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ACAD-UofA / Bioinformatics-Wiki

ACAD's Bioinformatics Wiki Pages
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PALEOMIX on ACAD1 #9

Closed EisenRa closed 6 years ago

EisenRa commented 7 years ago

Getting a bus error (damn that public transport)

[a1683110@acad1 corals]$ export MODULEPATH=/data/acad/apps/modules/all:$MODULEPATH [a1683110@acad1 corals]$ module load paleomix-meta [a1683110@acad1 corals]$ bam_pipeline run --jar-root $JAR_ROOT makefile.yaml Bus error (core dumped)

EisenRa commented 7 years ago

Not getting this error anymore, instead:

Traceback (most recent call last): File "/apps/software/Python/2.7.13-foss-2016b/lib/python2.7/logging/init.py", line 885, in emit self.flush() File "/apps/software/Python/2.7.13-foss-2016b/lib/python2.7/logging/init.py", line 845, in flush self.stream.flush() IOError: [Errno 28] No space left on device Logged from file pipeline.py, line 78

grahamgower commented 7 years ago

I guess /tmp is the disk its complaining about? You might try changing the path for paleomix's temp files. E.g.

$ mkdir -p /localscratch/EisenRa/tmp
$ bam_pipeline run --jar-root $JAR_ROOT --temp-root=/localscratch/EisenRa/tmp makefile.yaml

Not sure why you're getting the Bus error though.

EisenRa commented 7 years ago

That did the job, thanks!