error in 'gget setup alphafold'

[mikenada]

What happened?

receive an error while setting up alphafold

gget version

0.3.7

Operating System (OS)

Linux

User interface

Command-line

Are you using a computer with an Apple M1 chip?

Not applicable

What is the exact command that was run?

pip install --upgrade gget
** finish without error

gget setup alphafold
** see error below

Which output/error did you get?

** see error below 
(base) dostvip2@DESKTOP-L5H6T8M:/mnt/f$ gget setup alphafold
Traceback (most recent call last):
  File "/home/dostvip2/miniconda3_v2/bin/gget", line 5, in <module>
    from gget.main import main
  File "/home/dostvip2/miniconda3_v2/lib/python3.12/site-packages/gget/__init__.py", line 1, in <module>
    from .gget_ref import ref
  File "/home/dostvip2/miniconda3_v2/lib/python3.12/site-packages/gget/gget_ref.py", line 6, in <module>
    from .utils import (
  File "/home/dostvip2/miniconda3_v2/lib/python3.12/site-packages/gget/utils.py", line 11, in <module>
    from IPython.display import display, HTML
  File "/home/dostvip2/miniconda3_v2/lib/python3.12/site-packages/IPython/__init__.py", line 55, in <module>
    from .terminal.embed import embed
  File "/home/dostvip2/miniconda3_v2/lib/python3.12/site-packages/IPython/terminal/embed.py", line 15, in <module>
    from IPython.core.interactiveshell import DummyMod, InteractiveShell
  File "/home/dostvip2/miniconda3_v2/lib/python3.12/site-packages/IPython/core/interactiveshell.py", line 110, in <module>
    from IPython.core.history import HistoryManager
  File "/home/dostvip2/miniconda3_v2/lib/python3.12/site-packages/IPython/core/history.py", line 10, in <module>
    import sqlite3
  File "/home/dostvip2/miniconda3_v2/lib/python3.12/sqlite3/__init__.py", line 57, in <module>
    from sqlite3.dbapi2 import *
  File "/home/dostvip2/miniconda3_v2/lib/python3.12/sqlite3/dbapi2.py", line 27, in <module>
    from _sqlite3 import *
ImportError: /home/dostvip2/miniconda3_v2/lib/python3.12/lib-dynload/_sqlite3.cpython-312-x86_64-linux-gnu.so: undefined symbol: sqlite3_deserialize

[lauraluebbert]

It seems like an older version of SQLite is installed/being accessed, which does not have the sqlite3_deserialize function. Which version of SQLite do you have installed? You can in Python check with:

import sqlite3
print(sqlite3.sqlite_version)

Are you able to install a newer version of SQLite (3.24.0 or later)?

[mikenada]

Oh Its seems working now (hopefully) :

I created a new environment with python v3.10 and install everything on that environment. I also encountered several errors due to incompatibility in the installed versions. Hence, I installed specific version as listed below. I think it would be beneficial if the required version/s were also listed in the github page.

$ mamba create -n gget_alphafold2 python=3.10
$ conda activate gget_alphafold2
$ mamba install -c conda-forge requests==2.32.3
$ pip install --upgrade gget
$ mamba install -c conda-forge openmm=7.7.0
$ mamba install -c conda-forge sqlite==3.47.0
$ gget setup alphafold
$ pip install jax==0.4.34
$ pip install numpy==1.26.4
$ gget alphafold proteinsequenceshere

Will update this once the command finishes.

[mikenada]

after several hours, it ended with error :( Any suggestions would be appreciated.

