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bcbio / bcbio-nextgen

Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis
https://bcbio-nextgen.readthedocs.io
MIT License
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error running manta #1854

Closed PatrickJReed closed 7 years ago

PatrickJReed commented 7 years ago

Manta seems to run cleanly on some of my samples but not others that were all aligned and processed together with bcbio.

Config template:

details:

I am getting the following error:

[2017-03-10T18:43:46.531640] [ip-172-31-46-218.us-west-2.compute.internal] [118852_1] [TaskManager] [ERROR] Failed to complete command task: 'getAlignmentStats_generateStats_000' launched from master workflow, error code: 1, command: '/usr/local/share/bcbio/anaconda/share/manta-1.0.3-0/libexec/GetAlignmentStats --output-file /efs/SZ_Twins_Raw/SZ_Twins_SampleInfo-merged/work/bcbiotx/tmpfkPKvj/manta/workspace/alignmentStats.xml.tmpdir/alignmentStats.xml.000.xml --align-file /efs/SZ_Twins_Raw/SZ_Twins_SampleInfo-merged/work/align/2_NS_Fibro/2_NS_Fibro-sort.bam' [2017-03-10T18:43:46.536264] [ip-172-31-46-218.us-west-2.compute.internal] [118852_1] [TaskManager] [ERROR] [getAlignmentStats_generateStats_000] Error Message: [2017-03-10T18:43:46.536291] [ip-172-31-46-218.us-west-2.compute.internal] [118852_1] [TaskManager] [ERROR] [getAlignmentStats_generateStats_000] Last 11 stderr lines from task (of 11 total lines): [2017-03-10T18:43:46.536291] [ip-172-31-46-218.us-west-2.compute.internal] [118852_1] [TaskManager] [ERROR] [2017-03-10T18:43:46.219741] [ip-172-31-46-218.us-west-2.compute.internal] [118852_1] [getAlignmentStats_generateStats_000] FATAL_ERROR: GetAlignmentStats EXCEPTION: 2017-Mar-10 18:43:46: Operation not permitted: /builder/src/c++/lib/manta/ReadGroupStatsUtil.cpp(195): Throw in function void ReadGroupOrientTracker::finalize() [2017-03-10T18:43:46.536291] [ip-172-31-46-218.us-west-2.compute.internal] [118852_1] [TaskManager] [ERROR] [2017-03-10T18:43:46.233441] [ip-172-31-46-218.us-west-2.compute.internal] [118852_1] [getAlignmentStats_generateStats_000] Dynamic exception type: N5boost16exception_detail10clone_implIN8illumina6common14LogicExceptionEEE [2017-03-10T18:43:46.536291] [ip-172-31-46-218.us-west-2.compute.internal] [118852_1] [TaskManager] [ERROR] [2017-03-10T18:43:46.243936] [ip-172-31-46-218.us-west-2.compute.internal] [118852_1] [getAlignmentStats_generateStats_000] std::exception::what: ERROR: Too few observations (0) to determine pair orientation for read group '' in bam file '/efs/SZ_Twins_Raw/SZ_Twins_SampleInfo-merged/work/align/2_NS_Fibro/2_NS_Fibro-sort.bam' [2017-03-10T18:43:46.536291] [ip-172-31-46-218.us-west-2.compute.internal] [118852_1] [TaskManager] [ERROR] [2017-03-10T18:43:46.254876] [ip-172-31-46-218.us-west-2.compute.internal] [118852_1] [getAlignmentStats_generateStats_000] [2017-03-10T18:43:46.536291] [ip-172-31-46-218.us-west-2.compute.internal] [118852_1] [TaskManager] [ERROR] [2017-03-10T18:43:46.265807] [ip-172-31-46-218.us-west-2.compute.internal] [118852_1] [getAlignmentStats_generateStats_000] : ERROR: Too few observations (0) to determine pair orientation for read group '' in bam file '/efs/SZ_Twins_Raw/SZ_Twins_SampleInfo-merged/work/align/2_NS_Fibro/2_NS_Fibro-sort.bam' [2017-03-10T18:43:46.536291] [ip-172-31-46-218.us-west-2.compute.internal] [118852_1] [TaskManager] [ERROR] [2017-03-10T18:43:46.274880] [ip-172-31-46-218.us-west-2.compute.internal] [118852_1] [getAlignmentStats_generateStats_000] [2017-03-10T18:43:46.536291] [ip-172-31-46-218.us-west-2.compute.internal] [118852_1] [TaskManager] [ERROR] [2017-03-10T18:43:46.286380] [ip-172-31-46-218.us-west-2.compute.internal] [118852_1] [getAlignmentStats_generateStats_000] ...caught in program.run() [2017-03-10T18:43:46.536291] [ip-172-31-46-218.us-west-2.compute.internal] [118852_1] [TaskManager] [ERROR] [2017-03-10T18:43:46.295872] [ip-172-31-46-218.us-west-2.compute.internal] [118852_1] [getAlignmentStats_generateStats_000] cmdline: /usr/local/share/bcbio/anaconda/share/manta-1.0.3-0/libexec/GetAlignmentStats --output-file /efs/SZ_Twins_Raw/SZ_Twins_SampleInfo-merged/work/bcbiotx/tmpfkPKvj/manta/workspace/alignmentStats.xml.tmpdir/alignmentStats.xml.000.xml --align-file /efs/SZ_Twins_Raw/SZ_Twins_SampleInfo-merged/work/align/2_NS_Fibro/2_NS_Fibro-sort.bam [2017-03-10T18:43:46.536291] [ip-172-31-46-218.us-west-2.compute.internal] [118852_1] [TaskManager] [ERROR] [2017-03-10T18:43:46.304891] [ip-172-31-46-218.us-west-2.compute.internal] [118852_1] [getAlignmentStats_generateStats_000] version: 1.0.3 [2017-03-10T18:43:46.536291] [ip-172-31-46-218.us-west-2.compute.internal] [118852_1] [TaskManager] [ERROR] [2017-03-10T18:43:46.313940] [ip-172-31-46-218.us-west-2.compute.internal] [118852_1] [getAlignmentStats_generateStats_000] buildTime: 2016-11-15T15:58:15.020857Z [2017-03-10T18:43:46.536291] [ip-172-31-46-218.us-west-2.compute.internal] [118852_1] [TaskManager] [ERROR] [2017-03-10T18:43:46.324477] [ip-172-31-46-218.us-west-2.compute.internal] [118852_1] [getAlignmentStats_generateStats_000] compiler: g++-4.9.3 [2017-03-10T18:43:46.536370] [ip-172-31-46-218.us-west-2.compute.internal] [118852_1] [TaskManager] [ERROR] Shutting down task submission. Waiting for remaining tasks to complete.

PatrickJReed commented 7 years ago

Resolved, sample is SE