Question: Problems running ViromeScan - could not locate a Bowtie2 index
0
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
1

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
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1071 users visited in the last hour