Question: Unable to finish job for both RNA-STAR and tophat2
1
gravatar for chaoyuan
21 months ago by
chaoyuan80
chaoyuan80 wrote:

This is the problem I keep running into with both Tophat and RNA-Star on my locally installed Galaxy. They both cannot finish the job and save me the following error message:

Traceback (most recent call last):
File "/home/chuonglab/galaxy-dev/lib/galaxy/jobs/runners/local.py", line 128, in queue_job
job_wrapper.finish( stdout, stderr, exit_code )
File "/home/chuonglab/galaxy-dev/lib/galaxy/jobs/__init__.py", line 1248, in finish
dataset.datatype.set_meta( dataset, overwrite=False )
File "/home/chuonglab/galaxy-dev/lib/galaxy/datatypes/binary.py", line 339, in set_meta
exit_code = subprocess.call( args=command, stderr=open( stderr_name, 'wb' ) )
File "/usr/lib/python2.7/subprocess.py", line 522, in call
return Popen(*popenargs, **kwargs).wait()
File "/usr/lib/python2.7/subprocess.py", line 710, in __init__
errread, errwrite)
File "/usr/lib/python2.7/subprocess.py", line 1327, in _execute_child
raise child_exception
OSError: [Errno 2] No such file or directory

From my experience, I suspect this come from the fact that when Tophat and RNA-Star are run, the environment is not set up correctly for them so they can't find the samtools they need. Adding path to samtools binary to system PATH variable apparently might not be a good solution because different tools require different versions of samtools.

But when I monitored the process through top command, I see that tophat2 can find samtools 0.1.18 that it needs, even when I supply the path to samtools 0.1.19 system-side. It's in the last process when Galaxy is trying to finish up the task that it encounters a problem. So maybe at this point it's the samtools that's available system-wise that is needed? So probably just install a samtools package on Ubuntu should properly solve this problem? This package won't actually be used by different repository tools but only used by binary.py upon finishing a job?

ADD COMMENTlink modified 21 months ago by Jennifer Hillman Jackson23k • written 21 months ago by chaoyuan80
0
gravatar for chaoyuan
21 months ago by
chaoyuan80
chaoyuan80 wrote:

Ok. I think I finally understood this.

The samtools that's called by binary.py when converting SAM file to BAM file is independent from the samtools installed as dependency by other repository tools.

It occurred to me when I monitor the task with top : tophat is using samtools 0.1.18, which I did not make available system-wise. The binary.py actually makes a system call ( subprocess.call) and thus would be calling the system-wide samtools ( in my case 0.1.19).

So the right solution to this problem should be: install a samtools that will be available system-wide.

ADD COMMENTlink written 21 months ago by chaoyuan80
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