0s autopkgtest [16:52:11]: starting date and time: 2025-03-15 16:52:11+0000 0s autopkgtest [16:52:11]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [16:52:11]: host juju-7f2275-prod-proposed-migration-environment-9; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.6m0tjvj6/out --timeout-copy=6000 --setup-commands 'ln -s /dev/null /etc/systemd/system/bluetooth.service; printf "http_proxy=http://squid.internal:3128\nhttps_proxy=http://squid.internal:3128\nno_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com,radosgw.ps5.canonical.com\n" >> /etc/environment' --apt-pocket=proposed=src:glibc --apt-upgrade reapr --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=glibc/2.41-1ubuntu2 -- lxd -r lxd-armhf-10.145.243.85 lxd-armhf-10.145.243.85:autopkgtest/ubuntu/plucky/armhf 21s autopkgtest [16:52:32]: testbed dpkg architecture: armhf 23s autopkgtest [16:52:34]: testbed apt version: 2.9.33 27s autopkgtest [16:52:38]: @@@@@@@@@@@@@@@@@@@@ test bed setup 29s autopkgtest [16:52:40]: testbed release detected to be: None 37s autopkgtest [16:52:47]: updating testbed package index (apt update) 38s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 39s Get:2 http://ftpmaster.internal/ubuntu plucky InRelease [257 kB] 39s Get:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease [126 kB] 39s Get:4 http://ftpmaster.internal/ubuntu plucky-security InRelease [126 kB] 39s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [99.7 kB] 40s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.8 kB] 40s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [379 kB] 40s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf Packages [114 kB] 40s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf c-n-f Metadata [1832 B] 40s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted armhf c-n-f Metadata [116 B] 40s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf Packages [312 kB] 40s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf c-n-f Metadata [11.1 kB] 40s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse armhf Packages [3472 B] 40s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse armhf c-n-f Metadata [240 B] 40s Get:15 http://ftpmaster.internal/ubuntu plucky/multiverse Sources [299 kB] 41s Get:16 http://ftpmaster.internal/ubuntu plucky/main Sources [1394 kB] 43s Get:17 http://ftpmaster.internal/ubuntu plucky/universe Sources [21.0 MB] 65s Get:18 http://ftpmaster.internal/ubuntu plucky/main armhf Packages [1378 kB] 66s Get:19 http://ftpmaster.internal/ubuntu plucky/main armhf c-n-f Metadata [29.4 kB] 66s Get:20 http://ftpmaster.internal/ubuntu plucky/restricted armhf c-n-f Metadata [108 B] 66s Get:21 http://ftpmaster.internal/ubuntu plucky/universe armhf Packages [15.1 MB] 83s Get:22 http://ftpmaster.internal/ubuntu plucky/multiverse armhf Packages [172 kB] 85s Fetched 41.0 MB in 46s (890 kB/s) 86s Reading package lists... 91s autopkgtest [16:53:42]: upgrading testbed (apt dist-upgrade and autopurge) 93s Reading package lists... 94s Building dependency tree... 94s Reading state information... 95s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 95s Starting 2 pkgProblemResolver with broken count: 0 95s Done 96s Entering ResolveByKeep 97s 97s Calculating upgrade... 98s The following packages will be upgraded: 98s libc-bin libc6 locales pinentry-curses python3-jinja2 sos strace 98s 7 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 98s Need to get 8683 kB of archives. 98s After this operation, 23.6 kB of additional disk space will be used. 98s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf libc6 armhf 2.41-1ubuntu2 [2932 kB] 102s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf libc-bin armhf 2.41-1ubuntu2 [545 kB] 102s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf locales all 2.41-1ubuntu2 [4246 kB] 107s Get:4 http://ftpmaster.internal/ubuntu plucky/main armhf strace armhf 6.13+ds-1ubuntu1 [445 kB] 107s Get:5 http://ftpmaster.internal/ubuntu plucky/main armhf pinentry-curses armhf 1.3.1-2ubuntu3 [40.6 kB] 107s Get:6 http://ftpmaster.internal/ubuntu plucky/main armhf python3-jinja2 all 3.1.5-2ubuntu1 [109 kB] 107s Get:7 http://ftpmaster.internal/ubuntu plucky/main armhf sos all 4.9.0-5 [365 kB] 108s Preconfiguring packages ... 109s Fetched 8683 kB in 10s (889 kB/s) 109s (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 ... 64655 files and directories currently installed.) 109s Preparing to unpack .../libc6_2.41-1ubuntu2_armhf.deb ... 109s Unpacking libc6:armhf (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 109s Setting up libc6:armhf (2.41-1ubuntu2) ... 110s (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 ... 64655 files and directories currently installed.) 110s Preparing to unpack .../libc-bin_2.41-1ubuntu2_armhf.deb ... 110s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 110s Setting up libc-bin (2.41-1ubuntu2) ... 110s (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 ... 64655 files and directories currently installed.) 110s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ... 110s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 110s Preparing to unpack .../strace_6.13+ds-1ubuntu1_armhf.deb ... 110s Unpacking strace (6.13+ds-1ubuntu1) over (6.11-0ubuntu1) ... 111s Preparing to unpack .../pinentry-curses_1.3.1-2ubuntu3_armhf.deb ... 111s Unpacking pinentry-curses (1.3.1-2ubuntu3) over (1.3.1-2ubuntu2) ... 111s Preparing to unpack .../python3-jinja2_3.1.5-2ubuntu1_all.deb ... 111s Unpacking python3-jinja2 (3.1.5-2ubuntu1) over (3.1.5-2) ... 111s Preparing to unpack .../archives/sos_4.9.0-5_all.deb ... 113s Unpacking sos (4.9.0-5) over (4.9.0-4) ... 113s Setting up sos (4.9.0-5) ... 113s Setting up pinentry-curses (1.3.1-2ubuntu3) ... 113s Setting up locales (2.41-1ubuntu2) ... 114s Generating locales (this might take a while)... 117s en_US.UTF-8... done 117s Generation complete. 117s Setting up python3-jinja2 (3.1.5-2ubuntu1) ... 117s Setting up strace (6.13+ds-1ubuntu1) ... 117s Processing triggers for man-db (2.13.0-1) ... 118s Processing triggers for systemd (257.3-1ubuntu3) ... 121s Reading package lists... 122s Building dependency tree... 122s Reading state information... 123s Starting pkgProblemResolver with broken count: 0 123s Starting 2 pkgProblemResolver with broken count: 0 123s Done 124s Solving dependencies... 125s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 127s autopkgtest [16:54:18]: rebooting testbed after setup commands that affected boot 167s autopkgtest [16:54:58]: testbed running kernel: Linux 6.8.0-52-generic #53~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Wed Jan 15 18:10:51 UTC 2 192s autopkgtest [16:55:23]: @@@@@@@@@@@@@@@@@@@@ apt-source reapr 203s Get:1 http://ftpmaster.internal/ubuntu plucky/universe reapr 1.0.18+dfsg-7 (dsc) [2160 B] 203s Get:2 http://ftpmaster.internal/ubuntu plucky/universe reapr 1.0.18+dfsg-7 (tar) [74.6 kB] 203s Get:3 http://ftpmaster.internal/ubuntu plucky/universe reapr 1.0.18+dfsg-7 (diff) [320 kB] 203s gpgv: Signature made Sat Dec 21 22:15:37 2024 UTC 203s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 203s gpgv: issuer "tille@debian.org" 203s gpgv: Can't check signature: No public key 203s dpkg-source: warning: cannot verify inline signature for ./reapr_1.0.18+dfsg-7.dsc: no acceptable signature found 203s autopkgtest [16:55:34]: testing package reapr version 1.0.18+dfsg-7 205s autopkgtest [16:55:36]: build not needed 207s autopkgtest [16:55:38]: test test-example: preparing testbed 209s Reading package lists... 209s Building dependency tree... 209s Reading state information... 