Hi everyone,
I am having a problem with Tophat that has been posted here before here.
Basically, Tophat works fine, but in the last step when it writes all of the output, the operation fails, and we instead get the message:
[2012-10-16 07:44:11] Reporting output tracks
[FAILED]
Error running tophat-2.0.5/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 -p11 --inner-dist-mean 50 --inner-dist-std-dev 20 --no-closure-search --no-coverage-search --no-microexon-search --sam-header ./tophat_out/tmp/genome_ref_genome.bwt.samheader.sam --report-secondary-alignments --report-discordant-pair-alignments --report-mixed-alignments --samtools=/apps/group/bioinformatics/apps/samtools-0.1.18/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 ./tophat_out/tmp/genome_ref.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 246756 junctions
I originally received this message when running Tophat 2.0.5. The previous post I referenced had many people with the exact same problem, and they reported that switching to Tophat 2.0.4 often solved the error for some reason.
However, I've also tried using Tophat 2.0.4, with the exact same results.
Does anyone have any insight as to why this is happening? I appreciate your advice
I am having a problem with Tophat that has been posted here before here.
Basically, Tophat works fine, but in the last step when it writes all of the output, the operation fails, and we instead get the message:
[2012-10-16 07:44:11] Reporting output tracks
[FAILED]
Error running tophat-2.0.5/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 -p11 --inner-dist-mean 50 --inner-dist-std-dev 20 --no-closure-search --no-coverage-search --no-microexon-search --sam-header ./tophat_out/tmp/genome_ref_genome.bwt.samheader.sam --report-secondary-alignments --report-discordant-pair-alignments --report-mixed-alignments --samtools=/apps/group/bioinformatics/apps/samtools-0.1.18/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 ./tophat_out/tmp/genome_ref.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 246756 junctions
I originally received this message when running Tophat 2.0.5. The previous post I referenced had many people with the exact same problem, and they reported that switching to Tophat 2.0.4 often solved the error for some reason.
However, I've also tried using Tophat 2.0.4, with the exact same results.
Does anyone have any insight as to why this is happening? I appreciate your advice
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