Hi!
I am trying to run tophat, but I keep getting this very general error and I am not sure why.
[2014-05-27 09:46:02] Beginning TopHat run (v2.0.11)
-----------------------------------------------
[2014-05-27 09:46:02] Checking for Bowtie
Bowtie version: 2.2.2.0
[2014-05-27 09:46:02] Checking for Samtools
Samtools version: 0.1.19.0
[2014-05-27 09:46:02] Checking for Bowtie index files (genome)..
[2014-05-27 09:46:02] Checking for reference FASTA file
[2014-05-27 09:46:02] Generating SAM header for /afs/crc.nd.edu/user/k/kregan1/Daphnia/genome/Daphnia_pulex.main_genome.scaffolds.fasta
Error: Opening file /afs/crc.nd.edu/user/k/kregan1/Daphnia/genome
The file that it is trying to open is actually a directory that holds my reference genome and the bowtie index files. Have any of you seen this error and been able to fix it? Thanks so much!
I am trying to run tophat, but I keep getting this very general error and I am not sure why.
[2014-05-27 09:46:02] Beginning TopHat run (v2.0.11)
-----------------------------------------------
[2014-05-27 09:46:02] Checking for Bowtie
Bowtie version: 2.2.2.0
[2014-05-27 09:46:02] Checking for Samtools
Samtools version: 0.1.19.0
[2014-05-27 09:46:02] Checking for Bowtie index files (genome)..
[2014-05-27 09:46:02] Checking for reference FASTA file
[2014-05-27 09:46:02] Generating SAM header for /afs/crc.nd.edu/user/k/kregan1/Daphnia/genome/Daphnia_pulex.main_genome.scaffolds.fasta
Error: Opening file /afs/crc.nd.edu/user/k/kregan1/Daphnia/genome
The file that it is trying to open is actually a directory that holds my reference genome and the bowtie index files. Have any of you seen this error and been able to fix it? Thanks so much!
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