Mercurial > repos > kkonganti > cfsan_flye

comparison test-data/result1.log @ 0:96bb0635f0a0

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"planemo upload"
author kkonganti
date Fri, 24 Jun 2022 14:18:37 -0400
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-1:000000000000 0:96bb0635f0a0
1 [2021-11-22 18:13:09] root: INFO: Starting Flye 2.9-b1768
2 [2021-11-22 18:13:09] 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 [2021-11-22 18:13:09] root: DEBUG: Python version: 3.9.6 | packaged by conda-forge | (default, Jul 11 2021, 03:39:48)
4 [GCC 9.3.0]
5 [2021-11-22 18:13:09] root: INFO: >>>STAGE: configure
6 [2021-11-22 18:13:09] root: INFO: Configuring run
7 [2021-11-22 18:13:10] root: INFO: Total read length: 7249289
8 [2021-11-22 18:13:10] root: INFO: Reads N50/N90: 11150 / 5790
9 [2021-11-22 18:13:10] root: INFO: Minimum overlap set to 6000
10 [2021-11-22 18:13:10] root: INFO: >>>STAGE: assembly
11 [2021-11-22 18:13:10] root: INFO: Assembling disjointigs
12 [2021-11-22 18:13:10] root: DEBUG: -----Begin assembly log------
13 [2021-11-22 18:13:10] root: DEBUG: Running: flye-modules assemble --reads /tmp/tmpakmcmxzn/job_working_directory/000/8/working/input_0.fastq.gz,/tmp/tmpakmcmxzn/job_working_directory/000/8/working/input_1.fastq.gz,/tmp/tmpakmcmxzn/job_working_directory/000/8/working/input_2.fastq.gz,/tmp/tmpakmcmxzn/job_working_directory/000/8/working/input_3.fastq.gz,/tmp/tmpakmcmxzn/job_working_directory/000/8/working/input_4.fastq.gz,/tmp/tmpakmcmxzn/job_working_directory/000/8/working/input_5.fastq.gz,/tmp/tmpakmcmxzn/job_working_directory/000/8/working/input_6.fastq.gz --out-asm /tmp/tmpakmcmxzn/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/tmpakmcmxzn/job_working_directory/000/8/working/out_dir/flye.log --threads 1 --min-ovlp 6000
14 [2021-11-22 18:13:10] DEBUG: Build date: Aug 22 2021 04:46:17
15 [2021-11-22 18:13:10] DEBUG: Total RAM: 15 Gb
16 [2021-11-22 18:13:10] DEBUG: Available RAM: 9 Gb
17 [2021-11-22 18:13:10] DEBUG: Total CPUs: 8
18 [2021-11-22 18:13:10] DEBUG: Loading /usr/local/lib/python3.9/site-packages/flye/config/bin_cfg/asm_raw_reads.cfg
19 [2021-11-22 18:13:10] DEBUG: Loading /usr/local/lib/python3.9/site-packages/flye/config/bin_cfg/asm_defaults.cfg
20 [2021-11-22 18:13:10] DEBUG: big_genome_threshold=29000000
21 [2021-11-22 18:13:10] DEBUG: meta_read_filter_kmer_freq=100
22 [2021-11-22 18:13:10] DEBUG: chain_large_gap_penalty=2
23 [2021-11-22 18:13:10] DEBUG: chain_small_gap_penalty=0.5
24 [2021-11-22 18:13:10] DEBUG: chain_gap_jump_threshold=100
25 [2021-11-22 18:13:10] DEBUG: max_coverage_drop_rate=5
26 [2021-11-22 18:13:10] DEBUG: max_extensions_drop_rate=5
27 [2021-11-22 18:13:10] DEBUG: chimera_window=100
28 [2021-11-22 18:13:10] DEBUG: chimera_overhang=1000
29 [2021-11-22 18:13:10] DEBUG: min_reads_in_disjointig=4
30 [2021-11-22 18:13:10] DEBUG: max_inner_reads=10
31 [2021-11-22 18:13:10] DEBUG: max_inner_fraction=0.25
32 [2021-11-22 18:13:10] DEBUG: max_separation=500
33 [2021-11-22 18:13:10] DEBUG: unique_edge_length=50000
34 [2021-11-22 18:13:10] DEBUG: min_repeat_res_support=0.51
35 [2021-11-22 18:13:10] DEBUG: out_paths_ratio=5
36 [2021-11-22 18:13:10] DEBUG: graph_cov_drop_rate=5
37 [2021-11-22 18:13:10] DEBUG: coverage_estimate_window=100
38 [2021-11-22 18:13:10] DEBUG: max_bubble_length=50000
