Jobs that I run on a local Galaxy install on a Fedora 23 machine are completing but are erroring with the message below. Any idea why the metadata can not be written?
Thanks
galaxy.jobs.runners.local DEBUG 2016-06-03 17:30:02,044 execution finished: /home/anthony.underwood/galaxy/database/jobs_directory/000/142/galaxy_142.sh galaxy.model.metadata DEBUG 2016-06-03 17:30:02,158 setting metadata externally failed for HistoryDatasetAssociation 158: [Errno 2] No such file or directory galaxy.jobs.runners.local ERROR 2016-06-03 17:30:02,235 Job wrapper finish method failed Traceback (most recent call last): File "/home/anthony.underwood/galaxy/lib/galaxy/jobs/runners/local.py", line 128, in queue_job job_wrapper.finish( stdout, stderr, exit_code ) File "/home/anthony.underwood/galaxy/lib/galaxy/jobs/__init__.py", line 1257, in finish dataset.datatype.set_meta( dataset, overwrite=False ) File "/home/anthony.underwood/galaxy/lib/galaxy/datatypes/binary.py", line 339, in set_meta exit_code = subprocess.call( args=command, stderr=open( stderr_name, 'wb' ) ) File "/usr/lib64/python2.7/subprocess.py", line 522, in call return Popen(*popenargs, **kwargs).wait() File "/usr/lib64/python2.7/subprocess.py", line 710, in __init__ errread, errwrite) File "/usr/lib64/python2.7/subprocess.py", line 1335, in _execute_child raise child_exception OSError: [Errno 2] No such file or directory
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I think newer versions of Galaxy give a better error message - I am pretty sure the problem is you are missing samtools. It needs to be available on the PATH for Galaxy if you use bam data.
-John
On Fri, Jun 3, 2016 at 1:00 PM, Anthony Underwood Anthony.Underwood@phe.gov.uk wrote:
Jobs that I run on a local Galaxy install on a Fedora 23 machine are completing but are erroring with the message below. Any idea why the metadata can not be written?
Thanks
galaxy.jobs.runners.local DEBUG 2016-06-03 17:30:02,044 execution finished: /home/anthony.underwood/galaxy/database/jobs_directory/000/142/galaxy_142.sh galaxy.model.metadata DEBUG 2016-06-03 17:30:02,158 setting metadata externally failed for HistoryDatasetAssociation 158: [Errno 2] No such file or directory galaxy.jobs.runners.local ERROR 2016-06-03 17:30:02,235 Job wrapper finish method failed Traceback (most recent call last): File "/home/anthony.underwood/galaxy/lib/galaxy/jobs/runners/local.py", line 128, in queue_job job_wrapper.finish( stdout, stderr, exit_code ) File "/home/anthony.underwood/galaxy/lib/galaxy/jobs/__init__.py", line 1257, in finish dataset.datatype.set_meta( dataset, overwrite=False ) File "/home/anthony.underwood/galaxy/lib/galaxy/datatypes/binary.py", line 339, in set_meta exit_code = subprocess.call( args=command, stderr=open( stderr_name, 'wb' ) ) File "/usr/lib64/python2.7/subprocess.py", line 522, in call return Popen(*popenargs, **kwargs).wait() File "/usr/lib64/python2.7/subprocess.py", line 710, in __init__ errread, errwrite) File "/usr/lib64/python2.7/subprocess.py", line 1335, in _execute_child raise child_exception OSError: [Errno 2] No such file or directory
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Hi Anthony,
The line numbers for binary.py don't match the current latest source, but I would bet this is due to the samtools binary not being on the path of the cluster nodes. Note Galaxy itself needs samtools for dealing with BAM files and this is expected to be on the $PATH (and it not currently handled via the Galaxy Tool dependency system).
Peter
On Fri, Jun 3, 2016 at 6:00 PM, Anthony Underwood Anthony.Underwood@phe.gov.uk wrote:
Jobs that I run on a local Galaxy install on a Fedora 23 machine are completing but are erroring with the message below. Any idea why the metadata can not be written?
