"Np.contig_map_ref.gp", line 40733: unrecognized option - see 'help set'.

[wangjie07070910]

This tool looks great and I'm exploring it, but I'm having the following issues while using it, and I'd appreciate it if you could assist me with it. [Info] Paramater: refgenomefile=Np.fasta, mincontiglength=50000, minalignmentlength=10000, minalignmentidentity=0.9, prefix=Np_14703, threads=40, aligner=minimap2, nofilter=False, plot=False, overwrite=False, nucmeroption=, deltafilteroption=, minimapoption=-x asm5 -t 40 [Info] Filtering contigs input... [Info] Checking telomere in contigs... [Info] Running minimap2... [Error] Unexcepted error occur in gnuplot as follow: cmd: gnuplot Np.contig_map_ref.gp returncode: 1 stdout:

stderr:

set mouse format "%.0f" ^ "Np.contig_map_ref.gp", line 40733: unrecognized option - see 'help set'.

But I checked this file and it doesn't have line 40733 at all

vi +40733 Np.contig_map_ref.gp -c option, 1: Illegal address: only 39567 lines in the file

[Echoring]

I cannot make sure about this. Maybe this is an issue with incompatible gnuplot? Or png terminal not supported? By the way, too many sequence sometimes also cause error when ploting.

[kazumaxneo]

Hello I got same error. I have not specified any options for --plot but I am getting this. Could you Kindly provide an option to disable plotting? I am using the latest version 1.1.8.

$ python3 quartet.py AssemblyMapper -q hifiasm.fasta -r GCF_001433935.1.fasta -t 40 -a minimap2 --plot [Info] Paramater: refgenomefile=GCF_001433935.1.fasta, qryfile=hifiasm.fasta, mincontiglength=50000, minalignmentlength=10000, minalignmentidentity=0.9, prefix=quarTeT, threads=40, aligner=minimap2, nofilter=False, plot=True, overwrite=False, nucmeroption=, deltafilteroption=, minimapoption=-x asm5 -t 40 [Info] Filtering contigs input... [Info] Checking telomere in contigs... [Info] Running minimap2... [Error] Unexcepted error occur in gnuplot as follow: cmd: gnuplot quarTeT.contig_map_ref.gp returncode: 1 stdout:

stderr:

set mouse format "%.0f" ^ "quarTeT.contig_map_ref.gp", line 133: unrecognized option - see 'help set'.

[Echoring]

It most likely to be that the compiled gnuplot is not compatible with the quarTeT. I'm not sure what is lacking. This figure is a dotplot showing the colinearity between contigs and reference genome. If you do not require such a plot, try new option --noplot in v1.2.0.