Entering edit mode
6.5 years ago
rice.researcher
▴
210
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?
Hey,
In which directory are the indices actually located? How did you build the indices?
Kevin
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
Did you use bowtie2 or bowtie to build the indices yourself? It looks like the program requires bowtie2 indices?
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.!!
Great - I'm glad that it has been resolved.