mdmcleaner
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KIT-IBG-5
MDMcleaner the assessment, classification and refinement tool for microbial dark matter SAGs and MAGs
Dear mdmcleaner developers, I experienced a blastp error during `mdmclean clean`, which resulted in a `runtime error`. Could you have me troubleshoot please? I was running mdmcleaner in a compute...
Installation with conda: python=3.11.3 mdmcleaner=0.8.7 I got the next error when running `mdmcleaner makedb ` ``` You are running the following MDMcleaner command: '/mnt/extra/home/danielpalma/mambaforge/envs/mdmcleaner/bin/mdmcleaner makedb -o mdmcleaner' reading settings from...
Hi, I have been running MDMcleaner on 2 different bin sets. In one run, not all bins were processed without error (see #37). Using the same reference data, I am...
For compatibility with non-ascii version strings (e.g. non-english system language).
Hi! I'm trying to download database using mdmcleaner makedb, and I've got an error like this: 01a: download GTDB data-- Now downloading from gtdb: "gtdb_taxfiles" (attempt 1)... Now downloading from...
mdmcleaner is NOT designed to rescue terrible bins. It is only meant to validate good quality and to make good bins better! This needs to be reflected in the results,...
currently the output tables are a bit convoluted and not user friendly. Instead of outputing the infos "as is", digest them a bit more to be better readable
a positive list, containing the exact version of the reference -DB used along with all entires that were preiously assessed as "not contaminations" based on that database should be included...
- [x] add function to extract nucleotide references from blast-dbs - [ ] ~~add function to extract protein references from diamond dbs~~ use blast-DBs for diamond also - [ ]...