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ConcatVCF_Mutect2 recurring SIGPIPE #268

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sabackman opened this issue Aug 19, 2020 · 0 comments
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ConcatVCF_Mutect2 recurring SIGPIPE #268

sabackman opened this issue Aug 19, 2020 · 0 comments
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@szilvajuhos

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I've been running Sarek 2.6.1 on a number of normal-tumour sample pairs and quite often the runs crash due to a SIGPIPE in one or more of the ConcatVCF_Mutect2 jobs:

Process ConcatVCF_Mutect2 (SJ-2335-10703_vs_SJ-2335-1647) terminated with an error exit status (141)

Rerunning with the -resume always works, but typically some results are lost and need to be computed again. Some additions to the configuration file should solve the issue (similar to ConcatVCF).
This was referenced Aug 19, 2020
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maxulysse added a commit to maxulysse/nf-core_sarek that referenced this issue Aug 19, 2020
@maxulysse
fix issue nf-core#268
6c1a743
maxulysse added a commit that referenced this issue Aug 20, 2020
@maxulysse
Merge pull request #271 from MaxUlysse/CONCATVCF
131f9f6 
fix issue #268
@szilvajuhos szilvajuhos self-assigned this Aug 25, 2020
@szilvajuhos szilvajuhos mentioned this issue Aug 27, 2020
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@maxulysse @szilvajuhos @sabackman