jgi_summarize_bam_contig_depths: 'Killed'

[Sarah Turner]

I need to use jgi_summarize_bam_contig_depths to produce a depth file. I believe that MetaBAT and all of its requirements are correctly installed. I have eight .bam files that I want to generate a depth.txt file for.

My command:

jgi_summarize_bam_contig_depths --outputDepth depth.txt *.bam

It runs for a while, but then just says "Killed" and stops (no output file, nothing). Is there something I'm doing wrong? (For the record, I have both sorted .bam files and indexed .bam.bai files, but the files that I've been using are not the sorted ones. Is that the issue? I'd have to spend many hours downloading the sorted ones and the indexes, so I'm hoping to get some answers before I do that.)

Thanks in advance.

[Rob Egan]

That code expects the BAM data to be in sorted order, and I would not expect it work work on unsorted bams. I believe there are assertions in the code, but perhaps this is not enforced in the optimized build. You should be able to sort the bam files with "samtools sort" directly without downloading a new copy of the data. -Rob

[Rob Egan]

The usage states that sortedBams are the expected input