genomewalker
5/5/2017 - 12:02 PM
Log for mmseqs cluster DB cluDB tmp
Log for mmseqs cluster DB cluDB tmp
mmseqs cluster DB cluDB tmp
Program call:
DB cluDB tmp
MMseqs Version: 1c45613a4166130d040b52241dc66f7d687f4e54
Sub Matrix blosum62.out
Sensitivity 4
K-mer size 0
K-score 2147483647
Alphabet size 21
Max. sequence length 32000
Query queryProfile false
Target queryProfile false
Max. results per query 300
Offset result 0
Split DB 0
Split mode 2
Coverage threshold 0.8
Compositional bias 1
Diagonal Scoring 1
Mask Residues 1
Minimum Diagonal score 15
Include identical Seq. Id. false
Spaced Kmer 1
Threads 1
Verbosity 3
Add backtrace false
Alignment mode 2
E-value threshold 0.001
Seq. Id Threshold 0
Target Coverage threshold 0
Realign hit false
Max Reject 2147483647
Max Accept 2147483647
Cluster mode 0
Max depth connected component 1000
Similarity type 2
Cascaded clustering false
Cluster fragments false
Remove Temporary Files false
Sets the MPI runner
Rescore mode 0
Remove hits by seq.id. and coverage false
In substitution scoring mode, performs global alignment along the diagonal false
Set cluster settings automatic to s=6 cascaded=1
Program call:
DB tmp/clu_redundancy tmp/linclust --cluster-mode 0 --max-seqs 300 -v 3 --max-iterations 1000 --similarity-type 2 --threads 1 --sub-mat blosum62.out --alignment-mode 2 -e 0.001 --min-seq-id 0 -c 0.8 --target-cov 0 --max-seq-len 32000 --comp-bias-corr 1 --max-rejected 2147483647 --max-accept 2147483647 --rescore-mode 0
MMseqs Version: 1c45613a4166130d040b52241dc66f7d687f4e54
Cluster mode 0
Max. results per query 300
Verbosity 3
Max depth connected component 1000
Similarity type 2
Threads 1
Sub Matrix blosum62.out
Add backtrace false
Alignment mode 2
E-value threshold 0.001
Seq. Id Threshold 0
Coverage threshold 0.8
Target Coverage threshold 0
Max. sequence length 32000
Compositional bias 1
Query queryProfile false
Realign hit false
Max Reject 2147483647
Max Accept 2147483647
Include identical Seq. Id. false
Rescore mode 0
Remove hits by seq.id. and coverage false
In substitution scoring mode, performs global alignment along the diagonal false
Remove Temporary Files false
Sets the MPI runner
Program call:
DB tmp/linclust/pref --sub-mat blosum62.out --alph-size 13 --min-seq-id 0 --kmer-per-seq 20 --target-cov 0 -k 0 -c 0.8 --max-seq-len 32000 --threads 1 -v 3
MMseqs Version: 1c45613a4166130d040b52241dc66f7d687f4e54
Sub Matrix blosum62.out
Alphabet size 13
Seq. Id Threshold 0
Kmer per sequence 20
Target Coverage threshold 0
K-mer size 0
Coverage threshold 0.8
Max. sequence length 32000
Threads 1
Verbosity 3
Alphabet size: 13 k-mer size: 10
Y -> F
V -> I
M -> L
Q -> E
T -> S
R -> K
S -> A
N -> D
Reduced amino acid alphabet:
A C D E F G H I K L P W X
Check requirements
Needed memory (6369264 byte) of total memory (17179869184 byte)
Generate k-mers list ...
.Done.
Sort kmer ... Done.
Sort by rep. sequence ... Done
Time for merging files: 0 h 0 m 0 s
Time for processing: 0 h 0 m 2s
Rescore diagonals.
