problem in running demo

[ladimafakher]

Dear Xiaogen
thanks for your response. The contents of my uniclust30 folder can be seen in Figure 4
I thank you for helping me.
best regards

[xiaogenz]

Please rename your 'uniclust30' folder to 'uniclust30_2017_04'. Otherwise, the program won't be able to locate 'uniclust30_2017_04_a3m_db'. You can refer to line 161 in the 'runDEMO.py' script for clarification.

[ladimafakher]

Dear Xiaogen
As you said. I changed the e name of the 'uniclust30' folder to 'uniclust30_2017_04(figure6) and also changed the address in the run_DEMO2.py file(figure5). but I got the error "the library is not complete. Please check it!" again.
what is the problem and how can I solve it?
thanks for your helping
best regards

[xiaogenz]

Please carefully check lines 56 and 161 in 'run_DEMO2.py'. Ensure that 'hhblitsdb + "_a3m_db"' exists in your library. It's important to note that in line 56, 'hhblitsdb' should be set as your 'uniclust30' directory plus 'uniclust30_2017_04'.

Thanks,
Xiaogen

[ladimafakher]

Dear Xiaogen
I checked the 'run_DEMO2.py' the lone 56 is line 55 and the line 161 is 146(figure 9) in my file. I set the path of uniclust30_2017_04 in line 55 of my run_DEMO2.py file. Also, I checked that 'hhblitsdb + "_a3m_db"' file existed in the uniclust30_2017_04 directory. I found that this file existed in the uniclust30_2017_04 directory(Figure 8) with a file size of 50GB(Figure 7). so, I do not know what should I do now. please help me this this matter
best regards.

[xiaogenz]

Could you please show me the settings of NR_DB, hhblitsdb, jackhmmerdb, hmmsearchdb, and MDlibpath in lines 55-59 of runDEMO.py.
And please show me the content in local_library folder.

Best wishes,
Xiaogen

[ladimafakher]

Dear Xiaogen
the settings of NR_DB, hhblitsdb, jackhmmerdb, hmmsearchdb, and MDlibpath in lines 55-59 of runDEMO.py can be see in Figure 10. The content of local_library folder can be seen in Figure 6.

[xiaogenz]

Please change your settings to:

NR_DB = "/mdeia/ravis/data/DEMO/local_library/nr/nr"
hhblitsdb = "/mdeia/ravis/data/DEMO/local_library/uniclust30_2017_04/uniclust30_2017_04"
jackhmmerdb = "/mdeia/ravis/data/DEMO/local_library/uniref90.fasta/uniref90.fasta"
hmmsearchdb = "/mdeia/ravis/data/DEMO/local_library/metaclust/metaclust_2017_05.clean.fasta"
MDlibpath = "/mdeia/ravis/data/DEMO/local_library/multidomain_protein_CA"

Please confirm whether the following files exist:
1. "/mdeia/ravis/data/DEMO/local_library/uniclust30_2017_04/uniclust30_2017_04_a3m_db"
2. "/mdeia/ravis/data/DEMO/local_library/uniref90.fasta/uniref90.fasta"
3. "/mdeia/ravis/data/DEMO/local_library/metaclust/metaclust_2017_05.clean.fasta"

Best wishes,
Xiaogen

[ladimafakher]

dear Xiaogen
thanks for your response. I changed the path address of all libraries in the run_DEMO2.py file as you said in your previous message(Figure 11). I have one question why I should repeat the nr directory two times in the path for example /nr/nr and uniclust30_2017_04/uniclust30_2017_04? I also checked that I have these files:uniclust30_2017_04_a3m_db, uniref90.fasta, and metaclust_2017_05.clean.fasta in the library directory. I have all of them except this file metaclust_2017_05.clean.fasta. instead of metaclust_2017_05.clean.fasta file I have metaclust.fasta file with a volume of 164.0 GB (Figure 15). so, I changed the name of this file to metaclust_2017_05.clean.fasta put the path in the run_DEMO2.py file. is it correct? then I ran the Demo command and I got this information( Figure 14). Is DEMO now running correctly?
thanks so much for your help
best regards

[xiaogenz]

The first nr is your folder name and the second nr is the file name in the folder. Same as uniclust30_2017_04.
The settings of DEMO is correct now. But you should also change the settings of hhblitsdb, jackhmmerdb, and hmmsearchdb (lines 32-35) in /mdia/ravis/data/DEMO/external/runDistPre.pl. Otherwise, you cannot run DeepPotential for distance prediction.

Best wishes,
Xiaogen