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comparison test-data/diamond.log @ 27:b7e8663db1ec draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 327834d2ea9b16f0f0264fa4e9b675a2277f2fee
author iuc
date Tue, 18 Feb 2025 23:17:45 +0000
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26:1206c725e45a 27:b7e8663db1ec
1 diamond blastp --quiet --threads 1 --db ./database --query /tmp/tmpxfb7idqd/files/e/4/f/dataset_e4f75201-863d-4397-8ca7-7c0b79593e9d.dat --no-self-hits --outfmt 0 --out /tmp/tmpxfb7idqd/job_working_directory/000/3/outputs/dataset_0fb25f52-9d9b-4592-a709-7e516f37daa1.dat --compress 0 --algo 0 --matrix BLOSUM62 --comp-based-stats 1 --masking 1 --max-target-seqs 25 --evalue 0.001 --id 0 --query-cover 0 --subject-cover 0 --block-size 2.0 --motif-masking 0 --log
2 diamond v2.0.15.153
3 #CPU threads: 1
4 Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1)
5 CPU features detected: ssse3 popcnt sse4.1 avx2
6 Runtime dispatch: disabled
7 L3 cache size: 8388608
8 MAX_SHAPE_LEN=19 SEQ_MASK STRICT_BAND
9 Temporary directory: /tmp/tmpxfb7idqd/job_working_directory/000/3/outputs
10 #Target sequences to report alignments for: 25
11 DP fields: 1
12 Opening the database... [0s]
13 Database: ./database.dmnd (type: Diamond database, sequences: 2, letters: 568)
14 Block size = 2000000000
15 Opening the input file... [0s]
16 Opening the output file... [0s]
17 Loading query sequences... [0s]
18 Sequences = 2, letters = 566, average length = 283
19 Masking queries... [0s]
20 Current RSS: 6.8 MB, Peak RSS: 6.8 MB
21 Algorithm: Double-indexed
22 Shape configuration: 111101110111,111011010010111
23 Building query histograms... [0s]
24 Allocating buffers... [0s]
25 Current RSS: 6.9 MB, Peak RSS: 6.9 MB
26 Loading reference sequences... [0s]
27 Sequences = 2, letters = 568, average length = 284
28 Current RSS: 6.9 MB, Peak RSS: 6.9 MB
29 Masking reference... [0s]
30 Masked letters: 0
31 Initializing temporary storage... Async_buffer() 2,1
32 [0s]
