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comparison test-data/result1.log @ 12:3e4f8642c77e draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
author bgruening
date Mon, 26 Aug 2024 13:54:31 +0000
parents 276f5d8712d5
children
comparison
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11:291923e6f276 12:3e4f8642c77e
1 [2021-11-22 18:13:09] root: INFO: Starting Flye 2.9-b1768 1 [2024-08-19 09:44:19] root: INFO: Starting Flye 2.9.4-b1799
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 2 [2024-08-19 09:44:19] 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) 3 [2024-08-19 09:44:19] root: DEBUG: Python version: 3.11.9 | packaged by conda-forge | (main, Apr 19 2024, 18:36:13) [GCC 12.3.0]
4 [GCC 9.3.0] 4 [2024-08-19 09:44:19] root: INFO: >>>STAGE: configure
5 [2021-11-22 18:13:09] root: INFO: >>>STAGE: configure 5 [2024-08-19 09:44:19] root: INFO: Configuring run
6 [2021-11-22 18:13:09] root: INFO: Configuring run 6 [2024-08-19 09:44:19] root: INFO: Total read length: 7249289
7 [2021-11-22 18:13:10] root: INFO: Total read length: 7249289 7 [2024-08-19 09:44:19] root: INFO: Reads N50/N90: 11150 / 5790
8 [2021-11-22 18:13:10] root: INFO: Reads N50/N90: 11150 / 5790 8 [2024-08-19 09:44:19] root: INFO: Minimum overlap set to 6000
9 [2021-11-22 18:13:10] root: INFO: Minimum overlap set to 6000 9 [2024-08-19 09:44:19] root: INFO: >>>STAGE: assembly
10 [2021-11-22 18:13:10] root: INFO: >>>STAGE: assembly 10 [2024-08-19 09:44:19] root: INFO: Assembling disjointigs
11 [2021-11-22 18:13:10] root: INFO: Assembling disjointigs 11 [2024-08-19 09:44:19] root: DEBUG: -----Begin assembly log------
12 [2021-11-22 18:13:10] root: DEBUG: -----Begin assembly log------ 12 [2024-08-19 09:44:19] root: DEBUG: Running: flye-modules assemble --reads /tmp/tmpmmr8wbsp/job_working_directory/000/8/working/input_0.fastq.gz,/tmp/tmpmmr8wbsp/job_working_directory/000/8/working/input_1.fastq.gz,/tmp/tmpmmr8wbsp/job_working_directory/000/8/working/input_2.fastq.gz,/tmp/tmpmmr8wbsp/job_working_directory/000/8/working/input_3.fastq.gz,/tmp/tmpmmr8wbsp/job_working_directory/000/8/working/input_4.fastq.gz,/tmp/tmpmmr8wbsp/job_working_directory/000/8/working/input_5.fastq.gz,/tmp/tmpmmr8wbsp/job_working_directory/000/8/working/input_6.fastq.gz --out-asm /tmp/tmpmmr8wbsp/job_working_directory/000/8/working/out_dir/00-assembly/draft_assembly.fasta --config /usr/local/lib/python3.11/site-packages/flye/config/bin_cfg/asm_raw_reads.cfg --log /tmp/tmpmmr8wbsp/job_working_directory/000/8/working/out_dir/flye.log --threads 1 --min-ovlp 6000
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 13 [2024-08-19 09:44:19] DEBUG: Build date: Jul 26 2024 16:36:15
14 [2021-11-22 18:13:10] DEBUG: Build date: Aug 22 2021 04:46:17 14 [2024-08-19 09:44:19] DEBUG: Total RAM: 31 Gb
15 [2021-11-22 18:13:10] DEBUG: Total RAM: 15 Gb 15 [2024-08-19 09:44:19] DEBUG: Available RAM: 21 Gb
16 [2021-11-22 18:13:10] DEBUG: Available RAM: 9 Gb 16 [2024-08-19 09:44:19] DEBUG: Total CPUs: 12
17 [2021-11-22 18:13:10] DEBUG: Total CPUs: 8 17 [2024-08-19 09:44:19] DEBUG: Loading /usr/local/lib/python3.11/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 18 [2024-08-19 09:44:19] DEBUG: Loading /usr/local/lib/python3.11/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 19 [2024-08-19 09:44:19] DEBUG: big_genome_threshold=29000000
20 [2021-11-22 18:13:10] DEBUG: big_genome_threshold=29000000 20 [2024-08-19 09:44:19] DEBUG: meta_read_filter_kmer_freq=100
21 [2021-11-22 18:13:10] DEBUG: meta_read_filter_kmer_freq=100 21 [2024-08-19 09:44:19] DEBUG: chain_large_gap_penalty=2
22 [2021-11-22 18:13:10] DEBUG: chain_large_gap_penalty=2 22 [2024-08-19 09:44:19] DEBUG: chain_small_gap_penalty=0.5
23 [2021-11-22 18:13:10] DEBUG: chain_small_gap_penalty=0.5 23 [2024-08-19 09:44:19] DEBUG: chain_gap_jump_threshold=100
24 [2021-11-22 18:13:10] DEBUG: chain_gap_jump_threshold=100 24 [2024-08-19 09:44:19] DEBUG: max_jump_gap=500
25 [2021-11-22 18:13:10] DEBUG: max_coverage_drop_rate=5 25 [2024-08-19 09:44:19] DEBUG: max_coverage_drop_rate=5
26 [2021-11-22 18:13:10] DEBUG: max_extensions_drop_rate=5 26 [2024-08-19 09:44:19] DEBUG: max_extensions_drop_rate=5
27 [2021-11-22 18:13:10] DEBUG: chimera_window=100 27 [2024-08-19 09:44:19] DEBUG: chimera_window=100
28 [2021-11-22 18:13:10] DEBUG: chimera_overhang=1000 28 [2024-08-19 09:44:19] DEBUG: chimera_overhang=1000
29 [2021-11-22 18:13:10] DEBUG: min_reads_in_disjointig=4 29 [2024-08-19 09:44:19] DEBUG: min_reads_in_disjointig=4
30 [2021-11-22 18:13:10] DEBUG: max_inner_reads=10 30 [2024-08-19 09:44:19] DEBUG: max_inner_reads=10
31 [2021-11-22 18:13:10] DEBUG: max_inner_fraction=0.25 31 [2024-08-19 09:44:19] DEBUG: max_inner_fraction=0.25
32 [2021-11-22 18:13:10] DEBUG: max_separation=500 32 [2024-08-19 09:44:19] DEBUG: aggressive_dup_filter=1
33 [2021-11-22 18:13:10] DEBUG: unique_edge_length=50000 33 [2024-08-19 09:44:19] DEBUG: max_separation=500
34 [2021-11-22 18:13:10] DEBUG: min_repeat_res_support=0.51 34 [2024-08-19 09:44:19] DEBUG: unique_edge_length=50000
35 [2021-11-22 18:13:10] DEBUG: out_paths_ratio=5 35 [2024-08-19 09:44:19] DEBUG: min_repeat_res_support=0.51
36 [2021-11-22 18:13:10] DEBUG: graph_cov_drop_rate=5 36 [2024-08-19 09:44:19] DEBUG: out_paths_ratio=5
37 [2021-11-22 18:13:10] DEBUG: coverage_estimate_window=100 37 [2024-08-19 09:44:19] DEBUG: graph_cov_drop_rate=5
38 [2021-11-22 18:13:10] DEBUG: max_bubble_length=50000 38 [2024-08-19 09:44:19] DEBUG: coverage_estimate_window=100
39 [2021-11-22 18:13:10] DEBUG: loop_coverage_rate=1.5 39 [2024-08-19 09:44:19] DEBUG: max_bubble_length=50000
40 [2021-11-22 18:13:10] DEBUG: repeat_edge_cov_mult=1.75 40 [2024-08-19 09:44:19] DEBUG: loop_coverage_rate=1.5
41 [2021-11-22 18:13:10] DEBUG: weak_detach_rate=5 41 [2024-08-19 09:44:19] DEBUG: repeat_edge_cov_mult=1.75
42 [2021-11-22 18:13:10] DEBUG: tip_coverage_rate=2 42 [2024-08-19 09:44:19] DEBUG: weak_detach_rate=5
43 [2021-11-22 18:13:10] DEBUG: tip_length_rate=2 43 [2024-08-19 09:44:19] DEBUG: tip_coverage_rate=2
44 [2021-11-22 18:13:10] DEBUG: output_gfa_before_rr=0 44 [2024-08-19 09:44:19] DEBUG: tip_length_rate=2
45 [2021-11-22 18:13:10] DEBUG: low_cutoff_warning=1 45 [2024-08-19 09:44:19] DEBUG: output_gfa_before_rr=1
46 [2021-11-22 18:13:10] DEBUG: kmer_size=17 46 [2024-08-19 09:44:19] DEBUG: remove_alt_edges=0
47 [2021-11-22 18:13:10] DEBUG: use_minimizers=0 47 [2024-08-19 09:44:19] DEBUG: low_cutoff_warning=1