Program call:
DB DB tmp/linclust/pref tmp/linclust/pref_rescore1 --rescore-mode 0 --sub-mat blosum62.out -c 0.8 --target-cov 0 --min-seq-id 0.5 --threads 1 -v 3
MMseqs Version: 1c45613a4166130d040b52241dc66f7d687f4e54
Rescore mode 0
Sub Matrix blosum62.out
Remove hits by seq.id. and coverage false
In substitution scoring mode, performs global alignment along the diagonal false
Coverage threshold 0.8
Target Coverage threshold 0
Seq. Id Threshold 0.5
Include identical Seq. Id. false
Threads 1
Verbosity 3
Query file: DB
Target file: DB
Prefilter database: tmp/linclust/pref
Result database: tmp/linclust/pref_rescore1
.Done.
Time for merging files: 0 h 0 m 0 s
Time for diagonal calculation: 0 h 0 m 0s
Program call:
DB tmp/linclust/pref_rescore1 tmp/linclust/pre_clust --cluster-mode 0 --max-seqs 300 -v 3 --max-iterations 1000 --similarity-type 2 --threads 1
MMseqs Version: 1c45613a4166130d040b52241dc66f7d687f4e54
Cluster mode 0
Max. results per query 300
Verbosity 3
Max depth connected component 1000
Similarity type 2
Threads 1
Init...
Opening sequence database...
Opening alignment database...
done.
Clustering mode: Set Cover
.
Sort entries.
Find missing connections.
Found 11693 new connections.
Reconstruct initial order.
.
Add missing connections.
.
Time for Read in: 0 m 0s
Writing results...
...done.
Time for clustering: 0 m 0s
Time for merging files: 0 h 0 m 0 s
Total time: 0 m 0s
Size of the sequence database: 20000
Size of the alignment database: 20000
Number of clusters: 12074
Program call:
tmp/linclust/order_redundancy DB tmp/linclust/input_step_redundancy
MMseqs Version: 1c45613a4166130d040b52241dc66f7d687f4e54
Verbosity 3
Start writing to file tmp/linclust/input_step_redundancy
Time for merging files: 0 h 0 m 0 s
Program call:
tmp/linclust/order_redundancy tmp/linclust/pref tmp/linclust/pref_filter1
MMseqs Version: 1c45613a4166130d040b52241dc66f7d687f4e54
Verbosity 3
Start writing to file tmp/linclust/pref_filter1
Time for merging files: 0 h 0 m 0 s
Program call:
tmp/linclust/pref_filter1 tmp/linclust/pref_filter2 --filter-file tmp/linclust/order_redundancy
MMseqs Version: 1c45613a4166130d040b52241dc66f7d687f4e54
Filter column 1
Filter regex ^.*$
Positive filter true
Filter file tmp/linclust/order_redundancy
Mapping file
Threads 1
Verbosity 3
trim the results to one column false
Extract n lines 0
Numerical comparison operator
Numerical comparison value 0
Sort (increasing:1, decreasing: 2, shuffle: 3) the entries by numerical value 0
Include identical Seq. Id. false
Filtering with a filter files.
.Time for merging files: 0 h 0 m 0 s
Rescore diagonals.
Program call:
tmp/linclust/input_step_redundancy tmp/linclust/input_step_redundancy tmp/linclust/pref_filter2 tmp/linclust/pref_rescore2 --rescore-mode 1 --sub-mat blosum62.out --filter-hits -c 0.8 --target-cov 0 --min-seq-id 0 --threads 1 -v 3
MMseqs Version: 1c45613a4166130d040b52241dc66f7d687f4e54
Rescore mode 1
Sub Matrix blosum62.out
Remove hits by seq.id. and coverage true
In substitution scoring mode, performs global alignment along the diagonal false
Coverage threshold 0.8
Target Coverage threshold 0
Seq. Id Threshold 0
Include identical Seq. Id. false
Threads 1
Verbosity 3
Query file: tmp/linclust/input_step_redundancy
Target file: tmp/linclust/input_step_redundancy
Could not find any score per column for cov=0.8 seq.id=0
No hit will be filtered.
Prefilter database: tmp/linclust/pref_filter2
Result database: tmp/linclust/pref_rescore2
.Done.
