with erroneous connections 82s 0:00:00.036 1M / 20M INFO ECLoopRemover (erroneous_connection_remov: 406) Loops: accurately removed/deadend removed/other: 0/0/0 82s 0:00:00.036 1M / 20M INFO ECLoopRemover (erroneous_connection_remov: 407) RC loops: accurately removed/deadend removed/other: 0/0/0 82s 0:00:00.036 1M / 20M INFO StageManager (stage.cpp : 185) STAGE == Simplification (id: simplification) 82s 0:00:00.036 1M / 20M INFO General (simplification.cpp : 368) Graph simplification started 82s 0:00:00.036 1M / 20M INFO General (graph_simplification.hpp : 634) Creating parallel br instance 82s 0:00:00.036 1M / 20M INFO ConditionParser (graph_simplification.hpp : 179) Creating relative coverage EC condition with threshold 1 82s 0:00:00.036 1M / 20M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 1 82s 0:00:00.036 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 82s 0:00:00.036 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 1 times 82s 0:00:00.036 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 82s 0:00:00.036 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 0 times 82s 0:00:00.036 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 82s 0:00:00.036 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 82s 0:00:00.036 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 82s 0:00:00.036 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 82s 0:00:00.036 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 82s 0:00:00.036 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 0 times 82s 0:00:00.036 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 82s 0:00:00.036 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 82s 0:00:00.036 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 82s 0:00:00.036 1M / 20M INFO ConditionParser (graph_simplification.hpp : 179) Creating relative coverage EC condition with threshold 1 82s 0:00:00.036 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 0 times 82s 0:00:00.036 1M / 20M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 2 82s 0:00:00.036 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 82s 0:00:00.036 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 82s 0:00:00.036 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 82s 0:00:00.036 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 0 times 82s 0:00:00.036 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 82s 0:00:00.036 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 82s 0:00:00.036 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 82s 0:00:00.036 1M / 20M INFO ConditionParser (graph_simplification.hpp : 179) Creating relative coverage EC condition with threshold 1 82s 0:00:00.036 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 0 times 82s 0:00:00.036 1M / 20M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 3 82s 0:00:00.036 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 82s 0:00:00.036 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 82s 0:00:00.036 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 82s 0:00:00.036 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 0 times 82s 0:00:00.036 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 82s 0:00:00.036 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 82s 0:00:00.036 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 82s 0:00:00.036 1M / 20M INFO ConditionParser (graph_simplification.hpp : 179) Creating relative coverage EC condition with threshold 1 82s 0:00:00.036 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 0 times 82s 0:00:00.036 1M / 20M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 4 82s 0:00:00.036 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 82s 0:00:00.036 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 82s 0:00:00.036 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 82s 0:00:00.036 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 0 times 82s 0:00:00.036 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 82s 