Re: [galaxy-dev] Bowtie2 error: Creates a 62 kb file.
[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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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
___________________________________________________________ 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/
___________________________________________________________ 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/
participants (2)
-
Jeremy Goecks -
Maddhi, Srinivas