{"action":"created","issue":{"url":"https://api.github.com/repos/soedinglab/MMseqs2/issues/88","repository_url":"https://api.github.com/repos/soedinglab/MMseqs2","labels_url":"https://api.github.com/repos/soedinglab/MMseqs2/issues/88/labels{/name}","comments_url":"https://api.github.com/repos/soedinglab/MMseqs2/issues/88/comments","events_url":"https://api.github.com/repos/soedinglab/MMseqs2/issues/88/events","html_url":"https://github.com/soedinglab/MMseqs2/issues/88","id":326128460,"node_id":"MDU6SXNzdWUzMjYxMjg0NjA=","number":88,"title":"Identical sequences are not clustered together.","user":{"login":"ggautreau","id":17834092,"node_id":"MDQ6VXNlcjE3ODM0MDky","avatar_url":"https://avatars3.githubusercontent.com/u/17834092?v=4","gravatar_id":"","url":"https://api.github.com/users/ggautreau","html_url":"https://github.com/ggautreau","followers_url":"https://api.github.com/users/ggautreau/followers","following_url":"https://api.github.com/users/ggautreau/following{/other_user}","gists_url":"https://api.github.com/users/ggautreau/gists{/gist_id}","starred_url":"https://api.github.com/users/ggautreau/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ggautreau/subscriptions","organizations_url":"https://api.github.com/users/ggautreau/orgs","repos_url":"https://api.github.com/users/ggautreau/repos","events_url":"https://api.github.com/users/ggautreau/events{/privacy}","received_events_url":"https://api.github.com/users/ggautreau/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":9,"created_at":"2018-05-24T13:43:45Z","updated_at":"2018-06-28T16:28:19Z","closed_at":"2018-06-06T15:06:35Z","author_association":"NONE","body":"## Expected Behavior\r\nSome identical sequence must be clustered together.\r\n\r\nFor example in the pan.fasta file :\r\n```\r\n>GCF_001259475.1_4370_2_2_genomic_00977\r\nMFSNLKHVVMLMLLASAASYALAAPAPVSDLGSNVSGGSRSSEIERLERLLESRNLVQLQMQKQLDDMALEVNELRGQIEKNNYDMQQMLQRQRELFVELDRVRGEMKSPSSGAGQLPTSSNDEAAQGTFSSDANEQAAYQNAVDLILKKRDYAGAIAAFQKFQTDYPNSTFSANAHYWLGQLYFAKKEDKEAAKSFAAVVSDKGSNKRADALVKLGDIAKRNNNAEQARKFYQQAVDEYPDSASAKIAKENLK\r\n\r\n>GCF_001249795.1_3002_8_6_genomic_02902\r\nMFSNLKHVVMLMLLASAASYALAAPAPVSDLGSNVSGGSRSSEIERLERLLESRNLVQLQMQKQLDDMALEVNELRGQIEKNNYDMQQMLQRQRELFVELDRVRGEMKSPSSGAGQLPTSSNDEAAQGTFSSDANEQAAYQNAVDLILKKRDYAGAIAAFQKFQTDYPNSTFSANAHYWLGQLYFAKKEDKEAAKSFAAVVSDKGSNKRADALVKLGDIAKRNNNAEQARKFYQQAVDEYPDSASAKIAKENLK\r\n```\r\n\r\nThe 2 sequences are identical and must be clustered in the same cluster.\r\n\r\n## Current Behavior\r\n\r\nThe two previous sequences are not clustered together.\r\nThe fam.tsv output result is:\r\n\r\n```\r\nGCF_001249795.1_3002_8_6_genomic_02902  GCF_001249795.1_3002_8_6_genomic_02902  \r\nGCF_001249795.1_3002_8_6_genomic_02902  GCF_001259475.1_4370_2_2_genomic_00977\r\n```\r\n\r\n\r\n## Steps to Reproduce (for bugs)\r\n\r\nmmseqs createdb pan.fasta pan.db\r\nmmseqs cluster pan.db fam.db /tmp/ --min-seq-id 0.8 -c 0.8 --threads 1\r\nmmseqs createtsv pan.db pan.db fam.db fam.tsv --first-seq-as-repr true\r\n\r\n## MMseqs Output (for bugs)\r\n\r\n```\r\nProgram call:\r\npan.fasta pan.db \r\n\r\nMMseqs Version:      \tGITDIR-NOTFOUND\r\nMax. sequence length \t32000\r\nSplit Seq. by len    \ttrue\r\nOffset of numeric ids\t0\r\nVerbosity            \t3\r\n\r\nTime for merging files: 0 h 0 m 0 s\r\nTime for merging files: 0 h 0 m 0 s\r\n```\r\n```\r\nProgram call:\r\npan.db fam.db /tmp/ --min-seq-id 0.8 -c 0.8 --threads 1 \r\n\r\nMMseqs Version:                                                           \tGITDIR-NOTFOUND\r\nSub Matrix                                                                \tblosum62.out\r\nSensitivity                                                               \t4\r\nK-mer size                                                                \t0\r\nK-score                                                                   \t2147483647\r\nAlphabet size                                                             \t21\r\nMax. sequence length                                                      \t32000\r\nMax. results per query                                                    \t20\r\nOffset result                                                             \t0\r\nSplit DB                                                                  \t0\r\nSplit mode                                                                \t2\r\nSplit Memory Limit                                                        \t0\r\nCoverage threshold                                                        \t0.8\r\nCoverage Mode                                                             \t0\r\nCompositional bias                                                        \t1\r\nDiagonal Scoring                                                          \t1\r\nMask Residues                                                             \t1\r\nMinimum Diagonal score                                                    \t15\r\nInclude identical Seq. Id.                                                \tfalse\r\nSpaced Kmer                                                               \t1\r\nNo preload                                                                \tfalse\r\nEarly exit                                                                \tfalse\r\nPseudo count a                                                            \t1\r\nPseudo count b                                                            \t1.5\r\nThreads                                                                   \t1\r\nVerbosity                                                                 \t3\r\nAdd backtrace                                                             \tfalse\r\nAlignment mode                                                            \t3\r\nE-value threshold                                                         \t0.001\r\nSeq. Id Threshold                                                         \t0.8\r\nRealign hit                                                               \tfalse\r\nMax Reject                                                                \t2147483647\r\nMax Accept                                                                \t2147483647\r\nCluster mode                                                              \t0\r\nMax depth connected component                                             \t1000\r\nSimilarity type                                                           \t2\r\nSingle step clustering                                                    \ttrue\r\nCascaded clustering steps                                                 \t3\r\nRemove Temporary Files                                                    \tfalse\r\nSets the MPI runner                                                       \t\r\nKmer per sequence                                                         \t20\r\nShift hash                                                                \t5\r\nRescore mode                                                              \t0\r\nRemove hits by seq.id. and coverage                                       \tfalse\r\nIn substitution scoring mode, performs global alignment along the diagonal\tfalse\r\n\r\nSet cluster settings automatic to s=1\r\nSet cluster mode SET COVER.\r\nSet cluster iterations to 1\r\nProgram call:\r\npan.db /tmp//589280515582180421/clu_redundancy /tmp//589280515582180421/linclust --cluster-mode 0 -v 3 --max-iterations 1000 --similarity-type 2 --threads 1 --sub-mat blosum62.out --alignment-mode 3 -e 0.001 --min-seq-id 0.8 -c 0.8 --cov-mode 0 --max-seq-len 32000 --max-seqs 20 --comp-bias-corr 0 --max-rejected 2147483647 --max-accept 2147483647 --pca 1 --pcb 1.5 --alph-size 13 --kmer-per-seq 20 --mask 0 -k 0 --hash-shift 5 --split-memory-limit 0 --rescore-mode 0 \r\n\r\nMMseqs Version:                                                           \tGITDIR-NOTFOUND\r\nCluster mode                                                              \t0\r\nVerbosity                                                                 \t3\r\nMax depth connected component                                             \t1000\r\nSimilarity type                                                           \t2\r\nThreads                                                                   \t1\r\nSub Matrix                                                                \tblosum62.out\r\nAdd backtrace                                                             \tfalse\r\nAlignment mode                                                            \t3\r\nE-value threshold                                                         \t0.001\r\nSeq. Id Threshold                                                         \t0.8\r\nCoverage threshold                                                        \t0.8\r\nCoverage Mode                                                             \t0\r\nMax. sequence length                                                      \t32000\r\nMax. results per query                                                    \t20\r\nCompositional bias                                                        \t0\r\nRealign hit                                                               \tfalse\r\nMax Reject                                                                \t2147483647\r\nMax Accept                                                                \t2147483647\r\nInclude identical Seq. Id.                                                \tfalse\r\nNo preload                                                                \tfalse\r\nEarly exit                                                                \tfalse\r\nPseudo count a                                                            \t1\r\nPseudo count b                                                            \t1.5\r\nAlphabet size                                                             \t13\r\nKmer per sequence                                                         \t20\r\nMask Residues                                                             \t0\r\nK-mer size                                                                \t0\r\nShift hash                                                                \t5\r\nSplit Memory Limit                                                        \t0\r\nRescore mode                                                              \t0\r\nRemove hits by seq.id. and coverage                                       \tfalse\r\nIn substitution scoring mode, performs global alignment along the diagonal\tfalse\r\nRemove Temporary Files                                                    \tfalse\r\nSets the MPI runner                                                       \t\r\n\r\nProgram call:\r\npan.db /tmp//589280515582180421/linclust/13903844144087712329/pref --sub-mat blosum62.out --alph-size 13 --min-seq-id 0.8 --kmer-per-seq 20 --mask 0 --cov-mode 0 -k 0 -c 0.8 --max-seq-len 32000 --hash-shift 5 --split-memory-limit 0 --threads 1 -v 3 \r\n\r\nMMseqs Version:     \tGITDIR-NOTFOUND\r\nSub Matrix          \tblosum62.out\r\nAlphabet size       \t13\r\nSeq. Id Threshold   \t0.8\r\nKmer per sequence   \t20\r\nMask Residues       \t0\r\nCoverage Mode       \t0\r\nK-mer size          \t0\r\nCoverage threshold  \t0.8\r\nMax. sequence length\t32000\r\nShift hash          \t5\r\nSplit Memory Limit  \t0\r\nThreads             \t1\r\nVerbosity           \t3\r\n\r\nAlphabet size: 13 k-mer size: 10\r\nV -> I\r\nM -> L\r\nQ -> E\r\nT -> S\r\nR -> K\r\nY -> F\r\nS -> A\r\nN -> D\r\nReduced amino acid alphabet:\r\nA C D E F G H I K L P W X \r\nChecking requirements\r\nNeeded memory (640 byte) of total memory (182764221235 byte)\r\nProcess file into 1 parts\r\nGenerate k-mers list 0\r\n\r\nTime for fill: 0 h 0 m 0s\r\nDone.\r\nSort kmer ... Done.\r\nTime for sort: 0 h 0 m 0s\r\nSort by rep. sequence ... Done\r\nTime for sort: 0 h 0 m 0s\r\nTime for fill: 0 h 0 m 0s\r\nTime for merging files: 0 h 0 m 0 s\r\nTime for processing: 0 h 0 m 0s\r\nRescore diagonals.