39 [2021-11-22 18:13:10] DEBUG: loop_coverage_rate=1.5
40 [2021-11-22 18:13:10] DEBUG: repeat_edge_cov_mult=1.75
41 [2021-11-22 18:13:10] DEBUG: weak_detach_rate=5
42 [2021-11-22 18:13:10] DEBUG: tip_coverage_rate=2
43 [2021-11-22 18:13:10] DEBUG: tip_length_rate=2
44 [2021-11-22 18:13:10] DEBUG: output_gfa_before_rr=0
45 [2021-11-22 18:13:10] DEBUG: low_cutoff_warning=1
46 [2021-11-22 18:13:10] DEBUG: kmer_size=17
47 [2021-11-22 18:13:10] DEBUG: use_minimizers=0
48 [2021-11-22 18:13:10] DEBUG: reads_base_alignment=0
49 [2021-11-22 18:13:10] DEBUG: meta_read_top_kmer_rate=0.40
50 [2021-11-22 18:13:10] DEBUG: maximum_jump=1500
51 [2021-11-22 18:13:10] DEBUG: maximum_overhang=1500
52 [2021-11-22 18:13:10] DEBUG: repeat_kmer_rate=100
53 [2021-11-22 18:13:10] DEBUG: assemble_ovlp_divergence=0.10
54 [2021-11-22 18:13:10] DEBUG: assemble_divergence_relative=1
55 [2021-11-22 18:13:10] DEBUG: repeat_graph_ovlp_divergence=0.08
56 [2021-11-22 18:13:10] DEBUG: read_align_ovlp_divergence=0.25
57 [2021-11-22 18:13:10] DEBUG: hpc_scoring_on=0
58 [2021-11-22 18:13:10] DEBUG: add_unassembled_reads=0
59 [2021-11-22 18:13:10] DEBUG: extend_contigs_with_repeats=0
60 [2021-11-22 18:13:10] DEBUG: min_read_cov_cutoff=3
61 [2021-11-22 18:13:10] DEBUG: short_tip_length=20000
62 [2021-11-22 18:13:10] DEBUG: long_tip_length=100000
63 [2021-11-22 18:13:10] DEBUG: Running with k-mer size: 17
64 [2021-11-22 18:13:10] DEBUG: Running with minimum overlap 6000
65 [2021-11-22 18:13:10] DEBUG: Metagenome mode: N
66 [2021-11-22 18:13:10] DEBUG: Short mode: N
67 [2021-11-22 18:13:10] INFO: Reading sequences
68 [2021-11-22 18:13:10] DEBUG: Building positional index
69 [2021-11-22 18:13:10] DEBUG: Total sequence: 6471580 bp
70 [2021-11-22 18:13:12] INFO: Counting k-mers:
71 [2021-11-22 18:13:13] DEBUG: Updating k-mer histogram
72 [2021-11-22 18:13:56] DEBUG: Hash size: 29
73 [2021-11-22 18:13:56] DEBUG: Total k-mers 5958598
74 [2021-11-22 18:13:56] INFO: Filling index table (1/2)
75 [2021-11-22 18:13:59] DEBUG: Mean k-mer frequency: 2.57396
76 [2021-11-22 18:13:59] DEBUG: Repetitive k-mer frequency: 257
77 [2021-11-22 18:13:59] DEBUG: Filtered 0 repetitive k-mers (0)
78 [2021-11-22 18:13:59] INFO: Filling index table (2/2)
79 [2021-11-22 18:14:01] DEBUG: Sorting k-mer index
80 [2021-11-22 18:14:01] DEBUG: Selected k-mers: 319695
81 [2021-11-22 18:14:01] DEBUG: Index size: 822885
82 [2021-11-22 18:14:01] DEBUG: Mean k-mer index frequency: 2.57397
83 [2021-11-22 18:14:01] DEBUG: Peak RAM usage: 8 Gb
84 [2021-11-22 18:14:01] DEBUG: Estimating k-mer identity bias
85 [2021-11-22 18:14:05] DEBUG: Initial divergence estimate : 0.237684
86 [2021-11-22 18:14:05] DEBUG: Relative threshold: Y
87 [2021-11-22 18:14:05] DEBUG: Max divergence threshold set to 0.337684
88 [2021-11-22 18:14:05] INFO: Extending reads
89 [2021-11-22 18:14:05] DEBUG: Estimating overlap coverage
90 [2021-11-22 18:14:07] INFO: Overlap-based coverage: 10
91 [2021-11-22 18:14:07] INFO: Median overlap divergence: 0.235584
92 [2021-11-22 18:14:07] DEBUG: Sequence divergence distribution:
93
94 | * |
95 | * |
96 | *** |
97 | * *** |
98 | ****** |
99 | ******* |
100 | ******* |
101 | ******** |
102 | ******** |
103 | ********* |
104 | ********* |
105 | ********* |
106 | ********** |
107 | ************ |
108 | ************ |
109 | ************** |
110 | ************** |
111 | **************** |
