hi,all: when i do tophat fusion,i got an error like below.I browse many similar post in this forum and try to solve it ,but failed.Hope someone could give me a guidance.thx.
my script: /share/software/Alignment/tophat/tophat-2.1.1.Linux_x86_64/tophat -n 3 -o standard_test -p 24 -G /share/PROJ/20151008_RenalCellCarcinoma/Homo_sapiens.GRCh37.75.gtf --fusion-search --keep-fasta-order --no-coverage-search --bowtie1 --mate-std-dev 80 --fusion-anchor-length 13 --fusion-ignore-chromosome chrM /share/work/renyongzhe/software/index/human19_genome /share/work/renyongzhe/rna_fusion/RNAFFRK1I160181-A1_S5_R1_001.fastq.gz /share/work/renyongzhe/rna_fusion/RNAFFRK1I160181-A1_S5_R2_001.fastq.gz
Error running /share/software/Alignment/tophat/tophat-2.1.1.Linux_x86_64/tophat_reports --min-anchor 8 --splice-mismatches 0 --min-report-intron 50 --max-report-intron 500000 --min-isoform-fraction 0.15 --output-dir sample_test/ --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 --bowtie1 --fusion-search --fusion-anchor-length 13 --fusion-min-dist 10000000 --fusion-read-mismatches 2 --fusion-multireads 2 --fusion-multipairs 2 --fusion-ignore-chromosomes chrM -z gzip -p24 --inner-dist-mean 50 --inner-dist-std-dev 80 --gtf-annotations /share/PROJ/20151008_RenalCellCarcinoma/Homo_sapiens.GRCh37.75.gtf --gtf-juncs sample_test/tmp/Homo_sapiens.juncs --no-closure-search --no-coverage-search --no-microexon-search --sam-header sample_test/tmp/human19_genome_genome.bwt.samheader.sam --report-discordant-pair-alignments --report-mixed-alignments --samtools=/share/software/Alignment/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 /share/work/renyongzhe/software/index/human19_genome.fa sample_test/junctions.bed sample_test/insertions.bed sample_test/deletions.bed sample_test/fusions.out sample_test/tmp/accepted_hits sample_test/tmp/left_kept_reads.m2g.bam,sample_test/tmp/left_kept_reads.m2g_um.mapped.bam,sample_test/tmp/left_kept_reads.m2g_um.candidates sample_test/tmp/left_kept_reads.bam sample_test/tmp/right_kept_reads.m2g.bam,sample_test/tmp/right_kept_reads.m2g_um.mapped.bam,sample_test/tmp/right_kept_reads.m2g_um.candidates sample_test/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)
Perhaps try another version of tophat as suggested here.