Expected Behavior

I am trying to generate MSAs by querying uniref50 to uniref30.

Current Behavior

No output for the expandaln step

Steps to Reproduce (for bugs)

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

MMseqs Output (for bugs)

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.

Your Environment

Include as many relevant details about the environment you experienced the bug in. MMseqs Version: 7b95387f93e38c3911f9188bc702d63ed3194013 Run under a linux server.


You need to call the search module with the -a flag.


You need to call the search module with the -a flag.

I will search again.

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