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> https://bitbucket.org/peterjc/galaxy-central/changeset/d2c80e51d1fc 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 &> /home/pjcock/repositories/galaxy-central/database/tmp/GALAXY_VERSION_STRING_192; python /home/pjcock/repositories/galaxy-central/tools/sr_assembly/mira.py mira /home/pjcock/repositories/galaxy-central/database/files/000/dataset_403.dat /home/pjcock/repositories/galaxy-central/database/files/000/dataset_404.dat /home/pjcock/repositories/galaxy-central/database/files/000/dataset_406.dat /home/pjcock/repositories/galaxy-central/database/files/000/dataset_405.dat /home/pjcock/repositories/galaxy-central/database/files/000/dataset_407.dat /home/pjcock/repositories/galaxy-central/database/files/000/dataset_408.dat mira --job=denovo,genome,accurate 454_SETTINGS -LR:lsd=yes -LR:mxti=no -LR:ft=fastq -FN:fqi=/home/pjcock/repositories/galaxy-central/database/files/000/dataset_402.dat COMMON_SETTINGS -OUT:rrot=yes -OUT:rtd=yes MIRA took 4.98 minutes Done 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? Peter ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