48 [2021-11-22 18:13:10] DEBUG: reads_base_alignment=0 48 [2024-08-19 09:44:19] DEBUG: kmer_size=17
49 [2021-11-22 18:13:10] DEBUG: meta_read_top_kmer_rate=0.40 49 [2024-08-19 09:44:19] DEBUG: use_minimizers=0
50 [2021-11-22 18:13:10] DEBUG: maximum_jump=1500 50 [2024-08-19 09:44:19] DEBUG: reads_base_alignment=0
51 [2021-11-22 18:13:10] DEBUG: maximum_overhang=1500 51 [2024-08-19 09:44:19] DEBUG: meta_read_top_kmer_rate=0.40
52 [2021-11-22 18:13:10] DEBUG: repeat_kmer_rate=100 52 [2024-08-19 09:44:19] DEBUG: maximum_jump=1500
53 [2021-11-22 18:13:10] DEBUG: assemble_ovlp_divergence=0.10 53 [2024-08-19 09:44:19] DEBUG: maximum_overhang=1500
54 [2021-11-22 18:13:10] DEBUG: assemble_divergence_relative=1 54 [2024-08-19 09:44:19] DEBUG: repeat_kmer_rate=100
55 [2021-11-22 18:13:10] DEBUG: repeat_graph_ovlp_divergence=0.08 55 [2024-08-19 09:44:19] DEBUG: assemble_ovlp_divergence=0.10
56 [2021-11-22 18:13:10] DEBUG: read_align_ovlp_divergence=0.25 56 [2024-08-19 09:44:19] DEBUG: assemble_divergence_relative=1
57 [2021-11-22 18:13:10] DEBUG: hpc_scoring_on=0 57 [2024-08-19 09:44:19] DEBUG: repeat_graph_ovlp_divergence=0.08
58 [2021-11-22 18:13:10] DEBUG: add_unassembled_reads=0 58 [2024-08-19 09:44:19] DEBUG: read_align_ovlp_divergence=0.25
59 [2021-11-22 18:13:10] DEBUG: extend_contigs_with_repeats=0 59 [2024-08-19 09:44:19] DEBUG: hpc_scoring_on=0
60 [2021-11-22 18:13:10] DEBUG: min_read_cov_cutoff=3 60 [2024-08-19 09:44:19] DEBUG: add_unassembled_reads=0
61 [2021-11-22 18:13:10] DEBUG: short_tip_length=20000 61 [2024-08-19 09:44:19] DEBUG: extend_contigs_with_repeats=0
62 [2021-11-22 18:13:10] DEBUG: long_tip_length=100000 62 [2024-08-19 09:44:19] DEBUG: min_read_cov_cutoff=3
63 [2021-11-22 18:13:10] DEBUG: Running with k-mer size: 17 63 [2024-08-19 09:44:19] DEBUG: short_tip_length=20000
64 [2021-11-22 18:13:10] DEBUG: Running with minimum overlap 6000 64 [2024-08-19 09:44:19] DEBUG: long_tip_length=100000
65 [2021-11-22 18:13:10] DEBUG: Metagenome mode: N 65 [2024-08-19 09:44:19] DEBUG: Running with k-mer size: 17
66 [2021-11-22 18:13:10] DEBUG: Short mode: N 66 [2024-08-19 09:44:19] DEBUG: Running with minimum overlap 6000
67 [2021-11-22 18:13:10] INFO: Reading sequences 67 [2024-08-19 09:44:19] DEBUG: Metagenome mode: N
68 [2021-11-22 18:13:10] DEBUG: Building positional index 68 [2024-08-19 09:44:19] DEBUG: Short mode: N
69 [2021-11-22 18:13:10] DEBUG: Total sequence: 6471580 bp 69 [2024-08-19 09:44:19] INFO: Reading sequences
70 [2021-11-22 18:13:12] INFO: Counting k-mers: 70 [2024-08-19 09:44:19] DEBUG: Building positional index
71 [2021-11-22 18:13:13] DEBUG: Updating k-mer histogram 71 [2024-08-19 09:44:19] DEBUG: Total sequence: 6471580 bp
72 [2021-11-22 18:13:56] DEBUG: Hash size: 29 72 [2024-08-19 09:44:21] INFO: Counting k-mers:
73 [2021-11-22 18:13:56] DEBUG: Total k-mers 5958598 73 [2024-08-19 09:44:22] DEBUG: Updating k-mer histogram
74 [2021-11-22 18:13:56] INFO: Filling index table (1/2) 74 [2024-08-19 09:44:52] DEBUG: Hash size: 29
75 [2021-11-22 18:13:59] DEBUG: Mean k-mer frequency: 2.57396 75 [2024-08-19 09:44:52] DEBUG: Total k-mers 5958598
76 [2021-11-22 18:13:59] DEBUG: Repetitive k-mer frequency: 257 76 [2024-08-19 09:44:52] INFO: Filling index table (1/2)
77 [2021-11-22 18:13:59] DEBUG: Filtered 0 repetitive k-mers (0) 77 [2024-08-19 09:44:54] DEBUG: Mean k-mer frequency: 2.57396
78 [2021-11-22 18:13:59] INFO: Filling index table (2/2) 78 [2024-08-19 09:44:54] DEBUG: Repetitive k-mer frequency: 257
79 [2021-11-22 18:14:01] DEBUG: Sorting k-mer index 79 [2024-08-19 09:44:54] DEBUG: Filtered 0 repetitive k-mers (0)
80 [2021-11-22 18:14:01] DEBUG: Selected k-mers: 319695 80 [2024-08-19 09:44:54] INFO: Filling index table (2/2)
81 [2021-11-22 18:14:01] DEBUG: Index size: 822885 81 [2024-08-19 09:44:56] DEBUG: Sorting k-mer index
82 [2021-11-22 18:14:01] DEBUG: Mean k-mer index frequency: 2.57397 82 [2024-08-19 09:44:56] DEBUG: Selected k-mers: 319695
83 [2021-11-22 18:14:01] DEBUG: Peak RAM usage: 8 Gb 83 [2024-08-19 09:44:56] DEBUG: Index size: 822885
84 [2021-11-22 18:14:01] DEBUG: Estimating k-mer identity bias 84 [2024-08-19 09:44:56] DEBUG: Mean k-mer index frequency: 2.57397
85 [2021-11-22 18:14:05] DEBUG: Initial divergence estimate : 0.237684 85 [2024-08-19 09:44:56] DEBUG: Peak RAM usage: 8 Gb
86 [2021-11-22 18:14:05] DEBUG: Relative threshold: Y 86 [2024-08-19 09:44:56] DEBUG: Estimating k-mer identity bias
87 [2021-11-22 18:14:05] DEBUG: Max divergence threshold set to 0.337684 87 [2024-08-19 09:44:58] DEBUG: Initial divergence estimate : 0.237684
88 [2021-11-22 18:14:05] INFO: Extending reads 88 [2024-08-19 09:44:58] DEBUG: Relative threshold: Y
89 [2021-11-22 18:14:05] DEBUG: Estimating overlap coverage 89 [2024-08-19 09:44:58] DEBUG: Max divergence threshold set to 0.337684
90 [2021-11-22 18:14:07] INFO: Overlap-based coverage: 10 90 [2024-08-19 09:44:58] INFO: Extending reads
91 [2021-11-22 18:14:07] INFO: Median overlap divergence: 0.235584 91 [2024-08-19 09:44:58] DEBUG: Estimating overlap coverage
92 [2021-11-22 18:14:07] DEBUG: Sequence divergence distribution: 92 [2024-08-19 09:45:00] INFO: Overlap-based coverage: 10
93 [2024-08-19 09:45:00] INFO: Median overlap divergence: 0.235584
94 [2024-08-19 09:45:00] DEBUG: Sequence divergence distribution:
93 95
94 | * | 96 | * |
95 | * | 97 | * |
96 | *** | 98 | *** |
97 | * *** | 99 | * *** |
114 ---------------------------------------------------------------------------------------------------- 116 ----------------------------------------------------------------------------------------------------
115 0% 5% 10% 15% 20% 25% 30% 35% 40% 45% 117 0% 5% 10% 15% 20% 25% 30% 35% 40% 45%
116 118
117 Q25 = 0.22, Q50 = 0.24, Q75 = 0.25 119 Q25 = 0.22, Q50 = 0.24, Q75 = 0.25
118 120
119 [2021-11-22 18:14:08] DEBUG: Assembled disjointig 1 121 [2024-08-19 09:45:00] DEBUG: Assembled disjointig 1
120 With 83 reads 122 With 83 reads
121 Start read: +S1_395 123 Start read: +S1_395
122 At position: 40 124 At position: 40
123 leftTip: 1 rightTip: 1 125 leftTip: 1 rightTip: 1
124 Suspicious: 5 126 Suspicious: 5
126 Mean extensions: 9 128 Mean extensions: 9
127 Avg overlap len: 10043 129 Avg overlap len: 10043
128 Min overlap len: 4225 130 Min overlap len: 4225
129 Inner reads: 0 131 Inner reads: 0
130 Length: 434635 132 Length: 434635
