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
|