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
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