Hello. I apologize if this has been answered or addressed elsewhere, and I just wasn't able to find it through searching.
I am attempting to run velveth on a paired-end Illumina-generated sequence with short reads ( the two initial read files have been preprocessed, trimmed, and made into a single .fa file). I was trying to find the best hash length, so I wanted to use the
./velveth output_directory/ m,M,s (..data files..) function, where m-M is the range of values and s is the step. This is all being run on a cluster, so there shouldn't be any issues with computing ability. I compiled Velvet with a max kmer length of 149.
./velveth /output_directory_on_cluster/ 51,81,2 -shortPaired /path/to/sequence/files.fa with varying values for the m,M,s bit.
The job takes a while to run, and usually the first kmer value comes out correctly (makes a folder with Log, Roadmap, and Sequences files in it). However, the other ones don't have valid Sequence files; they are all empty files. I can use the typical velveth format (
.velveth /output_directory_on_cluster/ hash_length -shortPaired /path/to/sequence/files.fa) and it works if I separately run each kmer value that I'd like to test, but I was hoping to streamline it a little bit by using the m,M,s ability.
Has anyone experienced this problem before or know of a solution?