\r\nProgram call:\r\npan.db pan.db /tmp//589280515582180421/linclust/13903844144087712329/pref /tmp//589280515582180421/linclust/13903844144087712329/pref_rescore1 --rescore-mode 0 --sub-mat blosum62.out -c 0.8 -e 0.001 --cov-mode 0 --min-seq-id 0.8 --threads 1 -v 3 \r\n\r\nMMseqs Version:                                                           \tGITDIR-NOTFOUND\r\nRescore mode                                                              \t0\r\nSub Matrix                                                                \tblosum62.out\r\nRemove hits by seq.id. and coverage                                       \tfalse\r\nIn substitution scoring mode, performs global alignment along the diagonal\tfalse\r\nCoverage threshold                                                        \t0.8\r\nE-value threshold                                                         \t0.001\r\nCoverage Mode                                                             \t0\r\nSeq. Id Threshold                                                         \t0.8\r\nInclude identical Seq. Id.                                                \tfalse\r\nThreads                                                                   \t1\r\nVerbosity                                                                 \t3\r\n\r\nQuery  file: pan.db\r\nTarget  file: pan.db\r\nPrefilter database: /tmp//589280515582180421/linclust/13903844144087712329/pref\r\nResult database: /tmp//589280515582180421/linclust/13903844144087712329/pref_rescore1\r\nDone.\r\nTime for merging files: 0 h 0 m 0 s\r\nTime for diagonal calculation: 0 h 0 m 0s\r\nProgram call:\r\npan.db /tmp//589280515582180421/linclust/13903844144087712329/pref_rescore1 /tmp//589280515582180421/linclust/13903844144087712329/pre_clust --cluster-mode 0 -v 3 --max-iterations 1000 --similarity-type 2 --threads 1 \r\n\r\nMMseqs Version:              \tGITDIR-NOTFOUND\r\nCluster mode                 \t0\r\nVerbosity                    \t3\r\nMax depth connected component\t1000\r\nSimilarity type              \t2\r\nThreads                      \t1\r\n\r\nInit...\r\nOpening sequence database...\r\nOpening alignment database...\r\ndone.\r\nClustering mode: Set Cover\r\n\r\nSort entries.\r\n\r\nFind missing connections.\r\n\r\nFound 1 new connections.\r\n\r\nReconstruct initial order.\r\n\r\nAdd missing connections.\r\n\r\nTime for Read in: 0 m 0s\r\n\r\nWriting results...\r\n...done.\r\nTime for clustering: 0 m 0s\r\nTime for merging files: 0 h 0 m 0 s\r\nTotal time: 0 m 0s\r\n\r\nSize of the sequence database: 2\r\nSize of the alignment database: 2\r\nNumber of clusters: 1\r\nProgram call:\r\n/tmp//589280515582180421/linclust/13903844144087712329/order_redundancy pan.db /tmp//589280515582180421/linclust/13903844144087712329/input_step_redundancy \r\n\r\nMMseqs Version:\tGITDIR-NOTFOUND\r\nVerbosity\t3\r\n\r\nStart writing to file /tmp//589280515582180421/linclust/13903844144087712329/input_step_redundancy\r\nTime for merging files: 0 h 0 m 0 s\r\nProgram call:\r\n/tmp//589280515582180421/linclust/13903844144087712329/order_redundancy /tmp//589280515582180421/linclust/13903844144087712329/pref /tmp//589280515582180421/linclust/13903844144087712329/pref_filter1 \r\n\r\nMMseqs Version:\tGITDIR-NOTFOUND\r\nVerbosity\t3\r\n\r\nStart writing to file /tmp//589280515582180421/linclust/13903844144087712329/pref_filter1\r\nTime for merging files: 0 h 0 m 0 s\r\nProgram call:\r\n/tmp//589280515582180421/linclust/13903844144087712329/pref_filter1 /tmp//589280515582180421/linclust/13903844144087712329/pref_filter2 --filter-file /tmp//589280515582180421/linclust/13903844144087712329/order_redundancy \r\n\r\nMMseqs Version:               \tGITDIR-NOTFOUND\r\nFilter column                 \t1\r\nFilter regex                  \t^.*$\r\nPositive filter               \ttrue\r\nFilter file                   \t/tmp//589280515582180421/linclust/13903844144087712329/order_redundancy\r\nBeats first                   \tfalse\r\nMapping file                  \t\r\nThreads                       \t24\r\nVerbosity                     \t3\r\ntrim the results to one column\tfalse\r\nExtract n lines               \t0\r\nNumerical comparison operator \t\r\nNumerical comparison value    \t0\r\nSort entries                  \t0\r\nInclude identical Seq. Id.    \tfalse\r\njoin to DB                    \t\r\n\r\nFiltering with a filter files.