Question: Tophat2 "error running tophat_reports"
2
gravatar for Bibi
3.0 years ago by
Bibi20
Bibi20 wrote:

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.

rna-seq tophat2 tophat • 3.3k views
ADD COMMENTlink modified 2.6 years ago by cnhuangxy0 • written 3.0 years ago by Bibi20
1

I am facing the same problem! Help!

ADD REPLYlink written 3.0 years ago by sheepyuanyang10

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

ADD REPLYlink written 2.9 years ago by Beifish50

I am facing the same problem! Help!

ADD REPLYlink written 2.6 years ago by cnhuangxy0

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

ADD REPLYlink written 2.6 years ago by Satyajeet Khare1.3k
5
gravatar for Beifish
2.9 years ago by
Beifish50
Wuhan, China
Beifish50 wrote:

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

ADD COMMENTlink written 2.9 years ago by Beifish50

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

ADD REPLYlink written 16 months ago by xia177205076720

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.

ADD REPLYlink written 8 months ago by archana.bioinfo87100
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1135 users visited in the last hour