Hi Greg,

The problem here and the confusion between the Bowtie loc files are likely related. Do you have both bowtie/bowtie2 and tophat/tophat2 installed? And the tool wrappers for all versions are active? I though we resolved this earlier but maybe you installed a new tool or updated?


The wrappers for the tools that have dependencies on bowtie vs bowtie2 (and the associated indexes) are not interchangeable. You will need to chech your paths to see which tool is being used for each - be sure to check any symbolic paths that may have been created when the tools were installed (these tools are known to create links such as bowtie -> bowtie2, that you will want to get rid of).

Reviewing tool dependencies is the best way to troubleshoot:
http://wiki.galaxyproject.org/Admin/Tools/Tool%20Dependencies

Hopefully this helps. Be sure to keep any followup on the mailing list so the dev community can continue to have input,

Jen
Galaxy team

On 2/21/13 7:50 AM, greg wrote:
Hi guys,

On our local galaxy install I'm getting the error below when I run
tophat for illumina like this:

http://snag.gy/HsWyS.jpg

Any ideas?

Thanks,

Greg


Error:

Dataset generation errors

Dataset 27: Tophat for Illumina on data 15: deletions

Tool execution generated the following error message:

Error in tophat:
tophat: option --no-closure-search not recognized
     for detailed help see http://tophat.cbcb.umd.edu/manual.html

cp: cannot stat
`/home/galaxy/job_working_directory/000/238/tophat_out/junctions.bed':
No such file or directory
cp: cannot stat
`/home/galaxy/job_working_directory/000/238/tophat_out/insertions.bed':
No such file or directory
cp: cannot stat
`/home/galaxy/job_working_directory/000/238/tophat_out/accepted_hits.bam':
No such file or directory
cp: cannot stat
`/home/galaxy/job_working_directory/000/238/tophat_out/deletions.bed':
No such file or directory

The tool produced the following additional output:

TopHat v2.0.6
tophat -p 4  -a 8 -m 0 -i 70 -I 500000 -g 20 --library-type
fr-unstranded --max-insertion-length 3 --max-deletion-length 3
--coverage-search --min-coverage-intron 50 --max-coverage-intron 20000
--no-closure-search --initial-read-mismatches 2 --segment-mismatches 2
--segment-length 25 --min-segment-intron 50 --max-segment-intron
500000 
/usr/local/galaxy/indexes/Mus_musculus/UCSC/mm10/Sequence/Bowtie2Index/genome
/home/galaxy/000/dataset_306.dat
___________________________________________________________
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/


--
Jennifer Hillman-Jackson
Galaxy Support and Training
http://galaxyproject.org
___________________________________________________________
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/

Reply via email to