Question: Problems running ViromeScan - could not locate a Bowtie2 index
gravatar for Guillermo D. Huerta
7 months ago by
Columbus (Ohio)
Guillermo D. Huerta10 wrote:

Hi all,

I'm trying to run ViromeScan, and used the following:

$ module use /fs/project/PAS1117/modulefiles
$ module load viromescan/viromescan
$ module load bowtie2
viromescan -p 3 -m /fs/PAS1117/modulefiles/viromescan -d virus_ALL -1 /fs/project/PAS1117/Tara_Euk/upwelling-v2/ERR1719154_1.fastq.gz -2 /fs/project/PAS1117/Tara_Euk/upwelling-v2/ERR1719154_2.fastq.gz -o viromescan_out

but received...

Could not locate a Bowtie index corresponding to basename "/fs/PAS1117/modulefiles/viromescan/viromescan/database/bowtie2/virus_ALL"
Error: Encountered internal Bowtie 2 exception (#1)
Command: /usr/local/bowtie2/bowtie2-2.2.9/bowtie2-align-s --wrapper basic-0 -x /fs/PAS1117/modulefiles/viromescan/viromescan/database/bowtie2/virus_ALL --sensitive-local -p 3 --passthrough -1 /tmp/13722.inpipe1 -2 /tmp/13722.inpipe2 
(ERR): bowtie2-align exited with value 1

Would you know how to solve this?

thanks, Guillermo

rna-seq viromescan bowtie • 253 views
ADD COMMENTlink modified 7 months ago by genomax63k • written 7 months ago by Guillermo D. Huerta10

Where are the files for your bowtie2 index located? It looks like viromescan is looking for them in /fs/PAS1117/modulefiles/viromescan/viromescan/database/bowtie2/.

You could add the directory containing index to your $PATHby doing export PATH=$PATH=/path_to_dir_with_virus_ALL.

ADD REPLYlink modified 7 months ago • written 7 months ago by genomax63k
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