GPU version, mmseqs expandaln err : getData: local id (4294967295) >= db size (17)

[kehan777]

INFO:colabfold.mmseqs.search:Running mmseqs expandaln out3/qdb /mnt/d/conda/jupyter/ColabFold/database/uniref30_2302_gpu.idx out3/res /mnt/d/conda/jupyter/ColabFold/database/uniref30_2302_gpu.idx out3/res_exp --db-load-mode 0 --threads 18 --expansion-mode 0 -e inf --expand-filter-clusters 1 --max-seq-id 0.95
expandaln out3/qdb /mnt/d/conda/jupyter/ColabFold/database/uniref30_2302_gpu.idx out3/res /mnt/d/conda/jupyter/ColabFold/database/uniref30_2302_gpu.idx out3/res_exp --db-load-mode 0 --threads 18 --expansion-mode 0 -e inf --expand-filter-clusters 1 --max-seq-id 0.95

Index version: 16
Generated by: 2348eb6
ScoreMatrix: VTML80.out
Index version: 16
Generated by: 2348eb6
ScoreMatrix: VTML80.out
Invalid database read for database data file=/mnt/d/conda/jupyter/ColabFold/database/uniref30_2302_gpu.idx, database index=/mnt/d/conda/jupyter/ColabFold/database/uniref30_2302_gpu.idx.index
getData: local id (4294967295) >= db size (17)

//
uniref30_2302_db & colabfold_envdb_202108_db database download from colabfolad database, and work well using colabfold/mmseq cpu version.
then i change env to gpu version;
error when using mmseqs-linux-gpu.tar.gz 20-Sep-2025 10:46, i have covert db by using
mmseqs makepaddedseqdb uniref30_2302_db uniref30_2302_gpu;
mmseqs createindex uniref30_2302_gpu;
It's that right? & Could you tell me how to convert database correctly and how to solve "mmseqs expandaln error"？

thank you!

[martin-steinegger]

@milot-mirdita has updated the script. Could you please update your repository and try again?

[kehan777]

i have download https://dev.mmseqs.com/latest/mmseqs-linux-gpu.tar.gz 20-Sep-2025 10:46,
mmseqs createdb examples/DB.fasta targetDB
mmseqs makepaddedseqdb targetDB targetDB_padded
mmseqs easy-search examples/QUERY.fasta targetDB_padded alnRes.m8 tmp --gpu 1,work well;

then i use colabfold_search, when mmseqs expandaln out3/qdb uniref30_2302_gpu.idx out3/res uniref30_2302_gpu.idx out3/res_exp --db-load-mode 0 --threads 18 --expansion-mode 0 -e inf --expand-filter-clusters 1 --max-seq-id 0.95

MMseqs Version: 1046260
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 scale 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 18
Verbosity 3

Index version: 16
Generated by: 2348eb6
ScoreMatrix: VTML80.out
Index version: 16
Generated by: 2348eb6
ScoreMatrix: VTML80.out
Invalid database read for database data file=uniref30_2302_gpu.idx, database index=uniref30_2302_gpu.idx.index
getData: local id (4294967295) >= db size (17) , error

while i change ~/.bashrc env to mmseqs cpu version and using cpu database, success.

now the gpu version "mmseqs expandaln" still have read database problem..

[milot-mirdita]

Can you post a directory listing of the database directory (i.e. where uniref30_2302_gpu.idx is) and also post the contents of this file:

cat uniref30_2302_gpu.idx.index

[milot-mirdita]

It looks like it did not add the _aln* database to the .idx. Not sure how this might have happened. I recommend to rerun the setup_databases.sh script (https://raw.githubusercontent.com/sokrypton/ColabFold/refs/heads/main/setup_databases.sh) from scratch.