error while running Manta v1.2.2

[ricchasethi]

Hello,

I am running manta version 1.2.2 with hg19 as reference with paired tumor-normal sample. While executing the second step I get the error below. Can you please help me understand why this error is generated.
[25587_1] [TaskManager] [ERROR] Failed to complete command task: 'getChromDepth_sample000_estimateChromDepth_002_chr1_gl000192_random'
launched from master workflow, error code: 1, command: '/manta/build_manta1.2.2/libexec/GetChromDepth --ref hg19_SORTED.fa --align-file normal.sortedCO.bam --output manta/workspace/chromDepth.txt.tmpdir/chromDepth.txt.000.txt.tmpdir/chromDepth.txt.0
00.txt_002_chr1_gl000192_random --chrom chr1_gl000192_random'
[2017-11-16T15:59:45.399905] [25587_1] [TaskManager] [ERROR] [getChromDepth_sample000_estimateChromDepth_002_chr1_gl000192_random] Error Message:
[2017-11-16T15:59:45.406896] [25587_1] [TaskManager] [ERROR] [getChromDepth_sample000_estimateChromDepth_002_chr1_gl000192_random] Anomalous task wrapper stderr output. Wrapper signal file: 'manta/workspace/pyflow.data/logs/tmp/taskWrapperLogs/000/010/pyflowTaskWrapper.signal.txt'
[2017-11-16T15:59:45.416123] [25587_1] [TaskManager] [ERROR] [getChromDepth_sample000_estimateChromDepth_002_chr1_gl000192_random] Logging 6 line(s) of task wrapper
log output below:
[2017-11-16T15:59:45.427165] [25587_1] [TaskManager] [ERROR] [getChromDepth_sample000_estimateChromDepth_002_chr1_gl000192_random] [taskWrapper-stderr] [2017-11-16T
15:59:43.981317] [25587_1] [pyflowTaskWrapper:getChromDepth_sample000_estimateChromDepth_002_chr1_gl000192_random] [wrapperSignal] wrapperStart
[2017-11-16T15:59:45.435443] [25587_1] [TaskManager] [ERROR] [getChromDepth_sample000_estimateChromDepth_002_chr1_gl000192_random] [taskWrapper-stderr] [2017-11-16T
15:59:44.036707] [25587_1] [pyflowTaskWrapper:getChromDepth_sample000_estimateChromDepth_002_chr1_gl000192_random] [wrapperSignal] taskStart
[2017-11-16T15:59:45.480669] [25587_1] [TaskManager] [ERROR] [getChromDepth_sample000_estimateChromDepth_002_chr1_gl000192_random] [taskWrapper-stderr] [2017-11-16T
15:59:44.339082] [25587_1] [pyflowTaskWrapper:getChromDepth_sample000_estimateChromDepth_002_chr1_gl000192_random] [wrapperSignal] taskExitCode -6
[2017-11-16T15:59:45.522266] [25587_1] [TaskManager] [ERROR] [getChromDepth_sample000_estimateChromDepth_002_chr1_gl000192_random] [taskWrapper-stderr] [2017-11-16T
15:59:44.375386] [25587_1] [pyflowTaskWrapper:getChromDepth_sample000_estimateChromDepth_002_chr1_gl000192_random] [wrapperSignal] taskStderrTail 2
[2017-11-16T15:59:45.536006] [25587_1] [TaskManager] [ERROR] [getChromDepth_sample000_estimateChromDepth_002_chr1_gl000192_random] [taskWrapper-stderr] Last 1 stderr lines from task (of 1 total lines):
[2017-11-16T15:59:45.544465] [25587_1] [TaskManager] [ERROR] [getChromDepth_sample000_estimateChromDepth_002_chr1_gl000192_random] [taskWrapper-stderr] [2017-11-16T
15:59:44.304131] [25587_1] [getChromDepth_sample000_estimateChromDepth_002_chr1_gl000192_random] GetChromDepth: manta-1.2.2.release_src/src/c++/lib/blt_util/depth_buffer.hh:139: void depth_buffer_compressible::inc(pos_t, unsigned int): Assertion `posRange>=1' failed.

Thanks,
Riccha

[ctsa]

Thanks for reporting this @ricchasethi , this error hasn't been observed before.

Is this data you could share with us? If so, it looks like we could reproduce/fix this issue with just the sequences mapping to contig chr1_gl000192_random from normal sample normal.sortedCO.bam. Please contact me directly (csaunders@illumina.com) if you'd like to discuss options.

[ctsa]

Thank you for sharing data and helping us to debug this issue, for anyone else with this issue the improved error message (MANTA-1295) and fix for certain cases (MANTA-1296) preview is on branch https://github.com/Illumina/manta/tree/issue111Preview and will appear in the next point release.