Issue with GATK2 on Galaxy Repository. - galaxy-dev

31 May 2017

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:
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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
...
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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:
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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.
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...
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:
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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:
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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
...
...
...
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...
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
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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
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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
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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
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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
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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
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galaxy.jobs.runners.drmaa DEBUG 2017-05-29 10:37:21,424 Making
job_name, character 6 in proposed job_name u'_' is 95
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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
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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
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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
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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
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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
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galaxy.jobs.runners.drmaa DEBUG 2017-05-29 10:37:21,425 Making
job_name, character 12 in proposed job_name u'_' is 95
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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
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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
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galaxy.jobs.runners.drmaa DEBUG 2017-05-29 10:37:21,426 Making
job_name, character 15 in proposed job_name u'_' is 95
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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
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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
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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
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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
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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
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galaxy.jobs.runners.drmaa DEBUG 2017-05-29 10:37:21,427 Making
job_name, character 21 in proposed job_name u'_' is 95
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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
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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
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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
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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
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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
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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
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galaxy.jobs.runners.drmaa DEBUG 2017-05-29 10:37:21,428 Making
job_name, character 28 in proposed job_name u'_' is 95
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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
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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
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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
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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
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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
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galaxy.jobs.runners.drmaa DEBUG 2017-05-29 10:37:21,429 Making
job_name, character 34 in proposed job_name u'@' is 64
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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
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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
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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
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galaxy.jobs.runners.drmaa DEBUG 2017-05-29 10:37:21,430 Making
job_name, character 38 in proposed job_name u'.' is 46
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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
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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
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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
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galaxy.jobs.runners ERROR 2017-05-29 10:37:21,431 (15132) Unhandled
exception calling queue_job
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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
...
...
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...
method(arg)
File "/panfs/pstor.storage/home/qbcglab/galaxy_run/galaxy-
dist/lib/galaxy/jobs/runners/drmaa.py", line 132, in queue_job
...
...
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...
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
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job_name = ''.join( x if x in ( string.letters + string.digits +
'_' ) else '_' for x in job_name )
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File "/panfs/pstor.storage/home/qbcglab/galaxy_run/galaxy-
dist/lib/galaxy/jobs/runners/drmaa.py", line 400, in <genexpr>
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job_name = ''.join( x if x in ( string.letters + string.digits +
'_' ) else '_' for x in job_name )
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UnicodeDecodeError: 'ascii' codec can't decode byte 0xa6 in position
52: ordinal not in range(128)
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There is no sign of the 0xa6 at position 52 (the job name is only 42
chars long) in the job name.
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Thanks!
-Raj
> On May 29, 2017, at 5:50 AM, Peter Cock p.j.a.cock@googlemail.com
wrote:
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...
...
...
...
>
> 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
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...
> (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
...
...
...
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> 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:
...
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...
>> Hello,
>>
>> I updated to the latest version (17.05) galaxy code. I was
updating from a very old version.
...
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...
>> I fixed all the issues with except one. I am getting the following
error when I submit a job.
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>>
>> galaxy.jobs.runners ERROR 2017-05-29 01:42:44,008 (15131)
Unhandled exception calling queue_job
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...
>> 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
...
...
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...
>>  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 )
...
...
...
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...
>> 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 )
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...
>> UnicodeDecodeError: 'ascii' codec can't decode byte 0xa6 in
position 52: ordinal not in range(128)
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>>
>> I spent a day trying to debug this and didn’t get anywhere. The
job_name looks OK.
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>>
>> I would really appreciate some help from the community.
>>
>> Thanks!
>> -Raj
>>
>> ___________________________________________________________
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>>
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-- 
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South Africa National Bioinformatics Institute(Msc In Progress)
Department of Computer Science
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