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.goecks@emory.edu>wrote:
This is not a known bug. For questions related to Tophat errors, you might try the Tophat mailing list:
tophat.cufflinks@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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