Picard error on local Galaxy

Question: Picard error on local Galaxy

3.8 years ago by

Guy Reeves • 1.0k

Germany

Guy Reeves • 1.0k wrote:

I am trying to use Picard Tools on a local galaxy machine I have set up which does not have e-mail reporting enabled.

I think i must have screwed up the installation of the Picard suit and uninstalling and reinstalling does not help.

Do you have any ideas what i have done wrong and how to correct it?

The error is below

Thanks Guy

Traceback (most recent call last):
  File "/home/galaxy/galaxy-dist/lib/galaxy/jobs/runners/local.py", line 129, in queue_job
    job_wrapper.finish( stdout, stderr, exit_code )
  File "/home/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py", line 1124, in finish
    dataset.datatype.set_meta( dataset, overwrite=False )  # call datatype.set_meta directly for the initial set_meta call during dataset creation
  File "/home/galaxy/galaxy-dist/lib/galaxy/datatypes/binary.py", line 244, in set_meta
    proc = subprocess.Popen( args=command, stderr=open( stderr_name, 'wb' ) )
  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 dir

galaxy picard • 1.3k views

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modified 3.0 years ago by Elena • 30 • written 3.8 years ago by Guy Reeves • 1.0k

Just a guess, but can you check the metadata status for the input dataset? Click on the pencil icon - problems will be reported near the bottom of the first tab. You can reset the metadata using the "Auto-detect" button. Thanks, Jen, Galaxy team

ADD REPLY • link written 3.8 years ago by Jennifer Hillman Jackson ♦ 25k

3.0 years ago by

Elena • 30

United Kingdom

Elena • 30 wrote:

I run into this problem and solution was to add samtools to the PATH. Somehow it is not mentioned in documentation about local installation (or I missed it) but as a part of picard processing galaxy checks whether bam file is sorted using samtools, so if shell does not know what is samtools it generates this error.

ADD COMMENT • link written 3.0 years ago by Elena • 30

Hi Elena

that is great you updated this. would you have time to explain what you mean by 'adding samtools to the path. even very briefly would be great. Thanks Guy

ADD REPLY • link written 3.0 years ago by Guy Reeves • 1.0k

3.8 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hi,

There wasn't any feedback for the comment, so I am assuming that this is resolved. Other potential issues could be a path problem or that dependencies are not installed (samtools, etc). As far as I know, this specific error could not be generated by missing Picard indexes for any input reference genomes (but there is a data manager for this, if you need it, in the tool shed).

Best, Jen, Galaxy team

ADD COMMENT • link written 3.8 years ago by Jennifer Hillman Jackson ♦ 25k

3.8 years ago by

Guy Reeves • 1.0k

Germany

Guy Reeves • 1.0k wrote:

Hi Jen

I had been away. I did try checking the the input data setting to .bam. But it did not help.

I then thought maybe there was something wrong with this file so I tried to import a new .bam file through an admin dataset, but while this had worked in the path I get the error below when I try to import. This error looks identical to the one above that I thought was picard specific. I think I must have screwed up something more general. Any ideas.

Some tools do still work without this error e.g. groomer.

THanks Guy

Job Standard Error

Traceback (most recent call last):
  File "/home/galaxy/galaxy-dist/tools/data_source/upload.py", line 409, in <module>
    __main__()
  File "/home/galaxy/galaxy-dist/tools/data_source/upload.py", line 398, in __main__
    add_file( dataset, registry, json_file, output_path )
  File "/home/galaxy/galaxy-dist/tools/data_source/upload.py", line 326, in add_file
    if link_data_only == 'copy_files' and datatype.dataset_content_needs_grooming( output_path ):
  File "/home/galaxy/galaxy-dist/lib/galaxy/datatypes/binary.py", line 148, in dataset_content_needs_grooming
    version = self._get_samtools_version()
  File "/home/galaxy/galaxy-dist/lib/galaxy/datatypes/binary.py", line 130, in _get_samtools_version
    output = subprocess.Popen( [ 'samtools' ], stderr=subprocess.PIPE, stdout=subprocess.PIPE ).communicate()[1]
  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

ADD COMMENT • link written 3.8 years ago by Guy Reeves • 1.0k

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