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DaehwanKimLab / tophat

Spliced read mapper for RNA-Seq
http://ccb.jhu.edu/software/tophat
Boost Software License 1.0
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Uncaught exception of type St12out_of_range: basic_string::substr #44

Closed komalsrathi closed 7 years ago

komalsrathi commented 7 years ago

Hi,

I am trying to call fusions in paired end RNAseq data using the following command:

tophat2 \
--num-threads=10 \
--output-dir=SKNAS \
--fusion-search \
--no-coverage-search \
--mate-std-dev 80 \
--max-intron-length 100000 \
--fusion-min-dist 100000 \
--fusion-anchor-length 13 \
--bowtie1 \
/mnt/isilon/cbmi/variome/reference/bowtie_indexes/hg38_no_alt/Homo_sapiens/NCBI/GRCh38/Sequence/BowtieIndex/genome \
SKNAS_R1.fastq.gz SKNAS_R2.fastq.gz

I am running into this error which I cannot understand:

tophat.log:

[2017-03-15 10:34:57] Beginning TopHat run (v2.1.1)
-----------------------------------------------
[2017-03-15 10:34:57] Checking for Bowtie
                  Bowtie version:        1.1.2.0
[2017-03-15 10:34:57] Checking for Bowtie index files (genome)..
[2017-03-15 10:34:57] Checking for reference FASTA file
[2017-03-15 10:34:57] Generating SAM header for /mnt/isilon/cbmi/variome/reference/bowtie_indexes/hg38_no_alt/Homo_sapiens/NCBI/GRCh38/Sequence/BowtieIndex/genome
[2017-03-15 10:35:01] Preparing reads
         left reads: min. length=35, max. length=101, 78249357 kept reads (81277 discarded)
        right reads: min. length=35, max. length=101, 78027666 kept reads (302968 discarded)
[2017-03-15 11:21:50] Mapping left_kept_reads to genome genome with Bowtie 
[2017-03-15 12:05:10] Mapping left_kept_reads_seg1 to genome genome with Bowtie (1/4)
[2017-03-15 12:19:12] Mapping left_kept_reads_seg2 to genome genome with Bowtie (2/4)
[2017-03-15 12:32:37] Mapping left_kept_reads_seg3 to genome genome with Bowtie (3/4)
[2017-03-15 12:45:25] Mapping left_kept_reads_seg4 to genome genome with Bowtie (4/4)
[2017-03-15 12:56:50] Mapping right_kept_reads to genome genome with Bowtie 
[2017-03-15 13:43:45] Mapping right_kept_reads_seg1 to genome genome with Bowtie (1/4)
[2017-03-15 13:57:57] Mapping right_kept_reads_seg2 to genome genome with Bowtie (2/4)
[2017-03-15 14:12:11] Mapping right_kept_reads_seg3 to genome genome with Bowtie (3/4)
[2017-03-15 14:26:15] Mapping right_kept_reads_seg4 to genome genome with Bowtie (4/4)
[2017-03-15 14:39:20] Searching for junctions via segment mapping
[2017-03-15 14:54:04] Retrieving sequences for splices
[2017-03-15 14:55:33] Indexing splices
[2017-03-15 15:04:04] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie (1/4)
[2017-03-15 15:09:47] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie (2/4)
[2017-03-15 15:15:43] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie (3/4)
[2017-03-15 15:21:30] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie (4/4)
[2017-03-15 15:26:46] Joining segment hits
[2017-03-15 15:42:04] Mapping right_kept_reads_seg1 to genome segment_juncs with Bowtie (1/4)
[2017-03-15 15:48:29] Mapping right_kept_reads_seg2 to genome segment_juncs with Bowtie (2/4)
[2017-03-15 15:55:05] Mapping right_kept_reads_seg3 to genome segment_juncs with Bowtie (3/4)
[2017-03-15 16:01:43] Mapping right_kept_reads_seg4 to genome segment_juncs with Bowtie (4/4)
[2017-03-15 16:07:53] Joining segment hits
[2017-03-15 16:23:41] Reporting output tracks
        [FAILED]
Error running /home/rathik/tools/miniconda3/envs/fusion-env/bin/tophat_reports --min-anchor 8 --splice-mismatches 0 --min-report-intron 50 --max-report-intron 100000 --min-isoform-fraction 0.15 --output-dir SKNAS/ --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 -z gzip -p10 --inner-dist-mean 50 --inner-dist-std-dev 80 --no-closure-search --no-coverage-search --no-microexon-search --sam-header SKNAS/tmp/genome_genome.bwt.samheader.sam --report-discordant-pair-alignments --report-mixed-alignments --samtools=/home/rathik/tools/miniconda3/envs/fusion-env/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 /mnt/isilon/cbmi/variome/reference/bowtie_indexes/hg38_no_alt/Homo_sapiens/NCBI/GRCh38/Sequence/BowtieIndex/genome.fa SKNAS/junctions.bed SKNAS/insertions.bed SKNAS/deletions.bed SKNAS/fusions.out SKNAS/tmp/accepted_hits SKNAS/tmp/left_kept_reads.mapped.bam,SKNAS/tmp/left_kept_reads.candidates SKNAS/tmp/left_kept_reads.bam SKNAS/tmp/right_kept_reads.mapped.bam,SKNAS/tmp/right_kept_reads.candidates SKNAS/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 help would be much appreciated.

Thanks, Komal

komalsrathi commented 7 years ago

UPDATE - I am running this with Tophat v2.1.0 now and it works. Maybe you could add this to the Wiki or Manual? This will save a lot of time on the users end.