Re: [galaxy-dev] BLAST Database error: No alias or index file found
On Wed, May 1, 2013 at 11:43 AM, Mike Dyall-Smith mike.dyallsm...@gmail.com wrote: Hi Peter, In biolinux, I start galaxy by a clicking on an application icon. If I open the terminal and run the suggested command: $ sh run.sh | grep -i blast I get the following output (long): $ sudo sh run.sh | grep -i blast python path is: /usr/lib/galaxy-server/eggs/numpy-1.6.0-py2.7-linux-x86_64-ucs4.egg, ... Traceback (most recent call last): socket.error: [Errno 98] Address already in use -- as might be expected from this output, it doesn't start up galaxy at localhost. That usually happens if Galaxy is already running and is using the port. The second Galaxy instance therefore can't grab the port and so won't start. check is the read permissions on the BLAST database Well, from the terminal, I have access to all those files. The permissions are all the same, e.g. -rwxrwx--- 1 root vboxsf 15721925 Apr 10 18:55 nr.00.phd Within galaxy, I can open them with the get data menu command. That appears to mean only the owner (root) and members of the group vboxsf can read the files. That may explain why BLAST can't use the files. The simplest option is to make the BLAST database files (and if needed, the containing folder too) world readable, e.g. $ sudo chmod a+r /media/sf_mikeds_bioinf/db/nr* Alternatively check the group memberships. What user is Galaxy running as? (One way to check would be via top or ps when Galaxy is running). My guess is whatever user that is, they are not a member of the vboxsf group. To fix this, you could add the Galaxy user to the vboxsf group. Peter ___ 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/
Re: [galaxy-dev] BLAST Database error: No alias or index file found
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) 127.0.0.1 - - [01/May/2013:20:49:58 +1100] POST /root/user_get_usage 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.manager DEBUG 2013-05-01 20:49:59,237 (23) Job assigned to handler 'main' 127.0.0.1 - - [01/May/2013:20:50:02 +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 DEBUG 2013-05-01 20:50:04,403 (23) Working directory for job is: /usr/lib/galaxy-server/database/job_working_directory/000/23 galaxy.jobs.handler DEBUG 2013-05-01 20:50:04,404 dispatching job 23 to local runner galaxy.jobs.handler INFO 2013-05-01 20:50:04,523 (23) Job dispatched galaxy.jobs.runners.local DEBUG 2013-05-01 20:50:04,727 executing: python /usr/lib/galaxy-server/tools/data_source/upload.py /usr/lib/galaxy-server /usr/lib/galaxy-server/database/tmp/tmpckvivx /usr/lib/galaxy-server/database/tmp/tmpED2TiJ 23:/usr/lib/galaxy-server/database/job_working_directory/000/23/dataset_23_files:/usr/lib/galaxy-server/database/files/000/dataset_23.dat galaxy.jobs.runners.local DEBUG 2013-05-01 20:50:05,459 execution finished: python /usr/lib/galaxy-server/tools/data_source/upload.py /usr/lib/galaxy-server /usr/lib/galaxy-server/database/tmp/tmpckvivx /usr/lib/galaxy-server/database/tmp/tmpED2TiJ 23:/usr/lib/galaxy-server/database/job_working_directory/000/23/dataset_23_files:/usr/lib/galaxy-server/database/files/000/dataset_23.dat galaxy.jobs.runners.local DEBUG 2013-05-01 20:50:05,592 executing external set_meta script for job 23: /usr/lib/galaxy-server/set_metadata.sh ./database/files /usr/lib/galaxy-server/database/job_working_directory/000/23 . /usr/lib/galaxy-server/universe_wsgi.ini /usr/lib/galaxy-server/database/tmp/tmpckvivx /usr/lib/galaxy-server/database/job_working_directory/000/23/galaxy.json /usr/lib/galaxy-server/database/job_working_directory/000/23/metadata_in_HistoryDatasetAssociation_23_mZBOP0,/usr/lib/galaxy-server/database/job_working_directory/000/23/metadata_kwds_HistoryDatasetAssociation_23_ogpRq8,/usr/lib/galaxy-server/database/job_working_directory/000/23/metadata_out_HistoryDatasetAssociation_23_3yS7Yh,/usr/lib/galaxy-server/database/job_working_directory/000/23/metadata_results_HistoryDatasetAssociation_23_71mkqj,,/usr/lib/galaxy-server/database/job_working_directory/000/23/metadata_override_HistoryDatasetAssociation_23_KhG0tM