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HI, I have followed the update documentation but I am having trouble running CAMISAM.
Running the docker command says the mini.biom file is not available. I try entering the docker container using…
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Currently, in MATAM_V1.5.2, the following filter is applied on RDP results:
when the RDP confidence threshold (at genus level) is under a threshold of 0.8, then tag all taxonomic nodes as "unclassifi…
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Hi there,
Running spades on an HPC and am getting the following error in ca. 1min after the submission:
```
[user@sl2 metaspades_assembly]$ cat bench.out.28552
Command line: /opt/SPAdes-3.13.0-Li…
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Currently, InSilicoSeq treats a draft genome assembly (having more than one contig) as a separate organism belonging to each contig (fasta record). Most bacterial genome assemblies contain more than …
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Hello,
Firstly, thank you for a fantastic tool - it has worked very well so far, however I have run into some problems for a couple of our larger metagenomes.
I ran the Canu 1.8 command (see be…
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During assembly of a low-quality old (2012) dataset:
input: 4 FASTQ files available from the SRA:
```
SRR497965
SRR497966
SRR497967
SRR497968
```
end of log:
```
[2018-01-05 14:29:03] I…
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Hi!
Is anyone running the rc.1 version of prodigal 3 successfully on metagenomes?
It works fine for me on isolates (first training and then normal mode).
But when I run it on fasta file containin…
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Hi,
I am trying to run CAMISIM, in order to verify the tool works on my computer, I tried the two demo files mini.biom and mini_config.ini, using
> python metagenome_from_profile.py -p defaults…
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I'm using Diamond for classifying metagenome contigs (HiSeq/MetaSpades) against NR using a high memory server, and it works great! This workflow is so much easier than it used to be thanks to recent u…
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When running the taxonomy.sh (after making changes to get it fully running), I found that the `mmseqs convertkb` generates millions "Could not find accession" warnings. Should this be expected? I'm gu…