Assembly – SparseAssembler (k 131) on Geoduck Sequence Data

After some runs with kmergenie, I’ve decided to try re-running SparseAssembler using a kmer setting of 131.

The job was run on our Mox HPC node.

• Slurm script: 20180422_sparse_assembler_kmer131_geoduck_slurm.sh

Results:

Output folder:

• 20180422_sparseassembler_kmer131_geoduck/

Slurm output file:

• 20180422_sparseassembler_kmer131_geoduck/slurm-163406.out

This failed with the following error message:

Error! K-mer size too large!

Looking into this, it’s because the maximum kmer size for kmergenie is 127! Doh!

It’d be nice if the program looked at that setting first before processign all the data files…

A bit disappointing, but I’ll give this a go with a lower kmer setting and see how it goes.