CheckM

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Hi! I have been attempting to analyse my bins from my metagenomic data using CheckM. I was successful in doing so yesterday and generating graphs; however, I am facing the...

kritical1326

FileNotFoundError: [Errno 2] No such file or directory: 'checkm_folder/storage/tree/concatenated.tre'

9

I am running the following command ``` checkm lineage_wf -f "mysample_downsample10pct_metabat.checkm.txt" -t 40 -x fa metabat_folder checkm_folder ``` Here is my traceback: ``` Traceback (most recent call last): File "/opt/conda/bin/checkm",...

spitfiredd

Having trouble interpreting the meaning of "root" as a marker lineage

1

Hello, I'm running CheckM on KBase (Assess Genome Quality with CheckM - v1.0.18). I first used MetaBAT2 on KBase (MetaBAT2 Contig Binning - v1.7) to bin an assembled metagenome, resulting...

jackieway

checkm was working totally fine for me just a few days ago, but now even running the checkm test gives me this following error: ``` checkm test ~/checkm_test_results [2024-01-31 17:56:43]...

kstagaman

checkm_coverage dropped some bins

1

Hello, I am running checkm v1.2.1. I ran `coverage` for my bins but the output seems to drop some of the bins, particularly those that I expect to have high...

emilyjunkins

checkm ssu_finder

2

Dear all, I am trying to run ssu_finder as below, and errors occurred. Any idea? `checkm ssu_finder -x fa 36_Inf3_11dpi_metasapdes.metagenome.assembly.fasta ` 36_Inf3_11dpi_metasapdes.metagenome.assembly.fasta.metabat-bins ssu_finder [2024-01-10 15:30:59] INFO: CheckM v1.2.2 [2024-01-10 15:30:59]...

mehmetdayi

IndexError: list index out of range

1

I am trying to work on a genome to analyze with checkm with the following commands checkm lineage_wf -x fa Galaxy80-\[GCA_009932715.2_ASM993271v2_genomic.fna\].fasta ../CheckM-output/ Got the following error:[2023-05-22 17:57:32] INFO: CheckM v1.2.2...

sandipandrils

FileNotFoundError: [Errno 2] No such file or directory: '/home/majorram/anaconda3/envs/checkm/hmms/phylo.hmm'

2

Hi, I am geeting this error. Pls suggest. checkm lineage_wf /media/majorram/Analysis_Data/singhrn/medaka_final2/s2mags_genomes/s2mags_contigs_16S/ /media/majorram/Analysis_Data/singhrn/checkM_metagenome/S2_metaAssmbly/S2mags/ --reduced_tree -x fasta -t 32 [2023-08-02 12:16:36] INFO: CheckM v1.2.0 [2023-08-02 12:16:36] INFO: checkm lineage_wf /media/majorram/Analysis_Data/singhrn/medaka_final2/s2mags_genomes/s2mags_contigs_16S/ /media/majorram/Analysis_Data/singhrn/checkM_metagenome/S2_metaAssmbly/S2mags/ --reduced_tree...

ramnageena11

Chekm test: line 1: 16491 Bus error (core dumped) pplacer -j 1

1

Hello, i am running checkm test after the checkm installed. But I got the **error**: ``` [2023-09-11 21:31:17] INFO: Placing 1 bins into the genome tree with pplacer (be patient)....

98jay

Unexpected error: <class 'KeyError'>

1

Some of my files have been able to run through the entire lineage_wf pipeline, however about 1/4 of them did not and kept running into this issue: [2023-07-12 00:03:31] INFO:...

gracedai23