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Hi Donovan,
I am trying to filter scaffolds following the methods presented on your paper (Parks DH et al. 2017. Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree…
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Hi,
I used dada2 for longer read than usual 300bp. The overlap of forward and reverse primers produces 444bp reads. So, my ASV length is 444bp. Usually i got 4000 to 5000 ASVs for 300bp length. Ho…
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I'm new to both dada2 and decontam, and am planning to implement a pipeline using both of these within my lab.
I followed the dada2 pipeline tutorial (1.4) through the creation of a phyloseq object…
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Hi,
I'm running refinem scaffold_stats and I'm getting this error:
```
ktImportText is not on the system path.
Controlled exit resulting from an unrecoverable error or warning.
```
I g…
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Can we modify the gather output to separate matches into columns based on taxonomic rank? It's sometimes difficult to do this at the command line when the species or strain id spans multiple fields. F…
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### Summary
- What does this package do? (explain in 50 words or less):
Parse and serialize Ecological Metadata Language ('EML') files into S4 objects.
- Paste the full DESCRIPTION file insid…
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Hi Donovan,
I am trying to use RefineM on my Server. It worked fine until the process
"Removing contamination based on taxonomic assignments", When I reach the process ">refinem taxon_profile -c 40…
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When I run gtdbtk classify_wf, it error message below:
```
[2018-03-07 10:42:06] INFO: GTDB-Tk v0.0.3
[2018-03-07 10:42:06] INFO: gtdbtk classify_wf --genome_dir ./test1/ --out_dir gtdbtk_outdir -x…
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Log info is as follows:
[2018-02-01 14:48:24] INFO: RefineM v0.0.22
[2018-02-01 14:48:24] INFO: refinem taxon_profile -c 10 predict_genes/ scaffolds_stats/scaffold_stats.tsv /share/home/test001/sdh/…
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We have had a few occasions where it would be useful to add [`ceterms:instructionalProgramType`](http://credreg.net/ctdl/terms/instructionalProgramType) to `ceterms:Credential` and its subclasses.
…