We have a local install of galaxy which has the mpileup 0.0.3 tool installed (we can't go higher as we need to use a 1.1.x version of samtools). When we run the tool it appears to run for a reasonable amount of time and the result dataset is written to disk and is of a non-zero size however we get the following errors:
Traceback (most recent call last):
File "/data/galaxy/app/lib/galaxy/jobs/runners/local.py", line 129, in queue_job
job_wrapper.finish( stdout, stderr, exit_code )
File "/data/galaxy/app/lib/galaxy/jobs/__init__.py", line 1204, in finish
dataset.datatype.set_meta( dataset, overwrite=False )
File "/data/galaxy/app/lib/galaxy/datatypes/binary.py", line 502, in set_meta
proc = subprocess.Popen( args=command, stderr=open( stderr_name, 'wb' ) )
File "/usr/lib64/python2.6/subprocess.py", line 642, in __init__
File "/usr/lib64/python2.6/subprocess.py", line 1238, in _execute_child
OSError: [Errno 2] No such file or directory
Unable to finish job
We have seen the same error with the 0.0.2 version as well.
Any assistance you can give to why we are seeing this would be gratefully received!