0:00:00.036 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 82s 0:00:00.036 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 82s 0:00:00.036 1M / 20M INFO ConditionParser (graph_simplification.hpp : 179) Creating relative coverage EC condition with threshold 1 82s 0:00:00.036 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 0 times 82s 0:00:00.036 1M / 20M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 5 82s 0:00:00.036 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 82s 0:00:00.036 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 82s 0:00:00.036 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 82s 0:00:00.036 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 0 times 82s 0:00:00.036 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 82s 0:00:00.036 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 82s 0:00:00.036 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 82s 0:00:00.036 1M / 20M INFO ConditionParser (graph_simplification.hpp : 179) Creating relative coverage EC condition with threshold 1 82s 0:00:00.036 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 0 times 82s 0:00:00.036 1M / 20M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 6 82s 0:00:00.036 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 82s 0:00:00.036 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 82s 0:00:00.036 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 82s 0:00:00.036 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 0 times 82s 0:00:00.036 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 82s 0:00:00.036 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 82s 0:00:00.036 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 82s 0:00:00.036 1M / 20M INFO ConditionParser (graph_simplification.hpp : 179) Creating relative coverage EC condition with threshold 1 82s 0:00:00.036 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 0 times 82s 0:00:00.036 1M / 20M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 7 82s 0:00:00.036 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 82s 0:00:00.036 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 82s 0:00:00.036 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 82s 0:00:00.036 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 0 times 82s 0:00:00.036 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 82s 0:00:00.036 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 82s 0:00:00.036 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 82s 0:00:00.036 1M / 20M INFO ConditionParser (graph_simplification.hpp : 179) Creating relative coverage EC condition with threshold 1 82s 0:00:00.036 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 0 times 82s 0:00:00.036 1M / 20M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 8 82s 0:00:00.036 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 82s 0:00:00.036 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 82s 0:00:00.036 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 82s 0:00:00.036 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 0 times 82s 0:00:00.036 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 82s 0:00:00.036 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 82s 0:00:00.036 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 82s 0:00:00.036 1M / 20M INFO ConditionParser (graph_simplification.hpp : 179) Creating relative coverage EC condition with threshold 1 82s 0:00:00.036 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 0 times 82s 0:00:00.036 1M / 20M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 9 82s 0:00:00.036 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 82s 0:00:00.036 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 82s 0:00:00.036 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 82s 0:00:00.036 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 0 times 82s 0:00:00.036 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 82s 0:00:00.036 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 82s 0:00:00.036 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 82s 0:00:00.036 1M / 20M INFO ConditionParser (graph_simplification.hpp : 179) Creating relative coverage EC condition with threshold 1 82s 0:00:00.036 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 0 times 82s 0:00:00.036 1M / 20M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 10 82s 0:00:00.036 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 82s 0:00:00.036 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 82s 0:00:00.036 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 82s 0:00:00.036 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 0 times 82s 0:00:00.036 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 82s 0:00:00.036 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 82s 0:00:00.036 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 82s 0:00:00.036 1M / 20M INFO ConditionParser (graph_simplification.hpp : 179) Creating relative coverage EC condition with threshold 1 82s 0:00:00.036 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 0 times 82s 0:00:00.036 1M / 20M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 11 82s 0:00:00.036 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 82s 0:00:00.036 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 82s 0:00:00.036 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 82s 0:00:00.036 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 0 times 82s 0:00:00.036 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 82s 0:00:00.036 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 82s 0:00:00.036 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 82s 0:00:00.036 1M / 20M INFO ConditionParser (graph_simplification.hpp : 179) Creating relative coverage EC condition with threshold 1 82s 0:00:00.036 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 0 times 82s 0:00:00.036 1M / 20M INFO StageManager (stage.cpp : 185) STAGE == Gap Closer (id: late_gapcloser) 82s 0:00:00.037 10M / 20M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 82s 0:00:00.038 10M / 20M INFO General (gap_closer.cpp : 101) Total edges in tip neighborhood: 2 out of 2, length: 1902 82s 0:00:00.038 10M / 20M INFO General (edge_index.hpp : 167) Using small index (max_id = 13) 82s 0:00:00.038 10M / 20M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices 82s 0:00:00.038 10M / 20M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 951 kmers, 1456 bytes occupied (12.2482 bits per kmer). 82s 0:00:00.038 10M / 20M INFO General (edge_index_builders.hpp : 265) Collecting edge information from graph, this takes a while. 82s 0:00:00.040 10M / 20M INFO General (sequence_mapper_notifier.h: 95) Total 2054 reads processed 82s 0:00:00.041 10M / 20M INFO General (gap_closer.cpp : 452) Initializing gap closer 82s 0:00:00.041 10M / 20M INFO GapCloser (gap_closer.cpp : 359) Closing short gaps 82s 0:00:00.041 10M / 20M INFO GapCloser (gap_closer.cpp : 391) Closing short gaps complete: filled 0 gaps after checking 0 candidates 82s 0:00:00.041 10M / 20M INFO General (gap_closer.cpp : 456) Gap closer done 82s 0:00:00.042 1M / 20M INFO StageManager (stage.cpp : 185) STAGE == Simplification Cleanup (id: simplification_cleanup) 82s 0:00:00.042 1M / 20M INFO General (simplification.cpp : 176) PROCEDURE == Post simplification 82s 0:00:00.042 1M / 20M INFO General (graph_simplification.hpp : 448) Disconnection of relatively low covered edges disabled 82s 0:00:00.042 1M / 20M INFO General (graph_simplification.hpp : 485) Complex tip clipping disabled 82s 0:00:00.042 1M / 20M INFO General (graph_simplification.hpp : 634) Creating parallel br instance 82s 0:00:00.042 1M / 20M INFO General (graph_simplification.hpp : 634) Creating parallel br instance 82s 0:00:00.042 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Relative coverage erroneous connection remover 82s 0:00:00.042 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Relative coverage