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comparison test-data/result1.log @ 8:e27815e82dd4 draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
author bgruening
date Wed, 30 Jun 2021 20:02:51 +0000
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children 276f5d8712d5
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7:8d4f03b5fe9d 8:e27815e82dd4
1 [2021-06-30 16:00:39] root: INFO: Starting Flye 2.8.3-b1695
2 [2021-06-30 16:00:39] root: DEBUG: Cmd: /usr/local/bin/flye --pacbio-raw ./input_0.fastq.gz ./input_1.fastq.gz ./input_2.fastq.gz ./input_3.fastq.gz ./input_4.fastq.gz ./input_5.fastq.gz ./input_6.fastq.gz -o out_dir -t 1 -i 0
3 [2021-06-30 16:00:39] root: DEBUG: Python version: 3.9.2 | packaged by conda-forge | (default, Feb 21 2021, 05:02:46)
4 [GCC 9.3.0]
5 [2021-06-30 16:00:39] root: INFO: >>>STAGE: configure
6 [2021-06-30 16:00:39] root: INFO: Configuring run
7 [2021-06-30 16:00:39] root: INFO: Total read length: 7249289
8 [2021-06-30 16:00:39] root: INFO: Reads N50/N90: 11150 / 5790
9 [2021-06-30 16:00:39] root: INFO: Minimum overlap set to 5000
10 [2021-06-30 16:00:39] root: INFO: >>>STAGE: assembly
11 [2021-06-30 16:00:39] root: INFO: Assembling disjointigs
12 [2021-06-30 16:00:39] root: DEBUG: -----Begin assembly log------
13 [2021-06-30 16:00:39] root: DEBUG: Running: flye-modules assemble --reads ./input_0.fastq.gz,./input_1.fastq.gz,./input_2.fastq.gz,./input_3.fastq.gz,./input_4.fastq.gz,./input_5.fastq.gz,./input_6.fastq.gz --out-asm /tmp/tmpicy_msib/job_working_directory/000/8/working/out_dir/00-assembly/draft_assembly.fasta --config /usr/local/lib/python3.9/site-packages/flye/config/bin_cfg/asm_raw_reads.cfg --log /tmp/tmpicy_msib/job_working_directory/000/8/working/out_dir/flye.log --threads 1 --min-ovlp 5000
14 [2021-06-30 16:00:39] DEBUG: Build date: Mar 27 2021 19:08:40
15 [2021-06-30 16:00:39] DEBUG: Total RAM: 15 Gb
16 [2021-06-30 16:00:39] DEBUG: Available RAM: 11 Gb
17 [2021-06-30 16:00:39] DEBUG: Total CPUs: 8
18 [2021-06-30 16:00:39] DEBUG: Loading /usr/local/lib/python3.9/site-packages/flye/config/bin_cfg/asm_raw_reads.cfg
19 [2021-06-30 16:00:39] DEBUG: Loading /usr/local/lib/python3.9/site-packages/flye/config/bin_cfg/asm_defaults.cfg
20 [2021-06-30 16:00:39] DEBUG: big_genome_threshold=29000000
21 [2021-06-30 16:00:39] DEBUG: meta_read_filter_kmer_freq=100
22 [2021-06-30 16:00:39] DEBUG: max_coverage_drop_rate=5
23 [2021-06-30 16:00:39] DEBUG: max_extensions_drop_rate=5
24 [2021-06-30 16:00:39] DEBUG: chimera_window=100
25 [2021-06-30 16:00:39] DEBUG: min_reads_in_disjointig=4
26 [2021-06-30 16:00:39] DEBUG: max_inner_reads=10
27 [2021-06-30 16:00:39] DEBUG: max_inner_fraction=0.25
28 [2021-06-30 16:00:39] DEBUG: max_separation=500
29 [2021-06-30 16:00:39] DEBUG: unique_edge_length=50000
30 [2021-06-30 16:00:39] DEBUG: min_repeat_res_support=0.51
31 [2021-06-30 16:00:39] DEBUG: out_paths_ratio=5
32 [2021-06-30 16:00:39] DEBUG: graph_cov_drop_rate=5
33 [2021-06-30 16:00:39] DEBUG: coverage_estimate_window=100
34 [2021-06-30 16:00:39] DEBUG: max_bubble_length=50000
