Hi!
I proceeded my RNA-seq sample alignment using tophat2. A folder was created containing some files, but the files "accepted_hits.bam" and "unmapped.bam" are missing. In my sample folder I only have:
two folders: "logs" and "tmp"
four files: "deletions.bed", "insertions.bed", "junctions.bed" "prep_reads.info".
I ran the alignment again and the same thing happened. Does anybody have the same problem or knows why this is happening?
The alignment process generated this message in the Terminal window:
[2014-05-26 10:38:52] Reporting output tracks
[FAILED]
Error running /usr/bin/tophat_reports --min-anchor 8 --splice-mismatches 0 --min-report-intron 50 --max-report-intron 500000 --min-isoform-fraction 0.15 --output-dir MSCd0Adip/ --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 -p5 --gtf-annotations Homo_sapiens.GRCh37.75.gtf --gtf-juncs MSCd0Adip/tmp/Homo_sapiens.juncs --no-closure-search --no-coverage-search --no-microexon-search --sam-header MSCd0Adip/tmp/Hsa_GRCh37_75_genome.bwt.samheader.sam --report-discordant-pair-alignments --report-mixed-alignments --samtools=/usr/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 MSCd0Adip/tmp/Hsa_GRCh37_75.fa MSCd0Adip/junctions.bed MSCd0Adip/insertions.bed MSCd0Adip/deletions.bed MSCd0Adip/fusions.out MSCd0Adip/tmp/accepted_hits MSCd0Adip/tmp/left_kept_reads.bam
Loaded 375801 GFF junctions from MSCd0Adip/tmp/Homo_sapiens.juncs.
Thanks
I proceeded my RNA-seq sample alignment using tophat2. A folder was created containing some files, but the files "accepted_hits.bam" and "unmapped.bam" are missing. In my sample folder I only have:
two folders: "logs" and "tmp"
four files: "deletions.bed", "insertions.bed", "junctions.bed" "prep_reads.info".
I ran the alignment again and the same thing happened. Does anybody have the same problem or knows why this is happening?
The alignment process generated this message in the Terminal window:
[2014-05-26 10:38:52] Reporting output tracks
[FAILED]
Error running /usr/bin/tophat_reports --min-anchor 8 --splice-mismatches 0 --min-report-intron 50 --max-report-intron 500000 --min-isoform-fraction 0.15 --output-dir MSCd0Adip/ --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 -p5 --gtf-annotations Homo_sapiens.GRCh37.75.gtf --gtf-juncs MSCd0Adip/tmp/Homo_sapiens.juncs --no-closure-search --no-coverage-search --no-microexon-search --sam-header MSCd0Adip/tmp/Hsa_GRCh37_75_genome.bwt.samheader.sam --report-discordant-pair-alignments --report-mixed-alignments --samtools=/usr/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 MSCd0Adip/tmp/Hsa_GRCh37_75.fa MSCd0Adip/junctions.bed MSCd0Adip/insertions.bed MSCd0Adip/deletions.bed MSCd0Adip/fusions.out MSCd0Adip/tmp/accepted_hits MSCd0Adip/tmp/left_kept_reads.bam
Loaded 375801 GFF junctions from MSCd0Adip/tmp/Homo_sapiens.juncs.
Thanks
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