Time for merging files: 0 h 0 m 0 s
Time for diagonal calculation: 0 h 0 m 0s
Program call:
tmp/linclust/input_step_redundancy tmp/linclust/input_step_redundancy tmp/linclust/pref_rescore2 tmp/linclust/aln --sub-mat blosum62.out --alignment-mode 2 -e 0.001 --min-seq-id 0 -c 0.8 --target-cov 0 --max-seq-len 32000 --max-seqs 300 --comp-bias-corr 1 --max-rejected 2147483647 --max-accept 2147483647 --threads 1 -v 3
MMseqs Version: 1c45613a4166130d040b52241dc66f7d687f4e54
Sub Matrix blosum62.out
Add backtrace false
Alignment mode 2
E-value threshold 0.001
Seq. Id Threshold 0
Coverage threshold 0.8
Target Coverage threshold 0
Max. sequence length 32000
Max. results per query 300
Compositional bias 1
Query queryProfile false
Realign hit false
Max Reject 2147483647
Max Accept 2147483647
Include identical Seq. Id. false
Threads 1
Verbosity 3
Init data structures...
Compute score and coverage.
Calculation of Smith-Waterman alignments.
.Time for merging files: 0 h 0 m 0 s
All sequences processed.
16087 alignments calculated.
15656 sequence pairs passed the thresholds (0.973208 of overall calculated).
1.29667 hits per query sequence.
Time for alignments calculation: 0 h 0 m 18s
Program call:
tmp/linclust/input_step_redundancy tmp/linclust/aln tmp/linclust/clust --cluster-mode 0 --max-seqs 300 -v 3 --max-iterations 1000 --similarity-type 2 --threads 1
MMseqs Version: 1c45613a4166130d040b52241dc66f7d687f4e54
Cluster mode 0
Max. results per query 300
Verbosity 3
Max depth connected component 1000
Similarity type 2
Threads 1
Init...
Opening sequence database...
Opening alignment database...
done.
Clustering mode: Set Cover
.
Sort entries.
Find missing connections.
Found 3582 new connections.
Reconstruct initial order.
.
Add missing connections.
.
Time for Read in: 0 m 0s
Writing results...
...done.
Time for clustering: 0 m 1s
Time for merging files: 0 h 0 m 0 s
Total time: 0 m 1s
Size of the sequence database: 12074
Size of the alignment database: 12074
Number of clusters: 9318
Program call:
DB tmp/linclust/clu tmp/linclust/pre_clust tmp/linclust/clust
MMseqs Version: 1c45613a4166130d040b52241dc66f7d687f4e54
Verbosity 3
List amount 20000
Clustering step 1...
Clustering step 2...
Writing the results...
Time for merging files: 0 h 0 m 0 s
...done.
Program call:
tmp/order_redundancy DB tmp/input_step_redundancy
MMseqs Version: 1c45613a4166130d040b52241dc66f7d687f4e54
Verbosity 3
Start writing to file tmp/input_step_redundancy
Time for merging files: 0 h 0 m 0 s
Program call:
tmp/input_step_redundancy tmp/input_step_redundancy tmp/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 -c 0.8 --comp-bias-corr 0 --diag-score 0 --mask 1 --min-ungapped-score 0 --spaced-kmer-mode 1 --threads 1 -v 3
MMseqs Version: 1c45613a4166130d040b52241dc66f7d687f4e54
Sub Matrix blosum62.out
Sensitivity 1
K-mer size 0
K-score 2147483647
Alphabet size 21
Max. sequence length 32000
Query queryProfile false
Target queryProfile false
Max. results per query 20
Offset result 0
Split DB 0
Split mode 2
Coverage threshold 0.8
Compositional bias 0
Diagonal Scoring 0
Mask Residues 1
Minimum Diagonal score 0
Include identical Seq. Id. false
Spaced Kmer 1
Threads 1
Verbosity 3
Initialising data structures...
Cound not find precomputed index. Compute index.
