Hello all,
I am attempting to build a three-spined stickleback transcriptome index with TopHat v2.0.14 but I keep getting an error. I've already indexed the reference genome using bowtie and Tophat aligns without to the genome. However as soon as I use the following command:
tophat -G Gac_genes.gtf --transcriptome-index=gac_transcript/known_gac gac
I get this output after a few seconds:
[2015-06-01 15:57:08] Building transcriptome files with TopHat v2.0.14
-----------------------------------------------
[2015-06-01 15:57:08] Checking for Bowtie
Bowtie version: 2.2.5.0
[2015-06-01 15:57:08] Checking for Bowtie index files (genome)..
[2015-06-01 15:57:08] Checking for reference FASTA file
[2015-06-01 15:57:08] Building transcriptome data files gac_transcript/known_gac
[2015-06-01 15:57:26] Building Bowtie index from known_gac.fa
[FAILED]
Error: Couldn't build bowtie index with err = -6
I have checked that the first column of the GTF and the genome indexes are identical. Can anyone shed any light on what a -6 error indicates?
Many thanks in advance
I am attempting to build a three-spined stickleback transcriptome index with TopHat v2.0.14 but I keep getting an error. I've already indexed the reference genome using bowtie and Tophat aligns without to the genome. However as soon as I use the following command:
tophat -G Gac_genes.gtf --transcriptome-index=gac_transcript/known_gac gac
I get this output after a few seconds:
[2015-06-01 15:57:08] Building transcriptome files with TopHat v2.0.14
-----------------------------------------------
[2015-06-01 15:57:08] Checking for Bowtie
Bowtie version: 2.2.5.0
[2015-06-01 15:57:08] Checking for Bowtie index files (genome)..
[2015-06-01 15:57:08] Checking for reference FASTA file
[2015-06-01 15:57:08] Building transcriptome data files gac_transcript/known_gac
[2015-06-01 15:57:26] Building Bowtie index from known_gac.fa
[FAILED]
Error: Couldn't build bowtie index with err = -6
I have checked that the first column of the GTF and the genome indexes are identical. Can anyone shed any light on what a -6 error indicates?
Many thanks in advance
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