Question: Error running tophat2
1
gravatar for nelger
2.6 years ago by
nelger10
nelger10 wrote:

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.

 

tophat software error galaxy • 886 views
ADD COMMENTlink modified 23 months ago by deane30 • written 2.6 years ago by nelger10
0
gravatar for Jennifer Hillman Jackson
2.6 years ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

What distribution are you running? The latest was officially finalized/released yesterday, v 16.01. Perhaps upgrade to this master branch and see if the problem resolves? https://wiki.galaxyproject.org/News/2016_01_GalaxyRelease

Reinstalling the tool with the option to include dependencies is also a troubleshooting step.

Thanks, Jen, Galaxy team

ADD COMMENTlink written 2.6 years ago by Jennifer Hillman Jackson25k
0
gravatar for deane
23 months ago by
deane30
deane30 wrote:

I am having this same issue with 16.07 I tried tophat2 and older versions and got the same error.

galaxy.jobs.runners.local DEBUG 2016-10-18 12:33:03,293 execution finished: /home/galaxy/galaxy/database/jobs_directory/000/6/galaxy_6.sh galaxy.jobs.output_checker INFO 2016-10-18 12:33:03,305 Job 6: Log: tool progress galaxy.jobs.output_checker INFO 2016-10-18 12:33:03,305 Job 6: Log: tool progress galaxy.model.metadata DEBUG 2016-10-18 12:33:03,420 loading metadata from file for: HistoryDatasetAssociation 10 galaxy.model.metadata DEBUG 2016-10-18 12:33:03,492 loading metadata from file for: HistoryDatasetAssociation 11 galaxy.model.metadata DEBUG 2016-10-18 12:33:03,564 loading metadata from file for: HistoryDatasetAssociation 12 galaxy.model.metadata DEBUG 2016-10-18 12:33:03,638 loading metadata from file for: HistoryDatasetAssociation 13 galaxy.model.metadata DEBUG 2016-10-18 12:33:03,672 setting metadata externally failed for HistoryDatasetAssociation 14: [Errno 2] No such file or directory galaxy.jobs.runners.local ERROR 2016-10-18 12:33:03,747 Job wrapper finish method failed

Was this error resolved somehow?

deane@blazie.net

ADD COMMENTlink written 23 months ago by deane30
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