KIT-IBG-5/mdmcleaner issues and pull requests

#56 - UnboundLocalError 'prodigal_proc'

Issue - State: closed - Opened by AviHuene about 1 year ago - 1 comment

#55 - An error occured during blastp run with query '-'

Issue - State: open - Opened by rzhan186 over 1 year ago - 3 comments

#54 - Error when checking dependencies in mdmcleaner makedb

Issue - State: open - Opened by danpal96 over 1 year ago - 3 comments

#53 - Use utf8 encoding for `get_external_dependency_version_string`.

Pull Request - State: open - Opened by JuliaMuench over 1 year ago

#52 - Error in database downloading

Issue - State: open - Opened by uzun-masha over 1 year ago

#51 - failure to make reference database

Issue - State: closed - Opened by Yunliang81 almost 2 years ago - 3 comments

#50 - provide latest constructed database

Issue - State: closed - Opened by kingtom2016 almost 2 years ago - 2 comments
Labels: enhancement

#49 - Raise custom error if a directory which should be created is already a…

Pull Request - State: closed - Opened by did10 almost 2 years ago

#48 - Remove duplicated mdmcleaner py

Pull Request - State: closed - Opened by did10 almost 2 years ago

#47 - Remove duplicated mdmcleaner.py

Issue - State: closed - Opened by did10 almost 2 years ago

#46 - inconsistency in cleaner logs

Issue - State: closed - Opened by did10 almost 2 years ago - 2 comments

#45 - Use argparse error system to display makedb user input error

Pull Request - State: closed - Opened by did10 almost 2 years ago

#44 - Use argparse error system to display user input error

Pull Request - State: closed - Opened by did10 almost 2 years ago

#43 - enhancement add short help for refdb

Issue - State: closed - Opened by did10 almost 2 years ago - 3 comments
Labels: documentation, enhancement

#42 - Potential unintended behavior while directory checking and creating

Issue - State: closed - Opened by did10 almost 2 years ago - 3 comments
Labels: bug

#41 - Force list return even when no BLAST job to run

Pull Request - State: closed - Opened by cpauvert about 2 years ago - 1 comment

#40 - TypeError in clean.py prevent MDMcleaner to exit gracefully when no blast jobs should be run

Issue - State: closed - Opened by cpauvert about 2 years ago - 2 comments
Labels: bug

#39 - error with -M argument in "get_markers" workflow

Issue - State: closed - Opened by jvollme about 2 years ago

#38 - KeyError: 'Bacteria'

Issue - State: open - Opened by chassenr about 2 years ago - 4 comments

#37 - ERROR: evaluation result not accounted for: 'silva_conflict'

Issue - State: closed - Opened by chassenr about 2 years ago - 4 comments
Labels: bug

#35 - Threshold for contamination/completeness

Issue - State: closed - Opened by michoug about 2 years ago - 1 comment

#34 - Contamination percent calculation

Issue - State: closed - Opened by aelbehery about 2 years ago - 1 comment

#33 - silva url

Issue - State: closed - Opened by aelbehery about 2 years ago - 6 comments
Labels: enhancement

#32 - release tag 0.8.3 miss cutofftable_combined.tsv

Issue - State: closed - Opened by EricDeveaud about 2 years ago - 1 comment

#31 - Extracting the 'trustworthiness' score for an overall genome classification from the output files

Issue - State: closed - Opened by cpauvert over 2 years ago - 2 comments

#30 - "AttributeError: 'bindata' object has no attribute 'consensus_tax'" if NO contig yields ANY blast results

Issue - State: closed - Opened by jvollme over 2 years ago - 1 comment
Labels: bug, enhancement

#29 - highly contaminated bins should get a warning not to use filtered data even after cleaning

Issue - State: open - Opened by jvollme over 2 years ago - 1 comment
Labels: documentation, enhancement

#28 - t-rna based completeness estimations should not be returned for eukaryotic bins

Issue - State: open - Opened by jvollme over 2 years ago
Labels: bug

#27 - better error messages2

Issue - State: closed - Opened by jvollme over 2 years ago

#26 - better error messages

Issue - State: closed - Opened by jvollme over 2 years ago
Labels: enhancement

#25 - adjust dependencies

Issue - State: closed - Opened by jvollme over 2 years ago - 2 comments
Labels: bug

#24 - add a positive list for referencedb-ambiguities to speed things up

Issue - State: open - Opened by jvollme over 2 years ago
Labels: enhancement

#23 - Add trna-based completeness estimations to output table

Issue - State: closed - Opened by jvollme over 2 years ago
Labels: enhancement

#22 - problem with set_configs

Issue - State: closed - Opened by jvollme over 2 years ago
Labels: bug

#21 - dereplicate proteins on genus level to reduce database size

Issue - State: open - Opened by jvollme over 2 years ago

#20 - incorporate minHash

Issue - State: open - Opened by jvollme over 2 years ago

#19 - When workflows are aborted and then recontinued later, check that the database used is still the same...

Issue - State: open - Opened by jvollme over 2 years ago
Labels: bug, enhancement

#18 - "refdb_contams" workflow exits with error if outputblacklist does not already exist

Issue - State: closed - Opened by jvollme over 2 years ago - 1 comment
Labels: bug

#17 - review_refdb_contams shuld be run for each MAG/SAG during original contigs classifications...

Issue - State: closed - Opened by jvollme over 2 years ago
Labels: enhancement

#16 - review_refdbcontams needs to delete intermediate blast files when done

Issue - State: closed - Opened by jvollme over 2 years ago
Labels: bug, enhancement

#15 - instead of ncbi nr database, use MGnify in combination with RefSeq as reference db for ncbi-like taxonomy

Issue - State: closed - Opened by jvollme almost 3 years ago - 1 comment
Labels: enhancement, wontfix