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Hi, I am running gtdbtk denovo_wf on my Metagenome Assembled Genomes (MAGs) and seems it can't read the taxonomy file from classify_wf. May I seek your opinion on this matter?
I have uploaded the …
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Hello,
I ran `GTDB-Tk v1.7.0` on 246 genomes using the command:
`gtdbtk classify_wf --genome_dir ${LOCAL}/Genomes/ --out_dir ${LOCAL}/GTDB_OUT --extension $binExtension --cpus $coreNum`,
but …
MrOlm updated
8 months ago
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## Expected Behavior
Starting from nr which was already downloaded, generate all of the required files to run mmseqs taxonomy to assign taxonomy to metagenome assembled genomes.
## Current Behavio…
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Thank you for developing this tool!
I'm interested in automating spiec-easi as part of a pipeline that takes a table containing the abundances of metagenome assembled genomes as input.
However, I ha…
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Hey thanks for this tool. I'm getting the following error during the `run_genespace` step.
```
############################
1. Running orthofinder (or parsing existing results)
Checking …
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This is the first time I've ever used the software. So I don't know what do these numbers in the "Contamination" column mean? For example, bin 6 , does that mean the contamination is 2154.89%? Why is …
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Dear developer,
I can run the dbCAN2 tool without any issue when not using the CGC finder. However, when I specify a gff file with the "-c" option, I got the following error:
********************…
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Hey @shenwei356 and @nick-youngblut
Thank you so much for writing the python scripts to convert taxonomy between NCBI and GTDB. It will save so much time as compared to redoing the analysis using …
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Hello I'm trying to search hydrocarbon-degrading-genes over my metagenome assembled genomes (MAGs) using a hmm profile.
I'm testing the profile of the genes (my_genes.hmm) with one of my built geno…
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Hi,
I would like to align the list of metagenome-assembled genomes to merged-metatranscriptomics libraries. Please suggest a reasonable command to run MetaGT? I tried the following, but it complains…