I've turned on the Windows Subsystem for Linux feature on my Windows 10 desktop, installed Ubuntu and installed blast locally with this command
sudo apt-get install ncbi-blast+.
I'm trying to run a shell script that includes doing a local blastp search. The shell script line that's causing errors is below:
blastp -query protein_query.txt -db /mnt/c/Users/username/Desktop/Bioinformatics/refdata -out protein.blast.txt -evalue 1e-15 -outfmt "6 qseqid sseqid evalue stitle" -max_target_seqs 1000
I ran this shell script on bash by typing
/mnt/c/Users/username/Desktop/Bioinformatics/PROTEIN.sh, which gave me the following error:
command line argument error: Argument "query". File is not accessible: 'protein_query.txt'
I'm suspecting this has something to do with the location that blast was installed but I can't figure out where it got installed with the Ubuntu configuration... Can anyone provide any advice/suggestions?