131 [2021-11-22 18:14:08] DEBUG: Inner: 1024 covered: 1014 total: 1152 133 [2024-08-19 09:45:00] DEBUG: Inner: 1024 covered: 1014 total: 1152
132 [2021-11-22 18:14:08] DEBUG: Assembled disjointig 2 134 [2024-08-19 09:45:00] DEBUG: Assembled disjointig 2
133 With 6 reads 135 With 6 reads
134 Start read: +S1_921 136 Start read: +S1_921
135 At position: 4 137 At position: 4
136 leftTip: 0 rightTip: 0 138 leftTip: 0 rightTip: 0
137 Suspicious: 0 139 Suspicious: 0
139 Mean extensions: 4 141 Mean extensions: 4
140 Avg overlap len: 8689 142 Avg overlap len: 8689
141 Min overlap len: 7703 143 Min overlap len: 7703
142 Inner reads: 0 144 Inner reads: 0
143 Length: 34343 145 Length: 34343
144 [2021-11-22 18:14:08] DEBUG: Inner: 1040 covered: 1056 total: 1152 146 [2024-08-19 09:45:00] DEBUG: Inner: 1040 covered: 1056 total: 1152
145 [2021-11-22 18:14:08] INFO: Assembled 2 disjointigs 147 [2024-08-19 09:45:00] INFO: Assembled 2 disjointigs
146 [2021-11-22 18:14:08] INFO: Generating sequence 148 [2024-08-19 09:45:00] INFO: Generating sequence
147 [2021-11-22 18:14:08] DEBUG: Building positional index 149 [2024-08-19 09:45:00] DEBUG: Building positional index
148 [2021-11-22 18:14:08] DEBUG: Total sequence: 470346 bp 150 [2024-08-19 09:45:00] DEBUG: Total sequence: 470346 bp
149 [2021-11-22 18:14:08] DEBUG: Mean k-mer frequency: 1.00134 151 [2024-08-19 09:45:00] DEBUG: Mean k-mer frequency: 1.00134
150 [2021-11-22 18:14:08] DEBUG: Repetitive k-mer frequency: 100 152 [2024-08-19 09:45:00] DEBUG: Repetitive k-mer frequency: 100
151 [2021-11-22 18:14:08] DEBUG: Filtered 0 repetitive k-mers (0) 153 [2024-08-19 09:45:00] DEBUG: Filtered 0 repetitive k-mers (0)
152 [2021-11-22 18:14:08] DEBUG: Sorting k-mer index 154 [2024-08-19 09:45:00] DEBUG: Sorting k-mer index
153 [2021-11-22 18:14:08] DEBUG: Selected k-mers: 469680 155 [2024-08-19 09:45:00] DEBUG: Selected k-mers: 469680
154 [2021-11-22 18:14:08] DEBUG: K-mer index size: 470312 156 [2024-08-19 09:45:00] DEBUG: K-mer index size: 470312
155 [2021-11-22 18:14:08] DEBUG: Mean k-mer frequency: 1.00135 157 [2024-08-19 09:45:00] DEBUG: Mean k-mer frequency: 1.00135
156 [2021-11-22 18:14:08] DEBUG: Minimizer rate: 1.00007 158 [2024-08-19 09:45:00] DEBUG: Minimizer rate: 1.00007
157 [2021-11-22 18:14:08] INFO: Filtering contained disjointigs 159 [2024-08-19 09:45:00] INFO: Filtering contained disjointigs
158 [2021-11-22 18:14:09] DEBUG: Computing transitive closure for overlaps 160 [2024-08-19 09:45:00] DEBUG: Computing transitive closure for overlaps
159 [2021-11-22 18:14:09] DEBUG: Found 0 overlaps 161 [2024-08-19 09:45:00] DEBUG: Found 0 overlaps
160 [2021-11-22 18:14:09] DEBUG: Left 0 overlaps after filtering 162 [2024-08-19 09:45:00] DEBUG: Left 0 overlaps after filtering
161 [2021-11-22 18:14:09] INFO: Contained seqs: 0 163 [2024-08-19 09:45:00] INFO: Contained seqs: 0
162 [2021-11-22 18:14:09] DEBUG: Writing FASTA 164 [2024-08-19 09:45:00] DEBUG: Writing FASTA
163 [2021-11-22 18:14:09] DEBUG: Peak RAM usage: 8 Gb 165 [2024-08-19 09:45:00] DEBUG: Peak RAM usage: 8 Gb
164 -----------End assembly log------------ 166 -----------End assembly log------------
165 [2021-11-22 18:14:09] root: DEBUG: Disjointigs length: 470346, N50: 436173 167 [2024-08-19 09:45:00] root: DEBUG: Disjointigs length: 470346, N50: 436173
166 [2021-11-22 18:14:09] root: INFO: >>>STAGE: consensus 168 [2024-08-19 09:45:00] root: INFO: >>>STAGE: consensus
167 [2021-11-22 18:14:09] root: INFO: Running Minimap2 169 [2024-08-19 09:45:00] root: INFO: Running Minimap2
168 [2021-11-22 18:14:14] root: INFO: Computing consensus 170 [2024-08-19 09:45:04] root: INFO: Computing consensus
169 [2021-11-22 18:14:23] root: INFO: Alignment error rate: 0.197031 171 [2024-08-19 09:45:08] root: INFO: Alignment error rate: 0.196554
170 [2021-11-22 18:14:23] root: INFO: >>>STAGE: repeat 172 [2024-08-19 09:45:08] root: INFO: >>>STAGE: repeat
171 [2021-11-22 18:14:23] root: INFO: Building and resolving repeat graph 173 [2024-08-19 09:45:08] root: INFO: Building and resolving repeat graph
172 [2021-11-22 18:14:23] root: DEBUG: -----Begin repeat analyser log------ 174 [2024-08-19 09:45:08] 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 175 [2024-08-19 09:45:08] root: DEBUG: Running: flye-modules repeat --disjointigs /tmp/tmpmmr8wbsp/job_working_directory/000/8/working/out_dir/10-consensus/consensus.fasta --reads /tmp/tmpmmr8wbsp/job_working_directory/000/8/working/input_0.fastq.gz,/tmp/tmpmmr8wbsp/job_working_directory/000/8/working/input_1.fastq.gz,/tmp/tmpmmr8wbsp/job_working_directory/000/8/working/input_2.fastq.gz,/tmp/tmpmmr8wbsp/job_working_directory/000/8/working/input_3.fastq.gz,/tmp/tmpmmr8wbsp/job_working_directory/000/8/working/input_4.fastq.gz,/tmp/tmpmmr8wbsp/job_working_directory/000/8/working/input_5.fastq.gz,/tmp/tmpmmr8wbsp/job_working_directory/000/8/working/input_6.fastq.gz --out-dir /tmp/tmpmmr8wbsp/job_working_directory/000/8/working/out_dir/20-repeat --config /usr/local/lib/python3.11/site-packages/flye/config/bin_cfg/asm_raw_reads.cfg --log /tmp/tmpmmr8wbsp/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 04:47:01 176 [2024-08-19 09:45:08] DEBUG: Build date: Jul 26 2024 16:36:40
175 [2021-11-22 18:14:23] DEBUG: Total RAM: 15 Gb 177 [2024-08-19 09:45:08] DEBUG: Total RAM: 31 Gb
176 [2021-11-22 18:14:23] DEBUG: Available RAM: 9 Gb 178 [2024-08-19 09:45:08] DEBUG: Available RAM: 21 Gb
177 [2021-11-22 18:14:23] DEBUG: Total CPUs: 8 179 [2024-08-19 09:45:08] DEBUG: Total CPUs: 12
178 [2021-11-22 18:14:23] DEBUG: Loading /usr/local/lib/python3.9/site-packages/flye/config/bin_cfg/asm_raw_reads.cfg 180 [2024-08-19 09:45:08] DEBUG: Loading /usr/local/lib/python3.11/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 181 [2024-08-19 09:45:08] DEBUG: Loading /usr/local/lib/python3.11/site-packages/flye/config/bin_cfg/asm_defaults.cfg
180 [2021-11-22 18:14:23] DEBUG: big_genome_threshold=29000000 182 [2024-08-19 09:45:08] DEBUG: big_genome_threshold=29000000
181 [2021-11-22 18:14:23] DEBUG: meta_read_filter_kmer_freq=100 183 [2024-08-19 09:45:08] DEBUG: meta_read_filter_kmer_freq=100
182 [2021-11-22 18:14:23] DEBUG: chain_large_gap_penalty=2 184 [2024-08-19 09:45:08] DEBUG: chain_large_gap_penalty=2
183 [2021-11-22 18:14:23] DEBUG: chain_small_gap_penalty=0.5 185 [2024-08-19 09:45:08] DEBUG: chain_small_gap_penalty=0.5
184 [2021-11-22 18:14:23] DEBUG: chain_gap_jump_threshold=100 186 [2024-08-19 09:45:08] DEBUG: chain_gap_jump_threshold=100
