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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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Failed to process sequence file #327

Closed sapuizait closed 2 years ago

sapuizait commented 2 years ago

Hi

I have been trying to run checkm on a set of MAGs and I keep getting the above error but I dont have any additional info on why this is happening: Here is the log: [2022-03-18 12:16:41] INFO: CheckM v1.1.3 [2022-03-18 12:16:41] INFO: checkm lineage_wf -t 8 -x fas INPUT/ OUTPUT/ [2022-03-18 12:16:41] INFO: [CheckM - tree] Placing bins in reference genome tree. [2022-03-18 12:16:41] ERROR: Failed to process sequence file: INPUT/W11_DBSCAN_round2_2.txt.fas [2022-03-18 12:23:01] INFO: CheckM v1.1.3 [2022-03-18 12:23:01] INFO: checkm lineage_wf -t 8 -x fas INPUT/ OUTPUT/ [2022-03-18 12:23:01] INFO: [CheckM - tree] Placing bins in reference genome tree. [2022-03-18 12:23:01] ERROR: Failed to process sequence file: INPUT/W11_DBSCAN_round2_2.txt.fas

files are standard fasta files with fas extensions

Thanks for the help in advance P

donovan-h-parks commented 2 years ago

Hi,

Sorry for the slow reply. The input files must be standard FASTA files with sequences in nucleotide space. My best guess is that Prodigal is failing to identify any genes in your input files.

Cheers, Donovan

donovan-h-parks commented 2 years ago

If this remains a problem, please open this issue and attach one of the problematic bins.