Canu errors

Good evening,

I am running Canu on a remote desktop running a WSL.

The code I inputted to run the command was:

 canu -p canu_assem -d canu2 genomeSize=1.6g useGrid=false -nanopore nano_cat_filt.fastq.gz maxMemory=188 maxThreads=32 corMemory=16 cnsMemory=16

as when I tried initially running it cor and cns were not being allocated memory and now I am hitting this error

-- Running jobs.  First attempt out of 2.
----------------------------------------
-- Starting 'cormhap' concurrent execution on Tue Nov 26 20:02:58 2024 with 1002.719 GB free disk space (297 processes; 2 concurrently)

    cd correction/1-overlapper
    ./mhap.sh 1 > ./mhap.000001.out 2>&1
    ./mhap.sh 2 > ./mhap.000002.out 2>&1

-- Finished on Sun Nov 24 05:37:06 2024 (60155 seconds) with 998.261 GB free disk space
----------------------------------------
--
-- Mhap overlap jobs failed, retry.
--   job correction/1-overlapper/results/000004.ovb FAILED.
--   job correction/1-overlapper/results/000005.ovb FAILED.

And then it runs a second time but then give us. Any help would be much appreciated

genome assembly canu

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updated 1.7 years ago by colindaven

• written 1.7 years ago by joshua.j.wright •

I'd use a pure linux machine for assembly. How much RAM do you have ? Also maybe try Flye, it is a one command assembly which is nice.

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written 1.7 years ago by colindaven

Thank you for the reply!

Unfortunately I don't have access to a full linux machine with enough RAM - I am currently working with about 180Gb though on this WSL.

I've just tried Flye and that too crashed out because of not enough memory.

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written 1.7 years ago by joshua.j.wright •

A 1.6g genome might need 800+ GB RAM with flye in my experience. Shasta, which is faster, might need similar or more.

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written 1.7 years ago by colindaven

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