tophat2出现 Reporting output tracks [FAILED] ./SeqAn-1.4.2/seqan/basic/basic

本文链接：https://blog.csdn.net/Lt_sleep_early/article/details/129635417

使用tophat-2.1.1时出现以下错误，输出有误：

[2023-03-17 01:07:08] Reporting output tracks

[FAILED]

Error running /public/home/z*/**/**/tophat-2.1.1.Linux_x86_64/tophat_reports --min-anchor 8 --splice-mismatches 0 --mreport-intron 50 --max-report-intron 500000 --min-isoform-fraction 0.15 --output-dir tophat_fusion/ --max-multihits 20 --max-seg-multihits --segment-length 25 --segment-mismatches 2 --min-closure-exon 100 --min-closure-intron 50 --max-closure-intron 5000 --min-coverage-intron --max-coverage-intron 20000 --min-segment-intron 50 --max-segment-intron 500000 --read-mismatches 2 --read-gap-length 2 --read-edit-dist -read-realign-edit-dist 3 --max-insertion-length 3 --max-deletion-length 3 --bowtie1 --fusion-search --fusion-anchor-length 20 --fusion-miist 10000000 --fusion-read-mismatches 2 --fusion-multireads 2 --fusion-multipairs 2 -z gzip -p140 --inner-dist-mean 50 --inner-dist-std-de0 --no-closure-search --no-coverage-search --no-microexon-search --sam-header tophat_fusion/tmp/bowtie1_index_genome.bwt.samheader.sam --rrt-discordant-pair-alignments --report-mixed-alignments --samtools=/public/home/zhanglt/circrna/circexplorer2/tophat-2.1.1.Linux_x86_64/saols_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 -wtie2-ref-gap-open 5 --bowtie2-ref-gap-cont 3 tophat_fusion/tmp/bowtie1_index.fa tophat_fusion/junctions.bed tophat_fusion/insertions.bed hat_fusion/deletions.bed tophat_fusion/fusions.out tophat_fusion/tmp/accepted_hits tophat_fusion/tmp/left_kept_reads.mapped.bam,tophat_fus/tmp/left_kept_reads.candidates tophat_fusion/tmp/left_kept_reads.bam tophat_fusion/tmp/right_kept_reads.mapped.bam,tophat_fusion/tmp/righept_reads.candidates tophat_fusion/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)

能百度到关于tophat2输出出错的网页都看了，biostar都说别用tophat了，用STAR去做，但是后续工作依赖tophat的前期结果，无奈只好硬着头皮继续。然后尝试了tophat-2.1.0、2.0.9等版本都不行，甚至错误出现越来越早（甚至还没到结果输出这一步就报错了，说明可能更早的版本不能用），接着机缘巧合之下发现有可能是bowtie的问题，于是尝试将bowtie-2.5.0版本换成bowtie-2.5.1版本，此时tophat是2.1.0版本，第二天跑完，终于出现欣喜的结果了！！