Mercurial > repos > bgruening > flye
comparison test-data/result1.log @ 12:3e4f8642c77e draft default tip
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
author | bgruening |
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date | Mon, 26 Aug 2024 13:54:31 +0000 |
parents | 276f5d8712d5 |
children |
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11:291923e6f276 | 12:3e4f8642c77e |
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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 |