210s Starting pkgProblemResolver with broken count: 0 210s Starting 2 pkgProblemResolver with broken count: 0 210s Done 212s The following NEW packages will be installed: 212s bamtools fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono 212s libbambamc0 libbamtools2.5.2 libblas3 libcairo2 libdatrie1 libdeflate0 212s libfile-copy-link-perl libfontconfig1 libfreetype6 libgfortran5 libgomp1 212s libgraphite2-3 libharfbuzz0b libhts3t64 libhtscodecs2 libice6 libjbig0 212s libjpeg-turbo8 libjpeg8 libjsoncpp26 liblapack3 liblerc4 libpango-1.0-0 212s libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper2 libpixman-1-0 212s libsharpyuv0 libsm6 libtabixpp0t64 libtcl8.6 libthai-data libthai0 libtiff6 212s libtk8.6 libwebp7 libxcb-render0 libxcb-shm0 libxft2 libxrender1 libxss1 212s libxt6t64 r-base r-base-core r-cran-boot r-cran-class r-cran-cluster 212s r-cran-codetools r-cran-foreign r-cran-kernsmooth r-cran-lattice r-cran-mass 212s r-cran-matrix r-cran-mgcv r-cran-nlme r-cran-nnet r-cran-rpart 212s r-cran-spatial r-cran-survival r-recommended reapr samtools smalt snpomatic 212s tabix unzip x11-common xdg-utils zip 212s 0 upgraded, 75 newly installed, 0 to remove and 0 not upgraded. 212s Need to get 62.8 MB of archives. 212s After this operation, 108 MB of additional disk space will be used. 212s Get:1 http://ftpmaster.internal/ubuntu plucky/universe armhf libbamtools2.5.2 armhf 2.5.2+dfsg-6build1 [154 kB] 212s Get:2 http://ftpmaster.internal/ubuntu plucky/main armhf libjsoncpp26 armhf 1.9.6-3 [75.5 kB] 212s Get:3 http://ftpmaster.internal/ubuntu plucky/universe armhf bamtools armhf 2.5.2+dfsg-6build1 [197 kB] 213s Get:4 http://ftpmaster.internal/ubuntu plucky/main armhf libfreetype6 armhf 2.13.3+dfsg-1 [330 kB] 213s Get:5 http://ftpmaster.internal/ubuntu plucky/main armhf fonts-dejavu-mono all 2.37-8 [502 kB] 214s Get:6 http://ftpmaster.internal/ubuntu plucky/main armhf fonts-dejavu-core all 2.37-8 [835 kB] 215s Get:7 http://ftpmaster.internal/ubuntu plucky/main armhf fontconfig-config armhf 2.15.0-2ubuntu1 [37.5 kB] 215s Get:8 http://ftpmaster.internal/ubuntu plucky/main armhf libfontconfig1 armhf 2.15.0-2ubuntu1 [114 kB] 215s Get:9 http://ftpmaster.internal/ubuntu plucky/main armhf fontconfig armhf 2.15.0-2ubuntu1 [190 kB] 215s Get:10 http://ftpmaster.internal/ubuntu plucky/universe armhf libbambamc0 armhf 0.0.50-6build1 [34.1 kB] 215s Get:11 http://ftpmaster.internal/ubuntu plucky/main armhf libblas3 armhf 3.12.1-2 [132 kB] 215s Get:12 http://ftpmaster.internal/ubuntu plucky/main armhf libpixman-1-0 armhf 0.44.0-3 [183 kB] 215s Get:13 http://ftpmaster.internal/ubuntu plucky/main armhf libxcb-render0 armhf 1.17.0-2 [15.3 kB] 215s Get:14 http://ftpmaster.internal/ubuntu plucky/main armhf libxcb-shm0 armhf 1.17.0-2 [5774 B] 215s Get:15 http://ftpmaster.internal/ubuntu plucky/main armhf libxrender1 armhf 1:0.9.10-1.1build1 [16.0 kB] 215s Get:16 http://ftpmaster.internal/ubuntu plucky/main armhf libcairo2 armhf 1.18.2-2 [484 kB] 216s Get:17 http://ftpmaster.internal/ubuntu plucky/main armhf libdatrie1 armhf 0.2.13-3build1 [15.7 kB] 216s Get:18 http://ftpmaster.internal/ubuntu plucky/main armhf libdeflate0 armhf 1.23-1 [38.5 kB] 216s Get:19 http://ftpmaster.internal/ubuntu plucky/universe armhf libfile-copy-link-perl all 0.200-1 [12.8 kB] 216s Get:20 http://ftpmaster.internal/ubuntu plucky/main armhf libgfortran5 armhf 15-20250222-0ubuntu1 [330 kB] 216s Get:21 http://ftpmaster.internal/ubuntu plucky/main armhf libgomp1 armhf 15-20250222-0ubuntu1 [128 kB] 217s Get:22 http://ftpmaster.internal/ubuntu plucky/main armhf libgraphite2-3 armhf 1.3.14-2ubuntu1 [64.8 kB] 217s Get:23 http://ftpmaster.internal/ubuntu plucky/main armhf libharfbuzz0b armhf 10.2.0-1 [464 kB] 217s Get:24 http://ftpmaster.internal/ubuntu plucky/universe armhf libhtscodecs2 armhf 1.6.1-2 [67.5 kB] 217s Get:25 http://ftpmaster.internal/ubuntu plucky/universe armhf libhts3t64 armhf 1.21+ds-1 [399 kB] 218s Get:26 http://ftpmaster.internal/ubuntu plucky/main armhf x11-common all 1:7.7+23ubuntu3 [21.7 kB] 218s Get:27 http://ftpmaster.internal/ubuntu plucky/main armhf libice6 armhf 2:1.1.1-1 [36.5 kB] 218s Get:28 http://ftpmaster.internal/ubuntu plucky/main armhf libjpeg-turbo8 armhf 2.1.5-3ubuntu2 [127 kB] 218s Get:29 http://ftpmaster.internal/ubuntu plucky/main armhf libjpeg8 armhf 8c-2ubuntu11 [2148 B] 218s Get:30 http://ftpmaster.internal/ubuntu plucky/main armhf liblapack3 armhf 3.12.1-2 [2091 kB] 220s Get:31 http://ftpmaster.internal/ubuntu plucky/main armhf liblerc4 armhf 4.0.0+ds-5ubuntu1 [160 kB] 220s Get:32 http://ftpmaster.internal/ubuntu plucky/main armhf libthai-data all 0.1.29-2build1 [158 kB] 221s Get:33 http://ftpmaster.internal/ubuntu plucky/main armhf libthai0 armhf 0.1.29-2build1 [15.2 kB] 221s Get:34 http://ftpmaster.internal/ubuntu plucky/main armhf libpango-1.0-0 armhf 1.56.2-1 [216 kB] 221s Get:35 http://ftpmaster.internal/ubuntu plucky/main armhf libpangoft2-1.0-0 armhf 1.56.2-1 [43.6 kB] 221s Get:36 http://ftpmaster.internal/ubuntu plucky/main armhf libpangocairo-1.0-0 armhf 1.56.2-1 [25.1 kB] 221s Get:37 http://ftpmaster.internal/ubuntu plucky/main armhf libpaper2 armhf 2.2.5-0.3 [16.3 kB] 221s Get:38 http://ftpmaster.internal/ubuntu plucky/main armhf libpaper-utils armhf 2.2.5-0.3 [14.2 kB] 221s Get:39 http://ftpmaster.internal/ubuntu plucky/main armhf libsharpyuv0 armhf 1.5.0-0.1 [16.4 kB] 221s Get:40 http://ftpmaster.internal/ubuntu plucky/main armhf libsm6 armhf 2:1.2.4-1 [15.1 kB] 221s Get:41 http://ftpmaster.internal/ubuntu plucky/universe armhf libtabixpp0t64 armhf 1.1.2-2.1build1 [9456 B] 221s Get:42 http://ftpmaster.internal/ubuntu plucky/main armhf libtcl8.6 armhf 8.6.16+dfsg-1 [909 kB] 222s Get:43 http://ftpmaster.internal/ubuntu plucky/main armhf libjbig0 armhf 2.1-6.1ubuntu2 [24.9 kB] 222s Get:44 http://ftpmaster.internal/ubuntu plucky/main armhf libwebp7 armhf 1.5.0-0.1 [188 kB] 222s Get:45 http://ftpmaster.internal/ubuntu plucky/main armhf libtiff6 armhf 4.5.1+git230720-4ubuntu4 [179 kB] 223s Get:46 http://ftpmaster.internal/ubuntu plucky/main armhf libxft2 armhf 2.3.6-1build1 [37.4 kB] 223s Get:47 http://ftpmaster.internal/ubuntu plucky/main armhf libxss1 armhf 1:1.2.3-1build3 [6500 B] 223s Get:48 http://ftpmaster.internal/ubuntu plucky/main armhf libtk8.6 armhf 8.6.16-1 [686 kB] 224s Get:49 http://ftpmaster.internal/ubuntu plucky/main armhf libxt6t64 armhf 1:1.2.1-1.2build1 [145 kB] 224s Get:50 http://ftpmaster.internal/ubuntu plucky/main armhf zip armhf 3.0-14ubuntu2 [164 kB] 224s Get:51 http://ftpmaster.internal/ubuntu plucky/main armhf unzip armhf 6.0-28ubuntu6 [167 kB] 224s Get:52 http://ftpmaster.internal/ubuntu plucky/main armhf xdg-utils all 1.2.1-2ubuntu1 [66.0 kB] 224s Get:53 http://ftpmaster.internal/ubuntu plucky/universe armhf r-base-core armhf 4.4.3-1 [28.2 MB] 256s Get:54 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-boot all 1.3-31-1 [635 kB] 256s Get:55 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-cluster armhf 2.1.8-1 [563 kB] 257s Get:56 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-foreign armhf 0.8.88-1 [240 kB] 257s Get:57 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-mass armhf 7.3-64-1 [1105 kB] 258s Get:58 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-kernsmooth armhf 2.23-26-1 [91.6 kB] 258s Get:59 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-lattice armhf 0.22-6-1 [1363 kB] 260s Get:60 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-nlme armhf 3.1.167-1 [2306 kB] 262s Get:61 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-matrix armhf 1.7-3-1 [4039 kB] 267s Get:62 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-mgcv armhf 1.9-1-1 [3205 kB] 270s Get:63 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-survival armhf 3.8-3-1 [8196 kB] 280s