Peter,
The job name looks OK. Here is the output of the debug statements:
galaxy.jobs.runners.drmaa DEBUG 2017-05-29 10:37:21,423 Making job_name, tag was '15132', plan to use u'g15132_fastq_to_fasta_python_raj76@uga.edu' with underscores replacements galaxy.jobs.runners.drmaa DEBUG 2017-05-29 10:37:21,423 Making job_name, character 0 in proposed job_name u'g' is 103 galaxy.jobs.runners.drmaa DEBUG 2017-05-29 10:37:21,423 Making job_name, character 1 in proposed job_name u'1' is 49 galaxy.jobs.runners.drmaa DEBUG 2017-05-29 10:37:21,423 Making job_name, character 2 in proposed job_name u'5' is 53 galaxy.jobs.runners.drmaa DEBUG 2017-05-29 10:37:21,424 Making job_name, character 3 in proposed job_name u'1' is 49 galaxy.jobs.runners.drmaa DEBUG 2017-05-29 10:37:21,424 Making job_name, character 4 in proposed job_name u'3' is 51 galaxy.jobs.runners.drmaa DEBUG 2017-05-29 10:37:21,424 Making job_name, character 5 in proposed job_name u'2' is 50 galaxy.jobs.runners.drmaa DEBUG 2017-05-29 10:37:21,424 Making job_name, character 6 in proposed job_name u'_' is 95 galaxy.jobs.runners.drmaa DEBUG 2017-05-29 10:37:21,424 Making job_name, character 7 in proposed job_name u'f' is 102 galaxy.jobs.runners.drmaa DEBUG 2017-05-29 10:37:21,425 Making job_name, character 8 in proposed job_name u'a' is 97 galaxy.jobs.runners.drmaa DEBUG 2017-05-29 10:37:21,425 Making job_name, character 9 in proposed job_name u's' is 115 galaxy.jobs.runners.drmaa DEBUG 2017-05-29 10:37:21,425 Making job_name, character 10 in proposed job_name u't' is 116 galaxy.jobs.runners.drmaa DEBUG 2017-05-29 10:37:21,425 Making job_name, character 11 in proposed job_name u'q' is 113 galaxy.jobs.runners.drmaa DEBUG 2017-05-29 10:37:21,425 Making job_name, character 12 in proposed job_name u'_' is 95 galaxy.jobs.runners.drmaa DEBUG 2017-05-29 10:37:21,426 Making job_name, character 13 in proposed job_name u't' is 116 galaxy.jobs.runners.drmaa DEBUG 2017-05-29 10:37:21,426 Making job_name, character 14 in proposed job_name u'o' is 111 galaxy.jobs.runners.drmaa DEBUG 2017-05-29 10:37:21,426 Making job_name, character 15 in proposed job_name u'_' is 95 galaxy.jobs.runners.drmaa DEBUG 2017-05-29 10:37:21,426 Making job_name, character 16 in proposed job_name u'f' is 102 galaxy.jobs.runners.drmaa DEBUG 2017-05-29 10:37:21,426 Making job_name, character 17 in proposed job_name u'a' is 97 galaxy.jobs.runners.drmaa DEBUG 2017-05-29 10:37:21,426 Making job_name, character 18 in proposed job_name u's' is 115 galaxy.jobs.runners.drmaa DEBUG 2017-05-29 10:37:21,427 Making job_name, character 19 in proposed job_name u't' is 116 galaxy.jobs.runners.drmaa DEBUG 2017-05-29 10:37:21,427 Making job_name, character 20 in proposed job_name u'a' is 97 galaxy.jobs.runners.drmaa DEBUG 2017-05-29 10:37:21,427 Making job_name, character 21 in proposed job_name u'_' is 95 galaxy.jobs.runners.drmaa DEBUG 2017-05-29 10:37:21,427 Making job_name, character 22 in proposed job_name u'p' is 112 galaxy.jobs.runners.drmaa DEBUG 2017-05-29 10:37:21,427 Making job_name, character 23 in proposed job_name u'y' is 121 galaxy.jobs.runners.drmaa DEBUG 2017-05-29 10:37:21,427 Making job_name, character 24 in proposed job_name u't' is 116 galaxy.jobs.runners.drmaa DEBUG 2017-05-29 10:37:21,428 Making job_name, character 25 in proposed job_name u'h' is 104 galaxy.jobs.runners.drmaa DEBUG 2017-05-29 10:37:21,428 Making job_name, character 26 in proposed job_name u'o' is 111 galaxy.jobs.runners.drmaa DEBUG 2017-05-29 10:37:21,428 Making job_name, character 27 in proposed job_name u'n' is 110 galaxy.jobs.runners.drmaa DEBUG 2017-05-29 10:37:21,428 Making job_name, character 28 in proposed job_name u'_' is 95 galaxy.jobs.runners.drmaa DEBUG 2017-05-29 10:37:21,428 Making job_name, character 29 in proposed job_name u'r' is 114 galaxy.jobs.runners.drmaa DEBUG 2017-05-29 10:37:21,429 Making job_name, character 30 in proposed job_name u'a' is 97 galaxy.jobs.runners.drmaa DEBUG 2017-05-29 10:37:21,429 Making job_name, character 31 in proposed job_name u'j' is 106 galaxy.jobs.runners.drmaa DEBUG 2017-05-29 10:37:21,429 Making job_name, character 32 in proposed job_name u'7' is 55 galaxy.jobs.runners.drmaa DEBUG 2017-05-29 10:37:21,429 Making job_name, character 33 in proposed job_name u'6' is 54 galaxy.jobs.runners.drmaa DEBUG 2017-05-29 10:37:21,429 Making job_name, character 34 in proposed job_name