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lh3 / psmc

Implementation of the Pairwise Sequentially Markovian Coalescent (PSMC) model
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problem with psmc_plot.pl #59

Open cyadrogarcia opened 2 months ago

cyadrogarcia commented 2 months ago

I have run psmc and when trying to plot i am getting this error

psmc_plot.pl -R -u 0.53e-8 diploid diploid.psmc Use of uninitialized value in division (/) at /share/apps/psmc/utils/psmc_plot.pl line 119, <> line 1115. Use of uninitialized value in division (/) at /share/apps/psmc/utils/psmc_plot.pl line 119, <> line 1115. Illegal division by zero at /share/apps/psmc/utils/psmc_plot.pl line 119, <> line 1115.

has anyone dealed with this before? I was considering use ggplot, but not sure wich column to use or wich iteration

freshspaceoctopus commented 2 months ago

OK, so for any unfortunate soul who encounters this error, If your psmc files are not faulty (no NANs), the problem is just because the plotting function starts drawing by the 20th iteration by default. (option -n) You can override this option using -n , providing with the iteration of your plot.