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nloyfer / wgbs_tools

tools for working with Bisulfite Sequencing data while preserving reads intrinsic dependencies
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bam2pat invalid input argument empty bam file #50

Closed sc2936 closed 1 year ago

sc2936 commented 1 year ago

I tried wgbstools bam2pat directory/*.bam -r $region and it gives me 3 lines as a result. The first line says bam: directory/filename.bam The second line says Invalid input argument The third line says Empty bam file

When I check the size of my bam file in that directory, it says 1.85 KB.

I'm not sure why I am getting these errors. Any suggestions?

sc2936 commented 1 year ago

I used samtools view to check, and it turns out that yes, my bam file was empty. Bam files should have MB units for them to be converted to pat and beta files.