Add CheckM

[biocdgv]

Hi!!

I have finally finished CheckM's script. As a recall, CheckM did not run on my pc (the main reason for the delay). However, please find attached the input files (sample_human_gut.zip) that I used to test CheckM if you want to give it a try.

Hope you like it !! 🍶

[Nesper94]

Hi Cristian! I tried running CheckM and got an error, but I don't know if I am doing something wrong. This is my folder structure:

checkm_sample_human_gut/
└── sample_human_gut
    ├── concoct.17.fa
    ├── concoct.72.fa
    ├── concoct.77.fa
    ├── maxbin2.017.fa
    ├── maxbin2.032.fa
    ├── maxbin2.094.fa
    ├── maxbin2.109.fa
    ├── metabat.11.fa
    ├── metabat.25.fa
    ├── metabat.7.fa
    ├── metabat.85.fa
    └── metabat.8.fa

This is the command I ran:

metabiome checkm -i checkm_sample_human_gut/ -o results/checkm

And this is the error message:

metabiome checkm -i checkm_sample_human_gut/ -o results/checkm
Conda environment: metabiome-checkm
Input directory: /path/checkm_sample_human_gut
Number of threads: 1
CheckM workflow: lineage_wf
CheckM called with options: 
Perform lineage analysis workflow
Output directory path: /path/results/checkm
Name of the directory to be created: lineage_wf
Output directory path: /path/results/checkm/lineage_wf
Name of the directory to be created: sample_human_gut
[] INFO: CheckM v1.1.3
[] INFO: checkm lineage_wf /path/checkm_sample_human_gut/sample_human_gut /path/results/checkm/lineage_wf/sample_human_gut -t 1 -f /path/results/checkm/lineage_wf/sample_human_gut_results_summary.txt
[] INFO: [CheckM - tree] Placing bins in reference genome tree.
[] ERROR: No bins found. Check the extension (-x) used to identify bins.

[biocdgv]

Hello Juan!

Thanks for checking it out!!! I think the problem comes from the bins' extension. In your case, is fasta. So, try it this way:

metabiome checkm -i checkm_sample_human_gut/ -o results/checkm -opts -x fasta

C. 🦝

[Nesper94]

Hi! You were right, I ran

metabiome checkm -i checkm_sample_human_gut/ -o results/checkm -opts -x fa

and it worked. However my pc ran out of RAM and I could not check the results, but I think it is working fine.