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SysBioUAB / hpi_predictor

Bash+R tool to predict host-pathogen protein-protein interactions based on numerical encoding of physicochemical descriptors
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Tool no longer functional #4

Open pmaen opened 2 weeks ago

pmaen commented 2 weeks ago

When running the tool I get the following output:

14 CPU cores detected, using 13
Building the pathogen reference database
Retrieving ZIMJ680101 from pathogen database
Retrieving ZIMJ680101 from host database
Retrieving ZIMJ680104 from pathogen database
Retrieving ZIMJ680104 from host database
Retrieving GEIM800101 from pathogen database
Retrieving GEIM800101 from host database
Retrieving GEIM800105 from pathogen database
Retrieving GEIM800105 from host database
Retrieving GEIM800108 from pathogen database
Retrieving GEIM800108 from host database
Building the pathogen proteome database
Done!Time difference of 1.654454 secs
Building the host proteome database
[1] "/home/Software/hpi_predictor-main/datasets/hosts/Pseudomonas_aeruginosa_287/descriptors/h_results_lagmax_200_cutoff_0_4_ZIMJ680101.txt"
Error in aa2index(aa = as.vector(stri_list2matrix(str_extract_all(h.proteome$H_seq[x],  : 
  aa2index: 'window' must be smaller than the sequence length
Calls: lapply -> lapply -> FUN -> aa2index
Execution halted

This looks like a code error. I am running the tool on Ubuntu 24.04 LTS.