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[Issue] Pileup errors #30

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njspix opened this issue Sep 30, 2022 · 0 comments
Open

[Issue] Pileup errors #30

njspix opened this issue Sep 30, 2022 · 0 comments
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@njspix
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njspix commented Sep 30, 2022

Describe the bug
When running biscuit pileup -@ 4 -5 9 -3 5 -p -C 0 ${ref} ${bam} | bgzip -@ 4 > example.vcf.gz on some single-cell WGBS data against the grch38 reference, I will sometimes get the following error in stderr:
[refcache_fetch:96] Error, cannot retrieve reference chr1:0-0.
However, re-rerunning the command once or twice is usually enough to get the command to succeed without error.

BISCUIT version
Version: 1.0.2.20220113
(singularity container: https://depot.galaxyproject.org/singularity/mulled-v2-13ecc02e46375c1530003669d682d88af478b062:8f5ef05bea4d307d50ffcf518735290a84db36a5-0)

Minimally Reproducible Example
?? not consistently reproducible ??

Expected behavior
Pileup should exit with status > 0 or complete successfully.

Computer Resources

  • OS: Linux node110 3.10.0-1160.15.2.el7.x86_64 My QC.sh changes #1 SMP Wed Feb 3 15:06:38 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux
  • RAM: (default, node has 376G)
  • CPUs: 4
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