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songweizhi / Tax4Fun2_short_tutorial

A short tutorial for Tax4Fun2
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"Tax4Fun2_ReferenceData_v2/blast_bin/bin/blastn.exe' not found" #2

Open EsbergA opened 3 months ago

EsbergA commented 3 months ago

Dear all, I running the example files using the example code but I get the same error everytime: "Tax4Fun2_ReferenceData_v2/blast_bin/bin/blastn.exe' not found"

I have extracted the folder and as I see it everything should be in place, any suggestions?

modify the following 8 lines as needed

query_otu_seq = 'demo_OTU.fasta' # input OTU sequence file query_otu_table = 'demo_OTU_table.csv' # input OTU table pwd_op_folder = 'C:/Users/anes0001/Documents/Tax4Fun2/out1' # output directory pwd_ref_data = 'C:/Users/anes0001/Documents/Tax4Fun2/Tax4Fun2_ReferenceData_v2' # path to the default database (i.e., Tax4Fun2_ReferenceData_v2), need to be decompressed before use norm_by_cn = TRUE # normalize_by_copy_number (TRUE or FALSE) norm_path = TRUE # normalize_pathways (TRUE or FALSE) iden = 0.97 # min_identity_to_reference, please modify as needed num_of_threads = 2 # number of CPU cores to use, please modify as needed

predict functions

runRefBlast(path_to_otus = query_otu_seq, path_to_reference_data = pwd_ref_data, path_to_temp_folder = pwd_op_folder, database_mode = "Ref99NR", use_force = T, num_threads = num_of_threads)

makeFunctionalPrediction(path_to_otu_table = query_otu_table, path_to_reference_data = pwd_ref_data, path_to_temp_folder = pwd_op_folder, database_mode = "Ref99NR", normalize_by_copy_number = norm_by_cn, min_identity_to_reference = iden, normalize_pathways = norm_path)

Best regards, Anders

stalin-antony commented 3 months ago

You have to follow this step to solve the issue. (Mostly this problem occurs in the Windows version)

  1. If you are using R studio in Windows, try to Install the standalone version of the BLAST (https://ftp.ncbi.nlm.nih.gov/blast/executables/LATEST/)
  2. Once you have done the installation, go to the installation directory in Windows, (Example: C:\Program Files\NCBI\blast-2.15.0+\bin)
  3. copy all the binary files from the folder, and paste (replace) them into the binary folder of Tax4Fun2_ReferenceData_v2 (Tax4Fun2_ReferenceData_v2\blast_bin\bin).
  4. That's it. Now you can run the command. It will work.

good luck....

Dr. Antony Stalin