erroneous connection remover triggered 0 times 82s 0:00:00.042 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Relative coverage component remover 82s 0:00:00.042 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Relative coverage component remover triggered 0 times 82s 0:00:00.042 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Complex bulge remover 82s 0:00:00.042 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Complex bulge remover triggered 0 times 82s 0:00:00.042 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 82s 0:00:00.042 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 82s 0:00:00.042 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Final tip clipper 82s 0:00:00.042 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Final tip clipper triggered 0 times 82s 0:00:00.042 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 82s 0:00:00.042 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 82s 0:00:00.042 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Final bulge remover 82s 0:00:00.042 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Final bulge remover triggered 0 times 82s 0:00:00.042 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running AT Tips 82s 0:00:00.042 1M / 20M INFO Simplification (parallel_processing.hpp : 170) AT Tips triggered 0 times 82s 0:00:00.042 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Relative coverage erroneous connection remover 82s 0:00:00.042 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Relative coverage erroneous connection remover triggered 0 times 82s 0:00:00.042 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Relative coverage component remover 82s 0:00:00.042 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Relative coverage component remover triggered 0 times 82s 0:00:00.042 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Complex bulge remover 82s 0:00:00.042 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Complex bulge remover triggered 0 times 82s 0:00:00.042 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 82s 0:00:00.042 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 82s 0:00:00.042 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Final tip clipper 82s 0:00:00.042 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Final tip clipper triggered 0 times 82s 0:00:00.042 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 82s 0:00:00.042 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 82s 0:00:00.042 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Final bulge remover 82s 0:00:00.042 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Final bulge remover triggered 0 times 82s 0:00:00.042 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running AT Tips 82s 0:00:00.042 1M / 20M INFO Simplification (parallel_processing.hpp : 170) AT Tips triggered 0 times 82s 0:00:00.042 1M / 20M INFO General (simplification.cpp : 327) Disrupting self-conjugate edges 82s 0:00:00.042 1M / 20M INFO Simplification (parallel_processing.hpp : 167) Running Removing isolated edges 82s 0:00:00.042 1M / 20M INFO Simplification (parallel_processing.hpp : 170) Removing isolated edges triggered 0 times 82s 0:00:00.042 1M / 20M INFO General (simplification.cpp : 495) After simplification: 82s 0:00:00.042 1M / 20M INFO General (simplification.cpp : 496) Average coverage = 163.37 82s 0:00:00.042 1M / 20M INFO General (simplification.cpp : 497) Total length = 951 82s 0:00:00.042 1M / 20M INFO General (simplification.cpp : 498) Median edge length: 951 82s 0:00:00.042 1M / 20M INFO General (simplification.cpp : 499) Edges: 2 82s 0:00:00.042 1M / 20M INFO General (simplification.cpp : 500) Vertices: 4 82s 0:00:00.042 1M / 20M INFO StageManager (stage.cpp : 185) STAGE == Mismatch Correction (id: mismatch_correction) 82s 0:00:00.042 1M / 20M INFO General (graph_pack.cpp : 67) Index refill 82s 0:00:00.042 1M / 20M INFO General (edge_index.hpp : 156) Using small index (max_id = 13) 82s 0:00:00.042 1M / 20M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices 82s 0:00:00.042 1M / 20M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 951 kmers, 1456 bytes occupied (12.2482 bits per kmer). 