Description
https://github.com/bytedance/Protenix/blob/main/docs/colabfold_compatiable_msa.md
I follow the above url to perform the msa search
python3 scripts/colabfold_msa.py examples/dimer.fasta /data/colabfold_db dimer_colabfold_msa --db1 uniref30_2302_db --db3 colabfold_envdb_202108_db --mmseqs_path /home/cadd/programs/protenix/MMseqs2-16-747c6/build/bin/mmseqs
it raise an error,
Merging the results to dimer_colabfold_msa/res
[=================================================================] 100.00% 2 0s 0ms
Time for merging to res: 0h 0m 0s 0ms
Time for processing: 0h 0m 0s 1ms
rmdb dimer_colabfold_msa/tmp/17567987179003700171/aln_1
Time for processing: 0h 0m 0s 0ms
rmdb dimer_colabfold_msa/tmp/17567987179003700171/aln_tmp_2
Time for processing: 0h 0m 0s 0ms
mvdb dimer_colabfold_msa/tmp/latest/profile_1 dimer_colabfold_msa/prof_res
MMseqs Version: bd0fb80
Verbosity 3
Time for processing: 0h 0m 0s 0ms
lndb dimer_colabfold_msa/qdb_h dimer_colabfold_msa/prof_res_h
MMseqs Version: bd0fb80
Verbosity 3
Time for processing: 0h 0m 0s 0ms
expandaln dimer_colabfold_msa/qdb /data/colabfold_db/uniref30_2302_db_seq dimer_colabfold_msa/res /data/colabfold_db/uniref30_2302_db_aln dimer_colabfold_msa/res_exp --db-load-mode 0 --threads 64 --expansion-mode 0 -e inf --expand-filter-clusters 1 --max-seq-id 0.95
MMseqs Version: bd0fb80
Expansion mode 0
Substitution matrix aa:blosum62.out,nucl:nucleotide.out
Gap open cost aa:11,nucl:5
Gap extension cost aa:1,nucl:2
Max sequence length 65535
Score bias 0
Compositional bias 1
Compositional bias 1
E-value threshold inf
Seq. id. threshold 0
Coverage threshold 0
Coverage mode 0
Pseudo count mode 0
Pseudo count a substitution:1.100,context:1.400
Pseudo count b substitution:4.100,context:5.800
Expand filter clusters 1
Use filter only at N seqs 0
Maximum seq. id. threshold 0.95
Minimum seq. id. 0.0
Minimum score per column -20
Minimum coverage 0
Select N most diverse seqs 1000
Preload mode 0
Compressed 0
Threads 64
Verbosity 3
[=================================================================] 100.00% 2 0s 95ms
free(): invalid next size (normal)
Traceback (most recent call last):
File "/home/cadd/.conda/envs/proteinix/bin/colabfold_search", line 8, in
sys.exit(main())
File "/home/cadd/.conda/envs/proteinix/lib/python3.10/site-packages/colabfold/mmseqs/search.py", line 319, in main
mmseqs_search_monomer(
File "/home/cadd/.conda/envs/proteinix/lib/python3.10/site-packages/colabfold/mmseqs/search.py", line 94, in mmseqs_search_monomer
run_mmseqs(mmseqs, ["expandaln", base.joinpath("qdb"), dbbase.joinpath(f"{uniref_db}{dbSuffix1}"), base.joinpath("res"), dbbase.joinpath(f"{uniref_db}{dbSuffix2}"), base.joinpath("res_exp"), "--db-load-mode", str(db_load_mode), "--threads", str(threads)] + expand_param)
File "/home/cadd/.conda/envs/proteinix/lib/python3.10/site-packages/colabfold/mmseqs/search.py", line 25, in run_mmseqs
subprocess.check_call([mmseqs] + params)
File "/home/cadd/.conda/envs/proteinix/lib/python3.10/subprocess.py", line 369, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '[PosixPath('/home/cadd/programs/protenix/MMseqs2-16-747c6/build/bin/mmseqs'), 'expandaln', PosixPath('dimer_colabfold_msa/qdb'), PosixPath('/data/colabfold_db/uniref30_2302_db_seq'), PosixPath('dimer_colabfold_msa/res'), PosixPath('/data/colabfold_db/uniref30_2302_db_aln'), PosixPath('dimer_colabfold_msa/res_exp'), '--db-load-mode', '0', '--threads', '64', '--expansion-mode', '0', '-e', 'inf', '--expand-filter-clusters', '1', '--max-seq-id', '0.95']' died with <Signals.SIGABRT: 6>.
Traceback (most recent call last):
File "/home/cadd/programs/protenix/scripts/colabfold_msa.py", line 277, in
results_a3m = run_colabfold_search(config)
File "/home/cadd/programs/protenix/scripts/colabfold_msa.py", line 217, in run_colabfold_search
raise FileNotFoundError(f"No .a3m files found in {config.results_dir}")
FileNotFoundError: No .a3m files found in dimer_colabfold_msa