New subject: Bowtie2 error: Creates a 62 kb file.

24 Jul 2013

      [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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