Error with samtools - indexing alignments: Writing to standard output failed: broken pipe - python

Question

[coyot001]

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

[Jake Warner]

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.

[dr_bantz]

Sounds like your bam files might be too big. See here:

ANGSD hwrite error (wrong size)

[h.mon]

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.

[jnkoberstein]

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