185 [2021-11-22 18:14:23] DEBUG: max_coverage_drop_rate=5 187 [2024-08-19 09:45:08] DEBUG: max_jump_gap=500
186 [2021-11-22 18:14:23] DEBUG: max_extensions_drop_rate=5 188 [2024-08-19 09:45:08] DEBUG: max_coverage_drop_rate=5
187 [2021-11-22 18:14:23] DEBUG: chimera_window=100 189 [2024-08-19 09:45:08] DEBUG: max_extensions_drop_rate=5
188 [2021-11-22 18:14:23] DEBUG: chimera_overhang=1000 190 [2024-08-19 09:45:08] DEBUG: chimera_window=100
189 [2021-11-22 18:14:23] DEBUG: min_reads_in_disjointig=4 191 [2024-08-19 09:45:08] DEBUG: chimera_overhang=1000
190 [2021-11-22 18:14:23] DEBUG: max_inner_reads=10 192 [2024-08-19 09:45:08] DEBUG: min_reads_in_disjointig=4
191 [2021-11-22 18:14:23] DEBUG: max_inner_fraction=0.25 193 [2024-08-19 09:45:08] DEBUG: max_inner_reads=10
192 [2021-11-22 18:14:23] DEBUG: max_separation=500 194 [2024-08-19 09:45:08] DEBUG: max_inner_fraction=0.25
193 [2021-11-22 18:14:23] DEBUG: unique_edge_length=50000 195 [2024-08-19 09:45:08] DEBUG: aggressive_dup_filter=1
194 [2021-11-22 18:14:23] DEBUG: min_repeat_res_support=0.51 196 [2024-08-19 09:45:08] DEBUG: max_separation=500
195 [2021-11-22 18:14:23] DEBUG: out_paths_ratio=5 197 [2024-08-19 09:45:08] DEBUG: unique_edge_length=50000
196 [2021-11-22 18:14:23] DEBUG: graph_cov_drop_rate=5 198 [2024-08-19 09:45:08] DEBUG: min_repeat_res_support=0.51
197 [2021-11-22 18:14:23] DEBUG: coverage_estimate_window=100 199 [2024-08-19 09:45:08] DEBUG: out_paths_ratio=5
198 [2021-11-22 18:14:23] DEBUG: max_bubble_length=50000 200 [2024-08-19 09:45:08] DEBUG: graph_cov_drop_rate=5
199 [2021-11-22 18:14:23] DEBUG: loop_coverage_rate=1.5 201 [2024-08-19 09:45:08] DEBUG: coverage_estimate_window=100
200 [2021-11-22 18:14:23] DEBUG: repeat_edge_cov_mult=1.75 202 [2024-08-19 09:45:08] DEBUG: max_bubble_length=50000
201 [2021-11-22 18:14:23] DEBUG: weak_detach_rate=5 203 [2024-08-19 09:45:08] DEBUG: loop_coverage_rate=1.5
202 [2021-11-22 18:14:23] DEBUG: tip_coverage_rate=2 204 [2024-08-19 09:45:08] DEBUG: repeat_edge_cov_mult=1.75
203 [2021-11-22 18:14:23] DEBUG: tip_length_rate=2 205 [2024-08-19 09:45:08] DEBUG: weak_detach_rate=5
204 [2021-11-22 18:14:23] DEBUG: output_gfa_before_rr=0 206 [2024-08-19 09:45:08] DEBUG: tip_coverage_rate=2
205 [2021-11-22 18:14:23] DEBUG: low_cutoff_warning=1 207 [2024-08-19 09:45:08] DEBUG: tip_length_rate=2
206 [2021-11-22 18:14:23] DEBUG: kmer_size=17 208 [2024-08-19 09:45:08] DEBUG: output_gfa_before_rr=1
207 [2021-11-22 18:14:23] DEBUG: use_minimizers=0 209 [2024-08-19 09:45:08] DEBUG: remove_alt_edges=0
208 [2021-11-22 18:14:23] DEBUG: reads_base_alignment=0 210 [2024-08-19 09:45:08] DEBUG: low_cutoff_warning=1
209 [2021-11-22 18:14:23] DEBUG: meta_read_top_kmer_rate=0.40 211 [2024-08-19 09:45:08] DEBUG: kmer_size=17
210 [2021-11-22 18:14:23] DEBUG: maximum_jump=1500 212 [2024-08-19 09:45:08] DEBUG: use_minimizers=0
211 [2021-11-22 18:14:23] DEBUG: maximum_overhang=1500 213 [2024-08-19 09:45:08] DEBUG: reads_base_alignment=0
212 [2021-11-22 18:14:23] DEBUG: repeat_kmer_rate=100 214 [2024-08-19 09:45:08] DEBUG: meta_read_top_kmer_rate=0.40
213 [2021-11-22 18:14:23] DEBUG: assemble_ovlp_divergence=0.10 215 [2024-08-19 09:45:08] DEBUG: maximum_jump=1500
214 [2021-11-22 18:14:23] DEBUG: assemble_divergence_relative=1 216 [2024-08-19 09:45:08] DEBUG: maximum_overhang=1500
215 [2021-11-22 18:14:23] DEBUG: repeat_graph_ovlp_divergence=0.08 217 [2024-08-19 09:45:08] DEBUG: repeat_kmer_rate=100
216 [2021-11-22 18:14:23] DEBUG: read_align_ovlp_divergence=0.25 218 [2024-08-19 09:45:08] DEBUG: assemble_ovlp_divergence=0.10
217 [2021-11-22 18:14:23] DEBUG: hpc_scoring_on=0 219 [2024-08-19 09:45:08] DEBUG: assemble_divergence_relative=1
218 [2021-11-22 18:14:23] DEBUG: add_unassembled_reads=0 220 [2024-08-19 09:45:08] DEBUG: repeat_graph_ovlp_divergence=0.08
219 [2021-11-22 18:14:23] DEBUG: extend_contigs_with_repeats=0 221 [2024-08-19 09:45:08] DEBUG: read_align_ovlp_divergence=0.25
220 [2021-11-22 18:14:23] DEBUG: min_read_cov_cutoff=3 222 [2024-08-19 09:45:08] DEBUG: hpc_scoring_on=0
221 [2021-11-22 18:14:23] DEBUG: short_tip_length=20000 223 [2024-08-19 09:45:08] DEBUG: add_unassembled_reads=0
222 [2021-11-22 18:14:23] DEBUG: long_tip_length=100000 224 [2024-08-19 09:45:08] DEBUG: extend_contigs_with_repeats=0
223 [2021-11-22 18:14:23] DEBUG: Running with k-mer size: 17 225 [2024-08-19 09:45:08] DEBUG: min_read_cov_cutoff=3
224 [2021-11-22 18:14:23] DEBUG: Selected minimum overlap 6000 226 [2024-08-19 09:45:08] DEBUG: short_tip_length=20000
225 [2021-11-22 18:14:23] DEBUG: Metagenome mode: N 227 [2024-08-19 09:45:08] DEBUG: long_tip_length=100000
226 [2021-11-22 18:14:23] INFO: Parsing disjointigs 228 [2024-08-19 09:45:08] DEBUG: Running with k-mer size: 17
227 [2021-11-22 18:14:23] DEBUG: Building positional index 229 [2024-08-19 09:45:08] DEBUG: Selected minimum overlap 6000
228 [2021-11-22 18:14:23] DEBUG: Total sequence: 452437 bp 230 [2024-08-19 09:45:08] DEBUG: Metagenome mode: N
229 [2021-11-22 18:14:23] INFO: Building repeat graph 231 [2024-08-19 09:45:08] INFO: Parsing disjointigs
230 [2021-11-22 18:14:24] DEBUG: Mean k-mer frequency: 1.05543 232 [2024-08-19 09:45:08] DEBUG: Building positional index
231 [2021-11-22 18:14:24] DEBUG: Repetitive k-mer frequency: 105 233 [2024-08-19 09:45:08] DEBUG: Total sequence: 452901 bp
232 [2021-11-22 18:14:24] DEBUG: Filtered 0 repetitive k-mers (0) 234 [2024-08-19 09:45:08] INFO: Building repeat graph
233 [2021-11-22 18:14:24] DEBUG: Sorting k-mer index 235 [2024-08-19 09:45:08] DEBUG: Mean k-mer frequency: 1.03014
234 [2021-11-22 18:14:24] DEBUG: Selected k-mers: 428642 236 [2024-08-19 09:45:08] DEBUG: Repetitive k-mer frequency: 103
235 [2021-11-22 18:14:24] DEBUG: K-mer index size: 452403 237 [2024-08-19 09:45:08] DEBUG: Filtered 0 repetitive k-mers (0)
236 [2021-11-22 18:14:24] DEBUG: Mean k-mer frequency: 1.05543 238 [2024-08-19 09:45:08] DEBUG: Sorting k-mer index
237 [2021-11-22 18:14:24] DEBUG: Minimizer rate: 1.00008 239 [2024-08-19 09:45:08] DEBUG: Selected k-mers: 439615
238 [2021-11-22 18:14:24] DEBUG: Computing transitive closure for overlaps 240 [2024-08-19 09:45:08] DEBUG: K-mer index size: 452867
239 [2021-11-22 18:14:24] DEBUG: Found 10 overlaps 241 [2024-08-19 09:45:08] DEBUG: Mean k-mer frequency: 1.03014
240 [2021-11-22 18:14:24] DEBUG: Left 4 overlaps after filtering 242 [2024-08-19 09:45:08] DEBUG: Minimizer rate: 1.00008