Get:64 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-rpart armhf 4.1.24-1 [661 kB] 280s Get:65 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-class armhf 7.3-23-1 [88.8 kB] 281s Get:66 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-nnet armhf 7.3-20-1 [111 kB] 281s Get:67 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-spatial armhf 7.3-18-1 [131 kB] 281s Get:68 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-codetools all 0.2-20-1 [90.5 kB] 281s Get:69 http://ftpmaster.internal/ubuntu plucky/universe armhf r-recommended all 4.4.3-1 [2630 B] 281s Get:70 http://ftpmaster.internal/ubuntu plucky/universe armhf r-base all 4.4.3-1 [9290 B] 281s Get:71 http://ftpmaster.internal/ubuntu plucky/universe armhf samtools armhf 1.21-1 [619 kB] 282s Get:72 http://ftpmaster.internal/ubuntu plucky/universe armhf smalt armhf 0.7.6-13 [106 kB] 282s Get:73 http://ftpmaster.internal/ubuntu plucky/universe armhf snpomatic armhf 1.0-7 [82.9 kB] 282s Get:74 http://ftpmaster.internal/ubuntu plucky/universe armhf tabix armhf 1.21+ds-1 [433 kB] 282s Get:75 http://ftpmaster.internal/ubuntu plucky/universe armhf reapr armhf 1.0.18+dfsg-7 [198 kB] 283s Preconfiguring packages ... 283s Fetched 62.8 MB in 1min 11s (886 kB/s) 283s Selecting previously unselected package libbamtools2.5.2:armhf. 284s (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 ... 64655 files and directories currently installed.) 284s Preparing to unpack .../00-libbamtools2.5.2_2.5.2+dfsg-6build1_armhf.deb ... 284s Unpacking libbamtools2.5.2:armhf (2.5.2+dfsg-6build1) ... 284s Selecting previously unselected package libjsoncpp26:armhf. 284s Preparing to unpack .../01-libjsoncpp26_1.9.6-3_armhf.deb ... 284s Unpacking libjsoncpp26:armhf (1.9.6-3) ... 284s Selecting previously unselected package bamtools. 284s Preparing to unpack .../02-bamtools_2.5.2+dfsg-6build1_armhf.deb ... 284s Unpacking bamtools (2.5.2+dfsg-6build1) ... 284s Selecting previously unselected package libfreetype6:armhf. 284s Preparing to unpack .../03-libfreetype6_2.13.3+dfsg-1_armhf.deb ... 284s Unpacking libfreetype6:armhf (2.13.3+dfsg-1) ... 284s Selecting previously unselected package fonts-dejavu-mono. 284s Preparing to unpack .../04-fonts-dejavu-mono_2.37-8_all.deb ... 284s Unpacking fonts-dejavu-mono (2.37-8) ... 284s Selecting previously unselected package fonts-dejavu-core. 284s Preparing to unpack .../05-fonts-dejavu-core_2.37-8_all.deb ... 284s Unpacking fonts-dejavu-core (2.37-8) ... 284s Selecting previously unselected package fontconfig-config. 284s Preparing to unpack .../06-fontconfig-config_2.15.0-2ubuntu1_armhf.deb ... 284s Unpacking fontconfig-config (2.15.0-2ubuntu1) ... 284s Selecting previously unselected package libfontconfig1:armhf. 284s Preparing to unpack .../07-libfontconfig1_2.15.0-2ubuntu1_armhf.deb ... 284s Unpacking libfontconfig1:armhf (2.15.0-2ubuntu1) ... 284s Selecting previously unselected package fontconfig. 284s Preparing to unpack .../08-fontconfig_2.15.0-2ubuntu1_armhf.deb ... 284s Unpacking fontconfig (2.15.0-2ubuntu1) ... 284s Selecting previously unselected package libbambamc0:armhf. 284s Preparing to unpack .../09-libbambamc0_0.0.50-6build1_armhf.deb ... 284s Unpacking libbambamc0:armhf (0.0.50-6build1) ... 284s Selecting previously unselected package libblas3:armhf. 284s Preparing to unpack .../10-libblas3_3.12.1-2_armhf.deb ... 284s Unpacking libblas3:armhf (3.12.1-2) ... 284s Selecting previously unselected package libpixman-1-0:armhf. 284s Preparing to unpack .../11-libpixman-1-0_0.44.0-3_armhf.deb ... 284s Unpacking libpixman-1-0:armhf (0.44.0-3) ... 284s Selecting previously unselected package libxcb-render0:armhf. 284s Preparing to unpack .../12-libxcb-render0_1.17.0-2_armhf.deb ... 284s Unpacking libxcb-render0:armhf (1.17.0-2) ... 284s Selecting previously unselected package libxcb-shm0:armhf. 284s Preparing to unpack .../13-libxcb-shm0_1.17.0-2_armhf.deb ... 284s Unpacking libxcb-shm0:armhf (1.17.0-2) ... 285s Selecting previously unselected package libxrender1:armhf. 285s Preparing to unpack .../14-libxrender1_1%3a0.9.10-1.1build1_armhf.deb ... 285s Unpacking libxrender1:armhf (1:0.9.10-1.1build1) ... 285s Selecting previously unselected package libcairo2:armhf. 285s Preparing to unpack .../15-libcairo2_1.18.2-2_armhf.deb ... 285s Unpacking libcairo2:armhf (1.18.2-2) ... 285s Selecting previously unselected package libdatrie1:armhf. 285s Preparing to unpack .../16-libdatrie1_0.2.13-3build1_armhf.deb ... 285s Unpacking libdatrie1:armhf (0.2.13-3build1) ... 285s Selecting previously unselected package libdeflate0:armhf. 285s Preparing to unpack .../17-libdeflate0_1.23-1_armhf.deb ... 285s Unpacking libdeflate0:armhf (1.23-1) ... 285s Selecting previously unselected package libfile-copy-link-perl. 285s Preparing to unpack .../18-libfile-copy-link-perl_0.200-1_all.deb ... 285s Unpacking libfile-copy-link-perl (0.200-1) ... 285s Selecting previously unselected package libgfortran5:armhf. 285s Preparing to unpack .../19-libgfortran5_15-20250222-0ubuntu1_armhf.deb ... 285s Unpacking libgfortran5:armhf (15-20250222-0ubuntu1) ... 285s Selecting previously unselected package libgomp1:armhf. 285s Preparing to unpack .../20-libgomp1_15-20250222-0ubuntu1_armhf.deb ... 285s Unpacking libgomp1:armhf (15-20250222-0ubuntu1) ... 285s Selecting previously unselected package libgraphite2-3:armhf. 285s Preparing to unpack .../21-libgraphite2-3_1.3.14-2ubuntu1_armhf.deb ... 285s Unpacking libgraphite2-3:armhf (1.3.14-2ubuntu1) ... 285s Selecting previously unselected package libharfbuzz0b:armhf. 285s Preparing to unpack .../22-libharfbuzz0b_10.2.0-1_armhf.deb ... 285s Unpacking libharfbuzz0b:armhf (10.2.0-1) ... 285s Selecting previously unselected package libhtscodecs2:armhf. 285s Preparing to unpack .../23-libhtscodecs2_1.6.1-2_armhf.deb ... 285s Unpacking libhtscodecs2:armhf (1.6.1-2) ... 285s Selecting previously unselected package libhts3t64:armhf. 285s Preparing to unpack .../24-libhts3t64_1.21+ds-1_armhf.deb ... 285s Unpacking libhts3t64:armhf (1.21+ds-1) ... 285s Selecting previously unselected package x11-common. 285s Preparing to unpack .../25-x11-common_1%3a7.7+23ubuntu3_all.deb ... 285s Unpacking x11-common (1:7.7+23ubuntu3) ... 285s Selecting previously unselected package libice6:armhf. 285s Preparing to unpack .../26-libice6_2%3a1.1.1-1_armhf.deb ... 285s Unpacking libice6:armhf (2:1.1.1-1) ... 285s Selecting previously unselected package libjpeg-turbo8:armhf. 285s Preparing to unpack .../27-libjpeg-turbo8_2.1.5-3ubuntu2_armhf.deb ... 285s Unpacking libjpeg-turbo8:armhf (2.1.5-3ubuntu2) ... 285s Selecting previously unselected package libjpeg8:armhf. 285s Preparing to unpack .../28-libjpeg8_8c-2ubuntu11_armhf.deb ... 285s Unpacking libjpeg8:armhf (8c-2ubuntu11) ... 285s Selecting previously unselected package liblapack3:armhf. 285s Preparing to unpack .../29-liblapack3_3.12.1-2_armhf.deb ... 285s Unpacking liblapack3:armhf (3.12.1-2) ... 285s Selecting previously unselected package liblerc4:armhf. 285s Preparing to unpack .../30-liblerc4_4.0.0+ds-5ubuntu1_armhf.deb ... 285s Unpacking liblerc4:armhf (4.0.0+ds-5ubuntu1) ... 285s Selecting previously unselected package libthai-data. 285s Preparing to unpack .../31-libthai-data_0.1.29-2build1_all.deb ... 285s Unpacking libthai-data (0.1.29-2build1) ... 285s Selecting previously unselected package libthai0:armhf. 285s Preparing to unpack .../32-libthai0_0.1.29-2build1_armhf.deb ... 285s Unpacking libthai0:armhf (0.1.29-2build1) ... 285s Selecting previously unselected package libpango-1.0-0:armhf. 285s Preparing to unpack .../33-libpango-1.0-0_1.56.2-1_armhf.deb ... 285s Unpacking libpango-1.0-0:armhf (1.56.2-1) ... 