Mercurial > repos > bgruening > flye

comparison test-data/result1.log @ 9:276f5d8712d5 draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
author bgruening
date Tue, 23 Nov 2021 08:35:32 +0000
parents e27815e82dd4
children
comparison
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8:e27815e82dd4 9:276f5d8712d5
1 [2021-06-30 16:00:39] root: INFO: Starting Flye 2.8.3-b1695 1 [2021-11-22 18:13:09] root: INFO: Starting Flye 2.9-b1768
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 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 [2021-06-30 16:00:39] root: DEBUG: Python version: 3.9.2 | packaged by conda-forge | (default, Feb 21 2021, 05:02:46) 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] 4 [GCC 9.3.0]
5 [2021-06-30 16:00:39] root: INFO: >>>STAGE: configure 5 [2021-11-22 18:13:09] root: INFO: >>>STAGE: configure
6 [2021-06-30 16:00:39] root: INFO: Configuring run 6 [2021-11-22 18:13:09] root: INFO: Configuring run
7 [2021-06-30 16:00:39] root: INFO: Total read length: 7249289 7 [2021-11-22 18:13:10] root: INFO: Total read length: 7249289
8 [2021-06-30 16:00:39] root: INFO: Reads N50/N90: 11150 / 5790 8 [2021-11-22 18:13:10] root: INFO: Reads N50/N90: 11150 / 5790
9 [2021-06-30 16:00:39] root: INFO: Minimum overlap set to 5000 9 [2021-11-22 18:13:10] root: INFO: Minimum overlap set to 6000
10 [2021-06-30 16:00:39] root: INFO: >>>STAGE: assembly 10 [2021-11-22 18:13:10] root: INFO: >>>STAGE: assembly
11 [2021-06-30 16:00:39] root: INFO: Assembling disjointigs 11 [2021-11-22 18:13:10] root: INFO: Assembling disjointigs
12 [2021-06-30 16:00:39] root: DEBUG: -----Begin assembly log------ 12 [2021-11-22 18:13:10] 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 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 [2021-06-30 16:00:39] DEBUG: Build date: Mar 27 2021 19:08:40 14 [2021-11-22 18:13:10] DEBUG: Build date: Aug 22 2021 04:46:17
15 [2021-06-30 16:00:39] DEBUG: Total RAM: 15 Gb 15 [2021-11-22 18:13:10] DEBUG: Total RAM: 15 Gb
16 [2021-06-30 16:00:39] DEBUG: Available RAM: 11 Gb 16 [2021-11-22 18:13:10] DEBUG: Available RAM: 9 Gb
17 [2021-06-30 16:00:39] DEBUG: Total CPUs: 8 17 [2021-11-22 18:13:10] 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 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 [2021-06-30 16:00:39] DEBUG: Loading /usr/local/lib/python3.9/site-packages/flye/config/bin_cfg/asm_defaults.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 [2021-06-30 16:00:39] DEBUG: big_genome_threshold=29000000 20 [2021-11-22 18:13:10] DEBUG: big_genome_threshold=29000000
21 [2021-06-30 16:00:39] DEBUG: meta_read_filter_kmer_freq=100 21 [2021-11-22 18:13:10] DEBUG: meta_read_filter_kmer_freq=100
22 [2021-06-30 16:00:39] DEBUG: max_coverage_drop_rate=5 22 [2021-11-22 18:13:10] DEBUG: chain_large_gap_penalty=2
23 [2021-06-30 16:00:39] DEBUG: max_extensions_drop_rate=5 23 [2021-11-22 18:13:10] DEBUG: chain_small_gap_penalty=0.5
24 [2021-06-30 16:00:39] DEBUG: chimera_window=100 24 [2021-11-22 18:13:10] DEBUG: chain_gap_jump_threshold=100
25 [2021-06-30 16:00:39] DEBUG: min_reads_in_disjointig=4 25 [2021-11-22 18:13:10] DEBUG: max_coverage_drop_rate=5
26 [2021-06-30 16:00:39] DEBUG: max_inner_reads=10 26 [2021-11-22 18:13:10] DEBUG: max_extensions_drop_rate=5
27 [2021-06-30 16:00:39] DEBUG: max_inner_fraction=0.25 27 [2021-11-22 18:13:10] DEBUG: chimera_window=100
28 [2021-06-30 16:00:39] DEBUG: max_separation=500 28 [2021-11-22 18:13:10] DEBUG: chimera_overhang=1000
29 [2021-06-30 16:00:39] DEBUG: unique_edge_length=50000 29 [2021-11-22 18:13:10] DEBUG: min_reads_in_disjointig=4
30 [2021-06-30 16:00:39] DEBUG: min_repeat_res_support=0.51 30 [2021-11-22 18:13:10] DEBUG: max_inner_reads=10
31 [2021-06-30 16:00:39] DEBUG: out_paths_ratio=5 31 [2021-11-22 18:13:10] DEBUG: max_inner_fraction=0.25
32 [2021-06-30 16:00:39] DEBUG: graph_cov_drop_rate=5 32 [2021-11-22 18:13:10] DEBUG: max_separation=500
33 [2021-06-30 16:00:39] DEBUG: coverage_estimate_window=100 33 [2021-11-22 18:13:10] DEBUG: unique_edge_length=50000
34 [2021-06-30 16:00:39] DEBUG: max_bubble_length=50000 34 [2021-11-22 18:13:10] DEBUG: min_repeat_res_support=0.51
35 [2021-06-30 16:00:39] DEBUG: loop_coverage_rate=1.5 35 [2021-11-22 18:13:10] DEBUG: out_paths_ratio=5
36 [2021-06-30 16:00:39] DEBUG: repeat_edge_cov_mult=1.75 36 [2021-11-22 18:13:10] DEBUG: graph_cov_drop_rate=5
37 [2021-06-30 16:00:39] DEBUG: weak_detach_rate=5 37 [2021-11-22 18:13:10] DEBUG: coverage_estimate_window=100
38 [2021-06-30 16:00:39] DEBUG: tip_coverage_rate=2 38 [2021-11-22 18:13:10] DEBUG: max_bubble_length=50000
39 [2021-06-30 16:00:39] DEBUG: tip_length_rate=2 39 [2021-11-22 18:13:10] DEBUG: loop_coverage_rate=1.5
40 [2021-06-30 16:00:39] DEBUG: low_cutoff_warning=1 40 [2021-11-22 18:13:10] DEBUG: repeat_edge_cov_mult=1.75
41 [2021-06-30 16:00:39] DEBUG: hard_min_coverage_rate=10 41 [2021-11-22 18:13:10] DEBUG: weak_detach_rate=5
42 [2021-06-30 16:00:39] DEBUG: kmer_size=17 42 [2021-11-22 18:13:10] DEBUG: tip_coverage_rate=2
43 [2021-06-30 16:00:39] DEBUG: use_minimizers=0 43 [2021-11-22 18:13:10] DEBUG: tip_length_rate=2
44 [2021-06-30 16:00:39] DEBUG: reads_base_alignment=0 44 [2021-11-22 18:13:10] DEBUG: output_gfa_before_rr=0
45 [2021-06-30 16:00:39] DEBUG: assemble_kmer_sample=1 45 [2021-11-22 18:13:10] DEBUG: low_cutoff_warning=1
46 [2021-06-30 16:00:39] DEBUG: repeat_graph_kmer_sample=1 46 [2021-11-22 18:13:10] DEBUG: kmer_size=17
