Hi,
I've been running Bowtie with my RNAseq data, mapping the reads to the transcriptome (in .gtf format) and the genome.
I've kept getting an error which basically says:
I figured that it's some kind of error with the BAM file, but as its Bowtie/Tophat which produces the BAM file, I'm not sure what I can do. Any ideas?
I've been running Bowtie with my RNAseq data, mapping the reads to the transcriptome (in .gtf format) and the genome.
I've kept getting an error which basically says:
Code:
user@it053392:~$ tophat -G /home/user/Desktop/_sam/RNAseq_beta_data/Transcriptome/merged.remDup.gtf -o /home/user/Desktop/tophatout.sam /home/user/Downloads/Bowtie/bowtie2-2.2.6/indexes/hg19 /home/user/Desktop/_sam/RNAseq_beta_data/trimmed/36w62_trimmed.fastq [2015-11-02 11:46:46] Beginning TopHat run (v2.0.9) ----------------------------------------------- [2015-11-02 11:46:46] Checking for Bowtie Bowtie version: 2.1.0.0 [2015-11-02 11:46:46] Checking for Samtools Samtools version: 0.1.19.0 [2015-11-02 11:46:46] Checking for Bowtie index files (genome).. [2015-11-02 11:46:46] Checking for reference FASTA file Warning: Could not find FASTA file /home/user/Downloads/Bowtie/bowtie2-2.2.6/indexes/hg19.fa [2015-11-02 11:46:46] Reconstituting reference FASTA file from Bowtie index Executing: /usr/bin/bowtie2-inspect /home/user/Downloads/Bowtie/bowtie2-2.2.6/indexes/hg19 > /home/user/Desktop/tophatout.sam/tmp/hg19.fa [2015-11-02 11:46:59] Generating SAM header for /home/user/Downloads/Bowtie/bowtie2-2.2.6/indexes/hg19 format: fastq quality scale: phred33 (default) [2015-11-02 11:47:04] Reading known junctions from GTF file [2015-11-02 11:47:06] Preparing reads left reads: min. length=85, max. length=85, 25297338 kept reads (13185 discarded) [2015-11-02 11:54:01] Building transcriptome data files.. [2015-11-02 11:54:18] Building Bowtie index from merged.remDup.fa [2015-11-02 13:15:14] Mapping left_kept_reads to transcriptome merged.remDup with Bowtie2 [FAILED] Error running: /usr/bin/bam2fastx --all --fastq /home/user/Desktop/tophatout.sam/tmp/left_kept_reads.bam|/usr/bin/bowtie2-align -q -k 60 -D 15 -R 2 -N 0 -L 20 -i S,1,1.25 --gbar 4 --mp 6,2 --np 1 --rdg 5,3 --rfg 5,3 --score-min C,-14,0 -p 1 --sam-no-hd -x /home/user/Desktop/tophatout.sam/tmp/merged.remDup -|/usr/bin/fix_map_ordering --bowtie2-min-score 15 --read-mismatches 2 --read-gap-length 2 --read-edit-dist 2 --read-realign-edit-dist 3 --sam-header /home/user/Desktop/tophatout.sam/tmp/merged.remDup.bwt.samheader.sam - - /home/user/Desktop/tophatout.sam/tmp/left_kept_reads.m2g_um.bam | /usr/bin/map2gtf --sam-header /home/user/Desktop/tophatout.sam/tmp/hg19_genome.bwt.samheader.sam /home/user/Desktop/tophatout.sam/tmp/merged.remDup.fa.tlst - /home/user/Desktop/tophatout.sam/tmp/left_kept_reads.m2g.bam > /home/user/Desktop/tophatout.sam/logs/m2g_left_kept_reads.out user@it053392:~$ /usr/bin/bam2fastx --all --fastq /home/user/Desktop/tophatout.sam/tmp/left_kept_reads.bam|/usr/bin/bowtie2-align -q -k 60 -D 15 -R 2 -N 0 -L 20 -i S,1,1.25 --gbar 4 --mp 6,2 --np 1 --rdg 5,3 --rfg 5,3 --score-min C,-14,0 -p 1 --sam-no-hd -x /home/user/Desktop/tophatout.sam/tmp/merged.remDup -|/usr/bin/fix_map_ordering --bowtie2-min-score 15 --read-mismatches 2 --read-gap-length 2 --read-edit-dist 2 --read-realign-edit-dist 3 --sam-header /home/user/Desktop/tophatout.sam/tmp/merged.remDup.bwt.samheader.sam - - /home/user/Desktop/tophatout.sam/tmp/left_kept_reads.m2g_um.bam | /usr/bin/map2gtf --sam-header /home/user/Desktop/tophatout.sam/tmp/hg19_genome.bwt.samheader.sam /home/user/Desktop/tophatout.sam/tmp/merged.remDup.fa.tlst - /home/user/Desktop/tophatout.sam/tmp/left_kept_reads.m2g.bam > /home/user/Desktop/tophatout.sam/logs/m2g_left_kept_reads.out [bam_header_read] EOF marker is absent. The input is probably truncated. Error at parsing .tlst line (invalid strand): 31958 TCONS_00032473 scaffold40. 5-1634
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