35 [2021-06-30 16:00:39] DEBUG: loop_coverage_rate=1.5
36 [2021-06-30 16:00:39] DEBUG: repeat_edge_cov_mult=1.75
37 [2021-06-30 16:00:39] DEBUG: weak_detach_rate=5
38 [2021-06-30 16:00:39] DEBUG: tip_coverage_rate=2
39 [2021-06-30 16:00:39] DEBUG: tip_length_rate=2
40 [2021-06-30 16:00:39] DEBUG: low_cutoff_warning=1
41 [2021-06-30 16:00:39] DEBUG: hard_min_coverage_rate=10
42 [2021-06-30 16:00:39] DEBUG: kmer_size=17
43 [2021-06-30 16:00:39] DEBUG: use_minimizers=0
44 [2021-06-30 16:00:39] DEBUG: reads_base_alignment=0
45 [2021-06-30 16:00:39] DEBUG: assemble_kmer_sample=1
46 [2021-06-30 16:00:39] DEBUG: repeat_graph_kmer_sample=1
47 [2021-06-30 16:00:39] DEBUG: read_align_kmer_sample=1
48 [2021-06-30 16:00:39] DEBUG: meta_read_top_kmer_rate=0.40
49 [2021-06-30 16:00:39] DEBUG: maximum_jump=1500
50 [2021-06-30 16:00:39] DEBUG: maximum_overhang=1500
51 [2021-06-30 16:00:39] DEBUG: repeat_kmer_rate=100
52 [2021-06-30 16:00:39] DEBUG: assemble_ovlp_divergence=0.10
53 [2021-06-30 16:00:39] DEBUG: assemble_divergence_relative=1
54 [2021-06-30 16:00:39] DEBUG: repeat_graph_ovlp_divergence=0.08
55 [2021-06-30 16:00:39] DEBUG: read_align_ovlp_divergence=0.25
56 [2021-06-30 16:00:39] DEBUG: hpc_scoring_on=0
57 [2021-06-30 16:00:39] DEBUG: add_unassembled_reads=0
58 [2021-06-30 16:00:39] DEBUG: extend_contigs_with_repeats=0
59 [2021-06-30 16:00:39] DEBUG: min_read_cov_cutoff=3
60 [2021-06-30 16:00:39] DEBUG: short_tip_length=20000
61 [2021-06-30 16:00:39] DEBUG: long_tip_length=100000
62 [2021-06-30 16:00:39] DEBUG: Running with k-mer size: 17
63 [2021-06-30 16:00:39] DEBUG: Running with minimum overlap 5000
64 [2021-06-30 16:00:39] DEBUG: Metagenome mode: N
65 [2021-06-30 16:00:39] INFO: Reading sequences
66 [2021-06-30 16:00:39] DEBUG: Building positional index
67 [2021-06-30 16:00:39] DEBUG: Total sequence: 6702247 bp
68 [2021-06-30 16:00:42] INFO: Counting k-mers:
69 [2021-06-30 16:00:42] DEBUG: Updating k-mer histogram
70 [2021-06-30 16:01:29] DEBUG: Hash size: 32
71 [2021-06-30 16:01:29] DEBUG: Total k-mers 6159182
72 [2021-06-30 16:01:29] INFO: Filling index table (1/2)
73 [2021-06-30 16:01:32] DEBUG: Mean k-mer frequency: 2.59564
74 [2021-06-30 16:01:32] DEBUG: Repetitive k-mer frequency: 259
75 [2021-06-30 16:01:32] DEBUG: Filtered 0 repetitive k-mers (0)
76 [2021-06-30 16:01:32] INFO: Filling index table (2/2)
77 [2021-06-30 16:01:35] DEBUG: Sorting k-mer index
78 [2021-06-30 16:01:35] DEBUG: Selected k-mers: 333758
79 [2021-06-30 16:01:35] DEBUG: Index size: 866317
80 [2021-06-30 16:01:35] DEBUG: Mean k-mer index frequency: 2.59564
81 [2021-06-30 16:01:35] DEBUG: Peak RAM usage: 8 Gb
82 [2021-06-30 16:01:35] DEBUG: Estimating k-mer identity bias
83 [2021-06-30 16:01:39] DEBUG: Initial divergence estimate : 0.235584
84 [2021-06-30 16:01:39] DEBUG: Relative threshold: Y
85 [2021-06-30 16:01:39] DEBUG: Max divergence threshold set to 0.335584
86 [2021-06-30 16:01:39] INFO: Extending reads
87 [2021-06-30 16:01:39] DEBUG: Estimating overlap coverage
88 [2021-06-30 16:01:42] INFO: Overlap-based coverage: 11
