Tophat complains

[Assaf]

Hi all,

It is my first post here, and it is nice to e-meet you.

I have 454 transcriptome sequencing results, which I want to map to their reference genome, in order to identify splice junctions, reads depth, and to produce contigs. I decided to do that in a pipeline with the Bowtie, Tophat, and cufflinks programs.

I first created bowtie index files based on the genome reference (*.ebwt), and also converted my sff transcriptome files into fastq files (using biopython). And now i'm trying to run Tophat with the basename of bowtie index files, and the fastq.

After about 10min Tophat is terminated with the following complain:
....
[Mon Jan 2 16:33:02 2012] Joining segment hits
[FAILED]
Error executing: /home/assaf/programs1/tophat-1.3.3.Linux_x86_64/bam_merge ./tophat_out/tmp/left_kept_reads.candidates_and_unspl.bam ./tophat_out/tmp/left_kept_reads.unspl.bam ./tophat_out/tmp/left_kept_reads.candidates.bam

In the file sam_merge.log
this is what I got:

Warning: no input BAM records found.
GList error (GList.hh:932):Invalid list index: 0

I can indeed see that the file left_kept_reads.candidates_and_unspl.bam was not created, so bam_merge is in troubles, but why ?

Maybe you can give me a hint ?

Thanks in advanced,
Assaf

[Ambily]

Hi Assaf,

I am getting the same error too with the latest version of TopHat. Did you manage to fix it?

Looking forward to you response.
Ambily