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.cock@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 <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:
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>>>>>>>
>>>>>>> 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

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