Issue with job_name, UnicodeDecodeError in drmaa
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
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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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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Curious, my new guess is this is position 52 a temporary string from this expression: string.letters + string.digits + '_' This would fit with it being something unusual about the locale of your Galaxy server, and my suggested hack may work - replace string.letters with string.ascii_letters Separately at the Linux command line of the server running Galaxy, and on a cluster node, what does the command "locale" give? e.g. I get: $ locale LANG=en_US.UTF-8 LC_CTYPE="en_US.UTF-8" LC_NUMERIC="en_US.UTF-8" LC_TIME="en_US.UTF-8" LC_COLLATE="en_US.UTF-8" LC_MONETARY="en_US.UTF-8" LC_MESSAGES="en_US.UTF-8" LC_PAPER="en_US.UTF-8" LC_NAME="en_US.UTF-8" LC_ADDRESS="en_US.UTF-8" LC_TELEPHONE="en_US.UTF-8" LC_MEASUREMENT="en_US.UTF-8" LC_IDENTIFICATION="en_US.UTF-8" LC_ALL= Peter On Mon, May 29, 2017 at 3:43 PM, Saravanaraj Ayyampalayam <raj76@uga.edu> wrote:
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
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/
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Peter, You are correct. Changing string.letters to string.ascii_letters fixed it. I had to change it in two places. My locale is : LANG=en_US.iso885915 LC_CTYPE="en_US.iso885915" LC_NUMERIC="en_US.iso885915" LC_TIME="en_US.iso885915" LC_COLLATE="en_US.iso885915" LC_MONETARY="en_US.iso885915" LC_MESSAGES="en_US.iso885915" LC_PAPER="en_US.iso885915" LC_NAME="en_US.iso885915" LC_ADDRESS="en_US.iso885915" LC_TELEPHONE="en_US.iso885915" LC_MEASUREMENT="en_US.iso885915" LC_IDENTIFICATION="en_US.iso885915" LC_ALL= I will talk to our sysadmin and see if I can change the locale to en_US.UTF-8. Thank you very much. -Raj
On May 29, 2017, at 10:58 AM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
Curious, my new guess is this is position 52 a temporary string from this expression:
string.letters + string.digits + '_'
This would fit with it being something unusual about the locale of your Galaxy server, and my suggested hack may work - replace string.letters with string.ascii_letters
Separately at the Linux command line of the server running Galaxy, and on a cluster node, what does the command "locale" give? e.g. I get:
$ locale LANG=en_US.UTF-8 LC_CTYPE="en_US.UTF-8" LC_NUMERIC="en_US.UTF-8" LC_TIME="en_US.UTF-8" LC_COLLATE="en_US.UTF-8" LC_MONETARY="en_US.UTF-8" LC_MESSAGES="en_US.UTF-8" LC_PAPER="en_US.UTF-8" LC_NAME="en_US.UTF-8" LC_ADDRESS="en_US.UTF-8" LC_TELEPHONE="en_US.UTF-8" LC_MEASUREMENT="en_US.UTF-8" LC_IDENTIFICATION="en_US.UTF-8" LC_ALL=
Peter
On Mon, May 29, 2017 at 3:43 PM, Saravanaraj Ayyampalayam <raj76@uga.edu> wrote:
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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Thanks Saravanaraj, You should not need to change the locale, after all many Galaxy servers and their users will be labelling their files in non-English with "special" characters - but perhaps en_US.UTF-8 would be safer in your case as it seems that few people use Galaxy with en_US.iso885915 otherwise this would have been reported before? Can you tell us both places you changed string.letters to string.ascii_letters please? I could then submit this as a pull request to get Galaxy itself updated for future release. Peter On Mon, May 29, 2017 at 4:28 PM, Saravanaraj Ayyampalayam <raj76@uga.edu> wrote:
Peter,
You are correct. Changing string.letters to string.ascii_letters fixed it. I had to change it in two places.
My locale is :
LANG=en_US.iso885915 LC_CTYPE="en_US.iso885915" LC_NUMERIC="en_US.iso885915" LC_TIME="en_US.iso885915" LC_COLLATE="en_US.iso885915" LC_MONETARY="en_US.iso885915" LC_MESSAGES="en_US.iso885915" LC_PAPER="en_US.iso885915" LC_NAME="en_US.iso885915" LC_ADDRESS="en_US.iso885915" LC_TELEPHONE="en_US.iso885915" LC_MEASUREMENT="en_US.iso885915" LC_IDENTIFICATION="en_US.iso885915" LC_ALL=
I will talk to our sysadmin and see if I can change the locale to en_US.UTF-8.
