Question: Canu assembler : meryl failed after 2 attempts
0
gravatar for Roxane Boyer
16 months ago by
Roxane Boyer430
France/Marseille/IBDM
Roxane Boyer430 wrote:

Hi everyone,

This is my first time using Canu assembler. I have PacBio reads in a fastq format, and here some informations about : -computer : 32 CPUs and 126 gigabytes of memory -java environment : Java(TM) Runtime Environment '1.8.0_91

I'm trying to make an assembly of a Drosophila genome : D. suzukii (Yes I did a little misstake in the output directory but it's not a big deal)

I tried the folowing command :

perl canu -assemble -p susuzkii_canu -d /media/loutre/DATAPART1/Documents/suzukii_assembly/canu_assembly genomeSize=150000000 -pacbio-raw /media/loutre/DATAPART1/Documents/suzukii_assembly/pacbio_reads/filtered_subreads.fastq

At first sight, it seems to work well, but after a while, I got this error :

*meryl failed.
Don't panic, but a mostly harmless error occurred and canu failed.
canu failed with 'failed to generate mer counts.  Made 2 attempts, jobs still failed'.*

I can't figure out what's wrong... Any ideas ? Thanks for your help !

Cheers,

Roxane

assembly software error • 683 views
ADD COMMENTlink modified 16 months ago by genomax37k • written 16 months ago by Roxane Boyer430

I finnaly found out whats was wrong.

By default, Canu is doing first a correction step, then a trimming.

By specifying the -assemble option, I just passed theses two previous steps, and this what should have caused the mistake.

So I tried : perl canu -p susuzkii_canu -d /media/loutre/DATAPART1/Documents/suzukii_assembly/canu_assembly genomeSize=150000000 -pacbio-raw /media/loutre/DATAPART1/Documents/suzukii_assembly/pacbio_reads/filtered_subreads.fastq

Now I'm waiting but it should work.

ADD REPLYlink modified 16 months ago by genomax37k • written 16 months ago by Roxane Boyer430

Well, finally that wasn't the problem, so the post is still open

ADD REPLYlink written 16 months ago by Roxane Boyer430
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