TopHat - Segment Join Failed

[fongchun]

Hi,

I've been searching around the forum for a solution to this problem, but I've haven't found any solutions which have worked for me. I am just trying to run TopHat on a bunch of paired-end read libraries and I keep running into this segment join failed issue.

[fong@beast fong]$ tophat -r 200 -o /share/lustre/fong/results/ABC_VS_GCB/tophat/HS0637,hg19 hg19 /share/lustre/gascoyne/WTSS/DLBCL/raw_data/HS0637/reads.1.fastq /share/lustre/gascoyne/WTSS/DLBCL/raw_data/HS0637/reads.2.fastq

[Thu May 12 10:21:34 2011] Beginning TopHat run (v1.2.0)
-----------------------------------------------
[Thu May 12 10:21:34 2011] Preparing output location /share/lustre/fong/results/ABC_VS_GCB/tophat/HS0637,hg19/
[Thu May 12 10:21:35 2011] Checking for Bowtie index files
[Thu May 12 10:21:35 2011] Checking for reference FASTA file
[Thu May 12 10:21:35 2011] Checking for Bowtie
Bowtie version: 0.12.7.0
[Thu May 12 10:21:35 2011] Checking for Samtools
Samtools Version: 0.1.11
[Thu May 12 10:22:43 2011] Checking reads
min read length: 50bp, max read length: 75bp
format: fastq
quality scale: phred33 (default)
[Thu May 12 11:42:29 2011] Mapping reads against hg19 with Bowtie
[Thu May 12 11:42:30 2011] Joining segment hits
[FAILED]
Error: Segment join failed with err = 1

I've tried taking a small subset of the reads and it works fine, but when I scale it to use all the reads it returns this error. Can anyone provide any advice on how to fix this problem? Thanks,

Fong

[fongchun]

If this means anything to anyone, I somehow solved the problem by just changing some of my parameters. I removed the 'comma' in my output dir and then gave the absolute path to the reference index. So the following command I used was:

tophat -r 200 -o /share/lustre/fong/results/ABC_VS_GCB/tophat/HS0637 /share/lustre/fong/annotation_files/bowtie/indexes/hg19 /share/lustre/gascoyne/WTSS/DLBCL/raw_data/HS0637/reads.1.fastq /share/lustre/gascoyne/WTSS/DLBCL/raw_data/HS0637/reads.2.fastq

I had the BOWTIE_INDEXES environment variable set to the directory "/share/lustre/fong/annotation_files/bowtie/indexes/" so I theoretically shouldn't need to give it the absolute path. And it should have complained at the mapping set and not the joining segment hits step if it was an index problem. But whatever the case, these two modifications made tophat work.

Fong