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comparison test-data/diamond_log.txt @ 20:0729ae1533e5 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 62db819c1db857d3fba94dc4e290ee0f50f7928d
author iuc
date Mon, 03 Feb 2025 16:00:43 +0000
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19:7ff284249149 20:0729ae1533e5
1 diamond blastx --quiet --threads 1 --db ./database --query /tmp/tmpb7mnrgbk/files/0/b/a/dataset_0bafd694-5276-4809-9258-1d272c89c442.dat --query-gencode 1 --strand both --min-orf 1 --outfmt 6 qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore --out /tmp/tmpb7mnrgbk/job_working_directory/000/34/outputs/dataset_9356bfe1-71ff-4289-b524-b07b2006b561.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 --soft-masking 0 --index-chunks 4 --file-buffer-size 67108864 --log
2 #CPU threads: 1
3 Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1)
4 CPU features detected: ssse3 popcnt sse4.1 avx2
5 L3 cache size: 12582912
6 MAX_SHAPE_LEN=19 SEQ_MASK STRICT_BAND
7 Temporary directory: /tmp/tmpb7mnrgbk/job_working_directory/000/34/outputs
8 #Target sequences to report alignments for: 25
9 DP fields: 510
10 Opening the database... [0s]
11 Database: ./database (type: Diamond database, sequences: 2, letters: 568)
12 Block size = 2000000000
13 Current RSS: 6.5 MB, Peak RSS: 6.5 MB
14 Opening the input file... [0s]
15 Opening the output file... [0s]
16 Current RSS: 6.6 MB, Peak RSS: 6.6 MB
17 Loading query sequences... Sequences = 6, letters = 1694, average length = 282
18 [0s]
19 Sequences = 6, letters = 1694, average length = 282
20 Masking queries... [0s]
21 Current RSS: 7.1 MB, Peak RSS: 7.1 MB
22 Seed partition bits = 8
23 Algorithm: Double-indexed
24 Shape configuration: 111101110111,111011010010111
25 Building query histograms... [0s]
26 Current RSS: 7.1 MB, Peak RSS: 7.1 MB
27 Seeking in database... [0s]
28 Loading reference sequences... Sequences = 2, letters = 568, average length = 284
29 [0s]
30 Current RSS: 7.1 MB, Peak RSS: 7.1 MB
31 Masking reference... [0s]
32 Masked letters: 0
33 Initializing temporary storage... Async_buffer() 1
34 [0s]