286s Selecting previously unselected package libpangoft2-1.0-0:armhf. 286s Preparing to unpack .../34-libpangoft2-1.0-0_1.56.2-1_armhf.deb ... 286s Unpacking libpangoft2-1.0-0:armhf (1.56.2-1) ... 286s Selecting previously unselected package libpangocairo-1.0-0:armhf. 286s Preparing to unpack .../35-libpangocairo-1.0-0_1.56.2-1_armhf.deb ... 286s Unpacking libpangocairo-1.0-0:armhf (1.56.2-1) ... 286s Selecting previously unselected package libpaper2:armhf. 286s Preparing to unpack .../36-libpaper2_2.2.5-0.3_armhf.deb ... 286s Unpacking libpaper2:armhf (2.2.5-0.3) ... 286s Selecting previously unselected package libpaper-utils. 286s Preparing to unpack .../37-libpaper-utils_2.2.5-0.3_armhf.deb ... 286s Unpacking libpaper-utils (2.2.5-0.3) ... 286s Selecting previously unselected package libsharpyuv0:armhf. 286s Preparing to unpack .../38-libsharpyuv0_1.5.0-0.1_armhf.deb ... 286s Unpacking libsharpyuv0:armhf (1.5.0-0.1) ... 286s Selecting previously unselected package libsm6:armhf. 286s Preparing to unpack .../39-libsm6_2%3a1.2.4-1_armhf.deb ... 286s Unpacking libsm6:armhf (2:1.2.4-1) ... 286s Selecting previously unselected package libtabixpp0t64:armhf. 286s Preparing to unpack .../40-libtabixpp0t64_1.1.2-2.1build1_armhf.deb ... 286s Unpacking libtabixpp0t64:armhf (1.1.2-2.1build1) ... 286s Selecting previously unselected package libtcl8.6:armhf. 286s Preparing to unpack .../41-libtcl8.6_8.6.16+dfsg-1_armhf.deb ... 286s Unpacking libtcl8.6:armhf (8.6.16+dfsg-1) ... 286s Selecting previously unselected package libjbig0:armhf. 286s Preparing to unpack .../42-libjbig0_2.1-6.1ubuntu2_armhf.deb ... 286s Unpacking libjbig0:armhf (2.1-6.1ubuntu2) ... 286s Selecting previously unselected package libwebp7:armhf. 286s Preparing to unpack .../43-libwebp7_1.5.0-0.1_armhf.deb ... 286s Unpacking libwebp7:armhf (1.5.0-0.1) ... 286s Selecting previously unselected package libtiff6:armhf. 286s Preparing to unpack .../44-libtiff6_4.5.1+git230720-4ubuntu4_armhf.deb ... 286s Unpacking libtiff6:armhf (4.5.1+git230720-4ubuntu4) ... 286s Selecting previously unselected package libxft2:armhf. 286s Preparing to unpack .../45-libxft2_2.3.6-1build1_armhf.deb ... 286s Unpacking libxft2:armhf (2.3.6-1build1) ... 286s Selecting previously unselected package libxss1:armhf. 286s Preparing to unpack .../46-libxss1_1%3a1.2.3-1build3_armhf.deb ... 286s Unpacking libxss1:armhf (1:1.2.3-1build3) ... 286s Selecting previously unselected package libtk8.6:armhf. 286s Preparing to unpack .../47-libtk8.6_8.6.16-1_armhf.deb ... 286s Unpacking libtk8.6:armhf (8.6.16-1) ... 286s Selecting previously unselected package libxt6t64:armhf. 286s Preparing to unpack .../48-libxt6t64_1%3a1.2.1-1.2build1_armhf.deb ... 286s Unpacking libxt6t64:armhf (1:1.2.1-1.2build1) ... 286s Selecting previously unselected package zip. 286s Preparing to unpack .../49-zip_3.0-14ubuntu2_armhf.deb ... 286s Unpacking zip (3.0-14ubuntu2) ... 286s Selecting previously unselected package unzip. 286s Preparing to unpack .../50-unzip_6.0-28ubuntu6_armhf.deb ... 286s Unpacking unzip (6.0-28ubuntu6) ... 286s Selecting previously unselected package xdg-utils. 286s Preparing to unpack .../51-xdg-utils_1.2.1-2ubuntu1_all.deb ... 286s Unpacking xdg-utils (1.2.1-2ubuntu1) ... 286s Selecting previously unselected package r-base-core. 286s Preparing to unpack .../52-r-base-core_4.4.3-1_armhf.deb ... 286s Unpacking r-base-core (4.4.3-1) ... 287s Selecting previously unselected package r-cran-boot. 287s Preparing to unpack .../53-r-cran-boot_1.3-31-1_all.deb ... 287s Unpacking r-cran-boot (1.3-31-1) ... 287s Selecting previously unselected package r-cran-cluster. 287s Preparing to unpack .../54-r-cran-cluster_2.1.8-1_armhf.deb ... 287s Unpacking r-cran-cluster (2.1.8-1) ... 287s Selecting previously unselected package r-cran-foreign. 287s Preparing to unpack .../55-r-cran-foreign_0.8.88-1_armhf.deb ... 287s Unpacking r-cran-foreign (0.8.88-1) ... 287s Selecting previously unselected package r-cran-mass. 287s Preparing to unpack .../56-r-cran-mass_7.3-64-1_armhf.deb ... 287s Unpacking r-cran-mass (7.3-64-1) ... 287s Selecting previously unselected package r-cran-kernsmooth. 287s Preparing to unpack .../57-r-cran-kernsmooth_2.23-26-1_armhf.deb ... 287s Unpacking r-cran-kernsmooth (2.23-26-1) ... 287s Selecting previously unselected package r-cran-lattice. 287s Preparing to unpack .../58-r-cran-lattice_0.22-6-1_armhf.deb ... 287s Unpacking r-cran-lattice (0.22-6-1) ... 287s Selecting previously unselected package r-cran-nlme. 287s Preparing to unpack .../59-r-cran-nlme_3.1.167-1_armhf.deb ... 287s Unpacking r-cran-nlme (3.1.167-1) ... 287s Selecting previously unselected package r-cran-matrix. 287s Preparing to unpack .../60-r-cran-matrix_1.7-3-1_armhf.deb ... 287s Unpacking r-cran-matrix (1.7-3-1) ... 287s Selecting previously unselected package r-cran-mgcv. 287s Preparing to unpack .../61-r-cran-mgcv_1.9-1-1_armhf.deb ... 287s Unpacking r-cran-mgcv (1.9-1-1) ... 288s Selecting previously unselected package r-cran-survival. 288s Preparing to unpack .../62-r-cran-survival_3.8-3-1_armhf.deb ... 288s Unpacking r-cran-survival (3.8-3-1) ... 288s Selecting previously unselected package r-cran-rpart. 288s Preparing to unpack .../63-r-cran-rpart_4.1.24-1_armhf.deb ... 288s Unpacking r-cran-rpart (4.1.24-1) ... 288s Selecting previously unselected package r-cran-class. 288s Preparing to unpack .../64-r-cran-class_7.3-23-1_armhf.deb ... 288s Unpacking r-cran-class (7.3-23-1) ... 288s Selecting previously unselected package r-cran-nnet. 288s Preparing to unpack .../65-r-cran-nnet_7.3-20-1_armhf.deb ... 288s Unpacking r-cran-nnet (7.3-20-1) ... 288s Selecting previously unselected package r-cran-spatial. 288s Preparing to unpack .../66-r-cran-spatial_7.3-18-1_armhf.deb ... 288s Unpacking r-cran-spatial (7.3-18-1) ... 288s Selecting previously unselected package r-cran-codetools. 288s Preparing to unpack .../67-r-cran-codetools_0.2-20-1_all.deb ... 288s Unpacking r-cran-codetools (0.2-20-1) ... 288s Selecting previously unselected package r-recommended. 288s Preparing to unpack .../68-r-recommended_4.4.3-1_all.deb ... 288s Unpacking r-recommended (4.4.3-1) ... 288s Selecting previously unselected package r-base. 288s Preparing to unpack .../69-r-base_4.4.3-1_all.deb ... 288s Unpacking r-base (4.4.3-1) ... 288s Selecting previously unselected package samtools. 288s Preparing to unpack .../70-samtools_1.21-1_armhf.deb ... 288s Unpacking samtools (1.21-1) ... 288s Selecting previously unselected package smalt. 288s Preparing to unpack .../71-smalt_0.7.6-13_armhf.deb ... 288s Unpacking smalt (0.7.6-13) ... 288s Selecting previously unselected package snpomatic. 288s Preparing to unpack .../72-snpomatic_1.0-7_armhf.deb ... 288s Unpacking snpomatic (1.0-7) ... 288s Selecting previously unselected package tabix. 288s Preparing to unpack .../73-tabix_1.21+ds-1_armhf.deb ... 288s Unpacking tabix (1.21+ds-1) ... 288s Selecting previously unselected package reapr. 288s Preparing to unpack .../74-reapr_1.0.18+dfsg-7_armhf.deb ... 288s Unpacking reapr (1.0.18+dfsg-7) ... 288s Setting up libhtscodecs2:armhf (1.6.1-2) ... 288s Setting up libgraphite2-3:armhf (1.3.14-2ubuntu1) ... 288s Setting up libpixman-1-0:armhf (0.44.0-3) ... 288s Setting up libsharpyuv0:armhf (1.5.0-0.1) ... 288s Setting up libfile-copy-link-perl (0.200-1) ... 288s Setting up liblerc4:armhf (4.0.0+ds-5ubuntu1) ... 288s Setting up libxrender1:armhf (1:0.9.10-1.1build1) ... 288s Setting up libdatrie1:armhf (0.2.13-3build1) ... 288s Setting up libxcb-render0:armhf (1.17.0-2) ... 288s Setting up unzip (6.0-28ubuntu6) ... 288s Setting up x11-common (1:7.7+23ubuntu3) ... 