search

LarsNauheimer / HybPhaser

Workflow to detect and phase hybrids in target capture data
GNU General Public License v3.0
15 stars 5 forks source link

1b_assess_dataset.R #16

Open judato89 opened 1 year ago

judato89 commented 1 year ago

Error in plot.window(xlim = xlim, ylim = ylim, log = log, yaxs = pars$yaxs) : need finite 'ylim' values Calls: boxplot ... boxplot.default -> do.call -> -> plot.window

evoyeyo commented 1 year ago

Hi all. Just to add that I had a similar output:

[1] FALSE Error in plot.window(xlim = xlim, ylim = ylim, log = log, yaxs = pars$yaxs) : need finite 'ylim' values Calls: boxplot ... boxplot.default -> do.call -> <Anonymous> -> plot.window In addition: Warning messages: 1: In min(x) : no non-missing arguments to min; returning Inf 2: In max(x) : no non-missing arguments to max; returning -Inf Execution halted

Thanks for the help!

evoyeyo commented 1 year ago

Hi @judato89. Found a solution that worked for me. I had the consensus sequences folder WITHIN another folder. The 1a_count_snps.R script looks for the cons seqs in the 01_data folder. So, I just needed to move this 01_data folder to the output directory stated in the config.txt. Hope it works for you!

laymonb commented 1 year ago

@evoyeyo I was also getting that error and I figured out that it was happening because I was trying to use a file containing a list of paralogs to remove in the "#paralogs" section of the config.txt file, however, to use this option you also have to have this line: remove_loci_for_all_samples_with_more_than_this_mean_proportion_of_SNPs = "file". I was leaving that variable empty, and it was causing the error.