112 | * ***************** * |
113 | * ** ************************ | * *
114 ----------------------------------------------------------------------------------------------------
115 0% 5% 10% 15% 20% 25% 30% 35% 40% 45%
116
117 Q25 = 0.22, Q50 = 0.24, Q75 = 0.25
118
119 [2021-11-22 18:14:08] DEBUG: Assembled disjointig 1
120 With 83 reads
121 Start read: +S1_395
122 At position: 40
123 leftTip: 1 rightTip: 1
124 Suspicious: 5
125 Short ext: 3
126 Mean extensions: 9
127 Avg overlap len: 10043
128 Min overlap len: 4225
129 Inner reads: 0
130 Length: 434635
131 [2021-11-22 18:14:08] DEBUG: Inner: 1024 covered: 1014 total: 1152
132 [2021-11-22 18:14:08] DEBUG: Assembled disjointig 2
133 With 6 reads
134 Start read: +S1_921
135 At position: 4
136 leftTip: 0 rightTip: 0
137 Suspicious: 0
138 Short ext: 0
139 Mean extensions: 4
140 Avg overlap len: 8689
141 Min overlap len: 7703
142 Inner reads: 0
143 Length: 34343
144 [2021-11-22 18:14:08] DEBUG: Inner: 1040 covered: 1056 total: 1152
145 [2021-11-22 18:14:08] INFO: Assembled 2 disjointigs
146 [2021-11-22 18:14:08] INFO: Generating sequence
147 [2021-11-22 18:14:08] DEBUG: Building positional index
148 [2021-11-22 18:14:08] DEBUG: Total sequence: 470346 bp
149 [2021-11-22 18:14:08] DEBUG: Mean k-mer frequency: 1.00134
150 [2021-11-22 18:14:08] DEBUG: Repetitive k-mer frequency: 100
151 [2021-11-22 18:14:08] DEBUG: Filtered 0 repetitive k-mers (0)
152 [2021-11-22 18:14:08] DEBUG: Sorting k-mer index
153 [2021-11-22 18:14:08] DEBUG: Selected k-mers: 469680
154 [2021-11-22 18:14:08] DEBUG: K-mer index size: 470312
155 [2021-11-22 18:14:08] DEBUG: Mean k-mer frequency: 1.00135
156 [2021-11-22 18:14:08] DEBUG: Minimizer rate: 1.00007
157 [2021-11-22 18:14:08] INFO: Filtering contained disjointigs
158 [2021-11-22 18:14:09] DEBUG: Computing transitive closure for overlaps
159 [2021-11-22 18:14:09] DEBUG: Found 0 overlaps
160 [2021-11-22 18:14:09] DEBUG: Left 0 overlaps after filtering
161 [2021-11-22 18:14:09] INFO: Contained seqs: 0
162 [2021-11-22 18:14:09] DEBUG: Writing FASTA
163 [2021-11-22 18:14:09] DEBUG: Peak RAM usage: 8 Gb
164 -----------End assembly log------------
165 [2021-11-22 18:14:09] root: DEBUG: Disjointigs length: 470346, N50: 436173
166 [2021-11-22 18:14:09] root: INFO: >>>STAGE: consensus
167 [2021-11-22 18:14:09] root: INFO: Running Minimap2
168 [2021-11-22 18:14:14] root: INFO: Computing consensus
169 [2021-11-22 18:14:23] root: INFO: Alignment error rate: 0.197031
170 [2021-11-22 18:14:23] root: INFO: >>>STAGE: repeat
171 [2021-11-22 18:14:23] root: INFO: Building and resolving repeat graph
172 [2021-11-22 18:14:23] root: DEBUG: -----Begin repeat analyser log------
173 [2021-11-22 18:14:23] root: DEBUG: Running: flye-modules repeat --disjointigs /tmp/tmpakmcmxzn/job_working_directory/000/8/working/out_dir/10-consensus/consensus.fasta --reads /tmp/tmpakmcmxzn/job_working_directory/000/8/working/input_0.fastq.gz,/tmp/tmpakmcmxzn/job_working_directory/000/8/working/input_1.fastq.gz,/tmp/tmpakmcmxzn/job_working_directory/000/8/working/input_2.fastq.gz,/tmp/tmpakmcmxzn/job_working_directory/000/8/working/input_3.fastq.gz,/tmp/tmpakmcmxzn/job_working_directory/000/8/working/input_4.fastq.gz,/tmp/tmpakmcmxzn/job_working_directory/000/8/working/input_5.fastq.gz,/tmp/tmpakmcmxzn/job_working_directory/000/8/working/input_6.fastq.gz --out-dir /tmp/tmpakmcmxzn/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/tmpakmcmxzn/job_working_directory/000/8/working/out_dir/flye.log --threads 1 --min-ovlp 6000