\r\nTime for merging files: 0 h 0 m 0 s\r\nRescore diagonals.\r\nProgram call:\r\n/tmp//589280515582180421/linclust/13903844144087712329/input_step_redundancy /tmp//589280515582180421/linclust/13903844144087712329/input_step_redundancy /tmp//589280515582180421/linclust/13903844144087712329/pref_filter2 /tmp//589280515582180421/linclust/13903844144087712329/pref_rescore2 --rescore-mode 1 --sub-mat blosum62.out --filter-hits -c 0.8 -e 0.001 --cov-mode 0 --min-seq-id 0.8 --threads 1 -v 3 \r\n\r\nMMseqs Version:                                                           \tGITDIR-NOTFOUND\r\nRescore mode                                                              \t1\r\nSub Matrix                                                                \tblosum62.out\r\nRemove hits by seq.id. and coverage                                       \ttrue\r\nIn substitution scoring mode, performs global alignment along the diagonal\tfalse\r\nCoverage threshold                                                        \t0.8\r\nE-value threshold                                                         \t0.001\r\nCoverage Mode                                                             \t0\r\nSeq. Id Threshold                                                         \t0.8\r\nInclude identical Seq. Id.                                                \tfalse\r\nThreads                                                                   \t1\r\nVerbosity                                                                 \t3\r\n\r\nQuery  file: /tmp//589280515582180421/linclust/13903844144087712329/input_step_redundancy\r\nTarget  file: /tmp//589280515582180421/linclust/13903844144087712329/input_step_redundancy\r\nPrefilter database: /tmp//589280515582180421/linclust/13903844144087712329/pref_filter2\r\nResult database: /tmp//589280515582180421/linclust/13903844144087712329/pref_rescore2\r\nDone.\r\nTime for merging files: 0 h 0 m 0 s\r\nTime for diagonal calculation: 0 h 0 m 0s\r\nProgram call:\r\n/tmp//589280515582180421/linclust/13903844144087712329/input_step_redundancy /tmp//589280515582180421/linclust/13903844144087712329/input_step_redundancy /tmp//589280515582180421/linclust/13903844144087712329/pref_rescore2 /tmp//589280515582180421/linclust/13903844144087712329/aln --sub-mat blosum62.out --alignment-mode 3 -e 0.001 --min-seq-id 0.8 -c 0.8 --cov-mode 0 --max-seq-len 32000 --max-seqs 20 --comp-bias-corr 0 --max-rejected 2147483647 --max-accept 2147483647 --pca 1 --pcb 1.5 --threads 1 -v 3 \r\n\r\nMMseqs Version:           \tGITDIR-NOTFOUND\r\nSub Matrix                \tblosum62.out\r\nAdd backtrace             \tfalse\r\nAlignment mode            \t3\r\nE-value threshold         \t0.001\r\nSeq. Id Threshold         \t0.8\r\nCoverage threshold        \t0.8\r\nCoverage Mode             \t0\r\nMax. sequence length      \t32000\r\nMax. results per query    \t20\r\nCompositional bias        \t0\r\nRealign hit               \tfalse\r\nMax Reject                \t2147483647\r\nMax Accept                \t2147483647\r\nInclude identical Seq. Id.\tfalse\r\nNo preload                \tfalse\r\nEarly exit                \tfalse\r\nPseudo count a            \t1\r\nPseudo count b            \t1.5\r\nThreads                   \t1\r\nVerbosity                 \t3\r\n\r\nInit data structures...\r\nCompute score, coverage and sequence id.\r\nUsing 1 threads.\r\nQuery database type: Aminoacid\r\nTarget database type: Aminoacid\r\nCalculation of Smith-Waterman alignments.\r\nTime for merging files: 0 h 0 m 0 s\r\n\r\nAll sequences processed.\r\n\r\n1 alignments calculated.\r\n1 sequence pairs passed the thresholds (1 of overall calculated).\r\n1 hits per query sequence.\r\nTime for alignments calculation: 0 h 0 m 0s\r\nProgram call:\r\n/tmp//589280515582180421/linclust/13903844144087712329/input_step_redundancy /tmp//589280515582180421/linclust/13903844144087712329/aln /tmp//589280515582180421/linclust/13903844144087712329/clust --cluster-mode 0 -v 3 --max-iterations 1000 --similarity-type 2 --threads 1 \r\n\r\nMMseqs Version:              \tGITDIR-NOTFOUND\r\nCluster mode                 \t0\r\nVerbosity                    \t3\r\nMax depth connected component\t1000\r\nSimilarity type              \t2\r\nThreads                      \t1\r\n\r\nInit...