82s 0:00:00.042 1M / 20M INFO General (edge_index_builders.hpp : 252) Collecting edge information from graph, this takes a while. 82s 0:00:00.042 1M / 20M INFO General (graph_pack.cpp : 77) Normalizing k-mer map. Total 0 kmers to process 82s 0:00:00.042 1M / 20M INFO General (graph_pack.cpp : 79) Normalizing done 82s 0:00:00.042 1M / 20M INFO General (mismatch_correction.cpp : 400) Collect potential mismatches 82s 0:00:00.042 1M / 20M INFO General (mismatch_correction.cpp : 192) Total 0 edges (out of 2) with 0 potential mismatch positions (-nan positions per edge) 82s 0:00:00.042 1M / 20M INFO General (mismatch_correction.cpp : 402) Potential mismatches collected 82s 0:00:00.046 1M / 20M INFO General (sequence_mapper_notifier.h: 95) Total 8216 reads processed 82s 0:00:00.046 1M / 20M INFO General (mismatch_correction.cpp : 395) All edges processed 82s 0:00:00.047 1M / 20M INFO General (mismatch_correction.cpp : 450) Corrected 0 nucleotides 82s 0:00:00.047 1M / 20M INFO StageManager (stage.cpp : 185) STAGE == Contig Output (id: contig_output) 82s 0:00:00.047 1M / 20M INFO General (contig_output.hpp : 16) Outputting contigs to /tmp/tmp.cMLX1ajB23/spades_test/K49/before_rr.fasta 82s 0:00:00.047 1M / 20M INFO General (contig_output_stage.cpp : 151) Writing GFA graph to /tmp/tmp.cMLX1ajB23/spades_test/K49/assembly_graph_after_simplification.gfa 82s 0:00:00.047 1M / 20M INFO StageManager (stage.cpp : 185) STAGE == Paired Information Counting (id: late_pair_info_count) 82s 0:00:00.047 1M / 20M INFO General (graph_pack.cpp : 77) Normalizing k-mer map. Total 0 kmers to process 82s 0:00:00.047 1M / 20M INFO General (graph_pack.cpp : 79) Normalizing done 82s 0:00:00.047 1M / 20M INFO General (pair_info_count.cpp : 339) Min edge length for estimation: 951 82s 0:00:00.047 1M / 20M INFO General (pair_info_count.cpp : 350) Estimating insert size for library #0 82s 0:00:00.047 1M / 20M INFO General (pair_info_count.cpp : 202) Estimating insert size (takes a while) 82s 0:00:00.067 49M / 59M INFO General (pair_info_count.cpp : 48) Selecting usual mapper 82s 0:00:00.090 49M / 59M INFO General (sequence_mapper_notifier.h: 95) Total 2054 reads processed 83s 0:00:00.154 49M / 59M INFO General (pair_info_count.cpp : 220) Edge pairs: 2 83s 0:00:00.154 49M / 59M INFO General (pair_info_count.cpp : 222) 1751 paired reads (85.2483% of all) aligned to long edges 83s 0:00:00.155 1M / 59M INFO General (pair_info_count.cpp : 369) Insert size = 214.709, deviation = 10.4946, left quantile = 201, right quantile = 228, read length = 100 83s 0:00:00.155 1M / 59M INFO General (pair_info_count.cpp : 402) Mapping library #0 83s 0:00:00.155 1M / 59M INFO General (pair_info_count.cpp : 404) Mapping paired reads (takes a while) 83s 0:00:00.155 1M / 59M INFO General (pair_info_count.cpp : 299) Left insert size quantile 201, right insert size quantile 228, filtering threshold 0, rounding threshold 0 83s 0:00:00.156 10M / 59M INFO General (pair_info_count.cpp : 48) Selecting usual mapper 83s 0:00:00.159 10M / 59M INFO General (sequence_mapper_notifier.h: 95) Total 2054 reads processed 83s 0:00:00.160 1M / 59M INFO General (pair_info_count.cpp : 411) Mapping single reads of library #0 83s 0:00:00.160 1M / 59M INFO General (pair_info_count.cpp : 266) Will calculate lib coverage as well 83s 0:00:00.160 1M / 59M INFO General (pair_info_count.cpp : 48) Selecting usual mapper 83s 0:00:00.162 1M / 59M INFO General (sequence_mapper_notifier.h: 95) Total 4108 reads processed 83s 0:00:00.162 1M / 59M INFO General (pair_info_count.cpp : 413) Total paths obtained from single reads: 0 83s 0:00:00.162 1M / 59M INFO StageManager (stage.cpp : 185) STAGE == Distance Estimation (id: distance_estimation) 83s 0:00:00.162 1M / 59M INFO General (distance_estimation.cpp : 179) Processing