47 [2021-06-30 16:00:39] DEBUG: read_align_kmer_sample=1 47 [2021-11-22 18:13:10] DEBUG: use_minimizers=0
48 [2021-06-30 16:00:39] DEBUG: meta_read_top_kmer_rate=0.40 48 [2021-11-22 18:13:10] DEBUG: reads_base_alignment=0
49 [2021-06-30 16:00:39] DEBUG: maximum_jump=1500 49 [2021-11-22 18:13:10] DEBUG: meta_read_top_kmer_rate=0.40
50 [2021-06-30 16:00:39] DEBUG: maximum_overhang=1500 50 [2021-11-22 18:13:10] DEBUG: maximum_jump=1500
51 [2021-06-30 16:00:39] DEBUG: repeat_kmer_rate=100 51 [2021-11-22 18:13:10] DEBUG: maximum_overhang=1500
52 [2021-06-30 16:00:39] DEBUG: assemble_ovlp_divergence=0.10 52 [2021-11-22 18:13:10] DEBUG: repeat_kmer_rate=100
53 [2021-06-30 16:00:39] DEBUG: assemble_divergence_relative=1 53 [2021-11-22 18:13:10] DEBUG: assemble_ovlp_divergence=0.10
54 [2021-06-30 16:00:39] DEBUG: repeat_graph_ovlp_divergence=0.08 54 [2021-11-22 18:13:10] DEBUG: assemble_divergence_relative=1
55 [2021-06-30 16:00:39] DEBUG: read_align_ovlp_divergence=0.25 55 [2021-11-22 18:13:10] DEBUG: repeat_graph_ovlp_divergence=0.08
56 [2021-06-30 16:00:39] DEBUG: hpc_scoring_on=0 56 [2021-11-22 18:13:10] DEBUG: read_align_ovlp_divergence=0.25
57 [2021-06-30 16:00:39] DEBUG: add_unassembled_reads=0 57 [2021-11-22 18:13:10] DEBUG: hpc_scoring_on=0
58 [2021-06-30 16:00:39] DEBUG: extend_contigs_with_repeats=0 58 [2021-11-22 18:13:10] DEBUG: add_unassembled_reads=0
59 [2021-06-30 16:00:39] DEBUG: min_read_cov_cutoff=3 59 [2021-11-22 18:13:10] DEBUG: extend_contigs_with_repeats=0
60 [2021-06-30 16:00:39] DEBUG: short_tip_length=20000 60 [2021-11-22 18:13:10] DEBUG: min_read_cov_cutoff=3
61 [2021-06-30 16:00:39] DEBUG: long_tip_length=100000 61 [2021-11-22 18:13:10] DEBUG: short_tip_length=20000
62 [2021-06-30 16:00:39] DEBUG: Running with k-mer size: 17 62 [2021-11-22 18:13:10] DEBUG: long_tip_length=100000
63 [2021-06-30 16:00:39] DEBUG: Running with minimum overlap 5000 63 [2021-11-22 18:13:10] DEBUG: Running with k-mer size: 17
64 [2021-06-30 16:00:39] DEBUG: Metagenome mode: N 64 [2021-11-22 18:13:10] DEBUG: Running with minimum overlap 6000
65 [2021-06-30 16:00:39] INFO: Reading sequences 65 [2021-11-22 18:13:10] DEBUG: Metagenome mode: N
66 [2021-06-30 16:00:39] DEBUG: Building positional index 66 [2021-11-22 18:13:10] DEBUG: Short mode: N
67 [2021-06-30 16:00:39] DEBUG: Total sequence: 6702247 bp 67 [2021-11-22 18:13:10] INFO: Reading sequences
68 [2021-06-30 16:00:42] INFO: Counting k-mers: 68 [2021-11-22 18:13:10] DEBUG: Building positional index
69 [2021-06-30 16:00:42] DEBUG: Updating k-mer histogram 69 [2021-11-22 18:13:10] DEBUG: Total sequence: 6471580 bp
70 [2021-06-30 16:01:29] DEBUG: Hash size: 32 70 [2021-11-22 18:13:12] INFO: Counting k-mers:
71 [2021-06-30 16:01:29] DEBUG: Total k-mers 6159182 71 [2021-11-22 18:13:13] DEBUG: Updating k-mer histogram
72 [2021-06-30 16:01:29] INFO: Filling index table (1/2) 72 [2021-11-22 18:13:56] DEBUG: Hash size: 29
73 [2021-06-30 16:01:32] DEBUG: Mean k-mer frequency: 2.59564 73 [2021-11-22 18:13:56] DEBUG: Total k-mers 5958598
74 [2021-06-30 16:01:32] DEBUG: Repetitive k-mer frequency: 259 74 [2021-11-22 18:13:56] INFO: Filling index table (1/2)
75 [2021-06-30 16:01:32] DEBUG: Filtered 0 repetitive k-mers (0) 75 [2021-11-22 18:13:59] DEBUG: Mean k-mer frequency: 2.57396
76 [2021-06-30 16:01:32] INFO: Filling index table (2/2) 76 [2021-11-22 18:13:59] DEBUG: Repetitive k-mer frequency: 257
77 [2021-06-30 16:01:35] DEBUG: Sorting k-mer index 77 [2021-11-22 18:13:59] DEBUG: Filtered 0 repetitive k-mers (0)
78 [2021-06-30 16:01:35] DEBUG: Selected k-mers: 333758 78 [2021-11-22 18:13:59] INFO: Filling index table (2/2)
79 [2021-06-30 16:01:35] DEBUG: Index size: 866317 79 [2021-11-22 18:14:01] DEBUG: Sorting k-mer index
80 [2021-06-30 16:01:35] DEBUG: Mean k-mer index frequency: 2.59564 80 [2021-11-22 18:14:01] DEBUG: Selected k-mers: 319695
81 [2021-06-30 16:01:35] DEBUG: Peak RAM usage: 8 Gb 81 [2021-11-22 18:14:01] DEBUG: Index size: 822885
82 [2021-06-30 16:01:35] DEBUG: Estimating k-mer identity bias 82 [2021-11-22 18:14:01] DEBUG: Mean k-mer index frequency: 2.57397
83 [2021-06-30 16:01:39] DEBUG: Initial divergence estimate : 0.235584 83 [2021-11-22 18:14:01] DEBUG: Peak RAM usage: 8 Gb
84 [2021-06-30 16:01:39] DEBUG: Relative threshold: Y 84 [2021-11-22 18:14:01] DEBUG: Estimating k-mer identity bias
85 [2021-06-30 16:01:39] DEBUG: Max divergence threshold set to 0.335584 85 [2021-11-22 18:14:05] DEBUG: Initial divergence estimate : 0.237684
86 [2021-06-30 16:01:39] INFO: Extending reads 86 [2021-11-22 18:14:05] DEBUG: Relative threshold: Y
87 [2021-06-30 16:01:39] DEBUG: Estimating overlap coverage 87 [2021-11-22 18:14:05] DEBUG: Max divergence threshold set to 0.337684
88 [2021-06-30 16:01:42] INFO: Overlap-based coverage: 11 88 [2021-11-22 18:14:05] INFO: Extending reads
89 [2021-06-30 16:01:42] INFO: Median overlap divergence: 0.235584 89 [2021-11-22 18:14:05] DEBUG: Estimating overlap coverage
90 [2021-06-30 16:01:42] DEBUG: Sequence divergence distribution: 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:
91 93
92 | * | 94 | * |
93 | * | 95 | * |
94 | * *** | 96 | *** |
95 | * *** | 97 | * *** |
96 | ****** | 98 | ****** |
97 | ******* | 99 | ******* |
98 | ******* | 100 | ******* |
99 | ******** | 101 | ******** |
101 | ********* | 103 | ********* |
102 | ********* | 104 | ********* |
103 | ********* | 105 | ********* |
104 | ********** | 106 | ********** |
105 | ************ | 107 | ************ |
106 | ************* | 108 | ************ |
107 | ************** | 109 | ************** |
108 | ************** | 110 | ************** |
109 | **************** | 111 | **************** |
110 | * ***************** * | 112 | * ***************** * |
111 | * ** ************************ | * * 113 | * ** ************************ | * *
112 ---------------------------------------------------------------------------------------------------- 114 ----------------------------------------------------------------------------------------------------
113 0% 5% 10% 15% 20% 25% 30% 35% 40% 45% 115 0% 5% 10% 15% 20% 25% 30% 35% 40% 45%
114 116
115 Q25 = 0.22, Q50 = 0.24, Q75 = 0.25 117 Q25 = 0.22, Q50 = 0.24, Q75 = 0.25
116 118
117 [2021-06-30 16:01:42] DEBUG: Assembled disjointig 1 119 [2021-11-22 18:14:08] DEBUG: Assembled disjointig 1
118 With 86 reads 120 With 83 reads
119 Start read: +S1_371 121 Start read: +S1_395
120 At position: 35 122 At position: 40
121 leftTip: 1 rightTip: 1 123 leftTip: 1 rightTip: 1
122 Suspicious: 3 124 Suspicious: 5
123 Short ext: 2 125 Short ext: 3
124 Mean extensions: 9 126 Mean extensions: 9
125 Avg overlap len: 10074 127 Avg overlap len: 10043
126 Min overlap len: 2570 128 Min overlap len: 4225
127 Inner reads: 0 129 Inner reads: 0
128 Length: 433999 130 Length: 434635
129 [2021-06-30 16:01:42] DEBUG: Inner: 1040 covered: 1110 total: 1236 131 [2021-11-22 18:14:08] DEBUG: Inner: 1024 covered: 1014 total: 1152
130 [2021-06-30 16:01:42] INFO: Assembled 1 disjointigs 132 [2021-11-22 18:14:08] DEBUG: Assembled disjointig 2
131 [2021-06-30 16:01:42] INFO: Generating sequence 133 With 6 reads
132 [2021-06-30 16:01:43] DEBUG: Writing FASTA 134 Start read: +S1_921
133 [2021-06-30 16:01:43] DEBUG: Peak RAM usage: 8 Gb 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
134 -----------End assembly log------------ 164 -----------End assembly log------------
135 [2021-06-30 16:01:43] root: DEBUG: Disjointigs length: 434844, N50: 434844 165 [2021-11-22 18:14:09] root: DEBUG: Disjointigs length: 470346, N50: 436173
136 [2021-06-30 16:01:43] root: INFO: >>>STAGE: consensus 166 [2021-11-22 18:14:09] root: INFO: >>>STAGE: consensus
137 [2021-06-30 16:01:43] root: INFO: Running Minimap2 167 [2021-11-22 18:14:09] root: INFO: Running Minimap2
138 [2021-06-30 16:01:48] root: INFO: Computing consensus 168 [2021-11-22 18:14:14] root: INFO: Computing consensus
139 [2021-06-30 16:01:57] root: INFO: Alignment error rate: 0.196236 169 [2021-11-22 18:14:23] root: INFO: Alignment error rate: 0.197031
140 [2021-06-30 16:01:57] root: INFO: >>>STAGE: repeat 170 [2021-11-22 18:14:23] root: INFO: >>>STAGE: repeat
141 [2021-06-30 16:01:57] root: INFO: Building and resolving repeat graph 171 [2021-11-22 18:14:23] root: INFO: Building and resolving repeat graph
142 [2021-06-30 16:01:57] root: DEBUG: -----Begin repeat analyser log------ 172 [2021-11-22 18:14:23] 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 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
144 [2021-06-30 16:01:57] DEBUG: Build date: Mar 27 2021 19:09:05 174 [2021-11-22 18:14:23] DEBUG: Build date: Aug 22 2021 04:47:01
145 [2021-06-30 16:01:57] DEBUG: Total RAM: 15 Gb 175 [2021-11-22 18:14:23] DEBUG: Total RAM: 15 Gb
146 [2021-06-30 16:01:57] DEBUG: Available RAM: 11 Gb 176 [2021-11-22 18:14:23] DEBUG: Available RAM: 9 Gb
147 [2021-06-30 16:01:57] DEBUG: Total CPUs: 8 177 [2021-11-22 18:14:23] 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 178 [2021-11-22 18:14:23] 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 179 [2021-11-22 18:14:23] 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 180 [2021-11-22 18:14:23] DEBUG: big_genome_threshold=29000000
151 [2021-06-30 16:01:57] DEBUG: meta_read_filter_kmer_freq=100 181 [2021-11-22 18:14:23] DEBUG: meta_read_filter_kmer_freq=100
152 [2021-06-30 16:01:57] DEBUG: max_coverage_drop_rate=5 182 [2021-11-22 18:14:23] DEBUG: chain_large_gap_penalty=2
153 [2021-06-30 16:01:57] DEBUG: max_extensions_drop_rate=5 183 [2021-11-22 18:14:23] DEBUG: chain_small_gap_penalty=0.5
154 [2021-06-30 16:01:57] DEBUG: chimera_window=100 184 [2021-11-22 18:14:23] DEBUG: chain_gap_jump_threshold=100
155 [2021-06-30 16:01:57] DEBUG: min_reads_in_disjointig=4 185 [2021-11-22 18:14:23] DEBUG: max_coverage_drop_rate=5
156 [2021-06-30 16:01:57] DEBUG: max_inner_reads=10 186 [2021-11-22 18:14:23] DEBUG: max_extensions_drop_rate=5
157 [2021-06-30 16:01:57] DEBUG: max_inner_fraction=0.25 187 [2021-11-22 18:14:23] DEBUG: chimera_window=100
158 [2021-06-30 16:01:57] DEBUG: max_separation=500 188 [2021-11-22 18:14:23] DEBUG: chimera_overhang=1000
159 [2021-06-30 16:01:57] DEBUG: unique_edge_length=50000 189 [2021-11-22 18:14:23] DEBUG: min_reads_in_disjointig=4
160 [2021-06-30 16:01:57] DEBUG: min_repeat_res_support=0.51 190 [2021-11-22 18:14:23] DEBUG: max_inner_reads=10
161 [2021-06-30 16:01:57] DEBUG: out_paths_ratio=5 191 [2021-11-22 18:14:23] DEBUG: max_inner_fraction=0.25
162 [2021-06-30 16:01:57] DEBUG: graph_cov_drop_rate=5 192 [2021-11-22 18:14:23] DEBUG: max_separation=500
163 [2021-06-30 16:01:57] DEBUG: coverage_estimate_window=100 193 [2021-11-22 18:14:23] DEBUG: unique_edge_length=50000
164 [2021-06-30 16:01:57] DEBUG: max_bubble_length=50000 194 [2021-11-22 18:14:23] DEBUG: min_repeat_res_support=0.51
165 [2021-06-30 16:01:57] DEBUG: loop_coverage_rate=1.5 195 [2021-11-22 18:14:23] DEBUG: out_paths_ratio=5
166 [2021-06-30 16:01:57] DEBUG: repeat_edge_cov_mult=1.75 196 [2021-11-22 18:14:23] DEBUG: graph_cov_drop_rate=5
167 [2021-06-30 16:01:57] DEBUG: weak_detach_rate=5 197 [2021-11-22 18:14:23] DEBUG: coverage_estimate_window=100
168 [2021-06-30 16:01:57] DEBUG: tip_coverage_rate=2 198 [2021-11-22 18:14:23] DEBUG: max_bubble_length=50000
169 [2021-06-30 16:01:57] DEBUG: tip_length_rate=2 199 [2021-11-22 18:14:23] DEBUG: loop_coverage_rate=1.5
170 [2021-06-30 16:01:57] DEBUG: low_cutoff_warning=1 200 [2021-11-22 18:14:23] DEBUG: repeat_edge_cov_mult=1.75
171 [2021-06-30 16:01:57] DEBUG: hard_min_coverage_rate=10 201 [2021-11-22 18:14:23] DEBUG: weak_detach_rate=5
172 [2021-06-30 16:01:57] DEBUG: kmer_size=17 202 [2021-11-22 18:14:23] DEBUG: tip_coverage_rate=2
173 [2021-06-30 16:01:57] DEBUG: use_minimizers=0 203 [2021-11-22 18:14:23] DEBUG: tip_length_rate=2
174 [2021-06-30 16:01:57] DEBUG: reads_base_alignment=0 204 [2021-11-22 18:14:23] DEBUG: output_gfa_before_rr=0
175 [2021-06-30 16:01:57] DEBUG: assemble_kmer_sample=1 205 [2021-11-22 18:14:23] DEBUG: low_cutoff_warning=1
176 [2021-06-30 16:01:57] DEBUG: repeat_graph_kmer_sample=1 206 [2021-11-22 18:14:23] DEBUG: kmer_size=17
177 [2021-06-30 16:01:57] DEBUG: read_align_kmer_sample=1 207 [2021-11-22 18:14:23] DEBUG: use_minimizers=0
178 [2021-06-30 16:01:57] DEBUG: meta_read_top_kmer_rate=0.40 208 [2021-11-22 18:14:23] DEBUG: reads_base_alignment=0
179 [2021-06-30 16:01:57] DEBUG: maximum_jump=1500 209 [2021-11-22 18:14:23] DEBUG: meta_read_top_kmer_rate=0.40
180 [2021-06-30 16:01:57] DEBUG: maximum_overhang=1500 210 [2021-11-22 18:14:23] DEBUG: maximum_jump=1500
181 [2021-06-30 16:01:57] DEBUG: repeat_kmer_rate=100 211 [2021-11-22 18:14:23] DEBUG: maximum_overhang=1500
182 [2021-06-30 16:01:57] DEBUG: assemble_ovlp_divergence=0.10 212 [2021-11-22 18:14:23] DEBUG: repeat_kmer_rate=100
183 [2021-06-30 16:01:57] DEBUG: assemble_divergence_relative=1 213 [2021-11-22 18:14:23] DEBUG: assemble_ovlp_divergence=0.10
184 [2021-06-30 16:01:57] DEBUG: repeat_graph_ovlp_divergence=0.08 214 [2021-11-22 18:14:23] DEBUG: assemble_divergence_relative=1
185 [2021-06-30 16:01:57] DEBUG: read_align_ovlp_divergence=0.25 215 [2021-11-22 18:14:23] DEBUG: repeat_graph_ovlp_divergence=0.08
186 [2021-06-30 16:01:57] DEBUG: hpc_scoring_on=0 216 [2021-11-22 18:14:23] DEBUG: read_align_ovlp_divergence=0.25
187 [2021-06-30 16:01:57] DEBUG: add_unassembled_reads=0 217 [2021-11-22 18:14:23] DEBUG: hpc_scoring_on=0
188 [2021-06-30 16:01:57] DEBUG: extend_contigs_with_repeats=0 218 [2021-11-22 18:14:23] DEBUG: add_unassembled_reads=0
189 [2021-06-30 16:01:57] DEBUG: min_read_cov_cutoff=3 219 [2021-11-22 18:14:23] DEBUG: extend_contigs_with_repeats=0
190 [2021-06-30 16:01:57] DEBUG: short_tip_length=20000 220 [2021-11-22 18:14:23] DEBUG: min_read_cov_cutoff=3
191 [2021-06-30 16:01:57] DEBUG: long_tip_length=100000 221 [2021-11-22 18:14:23] DEBUG: short_tip_length=20000
192 [2021-06-30 16:01:57] DEBUG: Running with k-mer size: 17 222 [2021-11-22 18:14:23] DEBUG: long_tip_length=100000
193 [2021-06-30 16:01:57] DEBUG: Selected minimum overlap 5000 223 [2021-11-22 18:14:23] DEBUG: Running with k-mer size: 17
194 [2021-06-30 16:01:57] DEBUG: Metagenome mode: N 224 [2021-11-22 18:14:23] DEBUG: Selected minimum overlap 6000
195 [2021-06-30 16:01:57] INFO: Parsing disjointigs 225 [2021-11-22 18:14:23] DEBUG: Metagenome mode: N
196 [2021-06-30 16:01:57] DEBUG: Building positional index 226 [2021-11-22 18:14:23] INFO: Parsing disjointigs
197 [2021-06-30 16:01:57] DEBUG: Total sequence: 418806 bp 227 [2021-11-22 18:14:23] DEBUG: Building positional index
198 [2021-06-30 16:01:57] INFO: Building repeat graph 228 [2021-11-22 18:14:23] DEBUG: Total sequence: 452437 bp
199 [2021-06-30 16:01:57] DEBUG: Mean k-mer frequency: 1.00896 229 [2021-11-22 18:14:23] INFO: Building repeat graph
200 [2021-06-30 16:01:57] DEBUG: Repetitive k-mer frequency: 100 230 [2021-11-22 18:14:24] DEBUG: Mean k-mer frequency: 1.05543
201 [2021-06-30 16:01:57] DEBUG: Filtered 0 repetitive k-mers (0) 231 [2021-11-22 18:14:24] DEBUG: Repetitive k-mer frequency: 105
202 [2021-06-30 16:01:57] DEBUG: Sorting k-mer index 232 [2021-11-22 18:14:24] DEBUG: Filtered 0 repetitive k-mers (0)
203 [2021-06-30 16:01:57] DEBUG: Selected k-mers: 415069 233 [2021-11-22 18:14:24] DEBUG: Sorting k-mer index
204 [2021-06-30 16:01:57] DEBUG: K-mer index size: 418789 234 [2021-11-22 18:14:24] DEBUG: Selected k-mers: 428642
205 [2021-06-30 16:01:57] DEBUG: Mean k-mer frequency: 1.00896 235 [2021-11-22 18:14:24] DEBUG: K-mer index size: 452403
206 [2021-06-30 16:01:57] DEBUG: Minimizer rate: 1.00004 236 [2021-11-22 18:14:24] DEBUG: Mean k-mer frequency: 1.05543
207 [2021-06-30 16:01:58] DEBUG: Computing transitive closure for overlaps 237 [2021-11-22 18:14:24] DEBUG: Minimizer rate: 1.00008
208 [2021-06-30 16:01:58] DEBUG: Found 0 overlaps 238 [2021-11-22 18:14:24] DEBUG: Computing transitive closure for overlaps
209 [2021-06-30 16:01:58] DEBUG: Left 0 overlaps after filtering 239 [2021-11-22 18:14:24] DEBUG: Found 10 overlaps
210 [2021-06-30 16:01:58] INFO: Median overlap divergence: 0 240 [2021-11-22 18:14:24] DEBUG: Left 4 overlaps after filtering
211 [2021-06-30 16:01:58] DEBUG: Sequence divergence distribution: 241 [2021-11-22 18:14:24] INFO: Median overlap divergence: 0.0343169
212 242 [2021-11-22 18:14:24] DEBUG: Sequence divergence distribution:
213 | | 243
214 | | 244 | * |
215 | | 245 | * |
216 | | 246 | * |
217 | | 247 | * |
218 | | 248 | * |
219 | | 249 | * |
220 | | 250 | * |
221 | | 251 | * |
222 | | 252 | * |
223 | | 253 | * |
224 | | 254 | * |
225 | | 255 | * |
226 | | 256 | * |
227 | | 257 | * |
228 | | 258 | * |
229 | | 259 | * |
230 | | 260 | * |
231 | | 261 | * |
232 | | 262 | * |
263 | * |
233 ---------------------------------------------------------------------------------------------------- 264 ----------------------------------------------------------------------------------------------------
234 0% 5% 10% 15% 20% 25% 30% 35% 40% 45% 265 0% 5% 10% 15% 20% 25% 30% 35% 40% 45%
235 266
236 Q25 = 0, Q50 = 0, Q75 = 0 267 Q25 = 0.034, Q50 = 0.034, Q75 = 0.034
237 268
238 [2021-06-30 16:01:58] DEBUG: Computing gluepoints 269 [2021-11-22 18:14:24] DEBUG: Computing gluepoints
239 [2021-06-30 16:01:58] DEBUG: Added 0 gluepoint projections 270 [2021-11-22 18:14:24] DEBUG: Added 0 gluepoint projections
240 [2021-06-30 16:01:58] DEBUG: Created 4 gluepoints 271 [2021-11-22 18:14:24] DEBUG: Created 12 gluepoints
241 [2021-06-30 16:01:58] DEBUG: Artificial loops removed: 0 left, 0 right, 0 both 272 [2021-11-22 18:14:24] DEBUG: Artificial loops removed: 0 left, 0 right, 0 both
242 [2021-06-30 16:01:58] DEBUG: Initializing edges 273 [2021-11-22 18:14:24] DEBUG: Initializing edges
243 [2021-06-30 16:01:58] DEBUG: Edges length checksum: 18446744073013520505 274 [2021-11-22 18:14:24] DEBUG: Edges length checksum: 2261029433
244 [2021-06-30 16:01:58] DEBUG: Filtered 0 singleton segments 275 [2021-11-22 18:14:24] DEBUG: Filtered 0 singleton segments
245 [2021-06-30 16:01:58] DEBUG: Removed 0 simple and 0 double chimeric junctions 276 [2021-11-22 18:14:24] DEBUG: Removed 0 simple and 0 double chimeric junctions
246 [2021-06-30 16:01:58] DEBUG: Collapsed 0 edges 277 [2021-11-22 18:14:24] DEBUG: Collapsed 2 edges
247 [2021-06-30 16:01:58] DEBUG: * 1 +disjointig_1 0 418805 418805 278 [2021-11-22 18:14:24] DEBUG: * 4 +disjointig_1 0 419576 419576
248 [2021-06-30 16:01:58] DEBUG: Total edges: 1 279 [2021-11-22 18:14:24] DEBUG: Total edges: 4
249 [2021-06-30 16:01:58] INFO: Parsing reads 280 [2021-11-22 18:14:24] INFO: Parsing reads
250 [2021-06-30 16:01:58] DEBUG: Building positional index 281 [2021-11-22 18:14:24] DEBUG: Building positional index
251 [2021-06-30 16:01:58] DEBUG: Total sequence: 7249289 bp 282 [2021-11-22 18:14:24] DEBUG: Total sequence: 7249289 bp
252 [2021-06-30 16:01:58] DEBUG: Building positional index 283 [2021-11-22 18:14:24] DEBUG: Building positional index
253 [2021-06-30 16:01:58] DEBUG: Total sequence: 418805 bp 284 [2021-11-22 18:14:24] DEBUG: Total sequence: 419576 bp
254 [2021-06-30 16:01:58] INFO: Aligning reads to the graph 285 [2021-11-22 18:14:24] INFO: Aligning reads to the graph
255 [2021-06-30 16:01:58] DEBUG: Mean k-mer frequency: 1.00896 286 [2021-11-22 18:14:24] DEBUG: Mean k-mer frequency: 1.00888
256 [2021-06-30 16:01:58] DEBUG: Repetitive k-mer frequency: 100 287 [2021-11-22 18:14:24] DEBUG: Repetitive k-mer frequency: 100
257 [2021-06-30 16:01:58] DEBUG: Filtered 0 repetitive k-mers (0) 288 [2021-11-22 18:14:24] DEBUG: Filtered 0 repetitive k-mers (0)
258 [2021-06-30 16:01:58] DEBUG: Sorting k-mer index 289 [2021-11-22 18:14:24] DEBUG: Sorting k-mer index
259 [2021-06-30 16:01:58] DEBUG: Selected k-mers: 415068 290 [2021-11-22 18:14:24] DEBUG: Selected k-mers: 415865
260 [2021-06-30 16:01:58] DEBUG: K-mer index size: 418788 291 [2021-11-22 18:14:24] DEBUG: K-mer index size: 419559
261 [2021-06-30 16:01:58] DEBUG: Mean k-mer frequency: 1.00896 292 [2021-11-22 18:14:24] DEBUG: Mean k-mer frequency: 1.00888
262 [2021-06-30 16:01:58] DEBUG: Minimizer rate: 1.00004 293 [2021-11-22 18:14:24] DEBUG: Minimizer rate: 1.00004
263 [2021-06-30 16:02:00] DEBUG: Total reads : 618 294 [2021-11-22 18:14:26] DEBUG: Total reads : 576
264 [2021-06-30 16:02:00] DEBUG: Read with aligned parts : 610 295 [2021-11-22 18:14:26] DEBUG: Read with aligned parts : 566
265 [2021-06-30 16:02:00] DEBUG: Aligned in one piece : 610 296 [2021-11-22 18:14:26] DEBUG: Aligned in one piece : 566
266 [2021-06-30 16:02:00] INFO: Aligned read sequence: 6562529 / 6702247 (0.979154) 297 [2021-11-22 18:14:26] INFO: Aligned read sequence: 6321188 / 6471580 (0.976761)
267 [2021-06-30 16:02:00] INFO: Median overlap divergence: 0.129507 298 [2021-11-22 18:14:26] INFO: Median overlap divergence: 0.129819
268 [2021-06-30 16:02:00] DEBUG: Sequence divergence distribution: 299 [2021-11-22 18:14:26] DEBUG: Sequence divergence distribution:
269 300
270 | * |
271 | * | 301 | * |
272 | ** | 302 | ** |
273 | ** | 303 | ** |
274 | ** |
275 | *** | 304 | *** |
276 | *** * | 305 | *** |
277 | *** * | 306 | *** |
307 | ***** |
308 | ***** |
278 | ***** | 309 | ***** |
279 | ***** | 310 | ***** |
280 | ****** | 311 | ****** |
281 | ******* | 312 | ******* |
282 | ******* | 313 | ******* |
283 | ******** | 314 | ******** |
284 | ********* | 315 | ********* |
285 | ********* | 316 | ********* |
286 | ********** | 317 | ********** |
287 | *********** | 318 | ************ |
288 | ************ * | 319 | *************** |
289 | ***************** | 320 | **************** |
290 ---------------------------------------------------------------------------------------------------- 321 ----------------------------------------------------------------------------------------------------
291 0% 5% 10% 15% 20% 25% 30% 35% 40% 45% 322 0% 5% 10% 15% 20% 25% 30% 35% 40% 45%
292 323
293 Q25 = 0.12, Q50 = 0.13, Q75 = 0.14 324 Q25 = 0.12, Q50 = 0.13, Q75 = 0.14
294 325
295 [2021-06-30 16:02:00] INFO: Mean edge coverage: 14 326 [2021-11-22 18:14:27] INFO: Mean edge coverage: 14
