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KIT-IBG-5
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mdmcleaner
MDMcleaner the assessment, classification and refinement tool for microbial dark matter SAGs and MAGs
GNU General Public License v3.0
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UnboundLocalError 'prodigal_proc'
#56
AviHuene
closed
1 year ago
1
An error occured during blastp run with query '-'
#55
rzhan186
opened
1 year ago
3
Error when checking dependencies in mdmcleaner makedb
#54
danpal96
opened
1 year ago
3
Use utf8 encoding for `get_external_dependency_version_string`.
#53
JuliaMuench
opened
1 year ago
0
Error in database downloading
#52
uzun-masha
opened
1 year ago
0
failure to make reference database
#51
Yunliang81
closed
1 year ago
3
provide latest constructed database
#50
kingtom2016
closed
1 year ago
2
Raise custom error if a directory which should be created is already a…
#49
did10
closed
1 year ago
0
Remove duplicated mdmcleaner py
#48
did10
closed
1 year ago
0
Remove duplicated mdmcleaner.py
#47
did10
closed
1 year ago
0
inconsistency in cleaner logs
#46
did10
closed
1 year ago
2
Use argparse error system to display makedb user input error
#45
did10
closed
1 year ago
0
Use argparse error system to display user input error
#44
did10
closed
1 year ago
0
enhancement add short help for refdb
#43
did10
closed
1 year ago
3
Potential unintended behavior while directory checking and creating
#42
did10
closed
1 year ago
3
Force list return even when no BLAST job to run
#41
cpauvert
closed
1 year ago
1
TypeError in clean.py prevent MDMcleaner to exit gracefully when no blast jobs should be run
#40
cpauvert
closed
1 year ago
2
error with -M argument in "get_markers" workflow
#39
jvollme
closed
2 years ago
0
KeyError: 'Bacteria'
#38
chassenr
opened
2 years ago
4
ERROR: evaluation result not accounted for: 'silva_conflict'
#37
chassenr
closed
1 year ago
4
Threshold for contamination/completeness
#35
michoug
closed
2 years ago
1
Contamination percent calculation
#34
aelbehery
closed
2 years ago
1
silva url
#33
aelbehery
closed
2 years ago
6
release tag 0.8.3 miss cutofftable_combined.tsv
#32
EricDeveaud
closed
2 years ago
1
Extracting the 'trustworthiness' score for an overall genome classification from the output files
#31
cpauvert
closed
2 years ago
2
"AttributeError: 'bindata' object has no attribute 'consensus_tax'" if NO contig yields ANY blast results
#30
jvollme
closed
2 years ago
1
highly contaminated bins should get a warning not to use filtered data even after cleaning
#29
jvollme
opened
2 years ago
1
t-rna based completeness estimations should not be returned for eukaryotic bins
#28
jvollme
opened
2 years ago
0
better error messages2
#27
jvollme
closed
2 years ago
0
better error messages
#26
jvollme
closed
2 years ago
0
adjust dependencies
#25
jvollme
closed
2 years ago
2
add a positive list for referencedb-ambiguities to speed things up
#24
jvollme
opened
2 years ago
0
Add trna-based completeness estimations to output table
#23
jvollme
closed
2 years ago
0
problem with set_configs
#22
jvollme
closed
2 years ago
0
dereplicate proteins on genus level to reduce database size
#21
jvollme
opened
2 years ago
0
incorporate minHash
#20
jvollme
opened
2 years ago
0
When workflows are aborted and then recontinued later, check that the database used is still the same...
#19
jvollme
opened
2 years ago
0
"refdb_contams" workflow exits with error if outputblacklist does not already exist
#18
jvollme
closed
2 years ago
1
review_refdb_contams shuld be run for each MAG/SAG during original contigs classifications...
#17
jvollme
closed
2 years ago
0
review_refdbcontams needs to delete intermediate blast files when done
#16
jvollme
closed
2 years ago
0
instead of ncbi nr database, use MGnify in combination with RefSeq as reference db for ncbi-like taxonomy
#15
jvollme
closed
2 years ago
1
implement lock-files
#14
jvollme
opened
2 years ago
0
automatically repeat failed attempts to (re-)download data during db-building
#13
jvollme
closed
2 years ago
0
improve config file
#12
jvollme
closed
2 years ago
0
add functions to extract reference sequences from reference dbs
#11
jvollme
opened
2 years ago
2
check for all dependencies before running pipeline
#10
jvollme
closed
2 years ago
0
add workflow for evaluating potential refDB-contaminations
#9
jvollme
closed
2 years ago
0
add optional blacklist file to repository and add blacklist file location to config file
#8
jvollme
closed
2 years ago
0
add release to pip and conda
#7
jvollme
closed
2 years ago
0
Correct, Complete and improve all docstrings. Add documentation to "readthedocs"
#6
jvollme
opened
2 years ago
0
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