\r\nOpening sequence database...\r\nOpening alignment database...\r\ndone.\r\nClustering mode: Set Cover\r\n\r\nSort entries.\r\n\r\nFind missing connections.\r\n\r\nFound 0 new connections.\r\n\r\nReconstruct initial order.\r\n\r\nAdd missing connections.\r\n\r\nTime for Read in: 0 m 0s\r\n\r\nWriting results...\r\n...done.\r\nTime for clustering: 0 m 0s\r\nTime for merging files: 0 h 0 m 0 s\r\nTotal time: 0 m 0s\r\n\r\nSize of the sequence database: 1\r\nSize of the alignment database: 1\r\nNumber of clusters: 1\r\nProgram call:\r\npan.db /tmp//589280515582180421/linclust/13903844144087712329/clu /tmp//589280515582180421/linclust/13903844144087712329/pre_clust /tmp//589280515582180421/linclust/13903844144087712329/clust \r\n\r\nMMseqs Version:\tGITDIR-NOTFOUND\r\nThreads  \t24\r\nVerbosity\t3\r\n\r\nList amount 2\r\nClustering step 1...\r\nClustering step 2...\r\nWriting the results...\r\nTime for merging files: 0 h 0 m 0 s\r\n...done.\r\nProgram call:\r\n/tmp//589280515582180421/clu_redundancy pan.db /tmp//589280515582180421/input_step_redundancy \r\n\r\nMMseqs Version:\tGITDIR-NOTFOUND\r\nVerbosity\t3\r\n\r\nStart writing to file /tmp//589280515582180421/input_step_redundancy\r\nTime for merging files: 0 h 0 m 0 s\r\nProgram call:\r\n/tmp//589280515582180421/input_step_redundancy /tmp//589280515582180421/input_step_redundancy /tmp//589280515582180421/pref_step0 --sub-mat blosum62.out -s 1 -k 0 --k-score 2147483647 --alph-size 21 --max-seq-len 32000 --max-seqs 20 --offset-result 0 --split 0 --split-mode 2 --split-memory-limit 0 -c 0.8 --cov-mode 0 --comp-bias-corr 0 --diag-score 0 --mask 1 --min-ungapped-score 0 --spaced-kmer-mode 1 --pca 1 --pcb 1.5 --threads 1 -v 3 \r\n\r\nMMseqs Version:           \tGITDIR-NOTFOUND\r\nSub Matrix                \tblosum62.out\r\nSensitivity               \t1\r\nK-mer size                \t0\r\nK-score                   \t2147483647\r\nAlphabet size             \t21\r\nMax. sequence length      \t32000\r\nMax. results per query    \t20\r\nOffset result             \t0\r\nSplit DB                  \t0\r\nSplit mode                \t2\r\nSplit Memory Limit        \t0\r\nCoverage threshold        \t0.8\r\nCoverage Mode             \t0\r\nCompositional bias        \t0\r\nDiagonal Scoring          \t0\r\nMask Residues             \t1\r\nMinimum Diagonal score    \t0\r\nInclude identical Seq. Id.\tfalse\r\nSpaced Kmer               \t1\r\nNo preload                \tfalse\r\nEarly exit                \tfalse\r\nPseudo count a            \t1\r\nPseudo count b            \t1.5\r\nThreads                   \t1\r\nVerbosity                 \t3\r\n\r\nInitialising data structures...\r\nUsing 1 threads.\r\nCould not find precomputed index. Compute index.\r\nSubstitution matrices...\r\nUse kmer size 6 and split 1 using Target split mode.\r\nNeeded memory (1025282101 byte) of total memory (182764221235 byte)\r\nTarget database: /tmp//589280515582180421/input_step_redundancy(Size: 1)\r\nQuery database type: Aminoacid\r\nTarget database type: Aminoacid\r\nTime for init: 0 h 0 m 10s\r\n\r\n\r\nQuery database: /tmp//589280515582180421/input_step_redundancy(size=1)\r\nProcess prefiltering step 1 of 1\r\n\r\nIndex table: counting k-mers...\r\n\r\nIndex table: Masked residues: 24\r\nIndex table: fill...\r\nIndex table: removing duplicate entries...\r\nIndex table init done.\r\n\r\nDB statistic\r\nEntries:         17\r\nDB Size:         512000102 (byte)\r\nAvg Kmer Size:   2.65625e-07\r\nTop 10 Kmers\r\n   \tHYLQFA\t\t1\r\n\tYPSFNA\t\t1\r\n\tYQADPD\t\t1\r\n\tFQDPTF\t\t1\r\n\tAHWGYF\t\t1\r\n\tPNTSAH\t\t1\r\n\tYWGLAK\t\t1\r\n\tWLQYKK\t\t1\r\n\tANHWQL\t\t1\r\n\tTFAAWL\t\t1\r\nMin Kmer Size:   0\r\nEmpty list: 63999983\r\n\r\nTime for index table init: 0 h 0 m 2s\r\n\r\n\r\n\tk-mers per position = 0.354331, k-mer match probability: 2.22507e-308\r\nk-mer similarity threshold: 130\r\nk-mer match probability: 2.22507e-308\r\n\r\nStarting prefiltering scores calculation (step 1 of 1)\r\nQuery db start  1 to 1\r\nTarget db start  1 to 1\r\n\r\n0 k-mers per position.