174 [2021-11-22 18:14:23] DEBUG: Build date: Aug 22 2021 04:47:01
175 [2021-11-22 18:14:23] DEBUG: Total RAM: 15 Gb
176 [2021-11-22 18:14:23] DEBUG: Available RAM: 9 Gb
177 [2021-11-22 18:14:23] DEBUG: Total CPUs: 8
178 [2021-11-22 18:14:23] DEBUG: Loading /usr/local/lib/python3.9/site-packages/flye/config/bin_cfg/asm_raw_reads.cfg
179 [2021-11-22 18:14:23] DEBUG: Loading /usr/local/lib/python3.9/site-packages/flye/config/bin_cfg/asm_defaults.cfg
180 [2021-11-22 18:14:23] DEBUG: big_genome_threshold=29000000
181 [2021-11-22 18:14:23] DEBUG: meta_read_filter_kmer_freq=100
182 [2021-11-22 18:14:23] DEBUG: chain_large_gap_penalty=2
183 [2021-11-22 18:14:23] DEBUG: chain_small_gap_penalty=0.5
184 [2021-11-22 18:14:23] DEBUG: chain_gap_jump_threshold=100
185 [2021-11-22 18:14:23] DEBUG: max_coverage_drop_rate=5
186 [2021-11-22 18:14:23] DEBUG: max_extensions_drop_rate=5
187 [2021-11-22 18:14:23] DEBUG: chimera_window=100
188 [2021-11-22 18:14:23] DEBUG: chimera_overhang=1000
189 [2021-11-22 18:14:23] DEBUG: min_reads_in_disjointig=4
190 [2021-11-22 18:14:23] DEBUG: max_inner_reads=10
191 [2021-11-22 18:14:23] DEBUG: max_inner_fraction=0.25
192 [2021-11-22 18:14:23] DEBUG: max_separation=500
193 [2021-11-22 18:14:23] DEBUG: unique_edge_length=50000
194 [2021-11-22 18:14:23] DEBUG: min_repeat_res_support=0.51
195 [2021-11-22 18:14:23] DEBUG: out_paths_ratio=5
196 [2021-11-22 18:14:23] DEBUG: graph_cov_drop_rate=5
197 [2021-11-22 18:14:23] DEBUG: coverage_estimate_window=100
198 [2021-11-22 18:14:23] DEBUG: max_bubble_length=50000
199 [2021-11-22 18:14:23] DEBUG: loop_coverage_rate=1.5
200 [2021-11-22 18:14:23] DEBUG: repeat_edge_cov_mult=1.75
201 [2021-11-22 18:14:23] DEBUG: weak_detach_rate=5
202 [2021-11-22 18:14:23] DEBUG: tip_coverage_rate=2
203 [2021-11-22 18:14:23] DEBUG: tip_length_rate=2
204 [2021-11-22 18:14:23] DEBUG: output_gfa_before_rr=0
205 [2021-11-22 18:14:23] DEBUG: low_cutoff_warning=1
206 [2021-11-22 18:14:23] DEBUG: kmer_size=17
207 [2021-11-22 18:14:23] DEBUG: use_minimizers=0
208 [2021-11-22 18:14:23] DEBUG: reads_base_alignment=0
209 [2021-11-22 18:14:23] DEBUG: meta_read_top_kmer_rate=0.40
210 [2021-11-22 18:14:23] DEBUG: maximum_jump=1500
211 [2021-11-22 18:14:23] DEBUG: maximum_overhang=1500
212 [2021-11-22 18:14:23] DEBUG: repeat_kmer_rate=100
213 [2021-11-22 18:14:23] DEBUG: assemble_ovlp_divergence=0.10
214 [2021-11-22 18:14:23] DEBUG: assemble_divergence_relative=1
215 [2021-11-22 18:14:23] DEBUG: repeat_graph_ovlp_divergence=0.08
216 [2021-11-22 18:14:23] DEBUG: read_align_ovlp_divergence=0.25
217 [2021-11-22 18:14:23] DEBUG: hpc_scoring_on=0
218 [2021-11-22 18:14:23] DEBUG: add_unassembled_reads=0
219 [2021-11-22 18:14:23] DEBUG: extend_contigs_with_repeats=0
220 [2021-11-22 18:14:23] DEBUG: min_read_cov_cutoff=3
221 [2021-11-22 18:14:23] DEBUG: short_tip_length=20000
222 [2021-11-22 18:14:23] DEBUG: long_tip_length=100000
223 [2021-11-22 18:14:23] DEBUG: Running with k-mer size: 17
224 [2021-11-22 18:14:23] DEBUG: Selected minimum overlap 6000
225 [2021-11-22 18:14:23] DEBUG: Metagenome mode: N
226 [2021-11-22 18:14:23] INFO: Parsing disjointigs
227 [2021-11-22 18:14:23] DEBUG: Building positional index
