Tophat error running from bam2fastx?

[Triple_W]

Hi,
I just used TopHat v2.0.6 and came cross the following error


[2013-02-23 15:02:48] Beginning TopHat run (v2.0.6)
-----------------------------------------------
[2013-02-23 15:02:48] Checking for Bowtie
Bowtie version: 2.0.2.0
[2013-02-23 15:02:48] Checking for Samtools
Samtools version: 0.1.18.0
[2013-02-23 15:02:48] Checking for Bowtie index files
[2013-02-23 15:02:48] Checking for Bowtie index files
[2013-02-23 15:02:48] Checking for reference FASTA file
[2013-02-23 15:02:48] Generating SAM header for /home/yfenglab/wwwu/genomes/mm10/genome
format: fastq
quality scale: phred64 (reads generated with GA pipeline version >= 1.3)
[2013-02-23 15:02:52] Reading known junctions from GTF file
[2013-02-23 15:02:56] Preparing reads
left reads: min. length=90, max. length=90, 27839513 kept reads (589 discarded)
right reads: min. length=90, max. length=90, 27839658 kept reads (444 discarded)
[2013-02-23 15:23:44] Using pre-built transcriptome index..
[2013-02-23 15:23:46] Mapping left_kept_reads to transcriptome transcriptome with Bowtie2
[FAILED]
Error running:
/tophat/bam2fastx --all --fastq WT/tmp/left_kept_reads.bam|/bowtie2/bowtie2-align -q -k 60 --very-sensitive --gbar 4 --mp 6,2 --np 1 --rdg 5,3 --rfg 5,3 --score-min C,-32,0 -p 12 --sam-no-hd -x genomes/mm10/transcriptome -|/tophat/fix_map_ordering --bowtie2-min-score 30 --read-mismatches 4 --read-gap-length 2 --read-edit-dist 5 --read-realign-edit-dist 6 --sam-header WT/tmp/transcriptome.bwt.samheader.sam - - WT/tmp/left_kept_reads.m2g_um.bam | /tophat/map2gtf --sam-header WT/tmp/genome_genome.bwt.samheader.sam genomes/mm10/transcriptome.gff - WT/tmp/left_kept_reads.m2g.bam > WT/logs/m2g_left_kept_reads.out


Thanks!

[id0]

Were you able to resolve this error? I just got the same error with TopHat 2.0.9.

[dpryan]

The resolution to that is the run the

 /tophat/bam2fastx --all --fastq WT/tmp/left_kept_reads.bam|/bowtie2/bowtie2-align -q -k 60 --very-sensitive --gbar 4 --mp 6,2 --np 1 --rdg 5,3 --rfg 5,3 --score-min C,-32,0 -p 12 --sam-no-hd -x genomes/mm10/transcriptome -|/tophat/fix_map_ordering --bowtie2-min-score 30 --read-mismatches 4 --read-gap-length 2 --read-edit-dist 5 --read-realign-edit-dist 6 --sam-header WT/tmp/transcriptome.bwt.samheader.sam - - WT/tmp/left_kept_reads.m2g_um.bam | /tophat/map2gtf --sam-header WT/tmp/genome_genome.bwt.samheader.sam genomes/mm10/transcriptome.gff - WT/tmp/left_kept_reads.m2g.bam > WT/logs/m2g_left_kept_reads.out

command by itself and see exactly what error it produces. I may also be informative to split that command into its components, in case the error is being masked.

[id0]

Thanks for that suggestion. I erroneously assumed that all the errors were already output. After running that command by itself, there was additional useful info.

Turns out my input GTF had a few lines without strand info. After fixing those, TopHat finished running successfully.

[dpryan]

Cool, glad that worked out!

[Washington]

I was having the same problem.

This fixed it. Thanks a million guys,

-WLS