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Viromescan tool for metagenomics analysis: Bowtie not able to recognize index files

For viral community profiling and abundance estimation from metagenomics samples, I was working on Viromescan tool with the manual. However, I stuck with a problem related to bowtie index file recognition.

I executed the command for the paired end files from directory where index files are located,

:~/viromescan/database/bowtie2$ viromescan.sh -p 2 -d virus_ALL -1 /home/my_server/viromescan/a.fq -2 /home/my_server/viromescan/b.fq -o RESULT

and the command throws error like,

Could not locate a Bowtie index corresponding to basename "/viromescan/database/bowtie2/virus_ALL"
Error: Encountered internal Bowtie 2 exception (#1)
Command: /Tools/Mapping/bowtie2-2.3.2/bowtie2-align-s --wrapper basic-0 -x /viromescan/database/bowtie2/virus_ALL --sensitive-local -p 2 --passthrough -1 /home/my_server/viromescan/a.fq -2 /home/my_server/viromescan/b.fq 
(ERR): bowtie2-align exited with value 1

Looking at the error report, it is evident that something was wrong with index files for virus_ALL. I changed the bowtie index files with sample files (which worked well with some other RNASeq exp. Bowtie 2 version 2.3.2 ). Still same error is occurred. Can anyone give some direction?

bowtie software error alignment
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written by rice.researcher rice.researcher

Hey,

In which directory are the indices actually located? How did you build the indices?

Kevin

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written by Kevin Blighe Kevin Blighe

The downloaded tool has pre-made indices for viruses and human in a directory named 'bowtie2'. So I run commands from that location. To test whether the problem is with those indices files, I used another sample indices which was built like,

bowtie-build genome.fa genome

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written by rice.researcher rice.researcher

Did you use bowtie2 or bowtie to build the indices yourself? It looks like the program requires bowtie2 indices?

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written by Kevin Blighe Kevin Blighe

Previously, I tried both way, means indices built using bowtie and bowtie2. But got the same error. Now, I realized that a parameter -m (which is for pathway to viromescan folder) modifies the path for the bowtie indices and now solved the problem. The modified command I used is,

viromescan.sh -1 /home/my_server/viromescan/a.fq /home/my_server/viromescan/b.fq -d virus_ALL -p 2 -m /home/my_server -o testing

Thanks for your effort to looking into the problem.!!

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written by rice.researcher rice.researcher

Great - I'm glad that it has been resolved.

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written by Kevin Blighe Kevin Blighe

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