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?
___
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/
___
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/
