The software system of improving AlphaFold2- and AlphaFold-Multimer-based protein tertiary & quaternary structure prediction. It was developed by the Bioinformatics and Machine Learning Lab at the University of Missouri. It was blindly tested in CASP15 and ranked among the best server predictors in 2022. It improves AlphaFold's accuracy by 5-10%.
I would appreciate your assistance in running your app.
I am having difficulty running your app as a Singularity container on our HPC cluster with the example input for the monomer mode (examples/fasta/test_monomer.fasta). It appears that there should be a 'colabfold' directory in MULTICOM3/tools that contains the necessary scripts.
Could you please provide guidance on this issue?
Thank you!
stderr.log:
/sbin/ldconfig.real: Can't create temporary cache file /etc/ld.so.cache~: Read-only file system
I0627 18:33:07.009725 47128027451648 jackhmmer.py:108] Launching subprocess "/opt/conda/bin/jackhmmer -o /dev/null -A /mnt/output/N1_monomer_alignments_generation/mgnify_sto/test_monomer_mgnify.sto --noali --F1 0.0005 --F2 5e-05 --F3 5e-07 --incE 0.000$
I0627 18:33:07.009725 47128027451648 jackhmmer.py:108] Launching subprocess "/opt/conda/bin/jackhmmer -o /dev/null -A /mnt/output/N1_monomer_alignments_generation/uniref90_sto/test_monomer_uniref90.sto --noali --F1 0.0005 --F2 5e-05 --F3 5e-07 --incE 0$
I0627 18:33:07.009950 47128027451648 hhblits.py:112] Launching subprocess "/opt/conda/bin/hhblits -i /mnt/fasta_path/test_monomer.fasta -cpu 4 -oa3m /mnt/output/N1_monomer_alignments_generation/bfd_a3m/test_monomer_bfd.a3m -o /mnt/output/N1_monomer_ali$
I0627 18:33:07.010023 47128027451648 hhblits.py:112] Launching subprocess "/opt/conda/bin/hhblits -i /mnt/fasta_path/test_monomer.fasta -cpu 4 -oa3m /mnt/output/N1_monomer_alignments_generation/uniref30_bfd_a3m/test_monomer_uniref30_bfd.a3m -o /mnt/out$
I0627 18:33:07.010268 47128027451648 hhblits.py:112] Launching subprocess "/opt/conda/bin/hhblits -i /mnt/fasta_path/test_monomer.fasta -cpu 4 -oa3m /mnt/output/N1_monomer_alignments_generation/uniref30_a3m/test_monomer_uniref30.a3m -o /mnt/output/N1_m$
I0627 18:33:07.011448 47128027451648 hhblits.py:112] Launching subprocess "/opt/conda/bin/hhblits -i /mnt/fasta_path/test_monomer.fasta -cpu 4 -oa3m /mnt/output/N1_monomer_alignments_generation/uniclust30_bfd_a3m/test_monomer_uniclust30_bfd.a3m -o /mnt$
I0627 18:33:07.010956 47128027451648 hhblits.py:112] Launching subprocess "/opt/conda/bin/hhblits -i /mnt/fasta_path/test_monomer.fasta -cpu 4 -oa3m /mnt/output/N1_monomer_alignments_generation/uniclust30_a3m/test_monomer_uniclust30.a3m -o /mnt/output/$
I0627 18:33:07.012755 47128027451648 colabfold_msa_runner.py:56] Colabfold subprocess "python /app/MULTICOM3/tools/colabfold/search.py /mnt/fasta_path/test_monomer.fasta /mnt/multicom3_db/colabfold /mnt/output/N1_monomer_alignments_generation/colabfold$
I0627 18:33:07.021775 47128027451648 utils.py:23] Started Colabfold query
I0627 18:33:07.152521 47128027451648 utils.py:23] Started Jackhmmer (mgy_clusters_2022_05.fa) query
I0627 18:33:07.152528 47128027451648 utils.py:23] Started Jackhmmer (uniref90.fasta) query
I0627 18:33:07.156840 47128027451648 utils.py:27] Finished Colabfold query in 0.135 seconds
E0627 18:33:07.156933 47128027451648 colabfold_msa_runner.py:66] HHblits failed. Colabfold stderr begin:
