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genomewalker/mmseqs_20180926.log

Created September 26, 2018 08:02
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Raw
mmseqs_20180926.log
Program call:
search QUERY DB results tmp --num-iterations 2 -e 1e-5 -c 0.4
MMseqs Version: 199d9b81f8cd6af9e66f97ef4dc0bd53c8fce12b
Sub Matrix blosum62.out
Add backtrace true
Alignment mode 2
E-value threshold 1e-05
Seq. Id Threshold 0
Seq. Id. Mode 0
Alternative alignments 0
Coverage threshold 0.4
Coverage Mode 0
Max. sequence length 65535
Max. results per query 300
Compositional bias 1
Realign hit false
Max Reject 2147483647
Max Accept 2147483647
Include identical Seq. Id. false
No preload false
Pseudo count a 1
Pseudo count b 1.5
Score bias 0
Threads 8
Verbosity 3
Sensitivity 5.7
K-mer size 0
K-score 2147483647
Alphabet size 21
Offset result 0
Split DB 0
Split mode 2
Split Memory Limit 0
Diagonal Scoring 1
Exact k-mer matching 0
Mask Residues 1
Minimum Diagonal score 15
Spaced Kmer 1
Rescore mode 0
Remove hits by seq.id. and coverage false
Sort results 0
In substitution scoring mode, performs global alignment along the diagonal false
Mask profile 1
Profile e-value threshold 0.001
Use global sequence weighting false
Filter MSA 1
Maximum sequence identity threshold 0.9
Minimum seq. id. 0
Minimum score per column -20
Minimum coverage 0
Select n most diverse seqs 1000
Omit Consensus false
Min codons in orf 30
Max codons in length 32734
Max orf gaps 2147483647
Contig start mode 2
Contig end mode 2
Orf start mode 0
Forward Frames 1,2,3
Reverse Frames 1,2,3
Translation Table 1
Use all table starts false
Offset of numeric ids 0
Add Orf Stop false
Number search iterations 2
Start sensitivity 4
Search steps 1
Run a seq-profile search in slice mode 0
Sets the MPI runner
Remove Temporary Files false
Tmp tmp folder does not exist or is not a directory.
Created dir tmp
Program call:
prefilter QUERY DB tmp/1777218696978837010/pref_0 --sub-mat blosum62.out -s 5.7 -k 0 --k-score 2147483647 --alph-size 21 --max-seq-len 65535 --max-seqs 300 --offset-result 0 --split 0 --split-mode 2 --split-memory-limit 0 -c 0.4 --cov-mode 0 --comp-bias-corr 1 --diag-score 1 --exact-kmer-matching 0 --mask 1 --min-ungapped-score 15 --add-self-matches 0 --spaced-kmer-mode 1 --no-preload 0 --pca 1 --pcb 1.5 --threads 8 -v 3
MMseqs Version: 199d9b81f8cd6af9e66f97ef4dc0bd53c8fce12b
Sub Matrix blosum62.out
Sensitivity 5.7
K-mer size 0
K-score 2147483647
Alphabet size 21
Max. sequence length 65535
Max. results per query 300
Offset result 0
Split DB 0
Split mode 2
Split Memory Limit 0
Coverage threshold 0.4
Coverage Mode 0
Compositional bias 1
Diagonal Scoring 1
Exact k-mer matching 0
Mask Residues 1
Minimum Diagonal score 15
Include identical Seq. Id. false
Spaced Kmer 1
No preload false
Pseudo count a 1
Pseudo count b 1.5
Threads 8
Verbosity 3
Initialising data structures...
Using 8 threads.
Could not find precomputed index. Compute index.
Substitution matrices...
Use kmer size 6 and split 1 using Target split mode.
Needed memory (1096937783 byte) of total memory (30363914649 byte)
Target database: DB(Size: 20000)
Query database type: Aminoacid
Target database type: Aminoacid
Time for init: 0h 0m 0s 5ms
Query database: QUERY(size=500)
Process prefiltering step 1 of 1
Index table k-mer threshold: 88
Index table: counting k-mers...
.
Index table: Masked residues: 291826
Index table: fill...
.
Index table: removing duplicate entries...
Index table init done.
DB statistic
Entries: 8468505
DB Size: 562811030 (byte)
Avg Kmer Size: 0.13232
Top 10 Kmers
GQQVAR 190
QLGQRV 110
IHDKNI 105
ALGSGK 105
LLPGKT 102
SGGTLR 84
SGLGRV 75
VGSSST 61
VMHAGS 59
ATADTT 59
Min Kmer Size: 0
Empty list: 59185888
Time for index table init: 0h 0m 1s 688ms
k-mer similarity threshold: 88
k-mer match probability: 0
Starting prefiltering scores calculation (step 1 of 1)
Query db start 1 to 500
Target db start 1 to 20000
647 k-mers per position.
