0s autopkgtest [01:13:33]: starting date and time: 2026-02-05 01:13:33+0000 0s autopkgtest [01:13:33]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op 0s autopkgtest [01:13:33]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.qwu2u93r/out --timeout-copy=6000 --needs-internet=try --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:glibc,src:chiark-tcl --apt-upgrade augustus --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=glibc/2.42-2ubuntu5 chiark-tcl/1.3.7build1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-cpu2-ram4-disk20-arm64 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@sto01-arm64-24.secgroup --name adt-resolute-arm64-augustus-20260205-011333-juju-7f2275-prod-proposed-migration-environment-15-cf26fb65-ce2c-46f6-b5d0-ec1a82832656 --image adt/ubuntu-resolute-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --net-id=net_prod-autopkgtest-workers-arm64 -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 5s Creating nova instance adt-resolute-arm64-augustus-20260205-011333-juju-7f2275-prod-proposed-migration-environment-15-cf26fb65-ce2c-46f6-b5d0-ec1a82832656 from image adt/ubuntu-resolute-arm64-server-20260204.img (UUID f58d981d-b271-4157-b9b1-fd704695563c)... 61s autopkgtest [01:14:34]: testbed dpkg architecture: arm64 61s autopkgtest [01:14:34]: testbed apt version: 3.1.14 61s autopkgtest [01:14:34]: @@@@@@@@@@@@@@@@@@@@ test bed setup 61s autopkgtest [01:14:34]: testbed release detected to be: None 62s autopkgtest [01:14:35]: updating testbed package index (apt update) 63s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [124 kB] 63s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 63s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 63s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 63s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [1768 kB] 63s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [35.4 kB] 63s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/restricted Sources [5260 B] 63s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [228 kB] 63s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 Packages [262 kB] 63s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 c-n-f Metadata [7248 B] 63s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/restricted arm64 Packages [52.9 kB] 63s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/restricted arm64 c-n-f Metadata [328 B] 63s Get:13 http://ftpmaster.internal/ubuntu resolute-proposed/universe arm64 Packages [1540 kB] 63s Get:14 http://ftpmaster.internal/ubuntu resolute-proposed/universe arm64 c-n-f Metadata [40.2 kB] 63s Get:15 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse arm64 Packages [26.0 kB] 63s Get:16 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse arm64 c-n-f Metadata [776 B] 67s Fetched 4091 kB in 1s (4086 kB/s) 68s Reading package lists... 69s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 69s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 69s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 69s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 70s Reading package lists... 70s Reading package lists... 70s Building dependency tree... 70s Reading state information... 70s Calculating upgrade... 71s The following packages will be upgraded: 71s libc-bin libc-gconv-modules-extra libc6 locales python3-linkify-it 71s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 71s Need to get 7881 kB of archives. 71s After this operation, 0 B of additional disk space will be used. 71s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 libc-gconv-modules-extra arm64 2.42-2ubuntu5 [1413 kB] 71s Get:2 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 libc6 arm64 2.42-2ubuntu5 [1594 kB] 71s Get:3 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 libc-bin arm64 2.42-2ubuntu5 [599 kB] 71s Get:4 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 locales all 2.42-2ubuntu5 [4255 kB] 71s Get:5 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-linkify-it all 2.0.3-1ubuntu3 [19.4 kB] 71s dpkg-preconfigure: unable to re-open stdin: No such file or directory 71s Fetched 7881 kB in 0s (24.9 MB/s) 72s (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 ... 89360 files and directories currently installed.) 72s Preparing to unpack .../libc-gconv-modules-extra_2.42-2ubuntu5_arm64.deb ... 72s Unpacking libc-gconv-modules-extra:arm64 (2.42-2ubuntu5) over (2.42-2ubuntu4) ... 72s Setting up libc-gconv-modules-extra:arm64 (2.42-2ubuntu5) ... 72s (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 ... 89360 files and directories currently installed.) 72s Preparing to unpack .../libc6_2.42-2ubuntu5_arm64.deb ... 72s Unpacking libc6:arm64 (2.42-2ubuntu5) over (2.42-2ubuntu4) ... 72s Setting up libc6:arm64 (2.42-2ubuntu5) ... 72s (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 ... 89360 files and directories currently installed.) 72s Preparing to unpack .../libc-bin_2.42-2ubuntu5_arm64.deb ... 73s Unpacking libc-bin (2.42-2ubuntu5) over (2.42-2ubuntu4) ... 73s Setting up libc-bin (2.42-2ubuntu5) ... 73s (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 ... 89360 files and directories currently installed.) 73s Preparing to unpack .../locales_2.42-2ubuntu5_all.deb ... 73s Unpacking locales (2.42-2ubuntu5) over (2.42-2ubuntu4) ... 73s Preparing to unpack .../python3-linkify-it_2.0.3-1ubuntu3_all.deb ... 73s Unpacking python3-linkify-it (2.0.3-1ubuntu3) over (2.0.3-1ubuntu2) ... 73s Setting up locales (2.42-2ubuntu5) ... 74s Generating locales (this might take a while)... 76s en_US.UTF-8... done 76s Generation complete. 76s Setting up python3-linkify-it (2.0.3-1ubuntu3) ... 76s Processing triggers for man-db (2.13.1-1) ... 77s Processing triggers for systemd (259-1ubuntu3) ... 78s autopkgtest [01:14:51]: upgrading testbed (apt dist-upgrade and autopurge) 78s Reading package lists... 79s Building dependency tree... 79s Reading state information... 79s Calculating upgrade... 79s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 80s Reading package lists... 80s Building dependency tree... 80s Reading state information... 80s Solving dependencies... 80s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 83s autopkgtest [01:14:56]: testbed running kernel: Linux 6.18.0-9-generic #9-Ubuntu SMP PREEMPT_DYNAMIC Mon Jan 12 16:41:39 UTC 2026 83s autopkgtest [01:14:56]: @@@@@@@@@@@@@@@@@@@@ apt-source augustus 91s Get:1 http://ftpmaster.internal/ubuntu resolute/universe augustus 3.5.0+dfsg-5build3 (dsc) [2370 B] 91s Get:2 http://ftpmaster.internal/ubuntu resolute/universe augustus 3.5.0+dfsg-5build3 (tar) [152 MB] 91s Get:3 http://ftpmaster.internal/ubuntu resolute/universe augustus 3.5.0+dfsg-5build3 (diff) [20.6 kB] 91s gpgv: Signature made Sat Nov 1 18:44:53 2025 UTC 91s gpgv: using RSA key 4D0BE12F0E4776D8AACE9696E66C775AEBFE6C7D 91s gpgv: Can't check signature: No public key 91s dpkg-source: warning: cannot verify inline signature for ./augustus_3.5.0+dfsg-5build3.dsc: no acceptable signature found 100s autopkgtest [01:15:13]: testing package augustus version 3.5.0+dfsg-5build3 101s autopkgtest [01:15:14]: build not needed 137s autopkgtest [01:15:50]: test test-example: preparing testbed 137s Reading package lists... 138s Building dependency tree... 138s Reading state information... 138s Solving dependencies... 138s The following NEW packages will be installed: 138s augustus augustus-data augustus-doc libbamtools2.5.3 138s libboost-iostreams1.88.0 libcolamd3 libdeflate0 libgomp1 libgsl28 138s libgslcblas0 libhts3t64 libhtscodecs2 libmysql++3t64 libmysqlclient24 138s libsuitesparseconfig7 mysql-common 139s 0 upgraded, 16 newly installed, 0 to remove and 0 not upgraded. 139s Need to get 50.9 MB of archives. 139s After this operation, 315 MB of additional disk space will be used. 139s Get:1 http://ftpmaster.internal/ubuntu resolute/universe arm64 libbamtools2.5.3 arm64 2.5.3+dfsg-1 [134 kB] 139s Get:2 http://ftpmaster.internal/ubuntu resolute/main arm64 libboost-iostreams1.88.0 arm64 1.88.0-1.4ubuntu3 [261 kB] 139s Get:3 http://ftpmaster.internal/ubuntu resolute/main arm64 libgomp1 arm64 15.2.0-12ubuntu1 [147 kB] 139s Get:4 http://ftpmaster.internal/ubuntu resolute/main arm64 libsuitesparseconfig7 arm64 1:7.12.1+dfsg-1 [22.0 kB] 139s Get:5 http://ftpmaster.internal/ubuntu resolute/main arm64 libcolamd3 arm64 1:7.12.1+dfsg-1 [27.1 kB] 139s Get:6 http://ftpmaster.internal/ubuntu resolute/universe arm64 libgslcblas0 arm64 2.8+dfsg-6 [93.1 kB] 139s Get:7 http://ftpmaster.internal/ubuntu resolute/universe arm64 libgsl28 arm64 2.8+dfsg-6 [966 kB] 139s Get:8 http://ftpmaster.internal/ubuntu resolute/main arm64 libdeflate0 arm64 1.23-2 [46.4 kB] 139s Get:9 http://ftpmaster.internal/ubuntu resolute/universe arm64 libhtscodecs2 arm64 1.6.1-2build1 [83.8 kB] 139s Get:10 http://ftpmaster.internal/ubuntu resolute/universe arm64 libhts3t64 arm64 1.22.1+ds2-1 [442 kB] 139s Get:11 http://ftpmaster.internal/ubuntu resolute/main arm64 mysql-common all 5.8+1.1.1ubuntu2 [7002 B] 139s Get:12 http://ftpmaster.internal/ubuntu resolute/main arm64 libmysqlclient24 arm64 8.4.8-0ubuntu1 [1244 kB] 139s Get:13 http://ftpmaster.internal/ubuntu resolute/universe arm64 libmysql++3t64 arm64 3.2.5-2.3build2 [97.0 kB] 139s Get:14 http://ftpmaster.internal/ubuntu resolute/universe arm64 augustus-data all 3.5.0+dfsg-5build3 [22.3 MB] 140s Get:15 http://ftpmaster.internal/ubuntu resolute/universe arm64 augustus arm64 3.5.0+dfsg-5build3 [1666 kB] 140s Get:16 http://ftpmaster.internal/ubuntu resolute/universe arm64 augustus-doc all 3.5.0+dfsg-5build3 [23.4 MB] 142s Fetched 50.9 MB in 3s (17.9 MB/s) 142s Selecting previously unselected package libbamtools2.5.3:arm64. 142s (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 ... 89360 files and directories currently installed.) 142s Preparing to unpack .../00-libbamtools2.5.3_2.5.3+dfsg-1_arm64.deb ... 142s Unpacking libbamtools2.5.3:arm64 (2.5.3+dfsg-1) ... 142s Selecting previously unselected package libboost-iostreams1.88.0:arm64. 142s Preparing to unpack .../01-libboost-iostreams1.88.0_1.88.0-1.4ubuntu3_arm64.deb ... 142s Unpacking libboost-iostreams1.88.0:arm64 (1.88.0-1.4ubuntu3) ... 142s Selecting previously unselected package libgomp1:arm64. 142s Preparing to unpack .../02-libgomp1_15.2.0-12ubuntu1_arm64.deb ... 142s Unpacking libgomp1:arm64 (15.2.0-12ubuntu1) ... 142s Selecting previously unselected package libsuitesparseconfig7:arm64. 142s Preparing to unpack .../03-libsuitesparseconfig7_1%3a7.12.1+dfsg-1_arm64.deb ... 142s Unpacking libsuitesparseconfig7:arm64 (1:7.12.1+dfsg-1) ... 142s Selecting previously unselected package libcolamd3:arm64. 142s Preparing to unpack .../04-libcolamd3_1%3a7.12.1+dfsg-1_arm64.deb ... 142s Unpacking libcolamd3:arm64 (1:7.12.1+dfsg-1) ... 142s Selecting previously unselected package libgslcblas0:arm64. 142s Preparing to unpack .../05-libgslcblas0_2.8+dfsg-6_arm64.deb ... 142s Unpacking libgslcblas0:arm64 (2.8+dfsg-6) ... 142s Selecting previously unselected package libgsl28:arm64. 142s Preparing to unpack .../06-libgsl28_2.8+dfsg-6_arm64.deb ... 142s Unpacking libgsl28:arm64 (2.8+dfsg-6) ... 142s Selecting previously unselected package libdeflate0:arm64. 142s Preparing to unpack .../07-libdeflate0_1.23-2_arm64.deb ... 142s Unpacking libdeflate0:arm64 (1.23-2) ... 142s Selecting previously unselected package libhtscodecs2:arm64. 142s Preparing to unpack .../08-libhtscodecs2_1.6.1-2build1_arm64.deb ... 142s Unpacking libhtscodecs2:arm64 (1.6.1-2build1) ... 142s Selecting previously unselected package libhts3t64:arm64. 142s Preparing to unpack .../09-libhts3t64_1.22.1+ds2-1_arm64.deb ... 142s Unpacking libhts3t64:arm64 (1.22.1+ds2-1) ... 142s Selecting previously unselected package mysql-common. 142s Preparing to unpack .../10-mysql-common_5.8+1.1.1ubuntu2_all.deb ... 142s Unpacking mysql-common (5.8+1.1.1ubuntu2) ... 142s Selecting previously unselected package libmysqlclient24:arm64. 142s Preparing to unpack .../11-libmysqlclient24_8.4.8-0ubuntu1_arm64.deb ... 142s Unpacking libmysqlclient24:arm64 (8.4.8-0ubuntu1) ... 142s Selecting previously unselected package libmysql++3t64:arm64. 142s Preparing to unpack .../12-libmysql++3t64_3.2.5-2.3build2_arm64.deb ... 142s Unpacking libmysql++3t64:arm64 (3.2.5-2.3build2) ... 142s Selecting previously unselected package augustus-data. 142s Preparing to unpack .../13-augustus-data_3.5.0+dfsg-5build3_all.deb ... 142s Unpacking augustus-data (3.5.0+dfsg-5build3) ... 143s Selecting previously unselected package augustus. 143s Preparing to unpack .../14-augustus_3.5.0+dfsg-5build3_arm64.deb ... 143s Unpacking augustus (3.5.0+dfsg-5build3) ... 143s Selecting previously unselected package augustus-doc. 143s Preparing to unpack .../15-augustus-doc_3.5.0+dfsg-5build3_all.deb ... 143s Unpacking augustus-doc (3.5.0+dfsg-5build3) ... 144s Setting up libhtscodecs2:arm64 (1.6.1-2build1) ... 144s Setting up mysql-common (5.8+1.1.1ubuntu2) ... 144s update-alternatives: using /etc/mysql/my.cnf.fallback to provide /etc/mysql/my.cnf (my.cnf) in auto mode 144s Setting up libgslcblas0:arm64 (2.8+dfsg-6) ... 144s Setting up libdeflate0:arm64 (1.23-2) ... 144s Setting up libboost-iostreams1.88.0:arm64 (1.88.0-1.4ubuntu3) ... 144s Setting up libgomp1:arm64 (15.2.0-12ubuntu1) ... 144s Setting up libmysqlclient24:arm64 (8.4.8-0ubuntu1) ... 144s Setting up augustus-data (3.5.0+dfsg-5build3) ... 144s Setting up augustus-doc (3.5.0+dfsg-5build3) ... 144s Setting up libbamtools2.5.3:arm64 (2.5.3+dfsg-1) ... 144s Setting up libhts3t64:arm64 (1.22.1+ds2-1) ... 144s Setting up libsuitesparseconfig7:arm64 (1:7.12.1+dfsg-1) ... 144s Setting up libgsl28:arm64 (2.8+dfsg-6) ... 144s Setting up libmysql++3t64:arm64 (3.2.5-2.3build2) ... 144s Setting up libcolamd3:arm64 (1:7.12.1+dfsg-1) ... 144s Setting up augustus (3.5.0+dfsg-5build3) ... 144s Processing triggers for man-db (2.13.1-1) ... 144s Processing triggers for libc-bin (2.42-2ubuntu5) ... 146s autopkgtest [01:15:59]: test test-example: [----------------------- 146s # This output was generated with AUGUSTUS (version 3.5.0). 146s # AUGUSTUS is a gene prediction tool written by M. Stanke (mario.stanke@uni-greifswald.de), 146s # O. Keller, S. König, L. Gerischer, L. Romoth, Katharina Hoff, Henry Mehlan and Daniel Honsel. 146s # Please cite: Mario Stanke, Mark Diekhans, Robert Baertsch, David Haussler (2008), 146s # Using native and syntenically mapped cDNA alignments to improve de novo gene finding 146s # Bioinformatics 24: 637-644, doi 10.1093/bioinformatics/btn013 146s # No extrinsic information on sequences given. 146s # Sources of extrinsic information: M RM 146s # Initializing the parameters using config directory /usr/share/augustus/config/ ... 146s # human version. Using species specific transition matrix: /usr/share/augustus/config/species/human/human_trans_shadow_partial_utr.pbl 146s # Looks like /tmp/autopkgtest.axahEj/build.6tW/src/examples/example.fa is in fasta format. 146s # We have hints for 0 sequences and for 0 of the sequences in the input set. 146s # 146s # ----- prediction on sequence number 1 (length = 9453, name = HS04636) ----- 146s # 146s # Predicted genes for sequence number 1 on both strands 146s # start gene g1 146s HS04636 AUGUSTUS gene 836 8857 1 + . g1 146s HS04636 AUGUSTUS transcript 836 8857 . + . g1.t1 146s HS04636 AUGUSTUS tss 836 836 . + . transcript_id "g1.t1"; gene_id "g1"; 146s HS04636 AUGUSTUS exon 836 1017 . + . transcript_id "g1.t1"; gene_id "g1"; 146s HS04636 AUGUSTUS start_codon 966 968 . + 0 transcript_id "g1.t1"; gene_id "g1"; 146s HS04636 AUGUSTUS CDS 966 1017 . + 0 transcript_id "g1.t1"; gene_id "g1"; 146s HS04636 AUGUSTUS CDS 1818 1934 . + 2 transcript_id "g1.t1"; gene_id "g1"; 146s HS04636 AUGUSTUS exon 1818 1934 . + . transcript_id "g1.t1"; gene_id "g1"; 146s HS04636 AUGUSTUS CDS 2055 2198 . + 2 transcript_id "g1.t1"; gene_id "g1"; 146s HS04636 AUGUSTUS exon 2055 2198 . + . transcript_id "g1.t1"; gene_id "g1"; 146s HS04636 AUGUSTUS CDS 2852 2995 . + 2 transcript_id "g1.t1"; gene_id "g1"; 146s HS04636 AUGUSTUS exon 2852 2995 . + . transcript_id "g1.t1"; gene_id "g1"; 146s HS04636 AUGUSTUS CDS 3426 3607 . + 2 transcript_id "g1.t1"; gene_id "g1"; 146s HS04636 AUGUSTUS exon 3426 3607 . + . transcript_id "g1.t1"; gene_id "g1"; 146s HS04636 AUGUSTUS CDS 4340 4423 . + 0 transcript_id "g1.t1"; gene_id "g1"; 146s HS04636 AUGUSTUS exon 4340 4423 . + . transcript_id "g1.t1"; gene_id "g1"; 146s HS04636 AUGUSTUS CDS 4543 4789 . + 0 transcript_id "g1.t1"; gene_id "g1"; 146s HS04636 AUGUSTUS exon 4543 4789 . + . transcript_id "g1.t1"; gene_id "g1"; 146s HS04636 AUGUSTUS CDS 5072 5358 . + 2 transcript_id "g1.t1"; gene_id "g1"; 146s HS04636 AUGUSTUS exon 5072 5358 . + . transcript_id "g1.t1"; gene_id "g1"; 146s HS04636 AUGUSTUS CDS 5860 6007 . + 0 transcript_id "g1.t1"; gene_id "g1"; 146s HS04636 AUGUSTUS exon 5860 6007 . + . transcript_id "g1.t1"; gene_id "g1"; 146s HS04636 AUGUSTUS CDS 6494 6903 . + 2 transcript_id "g1.t1"; gene_id "g1"; 146s HS04636 AUGUSTUS exon 6494 8857 . + . transcript_id "g1.t1"; gene_id "g1"; 146s HS04636 AUGUSTUS stop_codon 6901 6903 . + 0 transcript_id "g1.t1"; gene_id "g1"; 146s HS04636 AUGUSTUS tts 8857 8857 . + . transcript_id "g1.t1"; gene_id "g1"; 146s # protein sequence = [MLARALLLCAVLALSHTANPCCSHPCQNRGVCMSVGFDQYKCDCTRTGFYGENCSTPEFLTRIKLFLKPTPNTVHYIL 146s # THFKGFWNVVNNIPFLRNAIMSYVLTSRSHLIDSPPTYNADYGYKSWEAFSNLSYYTRALPPVPDDCPTPLGVKGKKQLPDSNEIVEKLLLRRKFIPD 146s # PQGSNMMFAFFAQHFTHQFFKTDHKRGPAFTNGLGHGVDLNHIYGETLARQRKLRLFKDGKMKYQIIDGEMYPPTVKDTQAEMIYPPQVPEHLRFAVG 146s # QEVFGLVPGLMMYATIWLREHNRVCDVLKQEHPEWGDEQLFQTSRLILIGETIKIVIEDYVQHLSGYHFKLKFDPELLFNKQFQYQNRIAAEFNTLYH 146s # WHPLLPDTFQIHDQKYNYQQFIYNNSILLEHGITQFVESFTRQIAGRVAGGRNVPPAVQKVSQASIDQSRQMKYQSFNEYRKRFMLKPYESFEELTGE 146s # KEMSAELEALYGDIDAVELYPALLVEKPRPDAIFGETMVEVGAPFSLKGLMGNVICSPAYWKPSTFGGEVGFQIINTASIQSLICNNVKGCPFTSFSV 146s # PDPELIKTVTINASSSRSGLDDINPTVLLKERSTEL] 146s # Evidence for and against this transcript: 146s # % of transcript supported by hints (any source): 0 146s # CDS exons: 0/10 146s # CDS introns: 0/9 146s # 5'UTR exons and introns: 0/1 146s # 3'UTR exons and introns: 0/1 146s # hint groups fully obeyed: 0 146s # incompatible hint groups: 0 146s # end gene g1 146s ### 146s # 146s # ----- prediction on sequence number 2 (length = 2344, name = HS08198) ----- 146s # 146s # Predicted genes for sequence number 2 on both strands 147s # start gene g2 147s HS08198 AUGUSTUS gene 86 2344 1 + . g2 147s HS08198 AUGUSTUS transcript 86 2344 . + . g2.t1 147s HS08198 AUGUSTUS tss 86 86 . + . transcript_id "g2.t1"; gene_id "g2"; 147s HS08198 AUGUSTUS exon 86 582 . + . transcript_id "g2.t1"; gene_id "g2"; 147s HS08198 AUGUSTUS start_codon 445 447 . + 0 transcript_id "g2.t1"; gene_id "g2"; 147s HS08198 AUGUSTUS CDS 445 582 . + 0 transcript_id "g2.t1"; gene_id "g2"; 147s HS08198 AUGUSTUS CDS 812 894 . + 0 transcript_id "g2.t1"; gene_id "g2"; 147s HS08198 AUGUSTUS exon 812 894 . + . transcript_id "g2.t1"; gene_id "g2"; 147s HS08198 AUGUSTUS CDS 1053 1123 . + 1 transcript_id "g2.t1"; gene_id "g2"; 147s HS08198 AUGUSTUS exon 1053 1123 . + . transcript_id "g2.t1"; gene_id "g2"; 147s HS08198 AUGUSTUS CDS 1208 1315 . + 2 transcript_id "g2.t1"; gene_id "g2"; 147s HS08198 AUGUSTUS exon 1208 1315 . + . transcript_id "g2.t1"; gene_id "g2"; 147s HS08198 AUGUSTUS CDS 1587 1688 . + 2 transcript_id "g2.t1"; gene_id "g2"; 147s HS08198 AUGUSTUS exon 1587 1688 . + . transcript_id "g2.t1"; gene_id "g2"; 147s # protein sequence = [MLPPGTATLLTLLLAAGSLGQKPQRPRRPASPISTIQPKANFDAQQEQGHRAEATTLHVAPQGTAMAVSTFRKLDGIC 147s # WQVRQLYGDTGVLGRFLLQARGARGAVHVVVAETDYQSFAVLYLERAGQLSVKLYARSLPVSDSVLSGFEQRVQEAHLTEDQIFYFPKY] 147s # Evidence for and against this transcript: 147s # % of transcript supported by hints (any source): 0 147s # CDS exons: 0/5 147s # CDS introns: 0/5 147s # 5'UTR exons and introns: 0/1 147s # 3'UTR exons and introns: 0/0 147s # hint groups fully obeyed: 0 147s # incompatible hint groups: 0 147s # end gene g2 147s ### 147s # command line: 147s # augustus --species=human --UTR=on /tmp/autopkgtest.axahEj/build.6tW/src/examples/example.fa 147s # This output was generated with AUGUSTUS (version 3.5.0). 147s # AUGUSTUS is a gene prediction tool written by M. Stanke (mario.stanke@uni-greifswald.de), 147s # O. Keller, S. König, L. Gerischer, L. Romoth, Katharina Hoff, Henry Mehlan and Daniel Honsel. 147s # Please cite: Mario Stanke, Mark Diekhans, Robert Baertsch, David Haussler (2008), 147s # Using native and syntenically mapped cDNA alignments to improve de novo gene finding 147s # Bioinformatics 24: 637-644, doi 10.1093/bioinformatics/btn013 147s # Sources of extrinsic information: M P E RM 147s # Setting 1group1gene for E. 147s # reading in the file /tmp/autopkgtest.axahEj/build.6tW/src/examples/hints.gff ... 147s # Have extrinsic information about 2 sequences (in the specified range). 147s # Initializing the parameters using config directory /usr/share/augustus/config/ ... 147s # human version. Using default transition matrix. 147s # Looks like /tmp/autopkgtest.axahEj/build.6tW/src/examples/example.fa is in fasta format. 147s # We have hints for 2 sequences and for 2 of the sequences in the input set. 147s # 147s # ----- prediction on sequence number 1 (length = 9453, name = HS04636) ----- 147s # 147s # Predicted genes for sequence number 1 on both strands 149s # start gene g1 149s HS04636 AUGUSTUS gene 966 7633 1 + . g1 149s HS04636 AUGUSTUS transcript 966 7633 . + . g1.t1 149s HS04636 AUGUSTUS start_codon 966 968 . + 0 transcript_id "g1.t1"; gene_id "g1"; 149s HS04636 AUGUSTUS CDS 966 1017 . + 0 transcript_id "g1.t1"; gene_id "g1"; 149s HS04636 AUGUSTUS CDS 1818 1934 . + 2 transcript_id "g1.t1"; gene_id "g1"; 149s HS04636 AUGUSTUS CDS 2055 2198 . + 2 transcript_id "g1.t1"; gene_id "g1"; 149s HS04636 AUGUSTUS CDS 2852 2995 . + 2 transcript_id "g1.t1"; gene_id "g1"; 149s HS04636 AUGUSTUS CDS 3426 3607 . + 2 transcript_id "g1.t1"; gene_id "g1"; 149s HS04636 AUGUSTUS CDS 4340 4423 . + 0 transcript_id "g1.t1"; gene_id "g1"; 149s HS04636 AUGUSTUS CDS 4543 4789 . + 0 transcript_id "g1.t1"; gene_id "g1"; 149s HS04636 AUGUSTUS CDS 5072 5358 . + 2 transcript_id "g1.t1"; gene_id "g1"; 149s HS04636 AUGUSTUS CDS 5860 6007 . + 0 transcript_id "g1.t1"; gene_id "g1"; 149s HS04636 AUGUSTUS CDS 6494 6554 . + 2 transcript_id "g1.t1"; gene_id "g1"; 149s HS04636 AUGUSTUS CDS 7627 7633 . + 1 transcript_id "g1.t1"; gene_id "g1"; 149s HS04636 AUGUSTUS stop_codon 7631 7633 . + 0 transcript_id "g1.t1"; gene_id "g1"; 149s # protein sequence = [MLARALLLCAVLALSHTANPCCSHPCQNRGVCMSVGFDQYKCDCTRTGFYGENCSTPEFLTRIKLFLKPTPNTVHYIL 149s # THFKGFWNVVNNIPFLRNAIMSYVLTSRSHLIDSPPTYNADYGYKSWEAFSNLSYYTRALPPVPDDCPTPLGVKGKKQLPDSNEIVEKLLLRRKFIPD 149s # PQGSNMMFAFFAQHFTHQFFKTDHKRGPAFTNGLGHGVDLNHIYGETLARQRKLRLFKDGKMKYQIIDGEMYPPTVKDTQAEMIYPPQVPEHLRFAVG 149s # QEVFGLVPGLMMYATIWLREHNRVCDVLKQEHPEWGDEQLFQTSRLILIGETIKIVIEDYVQHLSGYHFKLKFDPELLFNKQFQYQNRIAAEFNTLYH 149s # WHPLLPDTFQIHDQKYNYQQFIYNNSILLEHGITQFVESFTRQIAGRVAGGRNVPPAVQKVSQASIDQSRQMKYQSFNEYRKRFMLKPYESFEELTGE 149s # KEMSAELEALYGDIDAVELV] 149s # Evidence for and against this transcript: 149s # % of transcript supported by hints (any source): 4.76 149s # CDS exons: 1/11 149s # P: 1 149s # CDS introns: 0/10 149s # 5'UTR exons and introns: 0/0 149s # 3'UTR exons and introns: 0/0 149s # hint groups fully obeyed: 2 149s # E: 1 149s # P: 1 149s # incompatible hint groups: 2 149s # M: 1 149s # P: 1 149s # end gene g1 149s ### 149s # 149s # ----- prediction on sequence number 2 (length = 2344, name = HS08198) ----- 149s # 149s # Predicted genes for sequence number 2 on both strands 149s autopkgtest [01:16:00]: test test-example: -----------------------] 149s # start gene g2 149s HS08198 AUGUSTUS gene 445 2344 1 + . g2 149s HS08198 AUGUSTUS transcript 445 2344 . + . g2.t1 149s HS08198 AUGUSTUS start_codon 445 447 . + 0 transcript_id "g2.t1"; gene_id "g2"; 149s HS08198 AUGUSTUS CDS 445 582 . + 0 transcript_id "g2.t1"; gene_id "g2"; 149s HS08198 AUGUSTUS CDS 758 894 . + 0 transcript_id "g2.t1"; gene_id "g2"; 149s HS08198 AUGUSTUS CDS 1053 1123 . + 1 transcript_id "g2.t1"; gene_id "g2"; 149s HS08198 AUGUSTUS CDS 1208 1315 . + 2 transcript_id "g2.t1"; gene_id "g2"; 149s HS08198 AUGUSTUS CDS 1587 1688 . + 2 transcript_id "g2.t1"; gene_id "g2"; 149s # protein sequence = [MLPPGTATLLTLLLAAGSLGQKPQRPRRPASPISTIQPKANFDAQQFAGTWLLVAVGSACRFLQEQGHRAEATTLHVA 149s # PQGTAMAVSTFRKLDGICWQVRQLYGDTGVLGRFLLQARGARGAVHVVVAETDYQSFAVLYLERAGQLSVKLYARSLPVSDSVLSGFEQRVQEAHLTE 149s # DQIFYFPKY] 149s # Evidence for and against this transcript: 149s # % of transcript supported by hints (any source): 10 149s # CDS exons: 0/5 149s # CDS introns: 1/5 149s # M: 1 149s # 5'UTR exons and introns: 0/0 149s # 3'UTR exons and introns: 0/0 149s # hint groups fully obeyed: 2 149s # E: 1 149s # M: 1 149s # incompatible hint groups: 1 149s # M: 1 149s # end gene g2 149s ### 149s # command line: 149s # augustus --species=human --hintsfile=/tmp/autopkgtest.axahEj/build.6tW/src/examples/hints.gff --extrinsicCfgFile=/usr/share/augustus/config/extrinsic/extrinsic.MPE.cfg /tmp/autopkgtest.axahEj/build.6tW/src/examples/example.fa 150s test-example PASS 150s autopkgtest [01:16:03]: test test-example: - - - - - - - - - - results - - - - - - - - - - 150s autopkgtest [01:16:03]: test test-example-with-training: preparing testbed 150s Reading package lists... 150s Building dependency tree... 150s Reading state information... 151s Solving dependencies... 151s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 152s autopkgtest [01:16:05]: test test-example-with-training: [----------------------- 153s '/usr/share/augustus/config' -> './config' 153s '/usr/share/augustus/config/cgp' -> './config/cgp' 153s '/usr/share/augustus/config/cgp/cgp_param_21features_accuracy_largerGrid.convDivCorrect.cfg' -> './config/cgp/cgp_param_21features_accuracy_largerGrid.convDivCorrect.cfg' 153s '/usr/share/augustus/config/cgp/log_reg_parameters_arabidopsis.cfg' -> './config/cgp/log_reg_parameters_arabidopsis.cfg' 153s '/usr/share/augustus/config/cgp/log_reg_parameters_default.cfg' -> './config/cgp/log_reg_parameters_default.cfg' 153s '/usr/share/augustus/config/cgp/log_reg_parameters_fly.cfg' -> './config/cgp/log_reg_parameters_fly.cfg' 153s '/usr/share/augustus/config/cgp/log_reg_parameters_human.cfg' -> './config/cgp/log_reg_parameters_human.cfg' 153s '/usr/share/augustus/config/cgp/log_reg_parameters_primates.cfg' -> './config/cgp/log_reg_parameters_primates.cfg' 153s '/usr/share/augustus/config/cgp/log_reg_parameters_s_aureus.cfg' -> './config/cgp/log_reg_parameters_s_aureus.cfg' 153s '/usr/share/augustus/config/extrinsic' -> './config/extrinsic' 153s '/usr/share/augustus/config/extrinsic/extrinsic-cgp.cfg' -> './config/extrinsic/extrinsic-cgp.cfg' 153s '/usr/share/augustus/config/extrinsic/extrinsic.E.XNT.cfg' -> './config/extrinsic/extrinsic.E.XNT.cfg' 153s '/usr/share/augustus/config/extrinsic/extrinsic.E.cfg' -> './config/extrinsic/extrinsic.E.cfg' 153s '/usr/share/augustus/config/extrinsic/extrinsic.M.RM.E.W.P.cfg' -> './config/extrinsic/extrinsic.M.RM.E.W.P.cfg' 153s '/usr/share/augustus/config/extrinsic/extrinsic.M.RM.E.W.cfg' -> './config/extrinsic/extrinsic.M.RM.E.W.cfg' 153s '/usr/share/augustus/config/extrinsic/extrinsic.M.RM.PB.cfg' -> './config/extrinsic/extrinsic.M.RM.PB.cfg' 153s '/usr/share/augustus/config/extrinsic/extrinsic.ME.cfg' -> './config/extrinsic/extrinsic.ME.cfg' 153s '/usr/share/augustus/config/extrinsic/extrinsic.MEMS.cfg' -> './config/extrinsic/extrinsic.MEMS.cfg' 153s '/usr/share/augustus/config/extrinsic/extrinsic.MP.cfg' -> './config/extrinsic/extrinsic.MP.cfg' 153s '/usr/share/augustus/config/extrinsic/extrinsic.MPE.cfg' -> './config/extrinsic/extrinsic.MPE.cfg' 153s '/usr/share/augustus/config/extrinsic/extrinsic.MT.cfg' -> './config/extrinsic/extrinsic.MT.cfg' 153s '/usr/share/augustus/config/extrinsic/extrinsic.cfg' -> './config/extrinsic/extrinsic.cfg' 153s '/usr/share/augustus/config/model' -> './config/model' 153s '/usr/share/augustus/config/model/constraints_shadow_partial.txt' -> './config/model/constraints_shadow_partial.txt' 153s '/usr/share/augustus/config/model/constraints_shadow_partial_utr.txt' -> './config/model/constraints_shadow_partial_utr.txt' 153s '/usr/share/augustus/config/model/ovlp_len.pbl' -> './config/model/ovlp_len.pbl' 153s '/usr/share/augustus/config/model/ovlp_len_archaea.pbl' -> './config/model/ovlp_len_archaea.pbl' 153s '/usr/share/augustus/config/model/states_shadow.cfg' -> './config/model/states_shadow.cfg' 153s '/usr/share/augustus/config/model/states_shadow_2igenic.cfg' -> './config/model/states_shadow_2igenic.cfg' 153s '/usr/share/augustus/config/model/states_shadow_bacterium.cfg' -> './config/model/states_shadow_bacterium.cfg' 153s '/usr/share/augustus/config/model/states_shadow_intronless.cfg' -> './config/model/states_shadow_intronless.cfg' 153s '/usr/share/augustus/config/model/states_shadow_utr.cfg' -> './config/model/states_shadow_utr.cfg' 153s '/usr/share/augustus/config/model/states_shadow_utr_nc.cfg' -> './config/model/states_shadow_utr_nc.cfg' 153s '/usr/share/augustus/config/model/states_singlestrand.cfg' -> './config/model/states_singlestrand.cfg' 153s '/usr/share/augustus/config/model/states_singlestrand_2igenic.cfg' -> './config/model/states_singlestrand_2igenic.cfg' 153s '/usr/share/augustus/config/model/trans_shadow_atleastone.pbl' -> './config/model/trans_shadow_atleastone.pbl' 153s '/usr/share/augustus/config/model/trans_shadow_bacterium.pbl' -> './config/model/trans_shadow_bacterium.pbl' 153s '/usr/share/augustus/config/model/trans_shadow_complete.pbl' -> './config/model/trans_shadow_complete.pbl' 153s '/usr/share/augustus/config/model/trans_shadow_complete_utr.pbl' -> './config/model/trans_shadow_complete_utr.pbl' 153s '/usr/share/augustus/config/model/trans_shadow_exactlyone.pbl' -> './config/model/trans_shadow_exactlyone.pbl' 153s '/usr/share/augustus/config/model/trans_shadow_intronless.pbl' -> './config/model/trans_shadow_intronless.pbl' 153s '/usr/share/augustus/config/model/trans_shadow_partial.pbl' -> './config/model/trans_shadow_partial.pbl' 153s '/usr/share/augustus/config/model/trans_shadow_partial_utr.pbl' -> './config/model/trans_shadow_partial_utr.pbl' 153s '/usr/share/augustus/config/model/trans_shadow_partial_utr_nc.pbl' -> './config/model/trans_shadow_partial_utr_nc.pbl' 153s '/usr/share/augustus/config/model/trans_singlestrand_atleastone.pbl' -> './config/model/trans_singlestrand_atleastone.pbl' 153s '/usr/share/augustus/config/model/trans_singlestrand_complete.pbl' -> './config/model/trans_singlestrand_complete.pbl' 153s '/usr/share/augustus/config/model/trans_singlestrand_exactlyone.pbl' -> './config/model/trans_singlestrand_exactlyone.pbl' 153s '/usr/share/augustus/config/model/trans_singlestrand_partial.pbl' -> './config/model/trans_singlestrand_partial.pbl' 153s '/usr/share/augustus/config/parameters' -> './config/parameters' 153s '/usr/share/augustus/config/parameters/AUG_CMDLN_PARAMETERS.md' -> './config/parameters/AUG_CMDLN_PARAMETERS.md' 153s '/usr/share/augustus/config/parameters/aug_cmdln_parameters.json' -> './config/parameters/aug_cmdln_parameters.json' 153s '/usr/share/augustus/config/profile' -> './config/profile' 153s '/usr/share/augustus/config/profile/blosum55.qij' -> './config/profile/blosum55.qij' 153s '/usr/share/augustus/config/profile/blosum62.qij' -> './config/profile/blosum62.qij' 153s '/usr/share/augustus/config/profile/default.qij' -> './config/profile/default.qij' 153s '/usr/share/augustus/config/species' -> './config/species' 153s '/usr/share/augustus/config/species/Anopheles_gambiae' -> './config/species/Anopheles_gambiae' 153s '/usr/share/augustus/config/species/Anopheles_gambiae/Anopheles_gambiae_exon_probs.pbl' -> './config/species/Anopheles_gambiae/Anopheles_gambiae_exon_probs.pbl' 153s '/usr/share/augustus/config/species/Anopheles_gambiae/Anopheles_gambiae_igenic_probs.pbl' -> './config/species/Anopheles_gambiae/Anopheles_gambiae_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/Anopheles_gambiae/Anopheles_gambiae_intron_probs.pbl' -> './config/species/Anopheles_gambiae/Anopheles_gambiae_intron_probs.pbl' 153s '/usr/share/augustus/config/species/Anopheles_gambiae/Anopheles_gambiae_metapars.cfg' -> './config/species/Anopheles_gambiae/Anopheles_gambiae_metapars.cfg' 153s '/usr/share/augustus/config/species/Anopheles_gambiae/Anopheles_gambiae_metapars.cgp.cfg' -> './config/species/Anopheles_gambiae/Anopheles_gambiae_metapars.cgp.cfg' 153s '/usr/share/augustus/config/species/Anopheles_gambiae/Anopheles_gambiae_metapars.utr.cfg' -> './config/species/Anopheles_gambiae/Anopheles_gambiae_metapars.utr.cfg' 153s '/usr/share/augustus/config/species/Anopheles_gambiae/Anopheles_gambiae_parameters.cfg' -> './config/species/Anopheles_gambiae/Anopheles_gambiae_parameters.cfg' 153s '/usr/share/augustus/config/species/Anopheles_gambiae/Anopheles_gambiae_weightmatrix.txt' -> './config/species/Anopheles_gambiae/Anopheles_gambiae_weightmatrix.txt' 153s '/usr/share/augustus/config/species/Anopheles_gambiae/README.txt' -> './config/species/Anopheles_gambiae/README.txt' 153s '/usr/share/augustus/config/species/Argopecten_irradians' -> './config/species/Argopecten_irradians' 153s '/usr/share/augustus/config/species/Argopecten_irradians/Argopecten_irradians_exon_probs.pbl' -> './config/species/Argopecten_irradians/Argopecten_irradians_exon_probs.pbl' 153s '/usr/share/augustus/config/species/Argopecten_irradians/Argopecten_irradians_igenic_probs.pbl' -> './config/species/Argopecten_irradians/Argopecten_irradians_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/Argopecten_irradians/Argopecten_irradians_intron_probs.pbl' -> './config/species/Argopecten_irradians/Argopecten_irradians_intron_probs.pbl' 153s '/usr/share/augustus/config/species/Argopecten_irradians/Argopecten_irradians_metapars.cfg' -> './config/species/Argopecten_irradians/Argopecten_irradians_metapars.cfg' 153s '/usr/share/augustus/config/species/Argopecten_irradians/Argopecten_irradians_metapars.cgp.cfg' -> './config/species/Argopecten_irradians/Argopecten_irradians_metapars.cgp.cfg' 153s '/usr/share/augustus/config/species/Argopecten_irradians/Argopecten_irradians_metapars.utr.cfg' -> './config/species/Argopecten_irradians/Argopecten_irradians_metapars.utr.cfg' 