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Ecogenomics
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CheckM
Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes
https://ecogenomics.github.io/CheckM/
GNU General Public License v3.0
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ERROR: Models must be parsed before identifying HMM hits
#353
sapuizait
closed
1 year ago
1
checkm.hmm
#352
yangfangming
closed
1 year ago
2
QA failed not placed in tree - root
#351
raw937
closed
1 year ago
5
CheckM installation fails due to "incompatible with your system: - feature:/linux-64::__glibc==2.28=0"
#350
annaedlund
opened
2 years ago
4
SafetyError: The package for checkm-genome located at [anaconda3_path]/pkgs/checkm-genome-1.1.3-py_1 appears to be corrupted. The path 'site-packages/checkm/DATA_CONFIG'
#349
jolespin
closed
3 months ago
4
Different results between lineage_wf runs
#348
cifuj
closed
3 months ago
1
AttributeError: 'MarkerGeneFinder' object has no attribute '__processBin'
#347
rachelmugge
closed
1 year ago
3
IndexError: Indez out of range when trying to perform a QC on a single bin
#346
reymonera
closed
1 year ago
3
error with checkM test
#345
ysevel
closed
2 years ago
3
Completeness analysis by checkm
#344
ramnageena11
closed
2 years ago
2
Compatibility with Python 3.6
#343
misialq
closed
2 years ago
1
URL for reference data not working
#342
yakshiUPR
closed
2 years ago
2
pplacer never ends
#341
lucaz88
closed
2 years ago
2
The positions of marker genes are shown in the hundreds of bp
#340
Abelcanc3rhack3r
closed
2 years ago
1
Extrapolate USCG sequences from samples
#339
ereynebeau
closed
2 years ago
1
How to interpret the headers in the genes.faa file?
#338
Laura-Alex
closed
2 years ago
1
guppy: loadlocale.c:129
#337
SilasK
closed
2 years ago
2
UnicodeDecodeError: 'utf-8' codec can't decode byte 0x8b in position 1: invalid start byte
#336
lfenske-93
closed
1 year ago
2
checkm python compatibility (<v.3.7.12)
#335
wshropshire
closed
2 years ago
3
Convert "checkm.results" to a easier analysis table
#334
B-1991-ing
closed
2 years ago
4
Rename private class methods
#333
misialq
closed
2 years ago
3
AttributeError: 'Namespace' object has no attribute 'bCalledGenes'
#332
neelam19051
closed
2 years ago
11
avoid UnboundLocalError
#331
alienzj
closed
2 years ago
1
Compressed files
#330
lfenske-93
closed
2 years ago
8
Support table as input for checkm bins
#329
alienzj
closed
2 years ago
2
FileNotFoundError: [Errno 2] No such file or directory: '/home/.checkm/hmms/phylo.hmm'
#328
yazhinia
closed
2 years ago
1
Failed to process sequence file
#327
sapuizait
closed
2 years ago
2
Allow user to specify path to `DATA_CONFIG` file, for use with Singularity containers
#326
maxibor
closed
2 years ago
1
Coverage not matching contig names
#325
ttubb
closed
2 years ago
2
Problem in Roary output
#324
akanksha-r
closed
2 years ago
1
inverse_transformed deprecated
#323
Gr1m3y
closed
2 years ago
2
Fix prettytable.
#322
jjacobson95
closed
2 years ago
1
Installation Error_Compatibility to others
#321
ramnageena11
closed
2 years ago
6
Make the -f option output default and add flag options for positional arguments
#320
tarunaaggarwal
closed
2 years ago
1
checkm setRoot not working
#319
dzolier
closed
2 years ago
1
Contamination is not in precentage?
#318
ZeweiSong
closed
2 years ago
1
Sharing databases on a cluster and .dmanifest problem...
#317
geboro
closed
2 years ago
2
checkm --ali error
#316
vasudhajain29
closed
2 years ago
1
Unable to install
#315
adoloman
closed
2 years ago
0
Problem calculating quality
#314
alejandrorgijon
closed
2 years ago
6
fix stringent matching while searching for genomes
#313
lijierr
closed
2 years ago
2
Genome problem
#312
Biofarmer
closed
2 years ago
6
checkm error
#311
Caiyulu-818
closed
2 years ago
7
checkm
#310
Caiyulu-818
closed
3 years ago
0
Issue 3770
#309
howla1ke
closed
3 years ago
6
CheckM cannot set Root directory:
#308
howla1ke
closed
3 years ago
0
error while bin_refinement
#307
Caiyulu-818
closed
3 years ago
1
How to check CheckM database version?
#306
jolespin
closed
3 years ago
2
Is there a way to get taxonomy ranks from the `lineage.ms` file from `lineage_wf`?
#305
jolespin
closed
3 years ago
1
[Question] Does `checkm lineage_wf` use CPR_43 marker set for Patescibacteria?
#304
jolespin
closed
3 years ago
5
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