How to run SNAP aligner on Windows correctly 10?

Question

[flight22121]

Trying code in Win CMD:

snap index H37Rv_reference.fa index -dir C:\Users\Friends\Documents\snap-beta.18-windows

and it throws error "Invalid argument: -dir"

How to set up the directory correctly and how to refer to it?

[GenoMax]

Looking at the command line you almost certainly have an error in it somewhere (have you looked at the manual/help?). You can't have index option twice. Does index-dir need to be one word?

[flight22121]

Found correct way on my own:

snap index H37Rv_reference.fa C:\Users\Friends\Documents\snap-beta.18-windows
Hash table slack 0.300000
Loading FASTA file 'H37Rv_reference.fa' into memory...0s
Saving genome...0s
Computing bias table.
Computed bias table in 0s
Allocating memory for hash tables...0s
Building hash tables.
41196(0%) seeds occur more than once, total of 112734(2%) genome locations are not unique, 498(0%) bad seeds, 0 both complements used 500 no string
Hash table build took 0s
Building overflow table.
Overflow table build and hash table save took 0s
Saving overflow table...0s
Index build and save took 0s (4412532 bases/s)

[flight22121]

and now get Unable to open file 'read1.fq' for QueryFileSize, 2 when aligning with code snap paired D:\snap-beta.18-windows\ read1.fq read2.fq -o output.sam , how to fix that? Thank you

[GenoMax]

I am just speculating. Check the manual/online help. If you are providing path for one of the fastq files then you may need to do it for the other as well. snap paired D:\snap-beta.18-windows\read1.fq D:\snap-beta.18-windows\read2.fq -o output.sam

Answer 1

[flight22121]

yes it works like:

snap single C:\Users\Friends\Documents\snap-beta.18-windows read1.fastq  -o output.sam
snap paired C:\Users\Friends\Documents\snap-beta.18-windows\ C:\Users\Friends\Documents\snap-beta.18-windows\read1.fastq  C:\Users\Friends\Documents\snap-beta.18-windows\read2.fastq   -o output.sam

Author of the software advised to write a separate path to an every single argument