153s '/usr/share/augustus/config/species/Argopecten_irradians/Argopecten_irradians_parameters.cfg' -> './config/species/Argopecten_irradians/Argopecten_irradians_parameters.cfg' 153s '/usr/share/augustus/config/species/Argopecten_irradians/Argopecten_irradians_weightmatrix.txt' -> './config/species/Argopecten_irradians/Argopecten_irradians_weightmatrix.txt' 153s '/usr/share/augustus/config/species/Argopecten_irradians/README.txt' -> './config/species/Argopecten_irradians/README.txt' 153s '/usr/share/augustus/config/species/Aurelia_aurita' -> './config/species/Aurelia_aurita' 153s '/usr/share/augustus/config/species/Aurelia_aurita/Aurelia_aurita_exon_probs.pbl' -> './config/species/Aurelia_aurita/Aurelia_aurita_exon_probs.pbl' 153s '/usr/share/augustus/config/species/Aurelia_aurita/Aurelia_aurita_igenic_probs.pbl' -> './config/species/Aurelia_aurita/Aurelia_aurita_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/Aurelia_aurita/Aurelia_aurita_intron_probs.pbl' -> './config/species/Aurelia_aurita/Aurelia_aurita_intron_probs.pbl' 153s '/usr/share/augustus/config/species/Aurelia_aurita/Aurelia_aurita_metapars.cfg' -> './config/species/Aurelia_aurita/Aurelia_aurita_metapars.cfg' 153s '/usr/share/augustus/config/species/Aurelia_aurita/Aurelia_aurita_metapars.cgp.cfg' -> './config/species/Aurelia_aurita/Aurelia_aurita_metapars.cgp.cfg' 153s '/usr/share/augustus/config/species/Aurelia_aurita/Aurelia_aurita_metapars.utr.cfg' -> './config/species/Aurelia_aurita/Aurelia_aurita_metapars.utr.cfg' 153s '/usr/share/augustus/config/species/Aurelia_aurita/Aurelia_aurita_parameters.cfg' -> './config/species/Aurelia_aurita/Aurelia_aurita_parameters.cfg' 153s '/usr/share/augustus/config/species/Aurelia_aurita/Aurelia_aurita_weightmatrix.txt' -> './config/species/Aurelia_aurita/Aurelia_aurita_weightmatrix.txt' 153s '/usr/share/augustus/config/species/Aurelia_aurita/README.txt' -> './config/species/Aurelia_aurita/README.txt' 153s '/usr/share/augustus/config/species/Bathycoccus_prasinos' -> './config/species/Bathycoccus_prasinos' 153s '/usr/share/augustus/config/species/Bathycoccus_prasinos/Bathycoccus_prasinos_exon_probs.pbl' -> './config/species/Bathycoccus_prasinos/Bathycoccus_prasinos_exon_probs.pbl' 153s '/usr/share/augustus/config/species/Bathycoccus_prasinos/Bathycoccus_prasinos_igenic_probs.pbl' -> './config/species/Bathycoccus_prasinos/Bathycoccus_prasinos_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/Bathycoccus_prasinos/Bathycoccus_prasinos_intron_probs.pbl' -> './config/species/Bathycoccus_prasinos/Bathycoccus_prasinos_intron_probs.pbl' 153s '/usr/share/augustus/config/species/Bathycoccus_prasinos/Bathycoccus_prasinos_metapars.cfg' -> './config/species/Bathycoccus_prasinos/Bathycoccus_prasinos_metapars.cfg' 153s '/usr/share/augustus/config/species/Bathycoccus_prasinos/Bathycoccus_prasinos_metapars.cgp.cfg' -> './config/species/Bathycoccus_prasinos/Bathycoccus_prasinos_metapars.cgp.cfg' 153s '/usr/share/augustus/config/species/Bathycoccus_prasinos/Bathycoccus_prasinos_metapars.utr.cfg' -> './config/species/Bathycoccus_prasinos/Bathycoccus_prasinos_metapars.utr.cfg' 153s '/usr/share/augustus/config/species/Bathycoccus_prasinos/Bathycoccus_prasinos_parameters.cfg' -> './config/species/Bathycoccus_prasinos/Bathycoccus_prasinos_parameters.cfg' 153s '/usr/share/augustus/config/species/Bathycoccus_prasinos/Bathycoccus_prasinos_weightmatrix.txt' -> './config/species/Bathycoccus_prasinos/Bathycoccus_prasinos_weightmatrix.txt' 153s '/usr/share/augustus/config/species/Bathycoccus_prasinos/README.txt' -> './config/species/Bathycoccus_prasinos/README.txt' 153s '/usr/share/augustus/config/species/Berviolum_minutum' -> './config/species/Berviolum_minutum' 153s '/usr/share/augustus/config/species/Berviolum_minutum/Berviolum_minutum_exon_probs.pbl' -> './config/species/Berviolum_minutum/Berviolum_minutum_exon_probs.pbl' 153s '/usr/share/augustus/config/species/Berviolum_minutum/Berviolum_minutum_igenic_probs.pbl' -> './config/species/Berviolum_minutum/Berviolum_minutum_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/Berviolum_minutum/Berviolum_minutum_intron_probs.pbl' -> './config/species/Berviolum_minutum/Berviolum_minutum_intron_probs.pbl' 153s '/usr/share/augustus/config/species/Berviolum_minutum/Berviolum_minutum_metapars.cfg' -> './config/species/Berviolum_minutum/Berviolum_minutum_metapars.cfg' 153s '/usr/share/augustus/config/species/Berviolum_minutum/Berviolum_minutum_metapars.cgp.cfg' -> './config/species/Berviolum_minutum/Berviolum_minutum_metapars.cgp.cfg' 153s '/usr/share/augustus/config/species/Berviolum_minutum/Berviolum_minutum_metapars.utr.cfg' -> './config/species/Berviolum_minutum/Berviolum_minutum_metapars.utr.cfg' 153s '/usr/share/augustus/config/species/Berviolum_minutum/Berviolum_minutum_parameters.cfg' -> './config/species/Berviolum_minutum/Berviolum_minutum_parameters.cfg' 153s '/usr/share/augustus/config/species/Berviolum_minutum/Berviolum_minutum_weightmatrix.txt' -> './config/species/Berviolum_minutum/Berviolum_minutum_weightmatrix.txt' 153s '/usr/share/augustus/config/species/Berviolum_minutum/README.txt' -> './config/species/Berviolum_minutum/README.txt' 153s '/usr/share/augustus/config/species/Branchiostoma_floridae' -> './config/species/Branchiostoma_floridae' 153s '/usr/share/augustus/config/species/Branchiostoma_floridae/Branchiostoma_floridae_exon_probs.pbl' -> './config/species/Branchiostoma_floridae/Branchiostoma_floridae_exon_probs.pbl' 153s '/usr/share/augustus/config/species/Branchiostoma_floridae/Branchiostoma_floridae_igenic_probs.pbl' -> './config/species/Branchiostoma_floridae/Branchiostoma_floridae_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/Branchiostoma_floridae/Branchiostoma_floridae_intron_probs.pbl' -> './config/species/Branchiostoma_floridae/Branchiostoma_floridae_intron_probs.pbl' 153s '/usr/share/augustus/config/species/Branchiostoma_floridae/Branchiostoma_floridae_metapars.cfg' -> './config/species/Branchiostoma_floridae/Branchiostoma_floridae_metapars.cfg' 153s '/usr/share/augustus/config/species/Branchiostoma_floridae/Branchiostoma_floridae_metapars.cgp.cfg' -> './config/species/Branchiostoma_floridae/Branchiostoma_floridae_metapars.cgp.cfg' 153s '/usr/share/augustus/config/species/Branchiostoma_floridae/Branchiostoma_floridae_metapars.utr.cfg' -> './config/species/Branchiostoma_floridae/Branchiostoma_floridae_metapars.utr.cfg' 153s '/usr/share/augustus/config/species/Branchiostoma_floridae/Branchiostoma_floridae_parameters.cfg' -> './config/species/Branchiostoma_floridae/Branchiostoma_floridae_parameters.cfg' 153s '/usr/share/augustus/config/species/Branchiostoma_floridae/Branchiostoma_floridae_weightmatrix.txt' -> './config/species/Branchiostoma_floridae/Branchiostoma_floridae_weightmatrix.txt' 153s '/usr/share/augustus/config/species/Branchiostoma_floridae/README.txt' -> './config/species/Branchiostoma_floridae/README.txt' 153s '/usr/share/augustus/config/species/Cassiopea_xamachana' -> './config/species/Cassiopea_xamachana' 153s '/usr/share/augustus/config/species/Cassiopea_xamachana/Cassiopea_xamachana_exon_probs.pbl' -> './config/species/Cassiopea_xamachana/Cassiopea_xamachana_exon_probs.pbl' 153s '/usr/share/augustus/config/species/Cassiopea_xamachana/Cassiopea_xamachana_igenic_probs.pbl' -> './config/species/Cassiopea_xamachana/Cassiopea_xamachana_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/Cassiopea_xamachana/Cassiopea_xamachana_intron_probs.pbl' -> './config/species/Cassiopea_xamachana/Cassiopea_xamachana_intron_probs.pbl' 153s '/usr/share/augustus/config/species/Cassiopea_xamachana/Cassiopea_xamachana_metapars.cfg' -> './config/species/Cassiopea_xamachana/Cassiopea_xamachana_metapars.cfg' 153s '/usr/share/augustus/config/species/Cassiopea_xamachana/Cassiopea_xamachana_metapars.cgp.cfg' -> './config/species/Cassiopea_xamachana/Cassiopea_xamachana_metapars.cgp.cfg' 153s '/usr/share/augustus/config/species/Cassiopea_xamachana/Cassiopea_xamachana_metapars.utr.cfg' -> './config/species/Cassiopea_xamachana/Cassiopea_xamachana_metapars.utr.cfg' 153s '/usr/share/augustus/config/species/Cassiopea_xamachana/Cassiopea_xamachana_parameters.cfg' -> './config/species/Cassiopea_xamachana/Cassiopea_xamachana_parameters.cfg' 153s '/usr/share/augustus/config/species/Cassiopea_xamachana/Cassiopea_xamachana_weightmatrix.txt' -> './config/species/Cassiopea_xamachana/Cassiopea_xamachana_weightmatrix.txt' 153s '/usr/share/augustus/config/species/Chlamydomonas_eustigma' -> './config/species/Chlamydomonas_eustigma' 153s '/usr/share/augustus/config/species/Chlamydomonas_eustigma/Chlamydomonas_eustigma_exon_probs.pbl' -> './config/species/Chlamydomonas_eustigma/Chlamydomonas_eustigma_exon_probs.pbl' 153s '/usr/share/augustus/config/species/Chlamydomonas_eustigma/Chlamydomonas_eustigma_igenic_probs.pbl' -> './config/species/Chlamydomonas_eustigma/Chlamydomonas_eustigma_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/Chlamydomonas_eustigma/Chlamydomonas_eustigma_intron_probs.pbl' -> './config/species/Chlamydomonas_eustigma/Chlamydomonas_eustigma_intron_probs.pbl' 153s '/usr/share/augustus/config/species/Chlamydomonas_eustigma/Chlamydomonas_eustigma_metapars.cfg' -> './config/species/Chlamydomonas_eustigma/Chlamydomonas_eustigma_metapars.cfg' 153s '/usr/share/augustus/config/species/Chlamydomonas_eustigma/Chlamydomonas_eustigma_metapars.cgp.cfg' -> './config/species/Chlamydomonas_eustigma/Chlamydomonas_eustigma_metapars.cgp.cfg' 153s '/usr/share/augustus/config/species/Chlamydomonas_eustigma/Chlamydomonas_eustigma_metapars.utr.cfg' -> './config/species/Chlamydomonas_eustigma/Chlamydomonas_eustigma_metapars.utr.cfg' 153s '/usr/share/augustus/config/species/Chlamydomonas_eustigma/Chlamydomonas_eustigma_parameters.cfg' -> './config/species/Chlamydomonas_eustigma/Chlamydomonas_eustigma_parameters.cfg' 153s '/usr/share/augustus/config/species/Chlamydomonas_eustigma/Chlamydomonas_eustigma_weightmatrix.txt' -> './config/species/Chlamydomonas_eustigma/Chlamydomonas_eustigma_weightmatrix.txt' 153s '/usr/share/augustus/config/species/Chlamydomonas_eustigma/README.txt' -> './config/species/Chlamydomonas_eustigma/README.txt' 153s '/usr/share/augustus/config/species/Chloropicon_primus' -> './config/species/Chloropicon_primus' 153s '/usr/share/augustus/config/species/Chloropicon_primus/Chloropicon_primus_exon_probs.pbl' -> './config/species/Chloropicon_primus/Chloropicon_primus_exon_probs.pbl' 153s '/usr/share/augustus/config/species/Chloropicon_primus/Chloropicon_primus_igenic_probs.pbl' -> './config/species/Chloropicon_primus/Chloropicon_primus_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/Chloropicon_primus/Chloropicon_primus_intron_probs.pbl' -> './config/species/Chloropicon_primus/Chloropicon_primus_intron_probs.pbl' 153s '/usr/share/augustus/config/species/Chloropicon_primus/Chloropicon_primus_metapars.cfg' -> './config/species/Chloropicon_primus/Chloropicon_primus_metapars.cfg' 153s '/usr/share/augustus/config/species/Chloropicon_primus/Chloropicon_primus_metapars.cgp.cfg' -> './config/species/Chloropicon_primus/Chloropicon_primus_metapars.cgp.cfg' 153s '/usr/share/augustus/config/species/Chloropicon_primus/Chloropicon_primus_metapars.utr.cfg' -> './config/species/Chloropicon_primus/Chloropicon_primus_metapars.utr.cfg' 153s '/usr/share/augustus/config/species/Chloropicon_primus/Chloropicon_primus_parameters.cfg' -> './config/species/Chloropicon_primus/Chloropicon_primus_parameters.cfg' 153s '/usr/share/augustus/config/species/Chloropicon_primus/Chloropicon_primus_weightmatrix.txt' -> './config/species/Chloropicon_primus/Chloropicon_primus_weightmatrix.txt' 153s '/usr/share/augustus/config/species/Chloropicon_primus/README.txt' -> './config/species/Chloropicon_primus/README.txt' 153s '/usr/share/augustus/config/species/Chrysaora_chesapeakei' -> './config/species/Chrysaora_chesapeakei' 153s '/usr/share/augustus/config/species/Chrysaora_chesapeakei/Chrysaora_chesapeakei_exon_probs.pbl' -> './config/species/Chrysaora_chesapeakei/Chrysaora_chesapeakei_exon_probs.pbl' 153s '/usr/share/augustus/config/species/Chrysaora_chesapeakei/Chrysaora_chesapeakei_igenic_probs.pbl' -> './config/species/Chrysaora_chesapeakei/Chrysaora_chesapeakei_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/Chrysaora_chesapeakei/Chrysaora_chesapeakei_intron_probs.pbl' -> './config/species/Chrysaora_chesapeakei/Chrysaora_chesapeakei_intron_probs.pbl' 153s '/usr/share/augustus/config/species/Chrysaora_chesapeakei/Chrysaora_chesapeakei_metapars.cfg' -> './config/species/Chrysaora_chesapeakei/Chrysaora_chesapeakei_metapars.cfg' 153s '/usr/share/augustus/config/species/Chrysaora_chesapeakei/Chrysaora_chesapeakei_metapars.cgp.cfg' -> './config/species/Chrysaora_chesapeakei/Chrysaora_chesapeakei_metapars.cgp.cfg' 153s '/usr/share/augustus/config/species/Chrysaora_chesapeakei/Chrysaora_chesapeakei_metapars.utr.cfg' -> './config/species/Chrysaora_chesapeakei/Chrysaora_chesapeakei_metapars.utr.cfg' 153s '/usr/share/augustus/config/species/Chrysaora_chesapeakei/Chrysaora_chesapeakei_parameters.cfg' -> './config/species/Chrysaora_chesapeakei/Chrysaora_chesapeakei_parameters.cfg' 153s '/usr/share/augustus/config/species/Chrysaora_chesapeakei/Chrysaora_chesapeakei_weightmatrix.txt' -> './config/species/Chrysaora_chesapeakei/Chrysaora_chesapeakei_weightmatrix.txt' 153s '/usr/share/augustus/config/species/Chrysaora_chesapeakei/README.txt' -> './config/species/Chrysaora_chesapeakei/README.txt' 153s '/usr/share/augustus/config/species/Conidiobolus_coronatus' -> './config/species/Conidiobolus_coronatus' 153s '/usr/share/augustus/config/species/Conidiobolus_coronatus/Conidiobolus_coronatus_exon_probs.pbl' -> './config/species/Conidiobolus_coronatus/Conidiobolus_coronatus_exon_probs.pbl' 153s '/usr/share/augustus/config/species/Conidiobolus_coronatus/Conidiobolus_coronatus_igenic_probs.pbl' -> './config/species/Conidiobolus_coronatus/Conidiobolus_coronatus_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/Conidiobolus_coronatus/Conidiobolus_coronatus_intron_probs.pbl' -> './config/species/Conidiobolus_coronatus/Conidiobolus_coronatus_intron_probs.pbl' 153s '/usr/share/augustus/config/species/Conidiobolus_coronatus/Conidiobolus_coronatus_metapars.cfg' -> './config/species/Conidiobolus_coronatus/Conidiobolus_coronatus_metapars.cfg' 153s '/usr/share/augustus/config/species/Conidiobolus_coronatus/Conidiobolus_coronatus_metapars.utr.cfg' -> './config/species/Conidiobolus_coronatus/Conidiobolus_coronatus_metapars.utr.cfg' 153s '/usr/share/augustus/config/species/Conidiobolus_coronatus/Conidiobolus_coronatus_parameters.cfg' -> './config/species/Conidiobolus_coronatus/Conidiobolus_coronatus_parameters.cfg' 153s '/usr/share/augustus/config/species/Conidiobolus_coronatus/Conidiobolus_coronatus_utr_probs.pbl' -> './config/species/Conidiobolus_coronatus/Conidiobolus_coronatus_utr_probs.pbl' 153s '/usr/share/augustus/config/species/Conidiobolus_coronatus/Conidiobolus_coronatus_weightmatrix.txt' -> './config/species/Conidiobolus_coronatus/Conidiobolus_coronatus_weightmatrix.txt' 153s '/usr/share/augustus/config/species/Cryptosporidium_hominis' -> './config/species/Cryptosporidium_hominis' 153s '/usr/share/augustus/config/species/Cryptosporidium_hominis/Cryptosporidium_hominis_exon_probs.pbl' -> './config/species/Cryptosporidium_hominis/Cryptosporidium_hominis_exon_probs.pbl' 153s '/usr/share/augustus/config/species/Cryptosporidium_hominis/Cryptosporidium_hominis_igenic_probs.pbl' -> './config/species/Cryptosporidium_hominis/Cryptosporidium_hominis_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/Cryptosporidium_hominis/Cryptosporidium_hominis_intron_probs.pbl' -> './config/species/Cryptosporidium_hominis/Cryptosporidium_hominis_intron_probs.pbl' 153s '/usr/share/augustus/config/species/Cryptosporidium_hominis/Cryptosporidium_hominis_metapars.cfg' -> './config/species/Cryptosporidium_hominis/Cryptosporidium_hominis_metapars.cfg' 153s '/usr/share/augustus/config/species/Cryptosporidium_hominis/Cryptosporidium_hominis_metapars.cgp.cfg' -> './config/species/Cryptosporidium_hominis/Cryptosporidium_hominis_metapars.cgp.cfg' 153s '/usr/share/augustus/config/species/Cryptosporidium_hominis/Cryptosporidium_hominis_metapars.utr.cfg' -> './config/species/Cryptosporidium_hominis/Cryptosporidium_hominis_metapars.utr.cfg' 153s '/usr/share/augustus/config/species/Cryptosporidium_hominis/Cryptosporidium_hominis_parameters.cfg' -> './config/species/Cryptosporidium_hominis/Cryptosporidium_hominis_parameters.cfg' 153s '/usr/share/augustus/config/species/Cryptosporidium_hominis/Cryptosporidium_hominis_weightmatrix.txt' -> './config/species/Cryptosporidium_hominis/Cryptosporidium_hominis_weightmatrix.txt' 153s '/usr/share/augustus/config/species/Cryptosporidium_hominis/README.txt' -> './config/species/Cryptosporidium_hominis/README.txt' 153s '/usr/share/augustus/config/species/Cyclotella_cryptica' -> './config/species/Cyclotella_cryptica' 153s '/usr/share/augustus/config/species/Cyclotella_cryptica/Cyclotella_cryptica_exon_probs.pbl' -> './config/species/Cyclotella_cryptica/Cyclotella_cryptica_exon_probs.pbl' 153s '/usr/share/augustus/config/species/Cyclotella_cryptica/Cyclotella_cryptica_igenic_probs.pbl' -> './config/species/Cyclotella_cryptica/Cyclotella_cryptica_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/Cyclotella_cryptica/Cyclotella_cryptica_intron_probs.pbl' -> './config/species/Cyclotella_cryptica/Cyclotella_cryptica_intron_probs.pbl' 153s '/usr/share/augustus/config/species/Cyclotella_cryptica/Cyclotella_cryptica_metapars.cfg' -> './config/species/Cyclotella_cryptica/Cyclotella_cryptica_metapars.cfg' 153s '/usr/share/augustus/config/species/Cyclotella_cryptica/Cyclotella_cryptica_metapars.cgp.cfg' -> './config/species/Cyclotella_cryptica/Cyclotella_cryptica_metapars.cgp.cfg' 153s '/usr/share/augustus/config/species/Cyclotella_cryptica/Cyclotella_cryptica_metapars.utr.cfg' -> './config/species/Cyclotella_cryptica/Cyclotella_cryptica_metapars.utr.cfg' 153s '/usr/share/augustus/config/species/Cyclotella_cryptica/Cyclotella_cryptica_parameters.cfg' -> './config/species/Cyclotella_cryptica/Cyclotella_cryptica_parameters.cfg' 153s '/usr/share/augustus/config/species/Cyclotella_cryptica/Cyclotella_cryptica_weightmatrix.txt' -> './config/species/Cyclotella_cryptica/Cyclotella_cryptica_weightmatrix.txt' 153s '/usr/share/augustus/config/species/Cyclotella_cryptica/README.txt' -> './config/species/Cyclotella_cryptica/README.txt' 153s '/usr/share/augustus/config/species/Dermasterias_imbricata' -> './config/species/Dermasterias_imbricata' 153s '/usr/share/augustus/config/species/Dermasterias_imbricata/Dermasterias_imbricata_exon_probs.pbl' -> './config/species/Dermasterias_imbricata/Dermasterias_imbricata_exon_probs.pbl' 153s '/usr/share/augustus/config/species/Dermasterias_imbricata/Dermasterias_imbricata_igenic_probs.pbl' -> './config/species/Dermasterias_imbricata/Dermasterias_imbricata_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/Dermasterias_imbricata/Dermasterias_imbricata_intron_probs.pbl' -> './config/species/Dermasterias_imbricata/Dermasterias_imbricata_intron_probs.pbl' 153s '/usr/share/augustus/config/species/Dermasterias_imbricata/Dermasterias_imbricata_metapars.cfg' -> './config/species/Dermasterias_imbricata/Dermasterias_imbricata_metapars.cfg' 153s '/usr/share/augustus/config/species/Dermasterias_imbricata/Dermasterias_imbricata_metapars.cgp.cfg' -> './config/species/Dermasterias_imbricata/Dermasterias_imbricata_metapars.cgp.cfg' 153s '/usr/share/augustus/config/species/Dermasterias_imbricata/Dermasterias_imbricata_metapars.utr.cfg' -> './config/species/Dermasterias_imbricata/Dermasterias_imbricata_metapars.utr.cfg' 153s '/usr/share/augustus/config/species/Dermasterias_imbricata/Dermasterias_imbricata_parameters.cfg' -> './config/species/Dermasterias_imbricata/Dermasterias_imbricata_parameters.cfg' 153s '/usr/share/augustus/config/species/Dermasterias_imbricata/Dermasterias_imbricata_weightmatrix.txt' -> './config/species/Dermasterias_imbricata/Dermasterias_imbricata_weightmatrix.txt' 153s '/usr/share/augustus/config/species/Dermasterias_imbricata/README.txt' -> './config/species/Dermasterias_imbricata/README.txt' 153s '/usr/share/augustus/config/species/Dunaliella_salina' -> './config/species/Dunaliella_salina' 153s '/usr/share/augustus/config/species/Dunaliella_salina/Dunaliella_salina_exon_probs.pbl' -> './config/species/Dunaliella_salina/Dunaliella_salina_exon_probs.pbl' 153s '/usr/share/augustus/config/species/Dunaliella_salina/Dunaliella_salina_igenic_probs.pbl' -> './config/species/Dunaliella_salina/Dunaliella_salina_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/Dunaliella_salina/Dunaliella_salina_intron_probs.pbl' -> './config/species/Dunaliella_salina/Dunaliella_salina_intron_probs.pbl' 153s '/usr/share/augustus/config/species/Dunaliella_salina/Dunaliella_salina_metapars.cfg' -> './config/species/Dunaliella_salina/Dunaliella_salina_metapars.cfg' 153s '/usr/share/augustus/config/species/Dunaliella_salina/Dunaliella_salina_metapars.cgp.cfg' -> './config/species/Dunaliella_salina/Dunaliella_salina_metapars.cgp.cfg' 153s '/usr/share/augustus/config/species/Dunaliella_salina/Dunaliella_salina_metapars.utr.cfg' -> './config/species/Dunaliella_salina/Dunaliella_salina_metapars.utr.cfg' 153s '/usr/share/augustus/config/species/Dunaliella_salina/Dunaliella_salina_parameters.cfg' -> './config/species/Dunaliella_salina/Dunaliella_salina_parameters.cfg' 153s '/usr/share/augustus/config/species/Dunaliella_salina/Dunaliella_salina_weightmatrix.txt' -> './config/species/Dunaliella_salina/Dunaliella_salina_weightmatrix.txt' 153s '/usr/share/augustus/config/species/Dunaliella_salina/README.txt' -> './config/species/Dunaliella_salina/README.txt' 153s '/usr/share/augustus/config/species/E_coli_K12' -> './config/species/E_coli_K12' 153s '/usr/share/augustus/config/species/E_coli_K12/E_coli_K12_exon_probs.pbl' -> './config/species/E_coli_K12/E_coli_K12_exon_probs.pbl' 153s '/usr/share/augustus/config/species/E_coli_K12/E_coli_K12_igenic_probs.pbl' -> './config/species/E_coli_K12/E_coli_K12_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/E_coli_K12/E_coli_K12_metapars.cfg' -> './config/species/E_coli_K12/E_coli_K12_metapars.cfg' 153s '/usr/share/augustus/config/species/E_coli_K12/E_coli_K12_metapars.utr.cfg' -> './config/species/E_coli_K12/E_coli_K12_metapars.utr.cfg' 153s '/usr/share/augustus/config/species/E_coli_K12/E_coli_K12_ovlp_len.pbl' -> './config/species/E_coli_K12/E_coli_K12_ovlp_len.pbl' 153s '/usr/share/augustus/config/species/E_coli_K12/E_coli_K12_parameters.cfg' -> './config/species/E_coli_K12/E_coli_K12_parameters.cfg' 153s '/usr/share/augustus/config/species/E_coli_K12/E_coli_K12_trans_shadow_bacterium.pbl' -> './config/species/E_coli_K12/E_coli_K12_trans_shadow_bacterium.pbl' 153s '/usr/share/augustus/config/species/E_coli_K12/E_coli_K12_weightmatrix.txt' -> './config/species/E_coli_K12/E_coli_K12_weightmatrix.txt' 153s '/usr/share/augustus/config/species/Ectocarpus_siliculosus' -> './config/species/Ectocarpus_siliculosus' 153s '/usr/share/augustus/config/species/Ectocarpus_siliculosus/Ectocarpus_siliculosus_exon_probs.pbl' -> './config/species/Ectocarpus_siliculosus/Ectocarpus_siliculosus_exon_probs.pbl' 153s '/usr/share/augustus/config/species/Ectocarpus_siliculosus/Ectocarpus_siliculosus_igenic_probs.pbl' -> './config/species/Ectocarpus_siliculosus/Ectocarpus_siliculosus_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/Ectocarpus_siliculosus/Ectocarpus_siliculosus_intron_probs.pbl' -> './config/species/Ectocarpus_siliculosus/Ectocarpus_siliculosus_intron_probs.pbl' 153s '/usr/share/augustus/config/species/Ectocarpus_siliculosus/Ectocarpus_siliculosus_metapars.cfg' -> './config/species/Ectocarpus_siliculosus/Ectocarpus_siliculosus_metapars.cfg' 153s '/usr/share/augustus/config/species/Ectocarpus_siliculosus/Ectocarpus_siliculosus_metapars.cgp.cfg' -> './config/species/Ectocarpus_siliculosus/Ectocarpus_siliculosus_metapars.cgp.cfg' 153s '/usr/share/augustus/config/species/Ectocarpus_siliculosus/Ectocarpus_siliculosus_metapars.utr.cfg' -> './config/species/Ectocarpus_siliculosus/Ectocarpus_siliculosus_metapars.utr.cfg' 153s '/usr/share/augustus/config/species/Ectocarpus_siliculosus/Ectocarpus_siliculosus_parameters.cfg' -> './config/species/Ectocarpus_siliculosus/Ectocarpus_siliculosus_parameters.cfg' 153s '/usr/share/augustus/config/species/Ectocarpus_siliculosus/Ectocarpus_siliculosus_weightmatrix.txt' -> './config/species/Ectocarpus_siliculosus/Ectocarpus_siliculosus_weightmatrix.txt' 153s '/usr/share/augustus/config/species/Ectocarpus_siliculosus/README.txt' -> './config/species/Ectocarpus_siliculosus/README.txt' 153s '/usr/share/augustus/config/species/Encephalitozoon_cuniculi' -> './config/species/Encephalitozoon_cuniculi' 153s '/usr/share/augustus/config/species/Encephalitozoon_cuniculi/Encephalitozoon_cuniculi_exon_probs.pbl' -> './config/species/Encephalitozoon_cuniculi/Encephalitozoon_cuniculi_exon_probs.pbl' 153s '/usr/share/augustus/config/species/Encephalitozoon_cuniculi/Encephalitozoon_cuniculi_igenic_probs.pbl' -> './config/species/Encephalitozoon_cuniculi/Encephalitozoon_cuniculi_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/Encephalitozoon_cuniculi/Encephalitozoon_cuniculi_intron_probs.pbl' -> './config/species/Encephalitozoon_cuniculi/Encephalitozoon_cuniculi_intron_probs.pbl' 153s '/usr/share/augustus/config/species/Encephalitozoon_cuniculi/Encephalitozoon_cuniculi_metapars.cfg' -> './config/species/Encephalitozoon_cuniculi/Encephalitozoon_cuniculi_metapars.cfg' 153s '/usr/share/augustus/config/species/Encephalitozoon_cuniculi/Encephalitozoon_cuniculi_metapars.cgp.cfg' -> './config/species/Encephalitozoon_cuniculi/Encephalitozoon_cuniculi_metapars.cgp.cfg' 153s '/usr/share/augustus/config/species/Encephalitozoon_cuniculi/Encephalitozoon_cuniculi_metapars.utr.cfg' -> './config/species/Encephalitozoon_cuniculi/Encephalitozoon_cuniculi_metapars.utr.cfg' 153s '/usr/share/augustus/config/species/Encephalitozoon_cuniculi/Encephalitozoon_cuniculi_parameters.cfg' -> './config/species/Encephalitozoon_cuniculi/Encephalitozoon_cuniculi_parameters.cfg' 153s '/usr/share/augustus/config/species/Encephalitozoon_cuniculi/Encephalitozoon_cuniculi_weightmatrix.txt' -> './config/species/Encephalitozoon_cuniculi/Encephalitozoon_cuniculi_weightmatrix.txt' 153s '/usr/share/augustus/config/species/Encephalitozoon_cuniculi/README.txt' -> './config/species/Encephalitozoon_cuniculi/README.txt' 153s '/usr/share/augustus/config/species/Fistulifera_solaris' -> './config/species/Fistulifera_solaris' 153s '/usr/share/augustus/config/species/Fistulifera_solaris/Fistulifera_solaris_exon_probs.pbl' -> './config/species/Fistulifera_solaris/Fistulifera_solaris_exon_probs.pbl' 153s '/usr/share/augustus/config/species/Fistulifera_solaris/Fistulifera_solaris_igenic_probs.pbl' -> './config/species/Fistulifera_solaris/Fistulifera_solaris_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/Fistulifera_solaris/Fistulifera_solaris_intron_probs.pbl' -> './config/species/Fistulifera_solaris/Fistulifera_solaris_intron_probs.pbl' 153s '/usr/share/augustus/config/species/Fistulifera_solaris/Fistulifera_solaris_metapars.cfg' -> './config/species/Fistulifera_solaris/Fistulifera_solaris_metapars.cfg' 153s '/usr/share/augustus/config/species/Fistulifera_solaris/Fistulifera_solaris_metapars.cgp.cfg' -> './config/species/Fistulifera_solaris/Fistulifera_solaris_metapars.cgp.cfg' 153s '/usr/share/augustus/config/species/Fistulifera_solaris/Fistulifera_solaris_metapars.utr.cfg' -> './config/species/Fistulifera_solaris/Fistulifera_solaris_metapars.utr.cfg' 153s '/usr/share/augustus/config/species/Fistulifera_solaris/Fistulifera_solaris_parameters.cfg' -> './config/species/Fistulifera_solaris/Fistulifera_solaris_parameters.cfg' 153s '/usr/share/augustus/config/species/Fistulifera_solaris/Fistulifera_solaris_weightmatrix.txt' -> './config/species/Fistulifera_solaris/Fistulifera_solaris_weightmatrix.txt' 153s '/usr/share/augustus/config/species/Fistulifera_solaris/README.txt' -> './config/species/Fistulifera_solaris/README.txt' 153s '/usr/share/augustus/config/species/Fragilariopsis_cylindrus_CCMP1102' -> './config/species/Fragilariopsis_cylindrus_CCMP1102' 153s '/usr/share/augustus/config/species/Fragilariopsis_cylindrus_CCMP1102/Fragilariopsis_cylindrus_CCMP1102_exon_probs.pbl' -> './config/species/Fragilariopsis_cylindrus_CCMP1102/Fragilariopsis_cylindrus_CCMP1102_exon_probs.pbl' 153s '/usr/share/augustus/config/species/Fragilariopsis_cylindrus_CCMP1102/Fragilariopsis_cylindrus_CCMP1102_igenic_probs.pbl' -> './config/species/Fragilariopsis_cylindrus_CCMP1102/Fragilariopsis_cylindrus_CCMP1102_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/Fragilariopsis_cylindrus_CCMP1102/Fragilariopsis_cylindrus_CCMP1102_intron_probs.pbl' -> './config/species/Fragilariopsis_cylindrus_CCMP1102/Fragilariopsis_cylindrus_CCMP1102_intron_probs.pbl' 153s '/usr/share/augustus/config/species/Fragilariopsis_cylindrus_CCMP1102/Fragilariopsis_cylindrus_CCMP1102_metapars.cfg' -> './config/species/Fragilariopsis_cylindrus_CCMP1102/Fragilariopsis_cylindrus_CCMP1102_metapars.cfg' 153s '/usr/share/augustus/config/species/Fragilariopsis_cylindrus_CCMP1102/Fragilariopsis_cylindrus_CCMP1102_metapars.cgp.cfg' -> './config/species/Fragilariopsis_cylindrus_CCMP1102/Fragilariopsis_cylindrus_CCMP1102_metapars.cgp.cfg' 153s '/usr/share/augustus/config/species/Fragilariopsis_cylindrus_CCMP1102/Fragilariopsis_cylindrus_CCMP1102_metapars.utr.cfg' -> './config/species/Fragilariopsis_cylindrus_CCMP1102/Fragilariopsis_cylindrus_CCMP1102_metapars.utr.cfg' 153s '/usr/share/augustus/config/species/Fragilariopsis_cylindrus_CCMP1102/Fragilariopsis_cylindrus_CCMP1102_parameters.cfg' -> './config/species/Fragilariopsis_cylindrus_CCMP1102/Fragilariopsis_cylindrus_CCMP1102_parameters.cfg' 153s '/usr/share/augustus/config/species/Fragilariopsis_cylindrus_CCMP1102/Fragilariopsis_cylindrus_CCMP1102_weightmatrix.txt' -> './config/species/Fragilariopsis_cylindrus_CCMP1102/Fragilariopsis_cylindrus_CCMP1102_weightmatrix.txt' 153s '/usr/share/augustus/config/species/Fragilariopsis_cylindrus_CCMP1102/README.txt' -> './config/species/Fragilariopsis_cylindrus_CCMP1102/README.txt' 153s '/usr/share/augustus/config/species/Gonapodya_prolifera' -> './config/species/Gonapodya_prolifera' 153s '/usr/share/augustus/config/species/Gonapodya_prolifera/Gonapodya_prolifera_exon_probs.pbl' -> './config/species/Gonapodya_prolifera/Gonapodya_prolifera_exon_probs.pbl' 153s '/usr/share/augustus/config/species/Gonapodya_prolifera/Gonapodya_prolifera_igenic_probs.pbl' -> './config/species/Gonapodya_prolifera/Gonapodya_prolifera_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/Gonapodya_prolifera/Gonapodya_prolifera_intron_probs.pbl' -> './config/species/Gonapodya_prolifera/Gonapodya_prolifera_intron_probs.pbl' 153s '/usr/share/augustus/config/species/Gonapodya_prolifera/Gonapodya_prolifera_metapars.cfg' -> './config/species/Gonapodya_prolifera/Gonapodya_prolifera_metapars.cfg' 153s '/usr/share/augustus/config/species/Gonapodya_prolifera/Gonapodya_prolifera_metapars.cgp.cfg' -> './config/species/Gonapodya_prolifera/Gonapodya_prolifera_metapars.cgp.cfg' 153s '/usr/share/augustus/config/species/Gonapodya_prolifera/Gonapodya_prolifera_metapars.utr.cfg' -> './config/species/Gonapodya_prolifera/Gonapodya_prolifera_metapars.utr.cfg' 153s '/usr/share/augustus/config/species/Gonapodya_prolifera/Gonapodya_prolifera_parameters.cfg' -> './config/species/Gonapodya_prolifera/Gonapodya_prolifera_parameters.cfg' 153s '/usr/share/augustus/config/species/Gonapodya_prolifera/Gonapodya_prolifera_weightmatrix.txt' -> './config/species/Gonapodya_prolifera/Gonapodya_prolifera_weightmatrix.txt' 153s '/usr/share/augustus/config/species/Gonapodya_prolifera/README.txt' -> './config/species/Gonapodya_prolifera/README.txt' 153s '/usr/share/augustus/config/species/Hydra_vulgaris' -> './config/species/Hydra_vulgaris' 153s '/usr/share/augustus/config/species/Hydra_vulgaris/Hydra_vulgaris_exon_probs.pbl' -> './config/species/Hydra_vulgaris/Hydra_vulgaris_exon_probs.pbl' 153s '/usr/share/augustus/config/species/Hydra_vulgaris/Hydra_vulgaris_igenic_probs.pbl' -> './config/species/Hydra_vulgaris/Hydra_vulgaris_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/Hydra_vulgaris/Hydra_vulgaris_intron_probs.pbl' -> './config/species/Hydra_vulgaris/Hydra_vulgaris_intron_probs.pbl' 153s '/usr/share/augustus/config/species/Hydra_vulgaris/Hydra_vulgaris_metapars.cfg' -> './config/species/Hydra_vulgaris/Hydra_vulgaris_metapars.cfg' 153s '/usr/share/augustus/config/species/Hydra_vulgaris/Hydra_vulgaris_metapars.cgp.cfg' -> './config/species/Hydra_vulgaris/Hydra_vulgaris_metapars.cgp.cfg' 153s '/usr/share/augustus/config/species/Hydra_vulgaris/Hydra_vulgaris_metapars.utr.cfg' -> './config/species/Hydra_vulgaris/Hydra_vulgaris_metapars.utr.cfg' 153s '/usr/share/augustus/config/species/Hydra_vulgaris/Hydra_vulgaris_parameters.cfg' -> './config/species/Hydra_vulgaris/Hydra_vulgaris_parameters.cfg' 153s '/usr/share/augustus/config/species/Hydra_vulgaris/Hydra_vulgaris_weightmatrix.txt' -> './config/species/Hydra_vulgaris/Hydra_vulgaris_weightmatrix.txt' 153s '/usr/share/augustus/config/species/Hydra_vulgaris/README.txt' -> './config/species/Hydra_vulgaris/README.txt' 153s '/usr/share/augustus/config/species/Leptasterias_sp' -> './config/species/Leptasterias_sp' 153s '/usr/share/augustus/config/species/Leptasterias_sp/Leptasterias_sp_exon_probs.pbl' -> './config/species/Leptasterias_sp/Leptasterias_sp_exon_probs.pbl' 153s '/usr/share/augustus/config/species/Leptasterias_sp/Leptasterias_sp_igenic_probs.pbl' -> './config/species/Leptasterias_sp/Leptasterias_sp_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/Leptasterias_sp/Leptasterias_sp_intron_probs.pbl' -> './config/species/Leptasterias_sp/Leptasterias_sp_intron_probs.pbl' 153s '/usr/share/augustus/config/species/Leptasterias_sp/Leptasterias_sp_metapars.cfg' -> './config/species/Leptasterias_sp/Leptasterias_sp_metapars.cfg' 153s '/usr/share/augustus/config/species/Leptasterias_sp/Leptasterias_sp_metapars.cgp.cfg' -> './config/species/Leptasterias_sp/Leptasterias_sp_metapars.cgp.cfg' 153s '/usr/share/augustus/config/species/Leptasterias_sp/Leptasterias_sp_metapars.utr.cfg' -> './config/species/Leptasterias_sp/Leptasterias_sp_metapars.utr.cfg' 153s '/usr/share/augustus/config/species/Leptasterias_sp/Leptasterias_sp_parameters.cfg' -> './config/species/Leptasterias_sp/Leptasterias_sp_parameters.cfg' 153s '/usr/share/augustus/config/species/Leptasterias_sp/Leptasterias_sp_weightmatrix.txt' -> './config/species/Leptasterias_sp/Leptasterias_sp_weightmatrix.txt' 153s '/usr/share/augustus/config/species/Leptasterias_sp/README.txt' -> './config/species/Leptasterias_sp/README.txt' 153s '/usr/share/augustus/config/species/Loa_loa' -> './config/species/Loa_loa' 153s '/usr/share/augustus/config/species/Loa_loa/Loa_loa_exon_probs.pbl' -> './config/species/Loa_loa/Loa_loa_exon_probs.pbl' 153s '/usr/share/augustus/config/species/Loa_loa/Loa_loa_igenic_probs.pbl' -> './config/species/Loa_loa/Loa_loa_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/Loa_loa/Loa_loa_intron_probs.pbl' -> './config/species/Loa_loa/Loa_loa_intron_probs.pbl' 153s '/usr/share/augustus/config/species/Loa_loa/Loa_loa_metapars.cfg' -> './config/species/Loa_loa/Loa_loa_metapars.cfg' 153s '/usr/share/augustus/config/species/Loa_loa/Loa_loa_metapars.cgp.cfg' -> './config/species/Loa_loa/Loa_loa_metapars.cgp.cfg' 153s '/usr/share/augustus/config/species/Loa_loa/Loa_loa_metapars.utr.cfg' -> './config/species/Loa_loa/Loa_loa_metapars.utr.cfg' 153s '/usr/share/augustus/config/species/Loa_loa/Loa_loa_parameters.cfg' -> './config/species/Loa_loa/Loa_loa_parameters.cfg' 153s '/usr/share/augustus/config/species/Loa_loa/Loa_loa_weightmatrix.txt' -> './config/species/Loa_loa/Loa_loa_weightmatrix.txt' 153s '/usr/share/augustus/config/species/Loa_loa/README.txt' -> './config/species/Loa_loa/README.txt' 153s '/usr/share/augustus/config/species/Micromonas_commoda' -> './config/species/Micromonas_commoda' 153s '/usr/share/augustus/config/species/Micromonas_commoda/Micromonas_commoda_exon_probs.pbl' -> './config/species/Micromonas_commoda/Micromonas_commoda_exon_probs.pbl' 153s '/usr/share/augustus/config/species/Micromonas_commoda/Micromonas_commoda_igenic_probs.pbl' -> './config/species/Micromonas_commoda/Micromonas_commoda_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/Micromonas_commoda/Micromonas_commoda_intron_probs.pbl' -> './config/species/Micromonas_commoda/Micromonas_commoda_intron_probs.pbl' 153s '/usr/share/augustus/config/species/Micromonas_commoda/Micromonas_commoda_metapars.cfg' -> './config/species/Micromonas_commoda/Micromonas_commoda_metapars.cfg' 153s '/usr/share/augustus/config/species/Micromonas_commoda/Micromonas_commoda_metapars.cgp.cfg' -> './config/species/Micromonas_commoda/Micromonas_commoda_metapars.cgp.cfg' 153s '/usr/share/augustus/config/species/Micromonas_commoda/Micromonas_commoda_metapars.utr.cfg' -> './config/species/Micromonas_commoda/Micromonas_commoda_metapars.utr.cfg' 153s '/usr/share/augustus/config/species/Micromonas_commoda/Micromonas_commoda_parameters.cfg' -> './config/species/Micromonas_commoda/Micromonas_commoda_parameters.cfg' 153s '/usr/share/augustus/config/species/Micromonas_commoda/Micromonas_commoda_weightmatrix.txt' -> './config/species/Micromonas_commoda/Micromonas_commoda_weightmatrix.txt' 153s '/usr/share/augustus/config/species/Micromonas_commoda/README.txt' -> './config/species/Micromonas_commoda/README.txt' 153s '/usr/share/augustus/config/species/Micromonas_pusilla' -> './config/species/Micromonas_pusilla' 153s '/usr/share/augustus/config/species/Micromonas_pusilla/Micromonas_pusilla_exon_probs.pbl' -> './config/species/Micromonas_pusilla/Micromonas_pusilla_exon_probs.pbl' 153s '/usr/share/augustus/config/species/Micromonas_pusilla/Micromonas_pusilla_igenic_probs.pbl' -> './config/species/Micromonas_pusilla/Micromonas_pusilla_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/Micromonas_pusilla/Micromonas_pusilla_intron_probs.pbl' -> './config/species/Micromonas_pusilla/Micromonas_pusilla_intron_probs.pbl' 153s '/usr/share/augustus/config/species/Micromonas_pusilla/Micromonas_pusilla_metapars.cfg' -> './config/species/Micromonas_pusilla/Micromonas_pusilla_metapars.cfg' 153s '/usr/share/augustus/config/species/Micromonas_pusilla/Micromonas_pusilla_metapars.cgp.cfg' -> './config/species/Micromonas_pusilla/Micromonas_pusilla_metapars.cgp.cfg' 153s '/usr/share/augustus/config/species/Micromonas_pusilla/Micromonas_pusilla_metapars.utr.cfg' -> './config/species/Micromonas_pusilla/Micromonas_pusilla_metapars.utr.cfg' 153s '/usr/share/augustus/config/species/Micromonas_pusilla/Micromonas_pusilla_parameters.cfg' -> './config/species/Micromonas_pusilla/Micromonas_pusilla_parameters.cfg' 153s '/usr/share/augustus/config/species/Micromonas_pusilla/Micromonas_pusilla_weightmatrix.txt' -> './config/species/Micromonas_pusilla/Micromonas_pusilla_weightmatrix.txt' 153s '/usr/share/augustus/config/species/Micromonas_pusilla/README.txt' -> './config/species/Micromonas_pusilla/README.txt' 153s '/usr/share/augustus/config/species/Monoraphidium_neglectum' -> './config/species/Monoraphidium_neglectum' 153s '/usr/share/augustus/config/species/Monoraphidium_neglectum/Monoraphidium_neglectum_exon_probs.pbl' -> './config/species/Monoraphidium_neglectum/Monoraphidium_neglectum_exon_probs.pbl' 153s '/usr/share/augustus/config/species/Monoraphidium_neglectum/Monoraphidium_neglectum_igenic_probs.pbl' -> './config/species/Monoraphidium_neglectum/Monoraphidium_neglectum_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/Monoraphidium_neglectum/Monoraphidium_neglectum_intron_probs.pbl' -> './config/species/Monoraphidium_neglectum/Monoraphidium_neglectum_intron_probs.pbl' 153s '/usr/share/augustus/config/species/Monoraphidium_neglectum/Monoraphidium_neglectum_metapars.cfg' -> './config/species/Monoraphidium_neglectum/Monoraphidium_neglectum_metapars.cfg' 153s '/usr/share/augustus/config/species/Monoraphidium_neglectum/Monoraphidium_neglectum_metapars.cgp.cfg' -> './config/species/Monoraphidium_neglectum/Monoraphidium_neglectum_metapars.cgp.cfg' 153s '/usr/share/augustus/config/species/Monoraphidium_neglectum/Monoraphidium_neglectum_metapars.utr.cfg' -> './config/species/Monoraphidium_neglectum/Monoraphidium_neglectum_metapars.utr.cfg' 153s '/usr/share/augustus/config/species/Monoraphidium_neglectum/Monoraphidium_neglectum_parameters.cfg' -> './config/species/Monoraphidium_neglectum/Monoraphidium_neglectum_parameters.cfg' 153s '/usr/share/augustus/config/species/Monoraphidium_neglectum/Monoraphidium_neglectum_weightmatrix.txt' -> './config/species/Monoraphidium_neglectum/Monoraphidium_neglectum_weightmatrix.txt' 153s '/usr/share/augustus/config/species/Monoraphidium_neglectum/README.txt' -> './config/species/Monoraphidium_neglectum/README.txt' 153s '/usr/share/augustus/config/species/Monosiga_brevicollis' -> './config/species/Monosiga_brevicollis' 153s '/usr/share/augustus/config/species/Monosiga_brevicollis/Monosiga_brevicollis_exon_probs.pbl' -> './config/species/Monosiga_brevicollis/Monosiga_brevicollis_exon_probs.pbl' 153s '/usr/share/augustus/config/species/Monosiga_brevicollis/Monosiga_brevicollis_igenic_probs.pbl' -> './config/species/Monosiga_brevicollis/Monosiga_brevicollis_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/Monosiga_brevicollis/Monosiga_brevicollis_intron_probs.pbl' -> './config/species/Monosiga_brevicollis/Monosiga_brevicollis_intron_probs.pbl' 153s '/usr/share/augustus/config/species/Monosiga_brevicollis/Monosiga_brevicollis_metapars.cfg' -> './config/species/Monosiga_brevicollis/Monosiga_brevicollis_metapars.cfg' 153s '/usr/share/augustus/config/species/Monosiga_brevicollis/Monosiga_brevicollis_metapars.cgp.cfg' -> './config/species/Monosiga_brevicollis/Monosiga_brevicollis_metapars.cgp.cfg' 153s '/usr/share/augustus/config/species/Monosiga_brevicollis/Monosiga_brevicollis_metapars.utr.cfg' -> './config/species/Monosiga_brevicollis/Monosiga_brevicollis_metapars.utr.cfg' 153s '/usr/share/augustus/config/species/Monosiga_brevicollis/Monosiga_brevicollis_parameters.cfg' -> './config/species/Monosiga_brevicollis/Monosiga_brevicollis_parameters.cfg' 153s '/usr/share/augustus/config/species/Monosiga_brevicollis/Monosiga_brevicollis_weightmatrix.txt' -> './config/species/Monosiga_brevicollis/Monosiga_brevicollis_weightmatrix.txt' 153s '/usr/share/augustus/config/species/Monosiga_brevicollis/README.txt' -> './config/species/Monosiga_brevicollis/README.txt' 153s '/usr/share/augustus/config/species/Naegleria_gruberi' -> './config/species/Naegleria_gruberi' 153s '/usr/share/augustus/config/species/Naegleria_gruberi/Naegleria_gruberi_exon_probs.pbl' -> './config/species/Naegleria_gruberi/Naegleria_gruberi_exon_probs.pbl' 153s '/usr/share/augustus/config/species/Naegleria_gruberi/Naegleria_gruberi_igenic_probs.pbl' -> './config/species/Naegleria_gruberi/Naegleria_gruberi_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/Naegleria_gruberi/Naegleria_gruberi_intron_probs.pbl' -> './config/species/Naegleria_gruberi/Naegleria_gruberi_intron_probs.pbl' 153s '/usr/share/augustus/config/species/Naegleria_gruberi/Naegleria_gruberi_metapars.cfg' -> './config/species/Naegleria_gruberi/Naegleria_gruberi_metapars.cfg' 153s '/usr/share/augustus/config/species/Naegleria_gruberi/Naegleria_gruberi_metapars.cgp.cfg' -> './config/species/Naegleria_gruberi/Naegleria_gruberi_metapars.cgp.cfg' 153s '/usr/share/augustus/config/species/Naegleria_gruberi/Naegleria_gruberi_metapars.utr.cfg' -> './config/species/Naegleria_gruberi/Naegleria_gruberi_metapars.utr.cfg' 153s '/usr/share/augustus/config/species/Naegleria_gruberi/Naegleria_gruberi_parameters.cfg' -> './config/species/Naegleria_gruberi/Naegleria_gruberi_parameters.cfg' 153s '/usr/share/augustus/config/species/Naegleria_gruberi/Naegleria_gruberi_weightmatrix.txt' -> './config/species/Naegleria_gruberi/Naegleria_gruberi_weightmatrix.txt' 153s '/usr/share/augustus/config/species/Naegleria_gruberi/README.txt' -> './config/species/Naegleria_gruberi/README.txt' 153s '/usr/share/augustus/config/species/Nemopilema_nomurai' -> './config/species/Nemopilema_nomurai' 153s '/usr/share/augustus/config/species/Nemopilema_nomurai/Nemopilema_nomurai_exon_probs.pbl' -> './config/species/Nemopilema_nomurai/Nemopilema_nomurai_exon_probs.pbl' 153s '/usr/share/augustus/config/species/Nemopilema_nomurai/Nemopilema_nomurai_igenic_probs.pbl' -> './config/species/Nemopilema_nomurai/Nemopilema_nomurai_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/Nemopilema_nomurai/Nemopilema_nomurai_intron_probs.pbl' -> './config/species/Nemopilema_nomurai/Nemopilema_nomurai_intron_probs.pbl' 153s '/usr/share/augustus/config/species/Nemopilema_nomurai/Nemopilema_nomurai_metapars.cfg' -> './config/species/Nemopilema_nomurai/Nemopilema_nomurai_metapars.cfg' 153s '/usr/share/augustus/config/species/Nemopilema_nomurai/Nemopilema_nomurai_metapars.cgp.cfg' -> './config/species/Nemopilema_nomurai/Nemopilema_nomurai_metapars.cgp.cfg' 153s '/usr/share/augustus/config/species/Nemopilema_nomurai/Nemopilema_nomurai_metapars.utr.cfg' -> './config/species/Nemopilema_nomurai/Nemopilema_nomurai_metapars.utr.cfg' 153s '/usr/share/augustus/config/species/Nemopilema_nomurai/Nemopilema_nomurai_parameters.cfg' -> './config/species/Nemopilema_nomurai/Nemopilema_nomurai_parameters.cfg' 153s '/usr/share/augustus/config/species/Nemopilema_nomurai/Nemopilema_nomurai_weightmatrix.txt' -> './config/species/Nemopilema_nomurai/Nemopilema_nomurai_weightmatrix.txt' 153s '/usr/share/augustus/config/species/Nemopilema_nomurai/README.txt' -> './config/species/Nemopilema_nomurai/README.txt' 153s '/usr/share/augustus/config/species/Notospermus_geniculatus' -> './config/species/Notospermus_geniculatus' 153s '/usr/share/augustus/config/species/Notospermus_geniculatus/Notospermus_geniculatus_exon_probs.pbl' -> './config/species/Notospermus_geniculatus/Notospermus_geniculatus_exon_probs.pbl' 153s '/usr/share/augustus/config/species/Notospermus_geniculatus/Notospermus_geniculatus_igenic_probs.pbl' -> './config/species/Notospermus_geniculatus/Notospermus_geniculatus_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/Notospermus_geniculatus/Notospermus_geniculatus_intron_probs.pbl' -> './config/species/Notospermus_geniculatus/Notospermus_geniculatus_intron_probs.pbl' 153s '/usr/share/augustus/config/species/Notospermus_geniculatus/Notospermus_geniculatus_metapars.cfg' -> './config/species/Notospermus_geniculatus/Notospermus_geniculatus_metapars.cfg' 153s '/usr/share/augustus/config/species/Notospermus_geniculatus/Notospermus_geniculatus_metapars.cgp.cfg' -> './config/species/Notospermus_geniculatus/Notospermus_geniculatus_metapars.cgp.cfg' 153s '/usr/share/augustus/config/species/Notospermus_geniculatus/Notospermus_geniculatus_metapars.utr.cfg' -> './config/species/Notospermus_geniculatus/Notospermus_geniculatus_metapars.utr.cfg' 153s '/usr/share/augustus/config/species/Notospermus_geniculatus/Notospermus_geniculatus_parameters.cfg' -> './config/species/Notospermus_geniculatus/Notospermus_geniculatus_parameters.cfg' 153s '/usr/share/augustus/config/species/Notospermus_geniculatus/Notospermus_geniculatus_weightmatrix.txt' -> './config/species/Notospermus_geniculatus/Notospermus_geniculatus_weightmatrix.txt' 153s '/usr/share/augustus/config/species/Notospermus_geniculatus/README.txt' -> './config/species/Notospermus_geniculatus/README.txt' 153s '/usr/share/augustus/config/species/Ostreococcus_sp_lucimarinus' -> './config/species/Ostreococcus_sp_lucimarinus' 153s '/usr/share/augustus/config/species/Ostreococcus_sp_lucimarinus/Ostreococcus_sp_lucimarinus_exon_probs.pbl' -> './config/species/Ostreococcus_sp_lucimarinus/Ostreococcus_sp_lucimarinus_exon_probs.pbl' 153s '/usr/share/augustus/config/species/Ostreococcus_sp_lucimarinus/Ostreococcus_sp_lucimarinus_igenic_probs.pbl' -> './config/species/Ostreococcus_sp_lucimarinus/Ostreococcus_sp_lucimarinus_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/Ostreococcus_sp_lucimarinus/Ostreococcus_sp_lucimarinus_intron_probs.pbl' -> './config/species/Ostreococcus_sp_lucimarinus/Ostreococcus_sp_lucimarinus_intron_probs.pbl' 153s '/usr/share/augustus/config/species/Ostreococcus_sp_lucimarinus/Ostreococcus_sp_lucimarinus_metapars.cfg' -> './config/species/Ostreococcus_sp_lucimarinus/Ostreococcus_sp_lucimarinus_metapars.cfg' 153s '/usr/share/augustus/config/species/Ostreococcus_sp_lucimarinus/Ostreococcus_sp_lucimarinus_metapars.cgp.cfg' -> './config/species/Ostreococcus_sp_lucimarinus/Ostreococcus_sp_lucimarinus_metapars.cgp.cfg' 153s '/usr/share/augustus/config/species/Ostreococcus_sp_lucimarinus/Ostreococcus_sp_lucimarinus_metapars.utr.cfg' -> './config/species/Ostreococcus_sp_lucimarinus/Ostreococcus_sp_lucimarinus_metapars.utr.cfg' 153s '/usr/share/augustus/config/species/Ostreococcus_sp_lucimarinus/Ostreococcus_sp_lucimarinus_parameters.cfg' -> './config/species/Ostreococcus_sp_lucimarinus/Ostreococcus_sp_lucimarinus_parameters.cfg' 153s '/usr/share/augustus/config/species/Ostreococcus_sp_lucimarinus/Ostreococcus_sp_lucimarinus_weightmatrix.txt' -> './config/species/Ostreococcus_sp_lucimarinus/Ostreococcus_sp_lucimarinus_weightmatrix.txt' 153s '/usr/share/augustus/config/species/Ostreococcus_sp_lucimarinus/README.txt' -> './config/species/Ostreococcus_sp_lucimarinus/README.txt' 153s '/usr/share/augustus/config/species/Ostreococcus_tauri' -> './config/species/Ostreococcus_tauri' 153s '/usr/share/augustus/config/species/Ostreococcus_tauri/Ostreococcus_tauri_exon_probs.pbl' -> './config/species/Ostreococcus_tauri/Ostreococcus_tauri_exon_probs.pbl' 153s '/usr/share/augustus/config/species/Ostreococcus_tauri/Ostreococcus_tauri_igenic_probs.pbl' -> './config/species/Ostreococcus_tauri/Ostreococcus_tauri_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/Ostreococcus_tauri/Ostreococcus_tauri_intron_probs.pbl' -> './config/species/Ostreococcus_tauri/Ostreococcus_tauri_intron_probs.pbl' 153s '/usr/share/augustus/config/species/Ostreococcus_tauri/Ostreococcus_tauri_metapars.cfg' -> './config/species/Ostreococcus_tauri/Ostreococcus_tauri_metapars.cfg' 153s '/usr/share/augustus/config/species/Ostreococcus_tauri/Ostreococcus_tauri_metapars.cgp.cfg' -> './config/species/Ostreococcus_tauri/Ostreococcus_tauri_metapars.cgp.cfg' 153s '/usr/share/augustus/config/species/Ostreococcus_tauri/Ostreococcus_tauri_metapars.utr.cfg' -> './config/species/Ostreococcus_tauri/Ostreococcus_tauri_metapars.utr.cfg' 153s '/usr/share/augustus/config/species/Ostreococcus_tauri/Ostreococcus_tauri_parameters.cfg' -> './config/species/Ostreococcus_tauri/Ostreococcus_tauri_parameters.cfg' 153s '/usr/share/augustus/config/species/Ostreococcus_tauri/Ostreococcus_tauri_weightmatrix.txt' -> './config/species/Ostreococcus_tauri/Ostreococcus_tauri_weightmatrix.txt' 153s '/usr/share/augustus/config/species/Ostreococcus_tauri/README.txt' -> './config/species/Ostreococcus_tauri/README.txt' 153s '/usr/share/augustus/config/species/Paramecium_tetraurelia' -> './config/species/Paramecium_tetraurelia' 153s '/usr/share/augustus/config/species/Paramecium_tetraurelia/Paramecium_tetraurelia_exon_probs.pbl' -> './config/species/Paramecium_tetraurelia/Paramecium_tetraurelia_exon_probs.pbl' 153s '/usr/share/augustus/config/species/Paramecium_tetraurelia/Paramecium_tetraurelia_igenic_probs.pbl' -> './config/species/Paramecium_tetraurelia/Paramecium_tetraurelia_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/Paramecium_tetraurelia/Paramecium_tetraurelia_intron_probs.pbl' -> './config/species/Paramecium_tetraurelia/Paramecium_tetraurelia_intron_probs.pbl' 153s '/usr/share/augustus/config/species/Paramecium_tetraurelia/Paramecium_tetraurelia_metapars.cfg' -> './config/species/Paramecium_tetraurelia/Paramecium_tetraurelia_metapars.cfg' 153s '/usr/share/augustus/config/species/Paramecium_tetraurelia/Paramecium_tetraurelia_metapars.cgp.cfg' -> './config/species/Paramecium_tetraurelia/Paramecium_tetraurelia_metapars.cgp.cfg' 153s '/usr/share/augustus/config/species/Paramecium_tetraurelia/Paramecium_tetraurelia_metapars.utr.cfg' -> './config/species/Paramecium_tetraurelia/Paramecium_tetraurelia_metapars.utr.cfg' 153s '/usr/share/augustus/config/species/Paramecium_tetraurelia/Paramecium_tetraurelia_parameters.cfg' -> './config/species/Paramecium_tetraurelia/Paramecium_tetraurelia_parameters.cfg' 153s '/usr/share/augustus/config/species/Paramecium_tetraurelia/Paramecium_tetraurelia_weightmatrix.txt' -> './config/species/Paramecium_tetraurelia/Paramecium_tetraurelia_weightmatrix.txt' 153s '/usr/share/augustus/config/species/Paramecium_tetraurelia/README.txt' -> './config/species/Paramecium_tetraurelia/README.txt' 153s '/usr/share/augustus/config/species/Pediculus_humanus' -> './config/species/Pediculus_humanus' 153s '/usr/share/augustus/config/species/Pediculus_humanus/Pediculus_humanus_exon_probs.pbl' -> './config/species/Pediculus_humanus/Pediculus_humanus_exon_probs.pbl' 153s '/usr/share/augustus/config/species/Pediculus_humanus/Pediculus_humanus_igenic_probs.pbl' -> './config/species/Pediculus_humanus/Pediculus_humanus_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/Pediculus_humanus/Pediculus_humanus_intron_probs.pbl' -> './config/species/Pediculus_humanus/Pediculus_humanus_intron_probs.pbl' 153s '/usr/share/augustus/config/species/Pediculus_humanus/Pediculus_humanus_metapars.cfg' -> './config/species/Pediculus_humanus/Pediculus_humanus_metapars.cfg' 153s '/usr/share/augustus/config/species/Pediculus_humanus/Pediculus_humanus_metapars.cgp.cfg' -> './config/species/Pediculus_humanus/Pediculus_humanus_metapars.cgp.cfg' 153s '/usr/share/augustus/config/species/Pediculus_humanus/Pediculus_humanus_metapars.utr.cfg' -> './config/species/Pediculus_humanus/Pediculus_humanus_metapars.utr.cfg' 153s '/usr/share/augustus/config/species/Pediculus_humanus/Pediculus_humanus_parameters.cfg' -> './config/species/Pediculus_humanus/Pediculus_humanus_parameters.cfg' 153s '/usr/share/augustus/config/species/Pediculus_humanus/Pediculus_humanus_weightmatrix.txt' -> './config/species/Pediculus_humanus/Pediculus_humanus_weightmatrix.txt' 153s '/usr/share/augustus/config/species/Pediculus_humanus/README.txt' -> './config/species/Pediculus_humanus/README.txt' 153s '/usr/share/augustus/config/species/Perkinsus_marinus' -> './config/species/Perkinsus_marinus' 153s '/usr/share/augustus/config/species/Perkinsus_marinus/Perkinsus_marinus_exon_probs.pbl' -> './config/species/Perkinsus_marinus/Perkinsus_marinus_exon_probs.pbl' 153s '/usr/share/augustus/config/species/Perkinsus_marinus/Perkinsus_marinus_igenic_probs.pbl' -> './config/species/Perkinsus_marinus/Perkinsus_marinus_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/Perkinsus_marinus/Perkinsus_marinus_intron_probs.pbl' -> './config/species/Perkinsus_marinus/Perkinsus_marinus_intron_probs.pbl' 153s '/usr/share/augustus/config/species/Perkinsus_marinus/Perkinsus_marinus_metapars.cfg' -> './config/species/Perkinsus_marinus/Perkinsus_marinus_metapars.cfg' 153s '/usr/share/augustus/config/species/Perkinsus_marinus/Perkinsus_marinus_metapars.cgp.cfg' -> './config/species/Perkinsus_marinus/Perkinsus_marinus_metapars.cgp.cfg' 153s '/usr/share/augustus/config/species/Perkinsus_marinus/Perkinsus_marinus_metapars.utr.cfg' -> './config/species/Perkinsus_marinus/Perkinsus_marinus_metapars.utr.cfg' 153s '/usr/share/augustus/config/species/Perkinsus_marinus/Perkinsus_marinus_parameters.cfg' -> './config/species/Perkinsus_marinus/Perkinsus_marinus_parameters.cfg' 153s '/usr/share/augustus/config/species/Perkinsus_marinus/Perkinsus_marinus_weightmatrix.txt' -> './config/species/Perkinsus_marinus/Perkinsus_marinus_weightmatrix.txt' 153s '/usr/share/augustus/config/species/Perkinsus_marinus/README.txt' -> './config/species/Perkinsus_marinus/README.txt' 153s '/usr/share/augustus/config/species/Phaeodactylum_tricornutum' -> './config/species/Phaeodactylum_tricornutum' 153s '/usr/share/augustus/config/species/Phaeodactylum_tricornutum/Phaeodactylum_tricornutum_exon_probs.pbl' -> './config/species/Phaeodactylum_tricornutum/Phaeodactylum_tricornutum_exon_probs.pbl' 153s '/usr/share/augustus/config/species/Phaeodactylum_tricornutum/Phaeodactylum_tricornutum_igenic_probs.pbl' -> './config/species/Phaeodactylum_tricornutum/Phaeodactylum_tricornutum_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/Phaeodactylum_tricornutum/Phaeodactylum_tricornutum_intron_probs.pbl' -> './config/species/Phaeodactylum_tricornutum/Phaeodactylum_tricornutum_intron_probs.pbl' 153s '/usr/share/augustus/config/species/Phaeodactylum_tricornutum/Phaeodactylum_tricornutum_metapars.cfg' -> './config/species/Phaeodactylum_tricornutum/Phaeodactylum_tricornutum_metapars.cfg' 153s '/usr/share/augustus/config/species/Phaeodactylum_tricornutum/Phaeodactylum_tricornutum_metapars.cgp.cfg' -> './config/species/Phaeodactylum_tricornutum/Phaeodactylum_tricornutum_metapars.cgp.cfg' 153s '/usr/share/augustus/config/species/Phaeodactylum_tricornutum/Phaeodactylum_tricornutum_metapars.utr.cfg' -> './config/species/Phaeodactylum_tricornutum/Phaeodactylum_tricornutum_metapars.utr.cfg' 153s '/usr/share/augustus/config/species/Phaeodactylum_tricornutum/Phaeodactylum_tricornutum_parameters.cfg' -> './config/species/Phaeodactylum_tricornutum/Phaeodactylum_tricornutum_parameters.cfg' 153s '/usr/share/augustus/config/species/Phaeodactylum_tricornutum/Phaeodactylum_tricornutum_weightmatrix.txt' -> './config/species/Phaeodactylum_tricornutum/Phaeodactylum_tricornutum_weightmatrix.txt' 153s '/usr/share/augustus/config/species/Phaeodactylum_tricornutum/README.txt' -> './config/species/Phaeodactylum_tricornutum/README.txt' 153s '/usr/share/augustus/config/species/Physcomitrium_patens' -> './config/species/Physcomitrium_patens' 153s '/usr/share/augustus/config/species/Physcomitrium_patens/Physcomitrium_patens_exon_probs.pbl' -> './config/species/Physcomitrium_patens/Physcomitrium_patens_exon_probs.pbl' 153s '/usr/share/augustus/config/species/Physcomitrium_patens/Physcomitrium_patens_igenic_probs.pbl' -> './config/species/Physcomitrium_patens/Physcomitrium_patens_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/Physcomitrium_patens/Physcomitrium_patens_intron_probs.pbl' -> './config/species/Physcomitrium_patens/Physcomitrium_patens_intron_probs.pbl' 153s '/usr/share/augustus/config/species/Physcomitrium_patens/Physcomitrium_patens_metapars.cfg' -> './config/species/Physcomitrium_patens/Physcomitrium_patens_metapars.cfg' 153s '/usr/share/augustus/config/species/Physcomitrium_patens/Physcomitrium_patens_metapars.cgp.cfg' -> './config/species/Physcomitrium_patens/Physcomitrium_patens_metapars.cgp.cfg' 153s '/usr/share/augustus/config/species/Physcomitrium_patens/Physcomitrium_patens_metapars.utr.cfg' -> './config/species/Physcomitrium_patens/Physcomitrium_patens_metapars.utr.cfg' 153s '/usr/share/augustus/config/species/Physcomitrium_patens/Physcomitrium_patens_parameters.cfg' -> './config/species/Physcomitrium_patens/Physcomitrium_patens_parameters.cfg' 153s '/usr/share/augustus/config/species/Physcomitrium_patens/Physcomitrium_patens_weightmatrix.txt' -> './config/species/Physcomitrium_patens/Physcomitrium_patens_weightmatrix.txt' 153s '/usr/share/augustus/config/species/Physcomitrium_patens/README.txt' -> './config/species/Physcomitrium_patens/README.txt' 153s '/usr/share/augustus/config/species/Populus_trichocarpa' -> './config/species/Populus_trichocarpa' 153s '/usr/share/augustus/config/species/Populus_trichocarpa/Populus_trichocarpa_exon_probs.pbl' -> './config/species/Populus_trichocarpa/Populus_trichocarpa_exon_probs.pbl' 153s '/usr/share/augustus/config/species/Populus_trichocarpa/Populus_trichocarpa_igenic_probs.pbl' -> './config/species/Populus_trichocarpa/Populus_trichocarpa_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/Populus_trichocarpa/Populus_trichocarpa_intron_probs.pbl' -> './config/species/Populus_trichocarpa/Populus_trichocarpa_intron_probs.pbl' 153s '/usr/share/augustus/config/species/Populus_trichocarpa/Populus_trichocarpa_metapars.cfg' -> './config/species/Populus_trichocarpa/Populus_trichocarpa_metapars.cfg' 153s '/usr/share/augustus/config/species/Populus_trichocarpa/Populus_trichocarpa_metapars.cgp.cfg' -> './config/species/Populus_trichocarpa/Populus_trichocarpa_metapars.cgp.cfg' 153s '/usr/share/augustus/config/species/Populus_trichocarpa/Populus_trichocarpa_metapars.utr.cfg' -> './config/species/Populus_trichocarpa/Populus_trichocarpa_metapars.utr.cfg' 153s '/usr/share/augustus/config/species/Populus_trichocarpa/Populus_trichocarpa_parameters.cfg' -> './config/species/Populus_trichocarpa/Populus_trichocarpa_parameters.cfg' 153s '/usr/share/augustus/config/species/Populus_trichocarpa/Populus_trichocarpa_weightmatrix.txt' -> './config/species/Populus_trichocarpa/Populus_trichocarpa_weightmatrix.txt' 153s '/usr/share/augustus/config/species/Pseudo-nitzschia_multistriata' -> './config/species/Pseudo-nitzschia_multistriata' 153s '/usr/share/augustus/config/species/Pseudo-nitzschia_multistriata/Pseudo-nitzschia_multistriata_exon_probs.pbl' -> './config/species/Pseudo-nitzschia_multistriata/Pseudo-nitzschia_multistriata_exon_probs.pbl' 153s '/usr/share/augustus/config/species/Pseudo-nitzschia_multistriata/Pseudo-nitzschia_multistriata_igenic_probs.pbl' -> './config/species/Pseudo-nitzschia_multistriata/Pseudo-nitzschia_multistriata_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/Pseudo-nitzschia_multistriata/Pseudo-nitzschia_multistriata_intron_probs.pbl' -> './config/species/Pseudo-nitzschia_multistriata/Pseudo-nitzschia_multistriata_intron_probs.pbl' 153s '/usr/share/augustus/config/species/Pseudo-nitzschia_multistriata/Pseudo-nitzschia_multistriata_metapars.cfg' -> './config/species/Pseudo-nitzschia_multistriata/Pseudo-nitzschia_multistriata_metapars.cfg' 153s '/usr/share/augustus/config/species/Pseudo-nitzschia_multistriata/Pseudo-nitzschia_multistriata_metapars.cgp.cfg' -> './config/species/Pseudo-nitzschia_multistriata/Pseudo-nitzschia_multistriata_metapars.cgp.cfg' 153s '/usr/share/augustus/config/species/Pseudo-nitzschia_multistriata/Pseudo-nitzschia_multistriata_metapars.utr.cfg' -> './config/species/Pseudo-nitzschia_multistriata/Pseudo-nitzschia_multistriata_metapars.utr.cfg' 153s '/usr/share/augustus/config/species/Pseudo-nitzschia_multistriata/Pseudo-nitzschia_multistriata_parameters.cfg' -> './config/species/Pseudo-nitzschia_multistriata/Pseudo-nitzschia_multistriata_parameters.cfg' 153s '/usr/share/augustus/config/species/Pseudo-nitzschia_multistriata/Pseudo-nitzschia_multistriata_weightmatrix.txt' -> './config/species/Pseudo-nitzschia_multistriata/Pseudo-nitzschia_multistriata_weightmatrix.txt' 153s '/usr/share/augustus/config/species/Pseudo-nitzschia_multistriata/README.txt' -> './config/species/Pseudo-nitzschia_multistriata/README.txt' 153s '/usr/share/augustus/config/species/Ptychodera_flava' -> './config/species/Ptychodera_flava' 153s '/usr/share/augustus/config/species/Ptychodera_flava/Ptychodera_flava_exon_probs.pbl' -> './config/species/Ptychodera_flava/Ptychodera_flava_exon_probs.pbl' 153s '/usr/share/augustus/config/species/Ptychodera_flava/Ptychodera_flava_igenic_probs.pbl' -> './config/species/Ptychodera_flava/Ptychodera_flava_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/Ptychodera_flava/Ptychodera_flava_intron_probs.pbl' -> './config/species/Ptychodera_flava/Ptychodera_flava_intron_probs.pbl' 153s '/usr/share/augustus/config/species/Ptychodera_flava/Ptychodera_flava_metapars.cfg' -> './config/species/Ptychodera_flava/Ptychodera_flava_metapars.cfg' 153s '/usr/share/augustus/config/species/Ptychodera_flava/Ptychodera_flava_metapars.cgp.cfg' -> './config/species/Ptychodera_flava/Ptychodera_flava_metapars.cgp.cfg' 153s '/usr/share/augustus/config/species/Ptychodera_flava/Ptychodera_flava_metapars.utr.cfg' -> './config/species/Ptychodera_flava/Ptychodera_flava_metapars.utr.cfg' 153s '/usr/share/augustus/config/species/Ptychodera_flava/Ptychodera_flava_parameters.cfg' -> './config/species/Ptychodera_flava/Ptychodera_flava_parameters.cfg' 153s '/usr/share/augustus/config/species/Ptychodera_flava/Ptychodera_flava_weightmatrix.txt' -> './config/species/Ptychodera_flava/Ptychodera_flava_weightmatrix.txt' 153s '/usr/share/augustus/config/species/Ptychodera_flava/README.txt' -> './config/species/Ptychodera_flava/README.txt' 153s '/usr/share/augustus/config/species/Pycnopodia_helianthoides' -> './config/species/Pycnopodia_helianthoides' 153s '/usr/share/augustus/config/species/Pycnopodia_helianthoides/Pycnopodia_helianthoides_exon_probs.pbl' -> './config/species/Pycnopodia_helianthoides/Pycnopodia_helianthoides_exon_probs.pbl' 153s '/usr/share/augustus/config/species/Pycnopodia_helianthoides/Pycnopodia_helianthoides_igenic_probs.pbl' -> './config/species/Pycnopodia_helianthoides/Pycnopodia_helianthoides_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/Pycnopodia_helianthoides/Pycnopodia_helianthoides_intron_probs.pbl' -> './config/species/Pycnopodia_helianthoides/Pycnopodia_helianthoides_intron_probs.pbl' 153s '/usr/share/augustus/config/species/Pycnopodia_helianthoides/Pycnopodia_helianthoides_metapars.cfg' -> './config/species/Pycnopodia_helianthoides/Pycnopodia_helianthoides_metapars.cfg' 153s '/usr/share/augustus/config/species/Pycnopodia_helianthoides/Pycnopodia_helianthoides_metapars.cgp.cfg' -> './config/species/Pycnopodia_helianthoides/Pycnopodia_helianthoides_metapars.cgp.cfg' 153s '/usr/share/augustus/config/species/Pycnopodia_helianthoides/Pycnopodia_helianthoides_metapars.utr.cfg' -> './config/species/Pycnopodia_helianthoides/Pycnopodia_helianthoides_metapars.utr.cfg' 153s '/usr/share/augustus/config/species/Pycnopodia_helianthoides/Pycnopodia_helianthoides_parameters.cfg' -> './config/species/Pycnopodia_helianthoides/Pycnopodia_helianthoides_parameters.cfg' 153s '/usr/share/augustus/config/species/Pycnopodia_helianthoides/Pycnopodia_helianthoides_weightmatrix.txt' -> './config/species/Pycnopodia_helianthoides/Pycnopodia_helianthoides_weightmatrix.txt' 153s '/usr/share/augustus/config/species/Pycnopodia_helianthoides/README.txt' -> './config/species/Pycnopodia_helianthoides/README.txt' 153s '/usr/share/augustus/config/species/Raphidocelis_subcapitata' -> './config/species/Raphidocelis_subcapitata' 153s '/usr/share/augustus/config/species/Raphidocelis_subcapitata/README.txt' -> './config/species/Raphidocelis_subcapitata/README.txt' 153s '/usr/share/augustus/config/species/Raphidocelis_subcapitata/Raphidocelis_subcapitata_exon_probs.pbl' -> './config/species/Raphidocelis_subcapitata/Raphidocelis_subcapitata_exon_probs.pbl' 153s '/usr/share/augustus/config/species/Raphidocelis_subcapitata/Raphidocelis_subcapitata_igenic_probs.pbl' -> './config/species/Raphidocelis_subcapitata/Raphidocelis_subcapitata_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/Raphidocelis_subcapitata/Raphidocelis_subcapitata_intron_probs.pbl' -> './config/species/Raphidocelis_subcapitata/Raphidocelis_subcapitata_intron_probs.pbl' 153s '/usr/share/augustus/config/species/Raphidocelis_subcapitata/Raphidocelis_subcapitata_metapars.cfg' -> './config/species/Raphidocelis_subcapitata/Raphidocelis_subcapitata_metapars.cfg' 153s '/usr/share/augustus/config/species/Raphidocelis_subcapitata/Raphidocelis_subcapitata_metapars.cgp.cfg' -> './config/species/Raphidocelis_subcapitata/Raphidocelis_subcapitata_metapars.cgp.cfg' 153s '/usr/share/augustus/config/species/Raphidocelis_subcapitata/Raphidocelis_subcapitata_metapars.utr.cfg' -> './config/species/Raphidocelis_subcapitata/Raphidocelis_subcapitata_metapars.utr.cfg' 153s '/usr/share/augustus/config/species/Raphidocelis_subcapitata/Raphidocelis_subcapitata_parameters.cfg' -> './config/species/Raphidocelis_subcapitata/Raphidocelis_subcapitata_parameters.cfg' 153s '/usr/share/augustus/config/species/Raphidocelis_subcapitata/Raphidocelis_subcapitata_weightmatrix.txt' -> './config/species/Raphidocelis_subcapitata/Raphidocelis_subcapitata_weightmatrix.txt' 153s '/usr/share/augustus/config/species/Rhopilema_esculentum' -> './config/species/Rhopilema_esculentum' 153s '/usr/share/augustus/config/species/Rhopilema_esculentum/README.txt' -> './config/species/Rhopilema_esculentum/README.txt' 153s '/usr/share/augustus/config/species/Rhopilema_esculentum/Rhopilema_esculentum_exon_probs.pbl' -> './config/species/Rhopilema_esculentum/Rhopilema_esculentum_exon_probs.pbl' 