Tophat Question: No Accepted_Hits.Bam Generated

Question

[Rnaer]

I am using tophat to map the SOLiD single-end 50mer reads to S.cerevisae genome. The commands I used are:

$ bowtie-build -C reads/sgd_genome.fa reads/sgd_genome  

$ qsub -V -o WT.1_tophat.O -e WT.1_tophat.E -N WT.1_tophat -l
nodes=1:ppn1,walltime=10:00:00 <<< " tophat --color --output-dir
cufflinks/WT.1 --GTF reads/gene_features.gff --quals reads/sgd_genome
reads/WT.1.csfasta reads/WT.1.qual"

The job ran without any error but there is no accepted_hits.bam generated and all the BED files are empty.

$ ls -l WT.1
total 16K
-rw-rw-r-- 1 zxu7 zxu7 0 07/19 15:15:24 deletions.bed
-rw-rw-r-- 1 zxu7 zxu7 0 07/19 15:15:24 insertions.bed
-rw-rw-r-- 1 zxu7 zxu7 0 07/19 15:15:24 junctions.bed
-rw-rw-r-- 1 zxu7 zxu7 70 07/19 12:30:42 leftkeptreads.info
drwxrwxr-x 2 zxu7 zxu7 8.0K 07/18 14:06:23 logs

$ cat WT.1tophat.E
[Mon Jul 18 10:36:07 2011] Beginning TopHat run (v1.3.1)
---------------------------------------------
[Mon Jul 18 10:36:07 2011] Preparing output location cufflinks/WT.1/
[Mon Jul 18 10:36:07 2011] Checking for Bowtie index files
[Mon Jul 18 10:36:07 2011] Checking for reference FASTA file
Warning: Could not find FASTA file cufflinks/genome.fa
[Mon Jul 18 10:36:07 2011] Reconstituting reference FASTA file from Bowtie index
Executing: /home/zxu7/Softwares/bowtie-0.12.7/bowtie-inspect
cufflinks/genome > cufflinks/WT.1/tmp/genome.fa
[Mon Jul 18 10:36:08 2011] Checking for Bowtie
Bowtie version: 0.12.7.0
[Mon Jul 18 10:36:08 2011] Checking for Samtools
Samtools Version: 0.1.14
[Mon Jul 18 10:36:08 2011] Generating SAM header for cufflinks/genome
[Mon Jul 18 10:36:11 2011] Preparing reads
format: fasta
[Mon Jul 18 10:36:11 2011] Reading known junctions from GTF file
Left reads: min. length=50, count=32186882
[Mon Jul 18 10:46:11 2011] Mapping leftkeptreads against genome with Bowtie
[Mon Jul 18 11:22:32 2011] Processing bowtie hits
[Mon Jul 18 11:56:23 2011] Mapping leftkeptreadsseg1 against genome with Bowtie (1/2)
[Mon Jul 18 12:26:07 2011] Mapping leftkeptreadsseg2 against genome with Bowtie (2/2)
[Mon Jul 18 13:01:47 2011] Searching for junctions via segment mapping
[Mon Jul 18 13:13:27 2011] Retrieving sequences for splices
[Mon Jul 18 13:13:28 2011] Indexing splices
[Mon Jul 18 13:13:29 2011] Mapping leftkeptreadsseg1 against segmentjuncs with Bowtie (1/2)
[Mon Jul 18 13:38:03 2011] Mapping leftkeptreadsseg2 against segment_juncs with Bowtie (2/2)
[Mon Jul 18 13:48:21 2011] Joining segment hits
[Mon Jul 18 14:06:53 2011] Reporting output tracks
-----------------------------------------------
Run complete [03:32:48 elapsed]

By the way, the gff files is in GFF version 3 format. Does anyone know what's wrong with my tophat command? Thanks

[Sukhi Singh]

Try running it again with --keep-tmp option, it might be a problem!!