ColabFold
ColabFold copied to clipboard
sokrypton
`colabfold_search` fails GPU search
TL;DR -> colabfold_search fails search on "GPU" DB setup
Error
INFO:colabfold.mmseqs.search:Running mmseqs align /home/ec2-user/result/prof_res /home/ec2-user/msa-work/db/uniref30_2302_db_seq /home/ec2-user/result/res_exp /home/ec2-user/result/res_exp_realign --db-load-mode 0 -e 10 --max-accept 100000 --threads 64 --alt-ali 10 -a
align /home/ec2-user/result/prof_res /home/ec2-user/msa-work/db/uniref30_2302_db_seq /home/ec2-user/result/res_exp /home/ec2-user/result/res_exp_realign --db-load-mode 0 -e 10 --max-accept 100000 --threads 64 --alt-ali 10 -a
Input /home/ec2-user/result/prof_res does not exist
Traceback (most recent call last):
File "/home/ec2-user/msa-work/localcolabfold/colabfold-conda/bin/colabfold_search", line 8, in <module>
sys.exit(main())
File "/home/ec2-user/msa-work/localcolabfold/colabfold-conda/lib/python3.10/site-packages/colabfold/mmseqs/search.py", line 461, in main
mmseqs_search_monomer(
File "/home/ec2-user/msa-work/localcolabfold/colabfold-conda/lib/python3.10/site-packages/colabfold/mmseqs/search.py", line 131, in mmseqs_search_monomer
run_mmseqs(mmseqs, ["align", base.joinpath("prof_res"), dbbase.joinpath(f"{uniref_db}{dbSuffix1}"), base.joinpath("res_exp"), base.joinpath("res_exp_realign"), "--db-load-mode", str(db_load_mode), "-e", str(align_eval), "--max-accept", str(max_accept), "--threads", str(threads), "--alt-ali", "10", "-a"])
File "/home/ec2-user/msa-work/localcolabfold/colabfold-conda/lib/python3.10/site-packages/colabfold/mmseqs/search.py", line 46, in run_mmseqs
subprocess.check_call([mmseqs] + params)
File "/home/ec2-user/msa-work/localcolabfold/colabfold-conda/lib/python3.10/subprocess.py", line 369, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '[PosixPath('mmseqs'), 'align', PosixPath('/home/ec2-user/result/prof_res'), PosixPath('/home/ec2-user/msa-work/db/uniref30_2302_db_seq'), PosixPath('/home/ec2-user/result/res_exp'), PosixPath('/home/ec2-user/result/res_exp_realign'), '--db-load-mode', '0', '-e', '10', '--max-accept', '100000', '--threads', '64', '--alt-ali', '10', '-a']' returned non-zero exit status 1.
Steps to reproduce
1. DB setup
git clone https://github.com/sokrypton/ColabFold.git
GPU=1 ./setup_databases.sh /path/to/db_folder
2. Install mmseqs
wget https://mmseqs.com/latest/mmseqs-linux-gpu.tar.gz;
tar xvfz mmseqs-linux-gpu.tar.gz;
# In ~/.bashrc
export PATH=$(pwd)/mmseqs/bin/:$PATH
source ~/.bashrc
3. Install localcolabfold
### INSTALL colabfold ###
wget https://raw.githubusercontent.com/YoshitakaMo/localcolabfold/main/install_colabbatch_linux.sh
bash install_colabbatch_linux.sh
# In ~/.bashrc
export PATH="/path/to/your/localcolabfold/colabfold-conda/bin:$PATH"
source ~/.bashrc
4. Running coldfold_search
colabfold_search --mmseqs mmseqs --gpu 1 input_sequences.fasta /home/ec2-user/msa-work/db/ ~/result/
Infrastructure setup
- Nvidia 1xL40S
- 16 CPU cores (AMD EPYC 7R13 Processor)
- 128GB Ram
- 3TB SSD
Can you upload the rest of the log too please? The snippet doesn't really reveal why /home/ec2-user/result/prof_res was not created.
Can you upload the rest of the log too please? The snippet doesn't really reveal why
/home/ec2-user/result/prof_reswas not created.
Full logs for colabfold_search --mmseqs mmseqs --gpu 1 input_sequences.fasta /home/ec2-user/msa-work/db/ ~/result/
colabfold_search --mmseqs mmseqs --gpu 1 input_sequences.fasta /home/ec2-user/msa-work/db/ ~/result/
INFO:colabfold.mmseqs.search:Running mmseqs createdb /home/ec2-user/result/query.fas /home/ec2-user/result/qdb --shuffle 0
createdb /home/ec2-user/result/query.fas /home/ec2-user/result/qdb --shuffle 0
Converting sequences
Time for merging to qdb_h: 0h 0m 0s 0ms
Time for merging to qdb: 0h 0m 0s 0ms
Database type: Nucleotide
Time for processing: 0h 0m 0s 0ms
INFO:colabfold.mmseqs.search:Search does not use index
INFO:colabfold.mmseqs.search:Running mmseqs search /home/ec2-user/result/qdb /home/ec2-user/msa-work/db/uniref30_2302_db /home/ec2-user/result/res /home/ec2-user/result/tmp --threads 64 --num-iterations 3 --db-load-mode 0 -a -e 0.1 --max-seqs 10000 --gpu 1 --prefilter-mode 1
Create directory /home/ec2-user/result/tmp
search /home/ec2-user/result/qdb /home/ec2-user/msa-work/db/uniref30_2302_db /home/ec2-user/result/res /home/ec2-user/result/tmp --threads 64 --num-iterations 3 --db-load-mode 0 -a -e 0.1 --max-seqs 10000 --gpu 1 --prefilter-mode 1
extractorfs /home/ec2-user/result/qdb /home/ec2-user/result/tmp/12810382096006738180/q_orfs_aa --min-length 30 --max-length 32734 --max-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 1 --use-all-table-starts 0 --id-offset 0 --create-lookup 0 --threads 64 --compressed 0 -v 3
[=================================================================] 100.00% 3 0s 7ms
Time for merging to q_orfs_aa_h: 0h 0m 0s 3ms
Time for merging to q_orfs_aa: 0h 0m 0s 3ms
Time for processing: 0h 0m 0s 103ms
ungappedprefilter /home/ec2-user/result/tmp/12810382096006738180/q_orfs_aa /home/ec2-user/msa-work/db/uniref30_2302_db.idx /home/ec2-user/result/tmp/12810382096006738180/search/pref_0 --sub-mat 'aa:blosum62.out,nucl:nucleotide.out' -c 0 -e 0.1 --cov-mode 0 --comp-bias-corr 1 --comp-bias-corr-scale 1 --min-ungapped-score 15 --max-seqs 10000 --db-load-mode 0 --gpu 1 --gpu-server 0 --gpu-server-wait-timeout 600 --prefilter-mode 1 --threads 64 --compressed 0 -v 3
Index version: 16
Generated by: 17.b804f
ScoreMatrix: VTML80.out
[=================================================================] 100.00% 4 1s 768ms
Time for merging to pref_0: 0h 0m 0s 0ms
Time for processing: 0h 1m 15s 686ms
align /home/ec2-user/result/tmp/12810382096006738180/q_orfs_aa /home/ec2-user/msa-work/db/uniref30_2302_db.idx /home/ec2-user/result/tmp/12810382096006738180/search/pref_0 /home/ec2-user/result/tmp/12810382096006738180/search/aln_0 --sub-mat 'aa:blosum62.out,nucl:nucleotide.out' -a 1 --alignment-mode 2 --alignment-output-mode 0 --wrapped-scoring 0 -e 0.1 --min-seq-id 0 --min-aln-len 0 --seq-id-mode 0 --alt-ali 0 -c 0 --cov-mode 0 --max-seq-len 65535 --comp-bias-corr 1 --comp-bias-corr-scale 1 --max-rejected 2147483647 --max-accept 2147483647 --add-self-matches 0 --db-load-mode 0 --pca substitution:1.100,context:1.400 --pcb substitution:4.100,context:5.800 --score-bias 0 --realign 1 --realign-score-bias -0.2 --realign-max-seqs 2147483647 --corr-score-weight 0 --gap-open aa:11,nucl:5 --gap-extend aa:1,nucl:2 --zdrop 40 --threads 64 --compressed 0 -v 3
Index version: 16
Generated by: 17.b804f
ScoreMatrix: VTML80.out
Compute score only
Query database size: 4 type: Aminoacid
Target database size: 36293491 type: Aminoacid
Calculation of alignments
[=================================================================] 100.00% 4 0s 509ms
Time for merging to aln_0: 0h 0m 0s 0ms
40000 alignments calculated
42 sequence pairs passed the thresholds (0.001050 of overall calculated)
10.500000 hits per query sequence
Time for processing: 0h 0m 1s 515ms
result2profile /home/ec2-user/result/tmp/12810382096006738180/q_orfs_aa /home/ec2-user/msa-work/db/uniref30_2302_db.idx /home/ec2-user/result/tmp/12810382096006738180/search/aln_0 /home/ec2-user/result/tmp/12810382096006738180/search/profile_0 --sub-mat 'aa:blosum62.out,nucl:nucleotide.out' -e 0.1 --mask-profile 1 --e-profile 0.1 --comp-bias-corr 1 --comp-bias-corr-scale 1 --wg 0 --allow-deletion 0 --filter-msa 1 --filter-min-enable 0 --max-seq-id 0.9 --qid '0.0' --qsc -20 --cov 0 --diff 1000 --pseudo-cnt-mode 0 --pca substitution:1.100,context:1.400 --pcb substitution:4.100,context:5.800 --db-load-mode 0 --gap-open aa:11,nucl:5 --gap-extend aa:1,nucl:2 --threads 64 --compressed 0 -v 3 --profile-output-mode 0
Index version: 16
Generated by: 17.b804f
ScoreMatrix: VTML80.out
Query database size: 4 type: Aminoacid
Target database size: 36293491 type: Aminoacid
[=================================================================] 100.00% 4 0s 4ms
Time for merging to profile_0: 0h 0m 0s 0ms
Time for processing: 0h 0m 0s 822ms
ungappedprefilter /home/ec2-user/result/tmp/12810382096006738180/search/profile_0 /home/ec2-user/msa-work/db/uniref30_2302_db.idx /home/ec2-user/result/tmp/12810382096006738180/search/pref_tmp_1 --sub-mat 'aa:blosum62.out,nucl:nucleotide.out' -c 0 -e 0.1 --cov-mode 0 --comp-bias-corr 1 --comp-bias-corr-scale 1 --min-ungapped-score 15 --max-seqs 10000 --db-load-mode 0 --gpu 1 --gpu-server 0 --gpu-server-wait-timeout 600 --prefilter-mode 1 --threads 64 --compressed 0 -v 3
Index version: 16
Generated by: 17.b804f
ScoreMatrix: VTML80.out
[=================================================================] 100.00% 4 1s 373ms
Time for merging to pref_tmp_1: 0h 0m 0s 0ms
Time for processing: 0h 0m 2s 227ms
subtractdbs /home/ec2-user/result/tmp/12810382096006738180/search/pref_tmp_1 /home/ec2-user/result/tmp/12810382096006738180/search/aln_0 /home/ec2-user/result/tmp/12810382096006738180/search/pref_1 --threads 64 --e-profile 0.1 -e 0.1 --compressed 0 -v 3
subtractdbs /home/ec2-user/result/tmp/12810382096006738180/search/pref_tmp_1 /home/ec2-user/result/tmp/12810382096006738180/search/aln_0 /home/ec2-user/result/tmp/12810382096006738180/search/pref_1 --threads 64 --e-profile 0.1 -e 0.1 --compressed 0 -v 3
Remove /home/ec2-user/result/tmp/12810382096006738180/search/aln_0 ids from /home/ec2-user/result/tmp/12810382096006738180/search/pref_tmp_1
[=================================================================] 100.00% 4 0s 10ms
Time for merging to pref_1: 0h 0m 0s 2ms
Time for processing: 0h 0m 0s 22ms
rmdb /home/ec2-user/result/tmp/12810382096006738180/search/pref_tmp_1
Time for processing: 0h 0m 0s 0ms
align /home/ec2-user/result/tmp/12810382096006738180/search/profile_0 /home/ec2-user/msa-work/db/uniref30_2302_db.idx /home/ec2-user/result/tmp/12810382096006738180/search/pref_1 /home/ec2-user/result/tmp/12810382096006738180/search/aln_tmp_1 --sub-mat 'aa:blosum62.out,nucl:nucleotide.out' -a 1 --alignment-mode 2 --alignment-output-mode 0 --wrapped-scoring 0 -e 0.1 --min-seq-id 0 --min-aln-len 0 --seq-id-mode 0 --alt-ali 0 -c 0 --cov-mode 0 --max-seq-len 65535 --comp-bias-corr 1 --comp-bias-corr-scale 1 --max-rejected 2147483647 --max-accept 2147483647 --add-self-matches 0 --db-load-mode 0 --pca substitution:1.100,context:1.400 --pcb substitution:4.100,context:5.800 --score-bias 0 --realign 0 --realign-score-bias -0.2 --realign-max-seqs 2147483647 --corr-score-weight 0 --gap-open aa:11,nucl:5 --gap-extend aa:1,nucl:2 --zdrop 40 --threads 64 --compressed 0 -v 3
Index version: 16
Generated by: 17.b804f
ScoreMatrix: VTML80.out
Compute score, coverage and sequence identity
Query database size: 4 type: Profile
Target database size: 36293491 type: Aminoacid
Calculation of alignments
[=================================================================] 100.00% 4 0s 455ms
Time for merging to aln_tmp_1: 0h 0m 0s 0ms
39958 alignments calculated
0 sequence pairs passed the thresholds (0.000000 of overall calculated)
0.000000 hits per query sequence
Time for processing: 0h 0m 1s 406ms
mergedbs /home/ec2-user/result/tmp/12810382096006738180/search/profile_0 /home/ec2-user/result/tmp/12810382096006738180/search/aln_1 /home/ec2-user/result/tmp/12810382096006738180/search/aln_0 /home/ec2-user/result/tmp/12810382096006738180/search/aln_tmp_1
Merging the results to /home/ec2-user/result/tmp/12810382096006738180/search/aln_1
[=================================================================] 100.00% 4 0s 0ms
Time for merging to aln_1: 0h 0m 0s 0ms
Time for processing: 0h 0m 0s 2ms
rmdb /home/ec2-user/result/tmp/12810382096006738180/search/aln_0
Time for processing: 0h 0m 0s 0ms
rmdb /home/ec2-user/result/tmp/12810382096006738180/search/aln_tmp_1
Time for processing: 0h 0m 0s 0ms
result2profile /home/ec2-user/result/tmp/12810382096006738180/search/profile_0 /home/ec2-user/msa-work/db/uniref30_2302_db.idx /home/ec2-user/result/tmp/12810382096006738180/search/aln_1 /home/ec2-user/result/tmp/12810382096006738180/search/profile_1 --sub-mat 'aa:blosum62.out,nucl:nucleotide.out' -e 0.1 --mask-profile 1 --e-profile 0.1 --comp-bias-corr 1 --comp-bias-corr-scale 1 --wg 0 --allow-deletion 0 --filter-msa 1 --filter-min-enable 0 --max-seq-id 0.9 --qid '0.0' --qsc -20 --cov 0 --diff 1000 --pseudo-cnt-mode 0 --pca substitution:1.100,context:1.400 --pcb substitution:4.100,context:5.800 --db-load-mode 0 --gap-open aa:11,nucl:5 --gap-extend aa:1,nucl:2 --threads 64 --compressed 0 -v 3 --profile-output-mode 0
Index version: 16
Generated by: 17.b804f
ScoreMatrix: VTML80.out
Query database size: 4 type: Profile
Target database size: 36293491 type: Aminoacid
[=================================================================] 100.00% 4 0s 8ms
Time for merging to profile_1: 0h 0m 0s 0ms
Time for processing: 0h 0m 0s 824ms
ungappedprefilter /home/ec2-user/result/tmp/12810382096006738180/search/profile_1 /home/ec2-user/msa-work/db/uniref30_2302_db.idx /home/ec2-user/result/tmp/12810382096006738180/search/pref_tmp_2 --sub-mat 'aa:blosum62.out,nucl:nucleotide.out' -c 0 -e 0.1 --cov-mode 0 --comp-bias-corr 1 --comp-bias-corr-scale 1 --min-ungapped-score 15 --max-seqs 10000 --db-load-mode 0 --gpu 1 --gpu-server 0 --gpu-server-wait-timeout 600 --prefilter-mode 1 --threads 64 --compressed 0 -v 3
Index version: 16
Generated by: 17.b804f
ScoreMatrix: VTML80.out
[=================================================================] 100.00% 4 1s 371ms
Time for merging to pref_tmp_2: 0h 0m 0s 0ms
Time for processing: 0h 0m 2s 222ms
subtractdbs /home/ec2-user/result/tmp/12810382096006738180/search/pref_tmp_2 /home/ec2-user/result/tmp/12810382096006738180/search/aln_1 /home/ec2-user/result/tmp/12810382096006738180/search/pref_2 --threads 64 --e-profile 0.1 -e 0.1 --compressed 0 -v 3
subtractdbs /home/ec2-user/result/tmp/12810382096006738180/search/pref_tmp_2 /home/ec2-user/result/tmp/12810382096006738180/search/aln_1 /home/ec2-user/result/tmp/12810382096006738180/search/pref_2 --threads 64 --e-profile 0.1 -e 0.1 --compressed 0 -v 3
Remove /home/ec2-user/result/tmp/12810382096006738180/search/aln_1 ids from /home/ec2-user/result/tmp/12810382096006738180/search/pref_tmp_2
[=================================================================] 100.00% 4 0s 10ms
Time for merging to pref_2: 0h 0m 0s 2ms
Time for processing: 0h 0m 0s 21ms
rmdb /home/ec2-user/result/tmp/12810382096006738180/search/pref_tmp_2
Time for processing: 0h 0m 0s 0ms
align /home/ec2-user/result/tmp/12810382096006738180/search/profile_1 /home/ec2-user/msa-work/db/uniref30_2302_db.idx /home/ec2-user/result/tmp/12810382096006738180/search/pref_2 /home/ec2-user/result/tmp/12810382096006738180/search/aln_tmp_2 --sub-mat 'aa:blosum62.out,nucl:nucleotide.out' -a 1 --alignment-mode 2 --alignment-output-mode 0 --wrapped-scoring 0 -e 0.1 --min-seq-id 0 --min-aln-len 0 --seq-id-mode 0 --alt-ali 0 -c 0 --cov-mode 0 --max-seq-len 65535 --comp-bias-corr 1 --comp-bias-corr-scale 1 --max-rejected 2147483647 --max-accept 2147483647 --add-self-matches 0 --db-load-mode 0 --pca substitution:1.100,context:1.400 --pcb substitution:4.100,context:5.800 --score-bias 0 --realign 0 --realign-score-bias -0.2 --realign-max-seqs 2147483647 --corr-score-weight 0 --gap-open aa:11,nucl:5 --gap-extend aa:1,nucl:2 --zdrop 40 --threads 64 --compressed 0 -v 3
Index version: 16
Generated by: 17.b804f
ScoreMatrix: VTML80.out
Compute score, coverage and sequence identity
Query database size: 4 type: Profile
Target database size: 36293491 type: Aminoacid
Calculation of alignments
[=================================================================] 100.00% 4 0s 456ms
Time for merging to aln_tmp_2: 0h 0m 0s 0ms
39958 alignments calculated
0 sequence pairs passed the thresholds (0.000000 of overall calculated)
0.000000 hits per query sequence
Time for processing: 0h 0m 1s 405ms
mergedbs /home/ec2-user/result/tmp/12810382096006738180/search/profile_1 /home/ec2-user/result/tmp/12810382096006738180/aln /home/ec2-user/result/tmp/12810382096006738180/search/aln_1 /home/ec2-user/result/tmp/12810382096006738180/search/aln_tmp_2
Merging the results to /home/ec2-user/result/tmp/12810382096006738180/aln
[=================================================================] 100.00% 4 0s 0ms
Time for merging to aln: 0h 0m 0s 0ms
Time for processing: 0h 0m 0s 0ms
rmdb /home/ec2-user/result/tmp/12810382096006738180/search/aln_1
Time for processing: 0h 0m 0s 0ms
rmdb /home/ec2-user/result/tmp/12810382096006738180/search/aln_tmp_2
Time for processing: 0h 0m 0s 0ms
offsetalignment /home/ec2-user/result/qdb /home/ec2-user/result/tmp/12810382096006738180/q_orfs_aa /home/ec2-user/msa-work/db/uniref30_2302_db.idx /home/ec2-user/msa-work/db/uniref30_2302_db.idx /home/ec2-user/result/tmp/12810382096006738180/aln /home/ec2-user/result/res --chain-alignments 0 --merge-query 1 --search-type 0 --threads 64 --compressed 0 --db-load-mode 0 -v 3
Index version: 16
Generated by: 17.b804f
ScoreMatrix: VTML80.out
Computing ORF lookup Computing contig offsets
Computing contig lookup
Time for contig lookup: 0h 0m 0s 0ms
Writing results to: /home/ec2-user/result/res
[=================================================================] 100.00% 3 0s 0ms
Time for merging to res: 0h 0m 0s 0ms
Time for processing: 0h 6m 46s 21ms
INFO:colabfold.mmseqs.search:Running mmseqs mvdb /home/ec2-user/result/tmp/latest/profile_1 /home/ec2-user/result/prof_res
mvdb /home/ec2-user/result/tmp/latest/profile_1 /home/ec2-user/result/prof_res
Time for processing: 0h 0m 0s 0ms
INFO:colabfold.mmseqs.search:Running mmseqs lndb /home/ec2-user/result/qdb_h /home/ec2-user/result/prof_res_h
lndb /home/ec2-user/result/qdb_h /home/ec2-user/result/prof_res_h
Time for processing: 0h 0m 0s 0ms
INFO:colabfold.mmseqs.search:Running mmseqs expandaln /home/ec2-user/result/qdb /home/ec2-user/msa-work/db/uniref30_2302_db_seq /home/ec2-user/result/res /home/ec2-user/msa-work/db/uniref30_2302_db_aln /home/ec2-user/result/res_exp --db-load-mode 0 --threads 64 --expansion-mode 0 -e inf --expand-filter-clusters 1 --max-seq-id 0.95
expandaln /home/ec2-user/result/qdb /home/ec2-user/msa-work/db/uniref30_2302_db_seq /home/ec2-user/result/res /home/ec2-user/msa-work/db/uniref30_2302_db_aln /home/ec2-user/result/res_exp --db-load-mode 0 --threads 64 --expansion-mode 0 -e inf --expand-filter-clusters 1 --max-seq-id 0.95
Can not touch 134187960766 into main memory
[=================================================================] 100.00% 3 0s 904ms
Time for merging to res_exp: 0h 0m 0s 2ms
Time for processing: 0h 4m 53s 314ms
INFO:colabfold.mmseqs.search:Running mmseqs align /home/ec2-user/result/prof_res /home/ec2-user/msa-work/db/uniref30_2302_db_seq /home/ec2-user/result/res_exp /home/ec2-user/result/res_exp_realign --db-load-mode 0 -e 10 --max-accept 100000 --threads 64 --alt-ali 10 -a
align /home/ec2-user/result/prof_res /home/ec2-user/msa-work/db/uniref30_2302_db_seq /home/ec2-user/result/res_exp /home/ec2-user/result/res_exp_realign --db-load-mode 0 -e 10 --max-accept 100000 --threads 64 --alt-ali 10 -a
Input /home/ec2-user/result/prof_res does not exist
Traceback (most recent call last):
File "/home/ec2-user/msa-work/localcolabfold/colabfold-conda/bin/colabfold_search", line 8, in <module>
sys.exit(main())
File "/home/ec2-user/msa-work/localcolabfold/colabfold-conda/lib/python3.10/site-packages/colabfold/mmseqs/search.py", line 461, in main
mmseqs_search_monomer(
File "/home/ec2-user/msa-work/localcolabfold/colabfold-conda/lib/python3.10/site-packages/colabfold/mmseqs/search.py", line 131, in mmseqs_search_monomer
run_mmseqs(mmseqs, ["align", base.joinpath("prof_res"), dbbase.joinpath(f"{uniref_db}{dbSuffix1}"), base.joinpath("res_exp"), base.joinpath("res_exp_realign"), "--db-load-mode", str(db_load_mode), "-e", str(align_eval), "--max-accept", str(max_accept), "--threads", str(threads), "--alt-ali", "10", "-a"])
File "/home/ec2-user/msa-work/localcolabfold/colabfold-conda/lib/python3.10/site-packages/colabfold/mmseqs/search.py", line 46, in run_mmseqs
subprocess.check_call([mmseqs] + params)
File "/home/ec2-user/msa-work/localcolabfold/colabfold-conda/lib/python3.10/subprocess.py", line 369, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '[PosixPath('mmseqs'), 'align', PosixPath('/home/ec2-user/result/prof_res'), PosixPath('/home/ec2-user/msa-work/db/uniref30_2302_db_seq'), PosixPath('/home/ec2-user/result/res_exp'), PosixPath('/home/ec2-user/result/res_exp_realign'), '--db-load-mode', '0', '-e', '10', '--max-accept', '100000', '--threads', '64', '--alt-ali', '10', '-a']' returned non-zero exit status 1.
What's the input? MMseqs2 detected nucleotide input, which doesn't work with colabfold.
What's the input? MMseqs2 detected nucleotide input, which doesn't work with colabfold.
That's my input cat input_sequences.fasta
>seq1_test
MFEARLVQGSILKKVLEALKDLINEACWDISSSGVNLQSMDSSHVSLVQLTLRSEGFDTYRCDRNLAMGVNLTSMSKILKCAGNEDIITLRAEDNADTLALVFEAPNQEKVSDYEMKLMDLDVEQLGIPEQEYSCVVKMPSGEFARICRDLSHIGDAVVISCAKDGVKFSASGELGNGNIKLSQTSNVDKEEEAVTIEMNEPVQLTFALRYLNFFTKATPLSSTVTLSMSADVPLVVEYKIADMGHLKYYLAPKIEDEEGS