35 Building reference histograms... [0s]
36 Allocating buffers... [0s]
37 Current RSS: 7.4 MB, Peak RSS: 7.4 MB
38 Processing query block 1, reference block 1/1, shape 1/2, index chunk 1/4.
39 Building reference seed array... [0s]
40 Current RSS: 7.4 MB, Peak RSS: 7.4 MB
41 Building query seed array... [0s]
42 Current RSS: 7.4 MB, Peak RSS: 7.4 MB
43 Indexed query seeds = 301/1694 (17.77%), reference seeds = 87/568 (15.32%)
44 Soft masked letters = 0/1694 (0.00%), 0/568 (0.00%)
45 Computing hash join... [0s]
46 Current RSS: 7.2 MB, Peak RSS: 7.4 MB
47 Masking low complexity seeds... [0s]
48 Masked seeds: 0/53 (0.00%)
49 Masked positions (query): 0/1694 (0.00%)
50 Masked positions (target): 0/568 (0.00%)
51 Current RSS: 7.4 MB, Peak RSS: 7.4 MB
52 Searching alignments... [0s]
53 Current RSS: 8.6 MB, Peak RSS: 9.5 MB
54 Deallocating memory... [0s]
55 Current RSS: 7.6 MB, Peak RSS: 9.5 MB
56 Processing query block 1, reference block 1/1, shape 1/2, index chunk 2/4.
57 Building reference seed array... [0s]
58 Current RSS: 7.6 MB, Peak RSS: 9.5 MB
59 Building query seed array... [0s]
60 Current RSS: 7.6 MB, Peak RSS: 9.5 MB
61 Indexed query seeds = 286/1694 (16.88%), reference seeds = 120/568 (21.13%)
62 Soft masked letters = 0/1694 (0.00%), 0/568 (0.00%)
63 Computing hash join... [0s]
64 Current RSS: 7.6 MB, Peak RSS: 9.5 MB
65 Masking low complexity seeds... [0s]
66 Masked seeds: 0/71 (0.00%)
67 Masked positions (query): 0/1694 (0.00%)
68 Masked positions (target): 0/568 (0.00%)
69 Current RSS: 7.6 MB, Peak RSS: 9.5 MB
70 Searching alignments... [0s]
71 Current RSS: 9.4 MB, Peak RSS: 9.5 MB
72 Deallocating memory... [0s]
73 Current RSS: 9.4 MB, Peak RSS: 9.5 MB
74 Processing query block 1, reference block 1/1, shape 1/2, index chunk 3/4.
75 Building reference seed array... [0s]
76 Current RSS: 9.4 MB, Peak RSS: 9.5 MB
77 Building query seed array... [0s]
78 Current RSS: 9.4 MB, Peak RSS: 9.5 MB
79 Indexed query seeds = 296/1694 (17.47%), reference seeds = 98/568 (17.25%)
80 Soft masked letters = 0/1694 (0.00%), 0/568 (0.00%)
81 Computing hash join... [0s]
82 Current RSS: 9.4 MB, Peak RSS: 9.5 MB
83 Masking low complexity seeds... [0s]
84 Masked seeds: 0/54 (0.00%)
85 Masked positions (query): 0/1694 (0.00%)
86 Masked positions (target): 0/568 (0.00%)
87 Current RSS: 9.4 MB, Peak RSS: 9.5 MB
88 Searching alignments... [0s]
89 Current RSS: 9.4 MB, Peak RSS: 9.5 MB
90 Deallocating memory... [0s]
91 Current RSS: 9.4 MB, Peak RSS: 9.5 MB
92 Processing query block 1, reference block 1/1, shape 1/2, index chunk 4/4.
93 Building reference seed array... [0s]
94 Current RSS: 9.4 MB, Peak RSS: 9.5 MB
95 Building query seed array... [0s]
96 Current RSS: 9.4 MB, Peak RSS: 9.5 MB
97 Indexed query seeds = 307/1694 (18.12%), reference seeds = 109/568 (19.19%)
98 Soft masked letters = 0/1694 (0.00%), 0/568 (0.00%)
99 Computing hash join... [0s]
100 Current RSS: 9.4 MB, Peak RSS: 9.5 MB
101 Masking low complexity seeds... [0s]
102 Masked seeds: 0/61 (0.00%)
103 Masked positions (query): 0/1694 (0.00%)
104 Masked positions (target): 0/568 (0.00%)
105 Current RSS: 9.4 MB, Peak RSS: 9.5 MB
