I have come across an error in the call to tophat_reports when running tophat 2.0.13 on a custom reference sequence. This error appears to occasionally occur when 0 reads map. When this is the case, the following error messages are produced...
You will notice that there are certain paramters that are missing in the call to tophat_reports. Even when you try to include these parameters manually, tophat_reports will still fail.
Updated (10/13/15):
I have come across an error in the call to tophat_reports when running tophat 2.0.13 on a custom reference sequence. This error appears to occasionally occur when 0 reads map. When this is the case, the following error messages are produced...
[2015-09-28 12:38:35] Reporting output tracks [FAILED] Error running /n/sw/fasrcsw/apps/Core/tophat/2.0.13-fasrc01/bin/tophat_reports --min-anchor 8 --splice-mismatches 0 --min-report-intron 50 --max-report-intron 500000 --min-isoform-fraction 0.15 --output-dir EH_2.9.17.thanno/ --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 -p16 --inner-dist-mean 50 --inner-dist-std-dev 20 --gtf-annotations /n/home09/msuperdock/regal/genome/crestinEGFP11/crestinEGFP.gtf --gtf-juncs EH_2.9.17.thanno/tmp/crestinEGFP.juncs --no-closure-search --no-coverage-search --no-microexon-search --sam-header EH_2.9.17.thanno/tmp/crestinEGFP_genome.bwt.samheader.sam --report-discordant-pair-alignments --report-mixed-alignments --samtools=/n/sw/fasrcsw/apps/Core/tophat/2.0.13-fasrc01/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 /n/home09/msuperdock/regal/genome/crestinEGFP11/crestinEGFP.fa EH_2.9.17.thanno/junctions.bed EH_2.9.17.thanno/insertions.bed EH_2.9.17.thanno/deletions.bed EH_2.9.17.thanno/fusions.out EH_2.9.17.thanno/tmp/accepted_hits EH_2.9.17.thanno/tmp/left_kept_reads.bam
You will notice that there are certain paramters that are missing in the call to tophat_reports. Even when you try to include these parameters manually, tophat_reports will still fail.