Last active
September 22, 2017 06:45
-
-
Save genomewalker/dc566892b5300bc62e166dac844a9b65 to your computer and use it in GitHub Desktop.
Log for mmseqs cluster DB cluDB tmp
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
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 |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment