search

lh3 / fermikit

De novo assembly based variant calling pipeline for Illumina short reads
Other
107 stars 22 forks source link

Error in last command of run-calling #7

Closed nextgenusfs closed 9 years ago

nextgenusfs commented 9 years ago

I'm getting an error in the last cmd of the run-calling script, specifically with the htsbox abreak command. The perl script, run-calling, has this syntax for the last command: $cmd .= "$root/htsbox abreak -cu $prefix.unsrt.sam.gz | gzip -1 > $prefix.sv.vcf.gz;\n";

Which looks like it is passing "-cu" flag to htsbox abreak, however those don't appear to be valid options:

Usage: htscmd abreak [options] |

Options: -b assume the input is BAM (default is SAM) -l INT exclude contigs shorter than INT [150] -q INT exclude alignments with mapQ below INT [10] -m FLOAT exclude alignments overlapping another long alignment by FLOAT fraction [0.5] -g INT join alignments separated by a gap shorter than INT bp [500]

Note: recommended BWA-SW setting is '-b9 -q16 -r1 -w500'

Thanks. Jon

lh3 commented 9 years ago

Perhaps you have another htsbox installed. Older htsbox doesn't have "-c" and "-u". Could you check? Thanks.

nextgenusfs commented 9 years ago

I installed through home-brew, which gave me this version. Version: htslib lite-r254, htsbox r266

So I take it that is an old version?

lh3 commented 9 years ago

It is very old.

nextgenusfs commented 9 years ago

Ok, thanks. I just cloned directly and all seems to be fine now. Thanks again for the help.

On Jul 13, 2015, at 11:24 AM, Heng Li notifications@github.com wrote:

It is very old.

— Reply to this email directly or view it on GitHub https://github.com/lh3/fermikit/issues/7#issuecomment-120985759.