296 [2021-06-30 16:02:00] DEBUG: 1 len:418805 cov:15 mult:1.07143 327 [2021-11-22 18:14:27] DEBUG: 4 len:419576 cov:14 mult:1
297 [2021-06-30 16:02:00] DEBUG: -1 len:418805 cov:15 mult:1.07143 328 [2021-11-22 18:14:27] DEBUG: -4 len:419576 cov:14 mult:1
298 [2021-06-30 16:02:00] DEBUG: Unique coverage threshold 26 329 [2021-11-22 18:14:27] DEBUG: Unique coverage threshold 24
299 [2021-06-30 16:02:00] INFO: Simplifying the graph 330 [2021-11-22 18:14:27] INFO: Simplifying the graph
300 [2021-06-30 16:02:00] DEBUG: Read coverage cutoff: 3 331 [2021-11-22 18:14:27] DEBUG: Read coverage cutoff: 3
301 [2021-06-30 16:02:00] DEBUG: [SIMPL] Removed 0 paths with low coverage 332 [2021-11-22 18:14:27] DEBUG: [SIMPL] Removed 0 paths with low coverage
302 [2021-06-30 16:02:00] DEBUG: Finding repeats 333 [2021-11-22 18:14:27] DEBUG: [SIMPL] Masked 0 heterozygous loops
303 [2021-06-30 16:02:00] DEBUG: Read coverage cutoff: 3 334 [2021-11-22 18:14:27] DEBUG: [SIMPL] Masked 0 simple bubbles
304 [2021-06-30 16:02:00] DEBUG: Repeat detection iteration 1 335 [2021-11-22 18:14:27] DEBUG: Finding repeats
305 [2021-06-30 16:02:00] DEBUG: Writing Dot 336 [2021-11-22 18:14:27] DEBUG: Read coverage cutoff: 3
306 [2021-06-30 16:02:00] DEBUG: Writing FASTA 337 [2021-11-22 18:14:27] DEBUG: Repeat detection iteration 1
307 [2021-06-30 16:02:00] DEBUG: [SIMPL] == Iteration 1 == 338 [2021-11-22 18:14:27] DEBUG: Writing Dot
308 [2021-06-30 16:02:00] DEBUG: Splitting nodes 339 [2021-11-22 18:14:27] DEBUG: Writing FASTA
309 [2021-06-30 16:02:00] DEBUG: [SIMPL] Split 0 nodes 340 [2021-11-22 18:14:27] DEBUG: [SIMPL] == Iteration 1 ==
310 [2021-06-30 16:02:00] DEBUG: [SIMPL] Clipped 0 short and 0 long tips 341 [2021-11-22 18:14:27] DEBUG: Splitting nodes
311 [2021-06-30 16:02:00] DEBUG: [SIMPL] Masked 0 heterozygous loops 342 [2021-11-22 18:14:27] DEBUG: [SIMPL] Split 0 nodes
312 [2021-06-30 16:02:00] DEBUG: [SIMPL] Masked 0 simple bubbles 343 [2021-11-22 18:14:27] DEBUG: [SIMPL] Clipped 0 short and 0 long tips
313 [2021-06-30 16:02:00] DEBUG: Finding repeats 344 [2021-11-22 18:14:27] DEBUG: [SIMPL] Masked 0 heterozygous loops
314 [2021-06-30 16:02:00] DEBUG: Read coverage cutoff: 3 345 [2021-11-22 18:14:27] DEBUG: [SIMPL] Masked 0 simple bubbles
315 [2021-06-30 16:02:00] DEBUG: Repeat detection iteration 1 346 [2021-11-22 18:14:27] DEBUG: Finding repeats
316 [2021-06-30 16:02:00] DEBUG: Total unique edges: 1 347 [2021-11-22 18:14:27] DEBUG: Read coverage cutoff: 3
317 [2021-06-30 16:02:00] DEBUG: [SIMPL] Resolved repeats: 0 348 [2021-11-22 18:14:27] DEBUG: Repeat detection iteration 1
318 [2021-06-30 16:02:00] DEBUG: RR links: 0 349 [2021-11-22 18:14:27] DEBUG: Total unique edges: 1
319 [2021-06-30 16:02:00] DEBUG: Unresolved: 0 350 [2021-11-22 18:14:27] DEBUG: [SIMPL] Resolved repeats: 0
320 [2021-06-30 16:02:00] DEBUG: Removed 0 simple and 0 double chimeric junctions 351 [2021-11-22 18:14:27] DEBUG: RR links: 0
321 [2021-06-30 16:02:00] DEBUG: [SIMPL] Collapsed 0 haplotypes 352 [2021-11-22 18:14:27] DEBUG: Unresolved: 0
322 [2021-06-30 16:02:00] DEBUG: [SIMPL] Resolved 0 simple repeats 353 [2021-11-22 18:14:27] DEBUG: Removed 0 simple and 0 double chimeric junctions
323 [2021-06-30 16:02:00] DEBUG: Read coverage cutoff: 3 354 [2021-11-22 18:14:27] DEBUG: [SIMPL] Collapsed 0 haplotypes
324 [2021-06-30 16:02:00] DEBUG: [SIMPL] Removed 0 paths with low coverage 355 [2021-11-22 18:14:27] DEBUG: [SIMPL] Resolved 0 simple repeats
325 [2021-06-30 16:02:00] DEBUG: Finding repeats 356 [2021-11-22 18:14:27] DEBUG: Read coverage cutoff: 3
326 [2021-06-30 16:02:00] DEBUG: Read coverage cutoff: 3 357 [2021-11-22 18:14:27] DEBUG: [SIMPL] Removed 0 paths with low coverage
327 [2021-06-30 16:02:00] DEBUG: Repeat detection iteration 1 358 [2021-11-22 18:14:27] DEBUG: Finding repeats
328 [2021-06-30 16:02:00] DEBUG: Writing Dot 359 [2021-11-22 18:14:27] DEBUG: Read coverage cutoff: 3
329 [2021-06-30 16:02:00] DEBUG: Writing FASTA 360 [2021-11-22 18:14:27] DEBUG: Repeat detection iteration 1
330 [2021-06-30 16:02:00] DEBUG: Peak RAM usage: 0 Gb 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
331 -----------End assembly log------------ 364 -----------End assembly log------------
332 [2021-06-30 16:02:00] root: INFO: >>>STAGE: contigger 365 [2021-11-22 18:14:27] root: INFO: >>>STAGE: contigger
333 [2021-06-30 16:02:00] root: INFO: Generating contigs 366 [2021-11-22 18:14:27] root: INFO: Generating contigs
334 [2021-06-30 16:02:00] root: DEBUG: -----Begin contigger analyser log------ 367 [2021-11-22 18:14:27] 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 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
336 [2021-06-30 16:02:00] DEBUG: Build date: Mar 27 2021 19:09:32 369 [2021-11-22 18:14:27] DEBUG: Build date: Aug 22 2021 04:47:48
337 [2021-06-30 16:02:00] DEBUG: Total RAM: 15 Gb 370 [2021-11-22 18:14:27] DEBUG: Total RAM: 15 Gb
338 [2021-06-30 16:02:00] DEBUG: Available RAM: 11 Gb 371 [2021-11-22 18:14:27] DEBUG: Available RAM: 9 Gb
339 [2021-06-30 16:02:00] DEBUG: Total CPUs: 8 372 [2021-11-22 18:14:27] 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 373 [2021-11-22 18:14:27] 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 374 [2021-11-22 18:14:27] 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 375 [2021-11-22 18:14:27] DEBUG: big_genome_threshold=29000000
343 [2021-06-30 16:02:00] DEBUG: meta_read_filter_kmer_freq=100 376 [2021-11-22 18:14:27] DEBUG: meta_read_filter_kmer_freq=100
