Problems running ViromeScan - could not locate a Bowtie2 index

Question

[Guillermo D. Huerta]

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

[GenoMax]

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.

[Mario]

Hello,

I've tried it as you suggested it and I'm keeping the same. I've exported the index to my PATH. It's weird because I downloaded it from viromescan's repository.

(viromescan) rhernandez@nautilus:~$ viromescan.sh -p 3 -m . -d virus_ALL -1 ASB_S11_L001_R1_001_prueba.fastq -o test_mario18 (ERR): "./viromescan/database/bowtie2/virus_ALL" does not exist or is not a Bowtie 2 index Exiting now ...

Hope you can help me.

Thanks,

Mario.

[GenoMax]

Can you post listing of ls -l virus_ALL* command from `bowtie2 directory?

[Mario]

Sure!

(viromescan) user@nautilus:~/miniconda3/envs/viromescan/database/bowtie2$ ls -l virus_ALL*

-rwxrwxrwx 1 user user 31136510 ene  6 17:33 virus_ALL.1.bt2

-rwxrwxrwx 1 user user 19867076 ene  6 17:33 virus_ALL.2.bt2

-rwxrwxrwx 1 user user    52604 ene  6 17:33 virus_ALL.3.bt2

-rwxrwxrwx 1 user user 19867072 ene  6 17:33 virus_ALL.4.bt2

-rwxrwxrwx 1 user user 31136510 ene  6 17:33 virus_ALL.rev.1.bt2

-rwxrwxrwx 1 user user 19867076 ene  6 17:33 virus_ALL.rev.2.bt2

virus_ALL: total 0

I followed the manual from viromescan website, and I decompress the bowtie2 folder.

[GenoMax]

So that looks ok. Simplest thing would be to try the command giving full path to the database. See if that works.

viromescan.sh -p 3 -m . -d ~/miniconda3/envs/viromescan/database/bowtie2/virus_ALL -1 ASB_S11_L001_R1_001_prueba.fastq -o test_mario18 

[Mario]

I did it, and I got the same error:

(viromescan) rhernandez@nautilus:~$ viromescan.sh -p 3 -m . -d /home/user/miniconda3/envs/viromescan/database/bowtie2/virus_ALL -1 ASB_S11_L001_R1_001_prueba.fastq -o test_mario23 (ERR): "./viromescan/database/bowtie2//home/user/miniconda3/envs/viromescan/database/bowtie2/virus_ALL" does not exist or is not a Bowtie 2 index Exiting now ...

Is there another way to get database in bowtie2 format?