All,
When running clustalW jobs, the only output we're getting is an error message
that appears to show the tool isn't receiving the proper run-time parameters:
Unknown option: I
Value "FILE=infile_copy" invalid for option N (number expected)
Unknown option: F
Unknown option: I
Unknown option: L
Unknown option: E
...
This appears to come from the rgClustalw.py wrapper:
cl = ['clustalw2 -INFILE=%s -OUTFILE=%s -OUTORDER=%s -TYPE=%s -OUTPUT=%s
' % (self.iname,self.opts.output,self.opts.out_order,self.opts.dnarna,self.opts.
outform)]
Strangely, the log files appear to show the correct paramters:
galaxy.tools WARNING 2014-06-05 10:37:43,484 Failed to resolve dependency on
'clustalw2', ignoring
galaxy.jobs.runners.local DEBUG 2014-06-05 10:37:43,596 (779) executing: python
/home/galaxy/galaxy-dist/tools/rgenetics/rgClustalw.py -i
"/home/galaxy/galaxy-dist/database/files/001/dataset_1243.dat" -o
"/home/galaxy/galaxy-dist/database/files/001/dataset_1244.dat" -s "ALIGNED" -l
"/home/galaxy/galaxy-dist/database/files/001/dataset_1245.dat" -t "Clustal_run"
-d "DNA" -f "CLUSTAL"
I'll post the full output from the logs below, but I was hoping someone might
be able to offer some suggestions on how to debug this further.
Thanks!
Malcolm
10.28.56.101 - - [05/Jun/2014:10:37:42 -0500] "POST /tool_runner/index
HTTP/1.1" 200 - "http://galaxy.chpc.wustl.edu/tool_runner?tool_id=clustalw";
"Mozilla/5.0 (X11; Linux x86_64; rv:24.0) Gecko/20100101 Firefox/24.0"
galaxy.jobs DEBUG 2014-06-05 10:37:43,025 (779) Working directory for job is:
/home/galaxy/galaxy-dist/database/job_working_directory/000/779
galaxy.jobs.handler DEBUG 2014-06-05 10:37:43,057 (779) Dispatching to local
runner
galaxy.jobs DEBUG 2014-06-05 10:37:43,205 (779) Persisting job destination
(destination id: local)
galaxy.jobs.handler INFO 2014-06-05 10:37:43,258 (779) Job dispatched
10.28.56.101 - - [05/Jun/2014:10:37:42 -0500] "GET /history HTTP/1.1" 200 -
"http://galaxy.chpc.wustl.edu/tool_runner/index"; "Mozilla/5.0 (X11; Linux
x86_64; rv:24.0) Gecko/20100101 Firefox/24.0"
galaxy.tools DEBUG 2014-06-05 10:37:43,466 Building dependency shell command
for dependency 'clustalw2'
galaxy.tools WARNING 2014-06-05 10:37:43,484 Failed to resolve dependency on
'clustalw2', ignoring
galaxy.jobs.runners.local DEBUG 2014-06-05 10:37:43,596 (779) executing: python
/home/galaxy/galaxy-dist/tools/rgenetics/rgClustalw.py -i
"/home/galaxy/galaxy-dist/database/files/001/dataset_1243.dat" -o
"/home/galaxy/galaxy-dist/database/files/001/dataset_1244.dat" -s "ALIGNED" -l
"/home/galaxy/galaxy-dist/database/files/001/dataset_1245.dat" -t "Clustal_run"
-d "DNA" -f "CLUSTAL"
10.28.56.101 - - [05/Jun/2014:10:37:43 -0500] "GET
/api/histories/1ac3b66e11b8fe50 HTTP/1.1" 200 -
"http://galaxy.chpc.wustl.edu/history"; "Mozilla/5.0 (X11; Linux x86_64;
rv:24.0) Gecko/20100101 Firefox/24.0"
galaxy.datatypes.interval ERROR 2014-06-05 10:37:43,732 Exception caught
attempting to generate viewport for dataset '972'
Traceback (most recent call last):
File "/home/galaxy/galaxy-dist/lib/galaxy/datatypes/interval.py", line 159,
in get_estimated_display_viewport
fh = open( dataset.file_name )
IOError: [Errno 2] No such file or directory:
'/home/galaxy/galaxy-dist/database/files/000/dataset_769.dat'
galaxy.jobs DEBUG 2014-06-05 10:37:43,736 (779) Persisting job destination
(destination id: local)
galaxy.datatypes.interval ERROR 2014-06-05 10:37:43,776 Exception caught
attempting to generate viewport for dataset '985'