(gget_alphafold2) dostvip2@DESKTOP-L5H6T8M:~$ gget alphafold MTSPLLYRTTTTCTRKTGLWMIRMLNYLACCFVTVRRGRGTVSFRKLSRLMTVLARSQPRNIKKFSTSTTTPHTPATSLSNFKKINSPASAGFFIFGAQCMANIEKLGSSSPEVLLKNATNLDQLVNGRESESLPDRFGVLRKTWHGMEMIFSRFIDYITGRGEQAVAAIGWQELGNWAVGLAVDNRQQIVYYNGSWYKYLGELEHVIAGDSPENDGGVWSAVNPTGKWSNIGDAALRSEMGSSKTGMGAYLSAYQRQWALELINNVATYLNAGKVNLWEYRHLALDTIVDGAEVVDWTPALIQALVDGAKYKRQVYAPGGRYYFQKMPEFVNLDSSGSTTNMSMYSLVGDGHDKTIFWTDSLVGVEMHFSTCRFYFDKFSVQRVLQGDDAAYRDSTIPLMQLGRRTDISAARLGYMGDVRFNGSPWGLNIEHCWDSIFQDVIVHNFQTSGIRIGIHDVDNSNNLLFIRTHIESCQYKGENLCRAFADMSYKTGSRVNHNITLIQPHIEPVNLRCHIFYSSYGKNIKVINPAFNRNNGSVDKGLYLDPSLAAPAVYSSDGVNIHIDGGQIQHIGPRSDTVAPLFKFVGTHKGWRCDSYIDTGKATSRTDLLSSVDVSRSNNGLREISFKGATVNSFTSMSSVGDRLRVAPLNDLQKVFDLVAETFIPPGETGTIARIIAMYSNTQDLSTPQQKAWDITSAGHASFKALRGQQYIIQAGAVATVNVGVGALERRGTYLISGAENNNQLFAMFFNVPGWAPSEIKTGSGVNLSRDQPDASVTGKLCVYQNNQYINLENRTASAVTVNVNFFA
14:04:59 - INFO - Old pandas version detected. Patching DataFrame.map to DataFrame.applymap
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
2024-11-11 14:05:00.487027: I tensorflow/core/util/port.cc:113] oneDNN custom operations are on. You may see slightly different numerical results due to floating-point round-off errors from different computation orders. To turn them off, set the environment variable TF_ENABLE_ONEDNN_OPTS=0.
2024-11-11 14:05:01.347774: I tensorflow/core/platform/cpu_feature_guard.cc:210] This TensorFlow binary is optimized to use available CPU instructions in performance-critical operations.
To enable the following instructions: AVX2 AVX_VNNI FMA, in other operations, rebuild TensorFlow with the appropriate compiler flags.
14:05:03 - INFO - Validating input sequence(s).
14:05:03 - INFO - Using the single-chain (monomer) model.
14:05:03 - INFO - Finding closest source for reference database.
Jackhmmer search: 13%|█████████▌ | 26/199 [elapsed: 34:39 remaining: 3:40:45]Jackhmmer search: 33%|███████████████████████▏ | 65/199 [elapsed: 1:27:19 remaining: 3:00:02]
Traceback (most recent call last):
File "/home/dostvip2/miniconda3/envs/gget_alphafold2/bin/gget", line 8, in
sys.exit(main())
File "/home/dostvip2/miniconda3/envs/gget_alphafold2/lib/python3.10/site-packages/gget/main.py", line 3219, in main
alphafold(
File "/home/dostvip2/miniconda3/envs/gget_alphafold2/lib/python3.10/site-packages/gget/gget_alphafold.py", line 544, in alphafold
raw_msa_results = get_msa(
File "/home/dostvip2/miniconda3/envs/gget_alphafold2/lib/python3.10/site-packages/gget/gget_alphafold.py", line 147, in get_msa
raw_msa_results[db_name].extend(jackhmmer_runner.query(fasta_path))
File "/home/dostvip2/miniconda3/envs/gget_alphafold2/lib/python3.10/site-packages/alphafold/data/tools/jackhmmer.py", line 171, in query
return self.query_multiple([input_fasta_path], max_sequences)[0]
File "/home/dostvip2/miniconda3/envs/gget_alphafold2/lib/python3.10/site-packages/alphafold/data/tools/jackhmmer.py", line 210, in query_multiple
future.result()
File "/home/dostvip2/miniconda3/envs/gget_alphafold2/lib/python3.10/concurrent/futures/_base.py", line 451, in result
return self.__get_result()
File "/home/dostvip2/miniconda3/envs/gget_alphafold2/lib/python3.10/concurrent/futures/_base.py", line 403, in __get_result
raise self._exception
File "/home/dostvip2/miniconda3/envs/gget_alphafold2/lib/python3.10/concurrent/futures/thread.py", line 58, in run
result = self.fn(*self.args, **self.kwargs)
File "/home/dostvip2/miniconda3/envs/gget_alphafold2/lib/python3.10/urllib/request.py", line 270, in urlretrieve
block = fp.read(bs)
File "/home/dostvip2/miniconda3/envs/gget_alphafold2/lib/python3.10/http/client.py", line 466, in read
s = self.fp.read(amt)
File "/home/dostvip2/miniconda3/envs/gget_alphafold2/lib/python3.10/socket.py", line 717, in readinto
return self._sock.recv_into(b)
File "/home/dostvip2/miniconda3/envs/gget_alphafold2/lib/python3.10/ssl.py", line 1307, in recv_into
return self.read(nbytes, buffer)
File "/home/dostvip2/miniconda3/envs/gget_alphafold2/lib/python3.10/ssl.py", line 1163, in read
return self._sslobj.read(len, buffer)
ssl.SSLError: [SSL] record layer failure (_ssl.c:2578)

[lauraluebbert]

Hi Mike, I'm glad the installation worked out and thank you for sharing the steps! The error above suggests a problem during the data retrieval over HTTPS. This happens rarely, especially when the internet connection in not stable. Unfortunately, the only solution is to try again. If there is anything you can do to secure the internet connection while the command is running that would be great! A better internet connection will also decrease the runtime.

[mikenada]

Hello @lauraluebbert Thanks for confirming that the installation works. Will try to re-run the analysis with a better internet connection.