tariqjoosab
commented
1 year ago Hello. My apologies for the issue you're encountering. I did a fresh install of the latest TFBMiner version from this repository and I cannot seem to replicate your issue. Here are my outputs, and what it should look like:
C:\Users\tjoos>py -m TFBMiner C00259 -l 3 -g C:\Users\tjoos\Desktop\genome_files
Identifying enzymatic chains for C00259 with maximum chain length set to 3...
Chain identified: EC:2.7.1.46 => EC:2.7.7.64
Chain identified: EC:5.3.1.4 => EC:2.7.1.16
Chain identified: EC:1.1.1.376 => EC:3.1.1.15
Chain identified: EC:2.7.1.46 => EC:2.7.7.64 => EC:5.1.3.5
Chain identified: EC:5.3.1.4 => EC:2.7.1.16 => EC:5.1.3.22
Chain identified: EC:1.1.1.376 => EC:3.1.1.15 => EC:4.2.1.25
Chain identified: EC:5.3.1.4 => EC:2.7.1.16 => EC:5.1.3.4
Chain identified: EC:2.7.1.46 => EC:2.7.7.64 => EC:2.4.2.34
Chain identified: EC:2.7.1.46 => EC:2.7.7.64 => EC:5.4.99.9
Chain identified: EC:2.7.1.46 => EC:2.7.7.64 => EC:5.4.99.30
Chain identified: EC:1.1.1.46 => EC:3.1.1.15
Chain identified: EC:1.1.1.376 => EC:3.1.1.15
Chain identified: EC:1.1.1.46 => EC:3.1.1.15 => EC:4.2.1.25
Chain identified: EC:1.1.1.376 => EC:3.1.1.15 => EC:4.2.1.25
12 unique chains were identified.
Processing 12 chains...
100%|██████████████████████████████████████████████████████████████████████████████████| 12/12 [01:53<00:00, 9.44s/it]
Processing is complete. 2195 potential biosensors were identified for C00259. Results have been deposited to C:\Users\tjoos\TFB_predictions. Total runtime: 161.56s.In your case, TFBMiner has identified enzymatic chains but cannot seem to identify any biosensors -- this is usually because it cannot locate the bacterial genomes that it needs to analyze. This is either because it cannot find the genome_files folder, or because it cannot find the genomes within the folder. I recommend double checking whether there are in-fact genomes within /Users/jameslloyd/Documents/Main_Work_JPBL/LL/Future_fellowship/Protein_engineering/genome_files, which should have been downloaded from here. The genome_files folder should also be unzipped after being downloaded, and it should not contain any subfolders -- it should only contain the genomes.
It is more likely that TFBMiner simply cannot locate the folder. I'm unfamiliar with the Mac OS so I don't know for certain whether you specified the path to it correctly on the command line, however if you place the genome_files folder within your User directory (/Users/jameslloyd in your case), then you will not need to specify the location of genome_files on the command line because TFBMiner will default to searching within your User directory, and it should be able to automatically find the folder.
Below I have also provided my output for allowing TFBMiner find genome_files within the default location, which also seems to be working on my end. Please let me know whether any of this resolves your issue.
C:\Users\tjoos>py -m TFBMiner C00259 -l 3
Identifying enzymatic chains for C00259 with maximum chain length set to 3...
Chain identified: EC:5.3.1.4 => EC:2.7.1.16
Chain identified: EC:2.7.1.46 => EC:2.7.7.64
Chain identified: EC:1.1.1.376 => EC:3.1.1.15
Chain identified: EC:2.7.1.46 => EC:2.7.7.64 => EC:5.1.3.5
Chain identified: EC:5.3.1.4 => EC:2.7.1.16 => EC:5.1.3.22
Chain identified: EC:1.1.1.376 => EC:3.1.1.15 => EC:4.2.1.25
Chain identified: EC:5.3.1.4 => EC:2.7.1.16 => EC:5.1.3.4
Chain identified: EC:2.7.1.46 => EC:2.7.7.64 => EC:2.4.2.34
Chain identified: EC:2.7.1.46 => EC:2.7.7.64 => EC:5.4.99.9
Chain identified: EC:2.7.1.46 => EC:2.7.7.64 => EC:5.4.99.30
Chain identified: EC:1.1.1.46 => EC:3.1.1.15
Chain identified: EC:1.1.1.376 => EC:3.1.1.15
Chain identified: EC:1.1.1.46 => EC:3.1.1.15 => EC:4.2.1.25
Chain identified: EC:1.1.1.376 => EC:3.1.1.15 => EC:4.2.1.25
12 unique chains were identified.
Processing 12 chains...
100%|██████████████████████████████████████████████████████████████████████████████████| 12/12 [02:14<00:00, 11.23s/it]
Processing is complete. 2195 potential biosensors were identified for C00259. Results have been deposited to C:\Users\tjoos\TFB_predictions. Total runtime: 188.41s.
I just installed TFBMiner and was very excited to use it on a list of compounds that I had, but I ran l-arabinose (C00259) as a test to see if it would run properly but I got zero hits. I assume that is not supposed to be the case. Can you please advise? See my command and the outputs below: