This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Error with samtools - indexing alignments: Writing to standard output failed: broken pipe - python

I am trying to use a pipeline for aligning data from a technique developed by another lab: https://github.com/SavageLab/dipseq/blob/master/README.md It was written a couple years ago and I think that it's not compatible with the most up to date samtools distribution.

I am trying to debug it and fix it so I can use it for my data analysis. The current error I am having is:

[E::bgzf_flush] hwrite error (wrong size) samtools view: writing to standard output failed: Broken pipe [E::bgzf_close] file write error samtools view: error closing standard output: -1

Does anyone know why it might be incopatible with samtools and how to approach solving this problem?

Thanks Willow

alignment software error
• 7,055 views • link
updated by Biostar Biostar • written by coyot001 • coyot001

Not sure if this helps but I usually get a broken pipe if my computer sleeps during an analysis. If that's the case you can run it with nohup or use a screen.

• 0 views • link
written by Jake Warner Jake Warner

dipseq comes with a bunch of tests and concise instructions how to run them. Did you try the tests? That would be my first suggestion.

If you suspect a newer SAMtools is the culprit, install an old one, they are still available for download.

• 0 views • link
written by h.mon h.mon

I had the same error with samtools=1.8 so downgraded to 0.1.19 and this fixed the problem.

• 1 views • link
written by jnkoberstein • jnkoberstein

0 answers

No answers yet.

Log in to answer this question.

More posts like this