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Problem with bcbio-nextgen freebayes-variant gets stuck in bedtools
Entering edit mode
2.4 years ago
idedios • 30
USA/Irvine/NeoGenomics Laboratories

I'm running the freebayes-variant template in bcbio-nextgen 0.9.0 and it gets stuck on bedtools complaining about the bed file I supplied with my samples. Here's the error message:

Command was:

bedtools subtract -b .../work/bedprep/A.bed -a .../work/tx/tmpDFyTaE/pybedtools.joKpzl.tmp

Error message was:

* WARNING: File .../tx/tmpDFyTaE/pybedtools.joKpzI.tmp has inconsistent naming convention for record:

1 0 249250621

A.bed is sorted and formatted as follows:

chr1 2488104 2488172

chr2 25461999 25462084


Any idea what's going on?

Entering edit mode
16 months ago
Sam ♦ 2.3k
New York

Your bed file follow the chrXX naming whereas your other file follows the xx naming. Removing the chr from your bed file should solve your problem


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