Thanks
galaxy.jobs.runners.local DEBUG 2016-06-03 17:30:02,044 execution finished: /home/anthony.underwood/galaxy/database/jobs_directory/000/142/galaxy_142.sh galaxy.model.metadata DEBUG 2016-06-03 17:30:02,158 setting metadata externally failed for HistoryDatasetAssociation 158: [Errno 2] No such file or directory galaxy.jobs.runners.local ERROR 2016-06-03 17:30:02,235 Job wrapper finish method failed Traceback (most recent call last): File "/home/anthony.underwood/galaxy/lib/galaxy/jobs/runners/local.py", line 128, in queue_job job_wrapper.finish( stdout, stderr, exit_code ) File "/home/anthony.underwood/galaxy/lib/galaxy/jobs/__init__.py", line 1257, in finish dataset.datatype.set_meta( dataset, overwrite=False ) File "/home/anthony.underwood/galaxy/lib/galaxy/datatypes/binary.py", line 339, in set_meta exit_code = subprocess.call( args=command, stderr=open( stderr_name, 'wb' ) ) File "/usr/lib64/python2.7/subprocess.py", line 522, in call return Popen(*popenargs, **kwargs).wait() File "/usr/lib64/python2.7/subprocess.py", line 710, in __init__ errread, errwrite) File "/usr/lib64/python2.7/subprocess.py", line 1335, in _execute_child raise child_exception OSError: [Errno 2] No such file or directory
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Thanks Peter and John - this was exactly the issue- problem solved. Not very intuitive but an easy fix :)
On 3 June 2016 at 23:13:34, Peter Cock (p.j.a.cock@googlemail.commailto:p.j.a.cock@googlemail.com) wrote:
Hi Anthony,
The line numbers for binary.py don't match the current latest source, but I would bet this is due to the samtools binary not being on the path of the cluster nodes. Note Galaxy itself needs samtools for dealing with BAM files and this is expected to be on the $PATH (and it not currently handled via the Galaxy Tool dependency system).
Peter
On Fri, Jun 3, 2016 at 6:00 PM, Anthony Underwood Anthony.Underwood@phe.gov.uk wrote:
Jobs that I run on a local Galaxy install on a Fedora 23 machine are completing but are erroring with the message below. Any idea why the metadata can not be written?
Thanks
galaxy.jobs.runners.local DEBUG 2016-06-03 17:30:02,044 execution finished: /home/anthony.underwood/galaxy/database/jobs_directory/000/142/galaxy_142.sh galaxy.model.metadata DEBUG 2016-06-03 17:30:02,158 setting metadata externally failed for HistoryDatasetAssociation 158: [Errno 2] No such file or directory galaxy.jobs.runners.local ERROR 2016-06-03 17:30:02,235 Job wrapper finish method failed Traceback (most recent call last): File "/home/anthony.underwood/galaxy/lib/galaxy/jobs/runners/local.py", line 128, in queue_job job_wrapper.finish( stdout, stderr, exit_code ) File "/home/anthony.underwood/galaxy/lib/galaxy/jobs/__init__.py", line 1257, in finish dataset.datatype.set_meta( dataset, overwrite=False ) File "/home/anthony.underwood/galaxy/lib/galaxy/datatypes/binary.py", line 339, in set_meta exit_code = subprocess.call( args=command, stderr=open( stderr_name, 'wb' ) ) File "/usr/lib64/python2.7/subprocess.py", line 522, in call return Popen(*popenargs, **kwargs).wait() File "/usr/lib64/python2.7/subprocess.py", line 710, in __init__ errread, errwrite) File "/usr/lib64/python2.7/subprocess.py", line 1335, in _execute_child raise child_exception OSError: [Errno 2] No such file or directory
The information contained in the EMail and any attachments is confidential and intended solely and for the attention and use of the named addressee(s). It may not be disclosed to any other person without the express authority of Public Health England, or the intended recipient, or both. If you are not the intended recipient, you must not disclose, copy, distribute or retain this message or any part of it. This footnote also confirms that this EMail has been swept for computer viruses by Symantec.Cloud, but please re-sweep any attachments before opening or saving. http://www.gov.uk/PHE
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************************************************************************** The information contained in the EMail and any attachments is confidential and intended solely and for the attention and use of the named addressee(s). It may not be disclosed to any other person without the express authority of Public Health England, or the intended recipient, or both. If you are not the intended recipient, you must not disclose, copy, distribute or retain this message or any part of it. This footnote also confirms that this EMail has been swept for computer viruses by Symantec.Cloud, but please re-sweep any attachments before opening or saving. http://www.gov.uk/PHE **************************************************************************
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Anthony Underwood -
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Peter Cock