\r\n17 DB matches per sequence.\r\n0 Overflows.\r\n1 sequences passed prefiltering per query sequence.\r\nMedian result list size: 1\r\n0 sequences with 0 size result lists.\r\n\r\n\r\nTime for prefiltering scores calculation: 0 h 0 m 0s\r\nTime for merging files: 0 h 0 m 0 s\r\n\r\nOverall time for prefiltering run: 0 h 0 m 12s\r\nProgram call:\r\n/tmp//589280515582180421/input_step_redundancy /tmp//589280515582180421/input_step_redundancy /tmp//589280515582180421/pref_step0 /tmp//589280515582180421/aln_step0 --sub-mat blosum62.out --alignment-mode 3 -e 0.001 --min-seq-id 0.8 -c 0.8 --cov-mode 0 --max-seq-len 32000 --max-seqs 20 --comp-bias-corr 0 --max-rejected 2147483647 --max-accept 2147483647 --pca 1 --pcb 1.5 --threads 1 -v 3 \r\n\r\nMMseqs Version:           \tGITDIR-NOTFOUND\r\nSub Matrix                \tblosum62.out\r\nAdd backtrace             \tfalse\r\nAlignment mode            \t3\r\nE-value threshold         \t0.001\r\nSeq. Id Threshold         \t0.8\r\nCoverage threshold        \t0.8\r\nCoverage Mode             \t0\r\nMax. sequence length      \t32000\r\nMax. results per query    \t20\r\nCompositional bias        \t0\r\nRealign hit               \tfalse\r\nMax Reject                \t2147483647\r\nMax Accept                \t2147483647\r\nInclude identical Seq. Id.\tfalse\r\nNo preload                \tfalse\r\nEarly exit                \tfalse\r\nPseudo count a            \t1\r\nPseudo count b            \t1.5\r\nThreads                   \t1\r\nVerbosity                 \t3\r\n\r\nInit data structures...\r\nCompute score, coverage and sequence id.\r\nUsing 1 threads.\r\nQuery database type: Aminoacid\r\nTarget database type: Aminoacid\r\nCalculation of Smith-Waterman alignments.\r\nTime for merging files: 0 h 0 m 0 s\r\n\r\nAll sequences processed.\r\n\r\n1 alignments calculated.\r\n1 sequence pairs passed the thresholds (1 of overall calculated).\r\n1 hits per query sequence.\r\nTime for alignments calculation: 0 h 0 m 0s\r\nProgram call:\r\n/tmp//589280515582180421/input_step_redundancy /tmp//589280515582180421/aln_step0 /tmp//589280515582180421/clu_step0 --cluster-mode 0 -v 3 --max-iterations 1000 --similarity-type 2 --threads 1 \r\n\r\nMMseqs Version:              \tGITDIR-NOTFOUND\r\nCluster mode                 \t0\r\nVerbosity                    \t3\r\nMax depth connected component\t1000\r\nSimilarity type              \t2\r\nThreads                      \t1\r\n\r\nInit...\r\nOpening sequence database...\r\nOpening alignment database...\r\ndone.\r\nClustering mode: Set Cover\r\n\r\nSort entries.\r\n\r\nFind missing connections.\r\n\r\nFound 0 new connections.\r\n\r\nReconstruct initial order.\r\n\r\nAdd missing connections.\r\n\r\nTime for Read in: 0 m 0s\r\n\r\nWriting results...\r\n...done.\r\nTime for clustering: 0 m 0s\r\nTime for merging files: 0 h 0 m 0 s\r\nTotal time: 0 m 0s\r\n\r\nSize of the sequence database: 1\r\nSize of the alignment database: 1\r\nNumber of clusters: 1\r\nProgram call:\r\npan.db /tmp//589280515582180421/clu /tmp//589280515582180421/clu_redundancy /tmp//589280515582180421/clu_step0 \r\n\r\nMMseqs Version:\tGITDIR-NOTFOUND\r\nThreads  \t24\r\nVerbosity\t3\r\n\r\nList amount 2\r\nClustering step 1...\r\nClustering step 2...\r\nWriting the results...\r\nTime for merging files: 0 h 0 m 0 s\r\n...done.\r\n\r\n```\r\n\r\n```\r\nProgram call:\r\npan.db pan.db fam.db fam.tsv --first-seq-as-repr true \r\n\r\nMMseqs Version:                  \tGITDIR-NOTFOUND\r\nfirst sequence as respresentative\ttrue\r\n\r\nQuery file is pan.db\r\nData file is fam.db\r\nStart writing file to fam.tsv\r\nDone.