SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
tophat running error figo1019 Bioinformatics 9 05-03-2013 08:18 AM
Converting bam to fastq filee/bam2fastx error bob-loblaw Bioinformatics 0 12-10-2012 03:59 AM
TopHat error - error running prep_reads ajaffe RNA Sequencing 0 11-29-2012 08:09 AM
tophat Error running running 'prep_reads' victoryhe Bioinformatics 2 10-17-2011 05:53 AM
TopHat running error pfranchini Bioinformatics 2 08-10-2009 07:46 AM

Reply
 
Thread Tools
Old 02-24-2013, 06:05 PM   #1
Triple_W
Member
 
Location: China

Join Date: Jan 2012
Posts: 12
Default Tophat error running from bam2fastx?

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!
Triple_W is offline   Reply With Quote
Old 09-27-2013, 02:39 PM   #2
id0
Senior Member
 
Location: USA

Join Date: Sep 2012
Posts: 130
Default

Were you able to resolve this error? I just got the same error with TopHat 2.0.9.
id0 is offline   Reply With Quote
Old 09-28-2013, 07:12 AM   #3
dpryan
Devon Ryan
 
Location: Freiburg, Germany

Join Date: Jul 2011
Posts: 3,480
Default

The resolution to that is the run the
Code:
 /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.
dpryan is offline   Reply With Quote
Old 09-30-2013, 09:37 AM   #4
id0
Senior Member
 
Location: USA

Join Date: Sep 2012
Posts: 130
Default

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.
id0 is offline   Reply With Quote
Old 09-30-2013, 09:47 AM   #5
dpryan
Devon Ryan
 
Location: Freiburg, Germany

Join Date: Jul 2011
Posts: 3,480
Default

Cool, glad that worked out!
dpryan is offline   Reply With Quote
Old 01-12-2015, 06:15 AM   #6
Washington
Junior Member
 
Location: Ithaca, NY, USA

Join Date: Nov 2014
Posts: 1
Default

I was having the same problem.

This fixed it. Thanks a million guys,

-WLS
Washington is offline   Reply With Quote
Reply

Tags
bam2fastx tophat bowtie

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 05:54 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO