I have a local galaxy server that is encountering some strange issues. Previously, tophat2 was running fine, but now all of a sudden, I am encountering an error with all tophat2 jobs exiting with:
Dataset 51: TopHat on data 5: align_summary
The Galaxy framework encountered the following error while attempting to run the tool:
Traceback (most recent call last):
File "/opt/galaxy/lib/galaxy/jobs/runners/local.py", line 128, in queue_job
job_wrapper.finish( stdout, stderr, exit_code )
File "/opt/galaxy/lib/galaxy/jobs/__init__.py", line 1207, in finish
dataset.datatype.set_meta( dataset, overwrite=False )
File "/opt/galaxy/lib/galaxy/datatypes/binary.py", line 315, in set_meta
exit_code = subprocess.call( args=command, stderr=open( stderr_name, 'wb' ) )
File "/usr/lib64/python2.6/subprocess.py", line 478, in call
p = Popen(*popenargs, **kwargs)
File "/usr/lib64/python2.6/subprocess.py", line 642, in __init__
errread, errwrite)
File "/usr/lib64/python2.6/subprocess.py", line 1238, in _execute_child
raise child_exception
OSError: [Errno 2] No such file or directory
Tool execution generated the following error message:
Unable to finish job
The error in paster.log is:
galaxy.jobs.runners.local DEBUG 2016-02-25 01:59:38,957 execution finished: /opt/galaxy/database/job_working_directory/000/314/galaxy_314.sh
galaxy.jobs.output_checker INFO 2016-02-25 01:59:38,985 Job 314: Log: tool progress
galaxy.jobs.output_checker INFO 2016-02-25 01:59:38,985 Job 314: Log: tool progress
galaxy.datatypes.metadata DEBUG 2016-02-25 01:59:39,022 setting metadata externally failed for HistoryDatasetAssociation 565: [Errno 2] No such file or directory
galaxy.jobs.runners.local ERROR 2016-02-25 01:59:39,072 Job wrapper finish method failed
Traceback (most recent call last):
File "/opt/galaxy/lib/galaxy/jobs/runners/local.py", line 128, in queue_job
job_wrapper.finish( stdout, stderr, exit_code )
File "/opt/galaxy/lib/galaxy/jobs/__init__.py", line 1207, in finish
dataset.datatype.set_meta( dataset, overwrite=False )
File "/opt/galaxy/lib/galaxy/datatypes/binary.py", line 315, in set_meta
exit_code = subprocess.call( args=command, stderr=open( stderr_name, 'wb' ) )
File "/usr/lib64/python2.6/subprocess.py", line 478, in call
p = Popen(*popenargs, **kwargs)
File "/usr/lib64/python2.6/subprocess.py", line 642, in __init__
errread, errwrite)
File "/usr/lib64/python2.6/subprocess.py", line 1238, in _execute_child
raise child_exception
OSError: [Errno 2] No such file or directory
galaxy.datatypes.metadata DEBUG 2016-02-25 01:59:39,283 Cleaning up external metadata files
galaxy.datatypes.metadata DEBUG 2016-02-25 01:59:39,301 Failed to cleanup MetadataTempFile temp files from /opt/galaxy/database/job_working_directory/000/314/metadata_out_HistoryDatasetAssociation_565_r2iRVw: No JSON object could be decoded
A few days ago, I updated tophat2 to the latest version on galaxy, but jobs had been running fine up until now. The funny thing is that the tool runs for a while and produces some output- 1.1gb file on accepted hits, but I have no idea if this is complete or not.
Thanks,
Nathan
**EDIT: I just wanted to mention that I have verified that samtools is in my path- I threw the executable into /usr/local/bin after compiling.
