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  • Tophat error

    Hi, all

    When using tophat commands, I am confronted with the following errors.

    [root@** bin]# /home/bin/tophat -p 8 -G Ptrichocarpa_156_gene.gff3 -o CAR01 --max-intron-length 5000 -r 150 -m 2 --solexa1.3-quals /home/bin/bowtie-0.12.8/indexes/Pop_trichocarpa /home/****/Fastq/CAR01_1.fastq /home/****/Fastq/CAR01_2.fastq

    At the beginning, it runs well. Till the end, I got the following errors.

    [2012-05-22 16:37:26] Reporting output tracks
    [FAILED]
    Error running /home/bin/tophat_reports --min-anchor 8 --splice-mismatches 2 --min-report-intron 50 --max-report-intron 5000 --min-isoform-fraction 0.15 --output-dir CAR01/ --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 5000 --min-segment-intron 50 --max-segment-intron 5000 --max-mismatches 2 --max-insertion-length 3 --max-deletion-length 3 --bowtie1 -z gzip -p8 --inner-dist-mean 150 --inner-dist-std-dev 20 --gtf-annotations Ptrichocarpa_156_gene.gff3 --gtf-juncs CAR01/tmp/Ptrichocarpa_156_gene.juncs --no-closure-search --no-coverage-search --no-microexon-search --sam-header CAR01/tmp/Pop_trichocarpa_genome.bwt.samheader.sam --samtools=/home/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 /home/bin/bowtie-0.12.8/indexes/Pop_trichocarpa.fa CAR01/junctions.bed CAR01/insertions.bed CAR01/deletions.bed CAR01/fusions.out CAR01/tmp/accepted_hits CAR01/tmp/left_kept_reads.m2g_um.candidates_and_unspl.bam CAR01/tmp/left_kept_reads.bam CAR01/tmp/right_kept_reads.m2g_um.candidates_and_unspl.bam CAR01/tmp/right_kept_reads.bam

    ./SeqAn-1.3/seqan/sequence/segment_infix.h:81 Assertion failed : data_begin_position <= data_end_position was: 18446744073709551569 > 51

    In the output files, the accepted_hits.bam file doesnot exist.

    Any idea?

  • #2
    It seems the problem can be fixed by updating tophat.
    See http://tophat.cbcb.umd.edu/

    Comment


    • #3
      EDIT: Not the same problem. Will post a new question.
      Last edited by miseiler; 06-02-2012, 02:56 PM.

      Comment

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