New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

SEQ and QUAL are of different length #1639

deber1980 opened this Issue Nov 13, 2016 · 3 comments


None yet
2 participants

deber1980 commented Nov 13, 2016


I'm getting the error below while running pipeline. Is there any practical way to debug this? I guess the problem might be with the files themselves but they are huge....


[fputs] Broken pipe
[E::sam_parse1] incomplete aux field
[W::sam_read1] parse error at line 259549
[bam_sort_core] truncated file. Aborting.
[E::sam_parse1] SEQ and QUAL are of different length
[W::sam_read1] parse error at line 170753
[bam_sort_core] truncated file. Aborting.
[W::sam_read1] parse error at line 27387614
[main_samview] truncated file.
' returned non-zero exit status 1
' returned non-zero exit status 1


This comment has been minimized.


chapmanb commented Nov 14, 2016

Sorry about the problem, we'd likely need more information about your run to be able to debug this. It's typically due to some sort of memory issue during the run. If you're using 0.9.9 the latest development version has some fixes to try and improve resource usage during the alignment process and also does automatic splitting of alignments for giant BAM files to avoid problems. If you're already using the latest development, a full traceback and understanding of the sample YAML you're using could help us try to provide more helpful information.


This comment has been minimized.

deber1980 commented Nov 15, 2016

I'm running a version from about 1-2 weeks ago (dev).
I provided a description of the configuration and what I'm doing in #1526
Is there a way to work around it? Use less threads when running bcbio for instance? Can I increase samblaster memory?


This comment has been minimized.


chapmanb commented Nov 15, 2016

Thanks for the additional details. I'll answer these questions in the other thread and close this to keep the discussion in one place.

@chapmanb chapmanb closed this Nov 15, 2016

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment