Hi all,
I am trying to run a stairway plot analysis (from here - https://sites.google.com/site/jpopgen/stairway-plot using version 2) and I can get right to the end, before getting rebuffed while trying to get the results (using Stairway_output_summary_plot2.class). I wonder if anyone has much experience with this program (or java) and might be able to help. My input and the output error are both below.
Many thanks in advance,
James
Code input:
java -Xmx1g -cp stairway_plot_es/:stairway_plot_es/gral-core-0.11.jar:stairway_plot_es/VectorGraphics2D-0.9.3.jar Stairway_output_summary_plot2 two-epoch_fold.blueprint rand9/
Error:
(base) jamesdorey@Jamess-MacBook-Pro-4:~/Desktop/Uni/My_papers/Fijiensis_paper/Analyses/Stairway_plots/stairway_plot_v2/TEST$ java -Xmx1g -cp stairway_plot_es/:stairway_plot_es/gral-core-0.11.jar:stairway_plot_es/VectorGraphics2D-0.9.3.jar Stairway_output_summary_plot2 two-epoch_fold.blueprint rand9/
Exception in thread "main" java.util.NoSuchElementException
at java.util.StringTokenizer.nextToken(StringTokenizer.java:332)
at Stairway_output_summary_plot2.main(Stairway_output_summary_plot2.java:238)
Have a look at https://www.youtube.com/watch?v=R5wKjst_sMM
https://www.youtube.com/watch?v=5o-kdjv7FD0
Hi james, you have an exception of your Tokenizer the next element is not found. Since you are on macos i advice you to install EclipseIDE include your jar file into the library and start the debugger.
Using java on the console is not the right approach. We have powerful tools to identify bugs rapidely.
I worked on EclipseIDE on MacOS.. since its java it runs allover..
Hey Yueqi, sorry, I should have posted the answer when I figure it out! Indeed, it was a simple wrong character in the last section (that relates to the creation of the plots) of the .blueprint file. I think that I had input a full-stop instead of a comma in the xrange or yrange (below). My advice is to double check this, or copy in the default and see if the code will run then!
Perhaps also you might be able to get a similar or the same error for a similar mistake elsewhere in the .blueprint file, so have a look if the above doesn't work.
Let me know how you go!
#plot setting
plot_title: two-epoch # title of the plot
xrange: 0.1,10000 # Time (1k year) range; format: xmin,xmax; "0,0" for default
yrange: 0,0 # Ne (1k individual) range; format: xmin,xmax; "0,0" for default
xspacing: 2 # X axis spacing
yspacing: 2 # Y axis spacing
fontsize: 12 # Font size
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