Hi Dev,

I am running a local instance Galaxy for developing a variant calling
pipeline. I ran into this issue after configuring and installing GATK2 on
my local when running the GATK *Realigner Target Creator on the BAM file
generated by Mark duplicates.*
*Can some suggest how to resolve this issue or please point to how to debug
this issue from the GATK2 wrapper? BTW, I follow the instruction by
ensuring that my GATK3 environment was set as stated in the Galaxy GATk2
readme.txt.*

Below here was the issue I encountered;

##### ERROR 
------------------------------------------------------------------------------------------
##### ERROR A USER ERROR has occurred (version 2.0-7-g7323e98):
##### ERROR The invalid arguments or inputs must be corrected before
the GATK can proceed
##### ERROR Please do not post this error to the GATK forum
##### ERROR
##### ERROR See the documentation (rerun with -h) for this tool to
view allowable command-line arguments.
##### ERROR Visit our website and forum for extensive documentation
and answers to
##### ERROR commonly asked questions http://www.broadinstitute.org/gatk
##### ERROR
##### ERROR MESSAGE: Argument with name
'num_cpu_threads_per_data_thread' isn't defined.
##### ERROR 
------------------------------------------------------------------------------------------



On Mon, May 29, 2017 at 6:44 PM, Peter Cock <p.j.a.c...@googlemail.com>
wrote:

> Thanks, pull request submitted:
>
> https://github.com/galaxyproject/galaxy/pull/4121
>
> Peter
>
>
> On Mon, May 29, 2017 at 5:23 PM, Saravanaraj Ayyampalayam <ra...@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.c...@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 <
> ra...@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.c...@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 <
> ra...@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_ra...@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.c...@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 <
> ra...@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/
> >>>>>
> >>>
> >
> ___________________________________________________________
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>



-- 
Ajayi Olabode O.
University of the western cape
South Africa National Bioinformatics Institute(Msc In Progress)
Department of Computer Science
Computer Science  (B.sc & Hons)
SAP ERP,
MCSE,MCTS,MCP,MCSA
Mechanical Engineering
E-mail: boraton2...@gmail.com
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"You are the future. Believe in yourself, in your greatness... Become all
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