89 [2021-06-30 16:01:42] INFO: Median overlap divergence: 0.235584
90 [2021-06-30 16:01:42] DEBUG: Sequence divergence distribution:
91
92 | * |
93 | * |
94 | * *** |
95 | * *** |
96 | ****** |
97 | ******* |
98 | ******* |
99 | ******** |
100 | ******** |
101 | ********* |
102 | ********* |
103 | ********* |
104 | ********** |
105 | ************ |
106 | ************* |
107 | ************** |
108 | ************** |
109 | **************** |
110 | * ***************** * |
111 | * ** ************************ | * *
112 ----------------------------------------------------------------------------------------------------
113 0% 5% 10% 15% 20% 25% 30% 35% 40% 45%
114
115 Q25 = 0.22, Q50 = 0.24, Q75 = 0.25
116
117 [2021-06-30 16:01:42] DEBUG: Assembled disjointig 1
118 With 86 reads
119 Start read: +S1_371
120 At position: 35
121 leftTip: 1 rightTip: 1
122 Suspicious: 3
123 Short ext: 2
124 Mean extensions: 9
125 Avg overlap len: 10074
126 Min overlap len: 2570
127 Inner reads: 0
128 Length: 433999
129 [2021-06-30 16:01:42] DEBUG: Inner: 1040 covered: 1110 total: 1236
130 [2021-06-30 16:01:42] INFO: Assembled 1 disjointigs
131 [2021-06-30 16:01:42] INFO: Generating sequence
132 [2021-06-30 16:01:43] DEBUG: Writing FASTA
133 [2021-06-30 16:01:43] DEBUG: Peak RAM usage: 8 Gb
134 -----------End assembly log------------
135 [2021-06-30 16:01:43] root: DEBUG: Disjointigs length: 434844, N50: 434844
136 [2021-06-30 16:01:43] root: INFO: >>>STAGE: consensus
137 [2021-06-30 16:01:43] root: INFO: Running Minimap2
138 [2021-06-30 16:01:48] root: INFO: Computing consensus
139 [2021-06-30 16:01:57] root: INFO: Alignment error rate: 0.196236
140 [2021-06-30 16:01:57] root: INFO: >>>STAGE: repeat
141 [2021-06-30 16:01:57] root: INFO: Building and resolving repeat graph
142 [2021-06-30 16:01:57] root: DEBUG: -----Begin repeat analyser log------
143 [2021-06-30 16:01:57] root: DEBUG: Running: flye-modules repeat --disjointigs /tmp/tmpicy_msib/job_working_directory/000/8/working/out_dir/10-consensus/consensus.fasta --reads ./input_0.fastq.gz,./input_1.fastq.gz,./input_2.fastq.gz,./input_3.fastq.gz,./input_4.fastq.gz,./input_5.fastq.gz,./input_6.fastq.gz --out-dir /tmp/tmpicy_msib/job_working_directory/000/8/working/out_dir/20-repeat --config /usr/local/lib/python3.9/site-packages/flye/config/bin_cfg/asm_raw_reads.cfg --log /tmp/tmpicy_msib/job_working_directory/000/8/working/out_dir/flye.log --threads 1 --min-ovlp 5000
144 [2021-06-30 16:01:57] DEBUG: Build date: Mar 27 2021 19:09:05
145 [2021-06-30 16:01:57] DEBUG: Total RAM: 15 Gb
146 [2021-06-30 16:01:57] DEBUG: Available RAM: 11 Gb
147 [2021-06-30 16:01:57] DEBUG: Total CPUs: 8
148 [2021-06-30 16:01:57] DEBUG: Loading /usr/local/lib/python3.9/site-packages/flye/config/bin_cfg/asm_raw_reads.cfg
149 [2021-06-30 16:01:57] DEBUG: Loading /usr/local/lib/python3.9/site-packages/flye/config/bin_cfg/asm_defaults.cfg
150 [2021-06-30 16:01:57] DEBUG: big_genome_threshold=29000000
151 [2021-06-30 16:01:57] DEBUG: meta_read_filter_kmer_freq=100