228 [2021-11-22 18:14:23] DEBUG: Total sequence: 452437 bp
229 [2021-11-22 18:14:23] INFO: Building repeat graph
230 [2021-11-22 18:14:24] DEBUG: Mean k-mer frequency: 1.05543
231 [2021-11-22 18:14:24] DEBUG: Repetitive k-mer frequency: 105
232 [2021-11-22 18:14:24] DEBUG: Filtered 0 repetitive k-mers (0)
233 [2021-11-22 18:14:24] DEBUG: Sorting k-mer index
234 [2021-11-22 18:14:24] DEBUG: Selected k-mers: 428642
235 [2021-11-22 18:14:24] DEBUG: K-mer index size: 452403
236 [2021-11-22 18:14:24] DEBUG: Mean k-mer frequency: 1.05543
237 [2021-11-22 18:14:24] DEBUG: Minimizer rate: 1.00008
238 [2021-11-22 18:14:24] DEBUG: Computing transitive closure for overlaps
239 [2021-11-22 18:14:24] DEBUG: Found 10 overlaps
240 [2021-11-22 18:14:24] DEBUG: Left 4 overlaps after filtering
241 [2021-11-22 18:14:24] INFO: Median overlap divergence: 0.0343169
242 [2021-11-22 18:14:24] DEBUG: Sequence divergence distribution:
243
244 | * |
245 | * |
246 | * |
247 | * |
248 | * |
249 | * |
250 | * |
251 | * |
252 | * |
253 | * |
254 | * |
255 | * |
256 | * |
257 | * |
258 | * |
259 | * |
260 | * |
261 | * |
262 | * |
263 | * |
264 ----------------------------------------------------------------------------------------------------
265 0% 5% 10% 15% 20% 25% 30% 35% 40% 45%
266
267 Q25 = 0.034, Q50 = 0.034, Q75 = 0.034
268
269 [2021-11-22 18:14:24] DEBUG: Computing gluepoints
270 [2021-11-22 18:14:24] DEBUG: Added 0 gluepoint projections
271 [2021-11-22 18:14:24] DEBUG: Created 12 gluepoints
272 [2021-11-22 18:14:24] DEBUG: Artificial loops removed: 0 left, 0 right, 0 both
273 [2021-11-22 18:14:24] DEBUG: Initializing edges
274 [2021-11-22 18:14:24] DEBUG: Edges length checksum: 2261029433
275 [2021-11-22 18:14:24] DEBUG: Filtered 0 singleton segments
276 [2021-11-22 18:14:24] DEBUG: Removed 0 simple and 0 double chimeric junctions
277 [2021-11-22 18:14:24] DEBUG: Collapsed 2 edges
278 [2021-11-22 18:14:24] DEBUG: * 4 +disjointig_1 0 419576 419576
279 [2021-11-22 18:14:24] DEBUG: Total edges: 4
280 [2021-11-22 18:14:24] INFO: Parsing reads
281 [2021-11-22 18:14:24] DEBUG: Building positional index
282 [2021-11-22 18:14:24] DEBUG: Total sequence: 7249289 bp
283 [2021-11-22 18:14:24] DEBUG: Building positional index
284 [2021-11-22 18:14:24] DEBUG: Total sequence: 419576 bp
285 [2021-11-22 18:14:24] INFO: Aligning reads to the graph
286 [2021-11-22 18:14:24] DEBUG: Mean k-mer frequency: 1.00888
287 [2021-11-22 18:14:24] DEBUG: Repetitive k-mer frequency: 100
288 [2021-11-22 18:14:24] DEBUG: Filtered 0 repetitive k-mers (0)
289 [2021-11-22 18:14:24] DEBUG: Sorting k-mer index
290 [2021-11-22 18:14:24] DEBUG: Selected k-mers: 415865
291 [2021-11-22 18:14:24] DEBUG: K-mer index size: 419559
292 [2021-11-22 18:14:24] DEBUG: Mean k-mer frequency: 1.00888
293 [2021-11-22 18:14:24] DEBUG: Minimizer rate: 1.00004
294 [2021-11-22 18:14:26] DEBUG: Total reads : 576
295 [2021-11-22 18:14:26] DEBUG: Read with aligned parts : 566
296 [2021-11-22 18:14:26] DEBUG: Aligned in one piece : 566
297 [2021-11-22 18:14:26] INFO: Aligned read sequence: 6321188 / 6471580 (0.976761)
298 [2021-11-22 18:14:26] INFO: Median overlap divergence: 0.129819
299 [2021-11-22 18:14:26] DEBUG: Sequence divergence distribution:
300
301 | * |
302 | ** |
303 | ** |
304 | *** |
305 | *** |
306 | *** |
307 | ***** |
308 | ***** |