289s Setting up libdeflate0:armhf (1.23-1) ... 289s Setting up libxcb-shm0:armhf (1.17.0-2) ... 289s Setting up libgomp1:armhf (15-20250222-0ubuntu1) ... 289s Setting up libjbig0:armhf (2.1-6.1ubuntu2) ... 289s Setting up zip (3.0-14ubuntu2) ... 289s Setting up libblas3:armhf (3.12.1-2) ... 289s update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so.3 to provide /usr/lib/arm-linux-gnueabihf/libblas.so.3 (libblas.so.3-arm-linux-gnueabihf) in auto mode 289s Setting up libfreetype6:armhf (2.13.3+dfsg-1) ... 289s Setting up libjsoncpp26:armhf (1.9.6-3) ... 289s Setting up libbambamc0:armhf (0.0.50-6build1) ... 289s Setting up fonts-dejavu-mono (2.37-8) ... 289s Setting up libtcl8.6:armhf (8.6.16+dfsg-1) ... 289s Setting up fonts-dejavu-core (2.37-8) ... 289s Setting up libjpeg-turbo8:armhf (2.1.5-3ubuntu2) ... 289s Setting up libbamtools2.5.2:armhf (2.5.2+dfsg-6build1) ... 289s Setting up libgfortran5:armhf (15-20250222-0ubuntu1) ... 289s Setting up libwebp7:armhf (1.5.0-0.1) ... 289s Setting up bamtools (2.5.2+dfsg-6build1) ... 289s Setting up snpomatic (1.0-7) ... 289s Setting up libhts3t64:armhf (1.21+ds-1) ... 289s Setting up libharfbuzz0b:armhf (10.2.0-1) ... 289s Setting up libthai-data (0.1.29-2build1) ... 289s Setting up libxss1:armhf (1:1.2.3-1build3) ... 289s Setting up libpaper2:armhf (2.2.5-0.3) ... 289s Setting up tabix (1.21+ds-1) ... 289s Setting up xdg-utils (1.2.1-2ubuntu1) ... 289s update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode 289s Setting up libjpeg8:armhf (8c-2ubuntu11) ... 289s Setting up smalt (0.7.6-13) ... 289s Setting up libice6:armhf (2:1.1.1-1) ... 289s Setting up liblapack3:armhf (3.12.1-2) ... 289s update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so.3 to provide /usr/lib/arm-linux-gnueabihf/liblapack.so.3 (liblapack.so.3-arm-linux-gnueabihf) in auto mode 289s Setting up fontconfig-config (2.15.0-2ubuntu1) ... 289s Setting up libpaper-utils (2.2.5-0.3) ... 289s Setting up samtools (1.21-1) ... 289s Setting up libthai0:armhf (0.1.29-2build1) ... 289s Setting up libtiff6:armhf (4.5.1+git230720-4ubuntu4) ... 289s Setting up libtabixpp0t64:armhf (1.1.2-2.1build1) ... 289s Setting up libfontconfig1:armhf (2.15.0-2ubuntu1) ... 289s Setting up libsm6:armhf (2:1.2.4-1) ... 289s Setting up fontconfig (2.15.0-2ubuntu1) ... 291s Regenerating fonts cache... done. 291s Setting up libxft2:armhf (2.3.6-1build1) ... 291s Setting up libtk8.6:armhf (8.6.16-1) ... 291s Setting up libpango-1.0-0:armhf (1.56.2-1) ... 291s Setting up libcairo2:armhf (1.18.2-2) ... 291s Setting up libxt6t64:armhf (1:1.2.1-1.2build1) ... 291s Setting up libpangoft2-1.0-0:armhf (1.56.2-1) ... 291s Setting up libpangocairo-1.0-0:armhf (1.56.2-1) ... 291s Setting up r-base-core (4.4.3-1) ... 292s Creating config file /etc/R/Renviron with new version 292s Setting up r-cran-lattice (0.22-6-1) ... 292s Setting up r-cran-nlme (3.1.167-1) ... 292s Setting up r-cran-cluster (2.1.8-1) ... 292s Setting up r-cran-nnet (7.3-20-1) ... 292s Setting up r-cran-codetools (0.2-20-1) ... 292s Setting up r-cran-boot (1.3-31-1) ... 292s Setting up r-cran-spatial (7.3-18-1) ... 292s Setting up r-cran-mass (7.3-64-1) ... 292s Setting up r-cran-foreign (0.8.88-1) ... 292s Setting up r-cran-matrix (1.7-3-1) ... 292s Setting up r-cran-kernsmooth (2.23-26-1) ... 292s Setting up r-cran-mgcv (1.9-1-1) ... 292s Setting up r-cran-class (7.3-23-1) ... 292s Setting up r-cran-survival (3.8-3-1) ... 292s Setting up r-cran-rpart (4.1.24-1) ... 292s Setting up r-recommended (4.4.3-1) ... 292s Setting up r-base (4.4.3-1) ... 292s Setting up reapr (1.0.18+dfsg-7) ... 292s Processing triggers for man-db (2.13.0-1) ... 293s Processing triggers for install-info (7.1.1-1) ... 293s Processing triggers for libc-bin (2.41-1ubuntu2) ... 301s autopkgtest [16:57:12]: test test-example: [----------------------- 303s [wgsim] seed = 42 303s [wgsim_core] calculating the total length of the reference sequence... 303s [wgsim_core] 1 sequences, total length: 1000111 303s foo 1384 T K + 303s foo 4961 T W + 303s foo 5885 - T - 303s foo 9598 A C - 303s foo 10177 G R + 303s foo 11305 G K + 303s foo 11592 G R + 303s foo 13931 T - - 303s foo 15907 C A - 303s foo 17264 G K + 303s foo 17780 A - - 303s foo 18711 A W + 303s foo 19249 T W + 303s foo 19522 C S + 303s foo 23053 T K + 303s foo 23681 A R + 303s foo 23730 C S + 303s foo 24075 G S + 303s foo 24555 G C - 303s foo 26775 G K + 303s foo 26896 C M + 303s foo 27253 G K + 303s foo 28210 T Y + 303s foo 28224 A W + 303s foo 28377 - G + 303s foo 29035 G K + 303s foo 29898 C M + 303s foo 30274 A R + 303s foo 30542 G K + 303s foo 31566 A C - 303s foo 32252 - A - 303s foo 33303 T K + 303s foo 33390 - G + 303s foo 34073 A R + 303s foo 34171 G R + 303s foo 34718 T Y + 303s foo 34801 - C + 303s foo 35204 T W + 303s foo 35342 G S + 303s foo 35489 G T - 303s foo 36153 A M + 303s foo 36273 C S + 303s foo 37356 G T - 303s foo 37596 C S + 303s foo 39308 T - - 303s foo 40333 C G - 303s foo 42295 T K + 303s foo 42372 T Y + 303s foo 44433 C G - 303s foo 44630 - AG + 303s foo 44902 T C - 303s foo 47156 C A - 303s foo 48210 C M + 303s foo 48390 A R + 303s foo 49652 C M + 303s foo 52739 T Y + 303s foo 52858 A M + 303s foo 54737 A G - 303s foo 55306 C T - 303s foo 55434 C T - 303s foo 59204 A W + 303s foo 59300 G C - 303s foo 59335 T Y + 303s foo 59444 T - - 303s foo 59531 C S + 303s foo 59766 C Y + 303s foo 61950 C S + 303s foo 62887 G S + 303s foo 63390 A G - 303s foo 64365 G K + 303s foo 64703 C S + 303s foo 64932 C Y + 303s foo 68383 - CG + 303s foo 68464 A W + 303s foo 68727 A W + 303s foo 69080 A M + 303s foo 72071 T C - 303s foo 72720 - G - 303s foo 73354 C T - 303s foo 73637 G T - 303s foo 74741 A M + 303s foo 75101 C T - 303s foo 75207 T K + 303s foo 76400 T Y + 303s foo 76780 A C - 303s foo 77172 A W + 303s foo 78385 C Y + 303s foo 80705 C M + 303s foo 82440 A R + 303s foo 83021 G K + 303s foo 83116 A - - 303s foo 83846 T K + 303s foo 84633 G S + 303s foo 85891 G S + 303s foo 87759 A C - 303s foo 87778 T W + 303s foo 88581 T K + 303s foo 88606 T Y + 303s foo 88880 A G - 303s foo 89945 G C - 303s foo 90728 T K + 303s foo 91798 G R + 303s foo 95957 G C - 303s foo 96173 T W + 303s foo 96665 A M + 303s foo 98019 - G + 303s foo 98131 A M + 303s foo 98669 A R + 303s foo 98719 G T - 303s foo 99062 A W + 303s foo 99590 A T - 303s foo 100532 - TC + 303s foo 103015 A W + 303s foo 103172 G S + 303s foo 103609 G R + 303s foo 106549 T Y + 303s foo 108808 C Y + 303s foo 109191 G C - 303s foo 111686 C G - 303s foo 113436 C A - 303s foo 113763 A W + 303s foo 115671 C T - 303s foo 117460 - A - 303s foo 118193 G - - 303s foo 118585 T K + 303s foo 121219 A M + 303s foo 121876 T K + 303s foo 122071 T A - 303s foo 124918 C G - 303s foo 125300 G S + 303s foo 125967 C S + 303s foo 127443 G S + 303s foo 127565 C Y + 303s foo 128700 C A - 303s foo 129912 G A - 303s foo 130847 T W + 303s foo 131677 G S + 303s foo 132189 T C - 303s foo 135878 CGGC - - 303s foo 136825 T K + 303s foo 138881 TGT - - 303s foo 139288 A W + 303s foo 141054 A W + 303s foo 141055 - T + 303s foo 141101 C S + 303s foo 141404 A R + 303s foo 142698 T C - 303s foo 143990 C A - 303s foo 144167 T Y + 303s foo 144814 C Y + 303s foo 146381 T Y + 303s foo 146393 C A - 303s foo 146510 A C - 303s foo 147182 A W + 303s foo 148783 T C - 303s foo 149068 G S + 303s foo 150208 T K + 303s foo 151554 T W + 303s foo 151709 C G - 303s foo 153072 G R + 303s foo 153307 T Y + 303s foo 154050 G S + 303s foo 154415 C S + 303s foo 154594 G R + 303s foo 155839 G T - 303s foo 156106 G A - 303s foo 159356 T W + 303s foo 159926 A W + 303s foo 160303 T K + 303s foo 161323 C Y + 303s foo 161904 G S + 303s foo 162533 - ACC - 303s foo 164738 C