search

ohlab / SMEG

Strain-level Metagenomic Estimation of Growth rate (SMEG) measures growth rates of microbial strains from complex metagenomic dataset
17 stars 6 forks source link

Calls: removeStrains Execution halted #3

Closed stebliankin closed 4 years ago

stebliankin commented 4 years ago

I have the following error during the "BUILDING SMEG DATABASE(S)" step in _buildsp

Error in data[!rownames(data) %in% outlier, ] : 
  incorrect number of dimensions
Calls: removeStrains
Execution halted

The error disappears when I change until [ ! $count -lt 3 ] to until [ ! $count -lt 2 ] in the line 232 of _buildsp

For some reason, during the third iteration, the input is corrupted. Can you please advise what might be the problem? How the setting of less number of iterations going to affect the results?

Thank you!

aemiol commented 4 years ago

Hi, using lesser iterations will NOT affect your results. Multiple iteration is conducted to see if more unique SNPs can be generated for clusters. Infact, there is an option to run the build without iteration.

Without seeing the actual data (i.e. strains), it is hard to predict why it failed at the 3rd iteration.

Cheers, Tunde

stebliankin commented 4 years ago

Thank you so much for your quick response and for your great work!