tophat fusion error

Question

[dimitrischat]

Hi all. Trying to run tophat fusion with 2 fastq files from rna-seq. I am using the example command from here: https://ccb.jhu.edu/software/tophat/fusion_tutorial.shtml .

tophat -o Output -p 10 --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 '/home/app/..hg19bt1' S17_R1_001.fastq.gz S17_R2_001.fastq.gz

ERROR [2019-02-28 17:28:15] Reporting output tracks [FAILED] Error running /home/app/anaconda3/bin/tophat_reports --min-anchor 8 --splice-mismatches 0 --min-report-intron 50 --max-report-intron 100000 --min-isoform-fraction 0.15 --output-dir Glentis/ --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 --max-insertion-length 3 --max-deletion-length 3 --bowtie1 --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 -p10 --inner-dist-mean 0 --inner-dist-std-dev 80 --no-closure-search --no-coverage-search --no-microexon-search --sam-header Glentis/tmp/hg19bt1_genome.bwt.samheader.sam --report-discordant-pair-alignments --report-mixed-alignments --samtools=/home/app/anaconda3/bin/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 Glentis/tmp/hg19bt1.fa Glentis/junctions.bed Glentis/insertions.bed Glentis/deletions.bed Glentis/fusions.out Glentis/tmp/accepted_hits Glentis/tmp/left_kept_reads.mapped.bam,Glentis/tmp/left_kept_reads.candidates Glentis/tmp/left_kept_reads.bam Glentis/tmp/right_kept_reads.mapped.bam,Glentis/tmp/right_kept_reads.candidates Glentis/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)

Any suggestions ?

[Bastien Hervé]

Hello dimitrischat,

Note that TopHat is not the most recommended tool for RNAseq experiment, take a look at HISAT2 or STAR

Please stop using Tophat https://t.co/Es4ohxOEyx Cole and I developed the method in *2008*. It was greatly improved in TopHat2 then HISAT & HISAT2. There is no reason to use it anymore. I have been saying this for years yet it has more citations this year than last #methodsmatter

— Lior Pachter (@lpachter) December 2, 2017

Issue similar to this one I guess : Tophat2 "error running tophat_reports"