G - 303s foo 165413 A R + 303s foo 166944 C M + 303s foo 167464 T Y + 303s foo 168420 T C - 303s foo 168579 A M + 303s foo 168787 T W + 303s foo 168959 A T - 303s foo 169884 G S + 303s foo 170032 G T - 303s foo 172058 G K + 303s foo 174942 A R + 303s foo 175014 G K + 303s foo 178406 G A - 303s foo 179028 - A + 303s foo 182394 C M + 303s foo 182735 T Y + 303s foo 183384 T K + 303s foo 183893 - AT - 303s foo 185360 G A - 303s foo 185538 - G - 303s foo 187948 G S + 303s foo 188120 T G - 303s foo 188179 T W + 303s foo 188316 T Y + 303s foo 189963 - G + 303s foo 190093 C Y + 303s foo 192220 C M + 303s foo 192368 A W + 303s foo 192782 T K + 303s foo 193307 A R + 303s foo 193501 G K + 303s foo 194276 G S + 303s foo 194930 C S + 303s foo 196728 A W + 303s foo 197559 G C - 303s foo 198467 T W + 303s foo 199042 C Y + 303s foo 199259 AA - - 303s foo 199687 TT - - 303s foo 200287 C A - 303s foo 200678 A R + 303s foo 201208 C T - 303s foo 201882 A - - 303s foo 204456 T K + 303s foo 206327 G R + 303s foo 207311 G T - 303s foo 209184 G A - 303s foo 209279 C Y + 303s foo 211459 C Y + 303s foo 213807 T Y + 303s foo 213846 T Y + 303s foo 214635 A G - 303s foo 214884 C A - 303s foo 216244 A M + 303s foo 216652 A M + 303s foo 216745 T - - 303s foo 216909 A T - 303s foo 217579 A G - 303s foo 217895 C Y + 303s foo 218870 G K + 303s foo 223098 T A - 303s foo 223283 - C + 303s foo 223666 C A - 303s foo 224011 - C + 303s foo 225681 C S + 303s foo 227345 T C - 303s foo 228778 T G - 303s foo 229926 C - - 303s foo 230778 T K + 303s foo 230939 CG - - 303s foo 231988 CT - - 303s foo 234593 T W + 303s foo 235496 C S + 303s foo 235705 G K + 303s foo 235758 A G - 303s foo 236852 T C - 303s foo 238790 A M + 303s foo 238865 T K + 303s foo 239329 A M + 303s foo 239576 - C + 303s foo 243058 G S + 303s foo 244147 T - - 303s foo 244462 C G - 303s foo 245443 - A + 303s foo 246544 C Y + 303s foo 246744 T W + 303s foo 247473 C M + 303s foo 248129 C T - 303s foo 249060 A C - 303s foo 249515 G T - 303s foo 250138 G S + 303s foo 250567 C A - 303s foo 254381 G R + 303s foo 257864 C M + 303s foo 257879 C Y + 303s foo 259859 A M + 303s foo 260643 C S + 303s foo 261681 C G - 303s foo 262645 T Y + 303s foo 263279 A R + 303s foo 263575 A - - 303s foo 264587 - TA + 303s foo 264689 T K + 303s foo 265758 G K + 303s foo 266272 A M + 303s foo 268550 C M + 303s foo 269986 G S + 303s foo 270321 AC - - 303s foo 273346 C S + 303s foo 275367 C A - 303s foo 277334 C G - 303s foo 277629 G T - 303s foo 278431 C Y + 303s foo 281456 T Y + 303s foo 281556 T G - 303s foo 281737 G K + 303s foo 282290 AC - - 303s foo 282851 - C - 303s foo 284405 A C - 303s foo 288751 A C - 303s foo 290501 TAAA - - 303s foo 291315 A W + 303s foo 291368 C - - 303s foo 292154 A C - 303s foo 292385 C M + 303s foo 292555 G K + 303s foo 297709 G C - 303s foo 298183 A W + 303s foo 298228 T W + 303s foo 299902 T G - 303s foo 302575 A T - 303s foo 304823 G R + 303s foo 305308 T Y + 303s foo 305487 G S + 303s foo 305697 G T - 303s foo 306098 C G - 303s foo 306882 T Y + 303s foo 308201 A M + 303s foo 308833 A T - 303s foo 312033 A - - 303s foo 312895 C G - 303s foo 313889 C - - 303s foo 315109 A R + 303s foo 316083 C - - 303s foo 316466 A R + 303s foo 318040 G C - 303s foo 319446 T C - 303s foo 320236 C S + 303s foo 320652 A - - 303s foo 320716 T K + 303s foo 323644 A - - 303s foo 325359 G T - 303s foo 329476 - CA + 303s foo 329706 T G - 303s foo 330181 T Y + 303s foo 330703 C Y + 303s foo 331315 G S + 303s foo 332351 C A - 303s foo 333408 A R + 303s foo 333468 C S + 303s foo 336247 A G - 303s foo 336586 A M + 303s foo 337364 G K + 303s foo 337686 A T - 303s foo 338043 A - - 303s foo 338292 C G - 303s foo 338962 A C - 303s foo 339353 G K + 303s foo 340647 - A + 303s foo 341705 G R + 303s foo 344283 C M + 303s foo 345898 - AG - 303s foo 347959 T - - 303s foo 349162 C M + 303s foo 352072 T Y + 303s foo 354614 C Y + 303s foo 359304 T - - 303s foo 359312 - G + 303s foo 360972 C S + 303s foo 363857 C Y + 303s foo 366226 A C - 303s foo 367259 C M + 303s foo 372502 T Y + 303s foo 372747 A M + 303s foo 375140 C S + 303s foo 376298 T W + 303s foo 376313 C - - 303s foo 376760 T W + 303s foo 378494 A W + 303s foo 381137 T G - 303s foo 381186 A R + 303s foo 381701 A G - 303s foo 382614 A W + 303s foo 382761 C T - 303s foo 382854 T C - 303s foo 383201 C T - 303s foo 385104 G S + 303s foo 385233 - A + 303s foo 386138 C T - 303s foo 386316 A W + 303s foo 387072 A R + 303s foo 387642 - A + 303s foo 388232 T C - 303s foo 388890 GGG - - 303s foo 390508 C S + 303s foo 390625 C M + 303s foo 391921 C G - 303s foo 395256 G T - 303s foo 395542 G S + 303s foo 397015 A - - 303s foo 397516 C Y + 303s foo 397528 GC - - 303s foo 398152 C T - 303s foo 399802 A W + 303s foo 400972 T K + 303s foo 401419 - T + 303s foo 401477 T W + 303s foo 402437 A M + 303s foo 402722 G R + 303s foo 403452 C M + 303s foo 404234 - A + 303s foo 405344 A W + 303s foo 407040 G S + 303s foo 408483 G R + 303s foo 408586 A C - 303s foo 408721 A R + 303s foo 409494 A M + 303s foo 410078 A G - 303s foo 411170 C A - 303s foo 415342 T Y + 303s foo 416265 C G - 303s foo 417740 C A - 303s foo 418622 C S + 303s foo 420232 A W + 303s foo 420288 T Y + 303s foo 420908 A W + 303s foo 421109 T A - 303s foo 421357 A R + 303s foo 422799 G A - 303s foo 424383 C S + 303s foo 424871 - GCA + 303s foo 427273 T A - 303s foo 429822 C M + 303s foo 429846 T W + 303s foo 432015 A G - 303s foo 432414 G K + 303s foo 433606 C Y + 303s foo 433831 T Y + 303s foo 437721 - A - 303s foo 438402 G - - 303s foo 438799 A T - 303s foo 439422 C M + 303s foo 440734 C A - 303s foo 441840 T G - 303s foo 442021 - C + 303s foo 445021 T A - 303s foo 445591 G A - 303s foo 446138 T W + 303s foo 447757 A W + 303s foo 449156 T - - 303s foo 449161 G K + 303s foo 450114 A W + 303s foo 450688 A W + 303s foo 454421 C G - 303s foo 454718 T Y + 303s foo 455675 TC - - 303s foo 461721 G R + 303s foo 462526 G S + 303s foo 467296 G A - 303s foo 467510 G K + 303s foo 468267 T K + 303s foo 469118 G R + 303s foo 469830 C Y + 303s foo 471073 G T - 303s foo 472056 G A - 303s foo 472773 - A + 303s foo 473046 G R + 303s foo 473188 G A - 303s foo 473742 C - - 303s foo 474789 T A - 303s foo 477763 G R + 303s foo 478246 T W + 303s foo 478975 T G - 303s foo 479038 A R + 303s foo 480275 T Y + 303s foo 480317 G A - 303s foo 481512 T K + 303s foo 482069 G S + 303s foo 482534 A R + 303s foo 483760 C Y + 303s foo 485281 T W + 303s foo 486255 T C - 303s foo 487038 T K + 303s foo 487225 T A - 303s foo 488012 C Y + 303s foo 488795 T C - 303s foo 490241 A R + 303s foo 492595 - CGG + 303s foo 493224 C A - 303s foo 494284 A T - 303s foo 495990 - T - 303s foo 497306 A R + 303s foo 497403 T Y + 303s foo 499569 C Y + 303s foo 499651 T K + 303s foo 503139 T C - 303s foo 504660 A R + 303s foo 508679 C - - 303s foo 513643 G K + 303s foo 515668 CC - - 303s foo 515836 G R + 303s foo 516488 C S + 303s foo 517602 G R + 303s foo 517962 G K + 303s foo 517975 T K + 303s foo 519144 A T - 303s foo 520068 T K + 303s foo 520926 A W + 303s foo 521562 C S + 303s foo 522076 CG - - 303s foo 522838 T Y + 303s foo 523513 - C + 303s foo 523907 - TA + 303s foo 526271 T A - 303s foo 526533 AC - - 303s foo 526767 C Y + 303s foo 528217 C Y + 303s foo 531924 G S + 303s foo 532333 - TT + 303s foo 533132 C M + 303s foo 534689 A T - 303s foo 534779 A W + 303s foo 535594 C A - 303s foo 535795 G R + 303s foo 538368 A R + 303s foo 540879 G K + 303s foo 542530 A - - 303s foo 543620 G R + 303s foo 544733 - C - 303s foo 546300 - TT + 303s foo 548196 A T - 303s foo 548878 C M + 303s foo 548885 G R + 303s foo 549459 T K + 303s foo 550908 A G - 303s foo 551170 A - - 303s foo 553130 T Y + 303s foo 555293 T G - 