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.dat      
                 
--indexes-path="/data/db/fungidb/Ncrassa_OR74A/bowtie2/Ncrassa_wt_Chr01.Chr07.+ChrM.+rDNA_v12"
          --single-paired=paired          
--input1=/usr/local/galaxy/galaxy-dist/database/files/001/dataset_1668.dat      
                
--input2=/usr/local/galaxy/galaxy-dist/database/files/001/dataset_1669.dat      
       -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.dat      
                 
--indexes-path="/data/db/fungidb/Ncrassa_OR74A/bowtie2/Ncrassa_wt_Chr01.Chr07.+ChrM.+rDNA_v12"
          --single-paired=paired          
--input1=/usr/local/galaxy/galaxy-dist/database/files/001/dataset_1668.dat      
                
--input2=/usr/local/galaxy/galaxy-dist/database/files/001/dataset_1669.dat      
       -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/galaxy.json
 
/usr/local/galaxy/galaxy-dist/database/job_working_directory/001/1483/metadata_in_HistoryDatasetAssociation_1767_wqhEmr,/usr/local/galaxy/galaxy-dist/database/job_working_directory/001/1483/metadata_kwds_HistoryDatasetAssociation_1767_qVZjpG,/usr/local/galaxy/galaxy-dist/database/job_working_directory/001/1483/metadata_out_HistoryDatasetAssociation_1767_vIfpRO,/usr/local/galaxy/galaxy-dist/database/job_working_directory/001/1483/metadata_results_HistoryDatasetAssociation_1767_UNl6OR,,/usr/local/galaxy/galaxy-dist/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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