153s '/usr/share/augustus/config/species/Rhopilema_esculentum/Rhopilema_esculentum_igenic_probs.pbl' -> './config/species/Rhopilema_esculentum/Rhopilema_esculentum_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/Rhopilema_esculentum/Rhopilema_esculentum_intron_probs.pbl' -> './config/species/Rhopilema_esculentum/Rhopilema_esculentum_intron_probs.pbl' 153s '/usr/share/augustus/config/species/Rhopilema_esculentum/Rhopilema_esculentum_metapars.cfg' -> './config/species/Rhopilema_esculentum/Rhopilema_esculentum_metapars.cfg' 153s '/usr/share/augustus/config/species/Rhopilema_esculentum/Rhopilema_esculentum_metapars.cgp.cfg' -> './config/species/Rhopilema_esculentum/Rhopilema_esculentum_metapars.cgp.cfg' 153s '/usr/share/augustus/config/species/Rhopilema_esculentum/Rhopilema_esculentum_metapars.utr.cfg' -> './config/species/Rhopilema_esculentum/Rhopilema_esculentum_metapars.utr.cfg' 153s '/usr/share/augustus/config/species/Rhopilema_esculentum/Rhopilema_esculentum_parameters.cfg' -> './config/species/Rhopilema_esculentum/Rhopilema_esculentum_parameters.cfg' 153s '/usr/share/augustus/config/species/Rhopilema_esculentum/Rhopilema_esculentum_weightmatrix.txt' -> './config/species/Rhopilema_esculentum/Rhopilema_esculentum_weightmatrix.txt' 153s '/usr/share/augustus/config/species/Ricinus_communis' -> './config/species/Ricinus_communis' 153s '/usr/share/augustus/config/species/Ricinus_communis/README.txt' -> './config/species/Ricinus_communis/README.txt' 153s '/usr/share/augustus/config/species/Ricinus_communis/Ricinus_communis_exon_probs.pbl' -> './config/species/Ricinus_communis/Ricinus_communis_exon_probs.pbl' 153s '/usr/share/augustus/config/species/Ricinus_communis/Ricinus_communis_igenic_probs.pbl' -> './config/species/Ricinus_communis/Ricinus_communis_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/Ricinus_communis/Ricinus_communis_intron_probs.pbl' -> './config/species/Ricinus_communis/Ricinus_communis_intron_probs.pbl' 153s '/usr/share/augustus/config/species/Ricinus_communis/Ricinus_communis_metapars.cfg' -> './config/species/Ricinus_communis/Ricinus_communis_metapars.cfg' 153s '/usr/share/augustus/config/species/Ricinus_communis/Ricinus_communis_metapars.cgp.cfg' -> './config/species/Ricinus_communis/Ricinus_communis_metapars.cgp.cfg' 153s '/usr/share/augustus/config/species/Ricinus_communis/Ricinus_communis_metapars.utr.cfg' -> './config/species/Ricinus_communis/Ricinus_communis_metapars.utr.cfg' 153s '/usr/share/augustus/config/species/Ricinus_communis/Ricinus_communis_parameters.cfg' -> './config/species/Ricinus_communis/Ricinus_communis_parameters.cfg' 153s '/usr/share/augustus/config/species/Ricinus_communis/Ricinus_communis_weightmatrix.txt' -> './config/species/Ricinus_communis/Ricinus_communis_weightmatrix.txt' 153s '/usr/share/augustus/config/species/Sclerotinia_sclerotiorum' -> './config/species/Sclerotinia_sclerotiorum' 153s '/usr/share/augustus/config/species/Sclerotinia_sclerotiorum/README.txt' -> './config/species/Sclerotinia_sclerotiorum/README.txt' 153s '/usr/share/augustus/config/species/Sclerotinia_sclerotiorum/Sclerotinia_sclerotiorum_exon_probs.pbl' -> './config/species/Sclerotinia_sclerotiorum/Sclerotinia_sclerotiorum_exon_probs.pbl' 153s '/usr/share/augustus/config/species/Sclerotinia_sclerotiorum/Sclerotinia_sclerotiorum_igenic_probs.pbl' -> './config/species/Sclerotinia_sclerotiorum/Sclerotinia_sclerotiorum_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/Sclerotinia_sclerotiorum/Sclerotinia_sclerotiorum_intron_probs.pbl' -> './config/species/Sclerotinia_sclerotiorum/Sclerotinia_sclerotiorum_intron_probs.pbl' 153s '/usr/share/augustus/config/species/Sclerotinia_sclerotiorum/Sclerotinia_sclerotiorum_metapars.cfg' -> './config/species/Sclerotinia_sclerotiorum/Sclerotinia_sclerotiorum_metapars.cfg' 153s '/usr/share/augustus/config/species/Sclerotinia_sclerotiorum/Sclerotinia_sclerotiorum_metapars.cgp.cfg' -> './config/species/Sclerotinia_sclerotiorum/Sclerotinia_sclerotiorum_metapars.cgp.cfg' 153s '/usr/share/augustus/config/species/Sclerotinia_sclerotiorum/Sclerotinia_sclerotiorum_metapars.utr.cfg' -> './config/species/Sclerotinia_sclerotiorum/Sclerotinia_sclerotiorum_metapars.utr.cfg' 153s '/usr/share/augustus/config/species/Sclerotinia_sclerotiorum/Sclerotinia_sclerotiorum_parameters.cfg' -> './config/species/Sclerotinia_sclerotiorum/Sclerotinia_sclerotiorum_parameters.cfg' 153s '/usr/share/augustus/config/species/Sclerotinia_sclerotiorum/Sclerotinia_sclerotiorum_weightmatrix.txt' -> './config/species/Sclerotinia_sclerotiorum/Sclerotinia_sclerotiorum_weightmatrix.txt' 153s '/usr/share/augustus/config/species/Skeletonema_costatum' -> './config/species/Skeletonema_costatum' 153s '/usr/share/augustus/config/species/Skeletonema_costatum/README.txt' -> './config/species/Skeletonema_costatum/README.txt' 153s '/usr/share/augustus/config/species/Skeletonema_costatum/Skeletonema_costatum_exon_probs.pbl' -> './config/species/Skeletonema_costatum/Skeletonema_costatum_exon_probs.pbl' 153s '/usr/share/augustus/config/species/Skeletonema_costatum/Skeletonema_costatum_igenic_probs.pbl' -> './config/species/Skeletonema_costatum/Skeletonema_costatum_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/Skeletonema_costatum/Skeletonema_costatum_intron_probs.pbl' -> './config/species/Skeletonema_costatum/Skeletonema_costatum_intron_probs.pbl' 153s '/usr/share/augustus/config/species/Skeletonema_costatum/Skeletonema_costatum_metapars.cfg' -> './config/species/Skeletonema_costatum/Skeletonema_costatum_metapars.cfg' 153s '/usr/share/augustus/config/species/Skeletonema_costatum/Skeletonema_costatum_metapars.cgp.cfg' -> './config/species/Skeletonema_costatum/Skeletonema_costatum_metapars.cgp.cfg' 153s '/usr/share/augustus/config/species/Skeletonema_costatum/Skeletonema_costatum_metapars.utr.cfg' -> './config/species/Skeletonema_costatum/Skeletonema_costatum_metapars.utr.cfg' 153s '/usr/share/augustus/config/species/Skeletonema_costatum/Skeletonema_costatum_parameters.cfg' -> './config/species/Skeletonema_costatum/Skeletonema_costatum_parameters.cfg' 153s '/usr/share/augustus/config/species/Skeletonema_costatum/Skeletonema_costatum_weightmatrix.txt' -> './config/species/Skeletonema_costatum/Skeletonema_costatum_weightmatrix.txt' 153s '/usr/share/augustus/config/species/Sordaria_macrospora' -> './config/species/Sordaria_macrospora' 153s '/usr/share/augustus/config/species/Sordaria_macrospora/README.txt' -> './config/species/Sordaria_macrospora/README.txt' 153s '/usr/share/augustus/config/species/Sordaria_macrospora/Sordaria_macrospora_exon_probs.pbl' -> './config/species/Sordaria_macrospora/Sordaria_macrospora_exon_probs.pbl' 153s '/usr/share/augustus/config/species/Sordaria_macrospora/Sordaria_macrospora_igenic_probs.pbl' -> './config/species/Sordaria_macrospora/Sordaria_macrospora_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/Sordaria_macrospora/Sordaria_macrospora_intron_probs.pbl' -> './config/species/Sordaria_macrospora/Sordaria_macrospora_intron_probs.pbl' 153s '/usr/share/augustus/config/species/Sordaria_macrospora/Sordaria_macrospora_metapars.cfg' -> './config/species/Sordaria_macrospora/Sordaria_macrospora_metapars.cfg' 153s '/usr/share/augustus/config/species/Sordaria_macrospora/Sordaria_macrospora_metapars.cgp.cfg' -> './config/species/Sordaria_macrospora/Sordaria_macrospora_metapars.cgp.cfg' 153s '/usr/share/augustus/config/species/Sordaria_macrospora/Sordaria_macrospora_metapars.utr.cfg' -> './config/species/Sordaria_macrospora/Sordaria_macrospora_metapars.utr.cfg' 153s '/usr/share/augustus/config/species/Sordaria_macrospora/Sordaria_macrospora_parameters.cfg' -> './config/species/Sordaria_macrospora/Sordaria_macrospora_parameters.cfg' 153s '/usr/share/augustus/config/species/Sordaria_macrospora/Sordaria_macrospora_weightmatrix.txt' -> './config/species/Sordaria_macrospora/Sordaria_macrospora_weightmatrix.txt' 153s '/usr/share/augustus/config/species/Sphaceloma_murrayae' -> './config/species/Sphaceloma_murrayae' 153s '/usr/share/augustus/config/species/Sphaceloma_murrayae/README.txt' -> './config/species/Sphaceloma_murrayae/README.txt' 153s '/usr/share/augustus/config/species/Sphaceloma_murrayae/Sphaceloma_murrayae_exon_probs.pbl' -> './config/species/Sphaceloma_murrayae/Sphaceloma_murrayae_exon_probs.pbl' 153s '/usr/share/augustus/config/species/Sphaceloma_murrayae/Sphaceloma_murrayae_igenic_probs.pbl' -> './config/species/Sphaceloma_murrayae/Sphaceloma_murrayae_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/Sphaceloma_murrayae/Sphaceloma_murrayae_intron_probs.pbl' -> './config/species/Sphaceloma_murrayae/Sphaceloma_murrayae_intron_probs.pbl' 153s '/usr/share/augustus/config/species/Sphaceloma_murrayae/Sphaceloma_murrayae_metapars.cfg' -> './config/species/Sphaceloma_murrayae/Sphaceloma_murrayae_metapars.cfg' 153s '/usr/share/augustus/config/species/Sphaceloma_murrayae/Sphaceloma_murrayae_metapars.cgp.cfg' -> './config/species/Sphaceloma_murrayae/Sphaceloma_murrayae_metapars.cgp.cfg' 153s '/usr/share/augustus/config/species/Sphaceloma_murrayae/Sphaceloma_murrayae_metapars.utr.cfg' -> './config/species/Sphaceloma_murrayae/Sphaceloma_murrayae_metapars.utr.cfg' 153s '/usr/share/augustus/config/species/Sphaceloma_murrayae/Sphaceloma_murrayae_parameters.cfg' -> './config/species/Sphaceloma_murrayae/Sphaceloma_murrayae_parameters.cfg' 153s '/usr/share/augustus/config/species/Sphaceloma_murrayae/Sphaceloma_murrayae_weightmatrix.txt' -> './config/species/Sphaceloma_murrayae/Sphaceloma_murrayae_weightmatrix.txt' 153s '/usr/share/augustus/config/species/Taeniopygia_guttata' -> './config/species/Taeniopygia_guttata' 153s '/usr/share/augustus/config/species/Taeniopygia_guttata/README.txt' -> './config/species/Taeniopygia_guttata/README.txt' 153s '/usr/share/augustus/config/species/Taeniopygia_guttata/Taeniopygia_guttata_exon_probs.pbl' -> './config/species/Taeniopygia_guttata/Taeniopygia_guttata_exon_probs.pbl' 153s '/usr/share/augustus/config/species/Taeniopygia_guttata/Taeniopygia_guttata_igenic_probs.pbl' -> './config/species/Taeniopygia_guttata/Taeniopygia_guttata_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/Taeniopygia_guttata/Taeniopygia_guttata_intron_probs.pbl' -> './config/species/Taeniopygia_guttata/Taeniopygia_guttata_intron_probs.pbl' 153s '/usr/share/augustus/config/species/Taeniopygia_guttata/Taeniopygia_guttata_metapars.cfg' -> './config/species/Taeniopygia_guttata/Taeniopygia_guttata_metapars.cfg' 153s '/usr/share/augustus/config/species/Taeniopygia_guttata/Taeniopygia_guttata_metapars.cgp.cfg' -> './config/species/Taeniopygia_guttata/Taeniopygia_guttata_metapars.cgp.cfg' 153s '/usr/share/augustus/config/species/Taeniopygia_guttata/Taeniopygia_guttata_metapars.utr.cfg' -> './config/species/Taeniopygia_guttata/Taeniopygia_guttata_metapars.utr.cfg' 153s '/usr/share/augustus/config/species/Taeniopygia_guttata/Taeniopygia_guttata_parameters.cfg' -> './config/species/Taeniopygia_guttata/Taeniopygia_guttata_parameters.cfg' 153s '/usr/share/augustus/config/species/Taeniopygia_guttata/Taeniopygia_guttata_weightmatrix.txt' -> './config/species/Taeniopygia_guttata/Taeniopygia_guttata_weightmatrix.txt' 153s '/usr/share/augustus/config/species/Thalassiosira_pseudonana_CCMP1335' -> './config/species/Thalassiosira_pseudonana_CCMP1335' 153s '/usr/share/augustus/config/species/Thalassiosira_pseudonana_CCMP1335/README.txt' -> './config/species/Thalassiosira_pseudonana_CCMP1335/README.txt' 153s '/usr/share/augustus/config/species/Thalassiosira_pseudonana_CCMP1335/Thalassiosira_pseudonana_CCMP1335_exon_probs.pbl' -> './config/species/Thalassiosira_pseudonana_CCMP1335/Thalassiosira_pseudonana_CCMP1335_exon_probs.pbl' 153s '/usr/share/augustus/config/species/Thalassiosira_pseudonana_CCMP1335/Thalassiosira_pseudonana_CCMP1335_igenic_probs.pbl' -> './config/species/Thalassiosira_pseudonana_CCMP1335/Thalassiosira_pseudonana_CCMP1335_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/Thalassiosira_pseudonana_CCMP1335/Thalassiosira_pseudonana_CCMP1335_intron_probs.pbl' -> './config/species/Thalassiosira_pseudonana_CCMP1335/Thalassiosira_pseudonana_CCMP1335_intron_probs.pbl' 153s '/usr/share/augustus/config/species/Thalassiosira_pseudonana_CCMP1335/Thalassiosira_pseudonana_CCMP1335_metapars.cfg' -> './config/species/Thalassiosira_pseudonana_CCMP1335/Thalassiosira_pseudonana_CCMP1335_metapars.cfg' 153s '/usr/share/augustus/config/species/Thalassiosira_pseudonana_CCMP1335/Thalassiosira_pseudonana_CCMP1335_metapars.cgp.cfg' -> './config/species/Thalassiosira_pseudonana_CCMP1335/Thalassiosira_pseudonana_CCMP1335_metapars.cgp.cfg' 153s '/usr/share/augustus/config/species/Thalassiosira_pseudonana_CCMP1335/Thalassiosira_pseudonana_CCMP1335_metapars.utr.cfg' -> './config/species/Thalassiosira_pseudonana_CCMP1335/Thalassiosira_pseudonana_CCMP1335_metapars.utr.cfg' 153s '/usr/share/augustus/config/species/Thalassiosira_pseudonana_CCMP1335/Thalassiosira_pseudonana_CCMP1335_parameters.cfg' -> './config/species/Thalassiosira_pseudonana_CCMP1335/Thalassiosira_pseudonana_CCMP1335_parameters.cfg' 153s '/usr/share/augustus/config/species/Thalassiosira_pseudonana_CCMP1335/Thalassiosira_pseudonana_CCMP1335_weightmatrix.txt' -> './config/species/Thalassiosira_pseudonana_CCMP1335/Thalassiosira_pseudonana_CCMP1335_weightmatrix.txt' 153s '/usr/share/augustus/config/species/Trichoplax_adhaerens' -> './config/species/Trichoplax_adhaerens' 153s '/usr/share/augustus/config/species/Trichoplax_adhaerens/README.txt' -> './config/species/Trichoplax_adhaerens/README.txt' 153s '/usr/share/augustus/config/species/Trichoplax_adhaerens/Trichoplax_adhaerens_exon_probs.pbl' -> './config/species/Trichoplax_adhaerens/Trichoplax_adhaerens_exon_probs.pbl' 153s '/usr/share/augustus/config/species/Trichoplax_adhaerens/Trichoplax_adhaerens_igenic_probs.pbl' -> './config/species/Trichoplax_adhaerens/Trichoplax_adhaerens_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/Trichoplax_adhaerens/Trichoplax_adhaerens_intron_probs.pbl' -> './config/species/Trichoplax_adhaerens/Trichoplax_adhaerens_intron_probs.pbl' 153s '/usr/share/augustus/config/species/Trichoplax_adhaerens/Trichoplax_adhaerens_metapars.cfg' -> './config/species/Trichoplax_adhaerens/Trichoplax_adhaerens_metapars.cfg' 153s '/usr/share/augustus/config/species/Trichoplax_adhaerens/Trichoplax_adhaerens_metapars.cgp.cfg' -> './config/species/Trichoplax_adhaerens/Trichoplax_adhaerens_metapars.cgp.cfg' 153s '/usr/share/augustus/config/species/Trichoplax_adhaerens/Trichoplax_adhaerens_metapars.utr.cfg' -> './config/species/Trichoplax_adhaerens/Trichoplax_adhaerens_metapars.utr.cfg' 153s '/usr/share/augustus/config/species/Trichoplax_adhaerens/Trichoplax_adhaerens_parameters.cfg' -> './config/species/Trichoplax_adhaerens/Trichoplax_adhaerens_parameters.cfg' 153s '/usr/share/augustus/config/species/Trichoplax_adhaerens/Trichoplax_adhaerens_weightmatrix.txt' -> './config/species/Trichoplax_adhaerens/Trichoplax_adhaerens_weightmatrix.txt' 153s '/usr/share/augustus/config/species/Trypanosoma_cruzi' -> './config/species/Trypanosoma_cruzi' 153s '/usr/share/augustus/config/species/Trypanosoma_cruzi/README.txt' -> './config/species/Trypanosoma_cruzi/README.txt' 153s '/usr/share/augustus/config/species/Trypanosoma_cruzi/Trypanosoma_cruzi_exon_probs.pbl' -> './config/species/Trypanosoma_cruzi/Trypanosoma_cruzi_exon_probs.pbl' 153s '/usr/share/augustus/config/species/Trypanosoma_cruzi/Trypanosoma_cruzi_igenic_probs.pbl' -> './config/species/Trypanosoma_cruzi/Trypanosoma_cruzi_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/Trypanosoma_cruzi/Trypanosoma_cruzi_intron_probs.pbl' -> './config/species/Trypanosoma_cruzi/Trypanosoma_cruzi_intron_probs.pbl' 153s '/usr/share/augustus/config/species/Trypanosoma_cruzi/Trypanosoma_cruzi_metapars.cfg' -> './config/species/Trypanosoma_cruzi/Trypanosoma_cruzi_metapars.cfg' 153s '/usr/share/augustus/config/species/Trypanosoma_cruzi/Trypanosoma_cruzi_metapars.cgp.cfg' -> './config/species/Trypanosoma_cruzi/Trypanosoma_cruzi_metapars.cgp.cfg' 153s '/usr/share/augustus/config/species/Trypanosoma_cruzi/Trypanosoma_cruzi_metapars.utr.cfg' -> './config/species/Trypanosoma_cruzi/Trypanosoma_cruzi_metapars.utr.cfg' 153s '/usr/share/augustus/config/species/Trypanosoma_cruzi/Trypanosoma_cruzi_parameters.cfg' -> './config/species/Trypanosoma_cruzi/Trypanosoma_cruzi_parameters.cfg' 153s '/usr/share/augustus/config/species/Trypanosoma_cruzi/Trypanosoma_cruzi_weightmatrix.txt' -> './config/species/Trypanosoma_cruzi/Trypanosoma_cruzi_weightmatrix.txt' 153s '/usr/share/augustus/config/species/Vitis_vinifera' -> './config/species/Vitis_vinifera' 153s '/usr/share/augustus/config/species/Vitis_vinifera/README.txt' -> './config/species/Vitis_vinifera/README.txt' 153s '/usr/share/augustus/config/species/Vitis_vinifera/Vitis_vinifera_exon_probs.pbl' -> './config/species/Vitis_vinifera/Vitis_vinifera_exon_probs.pbl' 153s '/usr/share/augustus/config/species/Vitis_vinifera/Vitis_vinifera_igenic_probs.pbl' -> './config/species/Vitis_vinifera/Vitis_vinifera_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/Vitis_vinifera/Vitis_vinifera_intron_probs.pbl' -> './config/species/Vitis_vinifera/Vitis_vinifera_intron_probs.pbl' 153s '/usr/share/augustus/config/species/Vitis_vinifera/Vitis_vinifera_metapars.cfg' -> './config/species/Vitis_vinifera/Vitis_vinifera_metapars.cfg' 153s '/usr/share/augustus/config/species/Vitis_vinifera/Vitis_vinifera_metapars.cgp.cfg' -> './config/species/Vitis_vinifera/Vitis_vinifera_metapars.cgp.cfg' 153s '/usr/share/augustus/config/species/Vitis_vinifera/Vitis_vinifera_metapars.utr.cfg' -> './config/species/Vitis_vinifera/Vitis_vinifera_metapars.utr.cfg' 153s '/usr/share/augustus/config/species/Vitis_vinifera/Vitis_vinifera_parameters.cfg' -> './config/species/Vitis_vinifera/Vitis_vinifera_parameters.cfg' 153s '/usr/share/augustus/config/species/Vitis_vinifera/Vitis_vinifera_weightmatrix.txt' -> './config/species/Vitis_vinifera/Vitis_vinifera_weightmatrix.txt' 153s '/usr/share/augustus/config/species/Vitrella_brassicaformis' -> './config/species/Vitrella_brassicaformis' 153s '/usr/share/augustus/config/species/Vitrella_brassicaformis/README.txt' -> './config/species/Vitrella_brassicaformis/README.txt' 153s '/usr/share/augustus/config/species/Vitrella_brassicaformis/Vitrella_brassicaformis_exon_probs.pbl' -> './config/species/Vitrella_brassicaformis/Vitrella_brassicaformis_exon_probs.pbl' 153s '/usr/share/augustus/config/species/Vitrella_brassicaformis/Vitrella_brassicaformis_igenic_probs.pbl' -> './config/species/Vitrella_brassicaformis/Vitrella_brassicaformis_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/Vitrella_brassicaformis/Vitrella_brassicaformis_intron_probs.pbl' -> './config/species/Vitrella_brassicaformis/Vitrella_brassicaformis_intron_probs.pbl' 153s '/usr/share/augustus/config/species/Vitrella_brassicaformis/Vitrella_brassicaformis_metapars.cfg' -> './config/species/Vitrella_brassicaformis/Vitrella_brassicaformis_metapars.cfg' 153s '/usr/share/augustus/config/species/Vitrella_brassicaformis/Vitrella_brassicaformis_metapars.cgp.cfg' -> './config/species/Vitrella_brassicaformis/Vitrella_brassicaformis_metapars.cgp.cfg' 153s '/usr/share/augustus/config/species/Vitrella_brassicaformis/Vitrella_brassicaformis_metapars.utr.cfg' -> './config/species/Vitrella_brassicaformis/Vitrella_brassicaformis_metapars.utr.cfg' 153s '/usr/share/augustus/config/species/Vitrella_brassicaformis/Vitrella_brassicaformis_parameters.cfg' -> './config/species/Vitrella_brassicaformis/Vitrella_brassicaformis_parameters.cfg' 153s '/usr/share/augustus/config/species/Vitrella_brassicaformis/Vitrella_brassicaformis_weightmatrix.txt' -> './config/species/Vitrella_brassicaformis/Vitrella_brassicaformis_weightmatrix.txt' 153s '/usr/share/augustus/config/species/Xenopus_tropicalis' -> './config/species/Xenopus_tropicalis' 153s '/usr/share/augustus/config/species/Xenopus_tropicalis/Xenopus_tropicalis_exon_probs.pbl' -> './config/species/Xenopus_tropicalis/Xenopus_tropicalis_exon_probs.pbl' 153s '/usr/share/augustus/config/species/Xenopus_tropicalis/Xenopus_tropicalis_igenic_probs.pbl' -> './config/species/Xenopus_tropicalis/Xenopus_tropicalis_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/Xenopus_tropicalis/Xenopus_tropicalis_intron_probs.pbl' -> './config/species/Xenopus_tropicalis/Xenopus_tropicalis_intron_probs.pbl' 153s '/usr/share/augustus/config/species/Xenopus_tropicalis/Xenopus_tropicalis_metapars.cfg' -> './config/species/Xenopus_tropicalis/Xenopus_tropicalis_metapars.cfg' 153s '/usr/share/augustus/config/species/Xenopus_tropicalis/Xenopus_tropicalis_metapars.cgp.cfg' -> './config/species/Xenopus_tropicalis/Xenopus_tropicalis_metapars.cgp.cfg' 153s '/usr/share/augustus/config/species/Xenopus_tropicalis/Xenopus_tropicalis_metapars.utr.cfg' -> './config/species/Xenopus_tropicalis/Xenopus_tropicalis_metapars.utr.cfg' 153s '/usr/share/augustus/config/species/Xenopus_tropicalis/Xenopus_tropicalis_parameters.cfg' -> './config/species/Xenopus_tropicalis/Xenopus_tropicalis_parameters.cfg' 153s '/usr/share/augustus/config/species/Xenopus_tropicalis/Xenopus_tropicalis_weightmatrix.txt' -> './config/species/Xenopus_tropicalis/Xenopus_tropicalis_weightmatrix.txt' 153s '/usr/share/augustus/config/species/Xiphophorus_maculatus' -> './config/species/Xiphophorus_maculatus' 153s '/usr/share/augustus/config/species/Xiphophorus_maculatus/README.txt' -> './config/species/Xiphophorus_maculatus/README.txt' 153s '/usr/share/augustus/config/species/Xiphophorus_maculatus/Xiphophorus_maculatus_exon_probs.pbl' -> './config/species/Xiphophorus_maculatus/Xiphophorus_maculatus_exon_probs.pbl' 153s '/usr/share/augustus/config/species/Xiphophorus_maculatus/Xiphophorus_maculatus_igenic_probs.pbl' -> './config/species/Xiphophorus_maculatus/Xiphophorus_maculatus_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/Xiphophorus_maculatus/Xiphophorus_maculatus_intron_probs.pbl' -> './config/species/Xiphophorus_maculatus/Xiphophorus_maculatus_intron_probs.pbl' 153s '/usr/share/augustus/config/species/Xiphophorus_maculatus/Xiphophorus_maculatus_parameters.cfg' -> './config/species/Xiphophorus_maculatus/Xiphophorus_maculatus_parameters.cfg' 153s '/usr/share/augustus/config/species/Xiphophorus_maculatus/Xiphophorus_maculatus_utr_probs.pbl' -> './config/species/Xiphophorus_maculatus/Xiphophorus_maculatus_utr_probs.pbl' 153s '/usr/share/augustus/config/species/Xiphophorus_maculatus/Xiphophorus_maculatus_weightmatrix.txt' -> './config/species/Xiphophorus_maculatus/Xiphophorus_maculatus_weightmatrix.txt' 153s '/usr/share/augustus/config/species/Xipophorus_maculatus' -> './config/species/Xipophorus_maculatus' 153s '/usr/share/augustus/config/species/Xipophorus_maculatus/Xipophorus_maculatus_exon_probs.pbl' -> './config/species/Xipophorus_maculatus/Xipophorus_maculatus_exon_probs.pbl' 153s '/usr/share/augustus/config/species/Xipophorus_maculatus/Xipophorus_maculatus_igenic_probs.pbl' -> './config/species/Xipophorus_maculatus/Xipophorus_maculatus_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/Xipophorus_maculatus/Xipophorus_maculatus_intron_probs.pbl' -> './config/species/Xipophorus_maculatus/Xipophorus_maculatus_intron_probs.pbl' 153s '/usr/share/augustus/config/species/Xipophorus_maculatus/Xipophorus_maculatus_parameters.cfg' -> './config/species/Xipophorus_maculatus/Xipophorus_maculatus_parameters.cfg' 153s '/usr/share/augustus/config/species/Xipophorus_maculatus/Xipophorus_maculatus_utr_probs.pbl' -> './config/species/Xipophorus_maculatus/Xipophorus_maculatus_utr_probs.pbl' 153s '/usr/share/augustus/config/species/Xipophorus_maculatus/Xipophorus_maculatus_weightmatrix.txt' -> './config/species/Xipophorus_maculatus/Xipophorus_maculatus_weightmatrix.txt' 153s '/usr/share/augustus/config/species/adorsata' -> './config/species/adorsata' 153s '/usr/share/augustus/config/species/adorsata/adorsata_parameters.cfg' -> './config/species/adorsata/adorsata_parameters.cfg' 153s '/usr/share/augustus/config/species/adorsata/adorsata_weightmatrix.txt' -> './config/species/adorsata/adorsata_weightmatrix.txt' 153s '/usr/share/augustus/config/species/adorsata/generic_exon_probs.pbl' -> './config/species/adorsata/generic_exon_probs.pbl' 153s '/usr/share/augustus/config/species/adorsata/generic_igenic_probs.pbl' -> './config/species/adorsata/generic_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/adorsata/generic_intron_probs.pbl' -> './config/species/adorsata/generic_intron_probs.pbl' 153s '/usr/share/augustus/config/species/adorsata/generic_weightmatrix.txt' -> './config/species/adorsata/generic_weightmatrix.txt' 153s '/usr/share/augustus/config/species/aedes' -> './config/species/aedes' 153s '/usr/share/augustus/config/species/aedes/aedes_exon_probs.pbl' -> './config/species/aedes/aedes_exon_probs.pbl' 153s '/usr/share/augustus/config/species/aedes/aedes_igenic_probs.pbl' -> './config/species/aedes/aedes_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/aedes/aedes_intron_probs.pbl' -> './config/species/aedes/aedes_intron_probs.pbl' 153s '/usr/share/augustus/config/species/aedes/aedes_parameters.cfg' -> './config/species/aedes/aedes_parameters.cfg' 153s '/usr/share/augustus/config/species/aedes/aedes_weightmatrix.txt' -> './config/species/aedes/aedes_weightmatrix.txt' 153s '/usr/share/augustus/config/species/amphimedon' -> './config/species/amphimedon' 153s '/usr/share/augustus/config/species/amphimedon/amphimedon_exon_probs.pbl' -> './config/species/amphimedon/amphimedon_exon_probs.pbl' 153s '/usr/share/augustus/config/species/amphimedon/amphimedon_igenic_probs.pbl' -> './config/species/amphimedon/amphimedon_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/amphimedon/amphimedon_intron_probs.pbl' -> './config/species/amphimedon/amphimedon_intron_probs.pbl' 153s '/usr/share/augustus/config/species/amphimedon/amphimedon_metapars.cfg' -> './config/species/amphimedon/amphimedon_metapars.cfg' 153s '/usr/share/augustus/config/species/amphimedon/amphimedon_parameters.cfg' -> './config/species/amphimedon/amphimedon_parameters.cfg' 153s '/usr/share/augustus/config/species/amphimedon/amphimedon_utr_probs.pbl' -> './config/species/amphimedon/amphimedon_utr_probs.pbl' 153s '/usr/share/augustus/config/species/amphimedon/amphimedon_weightmatrix.txt' -> './config/species/amphimedon/amphimedon_weightmatrix.txt' 153s '/usr/share/augustus/config/species/ancylostoma_ceylanicum' -> './config/species/ancylostoma_ceylanicum' 153s '/usr/share/augustus/config/species/ancylostoma_ceylanicum/README.TXT' -> './config/species/ancylostoma_ceylanicum/README.TXT' 153s '/usr/share/augustus/config/species/ancylostoma_ceylanicum/ancylostoma_ceylanicum_exon_probs.pbl' -> './config/species/ancylostoma_ceylanicum/ancylostoma_ceylanicum_exon_probs.pbl' 153s '/usr/share/augustus/config/species/ancylostoma_ceylanicum/ancylostoma_ceylanicum_igenic_probs.pbl' -> './config/species/ancylostoma_ceylanicum/ancylostoma_ceylanicum_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/ancylostoma_ceylanicum/ancylostoma_ceylanicum_intron_probs.pbl' -> './config/species/ancylostoma_ceylanicum/ancylostoma_ceylanicum_intron_probs.pbl' 153s '/usr/share/augustus/config/species/ancylostoma_ceylanicum/ancylostoma_ceylanicum_metapars.cfg' -> './config/species/ancylostoma_ceylanicum/ancylostoma_ceylanicum_metapars.cfg' 153s '/usr/share/augustus/config/species/ancylostoma_ceylanicum/ancylostoma_ceylanicum_metapars.utr.cfg' -> './config/species/ancylostoma_ceylanicum/ancylostoma_ceylanicum_metapars.utr.cfg' 153s '/usr/share/augustus/config/species/ancylostoma_ceylanicum/ancylostoma_ceylanicum_parameters.cfg' -> './config/species/ancylostoma_ceylanicum/ancylostoma_ceylanicum_parameters.cfg' 153s '/usr/share/augustus/config/species/ancylostoma_ceylanicum/ancylostoma_ceylanicum_weightmatrix.txt' -> './config/species/ancylostoma_ceylanicum/ancylostoma_ceylanicum_weightmatrix.txt' 153s '/usr/share/augustus/config/species/anidulans' -> './config/species/anidulans' 153s '/usr/share/augustus/config/species/anidulans/anidulans_exon_probs.pbl' -> './config/species/anidulans/anidulans_exon_probs.pbl' 153s '/usr/share/augustus/config/species/anidulans/anidulans_igenic_probs.pbl' -> './config/species/anidulans/anidulans_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/anidulans/anidulans_intron_probs.pbl' -> './config/species/anidulans/anidulans_intron_probs.pbl' 153s '/usr/share/augustus/config/species/anidulans/anidulans_parameters.cfg' -> './config/species/anidulans/anidulans_parameters.cfg' 153s '/usr/share/augustus/config/species/anidulans/anidulans_weightmatrix.txt' -> './config/species/anidulans/anidulans_weightmatrix.txt' 153s '/usr/share/augustus/config/species/arabidopsis' -> './config/species/arabidopsis' 153s '/usr/share/augustus/config/species/arabidopsis/arabidopsis_exon_probs.pbl' -> './config/species/arabidopsis/arabidopsis_exon_probs.pbl' 153s '/usr/share/augustus/config/species/arabidopsis/arabidopsis_igenic_probs.pbl' -> './config/species/arabidopsis/arabidopsis_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/arabidopsis/arabidopsis_intron_probs.pbl' -> './config/species/arabidopsis/arabidopsis_intron_probs.pbl' 153s '/usr/share/augustus/config/species/arabidopsis/arabidopsis_parameters.cfg' -> './config/species/arabidopsis/arabidopsis_parameters.cfg' 153s '/usr/share/augustus/config/species/arabidopsis/arabidopsis_utr_probs.pbl' -> './config/species/arabidopsis/arabidopsis_utr_probs.pbl' 153s '/usr/share/augustus/config/species/arabidopsis/arabidopsis_weightmatrix.txt' -> './config/species/arabidopsis/arabidopsis_weightmatrix.txt' 153s '/usr/share/augustus/config/species/aspergillus_fumigatus' -> './config/species/aspergillus_fumigatus' 153s '/usr/share/augustus/config/species/aspergillus_fumigatus/aspergillus_fumigatus_exon_probs.pbl' -> './config/species/aspergillus_fumigatus/aspergillus_fumigatus_exon_probs.pbl' 153s '/usr/share/augustus/config/species/aspergillus_fumigatus/aspergillus_fumigatus_igenic_probs.pbl' -> './config/species/aspergillus_fumigatus/aspergillus_fumigatus_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/aspergillus_fumigatus/aspergillus_fumigatus_intron_probs.pbl' -> './config/species/aspergillus_fumigatus/aspergillus_fumigatus_intron_probs.pbl' 153s '/usr/share/augustus/config/species/aspergillus_fumigatus/aspergillus_fumigatus_metapars.cfg' -> './config/species/aspergillus_fumigatus/aspergillus_fumigatus_metapars.cfg' 153s '/usr/share/augustus/config/species/aspergillus_fumigatus/aspergillus_fumigatus_parameters.cfg' -> './config/species/aspergillus_fumigatus/aspergillus_fumigatus_parameters.cfg' 153s '/usr/share/augustus/config/species/aspergillus_fumigatus/aspergillus_fumigatus_weightmatrix.txt' -> './config/species/aspergillus_fumigatus/aspergillus_fumigatus_weightmatrix.txt' 153s '/usr/share/augustus/config/species/aspergillus_nidulans' -> './config/species/aspergillus_nidulans' 153s '/usr/share/augustus/config/species/aspergillus_nidulans/aspergillus_nidulans_exon_probs.pbl' -> './config/species/aspergillus_nidulans/aspergillus_nidulans_exon_probs.pbl' 153s '/usr/share/augustus/config/species/aspergillus_nidulans/aspergillus_nidulans_igenic_probs.pbl' -> './config/species/aspergillus_nidulans/aspergillus_nidulans_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/aspergillus_nidulans/aspergillus_nidulans_intron_probs.pbl' -> './config/species/aspergillus_nidulans/aspergillus_nidulans_intron_probs.pbl' 153s '/usr/share/augustus/config/species/aspergillus_nidulans/aspergillus_nidulans_metapars.cfg' -> './config/species/aspergillus_nidulans/aspergillus_nidulans_metapars.cfg' 153s '/usr/share/augustus/config/species/aspergillus_nidulans/aspergillus_nidulans_parameters.cfg' -> './config/species/aspergillus_nidulans/aspergillus_nidulans_parameters.cfg' 153s '/usr/share/augustus/config/species/aspergillus_nidulans/aspergillus_nidulans_weightmatrix.txt' -> './config/species/aspergillus_nidulans/aspergillus_nidulans_weightmatrix.txt' 153s '/usr/share/augustus/config/species/aspergillus_oryzae' -> './config/species/aspergillus_oryzae' 153s '/usr/share/augustus/config/species/aspergillus_oryzae/aspergillus_oryzae_exon_probs.pbl' -> './config/species/aspergillus_oryzae/aspergillus_oryzae_exon_probs.pbl' 153s '/usr/share/augustus/config/species/aspergillus_oryzae/aspergillus_oryzae_igenic_probs.pbl' -> './config/species/aspergillus_oryzae/aspergillus_oryzae_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/aspergillus_oryzae/aspergillus_oryzae_intron_probs.pbl' -> './config/species/aspergillus_oryzae/aspergillus_oryzae_intron_probs.pbl' 153s '/usr/share/augustus/config/species/aspergillus_oryzae/aspergillus_oryzae_metapars.cfg' -> './config/species/aspergillus_oryzae/aspergillus_oryzae_metapars.cfg' 153s '/usr/share/augustus/config/species/aspergillus_oryzae/aspergillus_oryzae_parameters.cfg' -> './config/species/aspergillus_oryzae/aspergillus_oryzae_parameters.cfg' 153s '/usr/share/augustus/config/species/aspergillus_oryzae/aspergillus_oryzae_weightmatrix.txt' -> './config/species/aspergillus_oryzae/aspergillus_oryzae_weightmatrix.txt' 153s '/usr/share/augustus/config/species/aspergillus_terreus' -> './config/species/aspergillus_terreus' 153s '/usr/share/augustus/config/species/aspergillus_terreus/aspergillus_terreus_exon_probs.pbl' -> './config/species/aspergillus_terreus/aspergillus_terreus_exon_probs.pbl' 153s '/usr/share/augustus/config/species/aspergillus_terreus/aspergillus_terreus_igenic_probs.pbl' -> './config/species/aspergillus_terreus/aspergillus_terreus_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/aspergillus_terreus/aspergillus_terreus_intron_probs.pbl' -> './config/species/aspergillus_terreus/aspergillus_terreus_intron_probs.pbl' 153s '/usr/share/augustus/config/species/aspergillus_terreus/aspergillus_terreus_metapars.cfg' -> './config/species/aspergillus_terreus/aspergillus_terreus_metapars.cfg' 153s '/usr/share/augustus/config/species/aspergillus_terreus/aspergillus_terreus_parameters.cfg' -> './config/species/aspergillus_terreus/aspergillus_terreus_parameters.cfg' 153s '/usr/share/augustus/config/species/aspergillus_terreus/aspergillus_terreus_weightmatrix.txt' -> './config/species/aspergillus_terreus/aspergillus_terreus_weightmatrix.txt' 153s '/usr/share/augustus/config/species/b_pseudomallei' -> './config/species/b_pseudomallei' 153s '/usr/share/augustus/config/species/b_pseudomallei/b_pseudomallei_exon_probs.pbl' -> './config/species/b_pseudomallei/b_pseudomallei_exon_probs.pbl' 153s '/usr/share/augustus/config/species/b_pseudomallei/b_pseudomallei_igenic_probs.pbl' -> './config/species/b_pseudomallei/b_pseudomallei_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/b_pseudomallei/b_pseudomallei_metapars.cfg' -> './config/species/b_pseudomallei/b_pseudomallei_metapars.cfg' 153s '/usr/share/augustus/config/species/b_pseudomallei/b_pseudomallei_metapars.utr.cfg' -> './config/species/b_pseudomallei/b_pseudomallei_metapars.utr.cfg' 153s '/usr/share/augustus/config/species/b_pseudomallei/b_pseudomallei_ovlp_len.pbl' -> './config/species/b_pseudomallei/b_pseudomallei_ovlp_len.pbl' 153s '/usr/share/augustus/config/species/b_pseudomallei/b_pseudomallei_parameters.cfg' -> './config/species/b_pseudomallei/b_pseudomallei_parameters.cfg' 153s '/usr/share/augustus/config/species/b_pseudomallei/b_pseudomallei_parameters.cfg.orig1' -> './config/species/b_pseudomallei/b_pseudomallei_parameters.cfg.orig1' 153s '/usr/share/augustus/config/species/b_pseudomallei/b_pseudomallei_parameters.cfg.orig2' -> './config/species/b_pseudomallei/b_pseudomallei_parameters.cfg.orig2' 153s '/usr/share/augustus/config/species/b_pseudomallei/b_pseudomallei_trans_shadow_bacterium.pbl' -> './config/species/b_pseudomallei/b_pseudomallei_trans_shadow_bacterium.pbl' 153s '/usr/share/augustus/config/species/b_pseudomallei/b_pseudomallei_weightmatrix.txt' -> './config/species/b_pseudomallei/b_pseudomallei_weightmatrix.txt' 153s '/usr/share/augustus/config/species/bombus_impatiens1' -> './config/species/bombus_impatiens1' 153s '/usr/share/augustus/config/species/bombus_impatiens1/bombus_impatiens1_exon_probs.pbl' -> './config/species/bombus_impatiens1/bombus_impatiens1_exon_probs.pbl' 153s '/usr/share/augustus/config/species/bombus_impatiens1/bombus_impatiens1_exon_probs.pbl.withoutCRF' -> './config/species/bombus_impatiens1/bombus_impatiens1_exon_probs.pbl.withoutCRF' 153s '/usr/share/augustus/config/species/bombus_impatiens1/bombus_impatiens1_igenic_probs.pbl' -> './config/species/bombus_impatiens1/bombus_impatiens1_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/bombus_impatiens1/bombus_impatiens1_igenic_probs.pbl.withoutCRF' -> './config/species/bombus_impatiens1/bombus_impatiens1_igenic_probs.pbl.withoutCRF' 153s '/usr/share/augustus/config/species/bombus_impatiens1/bombus_impatiens1_intron_probs.pbl' -> './config/species/bombus_impatiens1/bombus_impatiens1_intron_probs.pbl' 153s '/usr/share/augustus/config/species/bombus_impatiens1/bombus_impatiens1_intron_probs.pbl.withoutCRF' -> './config/species/bombus_impatiens1/bombus_impatiens1_intron_probs.pbl.withoutCRF' 153s '/usr/share/augustus/config/species/bombus_impatiens1/bombus_impatiens1_metapars.cfg' -> './config/species/bombus_impatiens1/bombus_impatiens1_metapars.cfg' 153s '/usr/share/augustus/config/species/bombus_impatiens1/bombus_impatiens1_metapars.utr.cfg' -> './config/species/bombus_impatiens1/bombus_impatiens1_metapars.utr.cfg' 153s '/usr/share/augustus/config/species/bombus_impatiens1/bombus_impatiens1_parameters.cfg' -> './config/species/bombus_impatiens1/bombus_impatiens1_parameters.cfg' 153s '/usr/share/augustus/config/species/bombus_impatiens1/bombus_impatiens1_parameters.cfg.orig1' -> './config/species/bombus_impatiens1/bombus_impatiens1_parameters.cfg.orig1' 153s '/usr/share/augustus/config/species/bombus_impatiens1/bombus_impatiens1_parameters.cfg.orig2' -> './config/species/bombus_impatiens1/bombus_impatiens1_parameters.cfg.orig2' 153s '/usr/share/augustus/config/species/bombus_impatiens1/bombus_impatiens1_parameters.cfg.orig3' -> './config/species/bombus_impatiens1/bombus_impatiens1_parameters.cfg.orig3' 153s '/usr/share/augustus/config/species/bombus_impatiens1/bombus_impatiens1_parameters.cfg.orig4' -> './config/species/bombus_impatiens1/bombus_impatiens1_parameters.cfg.orig4' 153s '/usr/share/augustus/config/species/bombus_impatiens1/bombus_impatiens1_parameters.cfg.orig5' -> './config/species/bombus_impatiens1/bombus_impatiens1_parameters.cfg.orig5' 153s '/usr/share/augustus/config/species/bombus_impatiens1/bombus_impatiens1_weightmatrix.txt' -> './config/species/bombus_impatiens1/bombus_impatiens1_weightmatrix.txt' 153s '/usr/share/augustus/config/species/bombus_terrestris2' -> './config/species/bombus_terrestris2' 153s '/usr/share/augustus/config/species/bombus_terrestris2/bombus_terrestris2_exon_probs.pbl' -> './config/species/bombus_terrestris2/bombus_terrestris2_exon_probs.pbl' 153s '/usr/share/augustus/config/species/bombus_terrestris2/bombus_terrestris2_exon_probs.pbl.withoutCRF' -> './config/species/bombus_terrestris2/bombus_terrestris2_exon_probs.pbl.withoutCRF' 153s '/usr/share/augustus/config/species/bombus_terrestris2/bombus_terrestris2_igenic_probs.pbl' -> './config/species/bombus_terrestris2/bombus_terrestris2_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/bombus_terrestris2/bombus_terrestris2_igenic_probs.pbl.withoutCRF' -> './config/species/bombus_terrestris2/bombus_terrestris2_igenic_probs.pbl.withoutCRF' 153s '/usr/share/augustus/config/species/bombus_terrestris2/bombus_terrestris2_intron_probs.pbl' -> './config/species/bombus_terrestris2/bombus_terrestris2_intron_probs.pbl' 153s '/usr/share/augustus/config/species/bombus_terrestris2/bombus_terrestris2_intron_probs.pbl.withoutCRF' -> './config/species/bombus_terrestris2/bombus_terrestris2_intron_probs.pbl.withoutCRF' 153s '/usr/share/augustus/config/species/bombus_terrestris2/bombus_terrestris2_metapars.cfg' -> './config/species/bombus_terrestris2/bombus_terrestris2_metapars.cfg' 153s '/usr/share/augustus/config/species/bombus_terrestris2/bombus_terrestris2_metapars.utr.cfg' -> './config/species/bombus_terrestris2/bombus_terrestris2_metapars.utr.cfg' 153s '/usr/share/augustus/config/species/bombus_terrestris2/bombus_terrestris2_parameters.cfg' -> './config/species/bombus_terrestris2/bombus_terrestris2_parameters.cfg' 153s '/usr/share/augustus/config/species/bombus_terrestris2/bombus_terrestris2_parameters.cfg.orig1' -> './config/species/bombus_terrestris2/bombus_terrestris2_parameters.cfg.orig1' 153s '/usr/share/augustus/config/species/bombus_terrestris2/bombus_terrestris2_parameters.cfg.orig2' -> './config/species/bombus_terrestris2/bombus_terrestris2_parameters.cfg.orig2' 153s '/usr/share/augustus/config/species/bombus_terrestris2/bombus_terrestris2_parameters.cfg.orig3' -> './config/species/bombus_terrestris2/bombus_terrestris2_parameters.cfg.orig3' 153s '/usr/share/augustus/config/species/bombus_terrestris2/bombus_terrestris2_parameters.cfg.orig4' -> './config/species/bombus_terrestris2/bombus_terrestris2_parameters.cfg.orig4' 153s '/usr/share/augustus/config/species/bombus_terrestris2/bombus_terrestris2_utr_probs.pbl' -> './config/species/bombus_terrestris2/bombus_terrestris2_utr_probs.pbl' 153s '/usr/share/augustus/config/species/bombus_terrestris2/bombus_terrestris2_weightmatrix.txt' -> './config/species/bombus_terrestris2/bombus_terrestris2_weightmatrix.txt' 153s '/usr/share/augustus/config/species/botrytis_cinerea' -> './config/species/botrytis_cinerea' 153s '/usr/share/augustus/config/species/botrytis_cinerea/botrytis_cinerea_exon_probs.pbl' -> './config/species/botrytis_cinerea/botrytis_cinerea_exon_probs.pbl' 153s '/usr/share/augustus/config/species/botrytis_cinerea/botrytis_cinerea_igenic_probs.pbl' -> './config/species/botrytis_cinerea/botrytis_cinerea_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/botrytis_cinerea/botrytis_cinerea_intron_probs.pbl' -> './config/species/botrytis_cinerea/botrytis_cinerea_intron_probs.pbl' 153s '/usr/share/augustus/config/species/botrytis_cinerea/botrytis_cinerea_metapars.cfg' -> './config/species/botrytis_cinerea/botrytis_cinerea_metapars.cfg' 153s '/usr/share/augustus/config/species/botrytis_cinerea/botrytis_cinerea_parameters.cfg' -> './config/species/botrytis_cinerea/botrytis_cinerea_parameters.cfg' 153s '/usr/share/augustus/config/species/botrytis_cinerea/botrytis_cinerea_weightmatrix.txt' -> './config/species/botrytis_cinerea/botrytis_cinerea_weightmatrix.txt' 153s '/usr/share/augustus/config/species/brugia' -> './config/species/brugia' 153s '/usr/share/augustus/config/species/brugia/brugia_exon_probs.pbl' -> './config/species/brugia/brugia_exon_probs.pbl' 153s '/usr/share/augustus/config/species/brugia/brugia_igenic_probs.pbl' -> './config/species/brugia/brugia_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/brugia/brugia_intron_probs.pbl' -> './config/species/brugia/brugia_intron_probs.pbl' 153s '/usr/share/augustus/config/species/brugia/brugia_parameters.cfg' -> './config/species/brugia/brugia_parameters.cfg' 153s '/usr/share/augustus/config/species/brugia/brugia_splicefile' -> './config/species/brugia/brugia_splicefile' 153s '/usr/share/augustus/config/species/brugia/brugia_weightmatrix.txt' -> './config/species/brugia/brugia_weightmatrix.txt' 153s '/usr/share/augustus/config/species/c_elegans_trsk' -> './config/species/c_elegans_trsk' 153s '/usr/share/augustus/config/species/c_elegans_trsk/c_elegans_trsk_exon_probs.pbl' -> './config/species/c_elegans_trsk/c_elegans_trsk_exon_probs.pbl' 153s '/usr/share/augustus/config/species/c_elegans_trsk/c_elegans_trsk_exon_probs.pbl.withoutCRF' -> './config/species/c_elegans_trsk/c_elegans_trsk_exon_probs.pbl.withoutCRF' 153s '/usr/share/augustus/config/species/c_elegans_trsk/c_elegans_trsk_igenic_probs.pbl' -> './config/species/c_elegans_trsk/c_elegans_trsk_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/c_elegans_trsk/c_elegans_trsk_igenic_probs.pbl.withoutCRF' -> './config/species/c_elegans_trsk/c_elegans_trsk_igenic_probs.pbl.withoutCRF' 153s '/usr/share/augustus/config/species/c_elegans_trsk/c_elegans_trsk_intron_probs.pbl' -> './config/species/c_elegans_trsk/c_elegans_trsk_intron_probs.pbl' 153s '/usr/share/augustus/config/species/c_elegans_trsk/c_elegans_trsk_intron_probs.pbl.withoutCRF' -> './config/species/c_elegans_trsk/c_elegans_trsk_intron_probs.pbl.withoutCRF' 153s '/usr/share/augustus/config/species/c_elegans_trsk/c_elegans_trsk_metapars.cfg' -> './config/species/c_elegans_trsk/c_elegans_trsk_metapars.cfg' 153s '/usr/share/augustus/config/species/c_elegans_trsk/c_elegans_trsk_metapars.utr.cfg' -> './config/species/c_elegans_trsk/c_elegans_trsk_metapars.utr.cfg' 153s '/usr/share/augustus/config/species/c_elegans_trsk/c_elegans_trsk_parameters.cfg' -> './config/species/c_elegans_trsk/c_elegans_trsk_parameters.cfg' 153s '/usr/share/augustus/config/species/c_elegans_trsk/c_elegans_trsk_utr_probs.pbl' -> './config/species/c_elegans_trsk/c_elegans_trsk_utr_probs.pbl' 153s '/usr/share/augustus/config/species/c_elegans_trsk/c_elegans_trsk_weightmatrix.txt' -> './config/species/c_elegans_trsk/c_elegans_trsk_weightmatrix.txt' 153s '/usr/share/augustus/config/species/cacao' -> './config/species/cacao' 153s '/usr/share/augustus/config/species/cacao/cacao_exon_probs.pbl' -> './config/species/cacao/cacao_exon_probs.pbl' 153s '/usr/share/augustus/config/species/cacao/cacao_igenic_probs.pbl' -> './config/species/cacao/cacao_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/cacao/cacao_intron_probs.pbl' -> './config/species/cacao/cacao_intron_probs.pbl' 153s '/usr/share/augustus/config/species/cacao/cacao_metapars.cfg' -> './config/species/cacao/cacao_metapars.cfg' 153s '/usr/share/augustus/config/species/cacao/cacao_metapars.utr.cfg' -> './config/species/cacao/cacao_metapars.utr.cfg' 153s '/usr/share/augustus/config/species/cacao/cacao_parameters.cfg' -> './config/species/cacao/cacao_parameters.cfg' 153s '/usr/share/augustus/config/species/cacao/cacao_utr_probs.pbl' -> './config/species/cacao/cacao_utr_probs.pbl' 153s '/usr/share/augustus/config/species/cacao/cacao_weightmatrix.txt' -> './config/species/cacao/cacao_weightmatrix.txt' 153s '/usr/share/augustus/config/species/caenorhabditis' -> './config/species/caenorhabditis' 153s '/usr/share/augustus/config/species/caenorhabditis/caenorhabditis_exon_probs.pbl' -> './config/species/caenorhabditis/caenorhabditis_exon_probs.pbl' 153s '/usr/share/augustus/config/species/caenorhabditis/caenorhabditis_igenic_probs.pbl' -> './config/species/caenorhabditis/caenorhabditis_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/caenorhabditis/caenorhabditis_intron_probs.pbl' -> './config/species/caenorhabditis/caenorhabditis_intron_probs.pbl' 153s '/usr/share/augustus/config/species/caenorhabditis/caenorhabditis_metapars.cfg' -> './config/species/caenorhabditis/caenorhabditis_metapars.cfg' 153s '/usr/share/augustus/config/species/caenorhabditis/caenorhabditis_parameters.cfg' -> './config/species/caenorhabditis/caenorhabditis_parameters.cfg' 153s '/usr/share/augustus/config/species/caenorhabditis/caenorhabditis_trans_shadow_partial_utr.pbl' -> './config/species/caenorhabditis/caenorhabditis_trans_shadow_partial_utr.pbl' 153s '/usr/share/augustus/config/species/caenorhabditis/caenorhabditis_utr_probs.pbl' -> './config/species/caenorhabditis/caenorhabditis_utr_probs.pbl' 153s '/usr/share/augustus/config/species/caenorhabditis/caenorhabditis_weightmatrix.txt' -> './config/species/caenorhabditis/caenorhabditis_weightmatrix.txt' 153s '/usr/share/augustus/config/species/camponotus_floridanus' -> './config/species/camponotus_floridanus' 153s '/usr/share/augustus/config/species/camponotus_floridanus/README.TXT' -> './config/species/camponotus_floridanus/README.TXT' 153s '/usr/share/augustus/config/species/camponotus_floridanus/camponotus_floridanus_exon_probs.pbl' -> './config/species/camponotus_floridanus/camponotus_floridanus_exon_probs.pbl' 153s '/usr/share/augustus/config/species/camponotus_floridanus/camponotus_floridanus_igenic_probs.pbl' -> './config/species/camponotus_floridanus/camponotus_floridanus_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/camponotus_floridanus/camponotus_floridanus_intron_probs.pbl' -> './config/species/camponotus_floridanus/camponotus_floridanus_intron_probs.pbl' 153s '/usr/share/augustus/config/species/camponotus_floridanus/camponotus_floridanus_metapars.cfg' -> './config/species/camponotus_floridanus/camponotus_floridanus_metapars.cfg' 153s '/usr/share/augustus/config/species/camponotus_floridanus/camponotus_floridanus_metapars.utr.cfg' -> './config/species/camponotus_floridanus/camponotus_floridanus_metapars.utr.cfg' 153s '/usr/share/augustus/config/species/camponotus_floridanus/camponotus_floridanus_parameters.cfg' -> './config/species/camponotus_floridanus/camponotus_floridanus_parameters.cfg' 153s '/usr/share/augustus/config/species/camponotus_floridanus/camponotus_floridanus_weightmatrix.txt' -> './config/species/camponotus_floridanus/camponotus_floridanus_weightmatrix.txt' 153s '/usr/share/augustus/config/species/candida_albicans' -> './config/species/candida_albicans' 153s '/usr/share/augustus/config/species/candida_albicans/candida_albicans_exon_probs.pbl' -> './config/species/candida_albicans/candida_albicans_exon_probs.pbl' 153s '/usr/share/augustus/config/species/candida_albicans/candida_albicans_igenic_probs.pbl' -> './config/species/candida_albicans/candida_albicans_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/candida_albicans/candida_albicans_intron_probs.pbl' -> './config/species/candida_albicans/candida_albicans_intron_probs.pbl' 153s '/usr/share/augustus/config/species/candida_albicans/candida_albicans_metapars.cfg' -> './config/species/candida_albicans/candida_albicans_metapars.cfg' 153s '/usr/share/augustus/config/species/candida_albicans/candida_albicans_parameters.cfg' -> './config/species/candida_albicans/candida_albicans_parameters.cfg' 153s '/usr/share/augustus/config/species/candida_albicans/candida_albicans_weightmatrix.txt' -> './config/species/candida_albicans/candida_albicans_weightmatrix.txt' 153s '/usr/share/augustus/config/species/candida_guilliermondii' -> './config/species/candida_guilliermondii' 153s '/usr/share/augustus/config/species/candida_guilliermondii/candida_guilliermondii_exon_probs.pbl' -> './config/species/candida_guilliermondii/candida_guilliermondii_exon_probs.pbl' 153s '/usr/share/augustus/config/species/candida_guilliermondii/candida_guilliermondii_igenic_probs.pbl' -> './config/species/candida_guilliermondii/candida_guilliermondii_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/candida_guilliermondii/candida_guilliermondii_intron_probs.pbl' -> './config/species/candida_guilliermondii/candida_guilliermondii_intron_probs.pbl' 153s '/usr/share/augustus/config/species/candida_guilliermondii/candida_guilliermondii_metapars.cfg' -> './config/species/candida_guilliermondii/candida_guilliermondii_metapars.cfg' 153s '/usr/share/augustus/config/species/candida_guilliermondii/candida_guilliermondii_parameters.cfg' -> './config/species/candida_guilliermondii/candida_guilliermondii_parameters.cfg' 153s '/usr/share/augustus/config/species/candida_guilliermondii/candida_guilliermondii_weightmatrix.txt' -> './config/species/candida_guilliermondii/candida_guilliermondii_weightmatrix.txt' 153s '/usr/share/augustus/config/species/candida_tropicalis' -> './config/species/candida_tropicalis' 153s '/usr/share/augustus/config/species/candida_tropicalis/candida_tropicalis_exon_probs.pbl' -> './config/species/candida_tropicalis/candida_tropicalis_exon_probs.pbl' 153s '/usr/share/augustus/config/species/candida_tropicalis/candida_tropicalis_igenic_probs.pbl' -> './config/species/candida_tropicalis/candida_tropicalis_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/candida_tropicalis/candida_tropicalis_intron_probs.pbl' -> './config/species/candida_tropicalis/candida_tropicalis_intron_probs.pbl' 153s '/usr/share/augustus/config/species/candida_tropicalis/candida_tropicalis_metapars.cfg' -> './config/species/candida_tropicalis/candida_tropicalis_metapars.cfg' 153s '/usr/share/augustus/config/species/candida_tropicalis/candida_tropicalis_parameters.cfg' -> './config/species/candida_tropicalis/candida_tropicalis_parameters.cfg' 153s '/usr/share/augustus/config/species/candida_tropicalis/candida_tropicalis_weightmatrix.txt' -> './config/species/candida_tropicalis/candida_tropicalis_weightmatrix.txt' 153s '/usr/share/augustus/config/species/chaetomium_globosum' -> './config/species/chaetomium_globosum' 153s '/usr/share/augustus/config/species/chaetomium_globosum/chaetomium_globosum_exon_probs.pbl' -> './config/species/chaetomium_globosum/chaetomium_globosum_exon_probs.pbl' 153s '/usr/share/augustus/config/species/chaetomium_globosum/chaetomium_globosum_igenic_probs.pbl' -> './config/species/chaetomium_globosum/chaetomium_globosum_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/chaetomium_globosum/chaetomium_globosum_intron_probs.pbl' -> './config/species/chaetomium_globosum/chaetomium_globosum_intron_probs.pbl' 153s '/usr/share/augustus/config/species/chaetomium_globosum/chaetomium_globosum_metapars.cfg' -> './config/species/chaetomium_globosum/chaetomium_globosum_metapars.cfg' 153s '/usr/share/augustus/config/species/chaetomium_globosum/chaetomium_globosum_parameters.cfg' -> './config/species/chaetomium_globosum/chaetomium_globosum_parameters.cfg' 153s '/usr/share/augustus/config/species/chaetomium_globosum/chaetomium_globosum_weightmatrix.txt' -> './config/species/chaetomium_globosum/chaetomium_globosum_weightmatrix.txt' 153s '/usr/share/augustus/config/species/chicken' -> './config/species/chicken' 153s '/usr/share/augustus/config/species/chicken/README.TXT' -> './config/species/chicken/README.TXT' 153s '/usr/share/augustus/config/species/chicken/chicken_exon_probs.pbl' -> './config/species/chicken/chicken_exon_probs.pbl' 153s '/usr/share/augustus/config/species/chicken/chicken_igenic_probs.pbl' -> './config/species/chicken/chicken_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/chicken/chicken_intron_probs.pbl' -> './config/species/chicken/chicken_intron_probs.pbl' 153s '/usr/share/augustus/config/species/chicken/chicken_metapars.cfg' -> './config/species/chicken/chicken_metapars.cfg' 153s '/usr/share/augustus/config/species/chicken/chicken_metapars.utr.cfg' -> './config/species/chicken/chicken_metapars.utr.cfg' 153s '/usr/share/augustus/config/species/chicken/chicken_parameters.cfg' -> './config/species/chicken/chicken_parameters.cfg' 153s '/usr/share/augustus/config/species/chicken/chicken_weightmatrix.txt' -> './config/species/chicken/chicken_weightmatrix.txt' 153s '/usr/share/augustus/config/species/chiloscyllium' -> './config/species/chiloscyllium' 153s '/usr/share/augustus/config/species/chiloscyllium/chiloscyllium_exon_probs.pbl' -> './config/species/chiloscyllium/chiloscyllium_exon_probs.pbl' 153s '/usr/share/augustus/config/species/chiloscyllium/chiloscyllium_igenic_probs.pbl' -> './config/species/chiloscyllium/chiloscyllium_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/chiloscyllium/chiloscyllium_intron_probs.pbl' -> './config/species/chiloscyllium/chiloscyllium_intron_probs.pbl' 153s '/usr/share/augustus/config/species/chiloscyllium/chiloscyllium_metapars.cfg' -> './config/species/chiloscyllium/chiloscyllium_metapars.cfg' 153s '/usr/share/augustus/config/species/chiloscyllium/chiloscyllium_metapars.cgp.cfg' -> './config/species/chiloscyllium/chiloscyllium_metapars.cgp.cfg' 153s '/usr/share/augustus/config/species/chiloscyllium/chiloscyllium_metapars.utr.cfg' -> './config/species/chiloscyllium/chiloscyllium_metapars.utr.cfg' 153s '/usr/share/augustus/config/species/chiloscyllium/chiloscyllium_parameters.cfg' -> './config/species/chiloscyllium/chiloscyllium_parameters.cfg' 153s '/usr/share/augustus/config/species/chiloscyllium/chiloscyllium_parameters.cfg.orig1' -> './config/species/chiloscyllium/chiloscyllium_parameters.cfg.orig1' 153s '/usr/share/augustus/config/species/chiloscyllium/chiloscyllium_weightmatrix.txt' -> './config/species/chiloscyllium/chiloscyllium_weightmatrix.txt' 153s '/usr/share/augustus/config/species/chlamy2011' -> './config/species/chlamy2011' 153s '/usr/share/augustus/config/species/chlamy2011/chlamy2011_exon_probs.pbl' -> './config/species/chlamy2011/chlamy2011_exon_probs.pbl' 153s '/usr/share/augustus/config/species/chlamy2011/chlamy2011_igenic_probs.pbl' -> './config/species/chlamy2011/chlamy2011_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/chlamy2011/chlamy2011_intron_probs.pbl' -> './config/species/chlamy2011/chlamy2011_intron_probs.pbl' 153s '/usr/share/augustus/config/species/chlamy2011/chlamy2011_metapars.cfg' -> './config/species/chlamy2011/chlamy2011_metapars.cfg' 153s '/usr/share/augustus/config/species/chlamy2011/chlamy2011_metapars.utr.cfg' -> './config/species/chlamy2011/chlamy2011_metapars.utr.cfg' 153s '/usr/share/augustus/config/species/chlamy2011/chlamy2011_parameters.cfg' -> './config/species/chlamy2011/chlamy2011_parameters.cfg' 153s '/usr/share/augustus/config/species/chlamy2011/chlamy2011_trans_shadow_partial.pbl' -> './config/species/chlamy2011/chlamy2011_trans_shadow_partial.pbl' 153s '/usr/share/augustus/config/species/chlamy2011/chlamy2011_trans_shadow_partial_utr.pbl' -> './config/species/chlamy2011/chlamy2011_trans_shadow_partial_utr.pbl' 153s '/usr/share/augustus/config/species/chlamy2011/chlamy2011_utr_probs.pbl' -> './config/species/chlamy2011/chlamy2011_utr_probs.pbl' 153s '/usr/share/augustus/config/species/chlamy2011/chlamy2011_weightmatrix.txt' -> './config/species/chlamy2011/chlamy2011_weightmatrix.txt' 153s '/usr/share/augustus/config/species/chlamydomonas' -> './config/species/chlamydomonas' 153s '/usr/share/augustus/config/species/chlamydomonas/chlamydomonas_exon_probs.pbl' -> './config/species/chlamydomonas/chlamydomonas_exon_probs.pbl' 153s '/usr/share/augustus/config/species/chlamydomonas/chlamydomonas_igenic_probs.pbl' -> './config/species/chlamydomonas/chlamydomonas_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/chlamydomonas/chlamydomonas_intron_probs.pbl' -> './config/species/chlamydomonas/chlamydomonas_intron_probs.pbl' 153s '/usr/share/augustus/config/species/chlamydomonas/chlamydomonas_metapars.cfg' -> './config/species/chlamydomonas/chlamydomonas_metapars.cfg' 153s '/usr/share/augustus/config/species/chlamydomonas/chlamydomonas_parameters.cfg' -> './config/species/chlamydomonas/chlamydomonas_parameters.cfg' 153s '/usr/share/augustus/config/species/chlamydomonas/chlamydomonas_trans_shadow_partial.pbl' -> './config/species/chlamydomonas/chlamydomonas_trans_shadow_partial.pbl' 153s '/usr/share/augustus/config/species/chlamydomonas/chlamydomonas_trans_shadow_partial_utr.pbl' -> './config/species/chlamydomonas/chlamydomonas_trans_shadow_partial_utr.pbl' 153s '/usr/share/augustus/config/species/chlamydomonas/chlamydomonas_utr_probs.pbl' -> './config/species/chlamydomonas/chlamydomonas_utr_probs.pbl' 153s '/usr/share/augustus/config/species/chlamydomonas/chlamydomonas_weightmatrix.txt' -> './config/species/chlamydomonas/chlamydomonas_weightmatrix.txt' 153s '/usr/share/augustus/config/species/chlorella' -> './config/species/chlorella' 153s '/usr/share/augustus/config/species/chlorella/chlorella_exon_probs.pbl' -> './config/species/chlorella/chlorella_exon_probs.pbl' 153s '/usr/share/augustus/config/species/chlorella/chlorella_igenic_probs.pbl' -> './config/species/chlorella/chlorella_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/chlorella/chlorella_intron_probs.pbl' -> './config/species/chlorella/chlorella_intron_probs.pbl' 153s '/usr/share/augustus/config/species/chlorella/chlorella_metapars.cfg' -> './config/species/chlorella/chlorella_metapars.cfg' 153s '/usr/share/augustus/config/species/chlorella/chlorella_metapars.utr.cfg' -> './config/species/chlorella/chlorella_metapars.utr.cfg' 153s '/usr/share/augustus/config/species/chlorella/chlorella_parameters.cfg' -> './config/species/chlorella/chlorella_parameters.cfg' 153s '/usr/share/augustus/config/species/chlorella/chlorella_utr_probs.pbl' -> './config/species/chlorella/chlorella_utr_probs.pbl' 153s '/usr/share/augustus/config/species/chlorella/chlorella_weightmatrix.txt' -> './config/species/chlorella/chlorella_weightmatrix.txt' 153s '/usr/share/augustus/config/species/ciona' -> './config/species/ciona' 153s '/usr/share/augustus/config/species/ciona/README.TXT' -> './config/species/ciona/README.TXT' 153s '/usr/share/augustus/config/species/ciona/ciona_exon_probs.pbl' -> './config/species/ciona/ciona_exon_probs.pbl' 153s '/usr/share/augustus/config/species/ciona/ciona_igenic_probs.pbl' -> './config/species/ciona/ciona_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/ciona/ciona_intron_probs.pbl' -> './config/species/ciona/ciona_intron_probs.pbl' 153s '/usr/share/augustus/config/species/ciona/ciona_metapars.cfg' -> './config/species/ciona/ciona_metapars.cfg' 153s '/usr/share/augustus/config/species/ciona/ciona_metapars.cgp.cfg' -> './config/species/ciona/ciona_metapars.cgp.cfg' 153s '/usr/share/augustus/config/species/ciona/ciona_metapars.utr.cfg' -> './config/species/ciona/ciona_metapars.utr.cfg' 153s '/usr/share/augustus/config/species/ciona/ciona_parameters.cfg' -> './config/species/ciona/ciona_parameters.cfg' 153s '/usr/share/augustus/config/species/ciona/ciona_parameters.cfg.orig1' -> './config/species/ciona/ciona_parameters.cfg.orig1' 153s '/usr/share/augustus/config/species/ciona/ciona_weightmatrix.txt' -> './config/species/ciona/ciona_weightmatrix.txt' 153s '/usr/share/augustus/config/species/coccidioides_immitis' -> './config/species/coccidioides_immitis' 153s '/usr/share/augustus/config/species/coccidioides_immitis/coccidioides_immitis_exon_probs.pbl' -> './config/species/coccidioides_immitis/coccidioides_immitis_exon_probs.pbl' 153s '/usr/share/augustus/config/species/coccidioides_immitis/coccidioides_immitis_igenic_probs.pbl' -> './config/species/coccidioides_immitis/coccidioides_immitis_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/coccidioides_immitis/coccidioides_immitis_intron_probs.pbl' -> './config/species/coccidioides_immitis/coccidioides_immitis_intron_probs.pbl' 153s '/usr/share/augustus/config/species/coccidioides_immitis/coccidioides_immitis_metapars.cfg' -> './config/species/coccidioides_immitis/coccidioides_immitis_metapars.cfg' 153s '/usr/share/augustus/config/species/coccidioides_immitis/coccidioides_immitis_parameters.cfg' -> './config/species/coccidioides_immitis/coccidioides_immitis_parameters.cfg' 153s '/usr/share/augustus/config/species/coccidioides_immitis/coccidioides_immitis_weightmatrix.txt' -> './config/species/coccidioides_immitis/coccidioides_immitis_weightmatrix.txt' 153s '/usr/share/augustus/config/species/coprinus' -> './config/species/coprinus' 153s '/usr/share/augustus/config/species/coprinus/coprinus_exon_probs.pbl' -> './config/species/coprinus/coprinus_exon_probs.pbl' 153s '/usr/share/augustus/config/species/coprinus/coprinus_igenic_probs.pbl' -> './config/species/coprinus/coprinus_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/coprinus/coprinus_intron_probs.pbl' -> './config/species/coprinus/coprinus_intron_probs.pbl' 153s '/usr/share/augustus/config/species/coprinus/coprinus_parameters.cfg' -> './config/species/coprinus/coprinus_parameters.cfg' 153s '/usr/share/augustus/config/species/coprinus/coprinus_weightmatrix.txt' -> './config/species/coprinus/coprinus_weightmatrix.txt' 153s '/usr/share/augustus/config/species/coprinus_cinereus' -> './config/species/coprinus_cinereus' 153s '/usr/share/augustus/config/species/coprinus_cinereus/coprinus_cinereus_exon_probs.pbl' -> './config/species/coprinus_cinereus/coprinus_cinereus_exon_probs.pbl' 153s '/usr/share/augustus/config/species/coprinus_cinereus/coprinus_cinereus_igenic_probs.pbl' -> './config/species/coprinus_cinereus/coprinus_cinereus_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/coprinus_cinereus/coprinus_cinereus_intron_probs.pbl' -> './config/species/coprinus_cinereus/coprinus_cinereus_intron_probs.pbl' 153s '/usr/share/augustus/config/species/coprinus_cinereus/coprinus_cinereus_metapars.cfg' -> './config/species/coprinus_cinereus/coprinus_cinereus_metapars.cfg' 153s '/usr/share/augustus/config/species/coprinus_cinereus/coprinus_cinereus_parameters.cfg' -> './config/species/coprinus_cinereus/coprinus_cinereus_parameters.cfg' 153s '/usr/share/augustus/config/species/coprinus_cinereus/coprinus_cinereus_weightmatrix.txt' -> './config/species/coprinus_cinereus/coprinus_cinereus_weightmatrix.txt' 153s '/usr/share/augustus/config/species/coyote_tobacco' -> './config/species/coyote_tobacco' 153s '/usr/share/augustus/config/species/coyote_tobacco/coyote_tobacco_exon_probs.pbl' -> './config/species/coyote_tobacco/coyote_tobacco_exon_probs.pbl' 153s '/usr/share/augustus/config/species/coyote_tobacco/coyote_tobacco_igenic_probs.pbl' -> './config/species/coyote_tobacco/coyote_tobacco_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/coyote_tobacco/coyote_tobacco_intron_probs.pbl' -> './config/species/coyote_tobacco/coyote_tobacco_intron_probs.pbl' 153s '/usr/share/augustus/config/species/coyote_tobacco/coyote_tobacco_metapars.cfg' -> './config/species/coyote_tobacco/coyote_tobacco_metapars.cfg' 153s '/usr/share/augustus/config/species/coyote_tobacco/coyote_tobacco_metapars.utr.cfg' -> './config/species/coyote_tobacco/coyote_tobacco_metapars.utr.cfg' 153s '/usr/share/augustus/config/species/coyote_tobacco/coyote_tobacco_parameters.cfg' -> './config/species/coyote_tobacco/coyote_tobacco_parameters.cfg' 153s '/usr/share/augustus/config/species/coyote_tobacco/coyote_tobacco_trans_shadow_partial_utr.pbl' -> './config/species/coyote_tobacco/coyote_tobacco_trans_shadow_partial_utr.pbl' 153s '/usr/share/augustus/config/species/coyote_tobacco/coyote_tobacco_utr_probs.pbl' -> './config/species/coyote_tobacco/coyote_tobacco_utr_probs.pbl' 153s '/usr/share/augustus/config/species/coyote_tobacco/coyote_tobacco_weightmatrix.txt' -> './config/species/coyote_tobacco/coyote_tobacco_weightmatrix.txt' 153s '/usr/share/augustus/config/species/cryptococcus' -> './config/species/cryptococcus' 153s '/usr/share/augustus/config/species/cryptococcus/cryptococcus_exon_probs.pbl' -> './config/species/cryptococcus/cryptococcus_exon_probs.pbl' 153s '/usr/share/augustus/config/species/cryptococcus/cryptococcus_igenic_probs.pbl' -> './config/species/cryptococcus/cryptococcus_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/cryptococcus/cryptococcus_intron_probs.pbl' -> './config/species/cryptococcus/cryptococcus_intron_probs.pbl' 153s '/usr/share/augustus/config/species/cryptococcus/cryptococcus_parameters.cfg' -> './config/species/cryptococcus/cryptococcus_parameters.cfg' 153s '/usr/share/augustus/config/species/cryptococcus/cryptococcus_weightmatrix.txt' -> './config/species/cryptococcus/cryptococcus_weightmatrix.txt' 153s '/usr/share/augustus/config/species/cryptococcus_neoformans_gattii' -> './config/species/cryptococcus_neoformans_gattii' 153s '/usr/share/augustus/config/species/cryptococcus_neoformans_gattii/cryptococcus_neoformans_gattii_exon_probs.pbl' -> './config/species/cryptococcus_neoformans_gattii/cryptococcus_neoformans_gattii_exon_probs.pbl' 153s '/usr/share/augustus/config/species/cryptococcus_neoformans_gattii/cryptococcus_neoformans_gattii_igenic_probs.pbl' -> './config/species/cryptococcus_neoformans_gattii/cryptococcus_neoformans_gattii_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/cryptococcus_neoformans_gattii/cryptococcus_neoformans_gattii_intron_probs.pbl' -> './config/species/cryptococcus_neoformans_gattii/cryptococcus_neoformans_gattii_intron_probs.pbl' 153s '/usr/share/augustus/config/species/cryptococcus_neoformans_gattii/cryptococcus_neoformans_gattii_metapars.cfg' -> './config/species/cryptococcus_neoformans_gattii/cryptococcus_neoformans_gattii_metapars.cfg' 153s '/usr/share/augustus/config/species/cryptococcus_neoformans_gattii/cryptococcus_neoformans_gattii_parameters.cfg' -> './config/species/cryptococcus_neoformans_gattii/cryptococcus_neoformans_gattii_parameters.cfg' 153s '/usr/share/augustus/config/species/cryptococcus_neoformans_gattii/cryptococcus_neoformans_gattii_weightmatrix.txt' -> './config/species/cryptococcus_neoformans_gattii/cryptococcus_neoformans_gattii_weightmatrix.txt' 153s '/usr/share/augustus/config/species/cryptococcus_neoformans_neoformans_B' -> './config/species/cryptococcus_neoformans_neoformans_B' 153s '/usr/share/augustus/config/species/cryptococcus_neoformans_neoformans_B/cryptococcus_neoformans_neoformans_B_exon_probs.pbl' -> './config/species/cryptococcus_neoformans_neoformans_B/cryptococcus_neoformans_neoformans_B_exon_probs.pbl' 153s '/usr/share/augustus/config/species/cryptococcus_neoformans_neoformans_B/cryptococcus_neoformans_neoformans_B_igenic_probs.pbl' -> './config/species/cryptococcus_neoformans_neoformans_B/cryptococcus_neoformans_neoformans_B_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/cryptococcus_neoformans_neoformans_B/cryptococcus_neoformans_neoformans_B_intron_probs.pbl' -> './config/species/cryptococcus_neoformans_neoformans_B/cryptococcus_neoformans_neoformans_B_intron_probs.pbl' 153s '/usr/share/augustus/config/species/cryptococcus_neoformans_neoformans_B/cryptococcus_neoformans_neoformans_B_metapars.cfg' -> './config/species/cryptococcus_neoformans_neoformans_B/cryptococcus_neoformans_neoformans_B_metapars.cfg' 153s '/usr/share/augustus/config/species/cryptococcus_neoformans_neoformans_B/cryptococcus_neoformans_neoformans_B_parameters.cfg' -> './config/species/cryptococcus_neoformans_neoformans_B/cryptococcus_neoformans_neoformans_B_parameters.cfg' 153s '/usr/share/augustus/config/species/cryptococcus_neoformans_neoformans_B/cryptococcus_neoformans_neoformans_B_weightmatrix.txt' -> './config/species/cryptococcus_neoformans_neoformans_B/cryptococcus_neoformans_neoformans_B_weightmatrix.txt' 153s '/usr/share/augustus/config/species/cryptococcus_neoformans_neoformans_JEC21' -> './config/species/cryptococcus_neoformans_neoformans_JEC21' 153s '/usr/share/augustus/config/species/cryptococcus_neoformans_neoformans_JEC21/cryptococcus_neoformans_neoformans_JEC21_exon_probs.pbl' -> './config/species/cryptococcus_neoformans_neoformans_JEC21/cryptococcus_neoformans_neoformans_JEC21_exon_probs.pbl' 153s '/usr/share/augustus/config/species/cryptococcus_neoformans_neoformans_JEC21/cryptococcus_neoformans_neoformans_JEC21_igenic_probs.pbl' -> './config/species/cryptococcus_neoformans_neoformans_JEC21/cryptococcus_neoformans_neoformans_JEC21_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/cryptococcus_neoformans_neoformans_JEC21/cryptococcus_neoformans_neoformans_JEC21_intron_probs.pbl' -> './config/species/cryptococcus_neoformans_neoformans_JEC21/cryptococcus_neoformans_neoformans_JEC21_intron_probs.pbl' 153s '/usr/share/augustus/config/species/cryptococcus_neoformans_neoformans_JEC21/cryptococcus_neoformans_neoformans_JEC21_metapars.cfg' -> './config/species/cryptococcus_neoformans_neoformans_JEC21/cryptococcus_neoformans_neoformans_JEC21_metapars.cfg' 153s '/usr/share/augustus/config/species/cryptococcus_neoformans_neoformans_JEC21/cryptococcus_neoformans_neoformans_JEC21_parameters.cfg' -> './config/species/cryptococcus_neoformans_neoformans_JEC21/cryptococcus_neoformans_neoformans_JEC21_parameters.cfg' 153s '/usr/share/augustus/config/species/cryptococcus_neoformans_neoformans_JEC21/cryptococcus_neoformans_neoformans_JEC21_weightmatrix.txt' -> './config/species/cryptococcus_neoformans_neoformans_JEC21/cryptococcus_neoformans_neoformans_JEC21_weightmatrix.txt' 153s '/usr/share/augustus/config/species/culex' -> './config/species/culex' 153s '/usr/share/augustus/config/species/culex/culex_exon_probs.pbl' -> './config/species/culex/culex_exon_probs.pbl' 153s '/usr/share/augustus/config/species/culex/culex_exon_probs.pbl.wech' -> './config/species/culex/culex_exon_probs.pbl.wech' 153s '/usr/share/augustus/config/species/culex/culex_igenic_probs.pbl' -> './config/species/culex/culex_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/culex/culex_igenic_probs.pbl.wech' -> './config/species/culex/culex_igenic_probs.pbl.wech' 153s '/usr/share/augustus/config/species/culex/culex_intron_probs.pbl' -> './config/species/culex/culex_intron_probs.pbl' 153s '/usr/share/augustus/config/species/culex/culex_intron_probs.pbl.wech' -> './config/species/culex/culex_intron_probs.pbl.wech' 153s '/usr/share/augustus/config/species/culex/culex_metapars.cfg' -> './config/species/culex/culex_metapars.cfg' 153s '/usr/share/augustus/config/species/culex/culex_parameters.cfg' -> './config/species/culex/culex_parameters.cfg' 153s '/usr/share/augustus/config/species/culex/culex_parameters.old.cfg' -> './config/species/culex/culex_parameters.old.cfg' 153s '/usr/share/augustus/config/species/culex/culex_trans_shadow_partial_utr.pbl' -> './config/species/culex/culex_trans_shadow_partial_utr.pbl' 153s '/usr/share/augustus/config/species/culex/culex_utr_probs.pbl' -> './config/species/culex/culex_utr_probs.pbl' 153s '/usr/share/augustus/config/species/culex/culex_weightmatrix.txt' -> './config/species/culex/culex_weightmatrix.txt' 153s '/usr/share/augustus/config/species/debaryomyces_hansenii' -> './config/species/debaryomyces_hansenii' 153s '/usr/share/augustus/config/species/debaryomyces_hansenii/debaryomyces_hansenii_exon_probs.pbl' -> './config/species/debaryomyces_hansenii/debaryomyces_hansenii_exon_probs.pbl' 153s '/usr/share/augustus/config/species/debaryomyces_hansenii/debaryomyces_hansenii_igenic_probs.pbl' -> './config/species/debaryomyces_hansenii/debaryomyces_hansenii_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/debaryomyces_hansenii/debaryomyces_hansenii_intron_probs.pbl' -> './config/species/debaryomyces_hansenii/debaryomyces_hansenii_intron_probs.pbl' 153s '/usr/share/augustus/config/species/debaryomyces_hansenii/debaryomyces_hansenii_metapars.cfg' -> './config/species/debaryomyces_hansenii/debaryomyces_hansenii_metapars.cfg' 153s '/usr/share/augustus/config/species/debaryomyces_hansenii/debaryomyces_hansenii_parameters.cfg' -> './config/species/debaryomyces_hansenii/debaryomyces_hansenii_parameters.cfg' 153s '/usr/share/augustus/config/species/debaryomyces_hansenii/debaryomyces_hansenii_weightmatrix.txt' -> './config/species/debaryomyces_hansenii/debaryomyces_hansenii_weightmatrix.txt' 153s '/usr/share/augustus/config/species/elephant_shark' -> './config/species/elephant_shark' 153s '/usr/share/augustus/config/species/elephant_shark/elephant_shark_exon_probs.pbl' -> './config/species/elephant_shark/elephant_shark_exon_probs.pbl' 153s '/usr/share/augustus/config/species/elephant_shark/elephant_shark_igenic_probs.pbl' -> './config/species/elephant_shark/elephant_shark_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/elephant_shark/elephant_shark_intron_probs.pbl' -> './config/species/elephant_shark/elephant_shark_intron_probs.pbl' 153s '/usr/share/augustus/config/species/elephant_shark/elephant_shark_metapars.cfg' -> './config/species/elephant_shark/elephant_shark_metapars.cfg' 153s '/usr/share/augustus/config/species/elephant_shark/elephant_shark_metapars.utr.cfg' -> './config/species/elephant_shark/elephant_shark_metapars.utr.cfg' 153s '/usr/share/augustus/config/species/elephant_shark/elephant_shark_parameters.cfg' -> './config/species/elephant_shark/elephant_shark_parameters.cfg' 153s '/usr/share/augustus/config/species/elephant_shark/elephant_shark_weightmatrix.txt' -> './config/species/elephant_shark/elephant_shark_weightmatrix.txt' 153s '/usr/share/augustus/config/species/encephalitozoon_cuniculi_GB' -> './config/species/encephalitozoon_cuniculi_GB' 153s '/usr/share/augustus/config/species/encephalitozoon_cuniculi_GB/encephalitozoon_cuniculi_GB_exon_probs.pbl' -> './config/species/encephalitozoon_cuniculi_GB/encephalitozoon_cuniculi_GB_exon_probs.pbl' 153s '/usr/share/augustus/config/species/encephalitozoon_cuniculi_GB/encephalitozoon_cuniculi_GB_igenic_probs.pbl' -> './config/species/encephalitozoon_cuniculi_GB/encephalitozoon_cuniculi_GB_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/encephalitozoon_cuniculi_GB/encephalitozoon_cuniculi_GB_intron_probs.pbl' -> './config/species/encephalitozoon_cuniculi_GB/encephalitozoon_cuniculi_GB_intron_probs.pbl' 153s '/usr/share/augustus/config/species/encephalitozoon_cuniculi_GB/encephalitozoon_cuniculi_GB_metapars.cfg' -> './config/species/encephalitozoon_cuniculi_GB/encephalitozoon_cuniculi_GB_metapars.cfg' 153s '/usr/share/augustus/config/species/encephalitozoon_cuniculi_GB/encephalitozoon_cuniculi_GB_parameters.cfg' -> './config/species/encephalitozoon_cuniculi_GB/encephalitozoon_cuniculi_GB_parameters.cfg' 153s '/usr/share/augustus/config/species/encephalitozoon_cuniculi_GB/encephalitozoon_cuniculi_GB_weightmatrix.txt' -> './config/species/encephalitozoon_cuniculi_GB/encephalitozoon_cuniculi_GB_weightmatrix.txt' 153s '/usr/share/augustus/config/species/eremothecium_gossypii' -> './config/species/eremothecium_gossypii' 153s '/usr/share/augustus/config/species/eremothecium_gossypii/eremothecium_gossypii_exon_probs.pbl' -> './config/species/eremothecium_gossypii/eremothecium_gossypii_exon_probs.pbl' 153s '/usr/share/augustus/config/species/eremothecium_gossypii/eremothecium_gossypii_igenic_probs.pbl' -> './config/species/eremothecium_gossypii/eremothecium_gossypii_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/eremothecium_gossypii/eremothecium_gossypii_intron_probs.pbl' -> './config/species/eremothecium_gossypii/eremothecium_gossypii_intron_probs.pbl' 153s '/usr/share/augustus/config/species/eremothecium_gossypii/eremothecium_gossypii_metapars.cfg' -> './config/species/eremothecium_gossypii/eremothecium_gossypii_metapars.cfg' 153s '/usr/share/augustus/config/species/eremothecium_gossypii/eremothecium_gossypii_parameters.cfg' -> './config/species/eremothecium_gossypii/eremothecium_gossypii_parameters.cfg' 153s '/usr/share/augustus/config/species/eremothecium_gossypii/eremothecium_gossypii_weightmatrix.txt' -> './config/species/eremothecium_gossypii/eremothecium_gossypii_weightmatrix.txt' 153s '/usr/share/augustus/config/species/fly' -> './config/species/fly' 153s '/usr/share/augustus/config/species/fly/fly_exon_probs.pbl' -> './config/species/fly/fly_exon_probs.pbl' 153s '/usr/share/augustus/config/species/fly/fly_igenic_probs.pbl' -> './config/species/fly/fly_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/fly/fly_intron_probs.pbl' -> './config/species/fly/fly_intron_probs.pbl' 153s '/usr/share/augustus/config/species/fly/fly_metapars.cfg' -> './config/species/fly/fly_metapars.cfg' 153s '/usr/share/augustus/config/species/fly/fly_metapars.utr.cfg' -> './config/species/fly/fly_metapars.utr.cfg' 153s '/usr/share/augustus/config/species/fly/fly_parameters.cfg' -> './config/species/fly/fly_parameters.cfg' 153s '/usr/share/augustus/config/species/fly/fly_utr_probs.pbl' -> './config/species/fly/fly_utr_probs.pbl' 153s '/usr/share/augustus/config/species/fly/fly_weightmatrix.txt' -> './config/species/fly/fly_weightmatrix.txt' 153s '/usr/share/augustus/config/species/fly_exp' -> './config/species/fly_exp' 153s '/usr/share/augustus/config/species/fly_exp/fly_exp_exon_probs.pbl' -> './config/species/fly_exp/fly_exp_exon_probs.pbl' 153s '/usr/share/augustus/config/species/fly_exp/fly_exp_igenic_probs.pbl' -> './config/species/fly_exp/fly_exp_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/fly_exp/fly_exp_intron_probs.pbl' -> './config/species/fly_exp/fly_exp_intron_probs.pbl' 153s '/usr/share/augustus/config/species/fly_exp/fly_exp_metapars.cfg' -> './config/species/fly_exp/fly_exp_metapars.cfg' 153s '/usr/share/augustus/config/species/fly_exp/fly_exp_metapars.utr.cfg' -> './config/species/fly_exp/fly_exp_metapars.utr.cfg' 153s '/usr/share/augustus/config/species/fly_exp/fly_exp_parameters.cfg' -> './config/species/fly_exp/fly_exp_parameters.cfg' 153s '/usr/share/augustus/config/species/fly_exp/fly_exp_utr_probs.pbl' -> './config/species/fly_exp/fly_exp_utr_probs.pbl' 153s '/usr/share/augustus/config/species/fly_exp/fly_exp_weightmatrix.txt' -> './config/species/fly_exp/fly_exp_weightmatrix.txt' 153s '/usr/share/augustus/config/species/fusarium' -> './config/species/fusarium' 153s '/usr/share/augustus/config/species/fusarium/fusarium_exon_probs.pbl' -> './config/species/fusarium/fusarium_exon_probs.pbl' 153s '/usr/share/augustus/config/species/fusarium/fusarium_igenic_probs.pbl' -> './config/species/fusarium/fusarium_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/fusarium/fusarium_intron_probs.pbl' -> './config/species/fusarium/fusarium_intron_probs.pbl' 153s '/usr/share/augustus/config/species/fusarium/fusarium_parameters.cfg' -> './config/species/fusarium/fusarium_parameters.cfg' 153s '/usr/share/augustus/config/species/fusarium/fusarium_weightmatrix.txt' -> './config/species/fusarium/fusarium_weightmatrix.txt' 153s '/usr/share/augustus/config/species/fusarium_graminearum' -> './config/species/fusarium_graminearum' 153s '/usr/share/augustus/config/species/fusarium_graminearum/fusarium_graminearum_exon_probs.pbl' -> './config/species/fusarium_graminearum/fusarium_graminearum_exon_probs.pbl' 153s '/usr/share/augustus/config/species/fusarium_graminearum/fusarium_graminearum_igenic_probs.pbl' -> './config/species/fusarium_graminearum/fusarium_graminearum_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/fusarium_graminearum/fusarium_graminearum_intron_probs.pbl' -> './config/species/fusarium_graminearum/fusarium_graminearum_intron_probs.pbl' 153s '/usr/share/augustus/config/species/fusarium_graminearum/fusarium_graminearum_metapars.cfg' -> './config/species/fusarium_graminearum/fusarium_graminearum_metapars.cfg' 153s '/usr/share/augustus/config/species/fusarium_graminearum/fusarium_graminearum_parameters.cfg' -> './config/species/fusarium_graminearum/fusarium_graminearum_parameters.cfg' 153s '/usr/share/augustus/config/species/fusarium_graminearum/fusarium_graminearum_weightmatrix.txt' -> './config/species/fusarium_graminearum/fusarium_graminearum_weightmatrix.txt' 153s '/usr/share/augustus/config/species/galdieria' -> './config/species/galdieria' 153s '/usr/share/augustus/config/species/galdieria/extrinsic.PE.cfg' -> './config/species/galdieria/extrinsic.PE.cfg' 153s '/usr/share/augustus/config/species/galdieria/galdieria_exon_probs.pbl' -> './config/species/galdieria/galdieria_exon_probs.pbl' 153s '/usr/share/augustus/config/species/galdieria/galdieria_igenic_probs.pbl' -> './config/species/galdieria/galdieria_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/galdieria/galdieria_intron_probs.pbl' -> './config/species/galdieria/galdieria_intron_probs.pbl' 153s '/usr/share/augustus/config/species/galdieria/galdieria_metapars.cfg' -> './config/species/galdieria/galdieria_metapars.cfg' 153s '/usr/share/augustus/config/species/galdieria/galdieria_parameters.cfg' -> './config/species/galdieria/galdieria_parameters.cfg' 153s '/usr/share/augustus/config/species/galdieria/galdieria_splicefile' -> './config/species/galdieria/galdieria_splicefile' 153s '/usr/share/augustus/config/species/galdieria/galdieria_trans_shadow_partial_utr.pbl' -> './config/species/galdieria/galdieria_trans_shadow_partial_utr.pbl' 153s '/usr/share/augustus/config/species/galdieria/galdieria_utr_probs.pbl' -> './config/species/galdieria/galdieria_utr_probs.pbl' 153s '/usr/share/augustus/config/species/galdieria/galdieria_weightmatrix.txt' -> './config/species/galdieria/galdieria_weightmatrix.txt' 153s '/usr/share/augustus/config/species/generic' -> './config/species/generic' 153s '/usr/share/augustus/config/species/generic/generic_metapars.cfg' -> './config/species/generic/generic_metapars.cfg' 153s '/usr/share/augustus/config/species/generic/generic_metapars.cgp.cfg' -> './config/species/generic/generic_metapars.cgp.cfg' 153s '/usr/share/augustus/config/species/generic/generic_metapars.utr.cfg' -> './config/species/generic/generic_metapars.utr.cfg' 153s '/usr/share/augustus/config/species/generic/generic_parameters.cfg' -> './config/species/generic/generic_parameters.cfg' 153s '/usr/share/augustus/config/species/generic/generic_weightmatrix.txt' -> './config/species/generic/generic_weightmatrix.txt' 153s '/usr/share/augustus/config/species/gigaspora_margarita' -> './config/species/gigaspora_margarita' 153s '/usr/share/augustus/config/species/gigaspora_margarita/README.TXT' -> './config/species/gigaspora_margarita/README.TXT' 153s '/usr/share/augustus/config/species/gigaspora_margarita/gigaspora_margarita_exon_probs.pbl' -> './config/species/gigaspora_margarita/gigaspora_margarita_exon_probs.pbl' 153s '/usr/share/augustus/config/species/gigaspora_margarita/gigaspora_margarita_igenic_probs.pbl' -> './config/species/gigaspora_margarita/gigaspora_margarita_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/gigaspora_margarita/gigaspora_margarita_intron_probs.pbl' -> './config/species/gigaspora_margarita/gigaspora_margarita_intron_probs.pbl' 153s '/usr/share/augustus/config/species/gigaspora_margarita/gigaspora_margarita_metapars.cfg' -> './config/species/gigaspora_margarita/gigaspora_margarita_metapars.cfg' 153s '/usr/share/augustus/config/species/gigaspora_margarita/gigaspora_margarita_metapars.cgp.cfg' -> './config/species/gigaspora_margarita/gigaspora_margarita_metapars.cgp.cfg' 153s '/usr/share/augustus/config/species/gigaspora_margarita/gigaspora_margarita_metapars.utr.cfg' -> './config/species/gigaspora_margarita/gigaspora_margarita_metapars.utr.cfg' 153s '/usr/share/augustus/config/species/gigaspora_margarita/gigaspora_margarita_parameters.cfg' -> './config/species/gigaspora_margarita/gigaspora_margarita_parameters.cfg' 153s '/usr/share/augustus/config/species/gigaspora_margarita/gigaspora_margarita_weightmatrix.txt' -> './config/species/gigaspora_margarita/gigaspora_margarita_weightmatrix.txt' 153s '/usr/share/augustus/config/species/gigaspora_margarita/gth.cfg' -> './config/species/gigaspora_margarita/gth.cfg' 153s '/usr/share/augustus/config/species/heliconius_melpomene1' -> './config/species/heliconius_melpomene1' 153s '/usr/share/augustus/config/species/heliconius_melpomene1/heliconius_melpomene1_exon_probs.pbl' -> './config/species/heliconius_melpomene1/heliconius_melpomene1_exon_probs.pbl' 153s '/usr/share/augustus/config/species/heliconius_melpomene1/heliconius_melpomene1_igenic_probs.pbl' -> './config/species/heliconius_melpomene1/heliconius_melpomene1_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/heliconius_melpomene1/heliconius_melpomene1_intron_probs.pbl' -> './config/species/heliconius_melpomene1/heliconius_melpomene1_intron_probs.pbl' 153s '/usr/share/augustus/config/species/heliconius_melpomene1/heliconius_melpomene1_metapars.cfg' -> './config/species/heliconius_melpomene1/heliconius_melpomene1_metapars.cfg' 153s '/usr/share/augustus/config/species/heliconius_melpomene1/heliconius_melpomene1_metapars.utr.cfg' -> './config/species/heliconius_melpomene1/heliconius_melpomene1_metapars.utr.cfg' 153s '/usr/share/augustus/config/species/heliconius_melpomene1/heliconius_melpomene1_parameters.cfg' -> './config/species/heliconius_melpomene1/heliconius_melpomene1_parameters.cfg' 153s '/usr/share/augustus/config/species/heliconius_melpomene1/heliconius_melpomene1_weightmatrix.txt' -> './config/species/heliconius_melpomene1/heliconius_melpomene1_weightmatrix.txt' 153s '/usr/share/augustus/config/species/histoplasma' -> './config/species/histoplasma' 153s '/usr/share/augustus/config/species/histoplasma/histoplasma_exon_probs.pbl' -> './config/species/histoplasma/histoplasma_exon_probs.pbl' 153s '/usr/share/augustus/config/species/histoplasma/histoplasma_igenic_probs.pbl' -> './config/species/histoplasma/histoplasma_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/histoplasma/histoplasma_intron_probs.pbl' -> './config/species/histoplasma/histoplasma_intron_probs.pbl' 153s '/usr/share/augustus/config/species/histoplasma/histoplasma_parameters.cfg' -> './config/species/histoplasma/histoplasma_parameters.cfg' 153s '/usr/share/augustus/config/species/histoplasma/histoplasma_weightmatrix.txt' -> './config/species/histoplasma/histoplasma_weightmatrix.txt' 153s '/usr/share/augustus/config/species/histoplasma_capsulatum' -> './config/species/histoplasma_capsulatum' 153s '/usr/share/augustus/config/species/histoplasma_capsulatum/histoplasma_capsulatum_exon_probs.pbl' -> './config/species/histoplasma_capsulatum/histoplasma_capsulatum_exon_probs.pbl' 153s '/usr/share/augustus/config/species/histoplasma_capsulatum/histoplasma_capsulatum_igenic_probs.pbl' -> './config/species/histoplasma_capsulatum/histoplasma_capsulatum_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/histoplasma_capsulatum/histoplasma_capsulatum_intron_probs.pbl' -> './config/species/histoplasma_capsulatum/histoplasma_capsulatum_intron_probs.pbl' 153s '/usr/share/augustus/config/species/histoplasma_capsulatum/histoplasma_capsulatum_metapars.cfg' -> './config/species/histoplasma_capsulatum/histoplasma_capsulatum_metapars.cfg' 153s '/usr/share/augustus/config/species/histoplasma_capsulatum/histoplasma_capsulatum_parameters.cfg' -> './config/species/histoplasma_capsulatum/histoplasma_capsulatum_parameters.cfg' 153s '/usr/share/augustus/config/species/histoplasma_capsulatum/histoplasma_capsulatum_weightmatrix.txt' -> './config/species/histoplasma_capsulatum/histoplasma_capsulatum_weightmatrix.txt' 153s '/usr/share/augustus/config/species/honeybee1' -> './config/species/honeybee1' 153s '/usr/share/augustus/config/species/honeybee1/honeybee1_exon_probs.pbl' -> './config/species/honeybee1/honeybee1_exon_probs.pbl' 153s '/usr/share/augustus/config/species/honeybee1/honeybee1_exon_probs.pbl.withoutCRF' -> './config/species/honeybee1/honeybee1_exon_probs.pbl.withoutCRF' 153s '/usr/share/augustus/config/species/honeybee1/honeybee1_igenic_probs.pbl' -> './config/species/honeybee1/honeybee1_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/honeybee1/honeybee1_igenic_probs.pbl.withoutCRF' -> './config/species/honeybee1/honeybee1_igenic_probs.pbl.withoutCRF' 153s '/usr/share/augustus/config/species/honeybee1/honeybee1_intron_probs.pbl' -> './config/species/honeybee1/honeybee1_intron_probs.pbl' 153s '/usr/share/augustus/config/species/honeybee1/honeybee1_intron_probs.pbl.withoutCRF' -> './config/species/honeybee1/honeybee1_intron_probs.pbl.withoutCRF' 153s '/usr/share/augustus/config/species/honeybee1/honeybee1_metapars.cfg' -> './config/species/honeybee1/honeybee1_metapars.cfg' 153s '/usr/share/augustus/config/species/honeybee1/honeybee1_metapars.utr.cfg' -> './config/species/honeybee1/honeybee1_metapars.utr.cfg' 153s '/usr/share/augustus/config/species/honeybee1/honeybee1_parameters.cfg' -> './config/species/honeybee1/honeybee1_parameters.cfg' 153s '/usr/share/augustus/config/species/honeybee1/honeybee1_parameters.cfg.orig1' -> './config/species/honeybee1/honeybee1_parameters.cfg.orig1' 153s '/usr/share/augustus/config/species/honeybee1/honeybee1_utr_probs.pbl' -> './config/species/honeybee1/honeybee1_utr_probs.pbl' 153s '/usr/share/augustus/config/species/honeybee1/honeybee1_weightmatrix.txt' -> './config/species/honeybee1/honeybee1_weightmatrix.txt' 153s '/usr/share/augustus/config/species/human' -> './config/species/human' 153s '/usr/share/augustus/config/species/human/README.TXT' -> './config/species/human/README.TXT' 153s '/usr/share/augustus/config/species/human/human_exon_probs.pbl' -> './config/species/human/human_exon_probs.pbl' 153s '/usr/share/augustus/config/species/human/human_igenic_probs.pbl' -> './config/species/human/human_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/human/human_intron_probs.pbl' -> './config/species/human/human_intron_probs.pbl' 153s '/usr/share/augustus/config/species/human/human_parameters.cfg' -> './config/species/human/human_parameters.cfg' 153s '/usr/share/augustus/config/species/human/human_trans_shadow_partial_utr.pbl' -> './config/species/human/human_trans_shadow_partial_utr.pbl' 153s '/usr/share/augustus/config/species/human/human_utr_probs.pbl' -> './config/species/human/human_utr_probs.pbl' 153s '/usr/share/augustus/config/species/human/human_weightmatrix.txt' -> './config/species/human/human_weightmatrix.txt' 153s '/usr/share/augustus/config/species/hymenolepis_microstoma' -> './config/species/hymenolepis_microstoma' 153s '/usr/share/augustus/config/species/hymenolepis_microstoma/hymenolepis_microstoma_exon_probs.pbl' -> './config/species/hymenolepis_microstoma/hymenolepis_microstoma_exon_probs.pbl' 153s '/usr/share/augustus/config/species/hymenolepis_microstoma/hymenolepis_microstoma_igenic_probs.pbl' -> './config/species/hymenolepis_microstoma/hymenolepis_microstoma_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/hymenolepis_microstoma/hymenolepis_microstoma_intron_probs.pbl' -> './config/species/hymenolepis_microstoma/hymenolepis_microstoma_intron_probs.pbl' 153s '/usr/share/augustus/config/species/hymenolepis_microstoma/hymenolepis_microstoma_metapars.cfg' -> './config/species/hymenolepis_microstoma/hymenolepis_microstoma_metapars.cfg' 153s '/usr/share/augustus/config/species/hymenolepis_microstoma/hymenolepis_microstoma_metapars.cgp.cfg' -> './config/species/hymenolepis_microstoma/hymenolepis_microstoma_metapars.cgp.cfg' 153s '/usr/share/augustus/config/species/hymenolepis_microstoma/hymenolepis_microstoma_metapars.utr.cfg' -> './config/species/hymenolepis_microstoma/hymenolepis_microstoma_metapars.utr.cfg' 153s '/usr/share/augustus/config/species/hymenolepis_microstoma/hymenolepis_microstoma_parameters.cfg' -> './config/species/hymenolepis_microstoma/hymenolepis_microstoma_parameters.cfg' 153s '/usr/share/augustus/config/species/hymenolepis_microstoma/hymenolepis_microstoma_weightmatrix.txt' -> './config/species/hymenolepis_microstoma/hymenolepis_microstoma_weightmatrix.txt' 153s '/usr/share/augustus/config/species/hymenolepis_microstoma/make.doc' -> './config/species/hymenolepis_microstoma/make.doc' 153s '/usr/share/augustus/config/species/japaneselamprey' -> './config/species/japaneselamprey' 153s '/usr/share/augustus/config/species/japaneselamprey/japaneselamprey_exon_probs.pbl' -> './config/species/japaneselamprey/japaneselamprey_exon_probs.pbl' 153s '/usr/share/augustus/config/species/japaneselamprey/japaneselamprey_igenic_probs.pbl' -> './config/species/japaneselamprey/japaneselamprey_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/japaneselamprey/japaneselamprey_intron_probs.pbl' -> './config/species/japaneselamprey/japaneselamprey_intron_probs.pbl' 153s '/usr/share/augustus/config/species/japaneselamprey/japaneselamprey_metapars.cfg' -> './config/species/japaneselamprey/japaneselamprey_metapars.cfg' 153s '/usr/share/augustus/config/species/japaneselamprey/japaneselamprey_metapars.utr.cfg' -> './config/species/japaneselamprey/japaneselamprey_metapars.utr.cfg' 153s '/usr/share/augustus/config/species/japaneselamprey/japaneselamprey_parameters.cfg' -> './config/species/japaneselamprey/japaneselamprey_parameters.cfg' 153s '/usr/share/augustus/config/species/japaneselamprey/japaneselamprey_weightmatrix.txt' -> './config/species/japaneselamprey/japaneselamprey_weightmatrix.txt' 153s '/usr/share/augustus/config/species/kluyveromyces_lactis' -> './config/species/kluyveromyces_lactis' 153s '/usr/share/augustus/config/species/kluyveromyces_lactis/kluyveromyces_lactis_exon_probs.pbl' -> './config/species/kluyveromyces_lactis/kluyveromyces_lactis_exon_probs.pbl' 153s '/usr/share/augustus/config/species/kluyveromyces_lactis/kluyveromyces_lactis_igenic_probs.pbl' -> './config/species/kluyveromyces_lactis/kluyveromyces_lactis_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/kluyveromyces_lactis/kluyveromyces_lactis_intron_probs.pbl' -> './config/species/kluyveromyces_lactis/kluyveromyces_lactis_intron_probs.pbl' 153s '/usr/share/augustus/config/species/kluyveromyces_lactis/kluyveromyces_lactis_metapars.cfg' -> './config/species/kluyveromyces_lactis/kluyveromyces_lactis_metapars.cfg' 153s '/usr/share/augustus/config/species/kluyveromyces_lactis/kluyveromyces_lactis_parameters.cfg' -> './config/species/kluyveromyces_lactis/kluyveromyces_lactis_parameters.cfg' 153s '/usr/share/augustus/config/species/kluyveromyces_lactis/kluyveromyces_lactis_weightmatrix.txt' -> './config/species/kluyveromyces_lactis/kluyveromyces_lactis_weightmatrix.txt' 153s '/usr/share/augustus/config/species/laccaria_bicolor' -> './config/species/laccaria_bicolor' 153s '/usr/share/augustus/config/species/laccaria_bicolor/laccaria_bicolor_exon_probs.pbl' -> './config/species/laccaria_bicolor/laccaria_bicolor_exon_probs.pbl' 153s '/usr/share/augustus/config/species/laccaria_bicolor/laccaria_bicolor_igenic_probs.pbl' -> './config/species/laccaria_bicolor/laccaria_bicolor_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/laccaria_bicolor/laccaria_bicolor_intron_probs.pbl' -> './config/species/laccaria_bicolor/laccaria_bicolor_intron_probs.pbl' 153s '/usr/share/augustus/config/species/laccaria_bicolor/laccaria_bicolor_metapars.cfg' -> './config/species/laccaria_bicolor/laccaria_bicolor_metapars.cfg' 153s '/usr/share/augustus/config/species/laccaria_bicolor/laccaria_bicolor_parameters.cfg' -> './config/species/laccaria_bicolor/laccaria_bicolor_parameters.cfg' 153s '/usr/share/augustus/config/species/laccaria_bicolor/laccaria_bicolor_weightmatrix.txt' -> './config/species/laccaria_bicolor/laccaria_bicolor_weightmatrix.txt' 153s '/usr/share/augustus/config/species/leishmania_tarentolae' -> './config/species/leishmania_tarentolae' 153s '/usr/share/augustus/config/species/leishmania_tarentolae/leishmania_tarentolae_exon_probs.pbl' -> './config/species/leishmania_tarentolae/leishmania_tarentolae_exon_probs.pbl' 153s '/usr/share/augustus/config/species/leishmania_tarentolae/leishmania_tarentolae_igenic_probs.pbl' -> './config/species/leishmania_tarentolae/leishmania_tarentolae_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/leishmania_tarentolae/leishmania_tarentolae_metapars.cfg' -> './config/species/leishmania_tarentolae/leishmania_tarentolae_metapars.cfg' 153s '/usr/share/augustus/config/species/leishmania_tarentolae/leishmania_tarentolae_metapars.utr.cfg' -> './config/species/leishmania_tarentolae/leishmania_tarentolae_metapars.utr.cfg' 153s '/usr/share/augustus/config/species/leishmania_tarentolae/leishmania_tarentolae_parameters.cfg' -> './config/species/leishmania_tarentolae/leishmania_tarentolae_parameters.cfg' 153s '/usr/share/augustus/config/species/leishmania_tarentolae/leishmania_tarentolae_weightmatrix.txt' -> './config/species/leishmania_tarentolae/leishmania_tarentolae_weightmatrix.txt' 153s '/usr/share/augustus/config/species/lodderomyces_elongisporus' -> './config/species/lodderomyces_elongisporus' 153s '/usr/share/augustus/config/species/lodderomyces_elongisporus/lodderomyces_elongisporus_exon_probs.pbl' -> './config/species/lodderomyces_elongisporus/lodderomyces_elongisporus_exon_probs.pbl' 153s '/usr/share/augustus/config/species/lodderomyces_elongisporus/lodderomyces_elongisporus_igenic_probs.pbl' -> './config/species/lodderomyces_elongisporus/lodderomyces_elongisporus_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/lodderomyces_elongisporus/lodderomyces_elongisporus_intron_probs.pbl' -> './config/species/lodderomyces_elongisporus/lodderomyces_elongisporus_intron_probs.pbl' 153s '/usr/share/augustus/config/species/lodderomyces_elongisporus/lodderomyces_elongisporus_metapars.cfg' -> './config/species/lodderomyces_elongisporus/lodderomyces_elongisporus_metapars.cfg' 153s '/usr/share/augustus/config/species/lodderomyces_elongisporus/lodderomyces_elongisporus_parameters.cfg' -> './config/species/lodderomyces_elongisporus/lodderomyces_elongisporus_parameters.cfg' 153s '/usr/share/augustus/config/species/lodderomyces_elongisporus/lodderomyces_elongisporus_weightmatrix.txt' -> './config/species/lodderomyces_elongisporus/lodderomyces_elongisporus_weightmatrix.txt' 153s '/usr/share/augustus/config/species/magnaporthe_grisea' -> './config/species/magnaporthe_grisea' 153s '/usr/share/augustus/config/species/magnaporthe_grisea/magnaporthe_grisea_exon_probs.pbl' -> './config/species/magnaporthe_grisea/magnaporthe_grisea_exon_probs.pbl' 153s '/usr/share/augustus/config/species/magnaporthe_grisea/magnaporthe_grisea_igenic_probs.pbl' -> './config/species/magnaporthe_grisea/magnaporthe_grisea_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/magnaporthe_grisea/magnaporthe_grisea_intron_probs.pbl' -> './config/species/magnaporthe_grisea/magnaporthe_grisea_intron_probs.pbl' 153s '/usr/share/augustus/config/species/magnaporthe_grisea/magnaporthe_grisea_metapars.cfg' -> './config/species/magnaporthe_grisea/magnaporthe_grisea_metapars.cfg' 153s '/usr/share/augustus/config/species/magnaporthe_grisea/magnaporthe_grisea_parameters.cfg' -> './config/species/magnaporthe_grisea/magnaporthe_grisea_parameters.cfg' 153s '/usr/share/augustus/config/species/magnaporthe_grisea/magnaporthe_grisea_weightmatrix.txt' -> './config/species/magnaporthe_grisea/magnaporthe_grisea_weightmatrix.txt' 153s '/usr/share/augustus/config/species/maize' -> './config/species/maize' 153s '/usr/share/augustus/config/species/maize/maize_exon_probs.pbl' -> './config/species/maize/maize_exon_probs.pbl' 153s '/usr/share/augustus/config/species/maize/maize_igenic_probs.pbl' -> './config/species/maize/maize_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/maize/maize_intron_probs.pbl' -> './config/species/maize/maize_intron_probs.pbl' 153s '/usr/share/augustus/config/species/maize/maize_metapars.cfg' -> './config/species/maize/maize_metapars.cfg' 153s '/usr/share/augustus/config/species/maize/maize_parameters.cfg' -> './config/species/maize/maize_parameters.cfg' 153s '/usr/share/augustus/config/species/maize/maize_splicefile.txt.gz' -> './config/species/maize/maize_splicefile.txt.gz' 153s '/usr/share/augustus/config/species/maize/maize_weightmatrix.txt' -> './config/species/maize/maize_weightmatrix.txt' 153s '/usr/share/augustus/config/species/maize5' -> './config/species/maize5' 153s '/usr/share/augustus/config/species/maize5/maize5_exon_probs.pbl' -> './config/species/maize5/maize5_exon_probs.pbl' 153s '/usr/share/augustus/config/species/maize5/maize5_igenic_probs.pbl' -> './config/species/maize5/maize5_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/maize5/maize5_intron_probs.pbl' -> './config/species/maize5/maize5_intron_probs.pbl' 153s '/usr/share/augustus/config/species/maize5/maize5_metapars.cfg' -> './config/species/maize5/maize5_metapars.cfg' 153s '/usr/share/augustus/config/species/maize5/maize5_metapars.utr.cfg' -> './config/species/maize5/maize5_metapars.utr.cfg' 153s '/usr/share/augustus/config/species/maize5/maize5_parameters.cfg' -> './config/species/maize5/maize5_parameters.cfg' 153s '/usr/share/augustus/config/species/maize5/maize5_utr_probs.pbl' -> './config/species/maize5/maize5_utr_probs.pbl' 153s '/usr/share/augustus/config/species/maize5/maize5_weightmatrix.txt' -> './config/species/maize5/maize5_weightmatrix.txt' 153s '/usr/share/augustus/config/species/mnemiopsis_leidyi' -> './config/species/mnemiopsis_leidyi' 153s '/usr/share/augustus/config/species/mnemiopsis_leidyi/README.TXT' -> './config/species/mnemiopsis_leidyi/README.TXT' 153s '/usr/share/augustus/config/species/mnemiopsis_leidyi/mnemiopsis_leidyi_exon_probs.pbl' -> './config/species/mnemiopsis_leidyi/mnemiopsis_leidyi_exon_probs.pbl' 153s '/usr/share/augustus/config/species/mnemiopsis_leidyi/mnemiopsis_leidyi_igenic_probs.pbl' -> './config/species/mnemiopsis_leidyi/mnemiopsis_leidyi_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/mnemiopsis_leidyi/mnemiopsis_leidyi_intron_probs.pbl' -> './config/species/mnemiopsis_leidyi/mnemiopsis_leidyi_intron_probs.pbl' 153s '/usr/share/augustus/config/species/mnemiopsis_leidyi/mnemiopsis_leidyi_metapars.cfg' -> './config/species/mnemiopsis_leidyi/mnemiopsis_leidyi_metapars.cfg' 153s '/usr/share/augustus/config/species/mnemiopsis_leidyi/mnemiopsis_leidyi_metapars.cgp.cfg' -> './config/species/mnemiopsis_leidyi/mnemiopsis_leidyi_metapars.cgp.cfg' 153s '/usr/share/augustus/config/species/mnemiopsis_leidyi/mnemiopsis_leidyi_metapars.utr.cfg' -> './config/species/mnemiopsis_leidyi/mnemiopsis_leidyi_metapars.utr.cfg' 153s '/usr/share/augustus/config/species/mnemiopsis_leidyi/mnemiopsis_leidyi_parameters.cfg' -> './config/species/mnemiopsis_leidyi/mnemiopsis_leidyi_parameters.cfg' 153s '/usr/share/augustus/config/species/mnemiopsis_leidyi/mnemiopsis_leidyi_parameters.cgp.cfg' -> './config/species/mnemiopsis_leidyi/mnemiopsis_leidyi_parameters.cgp.cfg' 153s '/usr/share/augustus/config/species/mnemiopsis_leidyi/mnemiopsis_leidyi_utr_probs.pbl' -> './config/species/mnemiopsis_leidyi/mnemiopsis_leidyi_utr_probs.pbl' 153s '/usr/share/augustus/config/species/mnemiopsis_leidyi/mnemiopsis_leidyi_weightmatrix.txt' -> './config/species/mnemiopsis_leidyi/mnemiopsis_leidyi_weightmatrix.txt' 153s '/usr/share/augustus/config/species/nasonia' -> './config/species/nasonia' 153s '/usr/share/augustus/config/species/nasonia/nasonia_exon_probs.pbl' -> './config/species/nasonia/nasonia_exon_probs.pbl' 153s '/usr/share/augustus/config/species/nasonia/nasonia_igenic_probs.pbl' -> './config/species/nasonia/nasonia_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/nasonia/nasonia_intron_probs.pbl' -> './config/species/nasonia/nasonia_intron_probs.pbl' 153s '/usr/share/augustus/config/species/nasonia/nasonia_metapars.cfg' -> './config/species/nasonia/nasonia_metapars.cfg' 153s '/usr/share/augustus/config/species/nasonia/nasonia_parameters.cfg' -> './config/species/nasonia/nasonia_parameters.cfg' 153s '/usr/share/augustus/config/species/nasonia/nasonia_weightmatrix.txt' -> './config/species/nasonia/nasonia_weightmatrix.txt' 153s '/usr/share/augustus/config/species/nematostella_vectensis' -> './config/species/nematostella_vectensis' 153s '/usr/share/augustus/config/species/nematostella_vectensis/README.TXT' -> './config/species/nematostella_vectensis/README.TXT' 153s '/usr/share/augustus/config/species/nematostella_vectensis/nematostella_vectensis_exon_probs.pbl' -> './config/species/nematostella_vectensis/nematostella_vectensis_exon_probs.pbl' 153s '/usr/share/augustus/config/species/nematostella_vectensis/nematostella_vectensis_igenic_probs.pbl' -> './config/species/nematostella_vectensis/nematostella_vectensis_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/nematostella_vectensis/nematostella_vectensis_intron_probs.pbl' -> './config/species/nematostella_vectensis/nematostella_vectensis_intron_probs.pbl' 153s '/usr/share/augustus/config/species/nematostella_vectensis/nematostella_vectensis_parameters.cfg' -> './config/species/nematostella_vectensis/nematostella_vectensis_parameters.cfg' 153s '/usr/share/augustus/config/species/nematostella_vectensis/nematostella_vectensis_weightmatrix.txt' -> './config/species/nematostella_vectensis/nematostella_vectensis_weightmatrix.txt' 153s '/usr/share/augustus/config/species/neurospora' -> './config/species/neurospora' 153s '/usr/share/augustus/config/species/neurospora/neurospora_exon_probs.pbl' -> './config/species/neurospora/neurospora_exon_probs.pbl' 153s '/usr/share/augustus/config/species/neurospora/neurospora_igenic_probs.pbl' -> './config/species/neurospora/neurospora_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/neurospora/neurospora_intron_probs.pbl' -> './config/species/neurospora/neurospora_intron_probs.pbl' 153s '/usr/share/augustus/config/species/neurospora/neurospora_parameters.cfg' -> './config/species/neurospora/neurospora_parameters.cfg' 153s '/usr/share/augustus/config/species/neurospora/neurospora_weightmatrix.txt' -> './config/species/neurospora/neurospora_weightmatrix.txt' 153s '/usr/share/augustus/config/species/neurospora_crassa' -> './config/species/neurospora_crassa' 153s '/usr/share/augustus/config/species/neurospora_crassa/neurospora_crassa_exon_probs.pbl' -> './config/species/neurospora_crassa/neurospora_crassa_exon_probs.pbl' 153s '/usr/share/augustus/config/species/neurospora_crassa/neurospora_crassa_igenic_probs.pbl' -> './config/species/neurospora_crassa/neurospora_crassa_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/neurospora_crassa/neurospora_crassa_intron_probs.pbl' -> './config/species/neurospora_crassa/neurospora_crassa_intron_probs.pbl' 153s '/usr/share/augustus/config/species/neurospora_crassa/neurospora_crassa_metapars.cfg' -> './config/species/neurospora_crassa/neurospora_crassa_metapars.cfg' 153s '/usr/share/augustus/config/species/neurospora_crassa/neurospora_crassa_parameters.cfg' -> './config/species/neurospora_crassa/neurospora_crassa_parameters.cfg' 153s '/usr/share/augustus/config/species/neurospora_crassa/neurospora_crassa_weightmatrix.txt' -> './config/species/neurospora_crassa/neurospora_crassa_weightmatrix.txt' 153s '/usr/share/augustus/config/species/parasteatoda' -> './config/species/parasteatoda' 153s '/usr/share/augustus/config/species/parasteatoda/parasteatoda_exon_probs.pbl' -> './config/species/parasteatoda/parasteatoda_exon_probs.pbl' 153s '/usr/share/augustus/config/species/parasteatoda/parasteatoda_igenic_probs.pbl' -> './config/species/parasteatoda/parasteatoda_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/parasteatoda/parasteatoda_intron_probs.pbl' -> './config/species/parasteatoda/parasteatoda_intron_probs.pbl' 153s '/usr/share/augustus/config/species/parasteatoda/parasteatoda_parameters.cfg' -> './config/species/parasteatoda/parasteatoda_parameters.cfg' 153s '/usr/share/augustus/config/species/parasteatoda/parasteatoda_utr_probs.pbl' -> './config/species/parasteatoda/parasteatoda_utr_probs.pbl' 153s '/usr/share/augustus/config/species/parasteatoda/parasteatoda_weightmatrix.txt' -> './config/species/parasteatoda/parasteatoda_weightmatrix.txt' 153s '/usr/share/augustus/config/species/pchrysosporium' -> './config/species/pchrysosporium' 153s '/usr/share/augustus/config/species/pchrysosporium/pchrysosporium_exon_probs.pbl' -> './config/species/pchrysosporium/pchrysosporium_exon_probs.pbl' 153s '/usr/share/augustus/config/species/pchrysosporium/pchrysosporium_igenic_probs.pbl' -> './config/species/pchrysosporium/pchrysosporium_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/pchrysosporium/pchrysosporium_intron_probs.pbl' -> './config/species/pchrysosporium/pchrysosporium_intron_probs.pbl' 153s '/usr/share/augustus/config/species/pchrysosporium/pchrysosporium_parameters.cfg' -> './config/species/pchrysosporium/pchrysosporium_parameters.cfg' 153s '/usr/share/augustus/config/species/pchrysosporium/pchrysosporium_weightmatrix.txt' -> './config/species/pchrysosporium/pchrysosporium_weightmatrix.txt' 153s '/usr/share/augustus/config/species/pea_aphid' -> './config/species/pea_aphid' 153s '/usr/share/augustus/config/species/pea_aphid/pea_aphid_exon_probs.pbl' -> './config/species/pea_aphid/pea_aphid_exon_probs.pbl' 153s '/usr/share/augustus/config/species/pea_aphid/pea_aphid_igenic_probs.pbl' -> './config/species/pea_aphid/pea_aphid_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/pea_aphid/pea_aphid_intron_probs.pbl' -> './config/species/pea_aphid/pea_aphid_intron_probs.pbl' 153s '/usr/share/augustus/config/species/pea_aphid/pea_aphid_metapars.cfg' -> './config/species/pea_aphid/pea_aphid_metapars.cfg' 153s '/usr/share/augustus/config/species/pea_aphid/pea_aphid_parameters.cfg' -> './config/species/pea_aphid/pea_aphid_parameters.cfg' 153s '/usr/share/augustus/config/species/pea_aphid/pea_aphid_trans_shadow_partial_utr.pbl' -> './config/species/pea_aphid/pea_aphid_trans_shadow_partial_utr.pbl' 153s '/usr/share/augustus/config/species/pea_aphid/pea_aphid_utr_probs.pbl' -> './config/species/pea_aphid/pea_aphid_utr_probs.pbl' 153s '/usr/share/augustus/config/species/pea_aphid/pea_aphid_weightmatrix.txt' -> './config/species/pea_aphid/pea_aphid_weightmatrix.txt' 153s '/usr/share/augustus/config/species/pfalciparum' -> './config/species/pfalciparum' 153s '/usr/share/augustus/config/species/pfalciparum/pfalciparum_exon_probs.pbl' -> './config/species/pfalciparum/pfalciparum_exon_probs.pbl' 153s '/usr/share/augustus/config/species/pfalciparum/pfalciparum_igenic_probs.pbl' -> './config/species/pfalciparum/pfalciparum_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/pfalciparum/pfalciparum_intron_probs.pbl' -> './config/species/pfalciparum/pfalciparum_intron_probs.pbl' 153s '/usr/share/augustus/config/species/pfalciparum/pfalciparum_metapars.cfg' -> './config/species/pfalciparum/pfalciparum_metapars.cfg' 153s '/usr/share/augustus/config/species/pfalciparum/pfalciparum_parameters.cfg' -> './config/species/pfalciparum/pfalciparum_parameters.cfg' 153s '/usr/share/augustus/config/species/pfalciparum/pfalciparum_trans_shadow_partial.pbl' -> './config/species/pfalciparum/pfalciparum_trans_shadow_partial.pbl' 153s '/usr/share/augustus/config/species/pfalciparum/pfalciparum_weightmatrix.txt' -> './config/species/pfalciparum/pfalciparum_weightmatrix.txt' 153s '/usr/share/augustus/config/species/phanerochaete_chrysosporium' -> './config/species/phanerochaete_chrysosporium' 153s '/usr/share/augustus/config/species/phanerochaete_chrysosporium/phanerochaete_chrysosporium_exon_probs.pbl' -> './config/species/phanerochaete_chrysosporium/phanerochaete_chrysosporium_exon_probs.pbl' 153s '/usr/share/augustus/config/species/phanerochaete_chrysosporium/phanerochaete_chrysosporium_igenic_probs.pbl' -> './config/species/phanerochaete_chrysosporium/phanerochaete_chrysosporium_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/phanerochaete_chrysosporium/phanerochaete_chrysosporium_intron_probs.pbl' -> './config/species/phanerochaete_chrysosporium/phanerochaete_chrysosporium_intron_probs.pbl' 153s '/usr/share/augustus/config/species/phanerochaete_chrysosporium/phanerochaete_chrysosporium_metapars.cfg' -> './config/species/phanerochaete_chrysosporium/phanerochaete_chrysosporium_metapars.cfg' 153s '/usr/share/augustus/config/species/phanerochaete_chrysosporium/phanerochaete_chrysosporium_parameters.cfg' -> './config/species/phanerochaete_chrysosporium/phanerochaete_chrysosporium_parameters.cfg' 153s '/usr/share/augustus/config/species/phanerochaete_chrysosporium/phanerochaete_chrysosporium_weightmatrix.txt' -> './config/species/phanerochaete_chrysosporium/phanerochaete_chrysosporium_weightmatrix.txt' 153s '/usr/share/augustus/config/species/pichia_stipitis' -> './config/species/pichia_stipitis' 153s '/usr/share/augustus/config/species/pichia_stipitis/pichia_stipitis_exon_probs.pbl' -> './config/species/pichia_stipitis/pichia_stipitis_exon_probs.pbl' 153s '/usr/share/augustus/config/species/pichia_stipitis/pichia_stipitis_igenic_probs.pbl' -> './config/species/pichia_stipitis/pichia_stipitis_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/pichia_stipitis/pichia_stipitis_intron_probs.pbl' -> './config/species/pichia_stipitis/pichia_stipitis_intron_probs.pbl' 153s '/usr/share/augustus/config/species/pichia_stipitis/pichia_stipitis_metapars.cfg' -> './config/species/pichia_stipitis/pichia_stipitis_metapars.cfg' 153s '/usr/share/augustus/config/species/pichia_stipitis/pichia_stipitis_parameters.cfg' -> './config/species/pichia_stipitis/pichia_stipitis_parameters.cfg' 153s '/usr/share/augustus/config/species/pichia_stipitis/pichia_stipitis_weightmatrix.txt' -> './config/species/pichia_stipitis/pichia_stipitis_weightmatrix.txt' 153s '/usr/share/augustus/config/species/pisaster' -> './config/species/pisaster' 153s '/usr/share/augustus/config/species/pisaster/extrinsic.pisaster.cfg' -> './config/species/pisaster/extrinsic.pisaster.cfg' 153s '/usr/share/augustus/config/species/pisaster/pisaster_exon_probs.pbl' -> './config/species/pisaster/pisaster_exon_probs.pbl' 153s '/usr/share/augustus/config/species/pisaster/pisaster_igenic_probs.pbl' -> './config/species/pisaster/pisaster_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/pisaster/pisaster_intron_probs.pbl' -> './config/species/pisaster/pisaster_intron_probs.pbl' 153s '/usr/share/augustus/config/species/pisaster/pisaster_metapars.cfg' -> './config/species/pisaster/pisaster_metapars.cfg' 153s '/usr/share/augustus/config/species/pisaster/pisaster_metapars.cgp.cfg' -> './config/species/pisaster/pisaster_metapars.cgp.cfg' 153s '/usr/share/augustus/config/species/pisaster/pisaster_metapars.utr.cfg' -> './config/species/pisaster/pisaster_metapars.utr.cfg' 153s '/usr/share/augustus/config/species/pisaster/pisaster_parameters.cfg' -> './config/species/pisaster/pisaster_parameters.cfg' 153s '/usr/share/augustus/config/species/pisaster/pisaster_weightmatrix.txt' -> './config/species/pisaster/pisaster_weightmatrix.txt' 153s '/usr/share/augustus/config/species/pneumocystis' -> './config/species/pneumocystis' 153s '/usr/share/augustus/config/species/pneumocystis/README.TXT' -> './config/species/pneumocystis/README.TXT' 153s '/usr/share/augustus/config/species/pneumocystis/pneumocystis_exon_probs.pbl' -> './config/species/pneumocystis/pneumocystis_exon_probs.pbl' 153s '/usr/share/augustus/config/species/pneumocystis/pneumocystis_igenic_probs.pbl' -> './config/species/pneumocystis/pneumocystis_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/pneumocystis/pneumocystis_intron_probs.pbl' -> './config/species/pneumocystis/pneumocystis_intron_probs.pbl' 153s '/usr/share/augustus/config/species/pneumocystis/pneumocystis_metapars.cfg' -> './config/species/pneumocystis/pneumocystis_metapars.cfg' 153s '/usr/share/augustus/config/species/pneumocystis/pneumocystis_metaparsBAK.cfg' -> './config/species/pneumocystis/pneumocystis_metaparsBAK.cfg' 153s '/usr/share/augustus/config/species/pneumocystis/pneumocystis_parameters.cfg' -> './config/species/pneumocystis/pneumocystis_parameters.cfg' 153s '/usr/share/augustus/config/species/pneumocystis/pneumocystis_weightmatrix.txt' -> './config/species/pneumocystis/pneumocystis_weightmatrix.txt' 153s '/usr/share/augustus/config/species/rhincodon' -> './config/species/rhincodon' 153s '/usr/share/augustus/config/species/rhincodon/rhincodon_exon_probs.pbl' -> './config/species/rhincodon/rhincodon_exon_probs.pbl' 153s '/usr/share/augustus/config/species/rhincodon/rhincodon_igenic_probs.pbl' -> './config/species/rhincodon/rhincodon_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/rhincodon/rhincodon_intron_probs.pbl' -> './config/species/rhincodon/rhincodon_intron_probs.pbl' 153s '/usr/share/augustus/config/species/rhincodon/rhincodon_metapars.cfg' -> './config/species/rhincodon/rhincodon_metapars.cfg' 153s '/usr/share/augustus/config/species/rhincodon/rhincodon_metapars.cgp.cfg' -> './config/species/rhincodon/rhincodon_metapars.cgp.cfg' 153s '/usr/share/augustus/config/species/rhincodon/rhincodon_metapars.utr.cfg' -> './config/species/rhincodon/rhincodon_metapars.utr.cfg' 153s '/usr/share/augustus/config/species/rhincodon/rhincodon_parameters.cfg' -> './config/species/rhincodon/rhincodon_parameters.cfg' 153s '/usr/share/augustus/config/species/rhincodon/rhincodon_parameters.cfg.orig1' -> './config/species/rhincodon/rhincodon_parameters.cfg.orig1' 153s '/usr/share/augustus/config/species/rhincodon/rhincodon_weightmatrix.txt' -> './config/species/rhincodon/rhincodon_weightmatrix.txt' 153s '/usr/share/augustus/config/species/rhizopus_oryzae' -> './config/species/rhizopus_oryzae' 153s '/usr/share/augustus/config/species/rhizopus_oryzae/rhizopus_oryzae_exon_probs.pbl' -> './config/species/rhizopus_oryzae/rhizopus_oryzae_exon_probs.pbl' 153s '/usr/share/augustus/config/species/rhizopus_oryzae/rhizopus_oryzae_igenic_probs.pbl' -> './config/species/rhizopus_oryzae/rhizopus_oryzae_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/rhizopus_oryzae/rhizopus_oryzae_intron_probs.pbl' -> './config/species/rhizopus_oryzae/rhizopus_oryzae_intron_probs.pbl' 153s '/usr/share/augustus/config/species/rhizopus_oryzae/rhizopus_oryzae_metapars.cfg' -> './config/species/rhizopus_oryzae/rhizopus_oryzae_metapars.cfg' 153s '/usr/share/augustus/config/species/rhizopus_oryzae/rhizopus_oryzae_parameters.cfg' -> './config/species/rhizopus_oryzae/rhizopus_oryzae_parameters.cfg' 153s '/usr/share/augustus/config/species/rhizopus_oryzae/rhizopus_oryzae_weightmatrix.txt' -> './config/species/rhizopus_oryzae/rhizopus_oryzae_weightmatrix.txt' 153s '/usr/share/augustus/config/species/rhodnius' -> './config/species/rhodnius' 153s '/usr/share/augustus/config/species/rhodnius/rhodnius_exon_probs.pbl' -> './config/species/rhodnius/rhodnius_exon_probs.pbl' 153s '/usr/share/augustus/config/species/rhodnius/rhodnius_igenic_probs.pbl' -> './config/species/rhodnius/rhodnius_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/rhodnius/rhodnius_intron_probs.pbl' -> './config/species/rhodnius/rhodnius_intron_probs.pbl' 153s '/usr/share/augustus/config/species/rhodnius/rhodnius_metapars.cfg' -> './config/species/rhodnius/rhodnius_metapars.cfg' 153s '/usr/share/augustus/config/species/rhodnius/rhodnius_metapars.utr.cfg' -> './config/species/rhodnius/rhodnius_metapars.utr.cfg' 153s '/usr/share/augustus/config/species/rhodnius/rhodnius_parameters.cfg' -> './config/species/rhodnius/rhodnius_parameters.cfg' 153s '/usr/share/augustus/config/species/rhodnius/rhodnius_utr_probs.pbl' -> './config/species/rhodnius/rhodnius_utr_probs.pbl' 153s '/usr/share/augustus/config/species/rhodnius/rhodnius_weightmatrix.txt' -> './config/species/rhodnius/rhodnius_weightmatrix.txt' 153s '/usr/share/augustus/config/species/rice' -> './config/species/rice' 153s '/usr/share/augustus/config/species/rice/README.TXT' -> './config/species/rice/README.TXT' 153s '/usr/share/augustus/config/species/rice/rice_exon_probs.pbl' -> './config/species/rice/rice_exon_probs.pbl' 153s '/usr/share/augustus/config/species/rice/rice_igenic_probs.pbl' -> './config/species/rice/rice_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/rice/rice_intron_probs.pbl' -> './config/species/rice/rice_intron_probs.pbl' 153s '/usr/share/augustus/config/species/rice/rice_metapars.cfg' -> './config/species/rice/rice_metapars.cfg' 153s '/usr/share/augustus/config/species/rice/rice_metapars.utr.cfg' -> './config/species/rice/rice_metapars.utr.cfg' 153s '/usr/share/augustus/config/species/rice/rice_parameters.cfg' -> './config/species/rice/rice_parameters.cfg' 153s '/usr/share/augustus/config/species/rice/rice_utr_probs.pbl' -> './config/species/rice/rice_utr_probs.pbl' 153s '/usr/share/augustus/config/species/rice/rice_weightmatrix.txt' -> './config/species/rice/rice_weightmatrix.txt' 153s '/usr/share/augustus/config/species/s_aureus' -> './config/species/s_aureus' 153s '/usr/share/augustus/config/species/s_aureus/README.TXT' -> './config/species/s_aureus/README.TXT' 153s '/usr/share/augustus/config/species/s_aureus/s_aureus_exon_probs.pbl' -> './config/species/s_aureus/s_aureus_exon_probs.pbl' 153s '/usr/share/augustus/config/species/s_aureus/s_aureus_igenic_probs.pbl' -> './config/species/s_aureus/s_aureus_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/s_aureus/s_aureus_metapars.cfg' -> './config/species/s_aureus/s_aureus_metapars.cfg' 153s '/usr/share/augustus/config/species/s_aureus/s_aureus_metapars.utr.cfg' -> './config/species/s_aureus/s_aureus_metapars.utr.cfg' 153s '/usr/share/augustus/config/species/s_aureus/s_aureus_ovlp_len.pbl' -> './config/species/s_aureus/s_aureus_ovlp_len.pbl' 153s '/usr/share/augustus/config/species/s_aureus/s_aureus_parameters.cfg' -> './config/species/s_aureus/s_aureus_parameters.cfg' 153s '/usr/share/augustus/config/species/s_aureus/s_aureus_parameters.cgp.cfg' -> './config/species/s_aureus/s_aureus_parameters.cgp.cfg' 153s '/usr/share/augustus/config/species/s_aureus/s_aureus_trans_shadow_bacterium.pbl' -> './config/species/s_aureus/s_aureus_trans_shadow_bacterium.pbl' 153s '/usr/share/augustus/config/species/s_aureus/s_aureus_weightmatrix.txt' -> './config/species/s_aureus/s_aureus_weightmatrix.txt' 153s '/usr/share/augustus/config/species/s_pneumoniae' -> './config/species/s_pneumoniae' 153s '/usr/share/augustus/config/species/s_pneumoniae/s_pneumoniae_exon_probs.pbl' -> './config/species/s_pneumoniae/s_pneumoniae_exon_probs.pbl' 153s '/usr/share/augustus/config/species/s_pneumoniae/s_pneumoniae_igenic_probs.pbl' -> './config/species/s_pneumoniae/s_pneumoniae_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/s_pneumoniae/s_pneumoniae_metapars.cfg' -> './config/species/s_pneumoniae/s_pneumoniae_metapars.cfg' 153s '/usr/share/augustus/config/species/s_pneumoniae/s_pneumoniae_metapars.utr.cfg' -> './config/species/s_pneumoniae/s_pneumoniae_metapars.utr.cfg' 153s '/usr/share/augustus/config/species/s_pneumoniae/s_pneumoniae_ovlp_len.pbl' -> './config/species/s_pneumoniae/s_pneumoniae_ovlp_len.pbl' 153s '/usr/share/augustus/config/species/s_pneumoniae/s_pneumoniae_parameters.cfg' -> './config/species/s_pneumoniae/s_pneumoniae_parameters.cfg' 153s '/usr/share/augustus/config/species/s_pneumoniae/s_pneumoniae_parameters.cfg.orig1' -> './config/species/s_pneumoniae/s_pneumoniae_parameters.cfg.orig1' 153s '/usr/share/augustus/config/species/s_pneumoniae/s_pneumoniae_parameters.cfg.orig2' -> './config/species/s_pneumoniae/s_pneumoniae_parameters.cfg.orig2' 153s '/usr/share/augustus/config/species/s_pneumoniae/s_pneumoniae_parameters.cfg.orig3' -> './config/species/s_pneumoniae/s_pneumoniae_parameters.cfg.orig3' 153s '/usr/share/augustus/config/species/s_pneumoniae/s_pneumoniae_parameters.cfg.orig4' -> './config/species/s_pneumoniae/s_pneumoniae_parameters.cfg.orig4' 153s '/usr/share/augustus/config/species/s_pneumoniae/s_pneumoniae_trans_shadow_bacterium.pbl' -> './config/species/s_pneumoniae/s_pneumoniae_trans_shadow_bacterium.pbl' 153s '/usr/share/augustus/config/species/s_pneumoniae/s_pneumoniae_weightmatrix.txt' -> './config/species/s_pneumoniae/s_pneumoniae_weightmatrix.txt' 153s '/usr/share/augustus/config/species/saccharomyces' -> './config/species/saccharomyces' 153s '/usr/share/augustus/config/species/saccharomyces/saccharomyces_exon_probs.pbl' -> './config/species/saccharomyces/saccharomyces_exon_probs.pbl' 153s '/usr/share/augustus/config/species/saccharomyces/saccharomyces_igenic_probs.pbl' -> './config/species/saccharomyces/saccharomyces_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/saccharomyces/saccharomyces_intron_probs.pbl' -> './config/species/saccharomyces/saccharomyces_intron_probs.pbl' 153s '/usr/share/augustus/config/species/saccharomyces/saccharomyces_parameters.cfg' -> './config/species/saccharomyces/saccharomyces_parameters.cfg' 153s '/usr/share/augustus/config/species/saccharomyces/saccharomyces_weightmatrix.txt' -> './config/species/saccharomyces/saccharomyces_weightmatrix.txt' 153s '/usr/share/augustus/config/species/saccharomyces_cerevisiae_S288C' -> './config/species/saccharomyces_cerevisiae_S288C' 153s '/usr/share/augustus/config/species/saccharomyces_cerevisiae_S288C/saccharomyces_cerevisiae_S288C_exon_probs.pbl' -> './config/species/saccharomyces_cerevisiae_S288C/saccharomyces_cerevisiae_S288C_exon_probs.pbl' 153s '/usr/share/augustus/config/species/saccharomyces_cerevisiae_S288C/saccharomyces_cerevisiae_S288C_igenic_probs.pbl' -> './config/species/saccharomyces_cerevisiae_S288C/saccharomyces_cerevisiae_S288C_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/saccharomyces_cerevisiae_S288C/saccharomyces_cerevisiae_S288C_intron_probs.pbl' -> './config/species/saccharomyces_cerevisiae_S288C/saccharomyces_cerevisiae_S288C_intron_probs.pbl' 153s '/usr/share/augustus/config/species/saccharomyces_cerevisiae_S288C/saccharomyces_cerevisiae_S288C_metapars.cfg' -> './config/species/saccharomyces_cerevisiae_S288C/saccharomyces_cerevisiae_S288C_metapars.cfg' 153s '/usr/share/augustus/config/species/saccharomyces_cerevisiae_S288C/saccharomyces_cerevisiae_S288C_parameters.cfg' -> './config/species/saccharomyces_cerevisiae_S288C/saccharomyces_cerevisiae_S288C_parameters.cfg' 153s '/usr/share/augustus/config/species/saccharomyces_cerevisiae_S288C/saccharomyces_cerevisiae_S288C_weightmatrix.txt' -> './config/species/saccharomyces_cerevisiae_S288C/saccharomyces_cerevisiae_S288C_weightmatrix.txt' 153s '/usr/share/augustus/config/species/saccharomyces_cerevisiae_rm11-1a_1' -> './config/species/saccharomyces_cerevisiae_rm11-1a_1' 153s '/usr/share/augustus/config/species/saccharomyces_cerevisiae_rm11-1a_1/saccharomyces_cerevisiae_rm11-1a_1_exon_probs.pbl' -> './config/species/saccharomyces_cerevisiae_rm11-1a_1/saccharomyces_cerevisiae_rm11-1a_1_exon_probs.pbl' 153s '/usr/share/augustus/config/species/saccharomyces_cerevisiae_rm11-1a_1/saccharomyces_cerevisiae_rm11-1a_1_igenic_probs.pbl' -> './config/species/saccharomyces_cerevisiae_rm11-1a_1/saccharomyces_cerevisiae_rm11-1a_1_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/saccharomyces_cerevisiae_rm11-1a_1/saccharomyces_cerevisiae_rm11-1a_1_intron_probs.pbl' -> './config/species/saccharomyces_cerevisiae_rm11-1a_1/saccharomyces_cerevisiae_rm11-1a_1_intron_probs.pbl' 153s '/usr/share/augustus/config/species/saccharomyces_cerevisiae_rm11-1a_1/saccharomyces_cerevisiae_rm11-1a_1_metapars.cfg' -> './config/species/saccharomyces_cerevisiae_rm11-1a_1/saccharomyces_cerevisiae_rm11-1a_1_metapars.cfg' 153s '/usr/share/augustus/config/species/saccharomyces_cerevisiae_rm11-1a_1/saccharomyces_cerevisiae_rm11-1a_1_parameters.cfg' -> './config/species/saccharomyces_cerevisiae_rm11-1a_1/saccharomyces_cerevisiae_rm11-1a_1_parameters.cfg' 153s '/usr/share/augustus/config/species/saccharomyces_cerevisiae_rm11-1a_1/saccharomyces_cerevisiae_rm11-1a_1_weightmatrix.txt' -> './config/species/saccharomyces_cerevisiae_rm11-1a_1/saccharomyces_cerevisiae_rm11-1a_1_weightmatrix.txt' 153s '/usr/share/augustus/config/species/schistosoma' -> './config/species/schistosoma' 153s '/usr/share/augustus/config/species/schistosoma/schistosoma_exon_probs.pbl' -> './config/species/schistosoma/schistosoma_exon_probs.pbl' 153s '/usr/share/augustus/config/species/schistosoma/schistosoma_igenic_probs.pbl' -> './config/species/schistosoma/schistosoma_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/schistosoma/schistosoma_intron_probs.pbl' -> './config/species/schistosoma/schistosoma_intron_probs.pbl' 153s '/usr/share/augustus/config/species/schistosoma/schistosoma_metapars.cfg' -> './config/species/schistosoma/schistosoma_metapars.cfg' 153s '/usr/share/augustus/config/species/schistosoma/schistosoma_parameters.cfg' -> './config/species/schistosoma/schistosoma_parameters.cfg' 153s '/usr/share/augustus/config/species/schistosoma/schistosoma_parameters.cfg.opt' -> './config/species/schistosoma/schistosoma_parameters.cfg.opt' 153s '/usr/share/augustus/config/species/schistosoma/schistosoma_splicefile.txt' -> './config/species/schistosoma/schistosoma_splicefile.txt' 153s '/usr/share/augustus/config/species/schistosoma/schistosoma_weightmatrix.txt' -> './config/species/schistosoma/schistosoma_weightmatrix.txt' 153s '/usr/share/augustus/config/species/schistosoma2' -> './config/species/schistosoma2' 153s '/usr/share/augustus/config/species/schistosoma2/README.TXT' -> './config/species/schistosoma2/README.TXT' 153s '/usr/share/augustus/config/species/schistosoma2/schistosoma2_exon_probs.pbl' -> './config/species/schistosoma2/schistosoma2_exon_probs.pbl' 153s '/usr/share/augustus/config/species/schistosoma2/schistosoma2_igenic_probs.pbl' -> './config/species/schistosoma2/schistosoma2_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/schistosoma2/schistosoma2_intron_probs.pbl' -> './config/species/schistosoma2/schistosoma2_intron_probs.pbl' 153s '/usr/share/augustus/config/species/schistosoma2/schistosoma2_metapars.cfg' -> './config/species/schistosoma2/schistosoma2_metapars.cfg' 153s '/usr/share/augustus/config/species/schistosoma2/schistosoma2_metapars.cgp.cfg' -> './config/species/schistosoma2/schistosoma2_metapars.cgp.cfg' 153s '/usr/share/augustus/config/species/schistosoma2/schistosoma2_metapars.utr.cfg' -> './config/species/schistosoma2/schistosoma2_metapars.utr.cfg' 153s '/usr/share/augustus/config/species/schistosoma2/schistosoma2_parameters.cfg' -> './config/species/schistosoma2/schistosoma2_parameters.cfg' 153s '/usr/share/augustus/config/species/schistosoma2/schistosoma2_utr_probs.pbl' -> './config/species/schistosoma2/schistosoma2_utr_probs.pbl' 153s '/usr/share/augustus/config/species/schistosoma2/schistosoma2_weightmatrix.txt' -> './config/species/schistosoma2/schistosoma2_weightmatrix.txt' 153s '/usr/share/augustus/config/species/schizosaccharomyces_pombe' -> './config/species/schizosaccharomyces_pombe' 153s '/usr/share/augustus/config/species/schizosaccharomyces_pombe/schizosaccharomyces_pombe_exon_probs.pbl' -> './config/species/schizosaccharomyces_pombe/schizosaccharomyces_pombe_exon_probs.pbl' 153s '/usr/share/augustus/config/species/schizosaccharomyces_pombe/schizosaccharomyces_pombe_igenic_probs.pbl' -> './config/species/schizosaccharomyces_pombe/schizosaccharomyces_pombe_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/schizosaccharomyces_pombe/schizosaccharomyces_pombe_intron_probs.pbl' -> './config/species/schizosaccharomyces_pombe/schizosaccharomyces_pombe_intron_probs.pbl' 153s '/usr/share/augustus/config/species/schizosaccharomyces_pombe/schizosaccharomyces_pombe_metapars.cfg' -> './config/species/schizosaccharomyces_pombe/schizosaccharomyces_pombe_metapars.cfg' 153s '/usr/share/augustus/config/species/schizosaccharomyces_pombe/schizosaccharomyces_pombe_parameters.cfg' -> './config/species/schizosaccharomyces_pombe/schizosaccharomyces_pombe_parameters.cfg' 153s '/usr/share/augustus/config/species/schizosaccharomyces_pombe/schizosaccharomyces_pombe_weightmatrix.txt' -> './config/species/schizosaccharomyces_pombe/schizosaccharomyces_pombe_weightmatrix.txt' 153s '/usr/share/augustus/config/species/scyliorhinus' -> './config/species/scyliorhinus' 153s '/usr/share/augustus/config/species/scyliorhinus/scyliorhinus_exon_probs.pbl' -> './config/species/scyliorhinus/scyliorhinus_exon_probs.pbl' 153s '/usr/share/augustus/config/species/scyliorhinus/scyliorhinus_igenic_probs.pbl' -> './config/species/scyliorhinus/scyliorhinus_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/scyliorhinus/scyliorhinus_intron_probs.pbl' -> './config/species/scyliorhinus/scyliorhinus_intron_probs.pbl' 153s '/usr/share/augustus/config/species/scyliorhinus/scyliorhinus_metapars.cfg' -> './config/species/scyliorhinus/scyliorhinus_metapars.cfg' 153s '/usr/share/augustus/config/species/scyliorhinus/scyliorhinus_metapars.cgp.cfg' -> './config/species/scyliorhinus/scyliorhinus_metapars.cgp.cfg' 153s '/usr/share/augustus/config/species/scyliorhinus/scyliorhinus_metapars.utr.cfg' -> './config/species/scyliorhinus/scyliorhinus_metapars.utr.cfg' 153s '/usr/share/augustus/config/species/scyliorhinus/scyliorhinus_parameters.cfg' -> './config/species/scyliorhinus/scyliorhinus_parameters.cfg' 153s '/usr/share/augustus/config/species/scyliorhinus/scyliorhinus_parameters.cfg.orig1' -> './config/species/scyliorhinus/scyliorhinus_parameters.cfg.orig1' 153s '/usr/share/augustus/config/species/scyliorhinus/scyliorhinus_weightmatrix.txt' -> './config/species/scyliorhinus/scyliorhinus_weightmatrix.txt' 153s '/usr/share/augustus/config/species/sealamprey' -> './config/species/sealamprey' 153s '/usr/share/augustus/config/species/sealamprey/sealamprey_exon_probs.pbl' -> './config/species/sealamprey/sealamprey_exon_probs.pbl' 153s '/usr/share/augustus/config/species/sealamprey/sealamprey_igenic_probs.pbl' -> './config/species/sealamprey/sealamprey_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/sealamprey/sealamprey_intron_probs.pbl' -> './config/species/sealamprey/sealamprey_intron_probs.pbl' 153s '/usr/share/augustus/config/species/sealamprey/sealamprey_metapars.cfg' -> './config/species/sealamprey/sealamprey_metapars.cfg' 153s '/usr/share/augustus/config/species/sealamprey/sealamprey_parameters.cfg' -> './config/species/sealamprey/sealamprey_parameters.cfg' 153s '/usr/share/augustus/config/species/sealamprey/sealamprey_weightmatrix.txt' -> './config/species/sealamprey/sealamprey_weightmatrix.txt' 153s '/usr/share/augustus/config/species/strongylocentrotus_purpuratus' -> './config/species/strongylocentrotus_purpuratus' 153s '/usr/share/augustus/config/species/strongylocentrotus_purpuratus/README.TXT' -> './config/species/strongylocentrotus_purpuratus/README.TXT' 153s '/usr/share/augustus/config/species/strongylocentrotus_purpuratus/strongylocentrotus_purpuratus_exon_probs.pbl' -> './config/species/strongylocentrotus_purpuratus/strongylocentrotus_purpuratus_exon_probs.pbl' 153s '/usr/share/augustus/config/species/strongylocentrotus_purpuratus/strongylocentrotus_purpuratus_igenic_probs.pbl' -> './config/species/strongylocentrotus_purpuratus/strongylocentrotus_purpuratus_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/strongylocentrotus_purpuratus/strongylocentrotus_purpuratus_intron_probs.pbl' -> './config/species/strongylocentrotus_purpuratus/strongylocentrotus_purpuratus_intron_probs.pbl' 153s '/usr/share/augustus/config/species/strongylocentrotus_purpuratus/strongylocentrotus_purpuratus_metapars.cfg' -> './config/species/strongylocentrotus_purpuratus/strongylocentrotus_purpuratus_metapars.cfg' 