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Old 02-12-2013, 01:01 PM   #7
Ajayi Oyeyemi
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Location: Abeokuta

Join Date: Jul 2012
Posts: 30
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Hi,
I was running the alignment using tophat:

[2013-02-12 16:32:41] Beginning TopHat run (v2.0.7)
-----------------------------------------------
[2013-02-12 16:32:41] Checking for Bowtie
Bowtie version: 2.0.6.0
[2013-02-12 16:32:42] Checking for Samtools
Samtools version: 0.1.18.0
[2013-02-12 16:32:42] Checking for Bowtie index files
[2013-02-12 16:32:42] Checking for reference FASTA file
Warning: Could not find FASTA file /workdir/ooa4/index/bovine.fa
[2013-02-12 16:32:42] Reconstituting reference FASTA file from Bowtie index
Executing: /programs/bin/bowtie2/bowtie2-inspect /workdir/ooa4/index/bovine > tophat_output/tmp/bovine.fa
[2013-02-12 16:35:54] Generating SAM header for /workdir/ooa4/index/bovine
format: fastq
quality scale: phred33 (default)
[2013-02-12 16:36:56] Reading known junctions from GTF file
[2013-02-12 16:36:59] Preparing reads
left reads: min. length=72, max. length=72, 24813301 kept reads (29188 discarded)
[2013-02-12 16:47:07] Creating transcriptome data files..
[2013-02-12 16:48:19] Building Bowtie index from genes.fa
[FAILED]
Error: Couldn't build bowtie index with err = 1.

I went through the log file in my tophat output and it gave:
bowtie_inspect_recons.log g2f.err g2f.out gtf_juncs.log prep_reads.log run.log tophat.log

I used the code: tophat -o tophat_output -p 8 -G Bos_taurus/NCBI/Btau_4.6.1/Annotation/Archives/archive-2012-03-08-21-54-00/Genes/genes.gtf /workdir/ooa4/index/bovine SRR594497.fastq

All my .bt2 files are in the folder called index e.g bovine.bt1 etc...



I don't know whats happening and I need your help. I've been struggling real hard on this. Please help me out.

Yemi.
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