[Copying the list].
-----Original Message----- From: <Maddhi>, Srinivas Maddhi <srinivas-mad...@uiowa.edu> Date: Wednesday, July 24, 2013 10:01 AM To: "Perez, Ricardo" <ricky_...@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_...@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/
