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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.
Describe the bug
When running
biscuit pileup -@ 4 -5 9 -3 5 -p -C 0 ${ref} ${bam} | bgzip -@ 4 > example.vcf.gzon 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