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 - firstname.lastname@example.org