Hi Luqman, From your description, it sounds like everything was set up correctly, so I don't immediately know what went wrong. Could you share your history with me (kpvincent@bx.psu.edu)? Then I will be able to look into this in more detail. (To share your history, click on Options in the History pane and choose Share. You can enter the email here.) Regards, Kelly On Wed 13 Jan 2010, at 4:07 AM, galaxy-bugs@bx.psu.edu wrote:

GALAXY TOOL ERROR REPORT ------------------------

This error report was sent from the Galaxy instance hosted on the server "main.g2.bx.psu.edu" ----------------------------------------------------------------------------- This is in reference to dataset id 999375 from history id 312707 ----------------------------------------------------------------------------- You should be able to view the history containing the related history item

3: Map with Bowtie on data 2

by logging in as a Galaxy admin user to the Galaxy instance referenced above and pointing your browser to the following link.

main.g2.bx.psu.edu/history/view?id=e11c642116fd76eb ----------------------------------------------------------------------------- The user 'csilhah@nus.edu.sg' provided the following information:

Hi there,

Im having trouble running bowtie as you can see. Heres what i did:

1. I get example_sequence.txt file from my Illumina run. This is supposedly a fastq file (using the > 1.3 version).

2. I use FASTQ Groomer to convert it into fastqsanger format, bearing in mind to put the option as converting from Illumina 1.3 format.

3. Use output from 2. to align to hg19 on Bowtie.

Help is greatly appreciated!

Luqman ----------------------------------------------------------------------------- job id: 779082 tool id: bowtie_wrapper ----------------------------------------------------------------------------- job command line: python /galaxy/home/g2main/galaxy_main/tools/sr_mapping/ bowtie_wrapper.py --threads="4" --input1=/galaxy/home/ g2main/galaxy_main/database/files/000/999/dataset_999372.dat -- input2="None" --output=/galaxy/home/g2main/galaxy_main/database/ tmp/job_working_directory/779082/galaxy_dataset_999375.dat -- paired=single --genomeSource=indexed --ref=/depot/data2/ galaxy/hg19/bowtie_index/hg19 --params=pre_set -- skip="None" --alignLimit="None" --trimH="None" -- trimL="None" --mismatchSeed="None" -- mismatchQual="None" --seedLen="None" -- rounding="None" --maqSoapAlign="None" -- tryHard="None" --valAlign="None" -- allValAligns="None" --suppressAlign="None" -- best="None" --maxBacktracks="None" --strata="None" -- minInsert="None" --maxInsert="None" -- mateOrient="None" --maxAlignAttempt="None" -- forwardAlign="None" --reverseAlign="None" --offrate="Non e" --seed="None" --dbkey="None" -- indexSettings="None" --iauto_b="None" -- ipacked="None" --ibmax="None" --ibmaxdivn="None" -- idcv="None" --inodc="None" --inoref="None" -- ioffrate="None" --iftab="None" --intoa="None" -- iendian="None" --iseed="None" --icutoff="None" -- suppressHeader=true ----------------------------------------------------------------------------- job stderr: sh: line 1: 6372 Aborted bowtie -p 4 -S /depot/ data2/galaxy/hg19/bowtie_index/hg19 /galaxy/home/g2main/galaxy_main/ database/files/000/999/dataset_999372.dat > /galaxy/home/g2main/ galaxy_main/database/tmp/job_working_directory/779082/ galaxy_dataset_999375.dat 2> /dev/null

----------------------------------------------------------------------------- job stdout:

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