I am trying to generate MSAs by querying uniref50 to uniref30.
No output for the expandaln step
mmseqs createdb uniref50.fasta uniref50QueryDB
sudo vmtouch -t -l -d -w uniref30_2202_db.idx
mmseqs search uniref50QueryDB ../uniref30/uniref30_2202_db res tmp --db-load-mode 2
mmseqs expandaln uniref50QueryDB ../uniref30/uniref30_2202_db res ../uniref30/uniref30_2202_db_aln res_expanded --db-load-mode 2
This is the output for the last step (i.e. expandaln)
MMseqs Version: 7b95387f93e38c3911f9188bc702d63ed3194013
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 0.001
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 0
Use filter only at N seqs 0
Maximum seq. id. threshold 0.9
Minimum seq. id. 0.0
Minimum score per column -20
Minimum coverage 0
Select N most diverse seqs 1000
Preload mode 2
Compressed 0
Threads 64
Verbosity 3
Alignment must contain a backtrace.
Alignment must contain a backtrace. appears multiple times in red color.
Include as many relevant details about the environment you experienced the bug in. MMseqs Version: 7b95387f93e38c3911f9188bc702d63ed3194013 Run under a linux server.