search

walaj / bxtools

Tools for analyzing 10X Genomics data
MIT License
42 stars 10 forks source link

fail to open new bam file when splitting #15

Closed verne91 closed 7 years ago

verne91 commented 7 years ago

I want to split bam file with 10x barcodes. But it seemed that bxtools did not generate bam files for all barcodes. The error is "E::hts_open_format] fail to open file 'abc.bam' Could not open BAM: abc.bam"

walaj commented 7 years ago

abc.bam is the BAM that you would like to split? Can you check that samtools can operate on this BAM? This looks like something is corrupted with the BAM, since the error is direct from htslib code that is baked into bxtools.

verne91 commented 7 years ago

I got the reason. There are too many barcodes in the bam file and my system has the limitation of the number of opening files.

Thanks.