Problem with bcbio-nextgen freebayes-variant gets stuck in bedtools
1
0
Entering edit mode
5.7 years ago
idedios ▴ 30

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?

next-gen bcbio-nextgen bedtools • 1.3k views
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3
Entering edit mode
5.7 years ago
Sam ★ 3.4k

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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