303s foo 556198 G R + 303s foo 556355 A T - 303s foo 557688 G K + 303s foo 558415 G C - 303s foo 558461 - G + 303s foo 559287 T Y + 303s foo 559465 C M + 303s foo 560184 T W + 303s foo 560252 T W + 303s foo 562579 A M + 303s foo 562961 G A - 303s foo 566986 C A - 303s foo 568134 C A - 303s foo 569698 T C - 303s foo 570180 T K + 303s foo 570451 TG - - 303s foo 570832 - A - 303s foo 571589 A W + 303s foo 572208 C M + 303s foo 572871 C S + 303s foo 574334 G - - 303s foo 575673 T Y + 303s foo 576797 G S + 303s foo 578486 - C - 303s foo 578494 C S + 303s foo 579257 G A - 303s foo 580103 G T - 303s foo 580872 A W + 303s foo 580925 G S + 303s foo 580950 G C - 303s foo 581637 T Y + 303s foo 581654 A G - 303s foo 582538 A T - 303s foo 582691 C M + 303s foo 582938 A W + 303s foo 583104 T K + 303s foo 584763 T W + 303s foo 585723 T W + 303s foo 588253 T Y + 303s foo 588972 T C - 303s foo 589438 - C - 303s foo 591131 C Y + 303s foo 591950 G R + 303s foo 592194 T G - 303s foo 592310 G S + 303s foo 593892 G A - 303s foo 598556 A - - 303s foo 601660 G S + 303s foo 602112 G T - 303s foo 602412 T Y + 303s foo 607282 - C + 303s foo 607394 A M + 303s foo 608438 A T - 303s foo 609255 A W + 303s foo 609365 - T + 303s foo 611161 G K + 303s foo 612224 C G - 303s foo 614493 G R + 303s foo 614601 G A - 303s foo 614607 C Y + 303s foo 619507 C M + 303s foo 619798 T C - 303s foo 621872 C T - 303s foo 622375 C Y + 303s foo 623208 - G - 303s foo 624366 C A - 303s foo 625320 - ACA - 303s foo 626664 - G + 303s foo 627140 T C - 303s foo 627353 G T - 303s foo 628714 T Y + 303s foo 628744 A - - 303s foo 629152 A G - 303s foo 630110 T G - 303s foo 631744 G K + 303s foo 632763 C S + 303s foo 634419 G - - 303s foo 634459 A G - 303s foo 634571 G A - 303s foo 635366 - A + 303s foo 635604 G T - 303s foo 637057 T C - 303s foo 637525 A T - 303s foo 638412 A R + 303s foo 640547 A W + 303s foo 641514 T K + 303s foo 642219 A R + 303s foo 642427 A G - 303s foo 642612 A R + 303s foo 643553 T W + 303s foo 647316 - T + 303s foo 647598 C - - 303s foo 651093 G A - 303s foo 651718 G R + 303s foo 652235 A G - 303s foo 652579 A C - 303s foo 653355 A W + 303s foo 655174 C M + 303s foo 655487 A M + 303s foo 656849 G S + 303s foo 661081 T K + 303s foo 661134 G C - 303s foo 661935 A W + 303s foo 662010 A M + 303s foo 662040 G R + 303s foo 663030 A W + 303s foo 663268 - C + 303s foo 664991 T - - 303s foo 665489 T K + 303s foo 665555 C M + 303s foo 665965 C Y + 303s foo 668725 A C - 303s foo 668834 - G - 303s foo 668873 C S + 303s foo 669654 T W + 303s foo 671041 G S + 303s foo 671485 T W + 303s foo 671690 C M + 303s foo 673022 G R + 303s foo 674137 - T + 303s foo 674782 A C - 303s foo 676373 G T - 303s foo 676793 T C - 303s foo 677409 G S + 303s foo 677536 - AA - 303s foo 677620 G K + 303s foo 677686 C Y + 303s foo 678327 G S + 303s foo 678704 G S + 303s foo 678771 A C - 303s foo 678866 C T - 303s foo 679960 A W + 303s foo 680447 - C + 303s foo 682102 C T - 303s foo 685497 T A - 303s foo 686884 G S + 303s foo 687324 ACA - - 303s foo 687684 - AC + 303s foo 687823 T C - 303s foo 688590 G K + 303s foo 690802 C M + 303s foo 691388 T C - 303s foo 691403 T G - 303s foo 691790 G A - 303s foo 692973 C A - 303s foo 694058 G S + 303s foo 694550 G R + 303s foo 694968 T W + 303s foo 695898 A T - 303s foo 696721 C S + 303s foo 696787 C S + 303s foo 696935 A M + 303s foo 698024 - C + 303s foo 699813 A - - 303s foo 700179 G R + 303s foo 701421 A M + 303s foo 701989 T A - 303s foo 702862 C A - 303s foo 707020 G A - 303s foo 708420 A - - 303s foo 708669 C G - 303s foo 710521 T W + 303s foo 711801 G C - 303s foo 711913 T G - 303s foo 715830 C M + 303s foo 717664 TC - - 303s foo 718845 A W + 303s foo 719069 T Y + 303s foo 719565 A W + 303s foo 721136 T K + 303s foo 726116 T K + 303s foo 727809 T K + 303s foo 728864 G K + 303s foo 728918 G A - 303s foo 730296 - T + 303s foo 731988 C Y + 303s foo 734658 A M + 303s foo 734715 A W + 303s foo 736618 C G - 303s foo 737257 T Y + 303s foo 740864 C A - 303s foo 741640 G - - 303s foo 741859 - TA - 303s foo 742011 T K + 303s foo 742237 A R + 303s foo 742960 G K + 303s foo 743731 G R + 303s foo 743971 A W + 303s foo 744635 T K + 303s foo 746430 C G - 303s foo 746489 - GC - 303s foo 746881 C M + 303s foo 756997 TC - - 303s foo 757776 A M + 303s foo 759870 A T - 303s foo 760224 G K + 303s foo 760799 G C - 303s foo 761692 T C - 303s foo 762569 G S + 303s foo 763140 A G - 303s foo 763842 - T - 303s foo 764192 A M + 303s foo 764334 G A - 303s foo 764889 - AAT + 303s foo 766464 G S + 303s foo 768226 G A - 303s foo 770272 T G - 303s foo 771145 C Y + 303s foo 772209 T A - 303s foo 773672 T K + 303s foo 773932 G C - 303s foo 774658 C S + 303s foo 775969 A M + 303s foo 776816 T G - 303s foo 777591 C Y + 303s foo 777891 A M + 303s foo 778164 C M + 303s foo 778219 T W + 303s foo 779260 G T - 303s foo 779465 A W + 303s foo 779779 G S + 303s foo 780033 G K + 303s foo 783243 C M + 303s foo 783860 A R + 303s foo 788345 A M + 303s foo 789554 G - - 303s foo 790025 G K + 303s foo 791454 T K + 303s foo 792009 C A - 303s foo 792872 C G - 303s foo 794616 T W + 303s foo 795031 G R + 303s foo 796919 C M + 303s foo 797020 G S + 303s foo 797042 G C - 303s foo 797149 G A - 303s foo 797177 A C - 303s foo 799076 G C - 303s foo 799580 G S + 303s foo 800356 A R + 303s foo 802297 G T - 303s foo 802309 T Y + 303s foo 802343 - C + 303s foo 802769 A W + 303s foo 803104 C G - 303s foo 805819 C Y + 303s foo 805972 T Y + 303s foo 807503 T K + 303s foo 807950 C M + 303s foo 807994 - A - 303s foo 809167 A G - 303s foo 809658 A W + 303s foo 810152 A M + 303s foo 811506 G R + 303s foo 813494 A M + 303s foo 814035 G T - 303s foo 814476 A W + 303s foo 819399 T K + 303s foo 820171 T W + 303s foo 820445 G C - 303s foo 822178 C G - 303s foo 822504 C T - 303s foo 823378 C M + 303s foo 823591 CG - - 303s foo 824229 C M + 303s foo 824579 C T - 303s foo 824858 C M + 303s foo 826101 T K + 303s foo 827593 C G - 303s foo 827794 T Y + 303s foo 828228 A M + 303s foo 828367 T K + 303s foo 828788 C M + 303s foo 829002 C Y + 303s foo 830345 C M + 303s foo 831018 C A - 303s foo 831459 T K + 303s foo 832413 A T - 303s foo 832782 T Y + 303s foo 832908 T Y + 303s foo 833130 T - - 303s foo 833142 G S + 303s foo 833241 G A - 303s foo 836727 A T - 303s foo 836829 G S + 303s foo 838452 T G - 303s foo 838543 A T - 303s foo 838605 C M + 303s foo 838954 G C - 303s foo 841829 G K + 303s foo 842324 - TC + 303s foo 842996 - C + 303s foo 844390 C A - 303s foo 844793 A C - 303s foo 844925 C A - 303s foo 845082 G C - 303s foo 846202 G R + 303s foo 846707 A G - 303s foo 848713 G A - 303s foo 849372 C S + 303s foo 849742 G A - 303s foo 850499 C - - 303s foo 850927 GT - - 303s foo 851084 - G + 303s foo 852247 A R + 303s foo 852972 C A - 303s foo 854808 T W + 303s foo 855956 G K + 303s foo 856225 G A - 303s foo 856582 T K + 303s foo 857351 C M + 303s foo 857504 AC - - 303s foo 858324 A T - 303s foo 858858 T C - 303s foo 859488 T Y + 303s foo 862441 T Y + 303s foo 863827 C Y + 303s foo 864165 C A - 303s foo 865997 C M + 303s foo 866370 G S + 303s foo 867653 G S + 303s foo 867722 C Y + 303s foo 868696 C M + 303s foo 869005 T W + 303s foo 869791 T Y + 303s foo 875339 C Y + 303s foo 875347 C M + 303s foo 875584 T G - 303s foo 876780 C T - 303s foo 878368 A C - 303s foo 878916 - CAG + 303s foo 879005 A R + 303s foo 880112 G T - 303s foo 881021 - T - 303s foo 881175 T W + 303s foo 882168 - GGG + 303s foo 882223 - G - 303s foo 883033 TG - - 303s foo 883381 C G - 303s foo 884378 C - - 303s foo 885075 A M + 303s foo 885190 A W + 303s foo 885568 A W + 303s foo 885827 T Y + 303s foo 887610 TG - - 303s foo 889139 G R + 303s foo 890978 T - - 303s foo 891500 C Y + 303s foo 