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hahnlab / CAGEE

Computational Analysis of Gene Expression Evolution
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replicates in configuration file #26

Closed mtswanson2017 closed 2 months ago

mtswanson2017 commented 10 months ago

Hi!

Thanks for all of your work on CAGEE! I'm really excited to be using this tool!

I'm able to get cagee to work if I only have a single sample per species. However, when I try to include replicates I get the following error: Command line: cagee -t primate_pruned.nwk -i full_csn1s1t.tsv Discretization range set to 200 Summation probability calculation Searching for 1 sigmas

Optimizer strategy: Standard Nelder-Mead Iterations: 300 Expansion: 2 Reflection: 1 Starting Search for Initial Parameter Values Sigma^2:0.080301 terminate called after throwing an instance of 'std::runtime_error' what(): Attempt to access missing probability vector Aborted (core dumped)

Do you know what I could do to fix this? I've attached my configuration file in case it is formatted incorrectly.

full_csn1s1t.txt

benfulton commented 3 months ago

Sorry for leaving this so long. You need a replicate map to tell the application which items are considered replicates. The next version of CAGEE will alert to a failed transcript pruning rather than just dump core like that.