29042 DB matches per sequence.
0 Overflows.
205 sequences passed prefiltering per query sequence.
Median result list size: 237
1 sequences with 0 size result lists.
Time for prefiltering scores calculation: 0h 0m 1s 35ms
Time for merging files: 0h 0m 0s 2ms
Time for processing: 0h 0m 3s 261ms
Program call:
align QUERY DB tmp/1777218696978837010/pref_0 tmp/1777218696978837010/aln_0 --sub-mat blosum62.out -a 1 --alignment-mode 2 -e 0.1 --min-seq-id 0 --seq-id-mode 0 --alt-ali 0 -c 0.4 --cov-mode 0 --max-seq-len 65535 --max-seqs 300 --comp-bias-corr 1 --realign 1 --max-rejected 2147483647 --max-accept 2147483647 --add-self-matches 0 --no-preload 0 --pca 1 --pcb 1.5 --score-bias 0 --threads 8 -v 3
MMseqs Version: 199d9b81f8cd6af9e66f97ef4dc0bd53c8fce12b
Sub Matrix blosum62.out
Add backtrace true
Alignment mode 2
E-value threshold 0.1
Seq. Id Threshold 0
Seq. Id. Mode 0
Alternative alignments 0
Coverage threshold 0.4
Coverage Mode 0
Max. sequence length 65535
Max. results per query 300
Compositional bias 1
Realign hit true
Max Reject 2147483647
Max Accept 2147483647
Include identical Seq. Id. false
No preload false
Pseudo count a 1
Pseudo count b 1.5
Score bias 0
Threads 8
Verbosity 3
Init data structures...
Compute score only.
Using 8 threads.
Query database type: Aminoacid
Target database type: Aminoacid
Calculation of Smith-Waterman alignments.
Time for merging files: 0h 0m 0s 0ms
All sequences processed.
67957 alignments calculated.
0 sequence pairs passed the thresholds (0 of overall calculated).
0 hits per query sequence.
Time for processing: 0h 0m 1s 72ms
Program call:
result2profile QUERY DB tmp/1777218696978837010/aln_0 tmp/1777218696978837010/profile_0 --sub-mat blosum62.out --mask-profile 1 --e-profile 0.1 --comp-bias-corr 1 --wg 0 --filter-msa 1 --max-seq-id 0.9 --qid 0 --qsc -20 --cov 0 --diff 1000 --pca 0 --pcb 1.5 --omit-consensus 0 --no-preload 0 --threads 8 -v 3
MMseqs Version: 199d9b81f8cd6af9e66f97ef4dc0bd53c8fce12b
Sub Matrix blosum62.out
Mask profile 1
Profile e-value threshold 0.1
Compositional bias 1
Use global sequence weighting false
Filter MSA 1
Maximum sequence identity threshold 0.9
Minimum seq. id. 0
Minimum score per column -20
Minimum coverage 0
Select n most diverse seqs 1000
Pseudo count a 0
Pseudo count b 1.5
Omit Consensus false
No preload false
Threads 8
Verbosity 3
Start computing profiles.
Query database type: Aminoacid
Target database type: Aminoacid
Time for merging files: 0h 0m 0s 0ms
Time for merging files: 0h 0m 0s 5ms
Done.
Time for processing: 0h 0m 0s 95ms
Program call:
prefilter tmp/1777218696978837010/profile_0 DB tmp/1777218696978837010/pref_1 --sub-mat blosum62.out -s 5.7 -k 0 --k-score 2147483647 --alph-size 21 --max-seq-len 65535 --max-seqs 300 --offset-result 0 --split 0 --split-mode 2 --split-memory-limit 0 -c 0.4 --cov-mode 0 --comp-bias-corr 1 --diag-score 1 --exact-kmer-matching 0 --mask 1 --min-ungapped-score 15 --add-self-matches 0 --spaced-kmer-mode 1 --no-preload 0 --pca 1 --pcb 1.5 --threads 8 -v 3
MMseqs Version: 199d9b81f8cd6af9e66f97ef4dc0bd53c8fce12b
Sub Matrix blosum62.out
Sensitivity 5.7
K-mer size 0
K-score 2147483647
Alphabet size 21
Max. sequence length 65535
Max. results per query 300
Offset result 0
Split DB 0
Split mode 2
Split Memory Limit 0
Coverage threshold 0.4
Coverage Mode 0
Compositional bias 1
Diagonal Scoring 1
Exact k-mer matching 0
Mask Residues 1
Minimum Diagonal score 15
Include identical Seq. Id. false
Spaced Kmer 1
No preload false
Pseudo count a 1
Pseudo count b 1.5
Threads 8
Verbosity 3
Initialising data structures...
Using 8 threads.
Could not find precomputed index. Compute index.
Substitution matrices...
Use kmer size 6 and split 1 using Target split mode.
Needed memory (583657783 byte) of total memory (30363914649 byte)
Target database: DB(Size: 20000)
Query database type: Profile
Target database type: Aminoacid
Time for init: 0h 0m 0s 2ms
Query database: tmp/1777218696978837010/profile_0(size=500)
Process prefiltering step 1 of 1
Index table k-mer threshold: 0
Index table: counting k-mers...
.
Index table: Masked residues: 291826
Index table: fill...
.
Index table: removing duplicate entries...
Index table init done.
DB statistic
Entries: 8468505
DB Size: 562811030 (byte)
Avg Kmer Size: 0.13232
Top 10 Kmers
GQQVAR 190
QLGQRV 110
IHDKNI 105
ALGSGK 105
LLPGKT 102
SGGTLR 84
SGLGRV 75
VGSSST 61
VMHAGS 59
ATADTT 59
Min Kmer Size: 0
Empty list: 59185888
Time for index table init: 0h 0m 1s 392ms
k-mer similarity threshold: 105
k-mer match probability: 0
Starting prefiltering scores calculation (step 1 of 1)
Query db start 1 to 500
Target db start 1 to 20000
497 k-mers per position.
30552 DB matches per sequence.
0 Overflows.
201 sequences passed prefiltering per query sequence.
Median result list size: 219
1 sequences with 0 size result lists.
Time for prefiltering scores calculation: 0h 0m 0s 846ms
Time for merging files: 0h 0m 0s 0ms
Time for processing: 0h 0m 2s 246ms
Program call:
subtractdbs tmp/1777218696978837010/pref_1 tmp/1777218696978837010/aln_0 tmp/1777218696978837010/pref_next_1 --threads 8 --e-profile 0.1 -v 3
MMseqs Version: 199d9b81f8cd6af9e66f97ef4dc0bd53c8fce12b
Threads 8
Profile e-value threshold 0.1
Verbosity 3
Remove tmp/1777218696978837010/aln_0 ids from tmp/1777218696978837010/pref_1
Output databse: tmp/1777218696978837010/pref_next_1
Time for merging files: 0h 0m 0s 0ms
Time for processing: 0h 0m 0s 3ms
Program call:
align tmp/1777218696978837010/profile_0 DB tmp/1777218696978837010/pref_1 tmp/1777218696978837010/aln_1 --sub-mat blosum62.out -a 1 --alignment-mode 2 -e 1e-05 --min-seq-id 0 --seq-id-mode 0 --alt-ali 0 -c 0.4 --cov-mode 0 --max-seq-len 65535 --max-seqs 300 --comp-bias-corr 1 --realign 0 --max-rejected 2147483647 --max-accept 2147483647 --add-self-matches 0 --no-preload 0 --pca 1 --pcb 1.5 --score-bias 0 --threads 8 -v 3
MMseqs Version: 199d9b81f8cd6af9e66f97ef4dc0bd53c8fce12b
Sub Matrix blosum62.out
Add backtrace true
Alignment mode 2
E-value threshold 1e-05
Seq. Id Threshold 0
Seq. Id. Mode 0
Alternative alignments 0
Coverage threshold 0.4
Coverage Mode 0
Max. sequence length 65535
Max. results per query 300
Compositional bias 1
Realign hit false
Max Reject 2147483647
Max Accept 2147483647
Include identical Seq. Id. false
No preload false
Pseudo count a 1
Pseudo count b 1.5
Score bias 0
Threads 8
Verbosity 3
Init data structures...
Compute score, coverage and sequence id.
Using 8 threads.
Query database type: Profile
Target database type: Aminoacid
Calculation of Smith-Waterman alignments.
Time for merging files: 0h 0m 0s 0ms
All sequences processed.
0 alignments calculated.
0 sequence pairs passed the thresholds (-nan of overall calculated).
0 hits per query sequence.
Time for processing: 0h 0m 0s 99ms
Program call:
mergedbs tmp/1777218696978837010/profile_0 tmp/1777218696978837010/aln_new tmp/1777218696978837010/aln_0 tmp/1777218696978837010/aln_1
MMseqs Version: 199d9b81f8cd6af9e66f97ef4dc0bd53c8fce12b
Merge prefixes
Verbosity 3
Merging the results to tmp/1777218696978837010/aln_new
Done
Time for merging files: 0h 0m 0s 0ms
Time for processing: 0h 0m 0s 1ms
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