Error when correcting with reads about ragtag HOT 4 CLOSED

Sorry - I just realized the output got cutoff in my original post. I do have the following files. I'll check them out now.
c_reads_against_query.s.bam
c_reads_against_query.s.bam.bai

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It turned out to be an issue with my reads file. Thanks!

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Hi there,

Thanks for bringing this to my attention. It's not clear from the log, but the log is actually truncated. In future versions, I will add a log message that signals the end of the program. Something like "bye".

So something went wrong between compressing and sorting the read alignments. Is the sam/bam file empty? Aside from that bam file, we should also see a sorted bam file named c_reads_against_query.s.bam

It is strange that things failed yet there is no error message from pysam or anything else. Would you be willing to share the data so that I can reproduce the error? Unfortunately, it looks like the error is silent which makes it hard to debug.

You may be eager to get results in the meantime. Assuming the c_reads_against_query.sam looks ok, you can compress, sort and index it yourself with samtools (view, sort and index). Just be sure to name the sorted bam file c_reads_against_query.s.bam and put it in the same ragtag_output directory. Then, when you run ragtag with the same command, it will recognize the sorted bam file and it will (hopefully) proceed as normal.

Thanks,
Mike

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I should be more clear - aside from just checking if the SAM/BAM file is empty, please check the general integrity of the files with samtools. I have a feeling something is going wrong with pysam here.

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