Closed lntran26 closed 2 years ago
ah okay! this should be an easy enough bug fix. have you spotted the source of the issue yet?
I found the bug. The list of files stairwayplot intermediate files being handed to the all_plot
rule was incorrect, and had a list of all demographic models used. I will submit a simple PR to fix this.
Thank you @andrewkern ! @emanuelmfonseca and I have attempted to find/fix the bug ourselves but have been unsuccessful. Glad you can find it rather quickly!
@lntran26 I just authored a PR to fix this.
When running the N(t) analysis on two demographic models "Constant" and Out-Of-Africa (YRI), @emanuelmfonseca and I noticed that the stairway plot results for these models are virtually identical (while msmc and GONE results do differ). @lauterbur noticed this on one of the calls where we showed the initial 1 rep result. We confirm that this happens consistently across different runs and on multiple replicates.
I also found that when running multiple replicates, the number of lines plotted for stairway plots using the current pipeline often don't match with the number of replicates specified in the config file, while msmc and GONE always do. Since
tiny_config.yaml
currently only have 1 rep and 1 demography these issues might be missed when debugging.