metagenomic virome quality assessment

Question

[Petchimuthu]

I have collected viral contigs using GeNoMad software. I want to run checkv for quality assessment. Checkv is not properly working . It continuously shuts down in the gene-calling step. Can anyone assist in rectifying this issue?

$ checkv end_to_end "/mnt/d/metagenomic works _project/New_analysis_work/CSM7KOOH_contigs_virus.fna" "/mnt/d/metagenomic works _project/New_analysis_work/checkv" -t 8

CheckV v1.0.3: contamination
[1/8] Reading database info...
[2/8] Reading genome info...
[3/8] Calling genes with prodigal-gv...

Error: 8 prodigal-gv tasks failed. Program should be rerun.

Answer 1

[Mensur Dlakic]

The error message points to a problem with prodigal-gv. What happens when you type prodigal-gv on the command line?

It is never a good idea to have space characters (metagenomic works _project) in directory or file names when running Linux-based programs.