106 Searching alignments... [0s]
107 Current RSS: 9.4 MB, Peak RSS: 9.5 MB
108 Deallocating memory... [0s]
109 Current RSS: 9.4 MB, Peak RSS: 9.5 MB
110 Current RSS: 9.4 MB, Peak RSS: 9.5 MB
111 Processing query block 1, reference block 1/1, shape 2/2, index chunk 1/4.
112 Building reference seed array... [0s]
113 Current RSS: 9.4 MB, Peak RSS: 9.5 MB
114 Building query seed array... [0s]
115 Current RSS: 9.4 MB, Peak RSS: 9.5 MB
116 Indexed query seeds = 301/1694 (17.77%), reference seeds = 92/568 (16.20%)
117 Soft masked letters = 0/1694 (0.00%), 0/568 (0.00%)
118 Computing hash join... [0s]
119 Current RSS: 9.4 MB, Peak RSS: 9.5 MB
120 Masking low complexity seeds... [0s]
121 Masked seeds: 0/51 (0.00%)
122 Masked positions (query): 0/1694 (0.00%)
123 Masked positions (target): 0/568 (0.00%)
124 Current RSS: 9.4 MB, Peak RSS: 9.5 MB
125 Searching alignments... [0s]
126 Current RSS: 9.4 MB, Peak RSS: 9.5 MB
127 Deallocating memory... [0s]
128 Current RSS: 9.4 MB, Peak RSS: 9.5 MB
129 Processing query block 1, reference block 1/1, shape 2/2, index chunk 2/4.
130 Building reference seed array... [0s]
131 Current RSS: 9.4 MB, Peak RSS: 9.5 MB
132 Building query seed array... [0s]
133 Current RSS: 9.4 MB, Peak RSS: 9.5 MB
134 Indexed query seeds = 283/1694 (16.71%), reference seeds = 95/568 (16.73%)
135 Soft masked letters = 0/1694 (0.00%), 0/568 (0.00%)
136 Computing hash join... [0s]
137 Current RSS: 9.4 MB, Peak RSS: 9.5 MB
138 Masking low complexity seeds... [0s]
139 Masked seeds: 0/55 (0.00%)
140 Masked positions (query): 0/1694 (0.00%)
141 Masked positions (target): 0/568 (0.00%)
142 Current RSS: 9.4 MB, Peak RSS: 9.5 MB
143 Searching alignments... [0s]
144 Current RSS: 9.4 MB, Peak RSS: 9.5 MB
145 Deallocating memory... [0s]
146 Current RSS: 9.4 MB, Peak RSS: 9.5 MB
147 Processing query block 1, reference block 1/1, shape 2/2, index chunk 3/4.
148 Building reference seed array... [0s]
149 Current RSS: 9.4 MB, Peak RSS: 9.5 MB
150 Building query seed array... [0s]
151 Current RSS: 9.4 MB, Peak RSS: 9.5 MB
152 Indexed query seeds = 266/1694 (15.70%), reference seeds = 93/568 (16.37%)
153 Soft masked letters = 0/1694 (0.00%), 0/568 (0.00%)
154 Computing hash join... [0s]
155 Current RSS: 9.4 MB, Peak RSS: 9.5 MB
156 Masking low complexity seeds... [0s]
157 Masked seeds: 0/56 (0.00%)
158 Masked positions (query): 0/1694 (0.00%)
159 Masked positions (target): 0/568 (0.00%)
160 Current RSS: 9.4 MB, Peak RSS: 9.5 MB
161 Searching alignments... [0s]
162 Current RSS: 9.4 MB, Peak RSS: 9.5 MB
163 Deallocating memory... [0s]
164 Current RSS: 9.4 MB, Peak RSS: 9.5 MB
165 Processing query block 1, reference block 1/1, shape 2/2, index chunk 4/4.
166 Building reference seed array... [0s]
167 Current RSS: 9.4 MB, Peak RSS: 9.5 MB
168 Building query seed array... [0s]
169 Current RSS: 9.4 MB, Peak RSS: 9.5 MB
170 Indexed query seeds = 305/1694 (18.00%), reference seeds = 113/568 (19.89%)
171 Soft masked letters = 0/1694 (0.00%), 0/568 (0.00%)
172 Computing hash join... [0s]
173 Current RSS: 9.4 MB, Peak RSS: 9.5 MB
174 Masking low complexity seeds... [0s]
