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-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
>>> 
>>> ___________________________________________________________
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>> 
> 
> 
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