Query database: tmp/input_step_redundancy(size=9318)
Target database: tmp/input_step_redundancy(size=9318)
Use kmer size 6 and split 1 using split mode 0
Needed memory (1401997934 byte) of total memory (17179869184 byte)
Substitution matrices...
Time for init: 0 h 0 m 6s
Process prefiltering step 0 of 1
Index table: counting k-mers...
Index table: Masked residues: 151919
Index table: fill...
Index table: removing duplicate entries...
Index table init done.
DB statistic
Entries: 791058
DB Size: 690875316 (byte)
Avg Kmer Size: 0.00922343
Top 10 Kmers
HYCVLG 32
SRRWPI 21
PNGSFN 17
RCKCRW 16
GGTHAY 16
GLRGCR 14
VRRWWV 14
FFEMPR 13
VDYFCM 12
KCQFLM 12
Min Kmer Size: 0
Empty list: 85042352
Time for index table init: 0 h 0 m 2s
Error: Could not allocate memory by memalign. Please report this bug to developers
Program call:
tmp/input_step_redundancy tmp/input_step_redundancy tmp/pref_step0 tmp/aln_step0 --sub-mat blosum62.out --alignment-mode 2 -e 0.001 --min-seq-id 0 -c 0.8 --target-cov 0 --max-seq-len 32000 --max-seqs 20 --comp-bias-corr 0 --max-rejected 2147483647 --max-accept 2147483647 --threads 1 -v 3
MMseqs Version: 1c45613a4166130d040b52241dc66f7d687f4e54
Sub Matrix blosum62.out
Add backtrace false
Alignment mode 2
E-value threshold 0.001
Seq. Id Threshold 0
Coverage threshold 0.8
Target Coverage threshold 0
Max. sequence length 32000
Max. results per query 20
Compositional bias 0
Query queryProfile false
Realign hit false
Max Reject 2147483647
Max Accept 2147483647
Include identical Seq. Id. false
Threads 1
Verbosity 3
Init data structures...
Compute score and coverage.
Could not open data file tmp/pref_step0!
Program call:
tmp/input_step_redundancy tmp/aln_step0 tmp/clu_step0 --cluster-mode 0 --max-seqs 20 -v 3 --max-iterations 1000 --similarity-type 2 --threads 1
MMseqs Version: 1c45613a4166130d040b52241dc66f7d687f4e54
Cluster mode 0
Max. results per query 20
Verbosity 3
Max depth connected component 1000
Similarity type 2
Threads 1
Init...
Opening sequence database...
Opening alignment database...
Could not open data file tmp/aln_step0!
awk: fatal: cannot open file `tmp/clu_step0.index' for reading (No such file or directory)
Program call:
tmp/order_step0 tmp/input_step_redundancy tmp/input_step1
MMseqs Version: 1c45613a4166130d040b52241dc66f7d687f4e54
Verbosity 3
Start writing to file tmp/input_step1
Time for merging files: 0 h 0 m 0 s
Program call:
tmp/input_step1 tmp/input_step1 tmp/pref_step1 --sub-mat blosum62.out -s 2 -k 0 --k-score 2147483647 --alph-size 21 --max-seq-len 32000 --max-seqs 100 --offset-result 0 --split 0 --split-mode 2 -c 0.8 --comp-bias-corr 1 --diag-score 1 --mask 1 --min-ungapped-score 15 --spaced-kmer-mode 1 --threads 1 -v 3
MMseqs Version: 1c45613a4166130d040b52241dc66f7d687f4e54
Sub Matrix blosum62.out
Sensitivity 2
K-mer size 0
K-score 2147483647
Alphabet size 21
Max. sequence length 32000
Query queryProfile false
Target queryProfile false
Max. results per query 100
Offset result 0
Split DB 0
Split mode 2
Coverage threshold 0.8
Compositional bias 1
Diagonal Scoring 1
Mask Residues 1
Minimum Diagonal score 15
Include identical Seq. Id. false
Spaced Kmer 1
Threads 1
Verbosity 3
Initialising data structures...
