Jeremy,

But the tophat2 is running successfully in the command line. So, I guess
it's related to Galaxy. Why am I getting this error in Galaxy? Is it
because I don't have latest Galaxy? Is it file permission issue? I am using
Tophat V2.0.7 and latest Bowtie2 version.

On Fri, Feb 15, 2013 at 8:02 PM, Jeremy Goecks <jeremy.goe...@emory.edu>wrote:

> This is not a known bug. For questions related to Tophat errors, you might
> try the Tophat mailing list:
>
> tophat.cuffli...@gmail.com
>
> Good luck,
> J.
>
> On Feb 15, 2013, at 6:02 AM, Sachit Adhikari wrote:
>
> Galaxy is working fine in command line whereas in Galaxy at last i got
> this error:
>
>
> [2013-02-15 01:39:12] Reporting output tracks
>       [FAILED]
>
> Error running /usr/local/bin/tophat_reports --min-anchor 8 
> --splice-mismatches 0 --min-report-intron 50 --max-report-intron 500000 
> --min-isoform-fraction 0.15 --output-dir ./tophat_out/ --max-multihits 20 
> --max-seg-multihits 40 --segment-length 25 --segment-mismatches 2 
> --min-closure-exon 100 --min-closure-intron 50 --max-closure-intron 5000 
> --min-coverage-intron 50 --max-coverage-intron 20000 --min-segment-intron 50 
> --max-segment-intron 500000 --read-mismatches 2 --read-gap-length 2 
> --read-edit-dist 2 --read-realign-edit-dist 3 --max-insertion-length 3 
> --max-deletion-length 3 -z gzip -p4 --no-closure-search --no-coverage-search 
> --no-microexon-search --sam-header 
> ./tophat_out/tmp/genome_genome.bwt.samheader.sam 
> --report-discordant-pair-alignments --report-mixed-alignments 
> --samtools=/bin/samtools --bowtie2-max-penalty 6 --bowtie2-min-penalty 2 
> --bowtie2-penalty-for-N 1 --bowtie2-read-gap-open 5 --bowtie2-read-gap-cont 3 
> --bowtie2-ref-gap-open 5 --bowtie2-ref-gap-cont 3 
> /data/rathi/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.fa 
> ./tophat_out/junctions.bed ./tophat_out/insertions.bed 
> ./tophat_out/deletions.bed ./tophat_out/fusions.out 
> ./tophat_out/tmp/accepted_hits  ./tophat_out/tmp/left_kept_reads.bam
>       Loading ...done
>
>
> Is it a known bug?
>
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