309 | ***** |
310 | ***** |
311 | ****** |
312 | ******* |
313 | ******* |
314 | ******** |
315 | ********* |
316 | ********* |
317 | ********** |
318 | ************ |
319 | *************** |
320 | **************** |
321 ----------------------------------------------------------------------------------------------------
322 0% 5% 10% 15% 20% 25% 30% 35% 40% 45%
323
324 Q25 = 0.12, Q50 = 0.13, Q75 = 0.14
325
326 [2021-11-22 18:14:27] INFO: Mean edge coverage: 14
327 [2021-11-22 18:14:27] DEBUG: 4 len:419576 cov:14 mult:1
328 [2021-11-22 18:14:27] DEBUG: -4 len:419576 cov:14 mult:1
329 [2021-11-22 18:14:27] DEBUG: Unique coverage threshold 24
330 [2021-11-22 18:14:27] INFO: Simplifying the graph
331 [2021-11-22 18:14:27] DEBUG: Read coverage cutoff: 3
332 [2021-11-22 18:14:27] DEBUG: [SIMPL] Removed 0 paths with low coverage
333 [2021-11-22 18:14:27] DEBUG: [SIMPL] Masked 0 heterozygous loops
334 [2021-11-22 18:14:27] DEBUG: [SIMPL] Masked 0 simple bubbles
335 [2021-11-22 18:14:27] DEBUG: Finding repeats
336 [2021-11-22 18:14:27] DEBUG: Read coverage cutoff: 3
337 [2021-11-22 18:14:27] DEBUG: Repeat detection iteration 1
338 [2021-11-22 18:14:27] DEBUG: Writing Dot
339 [2021-11-22 18:14:27] DEBUG: Writing FASTA
340 [2021-11-22 18:14:27] DEBUG: [SIMPL] == Iteration 1 ==
341 [2021-11-22 18:14:27] DEBUG: Splitting nodes
342 [2021-11-22 18:14:27] DEBUG: [SIMPL] Split 0 nodes
343 [2021-11-22 18:14:27] DEBUG: [SIMPL] Clipped 0 short and 0 long tips
344 [2021-11-22 18:14:27] DEBUG: [SIMPL] Masked 0 heterozygous loops
345 [2021-11-22 18:14:27] DEBUG: [SIMPL] Masked 0 simple bubbles
346 [2021-11-22 18:14:27] DEBUG: Finding repeats
347 [2021-11-22 18:14:27] DEBUG: Read coverage cutoff: 3
348 [2021-11-22 18:14:27] DEBUG: Repeat detection iteration 1
349 [2021-11-22 18:14:27] DEBUG: Total unique edges: 1
350 [2021-11-22 18:14:27] DEBUG: [SIMPL] Resolved repeats: 0
351 [2021-11-22 18:14:27] DEBUG: RR links: 0
352 [2021-11-22 18:14:27] DEBUG: Unresolved: 0
353 [2021-11-22 18:14:27] DEBUG: Removed 0 simple and 0 double chimeric junctions
354 [2021-11-22 18:14:27] DEBUG: [SIMPL] Collapsed 0 haplotypes
355 [2021-11-22 18:14:27] DEBUG: [SIMPL] Resolved 0 simple repeats
356 [2021-11-22 18:14:27] DEBUG: Read coverage cutoff: 3
357 [2021-11-22 18:14:27] DEBUG: [SIMPL] Removed 0 paths with low coverage
358 [2021-11-22 18:14:27] DEBUG: Finding repeats
359 [2021-11-22 18:14:27] DEBUG: Read coverage cutoff: 3
360 [2021-11-22 18:14:27] DEBUG: Repeat detection iteration 1
361 [2021-11-22 18:14:27] DEBUG: Writing Dot
362 [2021-11-22 18:14:27] DEBUG: Writing FASTA
363 [2021-11-22 18:14:27] DEBUG: Peak RAM usage: 0 Gb
364 -----------End assembly log------------
365 [2021-11-22 18:14:27] root: INFO: >>>STAGE: contigger
366 [2021-11-22 18:14:27] root: INFO: Generating contigs
367 [2021-11-22 18:14:27] root: DEBUG: -----Begin contigger analyser log------
