Hi, I recently came across your tool and would like to try it. I used AMRFinderPlus on a unicycler assembly in conda environment with the --plus optiont and saved the output in a tsv file. When launchig pathotype with pathotypeR(indir =path/to/tsv, output = "patho_pred", "patho_prev") this error pops up:
Error in mutate():
ℹ In argument: Gene_name = Gene symbol.
Caused by error:
! 'Gene symbol' not found
Run rlang::last_trace() to see where the error occurred.
Called from: signal_abort(cnd, .file)
Looking at the AMRFinderPlus output file I have this columns:
Protein id, Contig id, Start, Stop, Strand, Element type, Element name, Scope, Type, Subtype, Class, Subclass, Method, Target length, Reference sequence length, % Coverage of reference, % Identity to reference, Alignment length, Closest reference accession, Closest reference name, HMM accession, HMM description.
Is there somthing I am missing? Should I edit the tsv output?
Thank you
Hi, I recently came across your tool and would like to try it. I used AMRFinderPlus on a unicycler assembly in conda environment with the --plus optiont and saved the output in a tsv file. When launchig pathotype with pathotypeR(indir =path/to/tsv, output = "patho_pred", "patho_prev") this error pops up:
Error in
mutate():ℹ In argument:
Gene_name = Gene symbol.Caused by error:
! 'Gene symbol' not found
Run
rlang::last_trace()to see where the error occurred.Called from: signal_abort(cnd, .file)
Looking at the AMRFinderPlus output file I have this columns:
Protein id, Contig id, Start, Stop, Strand, Element type, Element name, Scope, Type, Subtype, Class, Subclass, Method, Target length, Reference sequence length, % Coverage of reference, % Identity to reference, Alignment length, Closest reference accession, Closest reference name, HMM accession, HMM description.
Is there somthing I am missing? Should I edit the tsv output?
Thank you