Ecogenomics CheckM issues

Ecogenomics / 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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issues

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bioconda release broken due to setuptools not being shipped with python 3.12 anymore

#403 njohner opened 2 months ago
0
OSError: AF_UNIX path too long

#402 yqy6611 opened 2 months ago
1
checkm coverage NameError

#401 mv-mendes opened 2 months ago
0
CheckM failing at pplacer step

#400 priscalim00 closed 2 months ago
6
question about definition in # contigs column in ouput produced in Chdb.tsv file

#399 alicia-hgim opened 3 months ago
0
updated taxonomic data for marker sets?

#398 george-coulouris closed 3 months ago
6
ValueError: malformed node or string on line 1: <ast.Call object at 0x71dfb527dfd0>

#397 yqy6611 closed 3 months ago
4
np.float64 in binstats output causes ast error (fix included)

#396 george-coulouris closed 3 months ago
3
fail to run if AF_UNIX path is > 108 characters -

#395 handibles closed 3 months ago
1
For a specific bin, why is the Marker lineage in lineage.ms different with it in quality report?

#394 liuyun313 opened 6 months ago
0
No space left on device error in HMM step not caught

#393 boasvdp closed 3 months ago
2
question：Anaconda ——conda install pytorch==1.10.1 torchvision==0.11.2 torchaudio==0.10.1 cudatoolkit=11.3 -c pytorch -c conda-forge

#392 Sunflower-212 closed 6 months ago
0
Unexpected error: <class 'FileNotFoundError'>

#391 zzzzzoeyy closed 3 months ago
1
Having trouble running CheckM: Models must be parsed before identifying HMM hits.

#390 kritical1326 closed 6 months ago
0
Make sure pplacer is on your system path.

#389 apjim0527 closed 7 months ago
1
Having trouble interpreting the meaning of "root" as a marker lineage

#388 jackieway closed 3 months ago
1
NameError: free variable 'mask' referenced before assignment in enclosing scope

#387 kstagaman opened 8 months ago
0
checkm_coverage dropped some bins

#386 emilyjunkins opened 8 months ago
0
Fatal exception (source file p7_hmmfile.c, line 2095): hmm write failed. system error: No space left on device

#385 samuelmontgomery closed 8 months ago
2
checkm ssu_finder

#384 mehmetdayi closed 3 months ago
2
'utf-8' codec can't decode byte 0xb0 in position 37: invalid start byte

#383 tmossington closed 11 months ago
1
local variable 'seqId' referenced before assignment

#382 bheimbu closed 11 months ago
0
WARNING: Expected all files to contain sequences in amino acid space.

#381 mehmetday closed 1 year ago
1
maximum number of genomes/MAGs to run checkm

#380 sapuizait closed 1 year ago
2
Chekm test: line 1: 16491 Bus error (core dumped) pplacer -j 1

#379 98jay closed 3 months ago
2
FileNotFoundError: [Errno 2] No such file or directory: '/home/majorram/anaconda3/envs/checkm/hmms/phylo.hmm'

#378 ramnageena11 closed 3 months ago
3
Unexpected error: <class 'KeyError'>

#377 gracedai23 opened 1 year ago
0
added the dockerfile for checkm

#376 Louis-MG opened 1 year ago
0
ERROR conda.core.link:_execute(952): An error occurred while installing package 'bioconda::checkm-genome-1.2.2-pyhdfd78af_1'.

#375 RoyaRahmani closed 3 months ago
2
Understanding contamination value

#374 stephane-wang closed 1 year ago
2
IndexError: list index out of range

#373 sandipandrils closed 3 months ago
1
FileNotFoundError: [Errno 2] No such file or directory: 'checkm_folder/storage/tree/concatenated.tre'

#372 spitfiredd opened 1 year ago
9
don't find Strain heterogeneity info

#371 nashanghenzan closed 1 year ago
0
Reference data is missing

#370 tiagocabralborelli closed 3 months ago
1
Customizing CheckM Dataset & Gene Marker Selection for a Species

#369 Leytoncito opened 1 year ago
0
bin_qa_plot

#368 Anna-pro closed 3 months ago
1
AttributeError: 'Namespace' when running 'checkm coverage'

#367 Rene-Hoover closed 1 year ago
1
Placing 3 bins into the genome tree with pplacer Killed

#366 iquasere closed 1 year ago
4
Unexpected error: <class 'RecursionError'>

#365 MingyueCheng closed 3 months ago
2
FileNotFoundError for concatenated.tre file?

#364 sams898 closed 1 year ago
1
Is there a possibility to have the distance between the putative genome and the closest reference genome?

#363 dgrissa closed 3 months ago
1
Checkm data still available?

#362 standage closed 1 year ago
7
checkm coverage issue

#361 confusedWXX opened 1 year ago
0
checkm lineage_wf ------ BrokenPipeError: [Errno 32] Broken pipe

#360 PeterCx closed 1 year ago
2
Are bin_compare and bin_qa_plot functions still working?

#359 snehamurthy21 opened 1 year ago
4
ssu_finder

#358 joao1980 opened 1 year ago
1
Uncaught exception: Multiprocessing.Child_error

#357 zoubohao closed 1 year ago
3
No bins found. Check the extension (-x) used to identify bins.

#356 qussai96 closed 1 year ago
1
The effect of non-prokaryotes sequence

#355 neptuneyt closed 3 months ago
2
Support gzipped proteins as input

#354 alienzj closed 1 year ago
2