galaxyproject / galaxyproject/pulsar
AttributeError: 'AsynchronousJobState' object has no attribute 'get_id_tag'
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Description
Hi!
We are using pulsar on our cluster with a queued_drmaa configuration (Job scheduler is IBM LSF).
Things are working fine, except on tophat 2 when we want to use mm10 reference genome (sacCer2 is running properly).
We get the AttributeError => `'AsynchronousJobState' object has no attribute 'get_id_tag'`.
As the mm10 reference genome is way bigger than the sacCer2 reference genome, do you think it could be a memory reject from the cluster, resulting in the _AsynchronousJobState_?
Do you know when this error is occuring, and what does it mean for our job? Do you think we could then handle this type of error in a more detailed output to help people debug why Pulsar is returning this?
I can help on this, if needed!
Here are the full log we get in Galaxy:
##### Galaxy framework
```
Traceback (most recent call last):
File "/mnt/nfs/data/galaxy/galaxy-dist/lib/galaxy/jobs/runners/__init__.py", line 92, in run_next
job_id = arg.get_id_tag()
AttributeError: 'AsynchronousJobState' object has no attribute 'get_id_tag'
```
##### Tool execution error message
```
[2015-11-18 12:47:41] Beginning TopHat run (v2.0.14)
-----------------------------------------------
[2015-11-18 12:47:41] Checking for Bowtie
Bowtie version: 2.2.5.0
[2015-11-18 12:47:41] Checking for Bowtie index files (genome)..
[2015-11-18 12:47:41] Checking for reference FASTA file
[2015-11-18 12:47:41] Generating SAM header for /lustre/reference_data/mib-cri/galaxy/dmanager-data/mm10/bowtie2_index/mm10/mm10
Traceback (most recent call last):
File "/home/mib-cri/galaxysoftware/el5/dependencies/tophat/2.0.14/iuc/package_tophat_2_0_14/536f7bb5616d/bin/tophat", line 4095, in
sys.exit(main())
File "/home/mib-cri/galaxysoftware/el5/dependencies/tophat/2.0.14/iuc/package_tophat_2_0_14/536f7bb5616d/bin/tophat", line 3943, in main
sam_header_filename = get_index_sam_header(params, bwt_idx_prefix, "genome")
File "/home/mib-cri/galaxysoftware/el5/dependencies/tophat/2.0.14/iuc/package_tophat_2_0_14/536f7bb5616d/bin/tophat", line 1427, in get_index_sam_header
stderr=open('/dev/null'))
File "/home/mib-cri/galaxysoftware/el5/python-2.7/lib/python2.7/subprocess.py", line 522, in call
return Popen(*popenargs, **kwargs).wait()
File "/home/mib-cri/galaxysoftware/el5/python-2.7/lib/python2.7/subprocess.py", line 1384, in wait
pid, sts = _eintr_retry_call(os.waitpid, self.pid, 0)
File "/home/mib-cri/galaxysoftware/el5/python-2.7/lib/python2.7/subprocess.py", line 476, in _eintr_retry_call
return func(*args)
KeyboardInterrupt
```
Thanks for the help!
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