Question: Local Tophat Error "OSError: [Errno 2] No such file or directory"
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gravatar for deane
13 months ago by
deane30
deane30 wrote:

I have created a local Galaxy server to run RNA analysis. I am trying to run TOPHAT on a fastasanger file and am using a reference genome from my history. I was able to successfully run the Fasta-Groomer on my raw fasta file to create the fasta-sanger file. But running tophat on the Groomer output against the local reference genome gives this error output on all 5 of the output datasets:

Dataset generation errors Dataset 9: TopHat on data 2 and data 4: accepted_hits

The Galaxy framework encountered the following error while attempting to run the tool: Traceback (most recent call last): File "/home/galaxy/galaxy/lib/galaxy/jobs/runners/local.py", line 128, in queue_job job_wrapper.finish( stdout, stderr, exit_code ) File "/home/galaxy/galaxy/lib/galaxy/jobs/__init__.py", line 1265, in finish dataset.datatype.set_meta( dataset, overwrite=False ) File "/home/galaxy/galaxy/lib/galaxy/datatypes/binary.py", line 347, in set_meta exit_code = subprocess.call( args=command, stderr=open( stderr_name, 'wb' ) ) File "/usr/lib/python2.7/subprocess.py", line 523, in call return Popen(popenargs, *kwargs).wait() File "/usr/lib/python2.7/subprocess.py", line 711, in __init__ errread, errwrite) File "/usr/lib/python2.7/subprocess.py", line 1343, in _execute_child raise child_exception OSError: [Errno 2] No such file or directory

I created the local instance of Galaxy (July 2016) on a Ubuntu 16.04 workstation under user "galaxy".
I could not find a similar report on the Forums. I tried older versions of Tophat with the same results. I tried different reference genomes also with the same results. It appears that tophat had finished and generated good data but was unable to post the metadata and/or cleanup. I am not sure how to debug this error at this point.

Any help would be appreciated.

Deane Blazie - deane@blazie.net

path tophat admin local samtools • 1.0k views
ADD COMMENTlink modified 13 months ago by Jennifer Hillman Jackson23k • written 13 months ago by deane30
2
gravatar for deane
13 months ago by
deane30
deane30 wrote:

I solved this by adding a link to /usr/local/bin to the galaxy directory where the tool-shed installed samtools.

My search on the galaxy forums showed this to be a pretty common error. I can see where it may not be a samtools bug, but it would save a lot of research time if Galaxy took care of it somehow, possibly in the galaxy startup scripts.

I appreciate the help on this issue.

Thanks djevo1. Deane

ADD COMMENTlink written 13 months ago by deane30

The Galaxy dev team is reviewing ideas to make this process simpler in the future. Watch the release notes for upcoming Galaxy releases to find out when the solution is implemented.

ADD REPLYlink written 13 months ago by Jennifer Hillman Jackson23k
1
gravatar for djevo1
13 months ago by
djevo160
djevo160 wrote:

I believe your issue is that you haven't installed samtools and added it to your PATH. I had the same issue and rectified it by downloading samtools to a local directory visible to galaxy and then added the directory by using export PATH='directory to samtools':$PATH

ADD COMMENTlink modified 13 months ago • written 13 months ago by djevo160

Thank you for the response. I did try this but got the same error. Samtools was loaded and all dependencies seemed to be satisfied. The stdio error seems to indicate that it could not write to the database to store Metadata:

galaxy.jobs.output_checker INFO 2016-10-18 21:58:11,363 Job 7: Log: tool progress galaxy.jobs.output_checker INFO 2016-10-18 21:58:11,363 Job 7: Log: tool progress galaxy.model.metadata DEBUG 2016-10-18 21:58:11,455 loading metadata from file for: HistoryDatasetAssociation 15 galaxy.model.metadata DEBUG 2016-10-18 21:58:11,662 loading metadata from file for: HistoryDatasetAssociation 16 galaxy.model.metadata DEBUG 2016-10-18 21:58:11,732 loading metadata from file for: HistoryDatasetAssociation 17 galaxy.model.metadata DEBUG 2016-10-18 21:58:11,805 loading metadata from file for: HistoryDatasetAssociation 18 galaxy.model.metadata DEBUG 2016-10-18 21:58:11,838 setting metadata externally failed for HistoryDatasetAssociation 19: [Errno 2] No such file or directory galaxy.jobs.runners.local ERROR 2016-10-18 21:58:11,894 Job wrapper finish method failed

I'm not sure how to debug this.

Deane

ADD REPLYlink written 13 months ago by deane30

Can you paste the full error, probably 10 more lines above?

ADD REPLYlink written 13 months ago by djevo160
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