ColabFold
ColabFold copied to clipboard
sokrypton
Update setup-and-start-local.sh for GPU
Source: https://github.com/sokrypton/ColabFold/issues/766:
I need to update setup-and-start-local.sh for GPU, currently it will just break on the GPU databases. I forgot about this script. @milot-mirdita
Please update setup-and-start-local.sh for GPU as outlined in https://github.com/sokrypton/ColabFold/issues/766 by @milot-mirdita .
It currently fails like this:
$ ./setup-and-start-local.sh
uniref30_2302_db
uniref30_2302_db.GPU_READY
uniref30_2302_db.dbtype
uniref30_2302_db.index
uniref30_2302_db.lookup
uniref30_2302_db_aln
uniref30_2302_db_aln.dbtype
uniref30_2302_db_aln.index
uniref30_2302_db_h
uniref30_2302_db_h.dbtype
uniref30_2302_db_h.index
uniref30_2302_db_mapping
uniref30_2302_db_seq
uniref30_2302_db_seq.dbtype
uniref30_2302_db_seq.index
uniref30_2302_db_seq_h
uniref30_2302_db_seq_h.dbtype
uniref30_2302_db_seq_h.index
uniref30_2302_db_taxonomy
createindex uniref30_2302_db tmp1 --remove-tmp-files 1
MMseqs Version: 4589151554eb83a70ff0c4d04d21b83cabc203e4
Seed substitution matrix aa:VTML80.out,nucl:nucleotide.out
k-mer length 0
Alphabet size aa:21,nucl:5
Compositional bias 1
Compositional bias 1
Max sequence length 65535
Max results per query 300
Mask residues 1
Mask residues probability 0.9
Mask lower case residues 0
Spaced k-mers 1
Spaced k-mer pattern
Sensitivity 7.5
k-score seq:0,prof:0
Check compatible 0
Search type 0
Split database 0
Split memory limit 0
Verbosity 3
Threads 8
Min codons in orf 30
Max codons in length 32734
Max orf gaps 2147483647
Contig start mode 2
Contig end mode 2
Orf start mode 1
Forward frames 1,2,3
Reverse frames 1,2,3
Translation table 1
Translate orf 0
Use all table starts false
Offset of numeric ids 0
Create lookup 0
Compressed 0
Add orf stop false
Overlap between sequences 0
Sequence split mode 1
Header split mode 0
Strand selection 1
Remove temporary files true
createindex uniref30_2302_db tmp1 --remove-tmp-files 1
MMseqs Version: 4589151554eb83a70ff0c4d04d21b83cabc203e4
Seed substitution matrix aa:VTML80.out,nucl:nucleotide.out
k-mer length 0
Alphabet size aa:21,nucl:5
Compositional bias 1
Compositional bias 1
Max sequence length 65535
Max results per query 300
Mask residues 1
Mask residues probability 0.9
Mask lower case residues 0
Spaced k-mers 1
Spaced k-mer pattern
Sensitivity 7.5
k-score seq:0,prof:0
Check compatible 0
Search type 0
Split database 0
Split memory limit 0
Verbosity 3
Threads 8
Min codons in orf 30
Max codons in length 32734
Max orf gaps 2147483647
Contig start mode 2
Contig end mode 2
Orf start mode 1
Forward frames 1,2,3
Reverse frames 1,2,3
Translation table 1
Translate orf 0
Use all table starts false
Offset of numeric ids 0
Create lookup 0
Compressed 0
Add orf stop false
Overlap between sequences 0
Sequence split mode 1
Header split mode 0
Strand selection 1
Remove temporary files true
indexdb uniref30_2302_db uniref30_2302_db --seed-sub-mat 'aa:VTML80.out,nucl:nucleotide.out' -k 0 --alph-size aa:21,nucl:5 --comp-bias-corr 1 --comp-bias-corr-scale 1 --max-seq-len 65535 --max-seqs 300 --mask 1 --mask-prob 0.9 --mask-lower-case 0 --spaced-kmer-mode 1 -s 7.5 --k-score seq:0,prof:0 --check-compatible 0 --search-type 0 --split 0 --split-memory-limit 0 -v 3 --threads 8
Target split mode. Searching through 15 splits
Estimated memory consumption: 16G
Write VERSION (0)
Write META (1)
Write SCOREMATRIX3MER (4)
Write SCOREMATRIX2MER (3)
Write SCOREMATRIXNAME (2)
Write SPACEDPATTERN (23)
Write GENERATOR (22)
Write DBR1INDEX (5)
Write DBR1DATA (6)
Write DBR2INDEX (7)
Write DBR2DATA (8)
Write HDR1INDEX (18)
Write HDR1DATA (19)
Write ALNINDEX (24)
Write ALNDATA (25)
Index table: counting k-mers
[=================================================================] 100.00% 9.10M 4s 829ms
Index table: Masked residues: 0
No k-mer could be extracted for the database uniref30_2302_db.
Maybe the sequences length is less than 14 residues.
Error: indexdb died
I just pushed an update to the instructions and the scripts. Please let me know if they work for you