175 Masked seeds: 0/68 (0.00%)
176 Masked positions (query): 0/1694 (0.00%)
177 Masked positions (target): 0/568 (0.00%)
178 Current RSS: 9.4 MB, Peak RSS: 9.5 MB
179 Searching alignments... [0s]
180 Current RSS: 9.4 MB, Peak RSS: 9.5 MB
181 Deallocating memory... [0s]
182 Current RSS: 9.4 MB, Peak RSS: 9.5 MB
183 Current RSS: 9.4 MB, Peak RSS: 9.5 MB
184 Deallocating buffers... [0s]
185 Clearing query masking... [0s]
186 Current RSS: 9.4 MB, Peak RSS: 9.5 MB
187 Computing alignments... Async_buffer.load() 21(2.93367e-07 GB, 2.38419e-07 GB on disk)
188 Loading trace points... [0s]
189 Sorting trace points... [0s]
190 Computing partition... [0s]
191 Computing alignments... [0s]
192 Deallocating buffers... [0s]
193 Loading trace points... [0s]
194 [0.001s]
195 Deallocating reference... [0s]
196 Loading reference sequences... Current RSS: 10.1 MB, Peak RSS: 10.1 MB
197 [0s]
198 Deallocating buffers... [0s]
199 Current RSS: 10.1 MB, Peak RSS: 10.1 MB
200 Deallocating queries... [0s]
201 Current RSS: 10.1 MB, Peak RSS: 10.1 MB
202 Loading query sequences... [0s]
203 Closing the input file... [0s]
204 Closing the output file... [0s]
205 Closing the database... [0s]
206 Cleaning up... [0s]
207 Current RSS: 10.1 MB, Peak RSS: 10.1 MB
208 Total time = 0.017s
209 Hits (filter stage 0) = 774
210 Hits (filter stage 1) = 774 (100 %)
211 Hits (filter stage 2) = 774 (100 %)
212 Hits (filter stage 3) = 21 (2.71318 %)
213 Target hits (stage 0) = 2
214 Target hits (stage 1) = 0
215 Target hits (stage 2) = 2
216 Target hits (stage 3) = 2 (0 (0%) with CBS)
217 Target hits (stage 4) = 2
218 Target hits (stage 5) = 2
219 Target hits (stage 6) = 2
220 Swipe realignments = 0
221 Matrix adjusts = 0
222 Extensions (8 bit) = 0
223 Extensions (16 bit) = 4
224 Extensions (32 bit) = 0
225 Overflows (8 bit) = 0
226 Wasted (16 bit) = 0
227 Effort (Extension) = 8
228 Effort (Cells) = 0
229 Cells (8 bit) = 0
230 Cells (16 bit) = 0
231 SWIPE tasks = 2
232 SWIPE tasks (async) = 0
233 Trivial aln = 0
234 Hard queries = 0
235 Gapped filter (targets) = 0
236 Gapped filter (hits) stage 1 = 0
237 Gapped filter (hits) stage 2 = 0
238 Time (Load seed hit targets) = 5e-06s (CPU)
239 Time (Sort targets by score) = 0s (CPU)
240 Time (Gapped filter) = 0s (CPU)
241 Time (Matrix adjust) = 0s (CPU)
242 Time (Chaining) = 3.4e-05s (CPU)
243 Time (DP target sorting) = 0s (CPU)
244 Time (Query profiles) = 0s (CPU)
245 Time (Smith Waterman) = 0.000352s (CPU)
246 Time (Anchored SWIPE Alloc) = 0s (CPU)
247 Time (Anchored SWIPE Sort) = 0s (CPU)
248 Time (Anchored SWIPE Add) = 0s (CPU)
249 Time (Anchored SWIPE Output) = 0s (CPU)
250 Time (Anchored SWIPE) = 0s (CPU)
251 Time (Smith Waterman TB) = 0s (CPU)
252 Time (Smith Waterman-32) = 0s (CPU)
253 Time (Traceback) = 1.6e-05s (CPU)
254 Time (Target parallel) = 0s (wall)
255 Time (Load seed hits) = 0.000797s (wall)
256 Time (Sort seed hits) = 2.8e-05s (wall)
257 Time (Extension) = 0.000568s (wall)
258 Temporary disk space used (search): 2.38419e-07 GB
259 Reported 2 pairwise alignments, 2 HSPs.
260 1 queries aligned.
261 Current RSS: 10.1 MB, Peak RSS: 10.1 MB