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FilterAlignmentArtifacts Segfaulting #7162
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Update: I did some more cutting on the VCF and I can reproducibly cause a segfault with only these 4 variants in the VCF. I am attaching the associated VCF and log files here. The other files should remain the same as above. |
@takutosato @davidbenjamin Could one you comment on this one? |
Please let me know if there is anything I can do for further information. |
@michael-weinstein This looks like an issue in our accelerated Pair-HMM implementation from Intel. PR #7105 is in code review and will offer a work-around once merged. |
I am running into the same issue with v4.2.0.0. Has this been fixed yet? |
Bug Report
Affected tool(s) or class(es)
FilterAlignmentArtifact
Affected version(s)
Docker container running 4.1.9.0
Description
Appears to be causing a segfault
Steps to reproduce
COMMAND
COPY OF SHELL SESSION
RELEVANT FILES
hs_err_pid100.log
hs_err_pid164.log
hs_err_pid274.log
hs_err_pid400.log
hs_err_pid482.log
hs_err_pid711.log
hs_err_pid735.log
hs_err_pid801.log
hs_err_pid825.log
hs_err_pid849.log
otherFiles.zip
in2510-8.orientationFilter.vcf.txt
VCF extension appended with .txt to satisfy GitHub's upload requirements
Expected behavior
Worked on 7 other files generated with the same pipeline.
Actual behavior
Unsure why this last one is causing a segfault. The VCF included is not the whole VCF submitted originally. I went cutting out lines from the original until I could isolate it down to a minimal set required to reproduce the crash (I included all of the crash logs generated in case it can help). I was expecting to find a single line or maybe two that were required to reproduce this issue, but that range appears to be needed. Eliminating either the first or last line from the range will make the program work again. Did not attempt to remove lines from the middle of the range yet to see if they're necessary to cause the fault, but it's 2am and I should probably sleep.
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