152 [2021-06-30 16:01:57] DEBUG: max_coverage_drop_rate=5
153 [2021-06-30 16:01:57] DEBUG: max_extensions_drop_rate=5
154 [2021-06-30 16:01:57] DEBUG: chimera_window=100
155 [2021-06-30 16:01:57] DEBUG: min_reads_in_disjointig=4
156 [2021-06-30 16:01:57] DEBUG: max_inner_reads=10
157 [2021-06-30 16:01:57] DEBUG: max_inner_fraction=0.25
158 [2021-06-30 16:01:57] DEBUG: max_separation=500
159 [2021-06-30 16:01:57] DEBUG: unique_edge_length=50000
160 [2021-06-30 16:01:57] DEBUG: min_repeat_res_support=0.51
161 [2021-06-30 16:01:57] DEBUG: out_paths_ratio=5
162 [2021-06-30 16:01:57] DEBUG: graph_cov_drop_rate=5
163 [2021-06-30 16:01:57] DEBUG: coverage_estimate_window=100
164 [2021-06-30 16:01:57] DEBUG: max_bubble_length=50000
165 [2021-06-30 16:01:57] DEBUG: loop_coverage_rate=1.5
166 [2021-06-30 16:01:57] DEBUG: repeat_edge_cov_mult=1.75
167 [2021-06-30 16:01:57] DEBUG: weak_detach_rate=5
168 [2021-06-30 16:01:57] DEBUG: tip_coverage_rate=2
169 [2021-06-30 16:01:57] DEBUG: tip_length_rate=2
170 [2021-06-30 16:01:57] DEBUG: low_cutoff_warning=1
171 [2021-06-30 16:01:57] DEBUG: hard_min_coverage_rate=10
172 [2021-06-30 16:01:57] DEBUG: kmer_size=17
173 [2021-06-30 16:01:57] DEBUG: use_minimizers=0
174 [2021-06-30 16:01:57] DEBUG: reads_base_alignment=0
175 [2021-06-30 16:01:57] DEBUG: assemble_kmer_sample=1
176 [2021-06-30 16:01:57] DEBUG: repeat_graph_kmer_sample=1
177 [2021-06-30 16:01:57] DEBUG: read_align_kmer_sample=1
178 [2021-06-30 16:01:57] DEBUG: meta_read_top_kmer_rate=0.40
179 [2021-06-30 16:01:57] DEBUG: maximum_jump=1500
180 [2021-06-30 16:01:57] DEBUG: maximum_overhang=1500
181 [2021-06-30 16:01:57] DEBUG: repeat_kmer_rate=100
182 [2021-06-30 16:01:57] DEBUG: assemble_ovlp_divergence=0.10
183 [2021-06-30 16:01:57] DEBUG: assemble_divergence_relative=1
184 [2021-06-30 16:01:57] DEBUG: repeat_graph_ovlp_divergence=0.08
185 [2021-06-30 16:01:57] DEBUG: read_align_ovlp_divergence=0.25
186 [2021-06-30 16:01:57] DEBUG: hpc_scoring_on=0
187 [2021-06-30 16:01:57] DEBUG: add_unassembled_reads=0
188 [2021-06-30 16:01:57] DEBUG: extend_contigs_with_repeats=0
189 [2021-06-30 16:01:57] DEBUG: min_read_cov_cutoff=3
190 [2021-06-30 16:01:57] DEBUG: short_tip_length=20000
191 [2021-06-30 16:01:57] DEBUG: long_tip_length=100000
192 [2021-06-30 16:01:57] DEBUG: Running with k-mer size: 17
193 [2021-06-30 16:01:57] DEBUG: Selected minimum overlap 5000
194 [2021-06-30 16:01:57] DEBUG: Metagenome mode: N
195 [2021-06-30 16:01:57] INFO: Parsing disjointigs
196 [2021-06-30 16:01:57] DEBUG: Building positional index
197 [2021-06-30 16:01:57] DEBUG: Total sequence: 418806 bp
198 [2021-06-30 16:01:57] INFO: Building repeat graph
199 [2021-06-30 16:01:57] DEBUG: Mean k-mer frequency: 1.00896
200 [2021-06-30 16:01:57] DEBUG: Repetitive k-mer frequency: 100
201 [2021-06-30 16:01:57] DEBUG: Filtered 0 repetitive k-mers (0)
202 [2021-06-30 16:01:57] DEBUG: Sorting k-mer index
203 [2021-06-30 16:01:57] DEBUG: Selected k-mers: 415069
204 [2021-06-30 16:01:57] DEBUG: K-mer index size: 418789
205 [2021-06-30 16:01:57] DEBUG: Mean k-mer frequency: 1.00896