153s '/usr/share/augustus/config/species/strongylocentrotus_purpuratus/strongylocentrotus_purpuratus_metapars.cgp.cfg' -> './config/species/strongylocentrotus_purpuratus/strongylocentrotus_purpuratus_metapars.cgp.cfg' 153s '/usr/share/augustus/config/species/strongylocentrotus_purpuratus/strongylocentrotus_purpuratus_metapars.utr.cfg' -> './config/species/strongylocentrotus_purpuratus/strongylocentrotus_purpuratus_metapars.utr.cfg' 153s '/usr/share/augustus/config/species/strongylocentrotus_purpuratus/strongylocentrotus_purpuratus_parameters.cfg' -> './config/species/strongylocentrotus_purpuratus/strongylocentrotus_purpuratus_parameters.cfg' 153s '/usr/share/augustus/config/species/strongylocentrotus_purpuratus/strongylocentrotus_purpuratus_parameters.cgp.cfg' -> './config/species/strongylocentrotus_purpuratus/strongylocentrotus_purpuratus_parameters.cgp.cfg' 153s '/usr/share/augustus/config/species/strongylocentrotus_purpuratus/strongylocentrotus_purpuratus_utr_probs.pbl' -> './config/species/strongylocentrotus_purpuratus/strongylocentrotus_purpuratus_utr_probs.pbl' 153s '/usr/share/augustus/config/species/strongylocentrotus_purpuratus/strongylocentrotus_purpuratus_weightmatrix.txt' -> './config/species/strongylocentrotus_purpuratus/strongylocentrotus_purpuratus_weightmatrix.txt' 153s '/usr/share/augustus/config/species/sulfolobus_solfataricus' -> './config/species/sulfolobus_solfataricus' 153s '/usr/share/augustus/config/species/sulfolobus_solfataricus/sulfolobus_solfataricus_exon_probs.pbl' -> './config/species/sulfolobus_solfataricus/sulfolobus_solfataricus_exon_probs.pbl' 153s '/usr/share/augustus/config/species/sulfolobus_solfataricus/sulfolobus_solfataricus_igenic_probs.pbl' -> './config/species/sulfolobus_solfataricus/sulfolobus_solfataricus_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/sulfolobus_solfataricus/sulfolobus_solfataricus_metapars.cfg' -> './config/species/sulfolobus_solfataricus/sulfolobus_solfataricus_metapars.cfg' 153s '/usr/share/augustus/config/species/sulfolobus_solfataricus/sulfolobus_solfataricus_metapars.utr.cfg' -> './config/species/sulfolobus_solfataricus/sulfolobus_solfataricus_metapars.utr.cfg' 153s '/usr/share/augustus/config/species/sulfolobus_solfataricus/sulfolobus_solfataricus_ovlp_len.pbl' -> './config/species/sulfolobus_solfataricus/sulfolobus_solfataricus_ovlp_len.pbl' 153s '/usr/share/augustus/config/species/sulfolobus_solfataricus/sulfolobus_solfataricus_parameters.cfg' -> './config/species/sulfolobus_solfataricus/sulfolobus_solfataricus_parameters.cfg' 153s '/usr/share/augustus/config/species/sulfolobus_solfataricus/sulfolobus_solfataricus_trans_shadow_bacterium.pbl' -> './config/species/sulfolobus_solfataricus/sulfolobus_solfataricus_trans_shadow_bacterium.pbl' 153s '/usr/share/augustus/config/species/sulfolobus_solfataricus/sulfolobus_solfataricus_weightmatrix.txt' -> './config/species/sulfolobus_solfataricus/sulfolobus_solfataricus_weightmatrix.txt' 153s '/usr/share/augustus/config/species/sunflower' -> './config/species/sunflower' 153s '/usr/share/augustus/config/species/sunflower/README.TXT' -> './config/species/sunflower/README.TXT' 153s '/usr/share/augustus/config/species/sunflower/sunflower_exon_probs.pbl' -> './config/species/sunflower/sunflower_exon_probs.pbl' 153s '/usr/share/augustus/config/species/sunflower/sunflower_igenic_probs.pbl' -> './config/species/sunflower/sunflower_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/sunflower/sunflower_intron_probs.pbl' -> './config/species/sunflower/sunflower_intron_probs.pbl' 153s '/usr/share/augustus/config/species/sunflower/sunflower_metapars.cfg' -> './config/species/sunflower/sunflower_metapars.cfg' 153s '/usr/share/augustus/config/species/sunflower/sunflower_metapars.cgp.cfg' -> './config/species/sunflower/sunflower_metapars.cgp.cfg' 153s '/usr/share/augustus/config/species/sunflower/sunflower_metapars.utr.cfg' -> './config/species/sunflower/sunflower_metapars.utr.cfg' 153s '/usr/share/augustus/config/species/sunflower/sunflower_parameters.cfg' -> './config/species/sunflower/sunflower_parameters.cfg' 153s '/usr/share/augustus/config/species/sunflower/sunflower_weightmatrix.txt' -> './config/species/sunflower/sunflower_weightmatrix.txt' 153s '/usr/share/augustus/config/species/template_prokaryotic' -> './config/species/template_prokaryotic' 153s '/usr/share/augustus/config/species/template_prokaryotic/template_prokaryotic_metapars.cfg' -> './config/species/template_prokaryotic/template_prokaryotic_metapars.cfg' 153s '/usr/share/augustus/config/species/template_prokaryotic/template_prokaryotic_metapars.utr.cfg' -> './config/species/template_prokaryotic/template_prokaryotic_metapars.utr.cfg' 153s '/usr/share/augustus/config/species/template_prokaryotic/template_prokaryotic_ovlp_len.pbl' -> './config/species/template_prokaryotic/template_prokaryotic_ovlp_len.pbl' 153s '/usr/share/augustus/config/species/template_prokaryotic/template_prokaryotic_parameters.cfg' -> './config/species/template_prokaryotic/template_prokaryotic_parameters.cfg' 153s '/usr/share/augustus/config/species/template_prokaryotic/template_prokaryotic_trans_shadow_bacterium.pbl' -> './config/species/template_prokaryotic/template_prokaryotic_trans_shadow_bacterium.pbl' 153s '/usr/share/augustus/config/species/template_prokaryotic/template_prokaryotic_weightmatrix.txt' -> './config/species/template_prokaryotic/template_prokaryotic_weightmatrix.txt' 153s '/usr/share/augustus/config/species/tetrahymena' -> './config/species/tetrahymena' 153s '/usr/share/augustus/config/species/tetrahymena/tetrahymena_exon_probs.pbl' -> './config/species/tetrahymena/tetrahymena_exon_probs.pbl' 153s '/usr/share/augustus/config/species/tetrahymena/tetrahymena_igenic_probs.pbl' -> './config/species/tetrahymena/tetrahymena_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/tetrahymena/tetrahymena_intron_probs.pbl' -> './config/species/tetrahymena/tetrahymena_intron_probs.pbl' 153s '/usr/share/augustus/config/species/tetrahymena/tetrahymena_metapars.cfg' -> './config/species/tetrahymena/tetrahymena_metapars.cfg' 153s '/usr/share/augustus/config/species/tetrahymena/tetrahymena_parameters.cfg' -> './config/species/tetrahymena/tetrahymena_parameters.cfg' 153s '/usr/share/augustus/config/species/tetrahymena/tetrahymena_weightmatrix.txt' -> './config/species/tetrahymena/tetrahymena_weightmatrix.txt' 153s '/usr/share/augustus/config/species/thermoanaerobacter_tengcongensis' -> './config/species/thermoanaerobacter_tengcongensis' 153s '/usr/share/augustus/config/species/thermoanaerobacter_tengcongensis/thermoanaerobacter_tengcongensis_exon_probs.pbl' -> './config/species/thermoanaerobacter_tengcongensis/thermoanaerobacter_tengcongensis_exon_probs.pbl' 153s '/usr/share/augustus/config/species/thermoanaerobacter_tengcongensis/thermoanaerobacter_tengcongensis_igenic_probs.pbl' -> './config/species/thermoanaerobacter_tengcongensis/thermoanaerobacter_tengcongensis_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/thermoanaerobacter_tengcongensis/thermoanaerobacter_tengcongensis_metapars.cfg' -> './config/species/thermoanaerobacter_tengcongensis/thermoanaerobacter_tengcongensis_metapars.cfg' 153s '/usr/share/augustus/config/species/thermoanaerobacter_tengcongensis/thermoanaerobacter_tengcongensis_metapars.utr.cfg' -> './config/species/thermoanaerobacter_tengcongensis/thermoanaerobacter_tengcongensis_metapars.utr.cfg' 153s '/usr/share/augustus/config/species/thermoanaerobacter_tengcongensis/thermoanaerobacter_tengcongensis_ovlp_len.pbl' -> './config/species/thermoanaerobacter_tengcongensis/thermoanaerobacter_tengcongensis_ovlp_len.pbl' 153s '/usr/share/augustus/config/species/thermoanaerobacter_tengcongensis/thermoanaerobacter_tengcongensis_parameters.cfg' -> './config/species/thermoanaerobacter_tengcongensis/thermoanaerobacter_tengcongensis_parameters.cfg' 153s '/usr/share/augustus/config/species/thermoanaerobacter_tengcongensis/thermoanaerobacter_tengcongensis_trans_shadow_bacterium.pbl' -> './config/species/thermoanaerobacter_tengcongensis/thermoanaerobacter_tengcongensis_trans_shadow_bacterium.pbl' 153s '/usr/share/augustus/config/species/thermoanaerobacter_tengcongensis/thermoanaerobacter_tengcongensis_weightmatrix.txt' -> './config/species/thermoanaerobacter_tengcongensis/thermoanaerobacter_tengcongensis_weightmatrix.txt' 153s '/usr/share/augustus/config/species/tomato' -> './config/species/tomato' 153s '/usr/share/augustus/config/species/tomato/tomato_exon_probs.pbl' -> './config/species/tomato/tomato_exon_probs.pbl' 153s '/usr/share/augustus/config/species/tomato/tomato_igenic_probs.pbl' -> './config/species/tomato/tomato_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/tomato/tomato_intron_probs.pbl' -> './config/species/tomato/tomato_intron_probs.pbl' 153s '/usr/share/augustus/config/species/tomato/tomato_metapars.cfg' -> './config/species/tomato/tomato_metapars.cfg' 153s '/usr/share/augustus/config/species/tomato/tomato_metapars.utr.cfg' -> './config/species/tomato/tomato_metapars.utr.cfg' 153s '/usr/share/augustus/config/species/tomato/tomato_parameters.cfg' -> './config/species/tomato/tomato_parameters.cfg' 153s '/usr/share/augustus/config/species/tomato/tomato_utr_probs.pbl' -> './config/species/tomato/tomato_utr_probs.pbl' 153s '/usr/share/augustus/config/species/tomato/tomato_weightmatrix.txt' -> './config/species/tomato/tomato_weightmatrix.txt' 153s '/usr/share/augustus/config/species/toxoplasma' -> './config/species/toxoplasma' 153s '/usr/share/augustus/config/species/toxoplasma/toxoplasma_exon_probs.pbl' -> './config/species/toxoplasma/toxoplasma_exon_probs.pbl' 153s '/usr/share/augustus/config/species/toxoplasma/toxoplasma_igenic_probs.pbl' -> './config/species/toxoplasma/toxoplasma_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/toxoplasma/toxoplasma_intron_probs.pbl' -> './config/species/toxoplasma/toxoplasma_intron_probs.pbl' 153s '/usr/share/augustus/config/species/toxoplasma/toxoplasma_metaparameters.cfg' -> './config/species/toxoplasma/toxoplasma_metaparameters.cfg' 153s '/usr/share/augustus/config/species/toxoplasma/toxoplasma_parameters.cfg' -> './config/species/toxoplasma/toxoplasma_parameters.cfg' 153s '/usr/share/augustus/config/species/toxoplasma/toxoplasma_trans_shadow_partial_utr.pbl' -> './config/species/toxoplasma/toxoplasma_trans_shadow_partial_utr.pbl' 153s '/usr/share/augustus/config/species/toxoplasma/toxoplasma_utr_probs.pbl' -> './config/species/toxoplasma/toxoplasma_utr_probs.pbl' 153s '/usr/share/augustus/config/species/toxoplasma/toxoplasma_weightmatrix.txt' -> './config/species/toxoplasma/toxoplasma_weightmatrix.txt' 153s '/usr/share/augustus/config/species/tribolium2012' -> './config/species/tribolium2012' 153s '/usr/share/augustus/config/species/tribolium2012/tribolium2012_exon_probs.pbl' -> './config/species/tribolium2012/tribolium2012_exon_probs.pbl' 153s '/usr/share/augustus/config/species/tribolium2012/tribolium2012_exon_probs.pbl.HMM' -> './config/species/tribolium2012/tribolium2012_exon_probs.pbl.HMM' 153s '/usr/share/augustus/config/species/tribolium2012/tribolium2012_exon_probs.pbl1' -> './config/species/tribolium2012/tribolium2012_exon_probs.pbl1' 153s '/usr/share/augustus/config/species/tribolium2012/tribolium2012_exon_probs.pbl2' -> './config/species/tribolium2012/tribolium2012_exon_probs.pbl2' 153s '/usr/share/augustus/config/species/tribolium2012/tribolium2012_exon_probs.pbl3' -> './config/species/tribolium2012/tribolium2012_exon_probs.pbl3' 153s '/usr/share/augustus/config/species/tribolium2012/tribolium2012_exon_probs.pbl4' -> './config/species/tribolium2012/tribolium2012_exon_probs.pbl4' 153s '/usr/share/augustus/config/species/tribolium2012/tribolium2012_igenic_probs.pbl' -> './config/species/tribolium2012/tribolium2012_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/tribolium2012/tribolium2012_igenic_probs.pbl.HMM' -> './config/species/tribolium2012/tribolium2012_igenic_probs.pbl.HMM' 153s '/usr/share/augustus/config/species/tribolium2012/tribolium2012_igenic_probs.pbl1' -> './config/species/tribolium2012/tribolium2012_igenic_probs.pbl1' 153s '/usr/share/augustus/config/species/tribolium2012/tribolium2012_igenic_probs.pbl2' -> './config/species/tribolium2012/tribolium2012_igenic_probs.pbl2' 153s '/usr/share/augustus/config/species/tribolium2012/tribolium2012_igenic_probs.pbl3' -> './config/species/tribolium2012/tribolium2012_igenic_probs.pbl3' 153s '/usr/share/augustus/config/species/tribolium2012/tribolium2012_igenic_probs.pbl4' -> './config/species/tribolium2012/tribolium2012_igenic_probs.pbl4' 153s '/usr/share/augustus/config/species/tribolium2012/tribolium2012_intron_probs.pbl' -> './config/species/tribolium2012/tribolium2012_intron_probs.pbl' 153s '/usr/share/augustus/config/species/tribolium2012/tribolium2012_intron_probs.pbl.HMM' -> './config/species/tribolium2012/tribolium2012_intron_probs.pbl.HMM' 153s '/usr/share/augustus/config/species/tribolium2012/tribolium2012_intron_probs.pbl1' -> './config/species/tribolium2012/tribolium2012_intron_probs.pbl1' 153s '/usr/share/augustus/config/species/tribolium2012/tribolium2012_intron_probs.pbl2' -> './config/species/tribolium2012/tribolium2012_intron_probs.pbl2' 153s '/usr/share/augustus/config/species/tribolium2012/tribolium2012_intron_probs.pbl3' -> './config/species/tribolium2012/tribolium2012_intron_probs.pbl3' 153s '/usr/share/augustus/config/species/tribolium2012/tribolium2012_intron_probs.pbl4' -> './config/species/tribolium2012/tribolium2012_intron_probs.pbl4' 153s '/usr/share/augustus/config/species/tribolium2012/tribolium2012_metapars.cfg' -> './config/species/tribolium2012/tribolium2012_metapars.cfg' 153s '/usr/share/augustus/config/species/tribolium2012/tribolium2012_metapars.utr.cfg' -> './config/species/tribolium2012/tribolium2012_metapars.utr.cfg' 153s '/usr/share/augustus/config/species/tribolium2012/tribolium2012_parameters.cfg' -> './config/species/tribolium2012/tribolium2012_parameters.cfg' 153s '/usr/share/augustus/config/species/tribolium2012/tribolium2012_parameters.cfg.orig1' -> './config/species/tribolium2012/tribolium2012_parameters.cfg.orig1' 153s '/usr/share/augustus/config/species/tribolium2012/tribolium2012_parameters.cfg.orig2' -> './config/species/tribolium2012/tribolium2012_parameters.cfg.orig2' 153s '/usr/share/augustus/config/species/tribolium2012/tribolium2012_parameters.cfg.orig3' -> './config/species/tribolium2012/tribolium2012_parameters.cfg.orig3' 153s '/usr/share/augustus/config/species/tribolium2012/tribolium2012_parameters.cfg.orig4' -> './config/species/tribolium2012/tribolium2012_parameters.cfg.orig4' 153s '/usr/share/augustus/config/species/tribolium2012/tribolium2012_parameters.cfg.orig5' -> './config/species/tribolium2012/tribolium2012_parameters.cfg.orig5' 153s '/usr/share/augustus/config/species/tribolium2012/tribolium2012_parameters.cfg.orig6' -> './config/species/tribolium2012/tribolium2012_parameters.cfg.orig6' 153s '/usr/share/augustus/config/species/tribolium2012/tribolium2012_parameters.cfg.orig7' -> './config/species/tribolium2012/tribolium2012_parameters.cfg.orig7' 153s '/usr/share/augustus/config/species/tribolium2012/tribolium2012_trans_shadow_partial_utr.pbl' -> './config/species/tribolium2012/tribolium2012_trans_shadow_partial_utr.pbl' 153s '/usr/share/augustus/config/species/tribolium2012/tribolium2012_utr_probs.pbl' -> './config/species/tribolium2012/tribolium2012_utr_probs.pbl' 153s '/usr/share/augustus/config/species/tribolium2012/tribolium2012_utr_probs.pbl.HMM' -> './config/species/tribolium2012/tribolium2012_utr_probs.pbl.HMM' 153s '/usr/share/augustus/config/species/tribolium2012/tribolium2012_weightmatrix.txt' -> './config/species/tribolium2012/tribolium2012_weightmatrix.txt' 153s '/usr/share/augustus/config/species/trichinella' -> './config/species/trichinella' 153s '/usr/share/augustus/config/species/trichinella/trichinella_exon_probs.pbl' -> './config/species/trichinella/trichinella_exon_probs.pbl' 153s '/usr/share/augustus/config/species/trichinella/trichinella_igenic_probs.pbl' -> './config/species/trichinella/trichinella_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/trichinella/trichinella_intron_probs.pbl' -> './config/species/trichinella/trichinella_intron_probs.pbl' 153s '/usr/share/augustus/config/species/trichinella/trichinella_metapars.cfg' -> './config/species/trichinella/trichinella_metapars.cfg' 153s '/usr/share/augustus/config/species/trichinella/trichinella_metapars.utr.cfg' -> './config/species/trichinella/trichinella_metapars.utr.cfg' 153s '/usr/share/augustus/config/species/trichinella/trichinella_parameters.cfg' -> './config/species/trichinella/trichinella_parameters.cfg' 153s '/usr/share/augustus/config/species/trichinella/trichinella_utr_probs.pbl' -> './config/species/trichinella/trichinella_utr_probs.pbl' 153s '/usr/share/augustus/config/species/trichinella/trichinella_weightmatrix.txt' -> './config/species/trichinella/trichinella_weightmatrix.txt' 153s '/usr/share/augustus/config/species/ustilago' -> './config/species/ustilago' 153s '/usr/share/augustus/config/species/ustilago/ustilago_exon_probs.pbl' -> './config/species/ustilago/ustilago_exon_probs.pbl' 153s '/usr/share/augustus/config/species/ustilago/ustilago_igenic_probs.pbl' -> './config/species/ustilago/ustilago_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/ustilago/ustilago_intron_probs.pbl' -> './config/species/ustilago/ustilago_intron_probs.pbl' 153s '/usr/share/augustus/config/species/ustilago/ustilago_parameters.cfg' -> './config/species/ustilago/ustilago_parameters.cfg' 153s '/usr/share/augustus/config/species/ustilago/ustilago_weightmatrix.txt' -> './config/species/ustilago/ustilago_weightmatrix.txt' 153s '/usr/share/augustus/config/species/ustilago_maydis' -> './config/species/ustilago_maydis' 153s '/usr/share/augustus/config/species/ustilago_maydis/ustilago_maydis_exon_probs.pbl' -> './config/species/ustilago_maydis/ustilago_maydis_exon_probs.pbl' 153s '/usr/share/augustus/config/species/ustilago_maydis/ustilago_maydis_igenic_probs.pbl' -> './config/species/ustilago_maydis/ustilago_maydis_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/ustilago_maydis/ustilago_maydis_intron_probs.pbl' -> './config/species/ustilago_maydis/ustilago_maydis_intron_probs.pbl' 153s '/usr/share/augustus/config/species/ustilago_maydis/ustilago_maydis_metapars.cfg' -> './config/species/ustilago_maydis/ustilago_maydis_metapars.cfg' 153s '/usr/share/augustus/config/species/ustilago_maydis/ustilago_maydis_parameters.cfg' -> './config/species/ustilago_maydis/ustilago_maydis_parameters.cfg' 153s '/usr/share/augustus/config/species/ustilago_maydis/ustilago_maydis_weightmatrix.txt' -> './config/species/ustilago_maydis/ustilago_maydis_weightmatrix.txt' 153s '/usr/share/augustus/config/species/verticillium_albo_atrum1' -> './config/species/verticillium_albo_atrum1' 153s '/usr/share/augustus/config/species/verticillium_albo_atrum1/verticillium_albo_atrum1_exon_probs.pbl' -> './config/species/verticillium_albo_atrum1/verticillium_albo_atrum1_exon_probs.pbl' 153s '/usr/share/augustus/config/species/verticillium_albo_atrum1/verticillium_albo_atrum1_igenic_probs.pbl' -> './config/species/verticillium_albo_atrum1/verticillium_albo_atrum1_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/verticillium_albo_atrum1/verticillium_albo_atrum1_intron_probs.pbl' -> './config/species/verticillium_albo_atrum1/verticillium_albo_atrum1_intron_probs.pbl' 153s '/usr/share/augustus/config/species/verticillium_albo_atrum1/verticillium_albo_atrum1_metapars.cfg' -> './config/species/verticillium_albo_atrum1/verticillium_albo_atrum1_metapars.cfg' 153s '/usr/share/augustus/config/species/verticillium_albo_atrum1/verticillium_albo_atrum1_metapars.utr.cfg' -> './config/species/verticillium_albo_atrum1/verticillium_albo_atrum1_metapars.utr.cfg' 153s '/usr/share/augustus/config/species/verticillium_albo_atrum1/verticillium_albo_atrum1_parameters.cfg' -> './config/species/verticillium_albo_atrum1/verticillium_albo_atrum1_parameters.cfg' 153s '/usr/share/augustus/config/species/verticillium_albo_atrum1/verticillium_albo_atrum1_utr_probs.pbl' -> './config/species/verticillium_albo_atrum1/verticillium_albo_atrum1_utr_probs.pbl' 153s '/usr/share/augustus/config/species/verticillium_albo_atrum1/verticillium_albo_atrum1_weightmatrix.txt' -> './config/species/verticillium_albo_atrum1/verticillium_albo_atrum1_weightmatrix.txt' 153s '/usr/share/augustus/config/species/verticillium_longisporum1' -> './config/species/verticillium_longisporum1' 153s '/usr/share/augustus/config/species/verticillium_longisporum1/verticillium_longisporum1_exon_probs.pbl' -> './config/species/verticillium_longisporum1/verticillium_longisporum1_exon_probs.pbl' 153s '/usr/share/augustus/config/species/verticillium_longisporum1/verticillium_longisporum1_igenic_probs.pbl' -> './config/species/verticillium_longisporum1/verticillium_longisporum1_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/verticillium_longisporum1/verticillium_longisporum1_intron_probs.pbl' -> './config/species/verticillium_longisporum1/verticillium_longisporum1_intron_probs.pbl' 153s '/usr/share/augustus/config/species/verticillium_longisporum1/verticillium_longisporum1_metapars.cfg' -> './config/species/verticillium_longisporum1/verticillium_longisporum1_metapars.cfg' 153s '/usr/share/augustus/config/species/verticillium_longisporum1/verticillium_longisporum1_metapars.utr.cfg' -> './config/species/verticillium_longisporum1/verticillium_longisporum1_metapars.utr.cfg' 153s '/usr/share/augustus/config/species/verticillium_longisporum1/verticillium_longisporum1_parameters.cfg' -> './config/species/verticillium_longisporum1/verticillium_longisporum1_parameters.cfg' 153s '/usr/share/augustus/config/species/verticillium_longisporum1/verticillium_longisporum1_parameters.cfg.orig1' -> './config/species/verticillium_longisporum1/verticillium_longisporum1_parameters.cfg.orig1' 153s '/usr/share/augustus/config/species/verticillium_longisporum1/verticillium_longisporum1_utr_probs.pbl' -> './config/species/verticillium_longisporum1/verticillium_longisporum1_utr_probs.pbl' 153s '/usr/share/augustus/config/species/verticillium_longisporum1/verticillium_longisporum1_weightmatrix.txt' -> './config/species/verticillium_longisporum1/verticillium_longisporum1_weightmatrix.txt' 153s '/usr/share/augustus/config/species/volvox' -> './config/species/volvox' 153s '/usr/share/augustus/config/species/volvox/volvox_exon_probs.pbl' -> './config/species/volvox/volvox_exon_probs.pbl' 153s '/usr/share/augustus/config/species/volvox/volvox_igenic_probs.pbl' -> './config/species/volvox/volvox_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/volvox/volvox_intron_probs.pbl' -> './config/species/volvox/volvox_intron_probs.pbl' 153s '/usr/share/augustus/config/species/volvox/volvox_metapars.cfg' -> './config/species/volvox/volvox_metapars.cfg' 153s '/usr/share/augustus/config/species/volvox/volvox_metapars.cgp.cfg' -> './config/species/volvox/volvox_metapars.cgp.cfg' 153s '/usr/share/augustus/config/species/volvox/volvox_metapars.utr.cfg' -> './config/species/volvox/volvox_metapars.utr.cfg' 153s '/usr/share/augustus/config/species/volvox/volvox_parameters.cfg' -> './config/species/volvox/volvox_parameters.cfg' 153s '/usr/share/augustus/config/species/volvox/volvox_utr_probs.pbl' -> './config/species/volvox/volvox_utr_probs.pbl' 153s '/usr/share/augustus/config/species/volvox/volvox_weightmatrix.txt' -> './config/species/volvox/volvox_weightmatrix.txt' 153s '/usr/share/augustus/config/species/wheat' -> './config/species/wheat' 153s '/usr/share/augustus/config/species/wheat/README.txt' -> './config/species/wheat/README.txt' 153s '/usr/share/augustus/config/species/wheat/wheat_exon_probs.pbl' -> './config/species/wheat/wheat_exon_probs.pbl' 153s '/usr/share/augustus/config/species/wheat/wheat_igenic_probs.pbl' -> './config/species/wheat/wheat_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/wheat/wheat_intron_probs.pbl' -> './config/species/wheat/wheat_intron_probs.pbl' 153s '/usr/share/augustus/config/species/wheat/wheat_parameters.cfg' -> './config/species/wheat/wheat_parameters.cfg' 153s '/usr/share/augustus/config/species/wheat/wheat_utr_probs.pbl' -> './config/species/wheat/wheat_utr_probs.pbl' 153s '/usr/share/augustus/config/species/wheat/wheat_weightmatrix.txt' -> './config/species/wheat/wheat_weightmatrix.txt' 153s '/usr/share/augustus/config/species/yarrowia_lipolytica' -> './config/species/yarrowia_lipolytica' 153s '/usr/share/augustus/config/species/yarrowia_lipolytica/yarrowia_lipolytica_exon_probs.pbl' -> './config/species/yarrowia_lipolytica/yarrowia_lipolytica_exon_probs.pbl' 153s '/usr/share/augustus/config/species/yarrowia_lipolytica/yarrowia_lipolytica_igenic_probs.pbl' -> './config/species/yarrowia_lipolytica/yarrowia_lipolytica_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/yarrowia_lipolytica/yarrowia_lipolytica_intron_probs.pbl' -> './config/species/yarrowia_lipolytica/yarrowia_lipolytica_intron_probs.pbl' 153s '/usr/share/augustus/config/species/yarrowia_lipolytica/yarrowia_lipolytica_metapars.cfg' -> './config/species/yarrowia_lipolytica/yarrowia_lipolytica_metapars.cfg' 153s '/usr/share/augustus/config/species/yarrowia_lipolytica/yarrowia_lipolytica_metapars.utr.cfg' -> './config/species/yarrowia_lipolytica/yarrowia_lipolytica_metapars.utr.cfg' 153s '/usr/share/augustus/config/species/yarrowia_lipolytica/yarrowia_lipolytica_parameters.cfg' -> './config/species/yarrowia_lipolytica/yarrowia_lipolytica_parameters.cfg' 153s '/usr/share/augustus/config/species/yarrowia_lipolytica/yarrowia_lipolytica_utr_probs.pbl' -> './config/species/yarrowia_lipolytica/yarrowia_lipolytica_utr_probs.pbl' 153s '/usr/share/augustus/config/species/yarrowia_lipolytica/yarrowia_lipolytica_weightmatrix.txt' -> './config/species/yarrowia_lipolytica/yarrowia_lipolytica_weightmatrix.txt' 153s '/usr/share/augustus/config/species/zebrafish' -> './config/species/zebrafish' 153s '/usr/share/augustus/config/species/zebrafish/README.TXT' -> './config/species/zebrafish/README.TXT' 153s '/usr/share/augustus/config/species/zebrafish/zebrafish_exon_probs.pbl' -> './config/species/zebrafish/zebrafish_exon_probs.pbl' 153s '/usr/share/augustus/config/species/zebrafish/zebrafish_exon_probs.pbl.HMM' -> './config/species/zebrafish/zebrafish_exon_probs.pbl.HMM' 153s '/usr/share/augustus/config/species/zebrafish/zebrafish_igenic_probs.pbl' -> './config/species/zebrafish/zebrafish_igenic_probs.pbl' 153s '/usr/share/augustus/config/species/zebrafish/zebrafish_igenic_probs.pbl.HMM' -> './config/species/zebrafish/zebrafish_igenic_probs.pbl.HMM' 153s '/usr/share/augustus/config/species/zebrafish/zebrafish_intron_probs.pbl' -> './config/species/zebrafish/zebrafish_intron_probs.pbl' 153s '/usr/share/augustus/config/species/zebrafish/zebrafish_intron_probs.pbl.HMM' -> './config/species/zebrafish/zebrafish_intron_probs.pbl.HMM' 153s '/usr/share/augustus/config/species/zebrafish/zebrafish_metapars.cfg' -> './config/species/zebrafish/zebrafish_metapars.cfg' 153s '/usr/share/augustus/config/species/zebrafish/zebrafish_metapars.utr.cfg' -> './config/species/zebrafish/zebrafish_metapars.utr.cfg' 153s '/usr/share/augustus/config/species/zebrafish/zebrafish_parameters.cfg' -> './config/species/zebrafish/zebrafish_parameters.cfg' 153s '/usr/share/augustus/config/species/zebrafish/zebrafish_weightmatrix.txt' -> './config/species/zebrafish/zebrafish_weightmatrix.txt' 153s Will create parameters for a EUKARYOTIC species! 153s creating directory /tmp/tmp.q1M0E6hrua/config/species/test/ ... 153s creating /tmp/tmp.q1M0E6hrua/config/species/test/test_parameters.cfg ... 153s creating /tmp/tmp.q1M0E6hrua/config/species/test/test_weightmatrix.txt ... 153s creating /tmp/tmp.q1M0E6hrua/config/species/test/test_metapars.cfg ... 153s The necessary files for training test have been created. 153s Now, either run etraining or optimize_parameters.pl with --species=test. 153s etraining quickly estimates the parameters from a file with training genes. 153s optimize_augustus.pl alternates running etraining and augustus to find optimal metaparameters. 153s 153s # Read in 1 genbank sequences. 153s Quantiles of the GC contents in the training set: 153s 0% 0.402 153s 5% 0.402 10% 0.402 153s 15% 0.402 20% 0.402 153s 25% 0.402 30% 0.402 153s 35% 0.402 40% 0.402 153s 45% 0.402 50% 0.402 153s 55% 0.402 60% 0.402 153s 65% 0.402 70% 0.402 153s 75% 0.402 80% 0.402 153s 85% 0.402 90% 0.402 153s 95% 0.402 100% 0.402 153s HMM-training the parameters... 153s i= 0 bc= (0.237, 0.263, 0.263, 0.237) 153s ** building model for exons *EXON* 153s start codon frequencies: ATG(1) 153s # admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0) 153s number of bases in the reading frames: 570 571 570 153s --- frame = 0 --- minPatSum = 233 153s --- frame = 1 --- minPatSum = 233 153s --- frame = 2 --- minPatSum = 233 153s --- initial frame = 0 --- minPatSum = 233 153s --- initial frame = 1 --- minPatSum = 233 153s --- initial frame = 2 --- minPatSum = 233 153s --- internal exon terminal frame = 0 --- minPatSum = 233 153s --- internal exon terminal frame = 1 --- minPatSum = 233 153s --- internal exon terminal frame = 2 --- minPatSum = 233 153s single, initial, internal, terminal mean exon lengths : 153s n.a. 627 191 7 153s single exon : 0 153s initial exon 0 : 1 153s initial exon 1 : 0 153s initial exon 2 : 0 153s internal exon 0 : 3 153s internal exon 1 : 0 153s internal exon 2 : 3 153s terminal exon : 1 153s Frequency of stop codons: 153s tag: 0 (0) 153s taa: 1 (1) 153s tga: 0 (0) 153s end *EXON* 153s Storing parameters to file... 153s Writing exon model parameters [1] to file /tmp/tmp.q1M0E6hrua/config/species/test/test_exon_probs.pbl. 153s # This output was generated with AUGUSTUS (version 3.5.0). 153s # AUGUSTUS is a gene prediction tool written by M. Stanke (mario.stanke@uni-greifswald.de), 153s # O. Keller, S. König, L. Gerischer, L. Romoth, Katharina Hoff, Henry Mehlan and Daniel Honsel. 153s # Please cite: Mario Stanke, Mark Diekhans, Robert Baertsch, David Haussler (2008), 153s # Using native and syntenically mapped cDNA alignments to improve de novo gene finding 153s # Bioinformatics 24: 637-644, doi 10.1093/bioinformatics/btn013 153s # No extrinsic information on sequences given. 153s # Sources of extrinsic information: M RM 153s # Initializing the parameters using config directory /tmp/tmp.q1M0E6hrua/config/ ... 153s # test version. Using default transition matrix. 153s # admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0) 153s # Looks like /tmp/autopkgtest.axahEj/build.6tW/src/examples/example.fa is in fasta format. 153s # We have hints for 0 sequences and for 0 of the sequences in the input set. 153s # 153s # ----- prediction on sequence number 1 (length = 9453, name = HS04636) ----- 153s # 153s # Predicted genes for sequence number 1 on both strands 153s # start gene g1 153s HS04636 AUGUSTUS gene 1 1163 0.06 + . g1 153s HS04636 AUGUSTUS transcript 1 1163 0.06 + . g1.t1 153s HS04636 AUGUSTUS intron 1 350 0.36 + . transcript_id "g1.t1"; gene_id "g1"; 153s HS04636 AUGUSTUS intron 673 856 0.17 + . transcript_id "g1.t1"; gene_id "g1"; 153s HS04636 AUGUSTUS CDS 351 672 0.11 + 2 transcript_id "g1.t1"; gene_id "g1"; 153s HS04636 AUGUSTUS CDS 857 1163 0.32 + 1 transcript_id "g1.t1"; gene_id "g1"; 153s HS04636 AUGUSTUS stop_codon 1161 1163 . + 0 transcript_id "g1.t1"; gene_id "g1"; 153s # protein sequence = [VQTRHGGGGGRGDSLRPRTSGPLRFLERKPSVLLPSPGIPSKAISPELALGSARAKTAKKKRHLAETCAPGAVELGEE 153s # REGSDRRVGTTPSAPKLGQLPGFPIFSFPVRSTSRNSSAAPPSAPQPDALRQQSLPPRRALPAARMLARALLLCAVLALSHTGEYLAPRTGDSGSTHP 153s # GRVSALTSWVYPSTPTSLRIEKLRDLGKSLDR] 153s # Evidence for and against this transcript: 153s # % of transcript supported by hints (any source): 0 153s # CDS exons: 0/2 153s # CDS introns: 0/2 153s # 5'UTR exons and introns: 0/0 153s # 3'UTR exons and introns: 0/0 153s # hint groups fully obeyed: 0 153s # incompatible hint groups: 0 153s # end gene g1 153s ### 153s # 153s # ----- prediction on sequence number 2 (length = 2344, name = HS08198) ----- 153s # 153s # Predicted genes for sequence number 2 on both strands 154s # start gene g2 154s HS08198 AUGUSTUS gene 1 2271 0.02 - . g2 154s HS08198 AUGUSTUS transcript 1 2271 0.02 - . g2.t1 154s HS08198 AUGUSTUS intron 1 112 0.38 - . transcript_id "g2.t1"; gene_id "g2"; 154s HS08198 AUGUSTUS intron 950 1314 0.05 - . transcript_id "g2.t1"; gene_id "g2"; 154s HS08198 AUGUSTUS intron 2041 2116 0.39 - . transcript_id "g2.t1"; gene_id "g2"; 154s HS08198 AUGUSTUS CDS 113 949 0.16 - 1 transcript_id "g2.t1"; gene_id "g2"; 154s HS08198 AUGUSTUS CDS 1315 2040 0.26 - 1 transcript_id "g2.t1"; gene_id "g2"; 154s HS08198 AUGUSTUS CDS 2117 2271 0.39 - 0 transcript_id "g2.t1"; gene_id "g2"; 154s HS08198 AUGUSTUS start_codon 2269 2271 . - 0 transcript_id "g2.t1"; gene_id "g2"; 154s # protein sequence = [MAYAREDLPSQIPRAEIGPVTLRGLQPTGSAGLLKRRGGGREGLGGTGAGPDRQKIPCPGWQGPDLRLVSRRTGSGHP 154s # TGGVVSRGTDFSALELCAGLTSSLLQQRRDSAGASGPPHHAAMLAPAVHSPSRTWNWSAASQKPGAPRQGSGWTSAREWGWLSWGPAGDTHRTWGSRR 154s # SGPQSGGPPGPAAQTHSGPSRSQGASGLQGRQGSWGPGTRRRGGLWERGLCVPCPSGPSSLLPHQACLSLLPGPLLSRRIRMGERKCVPMAHPAPRGG 154s # PVSVQSLSACLVTEAGPHIPPGAERRVGVRVQGCSGTHSFRKVLTAMAVPWGATCSVVASARWPCSCRKRQAEPTATRSQVPANWGQTMGELEGTVGG 154s # PLTCFPLHPPQLHLLPSPPQQLLPVSLYPSHNFYLPPSTPPNFYLLRIKIGLGLDGADGGCGPAWPLRLLAQRASCQEQSQEGRSPRGQHGGGSRVAG 154s # LWEAKGSTTKSQDRVYSAVTEPSPGSPCPSVASPPPTSSLLVSLASICTSWQGLAPCPMYKVRVDLWLFIHFSCTPDFHRQSLALYTLSSLNHHPVVL 154s # SPWP] 154s # Evidence for and against this transcript: 154s # % of transcript supported by hints (any source): 0 154s # CDS exons: 0/3 154s # CDS introns: 0/3 154s # 5'UTR exons and introns: 0/0 154s # 3'UTR exons and introns: 0/0 154s # hint groups fully obeyed: 0 154s # incompatible hint groups: 0 154s # end gene g2 154s ### 154s # command line: 154s # augustus --species=test /tmp/autopkgtest.axahEj/build.6tW/src/examples/example.fa 154s autopkgtest [01:16:07]: test test-example-with-training: -----------------------] 154s test-example-with-training PASS 154s autopkgtest [01:16:07]: test test-example-with-training: - - - - - - - - - - results - - - - - - - - - - 155s autopkgtest [01:16:08]: @@@@@@@@@@@@@@@@@@@@ summary 155s test-example PASS 155s test-example-with-training PASS