library #0 83s 0:00:00.162 1M / 59M INFO General (distance_estimation.cpp : 150) Weight Filter Done 83s 0:00:00.162 1M / 59M INFO DistanceEstimator (distance_estimation.hpp : 116) Using SIMPLE distance estimator 83s 0:00:00.163 1M / 59M INFO General (distance_estimation.cpp : 37) Filtering info 83s 0:00:00.163 1M / 59M INFO General (pair_info_filters.hpp : 242) Start filtering; library index size: 2 83s 0:00:00.163 1M / 59M INFO General (pair_info_filters.hpp : 263) Done filtering; library index size: 2 83s 0:00:00.163 1M / 59M INFO General (distance_estimation.cpp : 156) Refining clustered pair information 83s 0:00:00.163 1M / 59M INFO General (distance_estimation.cpp : 158) The refining of clustered pair information has been finished 83s 0:00:00.163 1M / 59M INFO General (distance_estimation.cpp : 160) Improving paired information 83s 0:00:00.163 1M / 59M INFO PairInfoImprover (pair_info_improver.hpp : 104) Paired info stats: missing = 0; contradictional = 0 83s 0:00:00.163 1M / 59M INFO PairInfoImprover (pair_info_improver.hpp : 104) Paired info stats: missing = 0; contradictional = 0 83s 0:00:00.163 1M / 59M INFO StageManager (stage.cpp : 185) STAGE == Repeat Resolving (id: repeat_resolving) 83s 0:00:00.163 1M / 59M INFO General (repeat_resolving.cpp : 87) Using Path-Extend repeat resolving 83s 0:00:00.163 1M / 59M INFO General (launcher.cpp : 600) ExSPAnder repeat resolving tool started 83s 0:00:00.163 1M / 60M INFO General (launcher.cpp : 418) Creating main extenders, unique edge length = 2000 83s 0:00:00.163 1M / 60M INFO General (extenders_logic.cpp : 345) Creating extender; library index size: 2 83s 0:00:00.163 1M / 60M INFO General (extenders_logic.cpp : 345) Creating extender; library index size: 2 83s 0:00:00.163 1M / 60M INFO General (extenders_logic.cpp : 543) Using 1 paired-end library 83s 0:00:00.163 1M / 60M INFO General (extenders_logic.cpp : 544) Using 1 paired-end scaffolding library 83s 0:00:00.163 1M / 60M INFO General (extenders_logic.cpp : 545) Using 0 single read libraries 83s 0:00:00.163 1M / 60M INFO General (launcher.cpp : 447) Total number of extenders is 5 83s 0:00:00.163 1M / 60M INFO General (launcher.cpp : 250) Finalizing paths 83s 0:00:00.163 1M / 60M INFO General (launcher.cpp : 252) Deduplicating paths 83s 0:00:00.163 1M / 60M INFO General (launcher.cpp : 256) Paths deduplicated 83s 0:00:00.163 1M / 60M INFO General (launcher.cpp : 263) Overlaps will not be removed 83s 0:00:00.163 1M / 60M INFO General (launcher.cpp : 273) Paths finalized 83s 0:00:00.163 1M / 60M INFO General (launcher.cpp : 454) Closing gaps in paths 83s 0:00:00.163 1M / 60M INFO General (launcher.cpp : 484) Gap closing completed 83s 0:00:00.163 1M / 60M INFO General (launcher.cpp : 302) Traversing tandem repeats 83s 0:00:00.163 1M / 60M INFO General (launcher.cpp : 312) Traversed 0 loops 83s 0:00:00.163 1M / 60M INFO General (launcher.cpp : 250) Finalizing paths 83s 0:00:00.163 1M / 60M INFO General (launcher.cpp : 252) Deduplicating paths 83s 0:00:00.163 1M / 60M INFO General (launcher.cpp : 256) Paths deduplicated 83s 0:00:00.163 1M / 60M INFO General (launcher.cpp : 263) Overlaps will not be removed 83s 0:00:00.163 1M / 60M INFO General (launcher.cpp : 273) Paths finalized 83s 0:00:00.163 1M / 60M INFO General (launcher.cpp : 499) Finalizing paths - hard 83s 0:00:00.163 1M / 60M INFO General (launcher.cpp : 295) Read length relative cutoff 1.5 converted to 101 83s 0:00:00.163 1M / 60M INFO General (launcher.cpp : 296) Read length absolute cutoff 130 bp converted to 101 83s 0:00:00.163 1M / 60M INFO General (launcher.cpp : 297) Length cutoff: 101 83s 0:00:00.163 1M / 60M INFO General (launcher.cpp : 295) Read length relative cutoff 2 converted to 151 83s 0:00:00.163 1M / 60M INFO General (launcher.cpp : 296) Read length absolute cutoff 180 bp converted to 151 83s 0:00:00.163 1M / 60M INFO General (launcher.cpp : 297) Length cutoff: 151 83s 0:00:00.163 1M / 60M INFO General (launcher.cpp : 295) Read length