344 [2021-06-30 16:02:00] DEBUG: max_coverage_drop_rate=5 377 [2021-11-22 18:14:27] DEBUG: chain_large_gap_penalty=2
345 [2021-06-30 16:02:00] DEBUG: max_extensions_drop_rate=5 378 [2021-11-22 18:14:27] DEBUG: chain_small_gap_penalty=0.5
346 [2021-06-30 16:02:00] DEBUG: chimera_window=100 379 [2021-11-22 18:14:27] DEBUG: chain_gap_jump_threshold=100
347 [2021-06-30 16:02:00] DEBUG: min_reads_in_disjointig=4 380 [2021-11-22 18:14:27] DEBUG: max_coverage_drop_rate=5
348 [2021-06-30 16:02:00] DEBUG: max_inner_reads=10 381 [2021-11-22 18:14:27] DEBUG: max_extensions_drop_rate=5
349 [2021-06-30 16:02:00] DEBUG: max_inner_fraction=0.25 382 [2021-11-22 18:14:27] DEBUG: chimera_window=100
350 [2021-06-30 16:02:00] DEBUG: max_separation=500 383 [2021-11-22 18:14:27] DEBUG: chimera_overhang=1000
351 [2021-06-30 16:02:00] DEBUG: unique_edge_length=50000 384 [2021-11-22 18:14:27] DEBUG: min_reads_in_disjointig=4
352 [2021-06-30 16:02:00] DEBUG: min_repeat_res_support=0.51 385 [2021-11-22 18:14:27] DEBUG: max_inner_reads=10
353 [2021-06-30 16:02:00] DEBUG: out_paths_ratio=5 386 [2021-11-22 18:14:27] DEBUG: max_inner_fraction=0.25
354 [2021-06-30 16:02:00] DEBUG: graph_cov_drop_rate=5 387 [2021-11-22 18:14:27] DEBUG: max_separation=500
355 [2021-06-30 16:02:00] DEBUG: coverage_estimate_window=100 388 [2021-11-22 18:14:27] DEBUG: unique_edge_length=50000
356 [2021-06-30 16:02:00] DEBUG: max_bubble_length=50000 389 [2021-11-22 18:14:27] DEBUG: min_repeat_res_support=0.51
357 [2021-06-30 16:02:00] DEBUG: loop_coverage_rate=1.5 390 [2021-11-22 18:14:27] DEBUG: out_paths_ratio=5
358 [2021-06-30 16:02:00] DEBUG: repeat_edge_cov_mult=1.75 391 [2021-11-22 18:14:27] DEBUG: graph_cov_drop_rate=5
359 [2021-06-30 16:02:00] DEBUG: weak_detach_rate=5 392 [2021-11-22 18:14:27] DEBUG: coverage_estimate_window=100
360 [2021-06-30 16:02:00] DEBUG: tip_coverage_rate=2 393 [2021-11-22 18:14:27] DEBUG: max_bubble_length=50000
361 [2021-06-30 16:02:00] DEBUG: tip_length_rate=2 394 [2021-11-22 18:14:27] DEBUG: loop_coverage_rate=1.5
362 [2021-06-30 16:02:00] DEBUG: low_cutoff_warning=1 395 [2021-11-22 18:14:27] DEBUG: repeat_edge_cov_mult=1.75
363 [2021-06-30 16:02:00] DEBUG: hard_min_coverage_rate=10 396 [2021-11-22 18:14:27] DEBUG: weak_detach_rate=5
364 [2021-06-30 16:02:00] DEBUG: kmer_size=17 397 [2021-11-22 18:14:27] DEBUG: tip_coverage_rate=2
365 [2021-06-30 16:02:00] DEBUG: use_minimizers=0 398 [2021-11-22 18:14:27] DEBUG: tip_length_rate=2
366 [2021-06-30 16:02:00] DEBUG: reads_base_alignment=0 399 [2021-11-22 18:14:27] DEBUG: output_gfa_before_rr=0
367 [2021-06-30 16:02:00] DEBUG: assemble_kmer_sample=1 400 [2021-11-22 18:14:27] DEBUG: low_cutoff_warning=1
368 [2021-06-30 16:02:00] DEBUG: repeat_graph_kmer_sample=1 401 [2021-11-22 18:14:27] DEBUG: kmer_size=17
369 [2021-06-30 16:02:00] DEBUG: read_align_kmer_sample=1 402 [2021-11-22 18:14:27] DEBUG: use_minimizers=0
370 [2021-06-30 16:02:00] DEBUG: meta_read_top_kmer_rate=0.40 403 [2021-11-22 18:14:27] DEBUG: reads_base_alignment=0
371 [2021-06-30 16:02:00] DEBUG: maximum_jump=1500 404 [2021-11-22 18:14:27] DEBUG: meta_read_top_kmer_rate=0.40
372 [2021-06-30 16:02:00] DEBUG: maximum_overhang=1500 405 [2021-11-22 18:14:27] DEBUG: maximum_jump=1500
373 [2021-06-30 16:02:00] DEBUG: repeat_kmer_rate=100 406 [2021-11-22 18:14:27] DEBUG: maximum_overhang=1500
374 [2021-06-30 16:02:00] DEBUG: assemble_ovlp_divergence=0.10 407 [2021-11-22 18:14:27] DEBUG: repeat_kmer_rate=100
375 [2021-06-30 16:02:00] DEBUG: assemble_divergence_relative=1 408 [2021-11-22 18:14:27] DEBUG: assemble_ovlp_divergence=0.10
376 [2021-06-30 16:02:00] DEBUG: repeat_graph_ovlp_divergence=0.08 409 [2021-11-22 18:14:27] DEBUG: assemble_divergence_relative=1
377 [2021-06-30 16:02:00] DEBUG: read_align_ovlp_divergence=0.25 410 [2021-11-22 18:14:27] DEBUG: repeat_graph_ovlp_divergence=0.08
378 [2021-06-30 16:02:00] DEBUG: hpc_scoring_on=0 411 [2021-11-22 18:14:27] DEBUG: read_align_ovlp_divergence=0.25
379 [2021-06-30 16:02:00] DEBUG: add_unassembled_reads=0 412 [2021-11-22 18:14:27] DEBUG: hpc_scoring_on=0
380 [2021-06-30 16:02:00] DEBUG: extend_contigs_with_repeats=0 413 [2021-11-22 18:14:27] DEBUG: add_unassembled_reads=0
381 [2021-06-30 16:02:00] DEBUG: min_read_cov_cutoff=3 414 [2021-11-22 18:14:27] DEBUG: extend_contigs_with_repeats=0
382 [2021-06-30 16:02:00] DEBUG: short_tip_length=20000 415 [2021-11-22 18:14:27] DEBUG: min_read_cov_cutoff=3
383 [2021-06-30 16:02:00] DEBUG: long_tip_length=100000 416 [2021-11-22 18:14:27] DEBUG: short_tip_length=20000
384 [2021-06-30 16:02:00] DEBUG: Running with k-mer size: 17 417 [2021-11-22 18:14:27] DEBUG: long_tip_length=100000
385 [2021-06-30 16:02:00] DEBUG: Selected minimum overlap 5000 418 [2021-11-22 18:14:27] DEBUG: Running with k-mer size: 17
386 [2021-06-30 16:02:00] INFO: Reading sequences 419 [2021-11-22 18:14:27] DEBUG: Selected minimum overlap 6000
387 [2021-06-30 16:02:01] DEBUG: Building positional index 420 [2021-11-22 18:14:27] INFO: Reading sequences
388 [2021-06-30 16:02:01] DEBUG: Total sequence: 7249289 bp 421 [2021-11-22 18:14:27] DEBUG: Building positional index
389 [2021-06-30 16:02:01] DEBUG: Flipped 0 422 [2021-11-22 18:14:27] DEBUG: Total sequence: 7249289 bp
390 [2021-06-30 16:02:01] DEBUG: UPath 1: 1 423 [2021-11-22 18:14:27] DEBUG: Flipped 0
391 [2021-06-30 16:02:01] DEBUG: Final graph contiain 1 egdes 424 [2021-11-22 18:14:27] DEBUG: UPath 1: 4
