Question: Galaxy commits subprocess errors
0
gravatar for kaji331
4.0 years ago by
kaji33120
kaji33120 wrote:

Hello everyone:

Sorry to my English. I am installing Galaxy into my server with 12 cores and 128GB RAM. I manage it using SSH, use Apache and MySQL for a website that I can use Galaxy in my laptop. Recently, I am constructing a workflow for WES variants. When I use Markduplicates of Picards and BAM filter of Bamtools, they gave me errors below:

Traceback (most recent call last):
  File "/home/galaxy/galaxy-master/lib/galaxy/jobs/runners/local.py", line 129, in queue_job
    job_wrapper.finish( stdout, stderr, exit_code )
  File "/home/galaxy/galaxy-master/lib/galaxy/jobs/__init__.py", line 1199, in finish
    dataset.datatype.set_meta( dataset, overwrite=False )
  File "/home/galaxy/galaxy-master/lib/galaxy/datatypes/binary.py", line 281, in set_meta
    proc = subprocess.Popen( args=command, stderr=open( stderr_name, 'wb' ) )
  File "/usr/lib64/python2.6/subprocess.py", line 642, in __init__
    errread, errwrite)
  File "/usr/lib64/python2.6/subprocess.py", line 1234, in _execute_child
    raise child_exception
OSError: [Errno 13] Permission denied

When I run Galaxy with root user, I still get similar errors below Traceback (most recent call last):

Traceback (most recent call last):
  File "/home/galaxy/galaxy-master/lib/galaxy/jobs/runners/local.py", line 129, in queue_job
    job_wrapper.finish( stdout, stderr, exit_code )
  File "/home/galaxy/galaxy-master/lib/galaxy/jobs/__init__.py", line 1199, in finish
    dataset.datatype.set_meta( dataset, overwrite=False )
  File "/home/galaxy/galaxy-master/lib/galaxy/datatypes/binary.py", line 281, in set_meta
    proc = subprocess.Popen( args=command, stderr=open( stderr_name, 'wb' ) )
  File "/usr/lib64/python2.6/subprocess.py", line 642, in __init__
    errread, errwrite)
  File "/usr/lib64/python2.6/subprocess.py", line 1234, in _execute_child
    raise child_exception
OSError: [Errno 2] No such file or directory

I need your help, emergently. Thanks very very much !

galaxy • 1.2k views
ADD COMMENTlink modified 4.0 years ago • written 4.0 years ago by kaji33120

You'll likely have better luck at the dedicated Galaxy QA site: biostar.usegalaxy.org

ADD REPLYlink written 4.0 years ago by Dan D6.8k
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