Thank you very much. -Raj
On May 29, 2017, at 10:58 AM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
Curious, my new guess is this is position 52 a temporary string from this expression:
string.letters + string.digits + '_'
This would fit with it being something unusual about the locale of your Galaxy server, and my suggested hack may work - replace string.letters with string.ascii_letters
Separately at the Linux command line of the server running Galaxy, and on a cluster node, what does the command "locale" give? e.g. I get:
$ locale LANG=en_US.UTF-8 LC_CTYPE="en_US.UTF-8" LC_NUMERIC="en_US.UTF-8" LC_TIME="en_US.UTF-8" LC_COLLATE="en_US.UTF-8" LC_MONETARY="en_US.UTF-8" LC_MESSAGES="en_US.UTF-8" LC_PAPER="en_US.UTF-8" LC_NAME="en_US.UTF-8" LC_ADDRESS="en_US.UTF-8" LC_TELEPHONE="en_US.UTF-8" LC_MEASUREMENT="en_US.UTF-8" LC_IDENTIFICATION="en_US.UTF-8" LC_ALL=
Peter
On Mon, May 29, 2017 at 3:43 PM, Saravanaraj Ayyampalayam <raj76@uga.edu> wrote:
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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Peter, Here is the git diff output that shows the changes I made: diff --git a/lib/galaxy/jobs/runners/__init__.py b/lib/galaxy/jobs/runners/__init__.py index ebf4859..6ee51c8 100644 --- a/lib/galaxy/jobs/runners/__init__.py +++ b/lib/galaxy/jobs/runners/__init__.py @@ -419,7 +419,7 @@ class JobState( object ): job_name += '_%s' % self.job_wrapper.tool.old_id if self.job_wrapper.user: job_name += '_%s' % self.job_wrapper.user - self.job_name = ''.join( map( lambda x: x if x in ( string.letters + string.digits + '_' ) else '_', job_name ) ) + self.job_name = ''.join( map( lambda x: x if x in ( string.ascii_letters + string.digits + '_' ) else '_', job_name ) ) @staticmethod def default_job_file( files_dir, id_tag ): diff --git a/lib/galaxy/jobs/runners/drmaa.py b/lib/galaxy/jobs/runners/drmaa.py index 7c08984..5c5dc62 100644 --- a/lib/galaxy/jobs/runners/drmaa.py +++ b/lib/galaxy/jobs/runners/drmaa.py @@ -394,7 +394,7 @@ class DRMAAJobRunner( AsynchronousJobRunner ): job_name += '_%s' % job_wrapper.tool.old_id if external_runjob_script is None: job_name += '_%s' % job_wrapper.user - job_name = ''.join( x if x in ( string.letters + string.digits + '_' ) else '_' for x in job_name ) + job_name = ''.join( x if x in ( string.ascii_letters + string.digits + '_' ) else '_' for x in job_name ) if self.restrict_job_name_length: job_name = job_name[:self.restrict_job_name_length] return job_name -Raj
On May 29, 2017, at 11:33 AM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
Thanks Saravanaraj,
You should not need to change the locale, after all many Galaxy servers and their users will be labelling their files in non-English with "special" characters - but perhaps en_US.UTF-8 would be safer in your case as it seems that few people use Galaxy with en_US.iso885915 otherwise this would have been reported before?
Can you tell us both places you changed string.letters to string.ascii_letters please? I could then submit this as a pull request to get Galaxy itself updated for future release.
Peter
On Mon, May 29, 2017 at 4:28 PM, Saravanaraj Ayyampalayam <raj76@uga.edu> wrote:
Peter,
You are correct. Changing string.letters to string.ascii_letters fixed it. I had to change it in two places.
My locale is :
LANG=en_US.iso885915 LC_CTYPE="en_US.iso885915" LC_NUMERIC="en_US.iso885915" LC_TIME="en_US.iso885915" LC_COLLATE="en_US.iso885915" LC_MONETARY="en_US.iso885915" LC_MESSAGES="en_US.iso885915" LC_PAPER="en_US.iso885915" LC_NAME="en_US.iso885915" LC_ADDRESS="en_US.iso885915" LC_TELEPHONE="en_US.iso885915" LC_MEASUREMENT="en_US.iso885915" LC_IDENTIFICATION="en_US.iso885915" LC_ALL=
I will talk to our sysadmin and see if I can change the locale to en_US.UTF-8.
