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hahnlab / CAGEE

Computational Analysis of Gene Expression Evolution
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"WARNING: No math library available, calculations may be slow" #22

Closed emm-miller closed 3 weeks ago

emm-miller commented 1 year ago

Hello! I was trying to run CAGEE to estimate a single sigma over the whole tree. I was in the same directory as the below files so they could find them. I ran the command:

cagee --tree i.tre --infile i.tab

But it gave me the following message along with an empty results folder:

Values converted to LOG space Read input file i.tab. Command line: cagee --tree i.tre --infile i.tab Discretization range set to 200 WARNING: No math library available, calculations may be slow Using gamma prior with k=0.375, theta=1600) Summation probability calculation

Optimizer strategy: Standard Nelder-Mead Iterations: 300 Expansion: 2 Reflection: 1 Starting Search for Initial Parameter Values Sigma^2:nan Segmentation fault

To install CAGEE I ran: conda create --name cagee conda activate cagee conda install -n cagee -c bioconda cagee

These are the packages in my environment: `

Name Version Build Channel

_libgcc_mutex 0.1 conda_forge conda-forge _openmp_mutex 4.5 2_kmp_llvm conda-forge boost-cpp 1.74.0 h75c5d50_8 conda-forge bzip2 1.0.8 h7f98852_4 conda-forge cagee 1.0 hc5b1d88_0 bioconda icu 70.1 h27087fc_0 conda-forge libgcc-ng 12.2.0 h65d4601_19 conda-forge libstdcxx-ng 12.2.0 h46fd767_19 conda-forge libzlib 1.2.13 h166bdaf_4 conda-forge llvm-openmp 16.0.3 h4dfa4b3_0 conda-forge mkl 2020.4 h726a3e6_304 conda-forge xz 5.2.6 h166bdaf_0 conda-forge zlib 1.2.13 h166bdaf_4 conda-forge zstd 1.5.2 h3eb15da_6 conda-forge `

Would you have any recommendations? Thank you so much!!

benfulton commented 1 month ago

Sorry for leaving this so long. The missing math library shouldn't cause a segmentation fault. I'd guess there's an issue with your input files.