Traceback (most recent call last):
File "/home/galaxy/galaxy-dist/lib/galaxy/datatypes/interval.py", line 159,
in get_estimated_display_viewport
fh = open( dataset.file_name )
IOError: [Errno 2] No such file or directory:
'/home/galaxy/galaxy-dist/database/files/000/dataset_782.dat'
galaxy.datatypes.interval ERROR 2014-06-05 10:37:43,830 Exception caught
attempting to generate viewport for dataset '986'
Traceback (most recent call last):
File "/home/galaxy/galaxy-dist/lib/galaxy/datatypes/interval.py", line 159,
in get_estimated_display_viewport
fh = open( dataset.file_name )
IOError: [Errno 2] No such file or directory:
'/home/galaxy/galaxy-dist/database/files/000/dataset_783.dat'
galaxy.datatypes.interval ERROR 2014-06-05 10:37:43,876 Exception caught
attempting to generate viewport for dataset '987'
Traceback (most recent call last):
File "/home/galaxy/galaxy-dist/lib/galaxy/datatypes/interval.py", line 159,
in get_estimated_display_viewport
fh = open( dataset.file_name )
IOError: [Errno 2] No such file or directory:
'/home/galaxy/galaxy-dist/database/files/000/dataset_784.dat'
10.28.56.101 - - [05/Jun/2014:10:37:43 -0500] "GET
/history/get_display_application_links HTTP/1.1" 200 -
"http://galaxy.chpc.wustl.edu/history"; "Mozilla/5.0 (X11; Linux x86_64;
rv:24.0) Gecko/20100101 Firefox/24.0"
galaxy.jobs.runners.local DEBUG 2014-06-05 10:37:45,983 execution finished:
python /home/galaxy/galaxy-dist/tools/rgenetics/rgClustalw.py -i
"/home/galaxy/galaxy-dist/database/files/001/dataset_1243.dat" -o
"/home/galaxy/galaxy-dist/database/files/001/dataset_1244.dat" -s "ALIGNED" -l
"/home/galaxy/galaxy-dist/database/files/001/dataset_1245.dat" -t "Clustal_run"
-d "DNA" -f "CLUSTAL"
galaxy.jobs.runners DEBUG 2014-06-05 10:37:46,609 executing external set_meta
script for job 779: /home/galaxy/galaxy-dist/set_metadata.sh ./database/files
/home/galaxy/galaxy-dist/database/job_working_directory/000/779 .
/home/galaxy/galaxy-dist/universe_wsgi.ini
/home/galaxy/galaxy-dist/database/tmp/tmpsnNodx
/home/galaxy/galaxy-dist/database/job_working_directory/000/779/galaxy.json
/home/galaxy/galaxy-dist/database/job_working_directory/000/779/metadata_in_HistoryDatasetAssociation_1448_zaFZp3,/home/galaxy/galaxy-dist/database/job_working_directory/000/779/metadata_kwds_HistoryDatasetAssociation_1448_Rltsef,/home/galaxy/galaxy-dist/database/job_working_directory/000/779/metadata_out_HistoryDatasetAssociation_1448_12s67j,/home/galaxy/galaxy-dist/database/job_working_directory/000/779/metadata_results_HistoryDatasetAssociation_1448_Qucqzx,,/home/galaxy/galaxy-dist/database/job_working_directory/000/779/metadata_override_HistoryDatasetAssociation_1448_95Vr9q
/home/galaxy/galaxy-dist/database/job_working_directory/000/779/metadata_in_HistoryDatasetAssociation_1447_Zh2tCn,/home/galaxy/galaxy-dist/database/job_working_directory/000/779/metadata_kwds_HistoryDatasetAssociation_1447_UeH8AF,/home/galaxy/galaxy-dist/database/job_working_directory/000/779/metadata_out_HistoryDatasetAssociation_1447_cZxp2H,/home/galaxy/galaxy-dist/database/job_working_directory/000/779/metadata_results_HistoryDatasetAssociation_1447_ck1M8o,,/home/galaxy/galaxy-dist/database/job_working_directory/000/779/metadata_override_HistoryDatasetAssociation_1447_pefoLl
--
Malcolm Tobias
314.362.1594
___________________________________________________________
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:
http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/
