TopHat error - error running prep_reads

[ajaffe]

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.