206 [2021-06-30 16:01:57] DEBUG: Minimizer rate: 1.00004
207 [2021-06-30 16:01:58] DEBUG: Computing transitive closure for overlaps
208 [2021-06-30 16:01:58] DEBUG: Found 0 overlaps
209 [2021-06-30 16:01:58] DEBUG: Left 0 overlaps after filtering
210 [2021-06-30 16:01:58] INFO: Median overlap divergence: 0
211 [2021-06-30 16:01:58] DEBUG: Sequence divergence distribution:
212
213 | |
214 | |
215 | |
216 | |
217 | |
218 | |
219 | |
220 | |
221 | |
222 | |
223 | |
224 | |
225 | |
226 | |
227 | |
228 | |
229 | |
230 | |
231 | |
232 | |
233 ----------------------------------------------------------------------------------------------------
234 0% 5% 10% 15% 20% 25% 30% 35% 40% 45%
235
236 Q25 = 0, Q50 = 0, Q75 = 0
237
238 [2021-06-30 16:01:58] DEBUG: Computing gluepoints
239 [2021-06-30 16:01:58] DEBUG: Added 0 gluepoint projections
240 [2021-06-30 16:01:58] DEBUG: Created 4 gluepoints
241 [2021-06-30 16:01:58] DEBUG: Artificial loops removed: 0 left, 0 right, 0 both
242 [2021-06-30 16:01:58] DEBUG: Initializing edges
243 [2021-06-30 16:01:58] DEBUG: Edges length checksum: 18446744073013520505
244 [2021-06-30 16:01:58] DEBUG: Filtered 0 singleton segments
245 [2021-06-30 16:01:58] DEBUG: Removed 0 simple and 0 double chimeric junctions
246 [2021-06-30 16:01:58] DEBUG: Collapsed 0 edges
247 [2021-06-30 16:01:58] DEBUG: * 1 +disjointig_1 0 418805 418805
248 [2021-06-30 16:01:58] DEBUG: Total edges: 1
249 [2021-06-30 16:01:58] INFO: Parsing reads
250 [2021-06-30 16:01:58] DEBUG: Building positional index
251 [2021-06-30 16:01:58] DEBUG: Total sequence: 7249289 bp
252 [2021-06-30 16:01:58] DEBUG: Building positional index
253 [2021-06-30 16:01:58] DEBUG: Total sequence: 418805 bp
254 [2021-06-30 16:01:58] INFO: Aligning reads to the graph
255 [2021-06-30 16:01:58] DEBUG: Mean k-mer frequency: 1.00896
256 [2021-06-30 16:01:58] DEBUG: Repetitive k-mer frequency: 100
257 [2021-06-30 16:01:58] DEBUG: Filtered 0 repetitive k-mers (0)
258 [2021-06-30 16:01:58] DEBUG: Sorting k-mer index
259 [2021-06-30 16:01:58] DEBUG: Selected k-mers: 415068
260 [2021-06-30 16:01:58] DEBUG: K-mer index size: 418788
261 [2021-06-30 16:01:58] DEBUG: Mean k-mer frequency: 1.00896
262 [2021-06-30 16:01:58] DEBUG: Minimizer rate: 1.00004
263 [2021-06-30 16:02:00] DEBUG: Total reads : 618
264 [2021-06-30 16:02:00] DEBUG: Read with aligned parts : 610
265 [2021-06-30 16:02:00] DEBUG: Aligned in one piece : 610
266 [2021-06-30 16:02:00] INFO: Aligned read sequence: 6562529 / 6702247 (0.979154)
267 [2021-06-30 16:02:00] INFO: Median overlap divergence: 0.129507
268 [2021-06-30 16:02:00] DEBUG: Sequence divergence distribution:
269
270 | * |
271 | * |
272 | ** |
273 | ** |
274 | ** |
275 | *** |
276 | *** * |
277 | *** * |
278 | ***** |
279 | ***** |
280 | ****** |
281 | ******* |
282 | ******* |
283 | ******** |
284 | ********* |
285 | ********* |
286 | ********** |
287 | *********** |
288 | ************ * |
289 | ***************** |
290 ----------------------------------------------------------------------------------------------------