relative cutoff 2 converted to 151 83s 0:00:00.163 1M / 60M INFO General (launcher.cpp : 296) Read length absolute cutoff 180 bp converted to 151 83s 0:00:00.163 1M / 60M INFO General (launcher.cpp : 297) Length cutoff: 151 83s 0:00:00.163 1M / 60M INFO General (launcher.cpp : 499) Finalizing paths - soft 83s 0:00:00.163 1M / 60M INFO General (launcher.cpp : 295) Read length relative cutoff 1.05 converted to 56 83s 0:00:00.163 1M / 60M INFO General (launcher.cpp : 296) Read length absolute cutoff 85 bp converted to 56 83s 0:00:00.163 1M / 60M INFO General (launcher.cpp : 297) Length cutoff: 56 83s 0:00:00.163 1M / 60M INFO General (launcher.cpp : 295) Read length relative cutoff 1.5 converted to 101 83s 0:00:00.163 1M / 60M INFO General (launcher.cpp : 296) Read length absolute cutoff 130 bp converted to 101 83s 0:00:00.163 1M / 60M INFO General (launcher.cpp : 297) Length cutoff: 101 83s 0:00:00.163 1M / 60M INFO General (launcher.cpp : 295) Read length relative cutoff 1.2 converted to 71 83s 0:00:00.163 1M / 60M INFO General (launcher.cpp : 296) Read length absolute cutoff 100 bp converted to 71 83s 0:00:00.163 1M / 60M INFO General (launcher.cpp : 297) Length cutoff: 71 83s 0:00:00.163 1M / 60M INFO General (launcher.cpp : 507) Finalizing main paths 83s 0:00:00.163 1M / 60M INFO General (launcher.cpp : 295) Read length relative cutoff 1.3 converted to 81 83s 0:00:00.163 1M / 60M INFO General (launcher.cpp : 296) Read length absolute cutoff 110 bp converted to 81 83s 0:00:00.163 1M / 60M INFO General (launcher.cpp : 297) Length cutoff: 81 83s 0:00:00.163 1M / 60M INFO General (launcher.cpp : 295) Read length relative cutoff 1.6 converted to 111 83s 0:00:00.163 1M / 60M INFO General (launcher.cpp : 296) Read length absolute cutoff 140 bp converted to 111 83s 0:00:00.164 1M / 60M INFO General (launcher.cpp : 297) Length cutoff: 111 83s 0:00:00.164 1M / 60M INFO General (launcher.cpp : 295) Read length relative cutoff 1.5 converted to 101 83s 0:00:00.164 1M / 60M INFO General (launcher.cpp : 296) Read length absolute cutoff 130 bp converted to 101 83s 0:00:00.164 1M / 60M INFO General (launcher.cpp : 297) Length cutoff: 101 83s 0:00:00.164 1M / 60M INFO General (launcher.cpp : 664) ExSPAnder repeat resolving tool finished 83s 0:00:00.164 1M / 60M INFO StageManager (stage.cpp : 185) STAGE == Contig Output (id: contig_output) 83s 0:00:00.164 1M / 60M INFO General (contig_output.hpp : 16) Outputting contigs to /tmp/tmp.cMLX1ajB23/spades_test/K49/before_rr.fasta 83s 0:00:00.164 1M / 60M INFO General (contig_output_stage.cpp : 151) Writing GFA graph to /tmp/tmp.cMLX1ajB23/spades_test/K49/assembly_graph_with_scaffolds.gfa 83s 0:00:00.164 1M / 60M INFO General (contig_output_stage.cpp : 165) Outputting FastG graph to /tmp/tmp.cMLX1ajB23/spades_test/K49/assembly_graph.fastg 83s 0:00:00.164 1M / 60M INFO General (contig_output_stage.cpp : 98) Outputting contigs to /tmp/tmp.cMLX1ajB23/spades_test/K49/transcripts.fasta 83s 0:00:00.164 1M / 60M INFO General (contig_output_stage.cpp : 104) Outputting FastG paths to /tmp/tmp.cMLX1ajB23/spades_test/K49/transcripts.paths 83s 0:00:00.164 1M / 60M INFO General (contig_output_stage.cpp : 111) Populating GFA with scaffold paths 83s 0:00:00.164 1M / 60M INFO General (pipeline.cpp : 287) SPAdes finished 83s 0:00:00.164 1M / 60M INFO General (main.cpp : 136) Assembling time: 0 hours 0 minutes 0 seconds 83s 83s ===== K49 finished. 83s 83s 83s ===== Copy files started. 