galaxy.jobs.runners.local DEBUG 2013-05-01 20:50:06,549 execution of external set_meta for job 23 finished galaxy.jobs DEBUG 2013-05-01 20:50:06,626 The tool did not define exit code or stdio handling; checking stderr for success 127.0.0.1 - - [01/May/2013:20:50:06 +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.datatypes.metadata DEBUG 2013-05-01 20:50:06,773 loading metadata from file for: HistoryDatasetAssociation 23 galaxy.jobs DEBUG 2013-05-01 20:50:06,905 job 23 ended galaxy.datatypes.metadata DEBUG 2013-05-01 20:50:06,905 Cleaning up external metadata files 127.0.0.1 - - [01/May/2013:20:50:10 +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/20.0 127.0.0.1 - - [01/May/2013:20:50:10 +1100] POST /root/history_get_disk_size 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/20.0 127.0.0.1 - - [01/May/2013:20:50:11 +1100] GET /datasets/f09437b8822035f7/display/?preview=True 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/20.0 127.0.0.1 - - [01/May/2013:20:50:23 +1100] GET /tool_runner?tool_id=ncbi_blastp_wrapper HTTP/1.1 200 - http://127.0.0.1:8080/root/tool_menu; Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:20.0) Gecko/20100101 Firefox/20.0 127.0.0.1 - - [01/May/2013:20:50:36 +1100] POST /tool_runner/index HTTP/1.1 200 -
Re: [galaxy-dev] BLAST Database error: No alias or index file found
On Wed, May 1, 2013 at 12:09 PM, Mike Dyall-Smith mike.dyallsm...@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:
Re: [galaxy-dev] BLAST Database error: No alias or index file found
On Tue, Apr 30, 2013 at 3:56 AM, Mike Dyall-Smith mike.dyallsm...@gmail.com wrote: This follows on from Kenneth Auerbach's question Sep 12, 2012: Galaxy error running NCBI BLAST: blastx http://dev.list.galaxyproject.org/Galaxy-error-running-NCBI-BLAST-blastx-td4656210.html I wish to use a local copy of the genbank database for searches. The genbank db files are sitting in a folder on an external drive, and I have altered the blastdb_p.loc to point to them. I can see and select this database within galaxy, but when I try using blast+ blastp tool, I get the error BLAST Database error: No alias or index file found for protein database [/media/sf_mikeds_bioinf/GenbankDB_Files/nr/nr] in search path [/var/lib/galaxy-server/database/job_working_directory] As suggested previously by Peter Cock, I can list all the files with: ls /media/sf_mikeds_bioinf/GenbankDB_Files/nr/nr* which gives me the list: /media/sf_mikeds_bioinf/GenbankDB_Files/nr/nr.00.phd /media/sf_mikeds_bioinf/GenbankDB_Files/nr/nr.00.phi ... /media/sf_mikeds_bioinf/GenbankDB_Files/nr/nr.10.psq /media/sf_mikeds_bioinf/GenbankDB_Files/nr/nr.pal The alias file, nr.pal is the last one in the list above, so is present. I changed the default directory for the blast database: BLASTDB=/media/sf_mikeds_bioinf/GenbankDB_Files/nr - this made no difference to the error. I am running biolinux 7 (latest) in ubuntu within VirtualBox, on a macbook pro. The external drive is a shared folder, and I can see all the files within galaxy (e.g. I can import data data files). Any help would be appreciated. Regards, Mike DS Hi Mike, Have you been able to successfully run blastp with the nr database at the command line by hand? Could you share the (relevant lines from) your blastdb_p.loc file, and the matching error message from blastp when called from Galaxy? With your files here, /media/sf_mikeds_bioinf/GenbankDB_Files/nr/nr.* you should use /media/sf_mikeds_bioinf/GenbankDB_Files/nr/nr as the BLAST the database name (column 3 in blastdb_p.loc for use in Galaxy). (Personally I don't bother with the BLASTDB setting, it is just one more point of confusion when using BLAST on a cluster.) Regards, Peter ___ 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/
