Duration and Heterozygosity

[rmormando]

Hi I'm trying to run nPhase on a tetraploid yeast genome I seqeunced with PacBio HiFi reads.

Here is my code:

nphase pipeline --sampleName trialRun1 --reference s288c.fa --longReads pacbioHiFireads.fastq.gz --longReadPlatform pacbio --R1 illuminaShortRead_1.fastq --R2 illuminaShortRead_2.fastq --output trialRun1Output --threads 8

The issue I am having is that it's taking a long time to run - my computer accidentally restarted during its run so the progress I made running it for the past day or two is gone and before I run the code again I wanted to see if there was a tag or something I could add or do to the data to make it go faster.

I saw your messages in issue #11 and #10 but was wondering if there was anything done to the nPhase code to account for this. I also read up on your solution to #12 but I'm not sure how to go about doing that. I can run the code using the command I have written out above and I don't mind if it takes a longer amount of time but how much time on average would it take for a tetraploid yeast genome to run through nPhase?