291 0% 5% 10% 15% 20% 25% 30% 35% 40% 45%
292
293 Q25 = 0.12, Q50 = 0.13, Q75 = 0.14
294
295 [2021-06-30 16:02:00] INFO: Mean edge coverage: 14
296 [2021-06-30 16:02:00] DEBUG: 1 len:418805 cov:15 mult:1.07143
297 [2021-06-30 16:02:00] DEBUG: -1 len:418805 cov:15 mult:1.07143
298 [2021-06-30 16:02:00] DEBUG: Unique coverage threshold 26
299 [2021-06-30 16:02:00] INFO: Simplifying the graph
300 [2021-06-30 16:02:00] DEBUG: Read coverage cutoff: 3
301 [2021-06-30 16:02:00] DEBUG: [SIMPL] Removed 0 paths with low coverage
302 [2021-06-30 16:02:00] DEBUG: Finding repeats
303 [2021-06-30 16:02:00] DEBUG: Read coverage cutoff: 3
304 [2021-06-30 16:02:00] DEBUG: Repeat detection iteration 1
305 [2021-06-30 16:02:00] DEBUG: Writing Dot
306 [2021-06-30 16:02:00] DEBUG: Writing FASTA
307 [2021-06-30 16:02:00] DEBUG: [SIMPL] == Iteration 1 ==
308 [2021-06-30 16:02:00] DEBUG: Splitting nodes
309 [2021-06-30 16:02:00] DEBUG: [SIMPL] Split 0 nodes
310 [2021-06-30 16:02:00] DEBUG: [SIMPL] Clipped 0 short and 0 long tips
311 [2021-06-30 16:02:00] DEBUG: [SIMPL] Masked 0 heterozygous loops
312 [2021-06-30 16:02:00] DEBUG: [SIMPL] Masked 0 simple bubbles
313 [2021-06-30 16:02:00] DEBUG: Finding repeats
314 [2021-06-30 16:02:00] DEBUG: Read coverage cutoff: 3
315 [2021-06-30 16:02:00] DEBUG: Repeat detection iteration 1
316 [2021-06-30 16:02:00] DEBUG: Total unique edges: 1
317 [2021-06-30 16:02:00] DEBUG: [SIMPL] Resolved repeats: 0
318 [2021-06-30 16:02:00] DEBUG: RR links: 0
319 [2021-06-30 16:02:00] DEBUG: Unresolved: 0
320 [2021-06-30 16:02:00] DEBUG: Removed 0 simple and 0 double chimeric junctions
321 [2021-06-30 16:02:00] DEBUG: [SIMPL] Collapsed 0 haplotypes
322 [2021-06-30 16:02:00] DEBUG: [SIMPL] Resolved 0 simple repeats
323 [2021-06-30 16:02:00] DEBUG: Read coverage cutoff: 3
324 [2021-06-30 16:02:00] DEBUG: [SIMPL] Removed 0 paths with low coverage
325 [2021-06-30 16:02:00] DEBUG: Finding repeats
326 [2021-06-30 16:02:00] DEBUG: Read coverage cutoff: 3
327 [2021-06-30 16:02:00] DEBUG: Repeat detection iteration 1
328 [2021-06-30 16:02:00] DEBUG: Writing Dot
329 [2021-06-30 16:02:00] DEBUG: Writing FASTA
330 [2021-06-30 16:02:00] DEBUG: Peak RAM usage: 0 Gb
331 -----------End assembly log------------
332 [2021-06-30 16:02:00] root: INFO: >>>STAGE: contigger
333 [2021-06-30 16:02:00] root: INFO: Generating contigs
334 [2021-06-30 16:02:00] root: DEBUG: -----Begin contigger analyser log------
335 [2021-06-30 16:02:00] root: DEBUG: Running: flye-modules contigger --graph-edges /tmp/tmpicy_msib/job_working_directory/000/8/working/out_dir/20-repeat/repeat_graph_edges.fasta --reads ./input_0.fastq.gz,./input_1.fastq.gz,./input_2.fastq.gz,./input_3.fastq.gz,./input_4.fastq.gz,./input_5.fastq.gz,./input_6.fastq.gz --out-dir /tmp/tmpicy_msib/job_working_directory/000/8/working/out_dir/30-contigger --config /usr/local/lib/python3.9/site-packages/flye/config/bin_cfg/asm_raw_reads.cfg --repeat-graph /tmp/tmpicy_msib/job_working_directory/000/8/working/out_dir/20-repeat/repeat_graph_dump --graph-aln /tmp/tmpicy_msib/job_working_directory/000/8/working/out_dir/20-repeat/read_alignment_dump --log /tmp/tmpicy_msib/job_working_directory/000/8/working/out_dir/flye.log --threads 1 --min-ovlp 5000
