tophat reporting output problem

Question

[pavanraaz]

Hi

I new to rna seq analysis, I have reference genome and tried to map reads. After running Tophat I got below error. what might be the reason and how to solve it. I need your valuable suggestions.

 Joining segment hits
 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 --gtf-annotations /home/pavan/cajan_bowtie2-index/cajan.gff --gtf-juncs ./tophat_out/tmp/cajan.juncs --no-closure-search --no-coverage-search --no-microexon-search --sam-header ./tophat_out/tmp/cajan_genome.bwt.samheader.sam --report-discordant-pair-alignments --report-mixed-alignments --samtools=/usr/local/bin/samtools_0.1.18 --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 /home/pavan/cajan_bowtie2-index/cajan.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.m2g.bam,./tophat_out/tmp/left_kept_reads.m2g_um.mapped.bam,./tophat_out/tmp/left_kept_reads.m2g_um.candidates.bam ./tophat_out/tmp/left_kept_reads.bam
Loaded 125959 GFF junctions from ./tophat_out/tmp/cajan.juncs.

[Devon Ryan]

Try running that command manually so you can see the actual error message. For what it's worth, this seems to be a common place for tophat2 to die.