368 [2021-11-22 18:14:27] root: DEBUG: Running: flye-modules contigger --graph-edges /tmp/tmpakmcmxzn/job_working_directory/000/8/working/out_dir/20-repeat/repeat_graph_edges.fasta --reads /tmp/tmpakmcmxzn/job_working_directory/000/8/working/input_0.fastq.gz,/tmp/tmpakmcmxzn/job_working_directory/000/8/working/input_1.fastq.gz,/tmp/tmpakmcmxzn/job_working_directory/000/8/working/input_2.fastq.gz,/tmp/tmpakmcmxzn/job_working_directory/000/8/working/input_3.fastq.gz,/tmp/tmpakmcmxzn/job_working_directory/000/8/working/input_4.fastq.gz,/tmp/tmpakmcmxzn/job_working_directory/000/8/working/input_5.fastq.gz,/tmp/tmpakmcmxzn/job_working_directory/000/8/working/input_6.fastq.gz --out-dir /tmp/tmpakmcmxzn/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/tmpakmcmxzn/job_working_directory/000/8/working/out_dir/20-repeat/repeat_graph_dump --graph-aln /tmp/tmpakmcmxzn/job_working_directory/000/8/working/out_dir/20-repeat/read_alignment_dump --log /tmp/tmpakmcmxzn/job_working_directory/000/8/working/out_dir/flye.log --threads 1 --min-ovlp 6000
369 [2021-11-22 18:14:27] DEBUG: Build date: Aug 22 2021 04:47:48
370 [2021-11-22 18:14:27] DEBUG: Total RAM: 15 Gb
371 [2021-11-22 18:14:27] DEBUG: Available RAM: 9 Gb
372 [2021-11-22 18:14:27] DEBUG: Total CPUs: 8
373 [2021-11-22 18:14:27] DEBUG: Loading /usr/local/lib/python3.9/site-packages/flye/config/bin_cfg/asm_raw_reads.cfg
374 [2021-11-22 18:14:27] DEBUG: Loading /usr/local/lib/python3.9/site-packages/flye/config/bin_cfg/asm_defaults.cfg
375 [2021-11-22 18:14:27] DEBUG: big_genome_threshold=29000000
376 [2021-11-22 18:14:27] DEBUG: meta_read_filter_kmer_freq=100
377 [2021-11-22 18:14:27] DEBUG: chain_large_gap_penalty=2
378 [2021-11-22 18:14:27] DEBUG: chain_small_gap_penalty=0.5
379 [2021-11-22 18:14:27] DEBUG: chain_gap_jump_threshold=100
380 [2021-11-22 18:14:27] DEBUG: max_coverage_drop_rate=5
381 [2021-11-22 18:14:27] DEBUG: max_extensions_drop_rate=5
382 [2021-11-22 18:14:27] DEBUG: chimera_window=100
383 [2021-11-22 18:14:27] DEBUG: chimera_overhang=1000
384 [2021-11-22 18:14:27] DEBUG: min_reads_in_disjointig=4
385 [2021-11-22 18:14:27] DEBUG: max_inner_reads=10
386 [2021-11-22 18:14:27] DEBUG: max_inner_fraction=0.25
387 [2021-11-22 18:14:27] DEBUG: max_separation=500
388 [2021-11-22 18:14:27] DEBUG: unique_edge_length=50000
389 [2021-11-22 18:14:27] DEBUG: min_repeat_res_support=0.51
390 [2021-11-22 18:14:27] DEBUG: out_paths_ratio=5
391 [2021-11-22 18:14:27] DEBUG: graph_cov_drop_rate=5
392 [2021-11-22 18:14:27] DEBUG: coverage_estimate_window=100
393 [2021-11-22 18:14:27] DEBUG: max_bubble_length=50000
394 [2021-11-22 18:14:27] DEBUG: loop_coverage_rate=1.5
395 [2021-11-22 18:14:27] DEBUG: repeat_edge_cov_mult=1.75
396 [2021-11-22 18:14:27] DEBUG: weak_detach_rate=5
397 [2021-11-22 18:14:27] DEBUG: tip_coverage_rate=2
398 [2021-11-22 18:14:27] DEBUG: tip_length_rate=2
399 [2021-11-22 18:14:27] DEBUG: output_gfa_before_rr=0
400 [2021-11-22 18:14:27] DEBUG: low_cutoff_warning=1
401 [2021-11-22 18:14:27] DEBUG: kmer_size=17
402 [2021-11-22 18:14:27] DEBUG: use_minimizers=0
403 [2021-11-22 18:14:27] DEBUG: reads_base_alignment=0
404 [2021-11-22 18:14:27] DEBUG: meta_read_top_kmer_rate=0.40
405 [2021-11-22 18:14:27] DEBUG: maximum_jump=1500
406 [2021-11-22 18:14:27] DEBUG: maximum_overhang=1500
407 [2021-11-22 18:14:27] DEBUG: repeat_kmer_rate=100
408 [2021-11-22 18:14:27] DEBUG: assemble_ovlp_divergence=0.10
409 [2021-11-22 18:14:27] DEBUG: assemble_divergence_relative=1
410 [2021-11-22 18:14:27] DEBUG: repeat_graph_ovlp_divergence=0.08
411 [2021-11-22 18:14:27] DEBUG: read_align_ovlp_divergence=0.25
412 [2021-11-22 18:14:27] DEBUG: hpc_scoring_on=0
413 [2021-11-22 18:14:27] DEBUG: add_unassembled_reads=0
414 [2021-11-22 18:14:27] DEBUG: extend_contigs_with_repeats=0
415 [2021-11-22 18:14:27] DEBUG: min_read_cov_cutoff=3
