I am using tophat to map the RNA-seq data. But, I am getting the following error:
[Wed Jan 18 16:02:44 2012] Beginning TopHat run (v1.4.0)
-----------------------------------------------
[Wed Jan 18 16:02:44 2012] Preparing output location /home/RNA/Type_EM/Sample1/tophatNew/
[Wed Jan 18 16:02:44 2012] Checking for Bowtie index files
[Wed Jan 18 16:02:44 2012] Checking for reference FASTA file
[Wed Jan 18 16:02:44 2012] Checking for Bowtie
Bowtie version: 0.12.7.0
[Wed Jan 18 16:02:44 2012] Checking for Samtools
Samtools Version: 0.1.18
[Wed Jan 18 16:02:44 2012] Generating SAM header for /home/RefGenome/hg19/Homo_sapiens_assembly19_sorted
format: fastq
quality scale: phred33 (default)
[Wed Jan 18 16:02:47 2012] Reading known junctions from GTF file
[Wed Jan 18 16:03:00 2012] Preparing reads
left reads: min. length=101, count=18736919
right reads: min. length=101, count=18728487
[Wed Jan 18 16:49:23 2012] Creating transcriptome data files..
[Wed Jan 18 16:50:31 2012] Building Bowtie index from Homo_sapiens.GRCh37.65.fa
[FAILED]
Error: Couldn't build bowtie index with err = 1
The reference genome I used is Homo_sapiens_assembly19_sorted.fasta.
The transcriptome GTF file is Homo_sapiens.GRCh37.65.gtf.
why do I need Bowtie index from Homo_sapiens.GRCh37.65.fa ? Such file doesn't exit. Or do the reference genome fasta and the transcriptome gtf have to have the same name?
Thanks for any help.
[Wed Jan 18 16:02:44 2012] Beginning TopHat run (v1.4.0)
-----------------------------------------------
[Wed Jan 18 16:02:44 2012] Preparing output location /home/RNA/Type_EM/Sample1/tophatNew/
[Wed Jan 18 16:02:44 2012] Checking for Bowtie index files
[Wed Jan 18 16:02:44 2012] Checking for reference FASTA file
[Wed Jan 18 16:02:44 2012] Checking for Bowtie
Bowtie version: 0.12.7.0
[Wed Jan 18 16:02:44 2012] Checking for Samtools
Samtools Version: 0.1.18
[Wed Jan 18 16:02:44 2012] Generating SAM header for /home/RefGenome/hg19/Homo_sapiens_assembly19_sorted
format: fastq
quality scale: phred33 (default)
[Wed Jan 18 16:02:47 2012] Reading known junctions from GTF file
[Wed Jan 18 16:03:00 2012] Preparing reads
left reads: min. length=101, count=18736919
right reads: min. length=101, count=18728487
[Wed Jan 18 16:49:23 2012] Creating transcriptome data files..
[Wed Jan 18 16:50:31 2012] Building Bowtie index from Homo_sapiens.GRCh37.65.fa
[FAILED]
Error: Couldn't build bowtie index with err = 1
The reference genome I used is Homo_sapiens_assembly19_sorted.fasta.
The transcriptome GTF file is Homo_sapiens.GRCh37.65.gtf.
why do I need Bowtie index from Homo_sapiens.GRCh37.65.fa ? Such file doesn't exit. Or do the reference genome fasta and the transcriptome gtf have to have the same name?
Thanks for any help.
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