83s 83s 83s == Running: /usr/bin/python3 /usr/share/spades/spades_pipeline/scripts/copy_files.py /tmp/tmp.cMLX1ajB23/spades_test/K49/before_rr.fasta /tmp/tmp.cMLX1ajB23/spades_test/before_rr.fasta /tmp/tmp.cMLX1ajB23/spades_test/K49/assembly_graph_after_simplification.gfa /tmp/tmp.cMLX1ajB23/spades_test/assembly_graph_after_simplification.gfa /tmp/tmp.cMLX1ajB23/spades_test/K49/transcripts.fasta /tmp/tmp.cMLX1ajB23/spades_test/transcripts.fasta /tmp/tmp.cMLX1ajB23/spades_test/K49/transcripts.paths /tmp/tmp.cMLX1ajB23/spades_test/transcripts.paths /tmp/tmp.cMLX1ajB23/spades_test/K49/assembly_graph_with_scaffolds.gfa /tmp/tmp.cMLX1ajB23/spades_test/assembly_graph_with_scaffolds.gfa /tmp/tmp.cMLX1ajB23/spades_test/K49/assembly_graph.fastg /tmp/tmp.cMLX1ajB23/spades_test/assembly_graph.fastg /tmp/tmp.cMLX1ajB23/spades_test/K49/hard_filtered_final_paths.fasta /tmp/tmp.cMLX1ajB23/spades_test/hard_filtered_transcripts.fasta /tmp/tmp.cMLX1ajB23/spades_test/K49/soft_filtered_final_paths.fasta /tmp/tmp.cMLX1ajB23/spades_test/soft_filtered_transcripts.fasta 83s 83s 83s ===== Copy files finished. 83s 83s 83s ===== Assembling finished. 83s 83s 83s ===== Check test started. 83s 83s 83s == Running: /usr/bin/python3 /usr/share/spades/spades_pipeline/scripts/check_test_script.py --mode rna --result_transcripts_filename /tmp/tmp.cMLX1ajB23/spades_test/transcripts.fasta 83s 83s ========= TEST PASSED CORRECTLY. 83s 83s ===== Check test finished. 83s 83s 83s ===== Breaking scaffolds started. 83s 83s 83s == Running: /usr/bin/python3 /usr/share/spades/spades_pipeline/scripts/breaking_scaffolds_script.py --result_scaffolds_filename /tmp/tmp.cMLX1ajB23/spades_test/scaffolds.fasta --misc_dir /tmp/tmp.cMLX1ajB23/spades_test/misc --threshold_for_breaking_scaffolds 3 83s 83s 83s ===== Breaking scaffolds finished. 83s 83s 83s ===== Terminate started. 83s 83s 83s ===== Terminate finished. 83s 83s * Assembled contigs are in /tmp/tmp.cMLX1ajB23/spades_test/contigs.fasta 83s * Assembled transcripts are in /tmp/tmp.cMLX1ajB23/spades_test/transcripts.fasta 83s * Paths in the assembly graph corresponding to the transcripts are in /tmp/tmp.cMLX1ajB23/spades_test/transcripts.paths 83s * Hard filtered transcripts are in /tmp/tmp.cMLX1ajB23/spades_test/hard_filtered_transcripts.fasta 83s * Soft filtered transcripts are in /tmp/tmp.cMLX1ajB23/spades_test/soft_filtered_transcripts.fasta 83s * Assembly graph is in /tmp/tmp.cMLX1ajB23/spades_test/assembly_graph.fastg 83s * Assembly graph in GFA format is in /tmp/tmp.cMLX1ajB23/spades_test/assembly_graph_with_scaffolds.gfa 83s 83s ======= SPAdes pipeline finished. 83s 83s SPAdes log can be found here: /tmp/tmp.cMLX1ajB23/spades_test/spades.log 83s 83s Thank you for using SPAdes! 83s + command -v truspades 83s + truspades --test 83s WARNING: TruSPAdes is deprecated since version 3.15 83s Generating truseq dataset from input directories: 83s /usr/share/spades/test_dataset_truspades 83s Printing dataset to /tmp/tmp.cMLX1ajB23/spades_test_truspades/dataset.info 83s Dataset generated. See result in /tmp/tmp.cMLX1ajB23/spades_test_truspades/dataset.info 83s Launching truSPAdes assembly in 8 threads 83s You can find logs for separate barcodes in /tmp/tmp.cMLX1ajB23/spades_test_truspades/logs 83s Starting: BC_B 83s Starting: BC_A 85s Failed to finish: BC_A 85s Failed to finish: BC_B 85s 2 barcodes failed to assemble 85s Warning: could not find assembly results for barcode BC_B 85s Warning: could not find assembly results for barcode BC_A 85s Assembled virtual long TruSeq reads can be found in /tmp/tmp.cMLX1ajB23/spades_test_truspades/TSLR.fasta 85s TruSPAdes launch successfully finished 85s TruSPAdes test launch failed: incorrect output files 85s + echo W: truspades failed its self-test suite. 85s + rm -rf /tmp/tmp.cMLX1ajB23 85s W: truspades failed its self-test suite. 85s autopkgtest [03:41:50]: test run-upstreams-tests: -----------------------] 86s autopkgtest [03:41:51]: test run-upstreams-tests: - - - - - - - - - - results - - - - - - - - - - 86s run-upstreams-tests PASS 86s autopkgtest [03:41:51]: @@@@@@@@@@@@@@@@@@@@ summary 86s run-upstreams-tests PASS 89s nova [W] Skipping flock for amd64 89s Creating nova instance adt-questing-amd64-spades-20250504-034025-juju-7f2275-prod-proposed-migration-environment-21-a59e9744-b842-404b-b37a-ee2f7455a8a1 from image adt/ubuntu-questing-amd64-server-20250504.img (UUID 4574af64-5239-489d-bb56-4fb13b26ba3b)... 89s nova [W] Timed out waiting for c194371b-19a8-484d-b39b-e4e5dd36513b to get deleted.