416 [2021-11-22 18:14:27] DEBUG: short_tip_length=20000
417 [2021-11-22 18:14:27] DEBUG: long_tip_length=100000
418 [2021-11-22 18:14:27] DEBUG: Running with k-mer size: 17
419 [2021-11-22 18:14:27] DEBUG: Selected minimum overlap 6000
420 [2021-11-22 18:14:27] INFO: Reading sequences
421 [2021-11-22 18:14:27] DEBUG: Building positional index
422 [2021-11-22 18:14:27] DEBUG: Total sequence: 7249289 bp
423 [2021-11-22 18:14:27] DEBUG: Flipped 0
424 [2021-11-22 18:14:27] DEBUG: UPath 1: 4
425 [2021-11-22 18:14:27] DEBUG: Final graph contains 1 egdes
426 [2021-11-22 18:14:27] DEBUG: Extending contigs into repeats
427 [2021-11-22 18:14:27] DEBUG: Covered 0 repetitive contigs
428 [2021-11-22 18:14:27] INFO: Generated 1 contigs
429 [2021-11-22 18:14:27] DEBUG: Writing FASTA
430 [2021-11-22 18:14:27] DEBUG: Generating scaffold connections
431 [2021-11-22 18:14:27] INFO: Added 0 scaffold connections
432 [2021-11-22 18:14:27] DEBUG: Writing Dot
433 [2021-11-22 18:14:27] DEBUG: Writing FASTA
434 [2021-11-22 18:14:27] DEBUG: Writing Gfa
435 [2021-11-22 18:14:27] DEBUG: Peak RAM usage: 0 Gb
436 -----------End assembly log------------
437 [2021-11-22 18:14:27] root: INFO: >>>STAGE: finalize
438 [2021-11-22 18:14:27] root: DEBUG: ---Output dir contents:----
439 [2021-11-22 18:14:27] root: DEBUG: out_dir/
440 [2021-11-22 18:14:27] root: DEBUG: 367.0 B assembly_graph.gv
441 [2021-11-22 18:14:27] root: DEBUG: 416.0 K assembly.fasta
442 [2021-11-22 18:14:27] root: DEBUG: 92.0 B params.json
443 [2021-11-22 18:14:27] root: DEBUG: 28.0 K flye.log
444 [2021-11-22 18:14:27] root: DEBUG: 409.0 K assembly_graph.gfa
445 [2021-11-22 18:14:27] root: DEBUG: 10-consensus/
446 [2021-11-22 18:14:27] root: DEBUG: 1.0 K minimap.stderr
447 [2021-11-22 18:14:27] root: DEBUG: 449.0 K consensus.fasta
448 [2021-11-22 18:14:27] root: DEBUG: 3.0 K minimap.bam.bai
449 [2021-11-22 18:14:27] root: DEBUG: 30-contigger/
450 [2021-11-22 18:14:27] root: DEBUG: 409.0 K graph_final.gfa
451 [2021-11-22 18:14:27] root: DEBUG: 0.0 B scaffolds_links.txt
452 [2021-11-22 18:14:27] root: DEBUG: 111.0 B contigs_stats.txt
453 [2021-11-22 18:14:27] root: DEBUG: 367.0 B graph_final.gv
454 [2021-11-22 18:14:27] root: DEBUG: 414.0 K graph_final.fasta
455 [2021-11-22 18:14:27] root: DEBUG: 414.0 K contigs.fasta
456 [2021-11-22 18:14:27] root: DEBUG: 00-assembly/
457 [2021-11-22 18:14:27] root: DEBUG: 61.0 B draft_assembly.fasta.fai
458 [2021-11-22 18:14:27] root: DEBUG: 465.0 K draft_assembly.fasta
459 [2021-11-22 18:14:27] root: DEBUG: 20-repeat/
460 [2021-11-22 18:14:27] root: DEBUG: 414.0 K graph_before_rr.fasta
461 [2021-11-22 18:14:27] root: DEBUG: 183.0 B repeat_graph_dump
462 [2021-11-22 18:14:27] root: DEBUG: 367.0 B graph_before_rr.gv
463 [2021-11-22 18:14:27] root: DEBUG: 367.0 B graph_after_rr.gv
464 [2021-11-22 18:14:27] root: DEBUG: 414.0 K repeat_graph_edges.fasta
465 [2021-11-22 18:14:27] root: DEBUG: 119.0 K read_alignment_dump
466 [2021-11-22 18:14:27] root: DEBUG: --------------------------
467 [2021-11-22 18:14:27] root: INFO: Assembly statistics:
468
469 Total length: 419576
470 Fragments: 1
471 Fragments N50: 419576
472 Largest frg: 419576
473 Scaffolds: 0
474 Mean coverage: 14
475
476 [2021-11-22 18:14:27] root: INFO: Final assembly: /tmp/tmpakmcmxzn/job_working_directory/000/8/working/out_dir/assembly.fasta