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 questionshttp://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
<mailto:p.j.a.c...@googlemail.com>> wrote:
Thanks, pull request submitted:
https://github.com/galaxyproject/galaxy/pull/4121
<https://github.com/galaxyproject/galaxy/pull/4121>
Peter
On Mon, May 29, 2017 at 5:23 PM, Saravanaraj Ayyampalayam
<ra...@uga.edu <mailto: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 <mailto: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 <mailto: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 <mailto: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 <mailto: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
<mailto:u%27g15132_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 <mailto: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 <mailto: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/
<https://lists.galaxyproject.org/>
>>>>>>>
>>>>>>> To search Galaxy mailing lists use the unified search at:
>>>>>>> http://galaxyproject.org/search/
<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 <mailto:boraton2...@gmail.com>
Mobile Phone: 0791024568
"You are the future. Believe in yourself, in your greatness... Become
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