Hi, I am trying to do RNA analysis on local instance of Galaxy running in Linux mint. I have tried assembling the sequences using TopHat and got the error (see post: https://biostar.usegalaxy.org/p/19570/). I tried running HISAT, as I thought it may be a TopHat problem with the resources available. However when I run HISAT I am getting the same error (see below). I am not sure what the problem is, but I would really appreciate it if you can help me sort this out. I have been struggling with this error for over two weeks now. Any help and guidance will be greatly appreciated. Thanks in advance for your time.
Traceback (most recent call last):
File "/home/vythegi/galaxy1111/lib/galaxy/jobs/runners/local.py", line 128, in queue_job job_wrapper.finish( stdout, stderr, exit_code )
File "/home/vythegi/galaxy1111/lib/galaxy/jobs/__init__.py", line 1265, in finish dataset.datatype.set_meta( dataset, overwrite=False )
File "/home/vythegi/galaxy1111/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 1340, in _execute_child raise child_exception
OSError: [Errno 2] No such file or directory
The server is set up to run jobs on a cluster? This looks like a problem with that configuration.
Do other tools work that are deployed to the cluster? I am guessing not, but please confirm. (not just local jobs that run on the server)
The galaxy log would be a good place to find out where jobs are going and what the problems are a the root.
I should have asked this first: Is Samtools and Picard installed? Running any of those tools is successful?
This type of error can come up when a dependency is missing as explained in this other recent post: https://biostar.usegalaxy.org/p/19938/
Consider creating SAM and Picard indexes with Data Managers for any genome that you use to assign "database" to datasets for and use in routine analysis to avoid problems. The indexes are not always needed, but you won't be able to tell that from the tool form in most cases. Any genome that you indexed for mapping tools would need this anyway.
Hopefully one of these helps, Jen, Galaxy team