bgcflow
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NBChub
Snakemake workflow for the analysis of biosynthetic gene clusters across large collections of genomes (pangenomes)
Hi I'd like to inquire if bgcflow allows for the analysis of a specific region within a contig. For instance, I'm interested in examining the sequence NT_187580.1, spanning positions 169942...
I think it would be valuable to create a phylogenetic tree sub workflow. 1. autoMLST-based tree 2. GTDB tree using [de_novo_wf](https://ecogenomics.github.io/GTDBTk/commands/de_novo_wf.html) 3. Roary core genome alignment tree Perhaps we can...
This will be a neat feature for running bgcflow in a shared environments
I am creating an issue to list any feedback we get on improving documentation here. - [x] Provide warning and guide to install gcc. Many machine don't have gcc installed...
Use this approach to speed up emapper in large batch: https://github.com/eggnogdb/eggnog-mapper/wiki/eggNOG-mapper-v2.1.5-to-v2.1.12#user-content-Setting_up_large_annotation_jobs
Hi @ChMaWh, here is the first draft of `defense-finder` subworkflow: ## Usage: 1. Create a conda environment and install the [`BGCFlow` python wrapper](https://github.com/NBChub/bgcflow_wrapper) : ```bash # create and activate a...
It seems the latest python release cause error when reading the config resources, pinning the python to 3.11 fix the issue ``` DEBUG 05/10 10:32:05 Starting new HTTP connection (1):...
This common error was also found in BGC workflow when the list of BGCs in the sample set it too high. `/datadrive/bgcflow/.snakemake/shell_tmp.iz1795my/script.sh: line 10: /datadrive/bgcflow/.snakemake/conda/c2ac5875f1b6f2374bfd4dbe39acdefe_/bin/python: Argument list too long `...
Using pandas 2,1,0 and above cause this unnecessary warning: ```python /data/a/matinnu/bgcflow/workflow/rules/common.smk:369: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value...
``` run_status is now FEATURES_EXTRACTED Building GCF models... Dumping in-memory database content into /datadrive/data2/bgcflow/data/processed/strepto_combine/bigslice/cluster_as_6.1.1/result/data.db... Traceback (most recent call last): File "/datadrive/data2/bgcflow/.snakemake/conda/c53188cf74abfdc284d24b807d803856_/bin/bigslice", line 1828, in main clustering = BirchClustering.run( ^^^^^^^^^^^^^^^^^^^^ File...