241 [2021-11-22 18:14:24] INFO: Median overlap divergence: 0.0343169 243 [2024-08-19 09:45:10] DEBUG: Computing transitive closure for overlaps
242 [2021-11-22 18:14:24] DEBUG: Sequence divergence distribution: 244 [2024-08-19 09:45:10] DEBUG: Found 10 overlaps
243 245 [2024-08-19 09:45:10] DEBUG: Left 4 overlaps after filtering
244 | * | 246 [2024-08-19 09:45:10] INFO: Median overlap divergence: 0.083035
245 | * | 247 [2024-08-19 09:45:10] DEBUG: Sequence divergence distribution:
246 | * | 248
247 | * | 249 | *
248 | * | 250 | *
249 | * | 251 | *
250 | * | 252 | *
251 | * | 253 | *
252 | * | 254 | *
253 | * | 255 | *
254 | * | 256 | *
255 | * | 257 | *
256 | * | 258 | *
257 | * | 259 | *
258 | * | 260 | *
259 | * | 261 | *
260 | * | 262 | *
261 | * | 263 | *
262 | * | 264 | *
263 | * | 265 | *
266 | *
267 | *
268 | *
264 ---------------------------------------------------------------------------------------------------- 269 ----------------------------------------------------------------------------------------------------
265 0% 5% 10% 15% 20% 25% 30% 35% 40% 45% 270 0% 5% 10% 15% 20% 25% 30% 35% 40% 45%
266 271
267 Q25 = 0.034, Q50 = 0.034, Q75 = 0.034 272 Q25 = 0.083, Q50 = 0.083, Q75 = 0.083
268 273
269 [2021-11-22 18:14:24] DEBUG: Computing gluepoints 274 [2024-08-19 09:45:10] DEBUG: Computing gluepoints
270 [2021-11-22 18:14:24] DEBUG: Added 0 gluepoint projections 275 [2024-08-19 09:45:10] DEBUG: Added 0 gluepoint projections
271 [2021-11-22 18:14:24] DEBUG: Created 12 gluepoints 276 [2024-08-19 09:45:10] DEBUG: Created 14 gluepoints
272 [2021-11-22 18:14:24] DEBUG: Artificial loops removed: 0 left, 0 right, 0 both 277 [2024-08-19 09:45:10] DEBUG: Artificial loops removed: 0 left, 0 right, 0 both
273 [2021-11-22 18:14:24] DEBUG: Initializing edges 278 [2024-08-19 09:45:10] DEBUG: Initializing edges
274 [2021-11-22 18:14:24] DEBUG: Edges length checksum: 2261029433 279 [2024-08-19 09:45:10] DEBUG: Edges length checksum: 2641675703
275 [2021-11-22 18:14:24] DEBUG: Filtered 0 singleton segments 280 [2024-08-19 09:45:10] DEBUG: Filtered 0 singleton segments
276 [2021-11-22 18:14:24] DEBUG: Removed 0 simple and 0 double chimeric junctions 281 [2024-08-19 09:45:10] DEBUG: Removed 0 simple and 0 double chimeric junctions
277 [2021-11-22 18:14:24] DEBUG: Collapsed 2 edges 282 [2024-08-19 09:45:10] DEBUG: Collapsed 1 edges
278 [2021-11-22 18:14:24] DEBUG: * 4 +disjointig_1 0 419576 419576 283 [2024-08-19 09:45:10] DEBUG: * 1 +disjointig_1 0 370783 370783
279 [2021-11-22 18:14:24] DEBUG: Total edges: 4 284 [2024-08-19 09:45:10] DEBUG: * 5 +disjointig_1 370783 419825 49042
280 [2021-11-22 18:14:24] INFO: Parsing reads 285 [2024-08-19 09:45:10] DEBUG: * -3 +disjointig_2 0 26527 26527
281 [2021-11-22 18:14:24] DEBUG: Building positional index 286 [2024-08-19 09:45:10] DEBUG: Total edges: 5
282 [2021-11-22 18:14:24] DEBUG: Total sequence: 7249289 bp 287 [2024-08-19 09:45:10] INFO: Parsing reads
283 [2021-11-22 18:14:24] DEBUG: Building positional index 288 [2024-08-19 09:45:10] DEBUG: Building positional index
284 [2021-11-22 18:14:24] DEBUG: Total sequence: 419576 bp 289 [2024-08-19 09:45:10] DEBUG: Total sequence: 7249289 bp
285 [2021-11-22 18:14:24] INFO: Aligning reads to the graph 290 [2024-08-19 09:45:10] DEBUG: Building positional index
286 [2021-11-22 18:14:24] DEBUG: Mean k-mer frequency: 1.00888 291 [2024-08-19 09:45:10] DEBUG: Total sequence: 446352 bp
287 [2021-11-22 18:14:24] DEBUG: Repetitive k-mer frequency: 100 292 [2024-08-19 09:45:10] INFO: Aligning reads to the graph
288 [2021-11-22 18:14:24] DEBUG: Filtered 0 repetitive k-mers (0) 293 [2024-08-19 09:45:10] DEBUG: Mean k-mer frequency: 1.02577
289 [2021-11-22 18:14:24] DEBUG: Sorting k-mer index 294 [2024-08-19 09:45:10] DEBUG: Repetitive k-mer frequency: 102
290 [2021-11-22 18:14:24] DEBUG: Selected k-mers: 415865 295 [2024-08-19 09:45:10] DEBUG: Filtered 0 repetitive k-mers (0)
291 [2021-11-22 18:14:24] DEBUG: K-mer index size: 419559 296 [2024-08-19 09:45:10] DEBUG: Sorting k-mer index
292 [2021-11-22 18:14:24] DEBUG: Mean k-mer frequency: 1.00888 297 [2024-08-19 09:45:10] DEBUG: Selected k-mers: 435087
293 [2021-11-22 18:14:24] DEBUG: Minimizer rate: 1.00004 298 [2024-08-19 09:45:10] DEBUG: K-mer index size: 446301
294 [2021-11-22 18:14:26] DEBUG: Total reads : 576 299 [2024-08-19 09:45:10] DEBUG: Mean k-mer frequency: 1.02577
295 [2021-11-22 18:14:26] DEBUG: Read with aligned parts : 566 300 [2024-08-19 09:45:10] DEBUG: Minimizer rate: 1.00011
296 [2021-11-22 18:14:26] DEBUG: Aligned in one piece : 566 301 [2024-08-19 09:45:11] DEBUG: Total reads : 576
297 [2021-11-22 18:14:26] INFO: Aligned read sequence: 6321188 / 6471580 (0.976761) 302 [2024-08-19 09:45:11] DEBUG: Read with aligned parts : 566
298 [2021-11-22 18:14:26] INFO: Median overlap divergence: 0.129819 303 [2024-08-19 09:45:11] DEBUG: Aligned in one piece : 566
299 [2021-11-22 18:14:26] DEBUG: Sequence divergence distribution: 304 [2024-08-19 09:45:11] INFO: Aligned read sequence: 6321543 / 6471580 (0.976816)
305 [2024-08-19 09:45:11] INFO: Median overlap divergence: 0.12965
306 [2024-08-19 09:45:11] DEBUG: Sequence divergence distribution:
300 307
301 | * | 308 | * |
302 | ** |
303 | ** | 309 | ** |
304 | *** | 310 | *** |
305 | *** | 311 | *** |
306 | *** | 312 | *** |
313 | *** * |
307 | ***** | 314 | ***** |
308 | ***** | 315 | ***** |
309 | ***** | 316 | ***** |
310 | ***** | 317 | ****** |
311 | ****** | 318 | ****** |
312 | ******* | 319 | ******* |
313 | ******* | 320 | ******* |
314 | ******** | 321 | ******** |
315 | ********* | 322 | ********* |
316 | ********* | 323 | ********* |
317 | ********** | 324 | ********** |
318 | ************ | 325 | ************ * |
319 | *************** | 326 | ************ * |
320 | **************** | 327 | * **************** |
321 ---------------------------------------------------------------------------------------------------- 328 ----------------------------------------------------------------------------------------------------
322 0% 5% 10% 15% 20% 25% 30% 35% 40% 45% 329 0% 5% 10% 15% 20% 25% 30% 35% 40% 45%
323 330
324 Q25 = 0.12, Q50 = 0.13, Q75 = 0.14 331 Q25 = 0.12, Q50 = 0.13, Q75 = 0.14
325 332
326 [2021-11-22 18:14:27] INFO: Mean edge coverage: 14 333 [2024-08-19 09:45:11] INFO: Mean edge coverage: 13
327 [2021-11-22 18:14:27] DEBUG: 4 len:419576 cov:14 mult:1 334 [2024-08-19 09:45:11] DEBUG: 1 len:370783 cov:15 mult:1.15385