892257 G C - 303s foo 892642 G R + 303s foo 892644 T W + 303s foo 892757 C A - 303s foo 893222 T - - 303s foo 893348 T W + 303s foo 894161 - C - 303s foo 894447 A G - 303s foo 894614 A W + 303s foo 897817 T W + 303s foo 899408 C S + 303s foo 902450 A T - 303s foo 902970 AT - - 303s foo 905836 G K + 303s foo 906524 GA - - 303s foo 907484 A W + 303s foo 907537 C M + 303s foo 908515 G R + 303s foo 908642 C T - 303s foo 911145 T C - 303s foo 912220 T Y + 303s foo 912682 C Y + 303s foo 914260 C S + 303s foo 914757 T Y + 303s foo 916413 G C - 303s foo 916783 T G - 303s foo 917033 G C - 303s foo 917218 A - - 303s foo 918225 G - - 303s foo 918459 A - - 303s foo 918732 A M + 303s foo 919640 TC - - 303s foo 920824 T W + 303s foo 920836 G C - 303s foo 924560 G R + 303s foo 924659 GA - - 303s foo 925868 T A - 303s foo 928254 T G - 303s foo 928369 - A - 303s foo 928641 - AG + 303s foo 929857 C M + 303s foo 930211 T W + 303s foo 930935 C T - 303s foo 931986 A M + 303s foo 932852 G T - 303s foo 933965 T A - 303s foo 935564 A W + 303s foo 936034 T Y + 303s foo 936221 AC - - 303s foo 936670 C S + 303s foo 936704 T A - 303s foo 936786 T W + 303s foo 939218 C S + 303s foo 939312 A W + 303s foo 939467 A W + 303s foo 939934 C S + 303s foo 941603 C Y + 303s foo 942910 A W + 303s foo 944654 T Y + 303s foo 945301 A C - 303s foo 945770 C T - 303s foo 946078 G S + 303s foo 948833 G K + 303s foo 948999 A W + 303s foo 949193 A R + 303s foo 950276 C M + 303s foo 950414 A W + 303s foo 951285 G C - 303s foo 953158 G R + 303s foo 953287 A W + 303s foo 954150 C G - 303s foo 954258 G - - 303s foo 955396 CC - - 303s foo 956490 - AC + 303s foo 958129 A R + 303s foo 959027 T A - 303s foo 959964 A W + 303s foo 962042 A G - 303s foo 962742 C G - 303s foo 963306 T W + 303s foo 963422 G K + 303s foo 964082 G S + 303s foo 965561 C S + 303s foo 966531 T K + 303s foo 967324 T W + 303s foo 968419 - C - 303s foo 969054 G - - 303s foo 969158 G S + 303s foo 972658 C M + 303s foo 974266 T W + 303s foo 974629 G K + 303s foo 975034 A R + 303s foo 975636 T W + 303s foo 977078 - A - 303s foo 978321 G T - 303s foo 978595 C G - 303s foo 979090 C M + 303s foo 983855 TA - - 303s foo 985725 T A - 303s foo 988497 C Y + 303s foo 990171 C M + 303s foo 990804 - CA - 303s foo 990941 T W + 303s foo 991797 A W + 303s foo 992469 A M + 303s foo 994610 C Y + 303s foo 998107 - T + 303s foo 999725 G R + 303s [REAPR smaltmap] Running: smalt index -k 13 -s 2 out.bam.tmp.2047.smaltmap.smalt_index foo1.fasta 303s # Command line: smalt index -k 13 -s 2 out.bam.tmp.2047.smaltmap.smalt_index foo1.fasta 303s # Reading sequences ... 303s # Writing sequence set ... 303s # Setting up hash index with collisions ... 303s # word length = 13 bases, skip step = 2 bases ... 303s # number of bits for key = 18 with 0 perfect bits 303s # Counting keys ... 303s # Counting k-tuples ... 303s # Allocating k-tuple arrays ... 303s # Counting k-tuple occurrences ... 303s # Setting the k-tuple positions in index ... 304s # Hash table is set up. 304s # =-=-=-=-= Hash Index Stats =-=-=-=-= 304s # Hash index with collisions. 304s # Word length: 13 bases 304s # Skip step: 2 bases 304s # Number of hash keys: 262144 304s # Number of word positions: 499970 304s # Number of different words: 498076 304s # Maximum number of words per key: 11 304s # Number of keys without words: 39377 304s # =-=-= End of Hash Index Stats =-=-= 304s # Writing table to file ... 304s # smalt: Total elapsed wall clock time: 1 seconds 304s [REAPR smaltmap] Running: smalt sample -u 1000 -o out.bam.tmp.2047.smaltmap.smalt_sample out.bam.tmp.2047.smaltmap.smalt_index foofq.1.fastq foofq.2.fastq 304s # Command line: smalt sample -u 1000 -o out.bam.tmp.2047.smaltmap.smalt_sample out.bam.tmp.2047.smaltmap.smalt_index foofq.1.fastq foofq.2.fastq 304s # Opening read files ... 304s # Reading reference sequences ... 304s # Reading hash table ... 304s # =-=-=-=-= Hash Index Stats =-=-=-=-= 304s # Hash index with collisions. 304s # Word length: 13 bases 304s # Skip step: 2 bases 304s # Number of hash keys: 262144 304s # Number of word positions: 499970 304s # Number of different words: 498076 304s # Maximum number of words per key: 11 304s # Number of keys without words: 39377 304s # =-=-= End of Hash Index Stats =-=-= 304s # Check of read pairs ok ... 304s # Mate names match ... 304s # Sampling insert size distribution ... 308s [REAPR smaltmap] Running: smalt map -r 0 -x -y 0.5 -g out.bam.tmp.2047.smaltmap.smalt_sample -f samsoft out.bam.tmp.2047.smaltmap.smalt_index foofq.1.fastq foofq.2.fastq | awk '$1!~/^#/' | samtools view -S -T foo1.fasta -b - > out.bam.tmp.2047.smaltmap.raw.bam 308s # Processed 9999 read pairs. 308s # smalt: Time spent setting up hash index:0 seconds 308s # smalt: Time spent mapping reads:4 seconds 308s # smalt: Total elapsed wall clock time: 4 seconds 308s # Command line: smalt map -r 0 -x -y 0.5 -g out.bam.tmp.2047.smaltmap.smalt_sample -f samsoft out.bam.tmp.2047.smaltmap.smalt_index foofq.1.fastq foofq.2.fastq 308s # Reading distribution of insert sizes from file ... 308s # Sampled histogram 308s # Smoothed histogram 308s # Opening read files ... 308s # Reading reference sequences ... 308s # Reading hash table ... 308s # =-=-=-=-= Hash Index Stats =-=-=-=-= 308s # Hash index with collisions. 308s # Word length: 13 bases 308s # Skip step: 2 bases 308s # Number of hash keys: 262144 308s # Number of word positions: 499970 308s # Number of different words: 498076 308s # Maximum number of words per key: 11 308s # Number of keys without words: 39377 308s # =-=-= End of Hash Index Stats =-=-= 308s # Processing query reads ... 327s # Processed 10000 read pairs. 327s # smalt: Time spent setting up hash index:0 seconds 327s # smalt: Time spent mapping reads:19 seconds 327s # smalt: Total elapsed wall clock time: 19 seconds 327s [REAPR smaltmap] Running: samtools sort out.bam.tmp.2047.smaltmap.raw.bam -O bam -o out.bam.tmp.2047.smaltmap.raw.bam.sort.bam 327s [REAPR smaltmap] Running: samtools rmdup out.bam.tmp.2047.smaltmap.raw.bam.sort.bam out.bam.tmp.2047.smaltmap.rmdup.bam 327s [bam_rmdup_core] processing reference foo... 327s [bam_rmdup_core] 1 / 10000 = 0.0001 in library ' ' 327s [REAPR smaltmap] Running: echo "@HD VN:1.0 SO:coordinate" | awk '{OFS="\t"; $1=$1; print}' > out.bam.tmp.2047.smaltmap.header 327s [REAPR smaltmap] Running: samtools view -H out.bam.tmp.2047.smaltmap.rmdup.bam >> out.bam.tmp.2047.smaltmap.header 327s [REAPR smaltmap] Running: samtools reheader out.bam.tmp.2047.smaltmap.header out.bam.tmp.2047.smaltmap.rmdup.bam > out.bam 327s [REAPR smaltmap] Running: samtools index out.bam 328s [REAPR smaltmap] Running: rm out.bam.tmp.2047.smaltmap.* 328s Running reapr version 1.0.18 pipeline: 328s reapr foo1.fasta out.bam result 328s [REAPR pipeline] Running facheck 328s [REAPR pipeline] Running preprocess 330s [REAPR preprocess] sampling region foo:1169-3476. Already sampled 0 bases 330s [REAPR preprocess] sampling region foo:3492-5726. Already sampled 2308 bases 330s [REAPR preprocess] sampling region foo:5756-12551. Already sampled 4543 bases 330s [REAPR preprocess] sampling region foo:12591-998105. Already sampled 11339 bases 331s [REAPR preprocess] Sampled 996854 bases for GC/coverage estimation 335s [REAPR pipeline] Running stats 347s [REAPR pipeline] Running fcdrate 349s [REAPR pipeline] Running score 354s [REAPR pipeline] Running break 354s [REAPR pipeline] Running summary 354s autopkgtest [16:58:05]: test test-example: -----------------------] 358s test-example PASS 358s autopkgtest [16:58:09]: test test-example: - - - - - - - - - - results - - - - - - - - - - 362s autopkgtest [16:58:13]: @@@@@@@@@@@@@@@@@@@@ summary 362s test-example PASS