HiCanu settings

[Kirk3gaard]

Hi

Really excited to see your new results with pacbio HiFi data.

Is "HiCanu" activated when running canu (https://twitter.com/sergekoren/status/1217547604738732032) with the -pacbio-hifi option in v 1.9. Or is it necessary to build from github? (Canu V2.0 coming soon?)

Plus will additional settings be required?

Best regards
Rasmus

[skoren]

You need to use the GitHub tip, the 1.9 isn't going to have the most up to date version. Running:

git clone https://github.com/marbl/canu.git
cd canu
git checkout hicanu_rc
rm -r Linux-amd64
make

then run providing reads with -pacbio-hifi. We will make a release that includes these features soon, it has to go through the regular regression tests first.

[Kirk3gaard]

That sounds great. Thank you.

[Kirk3gaard]

Hi Sergey

I managed to run the above installation and confirmed that I got the hicanu branch.
canu -version
Canu branch hicanu_rc +325 changes (r9818 86bb2e2)

I then tried running it with some CCS data (with metagenome options from
https://speakerdeck.com/skoren/hicanu-resolving-repeats-and-haplotypes?slide=16). It starts out fine but then stops. I have attached the report and err files.

Command:
canu -p CANUASSEMBLY -d CANUASSEMBLY genomeSize=0.3g 'batOptions=-eg 0.0 -sb 0.001 -df 0 -db 3 -dr 0 -ca 2000 -cp 200' gridOptions="--account aauhpc_slim --time=24:00:00 --mail-user rhk@bio.aau.dk --mail-type FAIL" -pacbio-hifi PACBIOCCS_above1kbp.fastq

I tried the same command without the gridoptions on a different server and got the same result.

I cannot see what to do based on the error file so I would really appreciate if you can give me a hint.

CANUASSEMBLY.report.txt
CANUASSEMBLY.seqStore.err.txt

[skoren]

There is no error in these logs and it seems like the assembly was almost complete. Check the output of the canu.out file (and post it here) in the assembly folder.

[Kirk3gaard]

Thanks that file is really helpful. It appears that I have a typo in my command. Thanks for the help. I will change this and see if finishes.

canu.out.txt

[skoren]

Your bat options should be: 'batOptions=-eg 0.0 -sb 0.001 -dg 0 -db 3 -dr 0 -ca 2000 -cp 200' (dg instead of df).

[Kirk3gaard]

Yeah I noticed that and it completed successfully after restarting with g. Thanks a lot.

[mjfi2sb3]

Why do you specify batOptions? are they different from default for HiCanu? /sb

[skoren]

It's a metagenome so needs different settings than a clonal assembly.

[mjfi2sb3]

Ah, ok. Thanks

[skoren]

I'm guessing that you have 1.9 from your module load command. You shouldn't be using Canu 1.9 but 2.0 instead as 1.9 doesn't have full HiFi support. Other than that, the defaults work for almost all the HiFi datasets we have tried. The FAQ lists alternates to try which can help in cases where you have lower quality HiFi data: https://canu.readthedocs.io/en/latest/faq.html#what-parameters-should-i-use-for-my-reads