\r\n```\r\n\r\n## Context\r\n\r\nThese 2 sequences come from a vibro cholerae genome. \r\n\r\n\r\n## Your Environment\r\n\r\n* Git commit used (The string after \"MMseqs Version:\" when you execute MMseqs without any parameters): GITDIR-NOTFOUND (corresponds to the last release: 2-23394)\r\n\r\n* Which MMseqs version was used (Statically-compiled, self-compiled, Homebrew, etc.): self-compiled using GNU Make 3.81 and cmake version 2.8.12.2\r\n\r\n\r\n* For self-compiled and Homebrew: Compiler and Cmake versions used and their invocation: self-compiled using GNU Make 3.81 and cmake version 2.8.12.2\r\n* Server specifications (especially CPU support for AVX2/SSE and amount of system memory):\r\n```\r\nless /proc/cpuinfo\r\nprocessor       : 0\r\nvendor_id       : AuthenticAMD\r\ncpu family      : 21\r\nmodel           : 2\r\nmodel name      : AMD Opteron(tm) Processor 6344                 \r\nstepping        : 0\r\ncpu MHz         : 2599.862\r\ncache size      : 2048 KB\r\nphysical id     : 0\r\nsiblings        : 12\r\ncore id         : 0\r\ncpu cores       : 6\r\napicid          : 0\r\ninitial apicid  : 0\r\nfpu             : yes\r\nfpu_exception   : yes\r\ncpuid level     : 13\r\nwp              : yes\r\nflags           : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush mmx fxsr sse sse2 ht syscall nx mmxext\r\n fxsr_opt pdpe1gb rdtscp lm constant_tsc rep_good nonstop_tsc extd_apicid amd_dcm aperfmperf pni pclmulqdq monitor ssse3 fma cx16 sse4_1\r\n sse4_2 popcnt aes xsave avx f16c lahf_lm cmp_legacy svm extapic cr8_legacy abm sse4a misalignsse 3dnowprefetch osvw ibs xop skinit wdt \r\nlwp fma4 tce nodeid_msr tbm topoext perfctr_core perfctr_nb cpb npt lbrv svm_lock nrip_save tsc_scale vmcb_clean flushbyasid decodeassis\r\nts pausefilter pfthreshold bmi1\r\nbogomips        : 5199.72\r\nTLB size        : 1536 4K pages\r\nclflush size    : 64\r\ncache_alignment : 64\r\naddress sizes   : 48 bits physical, 48 bits virtual\r\npower management: ts ttp tm 100mhzsteps hwpstate cpb eff_freq_ro\r\n```\r\n* Operating system and version:\r\n```\r\n$uname -a\r\nLinux XXX 2.6.32-696.20.1.el6.x86_64 #1 SMP Fri Jan 26 17:51:45 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux\r\n```\r\n"},"comment":{"url":"https://api.github.com/repos/soedinglab/MMseqs2/issues/comments/401094316","html_url":"https://github.com/soedinglab/MMseqs2/issues/88#issuecomment-401094316","issue_url":"https://api.github.com/repos/soedinglab/MMseqs2/issues/88","id":401094316,"node_id":"MDEyOklzc3VlQ29tbWVudDQwMTA5NDMxNg==","user":{"login":"martin-steinegger","id":1413571,"node_id":"MDQ6VXNlcjE0MTM1NzE=","avatar_url":"https://avatars2.githubusercontent.com/u/1413571?v=4","gravatar_id":"","url":"https://api.github.com/users/martin-steinegger","html_url":"https://github.com/martin-steinegger","followers_url":"https://api.github.com/users/martin-steinegger/followers","following_url":"https://api.github.com/users/martin-steinegger/following{/other_user}","gists_url":"https://api.github.com/users/martin-steinegger/gists{/gist_id}","starred_url":"https://api.github.com/users/martin-steinegger/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/martin-steinegger/subscriptions","organizations_url":"https://api.github.com/users/martin-steinegger/orgs","repos_url":"https://api.github.com/users/martin-steinegger/repos","events_url":"https://api.github.com/users/martin-steinegger/events{/privacy}","received_events_url":"https://api.github.com/users/martin-steinegger/received_events","type":"User","site_admin":false},"created_at":"2018-06-28T16:28:19Z","updated_at":"2018-06-28T16:28:19Z","author_association":"MEMBER","body":"I clustered them with MMseqs2 version a59d9cdbc0f39f4cad75271866fffb70adaa8677 and the following command\r\n\r\n`mmseqs cluster panproteome.db panproteome.db_clu /tmp/clu/ --kmer-per-seq 80  --max-seqs 300`\r\n\r\nAll the sequences, you mentioned, are in one cluster.\r\n\r\n```\r\nGCF_000743805.1_BDQ_genomic_01916\tGCF_002025345.1_ASM202534v1_genomic_04754\t\r\nGCF_000743805.1_BDQ_genomic_01916\tGCF_000742655.1_ASM74265v1_genomic_01763\t\r\nGCF_000743805.1_BDQ_genomic_01916\tGCF_000793565.1_ASM79356v1_genomic_02850\t\r\nGCF_000743805.1_BDQ_genomic_01916\tGCF_000782995.1_ASM78299v1_genomic_04822\r\n```\r\n\r\nThe cluster `GCF_000743805.1_BDQ_genomic_01916\t` has a total size of 160 members. "}}
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