336 [2021-06-30 16:02:00] DEBUG: Build date: Mar 27 2021 19:09:32
337 [2021-06-30 16:02:00] DEBUG: Total RAM: 15 Gb
338 [2021-06-30 16:02:00] DEBUG: Available RAM: 11 Gb
339 [2021-06-30 16:02:00] DEBUG: Total CPUs: 8
340 [2021-06-30 16:02:00] DEBUG: Loading /usr/local/lib/python3.9/site-packages/flye/config/bin_cfg/asm_raw_reads.cfg
341 [2021-06-30 16:02:00] DEBUG: Loading /usr/local/lib/python3.9/site-packages/flye/config/bin_cfg/asm_defaults.cfg
342 [2021-06-30 16:02:00] DEBUG: big_genome_threshold=29000000
343 [2021-06-30 16:02:00] DEBUG: meta_read_filter_kmer_freq=100
344 [2021-06-30 16:02:00] DEBUG: max_coverage_drop_rate=5
345 [2021-06-30 16:02:00] DEBUG: max_extensions_drop_rate=5
346 [2021-06-30 16:02:00] DEBUG: chimera_window=100
347 [2021-06-30 16:02:00] DEBUG: min_reads_in_disjointig=4
348 [2021-06-30 16:02:00] DEBUG: max_inner_reads=10
349 [2021-06-30 16:02:00] DEBUG: max_inner_fraction=0.25
350 [2021-06-30 16:02:00] DEBUG: max_separation=500
351 [2021-06-30 16:02:00] DEBUG: unique_edge_length=50000
352 [2021-06-30 16:02:00] DEBUG: min_repeat_res_support=0.51
353 [2021-06-30 16:02:00] DEBUG: out_paths_ratio=5
354 [2021-06-30 16:02:00] DEBUG: graph_cov_drop_rate=5
355 [2021-06-30 16:02:00] DEBUG: coverage_estimate_window=100
356 [2021-06-30 16:02:00] DEBUG: max_bubble_length=50000
357 [2021-06-30 16:02:00] DEBUG: loop_coverage_rate=1.5
358 [2021-06-30 16:02:00] DEBUG: repeat_edge_cov_mult=1.75
359 [2021-06-30 16:02:00] DEBUG: weak_detach_rate=5
360 [2021-06-30 16:02:00] DEBUG: tip_coverage_rate=2
361 [2021-06-30 16:02:00] DEBUG: tip_length_rate=2
362 [2021-06-30 16:02:00] DEBUG: low_cutoff_warning=1
363 [2021-06-30 16:02:00] DEBUG: hard_min_coverage_rate=10
364 [2021-06-30 16:02:00] DEBUG: kmer_size=17
365 [2021-06-30 16:02:00] DEBUG: use_minimizers=0
366 [2021-06-30 16:02:00] DEBUG: reads_base_alignment=0
367 [2021-06-30 16:02:00] DEBUG: assemble_kmer_sample=1
368 [2021-06-30 16:02:00] DEBUG: repeat_graph_kmer_sample=1
369 [2021-06-30 16:02:00] DEBUG: read_align_kmer_sample=1
370 [2021-06-30 16:02:00] DEBUG: meta_read_top_kmer_rate=0.40
371 [2021-06-30 16:02:00] DEBUG: maximum_jump=1500
372 [2021-06-30 16:02:00] DEBUG: maximum_overhang=1500
373 [2021-06-30 16:02:00] DEBUG: repeat_kmer_rate=100
374 [2021-06-30 16:02:00] DEBUG: assemble_ovlp_divergence=0.10
375 [2021-06-30 16:02:00] DEBUG: assemble_divergence_relative=1
376 [2021-06-30 16:02:00] DEBUG: repeat_graph_ovlp_divergence=0.08
377 [2021-06-30 16:02:00] DEBUG: read_align_ovlp_divergence=0.25
378 [2021-06-30 16:02:00] DEBUG: hpc_scoring_on=0
379 [2021-06-30 16:02:00] DEBUG: add_unassembled_reads=0
380 [2021-06-30 16:02:00] DEBUG: extend_contigs_with_repeats=0
381 [2021-06-30 16:02:00] DEBUG: min_read_cov_cutoff=3
382 [2021-06-30 16:02:00] DEBUG: short_tip_length=20000
383 [2021-06-30 16:02:00] DEBUG: long_tip_length=100000
