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marbl / canu

A single molecule sequence assembler for genomes large and small.
http://canu.readthedocs.io/
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Fungal Genome Assembly #1185

Closed peflanag closed 5 years ago

peflanag commented 5 years ago

Hi, I'm using canu to assemble a fungal (Candida albicans) genome tahts approx 15Mb in size. Unlike when the bacteria guys in my lab us canu to assemble their genomes it seems to be taking far longer. I assume this is due to the genome size. However, Im just wondering is this normal? I've attached a screen shot. The bacteria guys in my lab that run canu said they never see the command window pump out this. I have to point out that I started canu 24hrs ago and about 12 hours ago it started pumping out whats in the screenshot

screen shot 2018-12-13 at 08 56 52

Also, this is a strain where I used CRISPR to delete a gene family. So I have deleted 15 genes from the organism. I'm assuming canu can still assemble and then if I view the assembled file in 3rd party software I should see gaps for where the genes are missing?

Cheers in advance,

Peter

skoren commented 5 years ago

This looks like a bug in Canu 1.7, is that the version you're using?

Either way, same solution as #1035, kill the job, remove the 3-overlapErrorAdjustment and restart adding the options redMemory=32 oeaMemory=32.

peflanag commented 5 years ago

Yea its 1.7. I dont know how to update to 1.8 cause I dont know how to tell the Mac to put it into the path to use the canu command. I had to have a computer guy do it for us originally in the lab! If I could pip install or brew install or conda install that would be great. Our lab is a microbiology lab and none of use have command line skills! We're just shooting in the dark! But I'll try the suggestion you mentioned above. Cheers!

peflanag commented 5 years ago

How do i remove the 3-overlapErrorAdjustment?

skoren commented 5 years ago

To remove, something like: rm -rf unitigging/3-overlapErrorAdjustment from inside the assembly folder.

FWIW, you don't need to put it in a special place to run (but if you care about how to do it I'd suggest this tutorial as a starting point: ftp://ftp.wayne.edu/ldp/en/Intro-Linux/Intro-Linux.pdf and the section on PATH on page 35). Download and extract the release following the commands on the release page then give the full path to wherever you put it. So after you extract it, run pwd and then to run canu put whatever that reports/*/bin/canu. But don't do that now since you're in the middle of an assembly and the new release isn't backwards compatible with a previously started assembly.

peflanag commented 5 years ago

Oh cool cheers!