Broken mDeepFRI installation and first prediction

[achousal]

• After running pip install mdeepfri, and mDeepFRI --help, I get error messages like the following:

(deepfri) /mnt/data2/andres/deepfri/databases$ mDeepFRI --help
Traceback (most recent call last):
File "/home/kuanguser/miniconda3/envs/deepfri/bin/mDeepFRI", line 5, in
from mDeepFRI.cli import main
File "/home/kuanguser/miniconda3/envs/deepfri/lib/python3.8/site-packages/mDeepFRI/cli.py", line 7, in
from mDeepFRI.pipeline import predict_protein_function
File "/home/kuanguser/miniconda3/envs/deepfri/lib/python3.8/site-packages/mDeepFRI/pipeline.py", line 10, in
from tqdm import tqdm

• The modules needed which did not install with the general command are: tqdm, pyopal, pysam, biotite, onnxruntime, MMseq2

• After installing the modules I get the help command working, but the default foldcomp and MMseq2 databases wont install properly after running a prediction.

• Command used:

• mDeepFRI predict-function -i /mnt/data2/andres/data/prediction_mgm/SRR1778453/SRR1778453_mH_fC_mS_genes.fna -d /mnt/data2/andres/deepfri/foldcomp/database -w /mnt/data2/andres/deepfri/weights/ -o /mnt/data2/andres/deepfri/output/ 2> log.txt &

• Note: at first, the prediction error log was asking for mmseq package, so I installed MMseq2 from "conda install -c conda-forge -c bioconda mmseqs2"
  Related error message:

[2024-11-26 13:55:20] cli.predict_function INFO: Minimum length: 60
[2024-11-26 13:55:20] cli.predict_function INFO: Maximum length: 1000
[2024-11-26 13:55:20] pipeline.predict_protein_function INFO: EC number prediction is not supported in version 1.1.
[2024-11-26 13:55:20] pipeline.predict_protein_function INFO: Creating PDB100 database. This may take a bit during a first run.
[2024-11-26 13:55:20] pdb.create_pdb_mmseqs INFO: Downloading PDB100 database.
[2024-11-26 13:55:44] pdb.create_pdb_mmseqs INFO: Creating MMSeqs2 database from PDB100.
Traceback (most recent call last):
File "/home/kuanguser/miniconda3/envs/deepfri/bin/mDeepFRI", line 8, in
sys.exit(main())
File "/home/kuanguser/miniconda3/envs/deepfri/lib/python3.8/site-packages/click/core.py", line 1157, in call
return self.main(*args, **kwargs)
File "/home/kuanguser/miniconda3/envs/deepfri/lib/python3.8/site-packages/click/core.py", line 1078, in main
rv = self.invoke(ctx)
File "/home/kuanguser/miniconda3/envs/deepfri/lib/python3.8/site-packages/click/core.py", line 1688, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/home/kuanguser/miniconda3/envs/deepfri/lib/python3.8/site-packages/click/core.py", line 1434, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/home/kuanguser/miniconda3/envs/deepfri/lib/python3.8/site-packages/click/core.py", line 783, in invoke
return __callback(*args, **kwargs)
File "/home/kuanguser/miniconda3/envs/deepfri/lib/python3.8/site-packages/click/decorators.py", line 33, in new_func
return f(get_current_context(), *args, **kwargs)
File "/home/kuanguser/miniconda3/envs/deepfri/lib/python3.8/site-packages/mDeepFRI/cli.py", line 231, in predict_function
predict_protein_function(
File "/home/kuanguser/miniconda3/envs/deepfri/lib/python3.8/site-packages/mDeepFRI/pipeline.py", line 80, in predict_protein_function
pdb100 = create_pdb_mmseqs()
File "/home/kuanguser/miniconda3/envs/deepfri/lib/python3.8/site-packages/mDeepFRI/pdb.py", line 65, in create_pdb_mmseqs
createdb(compressed_path, pdb100_mmseqs)
File "/home/kuanguser/miniconda3/envs/deepfri/lib/python3.8/site-packages/mDeepFRI/mmseqs.py", line 43, in createdb
run_command(f"mmseqs createdb {sequences_file} {db_path} --dbtype 1")
File "/home/kuanguser/miniconda3/envs/deepfri/lib/python3.8/site-packages/mDeepFRI/utils.py", line 32, in run_command
completed_process = subprocess.run(command,
File "/home/kuanguser/miniconda3/envs/deepfri/lib/python3.8/subprocess.py", line 493, in run
with Popen(*popenargs, **kwargs) as process:
File "/home/kuanguser/miniconda3/envs/deepfri/lib/python3.8/subprocess.py", line 858, in init
self._execute_child(args, executable, preexec_fn, close_fds,
File "/home/kuanguser/miniconda3/envs/deepfri/lib/python3.8/subprocess.py", line 1720, in _execute_child
raise child_exception_type(errno_num, err_msg, err_filename)
FileNotFoundError: [Errno 2] No such file or directory: 'mmseqs'

• Second try with MMseq2 installed in enviorment:

[2024-11-26 14:01:57] pipeline.predict_protein_function INFO: EC number prediction is not supported in version 1.1.
[2024-11-26 14:01:57] pipeline.predict_protein_function INFO: Creating PDB100 database. This may take a bit during a first run.
[2024-11-26 14:01:57] pipeline.predict_protein_function INFO: PDB100 database created.
[2024-11-26 14:01:57] database.build_database INFO: Building MMSeqs2 database from /mnt/data2/andres/deepfri/foldcomp/database
[2024-11-26 14:01:57] database.build_database INFO: Found /mnt/data2/andres/deepfri/foldcomp/database.fasta.gz in /mnt/data2/andres/deepfri/foldcomp
[2024-11-26 14:01:57] database.build_database INFO: Skipping extraction of FASTA file from FoldComp database.
[2024-11-26 14:01:57] database.build_database INFO: Creating and indexing MMSeqs2 database.
Traceback (most recent call last):
File "/home/kuanguser/miniconda3/envs/deepfri/lib/python3.8/site-packages/mDeepFRI/utils.py", line 32, in run_command
completed_process = subprocess.run(command,
File "/home/kuanguser/miniconda3/envs/deepfri/lib/python3.8/subprocess.py", line 516, in run
raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '['mmseqs', 'createdb', '/mnt/data2/andres/deepfri/foldcomp/database.fasta.gz', '/mnt/data2/andres/deepfri/foldcomp/database.mmseqsDB', '--dbtype', '1']' returned non-zero exit status 1.

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
File "/home/kuanguser/miniconda3/envs/deepfri/bin/mDeepFRI", line 8, in
sys.exit(main())
File "/home/kuanguser/miniconda3/envs/deepfri/lib/python3.8/site-packages/click/core.py", line 1157, in call
return self.main(*args, **kwargs)
File "/home/kuanguser/miniconda3/envs/deepfri/lib/python3.8/site-packages/click/core.py", line 1078, in main
rv = self.invoke(ctx)
File "/home/kuanguser/miniconda3/envs/deepfri/lib/python3.8/site-packages/click/core.py", line 1688, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/home/kuanguser/miniconda3/envs/deepfri/lib/python3.8/site-packages/click/core.py", line 1434, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/home/kuanguser/miniconda3/envs/deepfri/lib/python3.8/site-packages/click/core.py", line 783, in invoke
return __callback(*args, **kwargs)
File "/home/kuanguser/miniconda3/envs/deepfri/lib/python3.8/site-packages/click/decorators.py", line 33, in new_func
return f(get_current_context(), *args, **kwargs)
File "/home/kuanguser/miniconda3/envs/deepfri/lib/python3.8/site-packages/mDeepFRI/cli.py", line 231, in predict_function
predict_protein_function(
File "/home/kuanguser/miniconda3/envs/deepfri/lib/python3.8/site-packages/mDeepFRI/pipeline.py", line 89, in predict_protein_function
db = build_database(
File "/home/kuanguser/miniconda3/envs/deepfri/lib/python3.8/site-packages/mDeepFRI/database.py", line 87, in build_database
create_target_database(output_sequences, mmseqs_path, threads)
File "/home/kuanguser/miniconda3/envs/deepfri/lib/python3.8/site-packages/mDeepFRI/mmseqs.py", line 112, in create_target_database
createdb(foldcomp_fasta_path, mmseqs_db_path)
File "/home/kuanguser/miniconda3/envs/deepfri/lib/python3.8/site-packages/mDeepFRI/mmseqs.py", line 43, in createdb
run_command(f"mmseqs createdb {sequences_file} {db_path} --dbtype 1")
File "/home/kuanguser/miniconda3/envs/deepfri/lib/python3.8/site-packages/mDeepFRI/utils.py", line 42, in run_command
raise RuntimeError(
RuntimeError: Command 'mmseqs createdb /mnt/data2/andres/deepfri/foldcomp/database.fasta.gz /mnt/data2/andres/deepfri/foldcomp/database.mmseqsDB --dbtype 1' failed with exit code 1
The input files have no entry: - /mnt/data2/andres/deepfri/foldcomp/database.fasta.gz
Please check your input files. Only files in fasta/fastq[.gz|bz2] are supported

• This is how my foldcomp folder looks:

(deepfri) kuanguser@kuanglabnslook:/mnt/data2/andres/deepfri/foldcomp$ ls -hs
total 768K
128K database 0 database.mmseqsDB 0 database.mmseqsDB.index 0 database.mmseqsDB_h 0 database.mmseqsDB_h.index
128K database.fasta.gz 128K database.mmseqsDB.dbtype 128K database.mmseqsDB.source 128K database.mmseqsDB_h.dbtype 128K log.txt

• Trying to create a custom db with afdb_swissprot_v4:

(deepfri) kuanguser@kuanglabnslook:/mnt/data2/andres/deepfri$ foldcomp compress -t 40 afdb_swissprot_v4 databases/afdb_swissprot_v4.tar.gz
foldcomp: command not found

[valentynbez]

Hi @achousal!
Can you share you OS and python version?

I have a strong imprression that pip install failed.
Could you please rerun installation command and share log from it?
pip install mdeepfri --force-reinstall

Thanks for using my software and reporting back!
Valentyn