phac-nml
The oom error
Hello, dear mob-suite team
Thank you for developing this useful tool mob-suite, it helps us a lot in our work! However, I get the following error when using mobtyper. The operation seems to have exceeded the memory limit. What kind of sequence files would be appropriate?
slurmstepd: error: Detected 1 oom_kill event in StepId=52823311.batch. Some of the step tasks have been OOM Killed. slurm-52823311.out (END)
mob_typer --multi --infile 1000_sequences.ARGs.fa --out_file sequences_mobtyper_results.txt
The information of the fa file file format type num_seqs sum_len min_len avg_len max_len 1000_sequences.ARGs.fa FASTA DNA 36,819 151,255,110 1,001 4,108.1 376,906
Mob typer expects a single plasmid sequence to be type unless you use --multi option. A single Mob_recon can handle entire bacterial genomes and extract plasmids (note only a single genome per Fasta input).