E0627 18:33:07.156984 47128027451648 colabfold_msa_runner.py:69] python: can't open file '/app/MULTICOM3/tools/colabfold/search.py': [Errno 2] No such file or directory
E0627 18:33:07.157022 47128027451648 colabfold_msa_runner.py:70] Colabfold stderr end
I0627 18:33:07.163987 47128027451648 utils.py:23] Started HHblits query
I0627 18:33:07.163986 47128027451648 utils.py:23] Started HHblits query
I0627 18:33:07.163992 47128027451648 utils.py:23] Started HHblits query
I0627 18:33:07.164021 47128027451648 utils.py:23] Started HHblits query
I0627 18:33:07.164023 47128027451648 utils.py:23] Started HHblits query
I0627 18:34:48.832529 47128027451648 utils.py:27] Finished HHblits query in 101.668 seconds
I0627 19:00:08.474313 47128027451648 utils.py:27] Finished Jackhmmer (uniref90.fasta) query in 1621.320 seconds
I0627 19:22:34.567044 47128027451648 utils.py:27] Finished HHblits query in 2967.403 seconds
I0627 19:23:00.091713 47128027451648 utils.py:27] Finished HHblits query in 2992.927 seconds
I0627 19:23:19.643625 47128027451648 utils.py:27] Finished HHblits query in 3012.479 seconds
I0627 19:30:36.475643 47128027451648 utils.py:27] Finished HHblits query in 3449.311 seconds
I0627 21:02:51.629371 47128027451648 utils.py:27] Finished Jackhmmer (mgy_clusters_2022_05.fa) query in 8984.475 seconds
Traceback (most recent call last):
File "/app/MULTICOM3/bin/monomer.py", line 172, in
app.run(main)
File "/opt/conda/lib/python3.8/site-packages/absl/app.py", line 312, in run
_run_main(main, args)
File "/opt/conda/lib/python3.8/site-packages/absl/app.py", line 258, in _run_main
sys.exit(main(argv))
File "/app/MULTICOM3/bin/monomer.py", line 59, in main
raise RuntimeError('The monomer alignment generation has failed!')
RuntimeError: The monomer alignment generation has failed!
stdout.log:
Configuration....Done
Predicting structure for monomer
#################################################################################################
Start to generate alignments for monomers
Using database: /mnt/af_db/uniref90/uniref90.fasta
Using database: /mnt/af_db/bfd/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt
Using database: /mnt/af_db/uniref30/UniRef30_2021_03
Using database: /mnt/af_db/mgnify/mgy_clusters_2022_05.fa
Using database: /mnt/multicom3_db/uniclust30_2018_08/uniclust30_2018_08
Using database: /mnt/af_db/bfd/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt
Using database: /mnt/multicom3_db/uniclust30_2018_08/uniclust30_2018_08
Using database: /mnt/af_db/bfd/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt
Using database: /mnt/af_db/uniref30/UniRef30_2021_03
Using database: /mnt/multicom3_db/colabfold
Colabfold failed
stdout:
stderr:
python: can't open file '/app/MULTICOM3/tools/colabfold/search.py': [Errno 2] No such file or directory
Hello,
Thank you for sharing your code.
I would appreciate your assistance in running your app.
I am having difficulty running your app as a Singularity container on our HPC cluster with the example input for the monomer mode (examples/fasta/test_monomer.fasta). It appears that there should be a 'colabfold' directory in MULTICOM3/tools that contains the necessary scripts.
Could you please provide guidance on this issue?
Thank you! stderr.log:
stdout.log: