Issue with ColabFold_search (GPU version): MSA Order and Database Differences

Hi,

I searched for an MSA using ColabFold_search (GPU version) for more than 10,000 sequences and obtained a file named "uniref.a3m".

I have a few questions:

1. MSA Output: Is uniref.a3m my resulting MSA file, which was searched against the UniRef30 database?

2. Sequence Order: Does the order of sequences in uniref.a3m (starting from >101) correspond to the order in my query FASTA file? Do I need to split them manually?

3. Database Differences: When searching against the ColabFold database, the script seems to get stuck. Are there significant differences between UniRef30 and the ColabFold database that could be causing this issue?

INFO:colabfold.mmseqs.search:Running mmseqs search /data/junjie/AFDBcluster/a3ms/prof_res /data/junjie/genetic_databases_gpu/colabfold_envdb_202108_db /data/junjie/AFDBcluster/a3ms/res_env /data/junjie/AFDBcluster/a3ms/tmp3 --threads 64 --num-iterations 3 --db-load-mode 0 -a -e 0.1 --max-seqs 10000 --gpu 1 --prefilter-mode 1 --gpu-server 1
Create directory /data/junjie/AFDBcluster/a3ms/tmp3
search /data/junjie/AFDBcluster/a3ms/prof_res /data/junjie/genetic_databases_gpu/colabfold_envdb_202108_db /data/junjie/AFDBcluster/a3ms/res_env /data/junjie/AFDBcluster/a3ms/tmp3 --threads 64 --num-iterations 3 --db-load-mode 0 -a -e 0.1 --max-seqs 10000 --gpu 1 --prefilter-mode 1 --gpu-server 1

ungappedprefilter /data/junjie/AFDBcluster/a3ms/prof_res /data/junjie/genetic_databases_gpu/colabfold_envdb_202108_db.idx /data/junjie/AFDBcluster/a3ms/tmp3/12520996045656958086/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 1 --gpu-server-wait-timeout 600 --prefilter-mode 1 --threads 64 --compressed 0 -v 3

Index version: 16
Generated by: 8ef870f95af2a3ee474c2cdbb845f5f007fe5be6
ScoreMatrix: VTML80.out
[==============================================

Thanks so much for your help!

Start with the reported ColabFold_search GPU command and its final ungappedprefilter output. Compare the uniref.a3m/query mapping and the UniRef30 and ColabFold database paths; done requires a confirmed explanation of the output order, database differences, and apparent stall.