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When running the latest canu (built 20170206) it will not progress past canu1. I get canu.01.out claiming that it finished but there are no other .sh scripts, not outputs, not files created, no 'corre…
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I'm trying to figure out parameters via slurm to use multiple nodes for a canu assembly. I have invoked canu with or without slurm I get the same message regarding available threads. The grid has 57 n…
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I am assembling an heterogeneous sample (pool of sexually reproducing insects) using the latest version of canu. Raw coverage was 80X (avg length 7.2kb) that reduces to 26X after correction using canu…
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Hello -
I am trying to assemble a 2.8 Gbps tetraploid legume genome that has 25X PacBio data.
Looks like it crashed when finishing the following command,
/sw/compbio/canu/canu/Linux-amd64/bin/ovSt…
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Hi,
I run this command lines
```
module load bioinfo/Java8
/work/project/amaizing/bin/canu/Linux-amd64/bin/canu -s /work/project/amaizing/PacBio_FV2/canu.spec
-p F2PacBio1 -d F2PacBio1 genom…
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Hi
I am having what appears to be the same problem as in this post:
https://github.com/marbl/canu/issues/136. We are trying to assemble a 1.2 GB genome with ~66x PacBio coverage and are using Canu v…
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Hi Everyone,
I have been struggling with lsf system for 1 week to make it run Canu successfully but unfortunately I have not got any progress yet.
Please have a look at output below I will paste my…
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I've been using Mash with great success with plant read data, but I'm running into one weirdness. Some of my cultivars cluster in a way they shouldn't and I believe this is due to chloroplast differen…
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We are trying to increase our genomesize but the job fails saying 'Task bat can't run on any available machines.'. I have tried to use a size over 4gb on a single node with usegrid=false and I get th…
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I use stopBefore=correction, but canu says
ERROR: Invalid stopBefore specified (correction); must be one of:
ERROR: 'gatekeeper'
ERROR: 'meryl'
ERROR: 'trimReads'
ERROR: 'spl…