I'm having difficulty clustering using profiles when following the instructions in the wiki. Specifically I'm referring to this section:
# extract consensus sequences from profiles
mmseqs profile2consensus profileDB1 profileDB1_consensus
# search with profiles against consensus sequences of seqDB1
mmseqs search profileDB1 profileDB1_consensus resultDB2 tmp --add-self-matches -a # Add your cluster criteria here
# cluster the results
mmseqs clust profileDB1 resultDB2 profileDB1_clu
I can run mmseqs search without issue but when I run mmseqs clust I get the following error:
Create directory /final/db_cluster/low_1/Genus02938/Genus02938_DB
cluster /final/db_profile/low_1/Genus02938/Genus02938_DB /final/db_profile_vs_consensus/low_1/Genus02938/Genus02938_DB /final/db_cluster/low_1/Genus02938/Genus02938_DB
MMseqs Version: 15.6f452
Substitution matrix aa:blosum62.out,nucl:nucleotide.out
Seed substitution matrix aa:VTML80.out,nucl:nucleotide.out
Sensitivity 4
k-mer length 0
Target search mode 0
k-score seq:2147483647,prof:2147483647
Alphabet size aa:21,nucl:5
Max sequence length 65535
Max results per query 20
Split database 0
Split mode 2
Split memory limit 0
Coverage threshold 0.8
Coverage mode 0
Compositional bias 1
Compositional bias 1
Diagonal scoring true
Exact k-mer matching 0
Mask residues 1
Mask residues probability 0.9
Mask lower case residues 0
Minimum diagonal score 15
Selected taxa
Include identical seq. id. false
Spaced k-mers 1
Preload mode 0
Pseudo count a substitution:1.100,context:1.400
Pseudo count b substitution:4.100,context:5.800
Spaced k-mer pattern
Local temporary path
Threads 144
Compressed 0
Verbosity 3
Add backtrace false
Alignment mode 3
Alignment mode 0
Allow wrapped scoring false
E-value threshold 0.001
Seq. id. threshold 0
Min alignment length 0
Seq. id. mode 0
Alternative alignments 0
Max reject 2147483647
Max accept 2147483647
Score bias 0
Realign hits false
Realign score bias -0.2
Realign max seqs 2147483647
Correlation score weight 0
Gap open cost aa:11,nucl:5
Gap extension cost aa:1,nucl:2
Zdrop 40
Rescore mode 0
Remove hits by seq. id. and coverage false
Sort results 0
Cluster mode 0
Max connected component depth 1000
Similarity type 2
Weight file name
Cluster Weight threshold 0.9
Single step clustering false
Cascaded clustering steps 3
Cluster reassign false
Remove temporary files false
Force restart with latest tmp false
MPI runner
k-mers per sequence 21
Scale k-mers per sequence aa:0.000,nucl:0.200
Adjust k-mer length false
Shift hash 67
Include only extendable false
Skip repeating k-mers false
Set cluster sensitivity to -s 6.000000
Set cluster mode SET COVER
Set cluster iterations to 3
/final/db_profile_vs_consensus/low_1/Genus02938/Genus02938_DB.dbtype exists already!
Yes, /final/db_profile_vs_consensus/low_1/Genus02938/Genus02938_DB.dbtype already exists; it was created by mmseqs search. I'm not sure why mmseqs clust cares? Do you have any ideas - I can't figure this out. Many thanks!!
Hi,
I'm having difficulty clustering using profiles when following the instructions in the wiki. Specifically I'm referring to this section:
I can run
mmseqs search
without issue but when I runmmseqs clust
I get the following error:Yes,
/final/db_profile_vs_consensus/low_1/Genus02938/Genus02938_DB.dbtype
already exists; it was created bymmseqs search
. I'm not sure whymmseqs clust
cares? Do you have any ideas - I can't figure this out. Many thanks!!