Failed to mmap memory dataSize=0 File=tmp/input_step1
Program call:
tmp/input_step1 tmp/input_step1 tmp/pref_step1 tmp/aln_step1 --sub-mat blosum62.out --alignment-mode 2 -e 0.001 --min-seq-id 0 -c 0.8 --target-cov 0 --max-seq-len 32000 --max-seqs 100 --comp-bias-corr 1 --max-rejected 2147483647 --max-accept 2147483647 --threads 1 -v 3
MMseqs Version: 1c45613a4166130d040b52241dc66f7d687f4e54
Sub Matrix blosum62.out
Add backtrace false
Alignment mode 2
E-value threshold 0.001
Seq. Id Threshold 0
Coverage threshold 0.8
Target Coverage threshold 0
Max. sequence length 32000
Max. results per query 100
Compositional bias 1
Query queryProfile false
Realign hit false
Max Reject 2147483647
Max Accept 2147483647
Include identical Seq. Id. false
Threads 1
Verbosity 3
Init data structures...
Compute score and coverage.
Failed to mmap memory dataSize=0 File=tmp/input_step1
Program call:
tmp/input_step1 tmp/aln_step1 tmp/clu_step1 --cluster-mode 0 --max-seqs 100 -v 3 --max-iterations 1000 --similarity-type 2 --threads 1
MMseqs Version: 1c45613a4166130d040b52241dc66f7d687f4e54
Cluster mode 0
Max. results per query 100
Verbosity 3
Max depth connected component 1000
Similarity type 2
Threads 1
Init...
Opening sequence database...
Opening alignment database...
Could not open data file tmp/aln_step1!
awk: fatal: cannot open file `tmp/clu_step1.index' for reading (No such file or directory)
Program call:
tmp/order_step1 tmp/input_step1 tmp/input_step2
MMseqs Version: 1c45613a4166130d040b52241dc66f7d687f4e54
Verbosity 3
Failed to mmap memory dataSize=0 File=tmp/input_step1
Program call:
tmp/input_step2 tmp/input_step2 tmp/pref_step2 --sub-mat blosum62.out -s 4 -k 0 --k-score 2147483647 --alph-size 21 --max-seq-len 32000 --max-seqs 200 --offset-result 0 --split 0 --split-mode 2 -c 0.8 --comp-bias-corr 1 --diag-score 1 --mask 1 --min-ungapped-score 15 --spaced-kmer-mode 1 --threads 1 -v 3
MMseqs Version: 1c45613a4166130d040b52241dc66f7d687f4e54
Sub Matrix blosum62.out
Sensitivity 4
K-mer size 0
K-score 2147483647
Alphabet size 21
Max. sequence length 32000
Query queryProfile false
Target queryProfile false
Max. results per query 200
Offset result 0
Split DB 0
Split mode 2
Coverage threshold 0.8
Compositional bias 1
Diagonal Scoring 1
Mask Residues 1
Minimum Diagonal score 15
Include identical Seq. Id. false
Spaced Kmer 1
Threads 1
Verbosity 3
Initialising data structures...
Could not open data file tmp/input_step2!
Program call:
tmp/input_step2 tmp/input_step2 tmp/pref_step2 tmp/aln_step2 --sub-mat blosum62.out --alignment-mode 2 -e 0.001 --min-seq-id 0 -c 0.8 --target-cov 0 --max-seq-len 32000 --max-seqs 200 --comp-bias-corr 1 --max-rejected 2147483647 --max-accept 2147483647 --threads 1 -v 3
MMseqs Version: 1c45613a4166130d040b52241dc66f7d687f4e54
Sub Matrix blosum62.out
Add backtrace false
Alignment mode 2
E-value threshold 0.001
Seq. Id Threshold 0
Coverage threshold 0.8
Target Coverage threshold 0
Max. sequence length 32000
Max. results per query 200
Compositional bias 1
Query queryProfile false
Realign hit false
Max Reject 2147483647
Max Accept 2147483647
Include identical Seq. Id. false
Threads 1
Verbosity 3
Init data structures...
Compute score and coverage.
Could not open data file tmp/input_step2!
