{"action":"created","issue":{"url":"https://api.github.com/repos/Illumina/Isaac3/issues/5","repository_url":"https://api.github.com/repos/Illumina/Isaac3","labels_url":"https://api.github.com/repos/Illumina/Isaac3/issues/5/labels{/name}","comments_url":"https://api.github.com/repos/Illumina/Isaac3/issues/5/comments","events_url":"https://api.github.com/repos/Illumina/Isaac3/issues/5/events","html_url":"https://github.com/Illumina/Isaac3/issues/5","id":176346864,"number":5,"title":"ERROR: ***** Internal Program Error - assertion ([...]) failed in isaac::build::GapRealigner::GapChoice","user":{"login":"sklages","id":1837422,"avatar_url":"https://avatars.githubusercontent.com/u/1837422?v=3","gravatar_id":"","url":"https://api.github.com/users/sklages","html_url":"https://github.com/sklages","followers_url":"https://api.github.com/users/sklages/followers","following_url":"https://api.github.com/users/sklages/following{/other_user}","gists_url":"https://api.github.com/users/sklages/gists{/gist_id}","starred_url":"https://api.github.com/users/sklages/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/sklages/subscriptions","organizations_url":"https://api.github.com/users/sklages/orgs","repos_url":"https://api.github.com/users/sklages/repos","events_url":"https://api.github.com/users/sklages/events{/privacy}","received_events_url":"https://api.github.com/users/sklages/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":6,"created_at":"2016-09-12T10:52:40Z","updated_at":"2016-09-13T18:09:50Z","closed_at":"2016-09-13T18:09:50Z","body":"Hi,\r\n\r\nI have two PE125 fastq files (originally from bcl2fastq conversion) and wanted to map on `grcm38` with 40 threads. After ~90 min isaac crashed (reproducible) with:\r\n\r\n```\r\n2016-09-09 12:48:09  [7f88fc664700] Loading unsorted data\r\n2016-09-09 12:48:09  [7f88fc664700] Reading alignment records from BinMetadata(3id ReferencePosition(0:13680624:0f)bs 6840312bl 492742718ds 0do 0se 888256rs 869166f \r\n/scratch/cluster/mx/test_mouse/20160909_111202.mapping.mx.cpu40.vig1/3.ext_L7255-3_SJL.grcm38/temp/bin-00000001-00000003.dat)\r\n2016-09-09 12:48:09  [7f88f865c700] ERROR: ***** Internal Program Error - assertion (undoneAlignmentPos <= int64_t(undoPivotGap.getEndPos(false).getPosition())) failed \r\nin isaac::build::GapRealigner::GapChoice isaac::build::GapRealigner::findBetterGapsChoice(const isaac::build::gapRealigner::GapsRange&, const isaac::reference::ReferencePosition&, const isaac::reference::ReferencePosition&, const ContigList&, const isaac::io::FragmentAccessor&, const isaac::build::PackedFragmentBuffer::Index&, unsigned int&):/scratch/local2/build/illumina/Isaac3/src/c++/lib/build/GapRealigner.cpp(1092): \r\nundoPivotPos pos ReferencePosition(0:3309721:0f) overlapped by an existing deletion PackedFragmentBuffer::Index(ReferencePosition(0:3309721:0f),271963004do 271963291mdo, 22M25D102M)\r\n\r\n/scratch/cluster/mx/test_mouse/20160909_111202.mapping.mx.cpu40.vig1/3.ext_L7255-3_SJL.grcm38/run.3.isaac.sh: line 11: \r\n118927 Segmentation fault      \r\n/package/sequencer/illumina/isaac/current/bin/isaac-align \r\n--base-calls /scratch/cluster/mx/test_mouse/20160909_111202.mapping.mx.cpu40.vig1/3.ext_L7255-3_SJL.grcm38\r\n--base-calls-format fastq-gz \r\n--default-adapters Standard \r\n--reference-genome /project/genomes/Mus_musculus/NCBI/GRCm38/Sequence/iSAACIndex/sorted-reference.xml \r\n--realign-gaps sample\r\n--scatter-repeats 1\r\n--single-library-samples 0 \r\n--keep-duplicates 1 \r\n--bam-header-tag \"@RG\\tID:ext_L7255-3_SJL\\tLB:ext_L7255-3_SJL\\tSM:ext_L7255-3_SJL\\tPL:illumina\\tCN:MPIMG\\tDS:xxx, Mouse Whole Genome Sequencing (WGS)\" \r\n--keep-unaligned back \r\n--lane-number-max 3 \r\n--mark-duplicates 1 \r\n--clip-overlapping 1 \r\n--clip-semialigned 0 \r\n--description \"xxx, Mouse Whole Genome Sequencing (WGS)\" --jobs 40 \r\n--memory-limit 80 \r\n--input-concurrent-load 40 \r\n--temp-concurrent-load 8 \r\n--output-concurrent-save 40 \r\n--temp-concurrent-save 40 \r\n--cleanup-intermediary 1 \r\n--verbosity 3 \r\n--output-directory /scratch/cluster/mx/test_mouse/20160909_111202.mapping.mx.cpu40.vig1/3.ext_L7255-3_SJL.grcm38 \r\n--temp-directory /scratch/cluster/mx/test_mouse/20160909_111202.mapping.mx.cpu40.vig1/3.ext_L7255-3_SJL.grcm38/temp \r\n--realign-vigorously 1\r\n```\r\n\r\nSetting `--realign-vigorously 1` to `0` (which is the default) works like a charm.\r\n\r\nThis is `Version: iSAAC-03.16.06.06`.\r\n\r\nbest,\r\nSven"},"comment":{"url":"https://api.github.com/repos/Illumina/Isaac3/issues/comments/246771255","html_url":"https://github.com/Illumina/Isaac3/issues/5#issuecomment-246771255","issue_url":"https://api.github.com/repos/Illumina/Isaac3/issues/5","id":246771255,"user":{"login":"rpetrovski","id":3091569,"avatar_url":"https://avatars.githubusercontent.com/u/3091569?v=3","gravatar_id":"","url":"https://api.github.com/users/rpetrovski","html_url":"https://github.com/rpetrovski","followers_url":"https://api.github.com/users/rpetrovski/followers","following_url":"https://api.github.com/users/rpetrovski/following{/other_user}","gists_url":"https://api.github.com/users/rpetrovski/gists{/gist_id}","starred_url":"https://api.github.com/users/rpetrovski/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/rpetrovski/subscriptions","organizations_url":"https://api.github.com/users/rpetrovski/orgs","repos_url":"https://api.github.com/users/rpetrovski/repos","events_url":"https://api.github.com/users/rpetrovski/events{/privacy}","received_events_url":"https://api.github.com/users/rpetrovski/received_events","type":"User","site_admin":false},"created_at":"2016-09-13T18:09:50Z","updated_at":"2016-09-13T18:09:50Z","body":"Sven, I've just pushed the latest iSAAC-03 along with the fixes for vigorous realignment. Please let me know if you experience further issues.\r\n\r\nRoman."}}
{"actor":{"display_login":"rpetrovski"}}