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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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No bins found. Check the extension (-x) used to identify bins. #356

Closed qussai96 closed 1 year ago

qussai96 commented 2 years ago

Dear Donovan,

I am having trouble with running checkM on my machine. I am running the following command on the Arabidopsis Thaliana genome:

checkm lineage_wf -t 8 -x fa ~/Plants/Arabidopsis_Thaliana/genome/ ~/Plants/quality_check/checkM/ and I got the following error message.

[2022-11-09 11:58:28] INFO: CheckM v1.2.2
[2022-11-09 11:58:28] INFO: checkm lineage_wf -t 8 -x fa /home/students/q.abbas/Plants/Arabidopsis_Thaliana/genome/ /home/students/q.abbas/Plants/quality_check/checkM/
[2022-11-09 11:58:28] INFO: CheckM data: /home/students/q.abbas/Plants/Tools/checkM
[2022-11-09 11:58:28] INFO: [CheckM - tree] Placing bins in reference genome tree.
[2022-11-09 11:58:28] ERROR: No bins found. Check the extension (-x) used to identify bins.

I checked the bin folder and it contains the .fna file. PS. my genome is a multi-fasta file, could that be the problem?

best, ~Qussai

donovan-h-parks commented 2 years ago

Hi Qussai,

CheckM only works for bacterial and archaeal genomes. BUSCO may be more suited for your plant genome.

Cheers, Donovan