384 [2021-06-30 16:02:00] DEBUG: Running with k-mer size: 17
385 [2021-06-30 16:02:00] DEBUG: Selected minimum overlap 5000
386 [2021-06-30 16:02:00] INFO: Reading sequences
387 [2021-06-30 16:02:01] DEBUG: Building positional index
388 [2021-06-30 16:02:01] DEBUG: Total sequence: 7249289 bp
389 [2021-06-30 16:02:01] DEBUG: Flipped 0
390 [2021-06-30 16:02:01] DEBUG: UPath 1: 1
391 [2021-06-30 16:02:01] DEBUG: Final graph contiain 1 egdes
392 [2021-06-30 16:02:01] DEBUG: Extending contigs into repeats
393 [2021-06-30 16:02:01] DEBUG: Covered 0 repetitive contigs
394 [2021-06-30 16:02:01] INFO: Generated 1 contigs
395 [2021-06-30 16:02:01] DEBUG: Writing FASTA
396 [2021-06-30 16:02:01] DEBUG: Generating scaffold connections
397 [2021-06-30 16:02:01] INFO: Added 0 scaffold connections
398 [2021-06-30 16:02:01] DEBUG: Writing Dot
399 [2021-06-30 16:02:01] DEBUG: Writing FASTA
400 [2021-06-30 16:02:01] DEBUG: Writing Gfa
401 [2021-06-30 16:02:01] DEBUG: Peak RAM usage: 0 Gb
402 -----------End assembly log------------
403 [2021-06-30 16:02:01] root: INFO: >>>STAGE: finalize
404 [2021-06-30 16:02:01] root: DEBUG: ---Output dir contents:----
405 [2021-06-30 16:02:01] root: DEBUG: out_dir/
406 [2021-06-30 16:02:01] root: DEBUG: 367.0 B assembly_graph.gv
407 [2021-06-30 16:02:01] root: DEBUG: 415.0 K assembly.fasta
408 [2021-06-30 16:02:01] root: DEBUG: 92.0 B params.json
409 [2021-06-30 16:02:01] root: DEBUG: 26.0 K flye.log
410 [2021-06-30 16:02:01] root: DEBUG: 409.0 K assembly_graph.gfa
411 [2021-06-30 16:02:01] root: DEBUG: 10-consensus/
412 [2021-06-30 16:02:01] root: DEBUG: 415.0 K consensus.fasta
413 [2021-06-30 16:02:01] root: DEBUG: 37.0 B chunks.fasta.fai
414 [2021-06-30 16:02:01] root: DEBUG: 30-contigger/
415 [2021-06-30 16:02:01] root: DEBUG: 409.0 K graph_final.gfa
416 [2021-06-30 16:02:01] root: DEBUG: 0.0 B scaffolds_links.txt
417 [2021-06-30 16:02:01] root: DEBUG: 111.0 B contigs_stats.txt
418 [2021-06-30 16:02:01] root: DEBUG: 367.0 B graph_final.gv
419 [2021-06-30 16:02:01] root: DEBUG: 414.0 K graph_final.fasta
420 [2021-06-30 16:02:01] root: DEBUG: 414.0 K contigs.fasta
421 [2021-06-30 16:02:01] root: DEBUG: 00-assembly/
422 [2021-06-30 16:02:01] root: DEBUG: 429.0 K draft_assembly.fasta
423 [2021-06-30 16:02:01] root: DEBUG: 20-repeat/
424 [2021-06-30 16:02:01] root: DEBUG: 414.0 K graph_before_rr.fasta
425 [2021-06-30 16:02:01] root: DEBUG: 183.0 B repeat_graph_dump
426 [2021-06-30 16:02:01] root: DEBUG: 367.0 B graph_before_rr.gv
427 [2021-06-30 16:02:01] root: DEBUG: 367.0 B graph_after_rr.gv
428 [2021-06-30 16:02:01] root: DEBUG: 414.0 K repeat_graph_edges.fasta
429 [2021-06-30 16:02:01] root: DEBUG: 129.0 K read_alignment_dump
430 [2021-06-30 16:02:01] root: DEBUG: --------------------------
431 [2021-06-30 16:02:01] root: INFO: Assembly statistics:
432
433 Total length: 418805
434 Fragments: 1
435 Fragments N50: 418805
436 Largest frg: 418805
437 Scaffolds: 0
438 Mean coverage: 15
439
440 [2021-06-30 16:02:01] root: INFO: Final assembly: /tmp/tmpicy_msib/job_working_directory/000/8/working/out_dir/assembly.fasta