Tophat2 "error running tophat_reports"

Question

[Bibi]

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.

[sheepyuanyang]

I am facing the same problem! Help！

[Beifish]

someone help...........

[cnhuangxy]

I am facing the same problem! Help！

[Satyajeet Khare]

Read the answer by @Beifish above your comment. Use Tophat v2.1.0

Answer 1

[Beifish]

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

[xia17720507672]

Could you tell me your bowtie version for tophat-fusion? Thanks

[archana.bioinfo87]

Hi,

I am getting similar error in tophat v2.1.0

[2018-07-23 10:30:10] Beginning TopHat run (v2.1.0)

[2018-07-23 10:30:10] Checking for Bowtie Bowtie version: 1.1.2.0 [2018-07-23 10:30:11] Checking for Bowtie index files (genome).. [2018-07-23 10:30:11] Checking for reference FASTA file Warning: Could not find FASTA file ../bow_tie_build_hg19/hg19.fa [2018-07-23 10:30:11] Reconstituting reference FASTA file from Bowtie index Executing: /usr/bin/bowtie-inspect ../bow_tie_build_hg19/hg19 > final_tophat_fusion/tmp/hg19.fa [2018-07-23 10:32:36] Generating SAM header for ../bow_tie_build_hg19/hg19 [2018-07-23 10:32:56] Preparing reads left reads: min. length=48, max. length=48, 57435146 kept reads (2628 discarded) right reads: min. length=48, max. length=48, 57431378 kept reads (6396 discarded) [2018-07-23 10:49:38] Mapping left_kept_reads to genome hg19 with Bowtie [2018-07-23 11:44:57] Mapping left_kept_reads_seg1 to genome hg19 with Bowtie (1/2) [2018-07-23 12:03:16] Mapping left_kept_reads_seg2 to genome hg19 with Bowtie (2/2) [2018-07-23 12:29:38] Mapping right_kept_reads to genome hg19 with Bowtie [2018-07-23 13:41:25] Mapping right_kept_reads_seg1 to genome hg19 with Bowtie (1/2) [2018-07-23 14:14:02] Mapping right_kept_reads_seg2 to genome hg19 with Bowtie (2/2) [2018-07-23 15:02:24] Searching for junctions via segment mapping [2018-07-23 15:22:31] Retrieving sequences for splices [2018-07-23 15:24:50] Indexing splices [2018-07-23 15:26:29] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie (1/2) [2018-07-23 15:44:07] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie (2/2) [2018-07-23 16:03:37] Joining segment hits [2018-07-23 16:12:25] Mapping right_kept_reads_seg1 to genome segment_juncs with Bowtie (1/2) [2018-07-23 16:30:37] Mapping right_kept_reads_seg2 to genome segment_juncs with Bowtie (2/2) [2018-07-23 16:40:57] Joining segment hits [2018-07-23 16:50:07] Reporting output tracks [FAILED] Error running /usr/bin/tophat_reports --min-anchor 8 --splice-mismatches 0 --min-report-intron 50 --max-report-intron 500000 --min-isoform-fraction 0.15 --output-dir final_tophat_fusion/ --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 20 --fusion-min-dist 10000000 --fusion-read-mismatches 2 --fusion-multireads 2 --fusion-multipairs 2 -z gzip -p4 --inner-dist-mean 50 --inner-dist-std-dev 20 --no-closure-search --no-coverage-search --no-microexon-search --library-type fr-unstranded --sam-header final_tophat_fusion/tmp/hg19_genome.bwt.samheader.sam --report-discordant-pair-alignments --report-mixed-alignments --samtools=/usr/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 final_tophat_fusion/tmp/hg19.fa final_tophat_fusion/junctions.bed final_tophat_fusion/insertions.bed final_tophat_fusion/deletions.bed final_tophat_fusion/fusions.out final_tophat_fusion/tmp/accepted_hits final_tophat_fusion/tmp/left_kept_reads.mapped.bam,final_tophat_fusion/tmp/left_kept_reads.candidates final_tophat_fusion/tmp/left_kept_reads.bam final_tophat_fusion/tmp/right_kept_reads.mapped.bam,final_tophat_fusion/tmp/right_kept_reads.candidates final_tophat_fusion/tmp/right_kept_reads.bam what(): basic_string::substr: __pos (which is 40) > this->size() (which is 0)

Any help or suggestion is much appreciated.

Answer 2

[HaroonPakistan]

you need to activate the other version and then try. Was your problem solved?