Dear all,

While updating my MIRA wrapper for MIRA v3.4.0, with a test case
that takes about half an hour to run, I was sometimes getting the
following error message (on stderr):

uname: write error: Broken pipe

My hunch is this is a side effect of adding a version_command tag,
<version_command>mira --version | head -n 1</version_command>

This isn't down to the dataset or very long run times - I've tried a
small phage which assembles in about 5 minutes with the same
error on stdout. When I have repeated the exact same command
at the terminal, it has run without issue, e.g.

$ mira --version | head -n 1 &>
python /home/pjcock/repositories/galaxy-central/tools/sr_assembly/
mira /home/pjcock/repositories/galaxy-central/database/files/000/dataset_403.dat
mira --job=denovo,genome,accurate      454_SETTINGS     -LR:lsd=yes
 -LR:mxti=no -LR:ft=fastq
 COMMON_SETTINGS -OUT:rrot=yes -OUT:rtd=yes

MIRA took 4.98 minutes

One point which may be relevant is that the MIRA binary
produces quite a lot of output on stdout (often megabytes),
which my Python wrapper scripts is redirecting to a file (to
collect it as a Galaxy output). Perhaps this issue is related
to lots of data on stdout/stderr?

For the moment I am removing the version_command tag,
which appears to solve this problem, and I will report back
if the broken pipe error still happens.

Has anyone else noticed anything similar?

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