Problem with bcbio-nextgen freebayes-variant gets stuck in bedtools

Question

[idedios]

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?

Answer 1

[Sam]

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