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Hello,
I saw that pyrodigal can use different translation tables (issue #34), which is great!
Do you know if pyrodigal can correctly identify selenocysteine insertions? (And pyrrolysine too)
I …
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* pharokka version 1.7.3
* Python version 3.9.16
* Operating System debian 11
### Description
Dear George,
i have an issue with mmseqs:
pharokka.py \
-i /home/yana/download/Escherichia_phag…
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Hi,
I am trying to run the cat bins command with the pre-constructed database.
The available preconstructed database is build with diamond 2.0.6 which is not compatible with the cat 5.2.3 (dependenc…
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Hello, when I run gutsmash,I got these file in my output:
genome.gbk genome.json genome.zip css images index.html js regions.js svg
How do I know if there is an MGC in this genome in the o…
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Hello author,
Does your model support secondary development? If I want to make changes in your code, how should I retrain the model and what commands should I use to run the code?
Looking forward t…
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Hi,
I am using circlator in conda. When I run progcheck I get:
Circlator version: 1.5.5
External dependencies:
bwa 0.7.17 /Users/laura/miniconda3/envs/sanger/bin/bwa
WARNING: Didn't find ca…
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right now, the `fromfile` format doesn't support a simple way to produce translated sequence - presumably we'd need to add a CDS column or something, or else build workflows (elsewhere) to do prodigal…
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Hi.
I am encountering this problem: "RuntimeError: diamond failed to run: version -> Error: Option is not permitted for this workflow: threads". The following is my order: "python3 run_gutsmash.py …
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Hi Bastiaan,
I had a large contig file with many host sequences, which I removed using bbtools sketch, followed by parsing in R to generate a contig fasta (using the package Biostrings).
I then …
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Hello,
I'm using annotation program for the first time so I'm sorry if my question is obvious.
I have contig file with plasmid and .gb file with reference(--proteins). Not every CDS feature has ge…