I am using Tophat2 (v2.1.1) to find fusions on RNA-seq files.

To test the --fusion-search function, I launch the example in the manual :

    tophat -o tophat_outpu2 -p 8 --fusion-search --keep-fasta-order --bowtie1 --no-coverage-search -r 0 --mate-std-dev 80 --max-intron-length 100000 --fusion-min-dist 100000 --fusion-anchor-length 13 --fusion-ignore-chromosomes chrM /GenomeRef/hg19 SRR064286_1.fastq SRR064286_2.fastq

And everytime I got the same error :

    Error running /programs/tophat/tophat-2.1.1/install/bin/tophat_reports --min-anchor 8 --splice-mismatches 0 --min-report-intron 50 --max-report-intron 100000 --min-isoform-fraction 0.15 --output-dir tophat_output2/ --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 100000 --read-mismatches 2 --read-gap-length 2 --read-edit-dist 2 --read-realign-edit-dist 3 
        ...
    tophat_output2/insertions.bed tophat_output2/deletions.bed tophat_output2/fusions.out tophat_output2/tmp/accepted_hits tophat_output2/tmp/left_kept_reads.mapped.bam,tophat_output2/tmp/left_kept_reads.candidates tophat_output2/tmp/left_kept_reads.bam tophat_output2/tmp/right_kept_reads.mapped.bam,tophat_output2/tmp/right_kept_reads.candidates tophat_output2/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)

Dis someone can help me with this error ?

Thanks.
The right way to do is using Tophat2 v2.1.0...........
so simple but useful