On Wed, May 1, 2013 at 12:09 PM, Mike Dyall-Smith <mike.dyallsmith@gmail.com> wrote:
Hi Peter,
OK, I've worked out why the terminal did not start up galaxy. I have done that, performed a blastp search, and it failed with the usual error, but now I have the terminal output for that failure. Firstly the error report from galaxy:
---------------------------------------------------------------------- An error occurred running this job: blastp: 2.2.26+ Package: blast 2.2.26, build Aug 15 2012 17:48:54 BLAST Database error: No alias or index file found for protein database [/media/sf_mikeds_bioinf/haldb/HAL_collection] in search path [/var/lib/galaxy-server/database/job_working_directory/ ----------------------------------------------------------------------
Now, the log output in the terminal window for that galaxy session: (DEBUG flags are at the end) ---------------------------------------------------------------------------- ... galaxy.jobs.handler INFO 2013-05-01 20:50:46,580 (24) Job dispatched galaxy.jobs.runners.local DEBUG 2013-05-01 20:50:46,772 executing: blastp -version &> /usr/lib/galaxy-server/database/tmp/GALAXY_VERSION_STRING_24; python /usr/lib/galaxy-server/tools/ncbi_blast_plus/hide_stderr.py blastp -query "/usr/lib/galaxy-server/database/files/000/dataset_23.dat" -db "/media/sf_mikeds_bioinf/haldb/HAL_collection" -task blastp -evalue 0.001 -out /usr/lib/galaxy-server/database/files/000/dataset_24.dat -outfmt 6 -num_threads 8 127.0.0.1 - - [01/May/2013:20:50:49 +1100] "POST /root/history_item_updates HTTP/1.1" 200 - "http://127.0.0.1:8080/history" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:20.0) Gecko/20100101 Firefox/20.0" galaxy.jobs.runners.local DEBUG 2013-05-01 20:50:49,568 execution finished: blastp -version &> /usr/lib/galaxy-server/database/tmp/GALAXY_VERSION_STRING_24; python /usr/lib/galaxy-server/tools/ncbi_blast_plus/hide_stderr.py blastp -query "/usr/lib/galaxy-server/database/files/000/dataset_23.dat" -db "/media/sf_mikeds_bioinf/haldb/HAL_collection" -task blastp -evalue 0.001 -out /usr/lib/galaxy-server/database/files/000/dataset_24.dat -outfmt 6 -num_threads 8 galaxy.jobs.runners.local DEBUG 2013-05-01 20:50:49,658 executing external set_meta script for job 24: /usr/lib/galaxy-server/set_metadata.sh ./database/files /usr/lib/galaxy-server/database/job_working_directory/000/24 . /usr/lib/galaxy-server/universe_wsgi.ini /usr/lib/galaxy-server/database/tmp/tmpckvivx /usr/lib/galaxy-server/database/job_working_directory/000/24/galaxy.json /usr/lib/galaxy-server/database/job_working_directory/000/24/metadata_in_HistoryDatasetAssociation_24_Z7Rv70,/usr/lib/galaxy-server/database/job_working_directory/000/24/metadata_kwds_HistoryDatasetAssociation_24_NGaXc0,/usr/lib/galaxy-server/database/job_working_directory/000/24/metadata_out_HistoryDatasetAssociation_24_0FT0mx,/usr/lib/galaxy-server/database/job_working_directory/000/24/metadata_results_HistoryDatasetAssociation_24_U1RFk9,,/usr/lib/galaxy-server/database/job_working_directory/000/24/metadata_override_HistoryDatasetAssociation_24_PI3NHu galaxy.jobs.runners.local DEBUG 2013-05-01 20:50:50,616 execution of external set_meta for job 24 finished galaxy.jobs DEBUG 2013-05-01 20:50:50,635 The tool did not define exit code or stdio handling; checking stderr for success galaxy.jobs DEBUG 2013-05-01 20:50:50,686 setting dataset state to ERROR galaxy.jobs DEBUG 2013-05-01 20:50:50,817 job 24 ended ...
Great. From that we can see the command Galaxy ran, python /usr/lib/galaxy-server/tools/ncbi_blast_plus/hide_stderr.py blastp -query "/usr/lib/galaxy-server/database/files/000/dataset_23.dat" -db "/media/sf_mikeds_bioinf/haldb/HAL_collection" -task blastp -evalue 0.001 -out /usr/lib/galaxy-server/database/files/000/dataset_24.dat -outfmt 6 -num_threads 8 There are two (related) clues that this is not the latest BLAST wrapper, this warning: "The tool did not define exit code" and the fact that it is using the hide_stderr.py script to hide stderr from Galaxy. Since then Galaxy has allowed wrappers more flexibility to deal with stderr - which I tool advantage of in September 2012 with v0.0.13 of the BLAST+ wrappers. What does Galaxy say the version of the BLASTP wrapper is? I now suspect that the Galaxy you have from BioLinux is very old, and may still be using the BLAST+ wrappers as then bundled with Galaxy itself. Back in about August 2012, the BLAST+ wrappers were moved to the Tool Shed. Or, perhaps it is just using an old copy of the BLAST+ wrappers? Still, the BLAST+ wrappers from back then should work. I would suggest running this at the terminal (using a different file as the output) and seeing if this works: blastp -query "/usr/lib/galaxy-server/database/files/000/dataset_23.dat" -db "/media/sf_mikeds_bioinf/haldb/HAL_collection" -task blastp -evalue 0.001 -out test_blast.tabular -outfmt 6 -num_threads 8 If you've worked out which Linux user Galaxy is run under, try that here using: sudo -u the_galaxy_user blastp ... Also could do do this so I can check the database definition is sensible? ls -l /media/sf_mikeds_bioinf/haldb/HAL_collection* Thanks, Peter