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Hi,
I am trying to integrate `refinem` in an automated pipeline for assembly/binning of metagenomes. The pipeline in question would be run at various locations and therefore needs to include a down…
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Running ```./canu/Linux-amd64/bin/canu -p metagenome -d /scratch/metagenome_folder genomeSize=1g -nanopore-raw metagenome_folder/metagenome.fastq```, I'm getting a Error 7 as follows:
```-- Startin…
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hello, I have been looking into the contigs output by megahit and the resulting FASTG file (#20), and I noticed that in metagenomes with lots of strain variation, the FASTG file is for small k=27 is a…
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Hi there,
my canu process is stopping after cormhap. I restart the job, but the same error appeared.
Can't figure out what the problem is. Any help, please?
canu -p ONTassembly -d $WDR -fast -…
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The -fast option mentioned in the [version 1.8 release notes](https://github.com/marbl/canu/releases/tag/v1.8) does not appear to be documented in the QuickStart, FAQ or Tutorial, and does not appear …
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I'm running a metagenome assembly on a virtual machine with 96 cores, 360 GB RAM. We accidentally installed the latest commit of canu, commit
https://github.com/marbl/canu/commit/a50e26a75ffccc529bd…
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I've been running a pacbio-illumina hybrid assembly for a complex metagenome with the latest metaspades 3.12. This is a very complex dataset, and includes 800k pacbio reads totalling ~6.1 GB. The Illu…
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I'm using `quast 5.0.0 py27pl526ha92aebf_1 bioconda`
I get the following error when running `metaquast.py` on my metagenome:
```
ValueError: invalid literal for int() with base 10: '476978:…
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An assembled genome with about 2,000,000 bp was annotated with prokka. If one gene is ~1,000 bp, then it would be expected to return 2,000 genes. Yet my .faa file has ~4,000 genes in them.
It looks …
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Hi,
I tried to assemble a metagenome from simplified microbial community with canu v1.7 on a slurm cluster :
`canu -p canu-contig2 -d canu-metagenome2 genomeSize=0.4m corOutCoverage=all corMhapS…
jaube updated
6 years ago