Question: Error with samtools - indexing alignments: Writing to standard output failed: broken pipe - python
gravatar for coyot001
2.7 years ago by
coyot0010 wrote:

I am trying to use a pipeline for aligning data from a technique developed by another lab: 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 • 2.6k views
ADD COMMENTlink modified 2.6 years ago by Biostar ♦♦ 20 • written 2.7 years ago by coyot0010

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.

ADD REPLYlink written 2.7 years ago by Jake Warner800

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

ANGSD hwrite error (wrong size)

ADD REPLYlink written 2.6 years ago by dr_bantz80

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.

ADD REPLYlink modified 21 months ago • written 2.6 years ago by h.mon29k

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

ADD REPLYlink written 21 months ago by jnkoberstein0
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