392 [2021-06-30 16:02:01] DEBUG: Extending contigs into repeats 425 [2021-11-22 18:14:27] DEBUG: Final graph contains 1 egdes
393 [2021-06-30 16:02:01] DEBUG: Covered 0 repetitive contigs 426 [2021-11-22 18:14:27] DEBUG: Extending contigs into repeats
394 [2021-06-30 16:02:01] INFO: Generated 1 contigs 427 [2021-11-22 18:14:27] DEBUG: Covered 0 repetitive contigs
395 [2021-06-30 16:02:01] DEBUG: Writing FASTA 428 [2021-11-22 18:14:27] INFO: Generated 1 contigs
396 [2021-06-30 16:02:01] DEBUG: Generating scaffold connections 429 [2021-11-22 18:14:27] DEBUG: Writing FASTA
397 [2021-06-30 16:02:01] INFO: Added 0 scaffold connections 430 [2021-11-22 18:14:27] DEBUG: Generating scaffold connections
398 [2021-06-30 16:02:01] DEBUG: Writing Dot 431 [2021-11-22 18:14:27] INFO: Added 0 scaffold connections
399 [2021-06-30 16:02:01] DEBUG: Writing FASTA 432 [2021-11-22 18:14:27] DEBUG: Writing Dot
400 [2021-06-30 16:02:01] DEBUG: Writing Gfa 433 [2021-11-22 18:14:27] DEBUG: Writing FASTA
401 [2021-06-30 16:02:01] DEBUG: Peak RAM usage: 0 Gb 434 [2021-11-22 18:14:27] DEBUG: Writing Gfa
435 [2021-11-22 18:14:27] DEBUG: Peak RAM usage: 0 Gb
402 -----------End assembly log------------ 436 -----------End assembly log------------
403 [2021-06-30 16:02:01] root: INFO: >>>STAGE: finalize 437 [2021-11-22 18:14:27] root: INFO: >>>STAGE: finalize
404 [2021-06-30 16:02:01] root: DEBUG: ---Output dir contents:---- 438 [2021-11-22 18:14:27] root: DEBUG: ---Output dir contents:----
405 [2021-06-30 16:02:01] root: DEBUG: out_dir/ 439 [2021-11-22 18:14:27] root: DEBUG: out_dir/
406 [2021-06-30 16:02:01] root: DEBUG: 367.0 B assembly_graph.gv 440 [2021-11-22 18:14:27] root: DEBUG: 367.0 B assembly_graph.gv
407 [2021-06-30 16:02:01] root: DEBUG: 415.0 K assembly.fasta 441 [2021-11-22 18:14:27] root: DEBUG: 416.0 K assembly.fasta
408 [2021-06-30 16:02:01] root: DEBUG: 92.0 B params.json 442 [2021-11-22 18:14:27] root: DEBUG: 92.0 B params.json
409 [2021-06-30 16:02:01] root: DEBUG: 26.0 K flye.log 443 [2021-11-22 18:14:27] root: DEBUG: 28.0 K flye.log
410 [2021-06-30 16:02:01] root: DEBUG: 409.0 K assembly_graph.gfa 444 [2021-11-22 18:14:27] root: DEBUG: 409.0 K assembly_graph.gfa
411 [2021-06-30 16:02:01] root: DEBUG: 10-consensus/ 445 [2021-11-22 18:14:27] root: DEBUG: 10-consensus/
412 [2021-06-30 16:02:01] root: DEBUG: 415.0 K consensus.fasta 446 [2021-11-22 18:14:27] root: DEBUG: 1.0 K minimap.stderr
413 [2021-06-30 16:02:01] root: DEBUG: 37.0 B chunks.fasta.fai 447 [2021-11-22 18:14:27] root: DEBUG: 449.0 K consensus.fasta
414 [2021-06-30 16:02:01] root: DEBUG: 30-contigger/ 448 [2021-11-22 18:14:27] root: DEBUG: 3.0 K minimap.bam.bai
415 [2021-06-30 16:02:01] root: DEBUG: 409.0 K graph_final.gfa 449 [2021-11-22 18:14:27] root: DEBUG: 30-contigger/
416 [2021-06-30 16:02:01] root: DEBUG: 0.0 B scaffolds_links.txt 450 [2021-11-22 18:14:27] root: DEBUG: 409.0 K graph_final.gfa
417 [2021-06-30 16:02:01] root: DEBUG: 111.0 B contigs_stats.txt 451 [2021-11-22 18:14:27] root: DEBUG: 0.0 B scaffolds_links.txt
418 [2021-06-30 16:02:01] root: DEBUG: 367.0 B graph_final.gv 452 [2021-11-22 18:14:27] root: DEBUG: 111.0 B contigs_stats.txt
419 [2021-06-30 16:02:01] root: DEBUG: 414.0 K graph_final.fasta 453 [2021-11-22 18:14:27] root: DEBUG: 367.0 B graph_final.gv
420 [2021-06-30 16:02:01] root: DEBUG: 414.0 K contigs.fasta 454 [2021-11-22 18:14:27] root: DEBUG: 414.0 K graph_final.fasta
421 [2021-06-30 16:02:01] root: DEBUG: 00-assembly/ 455 [2021-11-22 18:14:27] root: DEBUG: 414.0 K contigs.fasta
422 [2021-06-30 16:02:01] root: DEBUG: 429.0 K draft_assembly.fasta 456 [2021-11-22 18:14:27] root: DEBUG: 00-assembly/
423 [2021-06-30 16:02:01] root: DEBUG: 20-repeat/ 457 [2021-11-22 18:14:27] root: DEBUG: 61.0 B draft_assembly.fasta.fai
424 [2021-06-30 16:02:01] root: DEBUG: 414.0 K graph_before_rr.fasta 458 [2021-11-22 18:14:27] root: DEBUG: 465.0 K draft_assembly.fasta
425 [2021-06-30 16:02:01] root: DEBUG: 183.0 B repeat_graph_dump 459 [2021-11-22 18:14:27] root: DEBUG: 20-repeat/
426 [2021-06-30 16:02:01] root: DEBUG: 367.0 B graph_before_rr.gv 460 [2021-11-22 18:14:27] root: DEBUG: 414.0 K graph_before_rr.fasta
427 [2021-06-30 16:02:01] root: DEBUG: 367.0 B graph_after_rr.gv 461 [2021-11-22 18:14:27] root: DEBUG: 183.0 B repeat_graph_dump
428 [2021-06-30 16:02:01] root: DEBUG: 414.0 K repeat_graph_edges.fasta 462 [2021-11-22 18:14:27] root: DEBUG: 367.0 B graph_before_rr.gv
429 [2021-06-30 16:02:01] root: DEBUG: 129.0 K read_alignment_dump 463 [2021-11-22 18:14:27] root: DEBUG: 367.0 B graph_after_rr.gv
430 [2021-06-30 16:02:01] root: DEBUG: -------------------------- 464 [2021-11-22 18:14:27] root: DEBUG: 414.0 K repeat_graph_edges.fasta
431 [2021-06-30 16:02:01] root: INFO: Assembly statistics: 465 [2021-11-22 18:14:27] root: DEBUG: 119.0 K read_alignment_dump
432 466 [2021-11-22 18:14:27] root: DEBUG: --------------------------
433 Total length: 418805 467 [2021-11-22 18:14:27] root: INFO: Assembly statistics:
468
469 Total length: 419576
434 Fragments: 1 470 Fragments: 1
435 Fragments N50: 418805 471 Fragments N50: 419576
436 Largest frg: 418805 472 Largest frg: 419576
437 Scaffolds: 0 473 Scaffolds: 0
438 Mean coverage: 15 474 Mean coverage: 14
439 475
440 [2021-06-30 16:02:01] root: INFO: Final assembly: /tmp/tmpicy_msib/job_working_directory/000/8/working/out_dir/assembly.fasta 476 [2021-11-22 18:14:27] root: INFO: Final assembly: /tmp/tmpakmcmxzn/job_working_directory/000/8/working/out_dir/assembly.fasta