CheckM

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Different results between lineage_wf runs

1

Hi @dparks1134, I have an issue with `checkm lineage_wf `. I have a set of bins that are annotated differently when I run them together or separately. I am using...

cifuj

UnicodeDecodeError: 'utf-8' codec can't decode byte 0x8b in position 1: invalid start byte

2

Hi, I'm trying to run checkm in the latest version, but it doesn't work. The commands are the same as I used before, however I get with: ` checkm lineage_wf...

lfenske-93

AttributeError: 'MarkerGeneFinder' object has no attribute '__processBin'

2

Hello, I am attempting to run CheckM after a successful install, but when I ran this command: `checkm lineage_wf -t 1 -x .fa --reduced_tree /Volumes/FireFly_Promise_Pegasus/RMugge/DISSERTATION/Ch3/Metagenome_Microcosm2.0/pipeline_3_assemblybased/09_das_tool/output/B001_DASTool_bins /Volumes/FireFly_Promise_Pegasus/RMugge/DISSERTATION/Ch3/Metagenome_Microcosm2.0/pipeline_3_assemblybased/10_checkM` It produced these errors:...

rachelmugge

IndexError: Indez out of range when trying to perform a QC on a single bin

2

Hi! After executing `$ checkm lineage_wf -t 4 -x fa bins.1.fa checkm/` I'm encountering this error: ``` [2022-07-14 00:46:22] INFO: CheckM v1.2.0 [2022-07-14 00:46:22] INFO: checkm lineage_wf -t 4 -x...

reymonera

CheckM installation fails due to "incompatible with your system: - feature:/linux-64::__glibc==2.28=0"

4

Hello, I am trying to install checkM using 'conda install -c bioconda/label/cf201901 checkm-genome' however the installation fails as I get the error message shown below. Any input on how to...

annaedlund

checkm.hmm

2

I have an issue with "checkm.hmm". I noticed that there are some phage-related HMMs in "checkm.hmm" file. If possible, how can I get the bacterial or archaea HMMs only? Thanks!...

yangfangming

QA failed not placed in tree - root

5

Good evening, I have a single circular contig from a cyanobacteria. When I run the standard: `checkm lineage_wf -t 36 -x fasta -f genome_checkm.tab --tab_table /data/folder /data/folder/checkm` I get no...

raw937

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'

2

Is there any insight on what causes the SafetyError for bioconda's CheckM v1.1.3? ``` (base) [jespinoz@exp-15-32 test]$ conda create -n checkm_env -c bioconda 'checkm-genome==1.1.3' Collecting package metadata (current_repodata.json): done Solving...

jolespin

No space left on device error in HMM step not caught

1

Hi there, I ran into an odd bug using CheckM today, where a no space left on device error was not caught and CheckM reported wrong output with exit code...

boasvdp

Unexpected error: Traceback (most recent call last): File "/Users/zhangluyao/anaconda3/bin/checkm", line 856, in checkmParser.parseOptions(args) File "/Users/zhangluyao/anaconda3/lib/python3.11/site-packages/checkm/main.py", line 980, in parseOptions self.lineageSet(options) File "/Users/zhangluyao/anaconda3/lib/python3.11/site-packages/checkm/main.py", line 261, in lineageSet treeParser.getBinMarkerSets(options.tree_dir, options.marker_file, File "/Users/zhangluyao/anaconda3/lib/python3.11/site-packages/checkm/treeParser.py",...

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