u'@' is 64 galaxy.jobs.runners.drmaa DEBUG 2017-05-29 10:37:21,430 Making job_name, character 35 in proposed job_name u'u' is 117 galaxy.jobs.runners.drmaa DEBUG 2017-05-29 10:37:21,430 Making job_name, character 36 in proposed job_name u'g' is 103 galaxy.jobs.runners.drmaa DEBUG 2017-05-29 10:37:21,430 Making job_name, character 37 in proposed job_name u'a' is 97 galaxy.jobs.runners.drmaa DEBUG 2017-05-29 10:37:21,430 Making job_name, character 38 in proposed job_name u'.' is 46 galaxy.jobs.runners.drmaa DEBUG 2017-05-29 10:37:21,430 Making job_name, character 39 in proposed job_name u'e' is 101 galaxy.jobs.runners.drmaa DEBUG 2017-05-29 10:37:21,431 Making job_name, character 40 in proposed job_name u'd' is 100 galaxy.jobs.runners.drmaa DEBUG 2017-05-29 10:37:21,431 Making job_name, character 41 in proposed job_name u'u' is 117 galaxy.jobs.runners ERROR 2017-05-29 10:37:21,431 (15132) Unhandled exception calling queue_job Traceback (most recent call last): File "/panfs/pstor.storage/home/qbcglab/galaxy_run/galaxy-dist/lib/galaxy/jobs/runners/__init__.py", line 104, in run_next method(arg) File "/panfs/pstor.storage/home/qbcglab/galaxy_run/galaxy-dist/lib/galaxy/jobs/runners/drmaa.py", line 132, in queue_job job_name = self._job_name(job_wrapper) File "/panfs/pstor.storage/home/qbcglab/galaxy_run/galaxy-dist/lib/galaxy/jobs/runners/drmaa.py", line 400, in _job_name job_name = ''.join( x if x in ( string.letters + string.digits + '_' ) else '_' for x in job_name ) File "/panfs/pstor.storage/home/qbcglab/galaxy_run/galaxy-dist/lib/galaxy/jobs/runners/drmaa.py", line 400, in <genexpr> job_name = ''.join( x if x in ( string.letters + string.digits + '_' ) else '_' for x in job_name ) UnicodeDecodeError: 'ascii' codec can't decode byte 0xa6 in position 52: ordinal not in range(128)
There is no sign of the 0xa6 at position 52 (the job name is only 42 chars long) in the job name.
Thanks! -Raj
On May 29, 2017, at 5:50 AM, Peter Cock p.j.a.cock@googlemail.com wrote:
Time for more debugging, try inserting something like this inserted the line above into /panfs/pstor.storage/home/qbcglab/galaxy_run/galaxy-dist/lib/galaxy/jobs/runners/drmaa.py (having backed up the file):
log.debug( 'Making job_name, tag was %r, plan to use %r with underscores replacements' % (galaxy_id_tag, job_name))
And if that doesn't help, check all the characters:
for i, letter in enumerate(job_name): log.debug( 'Making job_name, character %i in proposed job_name %r is %i' % (i, letter, ord(letter)))
My hunch is that the locale of the Galaxy server differs from that on the cluster, meaning DRMAA is stricter about allowed characters because Python's string.letters would be whatever is allowed on the Galaxy server's locale.
If I am right, a crude fix would be switching to using string.ascii_letters, i.e.
job_name = ''.join( x if x in ( string.ascii_letters + string.digits + '_' ) else '_' for x in job_name )
Peter
On Mon, May 29, 2017 at 6:54 AM, Saravanaraj Ayyampalayam raj76@uga.edu wrote:
Hello,
I updated to the latest version (17.05) galaxy code. I was updating from a very old version. I fixed all the issues with except one. I am getting the following error when I submit a job.
galaxy.jobs.runners ERROR 2017-05-29 01:42:44,008 (15131) Unhandled exception calling queue_job Traceback (most recent call last): File "/panfs/pstor.storage/home/qbcglab/galaxy_run/galaxy-dist/lib/galaxy/jobs/runners/__init__.py", line 104, in run_next method(arg) File "/panfs/pstor.storage/home/qbcglab/galaxy_run/galaxy-dist/lib/galaxy/jobs/runners/drmaa.py", line 132, in queue_job job_name = self._job_name(job_wrapper) File "/panfs/pstor.storage/home/qbcglab/galaxy_run/galaxy-dist/lib/galaxy/jobs/runners/drmaa.py", line 397, in _job_name job_name = ''.join( x if x in ( string.letters + string.digits + '_' ) else '_' for x in job_name ) File "/panfs/pstor.storage/home/qbcglab/galaxy_run/galaxy-dist/lib/galaxy/jobs/runners/drmaa.py", line 397, in <genexpr> job_name = ''.join( x if x in ( string.letters + string.digits + '_' ) else '_' for x in job_name ) UnicodeDecodeError: 'ascii' codec can't decode byte 0xa6 in position 52: ordinal not in range(128)
I spent a day trying to debug this and didn’t get anywhere. The job_name looks OK.
I would really appreciate some help from the community.
Thanks! -Raj
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