33 Building reference histograms... [0s]
34 Allocating buffers... [0s]
35 Current RSS: 6.9 MB, Peak RSS: 7.0 MB
36 Processing query block 1, reference block 1/1, shape 1/2, index chunk 1/4.
37 Building reference seed array... [0s]
38 Building query seed array... [0s]
39 Indexed query seeds = 97875695011120/566 (17292525620339.22%), reference seeds = 0/568 (0.00%)
40 Soft masked letters = 0/566 (0.00%), 0/568 (0.00%)
41 Computing hash join... [0s]
42 Masking low complexity seeds... [0s]
43 Masked seeds: 0/57 (0.00%)
44 Masked positions (query): 0/566 (0.00%)
45 Masked positions (target): 0/568 (0.00%)
46 Searching alignments... [0s]
47 Processing query block 1, reference block 1/1, shape 1/2, index chunk 2/4.
48 Building reference seed array... [0s]
49 Building query seed array... [0s]
50 Indexed query seeds = 2560271741526742528/566 (452344830658435072.00%), reference seeds = 0/568 (0.00%)
51 Soft masked letters = 0/566 (0.00%), 0/568 (0.00%)
52 Computing hash join... [0s]
53 Masking low complexity seeds... [0s]
54 Masked seeds: 0/57 (0.00%)
55 Masked positions (query): 0/566 (0.00%)
56 Masked positions (target): 0/568 (0.00%)
57 Searching alignments... [0s]
58 Processing query block 1, reference block 1/1, shape 1/2, index chunk 3/4.
59 Building reference seed array... [0s]
60 Building query seed array... [0s]
61 Indexed query seeds = 2560271741526742528/566 (452344830658435072.00%), reference seeds = 0/568 (0.00%)
62 Soft masked letters = 0/566 (0.00%), 0/568 (0.00%)
63 Computing hash join... [0s]
64 Masking low complexity seeds... [0s]
65 Masked seeds: 0/65 (0.00%)
66 Masked positions (query): 0/566 (0.00%)
67 Masked positions (target): 0/568 (0.00%)
68 Searching alignments... [0s]
69 Processing query block 1, reference block 1/1, shape 1/2, index chunk 4/4.
70 Building reference seed array... [0s]
71 Building query seed array... [0s]
72 Indexed query seeds = 129/566 (22.79%), reference seeds = 107/568 (18.84%)
73 Soft masked letters = 0/566 (0.00%), 0/568 (0.00%)
74 Computing hash join... [0s]
75 Masking low complexity seeds... [0s]
76 Masked seeds: 0/60 (0.00%)
77 Masked positions (query): 0/566 (0.00%)
78 Masked positions (target): 0/568 (0.00%)
79 Searching alignments... [0s]
80 Current RSS: 9.1 MB, Peak RSS: 9.2 MB
81 Processing query block 1, reference block 1/1, shape 2/2, index chunk 1/4.
82 Building reference seed array... [0s]
83 Building query seed array... [0s]
84 Indexed query seeds = 97875695011120/566 (17292525620339.22%), reference seeds = 107/568 (18.84%)
85 Soft masked letters = 0/566 (0.00%), 0/568 (0.00%)
86 Computing hash join... [0s]
87 Masking low complexity seeds... [0s]
88 Masked seeds: 0/58 (0.00%)
89 Masked positions (query): 0/566 (0.00%)
90 Masked positions (target): 0/568 (0.00%)
91 Searching alignments... [0s]
92 Processing query block 1, reference block 1/1, shape 2/2, index chunk 2/4.
93 Building reference seed array... [0s]
94 Building query seed array... [0s]
95 Indexed query seeds = 2560271741526742528/566 (452344830658435072.00%), reference seeds = 107/568 (18.84%)
96 Soft masked letters = 0/566 (0.00%), 0/568 (0.00%)
97 Computing hash join... [0s]
98 Masking low complexity seeds... [0s]
99 Masked seeds: 0/66 (0.00%)
100 Masked positions (query): 0/566 (0.00%)
101 Masked positions (target): 0/568 (0.00%)
102 Searching alignments... [0s]
103 Processing query block 1, reference block 1/1, shape 2/2, index chunk 3/4.
104 Building reference seed array... [0s]
105 Building query seed array... [0s]
106 Indexed query seeds = 2560271741526742528/566 (452344830658435072.00%), reference seeds = 107/568 (18.84%)
107 Soft masked letters = 0/566 (0.00%), 0/568 (0.00%)
108 Computing hash join... [0s]
109 Masking low complexity seeds... [0s]
110 Masked seeds: 0/46 (0.00%)
111 Masked positions (query): 0/566 (0.00%)
112 Masked positions (target): 0/568 (0.00%)
113 Searching alignments... [0s]
114 Processing query block 1, reference block 1/1, shape 2/2, index chunk 4/4.
115 Building reference seed array... [0s]
116 Building query seed array... [0s]
117 Indexed query seeds = 120/566 (21.20%), reference seeds = 102/568 (17.96%)
118 Soft masked letters = 0/566 (0.00%), 0/568 (0.00%)
119 Computing hash join... [0s]
120 Masking low complexity seeds... [0s]
121 Masked seeds: 0/60 (0.00%)
122 Masked positions (query): 0/566 (0.00%)
123 Masked positions (target): 0/568 (0.00%)
124 Searching alignments... [0s]
125 Deallocating buffers... [0s]
126 Clearing query masking... [0s]
127 Computing alignments... Async_buffer.load() 17(2.37487e-07 GB, 1.4063e-07 GB on disk)
128 Loading trace points... [0s]
129 Sorting trace points... [0s]
130 Computing alignments... [0.01s]
131 Deallocating buffers... [0s]
132 Loading trace points... [0s]
133 [0.011s]
134 Deallocating reference... [0s]
135 Loading reference sequences... [0s]
136 Current RSS: 9.6 MB, Peak RSS: 9.6 MB
137 Deallocating buffers... [0s]
138 Current RSS: 9.6 MB, Peak RSS: 9.6 MB
139 Deallocating queries... [0s]
140 Loading query sequences... [0s]
141 Closing the input file... [0s]
142 Closing the output file... [0s]
143 Cleaning up... [0s]
144 Current RSS: 9.6 MB, Peak RSS: 9.6 MB
145 Total time = 0.093s
146 Hits (filter stage 0) = 774
147 Hits (filter stage 1) = 774 (100 %)
148 Hits (filter stage 2) = 774 (100 %)
149 Hits (filter stage 3) = 17 (2.19638 %)
150 Target hits (stage 0) = 2
151 Target hits (stage 1) = 0
152 Target hits (stage 2) = 2
153 Target hits (stage 3) = 2 (0 (0%) with CBS)
154 Target hits (stage 4) = 2
155 Target hits (stage 5) = 2
156 Swipe realignments = 0
157 Matrix adjusts = 0
158 Extensions (8 bit) = 0
159 Extensions (16 bit) = 4
160 Extensions (32 bit) = 0
161 Hard queries = 0
162 Gapped filter (targets) = 0
163 Gapped filter (hits) stage 1 = 0
164 Gapped filter (hits) stage 2 = 0
165 Time (Load seed hit targets) = 4e-06s (CPU)
166 Time (Sort targets by score) = 0s (CPU)
167 Time (Gapped filter) = 0s (CPU)
168 Time (Matrix adjust) = 0s (CPU)
169 Time (Chaining) = 2e-05s (CPU)
170 Time (DP target sorting) = 0s (CPU)
171 Time (Smith Waterman) = 6.9e-05s (CPU)
172 Time (Smith Waterman TB) = 0.0001s (CPU)
173 Time (Traceback) = 8e-06s (CPU)
174 Time (Target parallel) = 0s (wall)
175 Time (Load seed hits) = 0.000495s (wall)
176 Time (Sort seed hits) = 2.4e-05s (wall)
177 Time (Extension) = 0.010185s (wall)
178 Temporary disk space used (search): 1.4063e-07 GB
179 Reported 2 pairwise alignments, 2 HSPs.
180 1 queries aligned.