328 [2021-11-22 18:14:27] DEBUG: -4 len:419576 cov:14 mult:1 335 [2024-08-19 09:45:11] DEBUG: -1 len:370783 cov:15 mult:1.15385
329 [2021-11-22 18:14:27] DEBUG: Unique coverage threshold 24 336 [2024-08-19 09:45:11] DEBUG: 3 len:26527 cov:7 mult:0.538462
330 [2021-11-22 18:14:27] INFO: Simplifying the graph 337 [2024-08-19 09:45:11] DEBUG: -3 len:26527 cov:7 mult:0.538462
331 [2021-11-22 18:14:27] DEBUG: Read coverage cutoff: 3 338 [2024-08-19 09:45:11] DEBUG: 5 len:49042 cov:12 mult:0.923077
332 [2021-11-22 18:14:27] DEBUG: [SIMPL] Removed 0 paths with low coverage 339 [2024-08-19 09:45:11] DEBUG: -5 len:49042 cov:12 mult:0.923077
333 [2021-11-22 18:14:27] DEBUG: [SIMPL] Masked 0 heterozygous loops 340 [2024-08-19 09:45:11] DEBUG: Unique coverage threshold 26
334 [2021-11-22 18:14:27] DEBUG: [SIMPL] Masked 0 simple bubbles 341 [2024-08-19 09:45:11] INFO: Simplifying the graph
335 [2021-11-22 18:14:27] DEBUG: Finding repeats 342 [2024-08-19 09:45:11] DEBUG: Read coverage cutoff: 3
336 [2021-11-22 18:14:27] DEBUG: Read coverage cutoff: 3 343 [2024-08-19 09:45:11] DEBUG: [SIMPL] Removed 0 paths with low coverage
337 [2021-11-22 18:14:27] DEBUG: Repeat detection iteration 1 344 [2024-08-19 09:45:11] DEBUG: [SIMPL] Masked 0 heterozygous loops
338 [2021-11-22 18:14:27] DEBUG: Writing Dot 345 [2024-08-19 09:45:11] DEBUG: [SIMPL] Masked 0 simple bubbles
339 [2021-11-22 18:14:27] DEBUG: Writing FASTA 346 [2024-08-19 09:45:11] DEBUG: Finding repeats
340 [2021-11-22 18:14:27] DEBUG: [SIMPL] == Iteration 1 == 347 [2024-08-19 09:45:11] DEBUG: Read coverage cutoff: 3
341 [2021-11-22 18:14:27] DEBUG: Splitting nodes 348 [2024-08-19 09:45:11] DEBUG: Repeat detection iteration 1
342 [2021-11-22 18:14:27] DEBUG: [SIMPL] Split 0 nodes 349 [2024-08-19 09:45:11] DEBUG: Starting -5 aln:7
343 [2021-11-22 18:14:27] DEBUG: [SIMPL] Clipped 0 short and 0 long tips 350 [2024-08-19 09:45:11] DEBUG: T -1 num:2 flank:9812 span:40
344 [2021-11-22 18:14:27] DEBUG: [SIMPL] Masked 0 heterozygous loops 351 [2024-08-19 09:45:11] DEBUG: T 3 num:5 flank:5809 span:11
345 [2021-11-22 18:14:27] DEBUG: [SIMPL] Masked 0 simple bubbles 352 [2024-08-19 09:45:11] DEBUG: Mult: 5 49042 12 (1,0)
346 [2021-11-22 18:14:27] DEBUG: Finding repeats 353 [2024-08-19 09:45:11] DEBUG: Writing Dot
347 [2021-11-22 18:14:27] DEBUG: Read coverage cutoff: 3 354 [2024-08-19 09:45:11] DEBUG: Writing FASTA
348 [2021-11-22 18:14:27] DEBUG: Repeat detection iteration 1 355 [2024-08-19 09:45:11] DEBUG: Writing Gfa
349 [2021-11-22 18:14:27] DEBUG: Total unique edges: 1 356 [2024-08-19 09:45:11] DEBUG: [SIMPL] == Iteration 1 ==
350 [2021-11-22 18:14:27] DEBUG: [SIMPL] Resolved repeats: 0 357 [2024-08-19 09:45:11] DEBUG: Splitting nodes
351 [2021-11-22 18:14:27] DEBUG: RR links: 0 358 [2024-08-19 09:45:11] DEBUG: [SIMPL] Split 0 nodes
352 [2021-11-22 18:14:27] DEBUG: Unresolved: 0 359 [2024-08-19 09:45:11] DEBUG: [SIMPL] Clipped 0 short and 0 long tips
353 [2021-11-22 18:14:27] DEBUG: Removed 0 simple and 0 double chimeric junctions 360 [2024-08-19 09:45:11] DEBUG: [SIMPL] Masked 0 heterozygous loops
354 [2021-11-22 18:14:27] DEBUG: [SIMPL] Collapsed 0 haplotypes 361 [2024-08-19 09:45:11] DEBUG: [SIMPL] Masked 0 simple bubbles
355 [2021-11-22 18:14:27] DEBUG: [SIMPL] Resolved 0 simple repeats 362 [2024-08-19 09:45:11] DEBUG: Finding repeats
356 [2021-11-22 18:14:27] DEBUG: Read coverage cutoff: 3 363 [2024-08-19 09:45:11] DEBUG: Read coverage cutoff: 3
357 [2021-11-22 18:14:27] DEBUG: [SIMPL] Removed 0 paths with low coverage 364 [2024-08-19 09:45:11] DEBUG: Repeat detection iteration 1
358 [2021-11-22 18:14:27] DEBUG: Finding repeats 365 [2024-08-19 09:45:11] DEBUG: Starting -5 aln:7
359 [2021-11-22 18:14:27] DEBUG: Read coverage cutoff: 3 366 [2024-08-19 09:45:11] DEBUG: T -1 num:2 flank:9812 span:40
360 [2021-11-22 18:14:27] DEBUG: Repeat detection iteration 1 367 [2024-08-19 09:45:11] DEBUG: T 3 num:5 flank:5809 span:11
361 [2021-11-22 18:14:27] DEBUG: Writing Dot 368 [2024-08-19 09:45:11] DEBUG: Mult: 5 49042 12 (1,0)
362 [2021-11-22 18:14:27] DEBUG: Writing FASTA 369 [2024-08-19 09:45:11] DEBUG: Total unique edges: 2
363 [2021-11-22 18:14:27] DEBUG: Peak RAM usage: 0 Gb 370 [2024-08-19 09:45:11] DEBUG: [SIMPL] Resolved repeats: 0
371 [2024-08-19 09:45:11] DEBUG: RR links: 0
372 [2024-08-19 09:45:11] DEBUG: Unresolved: 0
373 [2024-08-19 09:45:11] DEBUG: Removed 0 simple and 0 double chimeric junctions
374 [2024-08-19 09:45:11] DEBUG: [SIMPL] Collapsed 0 haplotypes
375 [2024-08-19 09:45:11] DEBUG: [SIMPL] Resolved 0 simple repeats
376 [2024-08-19 09:45:11] DEBUG: Read coverage cutoff: 3
377 [2024-08-19 09:45:11] DEBUG: [SIMPL] Removed 0 paths with low coverage
378 [2024-08-19 09:45:11] DEBUG: Finding repeats
379 [2024-08-19 09:45:11] DEBUG: Read coverage cutoff: 3
380 [2024-08-19 09:45:11] DEBUG: Repeat detection iteration 1
381 [2024-08-19 09:45:11] DEBUG: Starting -5 aln:7
382 [2024-08-19 09:45:11] DEBUG: T -1 num:2 flank:9812 span:40
383 [2024-08-19 09:45:11] DEBUG: T 3 num:5 flank:5809 span:11
384 [2024-08-19 09:45:11] DEBUG: Mult: 5 49042 12 (1,0)
385 [2024-08-19 09:45:11] DEBUG: Writing Dot
386 [2024-08-19 09:45:11] DEBUG: Writing FASTA
387 [2024-08-19 09:45:11] DEBUG: Peak RAM usage: 0 Gb
364 -----------End assembly log------------ 388 -----------End assembly log------------
365 [2021-11-22 18:14:27] root: INFO: >>>STAGE: contigger 389 [2024-08-19 09:45:11] root: INFO: >>>STAGE: contigger
366 [2021-11-22 18:14:27] root: INFO: Generating contigs 390 [2024-08-19 09:45:11] root: INFO: Generating contigs
367 [2021-11-22 18:14:27] root: DEBUG: -----Begin contigger analyser log------ 391 [2024-08-19 09:45:11] 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 392 [2024-08-19 09:45:11] root: DEBUG: Running: flye-modules contigger --graph-edges /tmp/tmpmmr8wbsp/job_working_directory/000/8/working/out_dir/20-repeat/repeat_graph_edges.fasta --reads /tmp/tmpmmr8wbsp/job_working_directory/000/8/working/input_0.fastq.gz,/tmp/tmpmmr8wbsp/job_working_directory/000/8/working/input_1.fastq.gz,/tmp/tmpmmr8wbsp/job_working_directory/000/8/working/input_2.fastq.gz,/tmp/tmpmmr8wbsp/job_working_directory/000/8/working/input_3.fastq.gz,/tmp/tmpmmr8wbsp/job_working_directory/000/8/working/input_4.fastq.gz,/tmp/tmpmmr8wbsp/job_working_directory/000/8/working/input_5.fastq.gz,/tmp/tmpmmr8wbsp/job_working_directory/000/8/working/input_6.fastq.gz --out-dir /tmp/tmpmmr8wbsp/job_working_directory/000/8/working/out_dir/30-contigger --config /usr/local/lib/python3.11/site-packages/flye/config/bin_cfg/asm_raw_reads.cfg --repeat-graph /tmp/tmpmmr8wbsp/job_working_directory/000/8/working/out_dir/20-repeat/repeat_graph_dump --graph-aln /tmp/tmpmmr8wbsp/job_working_directory/000/8/working/out_dir/20-repeat/read_alignment_dump --log /tmp/tmpmmr8wbsp/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 04:47:48 393 [2024-08-19 09:45:11] DEBUG: Build date: Jul 26 2024 16:37:08
