TopHat error - error running prep_reads

ajaffe · 11-29-2012, 08:09 AM

Hey all,

I came across a strange error affecting a subset of my samples. I ran TopHat2 on 71 paired end RNA seq samples, all with the same bowtie2 index and gtf gene annotation file, and 68/71 worked fine. however, 3 of the samples created the same error for TopHat2:

[2012-11-29 10:24:06] Beginning TopHat run (v2.0.6)
-----------------------------------------------
[2012-11-29 10:24:06] Checking for Bowtie
Bowtie version: 2.0.2.0
[2012-11-29 10:24:07] Checking for Samtools
Samtools version: 0.1.18.0
[2012-11-29 10:24:07] Checking for Bowtie index files
[2012-11-29 10:24:07] Checking for reference FASTA file
[2012-11-29 10:24:07] Generating SAM header for [GENOME FILE]
format: fastq
quality scale: phred33 (default)
[2012-11-29 10:26:12] Reading known junctions from GTF file
[2012-11-29 10:26:23] Preparing reads
[FAILED]
Error running 'prep_reads'
stdout: Broken pipe

any help would be greatly appreciated.

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11-29-2012, 08:09 AM	#1
ajaffe Junior Member Location: Baltimore, MD Join Date: Jan 2011 Posts: 4	TopHat error - error running prep_reads Hey all, I came across a strange error affecting a subset of my samples. I ran TopHat2 on 71 paired end RNA seq samples, all with the same bowtie2 index and gtf gene annotation file, and 68/71 worked fine. however, 3 of the samples created the same error for TopHat2: [2012-11-29 10:24:06] Beginning TopHat run (v2.0.6) ----------------------------------------------- [2012-11-29 10:24:06] Checking for Bowtie Bowtie version: 2.0.2.0 [2012-11-29 10:24:07] Checking for Samtools Samtools version: 0.1.18.0 [2012-11-29 10:24:07] Checking for Bowtie index files [2012-11-29 10:24:07] Checking for reference FASTA file [2012-11-29 10:24:07] Generating SAM header for [GENOME FILE] format: fastq quality scale: phred33 (default) [2012-11-29 10:26:12] Reading known junctions from GTF file [2012-11-29 10:26:23] Preparing reads [FAILED] Error running 'prep_reads' stdout: Broken pipe any help would be greatly appreciated.