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Hi
I am getting the following error when vamb is loading RPKM from a jgi depths file. Can you please let me know what the issue is?
(/pylon5/cc5piap/arghyam/vamb) [arghyam@login018 megahit-all-an…
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I can't make any sense of this error in the "predict_genes_genomes" rule. Any ideas?
Running on a linux cluster. Thanks!
Executing: snakemake --snakefile /stor/work/Ochman/sean/projects/atlas-tuto…
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Hi,
I was wondering if it's possible to add new genomes to the kodoja_db bypassing the ncbi download everytime.
Let me explain:
I already have my kodoja_db/ folder built and functional with virus…
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Hi there,
I am trying to run SNPgenie to calculate nucleotide diversity on my VCF file from a virus population study. SNPgenie has the following requirement for VCF 4 files;
"FORMAT (4): --v…
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Dear Authors,
I used Ragout on some viral genome and the analysis was very successful. However I can not use Ragout on all the viruses I usually work with because the minimum sequence size to be co…
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We are seeing a large number of virus genomes with a single protein. This appears to be a misannotation in the NCBI database. For example, Bovine mastadenovirus C is listed as a virus genome with ac…
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'Desktop/a.bib' does not appear to be a file, so autocomplete-bibtex will not try to parse it.
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This is not a network issue - Python 3 is working fine, but a download on Python 2.7 is failing:
(*updated*) - Initially thought it was failing in the call to ``ncbi-genome-download``
https://tr…
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Hi,
Is it possible to create a database containing the completely assembled and annotated reference genomes of Archaea, Bacteria, and viruses from the NCBI RefSeq database, as well as fungal RefSe…
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Hi,
using v6.1-master here
I got this error while trying to summarize a collection of viruses (after running the classic HMMs program):
```
anvi-summarize -c CONTIGS.db -p PROFILE/PROFILE.db…