Program call:
tmp/input_step2 tmp/aln_step2 tmp/clu_step2 --cluster-mode 0 --max-seqs 200 -v 3 --max-iterations 1000 --similarity-type 2 --threads 1
MMseqs Version: 1c45613a4166130d040b52241dc66f7d687f4e54
Cluster mode 0
Max. results per query 200
Verbosity 3
Max depth connected component 1000
Similarity type 2
Threads 1
Init...
Opening sequence database...
Opening alignment database...
Could not open data file tmp/aln_step2!
awk: fatal: cannot open file `tmp/clu_step2.index' for reading (No such file or directory)
Program call:
tmp/order_step2 tmp/input_step2 tmp/input_step3
MMseqs Version: 1c45613a4166130d040b52241dc66f7d687f4e54
Verbosity 3
Could not open data file tmp/input_step2!
Program call:
tmp/input_step3 tmp/input_step3 tmp/pref_step3 --sub-mat blosum62.out -s 6 -k 0 --k-score 2147483647 --alph-size 21 --max-seq-len 32000 --max-seqs 300 --offset-result 0 --split 0 --split-mode 2 -c 0.8 --comp-bias-corr 1 --diag-score 1 --mask 1 --min-ungapped-score 15 --spaced-kmer-mode 1 --threads 1 -v 3
MMseqs Version: 1c45613a4166130d040b52241dc66f7d687f4e54
Sub Matrix blosum62.out
Sensitivity 6
K-mer size 0
K-score 2147483647
Alphabet size 21
Max. sequence length 32000
Query queryProfile false
Target queryProfile false
Max. results per query 300
Offset result 0
Split DB 0
Split mode 2
Coverage threshold 0.8
Compositional bias 1
Diagonal Scoring 1
Mask Residues 1
Minimum Diagonal score 15
Include identical Seq. Id. false
Spaced Kmer 1
Threads 1
Verbosity 3
Initialising data structures...
Could not open data file tmp/input_step3!
Program call:
tmp/input_step3 tmp/input_step3 tmp/pref_step3 tmp/aln_step3 --sub-mat blosum62.out --alignment-mode 2 -e 0.001 --min-seq-id 0 -c 0.8 --target-cov 0 --max-seq-len 32000 --max-seqs 300 --comp-bias-corr 1 --max-rejected 2147483647 --max-accept 2147483647 --threads 1 -v 3
MMseqs Version: 1c45613a4166130d040b52241dc66f7d687f4e54
Sub Matrix blosum62.out
Add backtrace false
Alignment mode 2
E-value threshold 0.001
Seq. Id Threshold 0
Coverage threshold 0.8
Target Coverage threshold 0
Max. sequence length 32000
Max. results per query 300
Compositional bias 1
Query queryProfile false
Realign hit false
Max Reject 2147483647
Max Accept 2147483647
Include identical Seq. Id. false
Threads 1
Verbosity 3
Init data structures...
Compute score and coverage.
Could not open data file tmp/input_step3!
Program call:
tmp/input_step3 tmp/aln_step3 tmp/clu_step3 --cluster-mode 0 --max-seqs 300 -v 3 --max-iterations 1000 --similarity-type 2 --threads 1
MMseqs Version: 1c45613a4166130d040b52241dc66f7d687f4e54
Cluster mode 0
Max. results per query 300
Verbosity 3
Max depth connected component 1000
Similarity type 2
Threads 1
Init...
Opening sequence database...
Opening alignment database...
Could not open data file tmp/aln_step3!
Program call:
DB tmp/clu tmp/clu_redundancy tmp/clu_step0 tmp/clu_step1 tmp/clu_step2 tmp/clu_step3
MMseqs Version: 1c45613a4166130d040b52241dc66f7d687f4e54
Verbosity 3
List amount 20000
Clustering step 1...
Could not open data file tmp/clu_step0!
mv: rename tmp/clu to cluDB: No such file or directory
mv: rename tmp/clu.index to cluDB.index: No such file or directory
Could not move result to cluDB