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  • TopHat2 fusion-search : SeqAn error

    Hi everyone,

    I am using Tophat v2.1.1 with the option --fusion-search.

    I downloaded the example and tried exactly the code in the manual :
    tophat -o tophat_MCF7_out3 -p 8 --fusion-search --keep-fasta-order --bowtie1 --no-coverage-search -r 0 --mate-std-dev 80 --fusion-min-dist 100000 --fusion-anchor-length 13 --fusion-ignore-chromosomes chrM hg19 SRR064286_1.fastq SRR064286_2.fastq

    Everytime I launch it, I have the same error :
    Error running /programs/tophat/tophat-2.1.1/tophat_reports --min-anchor 8 --splice-mismatches 0 --min-report-intron 50 --max-report-intron 500000 --min-isoform-fraction 0.15 --output-dir tophat_MCF7_out3/ --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 --fusion-search --fusion-anchor-length 13 --fusion-min-dist 100000 --fusion-read-mismatches 2 --fusion-multireads 2 --fusion-multipairs 2 --fusion-ignore-chromosomes chrM -z gzip -p12 --inner-dist-mean 0 --inner-dist-std-dev 80 --no-closure-search --no-coverage-search --no-microexon-search --sam-header tophat_MCF7_out3/tmp/hg19_genome.bwt.samheader.sam --report-discordant-pair-alignments --report-mixed-alignments --samtools=/ngs/programs/tophat/tophat-2.1.1.Linux_x86_64/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 /GenomeRef/hg19.fa tophat_MCF7_out3/junctions.bed tophat_MCF7_out3/insertions.bed tophat_MCF7_out3/deletions.bed tophat_MCF7_out3/fusions.out tophat_MCF7_out3/tmp/accepted_hits tophat_MCF7_out3/tmp/left_kept_reads.mapped.bam,tophat_MCF7_out3/tmp/left_kept_reads.candidates tophat_MCF7_out3/tmp/left_kept_reads.bam tophat_MCF7_out3/tmp/right_kept_reads.mapped.bam,tophat_MCF7_out3/tmp/right_kept_reads.candidates tophat_MCF7_out3/tmp/right_kept_reads.bam

    ./SeqAn-1.4.2/seqan/basic/basic_exception.h:236 FAILED! (Uncaught exception of type St12out_of_range: basic_string::substr)


    Did someone already had this error ?
    Last edited by bibi; 04-20-2016, 11:28 PM.

  • #2
    Hi,

    I found a solution which worked for me. All I had to do is use an earlier version of tophat v2.1.0.
    See the link below



    Regards,
    Pramod

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