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Hello!
I have a question about the hallmark gene count reported in the output files of virsorter2 using --include-groups "NCLDV". Are these marker genes only of NCLDV (MCP, pATPase, primase, TFIIS,…
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Hello Mike,
I'm using Cenote-Taker2 to discover viral elements in my samples. I'm really glad that there are lots of viral genes are identified but I have two questions and hope to have you suggest…
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Hi,
I am struggling to find where the taxonomic classification is output. The CONTIG_SUMMARY has an ORGANISM_NAME, but no taxonomy. Is one meant to trace the ORGANISM_NAME to the database to find …
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Hi there,
I'm looking to trial annotating putative viral contigs via DRAM-v and was wondering if there is a `--prep-for-dramv` setting whereby *all* filtering in VirSorter2 can be fully silenced (i…
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Dear WTP team,
Thanks for this excellent pipeline!
I played a bit with my dataset and I got 86 viral positive contigs. However, the output from checkV only found very few with viral gene. Is check…
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I just run the nextflow pipeline again using `v0.3.0` on the `~/.nextflow/assets/EBI-Metagenomics/emg-viral-pipeline/nextflow/test/kleiner_virome_2015.fasta` example data set.
Now, the pipeline on…
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# Error at the PlasmidID step : gff_to_bed.sh
Hi
I am trying to run viral recon pipeline with assembly enabled, and has been encountering an error at the PlasmidID step. it would be very help…
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Hi,
I have met a strange error when I used virsorter2. It is like this:
[2021-07-16 10:29 INFO] # of seqs < 5000 bp and removed: 0
[2021-07-16 10:29 INFO] # of circular seqs: 0
[2021-07-16 10:29…
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Hi,jiarong ,
This software helps me a lot when I try to find the virus sequence in the metagenomic data. I found the viruses were classified into three categories as you described in the paper, but I…
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**Version info**
- bcbio version (`bcbio_nextgen.py --version`): 1.2.8
- OS name and version (`lsb_release -ds`): ubuntu20.04 docker container
**To Reproduce**
Exact bcbio command you hav…