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 50
--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 2 --min-segment-intron 50
--max-segment-intron 50 --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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