Thank you very much. -Raj
On May 29, 2017, at 10:58 AM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
Curious, my new guess is this is position 52 a temporary string from this expression:
string.letters + string.digits + '_'
This would fit with it being something unusual about the locale of your Galaxy server, and my suggested hack may work - replace string.letters with string.ascii_letters
Separately at the Linux command line of the server running Galaxy, and on a cluster node, what does the command "locale" give? e.g. I get:
$ locale LANG=en_US.UTF-8 LC_CTYPE="en_US.UTF-8" LC_NUMERIC="en_US.UTF-8" LC_TIME="en_US.UTF-8" LC_COLLATE="en_US.UTF-8" LC_MONETARY="en_US.UTF-8" LC_MESSAGES="en_US.UTF-8" LC_PAPER="en_US.UTF-8" LC_NAME="en_US.UTF-8" LC_ADDRESS="en_US.UTF-8" LC_TELEPHONE="en_US.UTF-8" LC_MEASUREMENT="en_US.UTF-8" LC_IDENTIFICATION="en_US.UTF-8" LC_ALL=
Peter
On Mon, May 29, 2017 at 3:43 PM, Saravanaraj Ayyampalayam <raj76@uga.edu> wrote:
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
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/
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Thanks, pull request submitted: https://github.com/galaxyproject/galaxy/pull/4121 Peter On Mon, May 29, 2017 at 5:23 PM, Saravanaraj Ayyampalayam <raj76@uga.edu> wrote:
Peter,
Here is the git diff output that shows the changes I made:
diff --git a/lib/galaxy/jobs/runners/__init__.py b/lib/galaxy/jobs/runners/__init__.py index ebf4859..6ee51c8 100644 --- a/lib/galaxy/jobs/runners/__init__.py +++ b/lib/galaxy/jobs/runners/__init__.py @@ -419,7 +419,7 @@ class JobState( object ): job_name += '_%s' % self.job_wrapper.tool.old_id if self.job_wrapper.user: job_name += '_%s' % self.job_wrapper.user - self.job_name = ''.join( map( lambda x: x if x in ( string.letters + string.digits + '_' ) else '_', job_name ) ) + self.job_name = ''.join( map( lambda x: x if x in ( string.ascii_letters + string.digits + '_' ) else '_', job_name ) )
@staticmethod def default_job_file( files_dir, id_tag ): diff --git a/lib/galaxy/jobs/runners/drmaa.py b/lib/galaxy/jobs/runners/drmaa.py index 7c08984..5c5dc62 100644 --- a/lib/galaxy/jobs/runners/drmaa.py +++ b/lib/galaxy/jobs/runners/drmaa.py @@ -394,7 +394,7 @@ class DRMAAJobRunner( AsynchronousJobRunner ): job_name += '_%s' % job_wrapper.tool.old_id if external_runjob_script is None: job_name += '_%s' % job_wrapper.user - job_name = ''.join( x if x in ( string.letters + string.digits + '_' ) else '_' for x in job_name ) + job_name = ''.join( x if x in ( string.ascii_letters + string.digits + '_' ) else '_' for x in job_name ) if self.restrict_job_name_length: job_name = job_name[:self.restrict_job_name_length] return job_name
-Raj
On May 29, 2017, at 11:33 AM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
Thanks Saravanaraj,
You should not need to change the locale, after all many Galaxy servers and their users will be labelling their files in non-English with "special" characters - but perhaps en_US.UTF-8 would be safer in your case as it seems that few people use Galaxy with en_US.iso885915 otherwise this would have been reported before?
Can you tell us both places you changed string.letters to string.ascii_letters please? I could then submit this as a pull request to get Galaxy itself updated for future release.
Peter
On Mon, May 29, 2017 at 4:28 PM, Saravanaraj Ayyampalayam <raj76@uga.edu> wrote:
Peter,
You are correct. Changing string.letters to string.ascii_letters fixed it. I had to change it in two places.
My locale is :
LANG=en_US.iso885915 LC_CTYPE="en_US.iso885915" LC_NUMERIC="en_US.iso885915" LC_TIME="en_US.iso885915" LC_COLLATE="en_US.iso885915" LC_MONETARY="en_US.iso885915" LC_MESSAGES="en_US.iso885915" LC_PAPER="en_US.iso885915" LC_NAME="en_US.iso885915" LC_ADDRESS="en_US.iso885915" LC_TELEPHONE="en_US.iso885915" LC_MEASUREMENT="en_US.iso885915" LC_IDENTIFICATION="en_US.iso885915" LC_ALL=
I will talk to our sysadmin and see if I can change the locale to en_US.UTF-8.
Thank you very much. -Raj
On May 29, 2017, at 10:58 AM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
Curious, my new guess is this is position 52 a temporary string from this expression:
string.letters + string.digits + '_'
This would fit with it being something unusual about the locale of your Galaxy server, and my suggested hack may work - replace string.letters with string.ascii_letters
Separately at the Linux command line of the server running Galaxy, and on a cluster node, what does the command "locale" give? e.g. I get:
$ locale LANG=en_US.UTF-8 LC_CTYPE="en_US.UTF-8" LC_NUMERIC="en_US.UTF-8" LC_TIME="en_US.UTF-8" LC_COLLATE="en_US.UTF-8" LC_MONETARY="en_US.UTF-8" LC_MESSAGES="en_US.UTF-8" LC_PAPER="en_US.UTF-8" LC_NAME="en_US.UTF-8" LC_ADDRESS="en_US.UTF-8" LC_TELEPHONE="en_US.UTF-8" LC_MEASUREMENT="en_US.UTF-8" LC_IDENTIFICATION="en_US.UTF-8" LC_ALL=
Peter
On Mon, May 29, 2017 at 3:43 PM, Saravanaraj Ayyampalayam <raj76@uga.edu> wrote:
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 > > ___________________________________________________________ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > https://lists.galaxyproject.org/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/
participants (2)
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Peter Cock -
Saravanaraj Ayyampalayam