It would be very useful to know what's in the 62kb file -- is it a BAM file or a long error message? Also, the Bowtie2 wrapper has been updated in -central, so you may want to check that out as well. J. On Jul 24, 2013, at 5:07 PM, Maddhi, Srinivas wrote:
[Copying the list].
-----Original Message----- From: <Maddhi>, Srinivas Maddhi <srinivas-maddhi@uiowa.edu> Date: Wednesday, July 24, 2013 10:01 AM To: "Perez, Ricardo" <ricky_pz2@neo.tamu.edu> Subject: Re: [galaxy-dev] Bowtie2 error: Creates a 62 kb file.
Hi Ricardo,
Ensuring that the appropriate reference indices are present, properly configured and selected when running bowtie2 might help address this problem.
-----Original Message----- From: <Perez>, Ricardo <ricky_pz2@neo.tamu.edu> Date: Wednesday, July 24, 2013 1:35 AM To: "galaxy-dev@lists.bx.psu.edu" <galaxy-dev@lists.bx.psu.edu> Subject: [galaxy-dev] Bowtie2 error: Creates a 62 kb file.
Dear all,
Today we ran some problems when running bowtie2. When we run bowtie2, the run manages to complete. However, bowtie2 creates a 62kb file. The error log that we get is the following:
galaxy.jobs DEBUG 2013-07-23 17:09:42,378 (1483) Persisting job destination (destination id: local:///) galaxy.jobs.handler INFO 2013-07-23 17:09:42,392 (1483) Job dispatched galaxy.tools DEBUG 2013-07-23 17:09:42,556 Building dependency shell command for dependency 'bowtie2' galaxy.tools WARNING 2013-07-23 17:09:42,556 Failed to resolve dependency on 'bowtie2', ignoring galaxy.tools DEBUG 2013-07-23 17:09:42,556 Building dependency shell command for dependency 'samtools' galaxy.tools WARNING 2013-07-23 17:09:42,556 Failed to resolve dependency on 'samtools', ignoring galaxy.jobs.runners.local DEBUG 2013-07-23 17:09:42,626 (1483) executing: bowtie2 --version &> /usr/local/galaxy/galaxy-dist/database/tmp/GALAXY_VERSION_STRING_1483; python /usr/local/galaxy/galaxy-dist/tools/sr_mapping/bowtie2_wrapper.py --num-threads="4" --output=/usr/local/galaxy/galaxy-dist/database/files/001/dataset_1673.da t
--indexes-path="/data/db/fungidb/Ncrassa_OR74A/bowtie2/Ncrassa_wt_Chr01.C h r07.+ChrM.+rDNA_v12" --single-paired=paired --input1=/usr/local/galaxy/galaxy-dist/database/files/001/dataset_1668.da t
--input2=/usr/local/galaxy/galaxy-dist/database/files/001/dataset_1669.da t -I 0 -X 250 --settings=preSet galaxy.jobs DEBUG 2013-07-23 17:09:42,696 (1483) Persisting job destination (destination id: local:///) galaxy.jobs.runners.local DEBUG 2013-07-23 17:09:42,766 execution finished: bowtie2 --version &> /usr/local/galaxy/galaxy-dist/database/tmp/GALAXY_VERSION_STRING_1483; python /usr/local/galaxy/galaxy-dist/tools/sr_mapping/bowtie2_wrapper.py --num-threads="4" --output=/usr/local/galaxy/galaxy-dist/database/files/001/dataset_1673.da t
--indexes-path="/data/db/fungidb/Ncrassa_OR74A/bowtie2/Ncrassa_wt_Chr01.C h r07.+ChrM.+rDNA_v12" --single-paired=paired --input1=/usr/local/galaxy/galaxy-dist/database/files/001/dataset_1668.da t
--input2=/usr/local/galaxy/galaxy-dist/database/files/001/dataset_1669.da t -I 0 -X 250 --settings=preSet galaxy.jobs.runners DEBUG 2013-07-23 17:09:42,850 executing external set_meta script for job 1483: /usr/local/galaxy/galaxy-dist/set_metadata.sh ./database/files /usr/local/galaxy/galaxy-dist/database/job_working_directory/001/1483 . /usr/local/galaxy/galaxy-dist/universe_wsgi.ini /usr/local/galaxy/galaxy-dist/database/tmp/tmpUiqpPD /usr/local/galaxy/galaxy-dist/database/job_working_directory/001/1483/gal a xy.json /usr/local/galaxy/galaxy-dist/database/job_working_directory/001/1483/met a data_in_HistoryDatasetAssociation_1767_wqhEmr,/usr/local/galaxy/galaxy-di s t/database/job_working_directory/001/1483/metadata_kwds_HistoryDatasetAss o ciation_1767_qVZjpG,/usr/local/galaxy/galaxy-dist/database/job_working_di r ectory/001/1483/metadata_out_HistoryDatasetAssociation_1767_vIfpRO,/usr/l o cal/galaxy/galaxy-dist/database/job_working_directory/001/1483/metadata_r e sults_HistoryDatasetAssociation_1767_UNl6OR,,/usr/local/galaxy/galaxy-dis t /database/job_working_directory/001/1483/metadata_over! ride_HistoryDatasetAssociation_1767_MZilrL 165.91.11.135 - - [23/Jul/2013:17:09:43 -0500] "GET /api/histories/ca8efa3c47500414 HTTP/1.1" 200 - "http://galaxy.tamu.edu/history" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.22 (KHTML, like Gecko) Ubuntu Chromium/25.0.1364.160 Chrome/25.0.1364.160 Safari/537.22" 165.91.11.231 - - [23/Jul/2013:17:09:43 -0500] "GET /history HTTP/1.1" 200 - "http://galaxy.tamu.edu/tool_runner/index" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_6_8) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/28.0.1500.71 Safari/537.36" 165.91.11.231 - - [23/Jul/2013:17:09:43 -0500] "GET /api/histories/1ab12f1e464820dd HTTP/1.1" 200 - "http://galaxy.tamu.edu/history" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_6_8) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/28.0.1500.71 Safari/537.36" 165.91.11.231 - - [23/Jul/2013:17:09:43 -0500] "GET /history/get_display_application_links HTTP/1.1" 200 - "http://galaxy.tamu.edu/history" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_6_8) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/28.0.1500.71 Safari/537.36" galaxy.jobs.runners DEBUG 2013-07-23 17:09:44,457 execution of external set_meta for job 1483 finished galaxy.datatypes.metadata DEBUG 2013-07-23 17:09:44,545 loading metadata from file for: HistoryDatasetAssociation 1767
We currently have the most recent version of bowtie2 and samtools. Anyone know how to fix this?
Thank you for your time, --Ricardo Perez
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