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Hi,
I try to use DRAM-v.py, but the output of DRAM-v.py distill only contains following files:
`amg_summary.tsv distill.log product.html vMAG_stats.tsv `
The `viral_genome_summary.tsv` and …
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Hi,
I have been running DRAM on some small assembled genomes (2Megabytes) and the computing time when using Uniref is getting really high. It has already been running for more than 24 hours on a cl…
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Step 5b fails when attempting to index fasq files. Full traceback:
Traceback (most recent call last):
File "/Users/xxxx/mambaforge/envs/metacerberus/bin/metacerberus.py", line 693, in
sys…
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Hi developers!
Thanks for your contribution to the study field of viral ecology!
Recently, I used the PHAMB tool to identify viral bins from my bulk metagenomes, and I had some questions about the o…
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Hi,
I used geNomad to identify viruses in addition to VirSorter2 and Cenote-taker2. Subsequently, I used geNomad's annotate module to assign taxonomy to all viral contigs, including those identifie…
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Hi Josh,
During viral binning, I am getting this error "ERROR: Paired-end reads were detected in single-end read library" at the featurecounts step. How do I indicate that there are paired-end read…
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Hi,
I have downloaded and built the kraken2 database with `kraken2-build --download-taxonomy`, as follows
```
kraken2-build --db krakendb --download-library bacteria
kraken2-build --db krak…
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## Expected Behavior
Out put a correct(common) gff file like here https://m.ensembl.org/info/website/upload/gff3.html.
## Current Behavior
1) The 2nd column of gff file is annotation source, and …
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Thank you for upgrading the VAMB tool.
I am keen on using phamb for viral binning. I am curious whether AAMB (z+y) can enhance vMAGs as well. As CheckM2 performs well with prokaryotes, I am unsure …
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Hi,
I don't know if I made some mistake or if we cannot select only "vae" in AVAMB snakemake pipeline.
My main goal is to get viral bins using phamb from output of VAMB.
So I used AVAMB 4.1.…