370 [2021-11-22 18:14:27] DEBUG: Total RAM: 15 Gb 394 [2024-08-19 09:45:11] DEBUG: Total RAM: 31 Gb
371 [2021-11-22 18:14:27] DEBUG: Available RAM: 9 Gb 395 [2024-08-19 09:45:11] DEBUG: Available RAM: 21 Gb
372 [2021-11-22 18:14:27] DEBUG: Total CPUs: 8 396 [2024-08-19 09:45:11] DEBUG: Total CPUs: 12
373 [2021-11-22 18:14:27] DEBUG: Loading /usr/local/lib/python3.9/site-packages/flye/config/bin_cfg/asm_raw_reads.cfg 397 [2024-08-19 09:45:11] DEBUG: Loading /usr/local/lib/python3.11/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 398 [2024-08-19 09:45:11] DEBUG: Loading /usr/local/lib/python3.11/site-packages/flye/config/bin_cfg/asm_defaults.cfg
375 [2021-11-22 18:14:27] DEBUG: big_genome_threshold=29000000 399 [2024-08-19 09:45:11] DEBUG: big_genome_threshold=29000000
376 [2021-11-22 18:14:27] DEBUG: meta_read_filter_kmer_freq=100 400 [2024-08-19 09:45:11] DEBUG: meta_read_filter_kmer_freq=100
377 [2021-11-22 18:14:27] DEBUG: chain_large_gap_penalty=2 401 [2024-08-19 09:45:11] DEBUG: chain_large_gap_penalty=2
378 [2021-11-22 18:14:27] DEBUG: chain_small_gap_penalty=0.5 402 [2024-08-19 09:45:11] DEBUG: chain_small_gap_penalty=0.5
379 [2021-11-22 18:14:27] DEBUG: chain_gap_jump_threshold=100 403 [2024-08-19 09:45:11] DEBUG: chain_gap_jump_threshold=100
380 [2021-11-22 18:14:27] DEBUG: max_coverage_drop_rate=5 404 [2024-08-19 09:45:11] DEBUG: max_jump_gap=500
381 [2021-11-22 18:14:27] DEBUG: max_extensions_drop_rate=5 405 [2024-08-19 09:45:11] DEBUG: max_coverage_drop_rate=5
382 [2021-11-22 18:14:27] DEBUG: chimera_window=100 406 [2024-08-19 09:45:11] DEBUG: max_extensions_drop_rate=5
383 [2021-11-22 18:14:27] DEBUG: chimera_overhang=1000 407 [2024-08-19 09:45:11] DEBUG: chimera_window=100
384 [2021-11-22 18:14:27] DEBUG: min_reads_in_disjointig=4 408 [2024-08-19 09:45:11] DEBUG: chimera_overhang=1000
385 [2021-11-22 18:14:27] DEBUG: max_inner_reads=10 409 [2024-08-19 09:45:11] DEBUG: min_reads_in_disjointig=4
386 [2021-11-22 18:14:27] DEBUG: max_inner_fraction=0.25 410 [2024-08-19 09:45:11] DEBUG: max_inner_reads=10
387 [2021-11-22 18:14:27] DEBUG: max_separation=500 411 [2024-08-19 09:45:11] DEBUG: max_inner_fraction=0.25
388 [2021-11-22 18:14:27] DEBUG: unique_edge_length=50000 412 [2024-08-19 09:45:11] DEBUG: aggressive_dup_filter=1
389 [2021-11-22 18:14:27] DEBUG: min_repeat_res_support=0.51 413 [2024-08-19 09:45:11] DEBUG: max_separation=500
390 [2021-11-22 18:14:27] DEBUG: out_paths_ratio=5 414 [2024-08-19 09:45:11] DEBUG: unique_edge_length=50000
391 [2021-11-22 18:14:27] DEBUG: graph_cov_drop_rate=5 415 [2024-08-19 09:45:11] DEBUG: min_repeat_res_support=0.51
392 [2021-11-22 18:14:27] DEBUG: coverage_estimate_window=100 416 [2024-08-19 09:45:11] DEBUG: out_paths_ratio=5
393 [2021-11-22 18:14:27] DEBUG: max_bubble_length=50000 417 [2024-08-19 09:45:11] DEBUG: graph_cov_drop_rate=5
394 [2021-11-22 18:14:27] DEBUG: loop_coverage_rate=1.5 418 [2024-08-19 09:45:11] DEBUG: coverage_estimate_window=100
395 [2021-11-22 18:14:27] DEBUG: repeat_edge_cov_mult=1.75 419 [2024-08-19 09:45:11] DEBUG: max_bubble_length=50000
396 [2021-11-22 18:14:27] DEBUG: weak_detach_rate=5 420 [2024-08-19 09:45:11] DEBUG: loop_coverage_rate=1.5
397 [2021-11-22 18:14:27] DEBUG: tip_coverage_rate=2 421 [2024-08-19 09:45:11] DEBUG: repeat_edge_cov_mult=1.75
398 [2021-11-22 18:14:27] DEBUG: tip_length_rate=2 422 [2024-08-19 09:45:11] DEBUG: weak_detach_rate=5
399 [2021-11-22 18:14:27] DEBUG: output_gfa_before_rr=0 423 [2024-08-19 09:45:11] DEBUG: tip_coverage_rate=2
400 [2021-11-22 18:14:27] DEBUG: low_cutoff_warning=1 424 [2024-08-19 09:45:11] DEBUG: tip_length_rate=2
401 [2021-11-22 18:14:27] DEBUG: kmer_size=17 425 [2024-08-19 09:45:11] DEBUG: output_gfa_before_rr=1
402 [2021-11-22 18:14:27] DEBUG: use_minimizers=0 426 [2024-08-19 09:45:11] DEBUG: remove_alt_edges=0
403 [2021-11-22 18:14:27] DEBUG: reads_base_alignment=0 427 [2024-08-19 09:45:11] DEBUG: low_cutoff_warning=1
404 [2021-11-22 18:14:27] DEBUG: meta_read_top_kmer_rate=0.40 428 [2024-08-19 09:45:11] DEBUG: kmer_size=17
405 [2021-11-22 18:14:27] DEBUG: maximum_jump=1500 429 [2024-08-19 09:45:11] DEBUG: use_minimizers=0
406 [2021-11-22 18:14:27] DEBUG: maximum_overhang=1500 430 [2024-08-19 09:45:11] DEBUG: reads_base_alignment=0
407 [2021-11-22 18:14:27] DEBUG: repeat_kmer_rate=100 431 [2024-08-19 09:45:11] DEBUG: meta_read_top_kmer_rate=0.40
408 [2021-11-22 18:14:27] DEBUG: assemble_ovlp_divergence=0.10 432 [2024-08-19 09:45:11] DEBUG: maximum_jump=1500
409 [2021-11-22 18:14:27] DEBUG: assemble_divergence_relative=1 433 [2024-08-19 09:45:11] DEBUG: maximum_overhang=1500
410 [2021-11-22 18:14:27] DEBUG: repeat_graph_ovlp_divergence=0.08 434 [2024-08-19 09:45:11] DEBUG: repeat_kmer_rate=100
411 [2021-11-22 18:14:27] DEBUG: read_align_ovlp_divergence=0.25 435 [2024-08-19 09:45:11] DEBUG: assemble_ovlp_divergence=0.10
412 [2021-11-22 18:14:27] DEBUG: hpc_scoring_on=0 436 [2024-08-19 09:45:11] DEBUG: assemble_divergence_relative=1
413 [2021-11-22 18:14:27] DEBUG: add_unassembled_reads=0 437 [2024-08-19 09:45:11] DEBUG: repeat_graph_ovlp_divergence=0.08
414 [2021-11-22 18:14:27] DEBUG: extend_contigs_with_repeats=0 438 [2024-08-19 09:45:11] DEBUG: read_align_ovlp_divergence=0.25
415 [2021-11-22 18:14:27] DEBUG: min_read_cov_cutoff=3 439 [2024-08-19 09:45:11] DEBUG: hpc_scoring_on=0
416 [2021-11-22 18:14:27] DEBUG: short_tip_length=20000 440 [2024-08-19 09:45:11] DEBUG: add_unassembled_reads=0
417 [2021-11-22 18:14:27] DEBUG: long_tip_length=100000 441 [2024-08-19 09:45:11] DEBUG: extend_contigs_with_repeats=0
418 [2021-11-22 18:14:27] DEBUG: Running with k-mer size: 17 442 [2024-08-19 09:45:11] DEBUG: min_read_cov_cutoff=3
419 [2021-11-22 18:14:27] DEBUG: Selected minimum overlap 6000 443 [2024-08-19 09:45:11] DEBUG: short_tip_length=20000
420 [2021-11-22 18:14:27] INFO: Reading sequences 444 [2024-08-19 09:45:11] DEBUG: long_tip_length=100000
421 [2021-11-22 18:14:27] DEBUG: Building positional index 445 [2024-08-19 09:45:11] DEBUG: Running with k-mer size: 17
422 [2021-11-22 18:14:27] DEBUG: Total sequence: 7249289 bp 446 [2024-08-19 09:45:11] DEBUG: Selected minimum overlap 6000
423 [2021-11-22 18:14:27] DEBUG: Flipped 0 447 [2024-08-19 09:45:11] INFO: Reading sequences
424 [2021-11-22 18:14:27] DEBUG: UPath 1: 4 448 [2024-08-19 09:45:11] DEBUG: Building positional index
425 [2021-11-22 18:14:27] DEBUG: Final graph contains 1 egdes 449 [2024-08-19 09:45:11] DEBUG: Total sequence: 7249289 bp
426 [2021-11-22 18:14:27] DEBUG: Extending contigs into repeats 450 [2024-08-19 09:45:11] DEBUG: Flipped 0
427 [2021-11-22 18:14:27] DEBUG: Covered 0 repetitive contigs 451 [2024-08-19 09:45:11] DEBUG: UPath 1: 1
428 [2021-11-22 18:14:27] INFO: Generated 1 contigs 452 [2024-08-19 09:45:11] DEBUG: UPath 2: 3
429 [2021-11-22 18:14:27] DEBUG: Writing FASTA 453 [2024-08-19 09:45:11] DEBUG: UPath 3: 5
430 [2021-11-22 18:14:27] DEBUG: Generating scaffold connections 454 [2024-08-19 09:45:11] DEBUG: Final graph contains 3 egdes
431 [2021-11-22 18:14:27] INFO: Added 0 scaffold connections 455 [2024-08-19 09:45:11] DEBUG: Extending contigs into repeats
432 [2021-11-22 18:14:27] DEBUG: Writing Dot 456 [2024-08-19 09:45:11] DEBUG: Covered 0 repetitive contigs
433 [2021-11-22 18:14:27] DEBUG: Writing FASTA 457 [2024-08-19 09:45:11] INFO: Generated 3 contigs
434 [2021-11-22 18:14:27] DEBUG: Writing Gfa 458 [2024-08-19 09:45:11] DEBUG: Writing FASTA
435 [2021-11-22 18:14:27] DEBUG: Peak RAM usage: 0 Gb 459 [2024-08-19 09:45:11] DEBUG: Generating scaffold connections
460 [2024-08-19 09:45:11] INFO: Added 0 scaffold connections
461 [2024-08-19 09:45:11] DEBUG: Writing Dot
462 [2024-08-19 09:45:11] DEBUG: Writing FASTA
463 [2024-08-19 09:45:11] DEBUG: Writing Gfa
464 [2024-08-19 09:45:11] DEBUG: Peak RAM usage: 0 Gb
436 -----------End assembly log------------ 465 -----------End assembly log------------
437 [2021-11-22 18:14:27] root: INFO: >>>STAGE: finalize 466 [2024-08-19 09:45:11] root: INFO: >>>STAGE: finalize
438 [2021-11-22 18:14:27] root: DEBUG: ---Output dir contents:---- 467 [2024-08-19 09:45:11] root: DEBUG: ---Output dir contents:----
439 [2021-11-22 18:14:27] root: DEBUG: out_dir/ 468 [2024-08-19 09:45:11] root: DEBUG: out_dir/
440 [2021-11-22 18:14:27] root: DEBUG: 367.0 B assembly_graph.gv 469 [2024-08-19 09:45:11] root: DEBUG: 705.0 B assembly_graph.gv
441 [2021-11-22 18:14:27] root: DEBUG: 416.0 K assembly.fasta 470 [2024-08-19 09:45:11] root: DEBUG: 464.0 K assembly.fasta
442 [2021-11-22 18:14:27] root: DEBUG: 92.0 B params.json 471 [2024-08-19 09:45:11] root: DEBUG: 92.0 B params.json
443 [2021-11-22 18:14:27] root: DEBUG: 28.0 K flye.log 472 [2024-08-19 09:45:11] root: DEBUG: 30.0 K flye.log
444 [2021-11-22 18:14:27] root: DEBUG: 409.0 K assembly_graph.gfa 473 [2024-08-19 09:45:11] root: DEBUG: 436.0 K assembly_graph.gfa
445 [2021-11-22 18:14:27] root: DEBUG: 10-consensus/ 474 [2024-08-19 09:45:11] root: DEBUG: 30-contigger/
446 [2021-11-22 18:14:27] root: DEBUG: 1.0 K minimap.stderr 475 [2024-08-19 09:45:11] root: DEBUG: 462.0 K contigs.fasta
447 [2021-11-22 18:14:27] root: DEBUG: 449.0 K consensus.fasta 476 [2024-08-19 09:45:11] root: DEBUG: 441.0 K graph_final.fasta
448 [2021-11-22 18:14:27] root: DEBUG: 3.0 K minimap.bam.bai 477 [2024-08-19 09:45:11] root: DEBUG: 182.0 B contigs_stats.txt
449 [2021-11-22 18:14:27] root: DEBUG: 30-contigger/ 478 [2024-08-19 09:45:11] root: DEBUG: 436.0 K graph_final.gfa
450 [2021-11-22 18:14:27] root: DEBUG: 409.0 K graph_final.gfa 479 [2024-08-19 09:45:11] root: DEBUG: 0.0 B scaffolds_links.txt
451 [2021-11-22 18:14:27] root: DEBUG: 0.0 B scaffolds_links.txt 480 [2024-08-19 09:45:11] root: DEBUG: 705.0 B graph_final.gv
452 [2021-11-22 18:14:27] root: DEBUG: 111.0 B contigs_stats.txt 481 [2024-08-19 09:45:11] root: DEBUG: 20-repeat/
453 [2021-11-22 18:14:27] root: DEBUG: 367.0 B graph_final.gv 482 [2024-08-19 09:45:11] root: DEBUG: 705.0 B graph_after_rr.gv
454 [2021-11-22 18:14:27] root: DEBUG: 414.0 K graph_final.fasta 483 [2024-08-19 09:45:11] root: DEBUG: 441.0 K repeat_graph_edges.fasta
455 [2021-11-22 18:14:27] root: DEBUG: 414.0 K contigs.fasta 484 [2024-08-19 09:45:11] root: DEBUG: 441.0 K graph_before_rr.fasta
456 [2021-11-22 18:14:27] root: DEBUG: 00-assembly/ 485 [2024-08-19 09:45:11] root: DEBUG: 705.0 B graph_before_rr.gv
457 [2021-11-22 18:14:27] root: DEBUG: 61.0 B draft_assembly.fasta.fai 486 [2024-08-19 09:45:11] root: DEBUG: 436.0 K graph_before_rr.gfa
458 [2021-11-22 18:14:27] root: DEBUG: 465.0 K draft_assembly.fasta 487 [2024-08-19 09:45:11] root: DEBUG: 564.0 B repeat_graph_dump
459 [2021-11-22 18:14:27] root: DEBUG: 20-repeat/ 488 [2024-08-19 09:45:11] root: DEBUG: 121.0 K read_alignment_dump
460 [2021-11-22 18:14:27] root: DEBUG: 414.0 K graph_before_rr.fasta 489 [2024-08-19 09:45:11] root: DEBUG: 10-consensus/
461 [2021-11-22 18:14:27] root: DEBUG: 183.0 B repeat_graph_dump 490 [2024-08-19 09:45:11] root: DEBUG: 449.0 K consensus.fasta
462 [2021-11-22 18:14:27] root: DEBUG: 367.0 B graph_before_rr.gv 491 [2024-08-19 09:45:11] root: DEBUG: 3.0 K minimap.bam.bai
463 [2021-11-22 18:14:27] root: DEBUG: 367.0 B graph_after_rr.gv 492 [2024-08-19 09:45:11] root: DEBUG: 1.0 K minimap.stderr
464 [2021-11-22 18:14:27] root: DEBUG: 414.0 K repeat_graph_edges.fasta 493 [2024-08-19 09:45:11] root: DEBUG: 00-assembly/
465 [2021-11-22 18:14:27] root: DEBUG: 119.0 K read_alignment_dump 494 [2024-08-19 09:45:11] root: DEBUG: 465.0 K draft_assembly.fasta
466 [2021-11-22 18:14:27] root: DEBUG: -------------------------- 495 [2024-08-19 09:45:11] root: DEBUG: 61.0 B draft_assembly.fasta.fai
467 [2021-11-22 18:14:27] root: INFO: Assembly statistics: 496 [2024-08-19 09:45:11] root: DEBUG: --------------------------
468 497 [2024-08-19 09:45:11] root: INFO: Assembly statistics:
469 Total length: 419576 498
470 Fragments: 1 499 Total length: 467534
471 Fragments N50: 419576 500 Fragments: 3
472 Largest frg: 419576 501 Fragments N50: 382469
502 Largest frg: 382469
473 Scaffolds: 0 503 Scaffolds: 0
474 Mean coverage: 14 504 Mean coverage: 14
475 505
476 [2021-11-22 18:14:27] root: INFO: Final assembly: /tmp/tmpakmcmxzn/job_working_directory/000/8/working/out_dir/assembly.fasta 506 [2024-08-19 09:45:11] root: INFO: Final assembly: /tmp/tmpmmr8wbsp/job_working_directory/000/8/working/out_dir/assembly.fasta