I'm trying to run tophat2.0.10 on some PE RNA-seq samples. However, tophat_reports fails at the reporting output tracks step with the error below. If I run tophat without the --no-discordant option then it runs fine. Any ideas? Thanks
[2014-01-07 21:09:50] Joining segment hits
[2014-01-07 21:14:07] Reporting output tracks
[FAILED]
Error running /N/hd01/jake/Mason/programs/tophat-2.0.10/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 1 --max-seg-multihits 10 --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 -p8 --inner-dist-mean 50 --inner-dist-std-dev 20 --no-closure-search --no-coverage-search --no-microexon-search --library-type fr-firststrand --sam-header ./tophat_out/tmp/genome_genome.bwt.samheader.sam --report-mixed-alignments --samtools=/N/u/jake/Mason/programs/samtools-0.1.19/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 /N/dc2/projects/RNA/jake/UCSC_mm10_bowtie/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.mapped.bam,./tophat_out/tmp/left_kept_reads.candidates ./tophat_out/tmp/left_kept_reads.bam ./tophat_out/tmp/right_kept_reads.mapped.bam,./tophat_out/tmp/right_kept_reads.candidates ./tophat_out/tmp/right_kept_reads.bam
Loaded 147930 junctions
[2014-01-07 21:09:50] Joining segment hits
[2014-01-07 21:14:07] Reporting output tracks
[FAILED]
Error running /N/hd01/jake/Mason/programs/tophat-2.0.10/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 1 --max-seg-multihits 10 --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 -p8 --inner-dist-mean 50 --inner-dist-std-dev 20 --no-closure-search --no-coverage-search --no-microexon-search --library-type fr-firststrand --sam-header ./tophat_out/tmp/genome_genome.bwt.samheader.sam --report-mixed-alignments --samtools=/N/u/jake/Mason/programs/samtools-0.1.19/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 /N/dc2/projects/RNA/jake/UCSC_mm10_bowtie/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.mapped.bam,./tophat_out/tmp/left_kept_reads.candidates ./tophat_out/tmp/left_kept_reads.bam ./tophat_out/tmp/right_kept_reads.mapped.bam,./tophat_out/tmp/right_kept_reads.candidates ./tophat_out/tmp/right_kept_reads.bam
Loaded 147930 junctions
Comment