Mercurial > repos > bgruening > flye
comparison test-data/result1.log @ 9:276f5d8712d5 draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
author | bgruening |
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date | Tue, 23 Nov 2021 08:35:32 +0000 |
parents | e27815e82dd4 |
children | 3e4f8642c77e |
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8:e27815e82dd4 | 9:276f5d8712d5 |
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1 [2021-06-30 16:00:39] root: INFO: Starting Flye 2.8.3-b1695 | 1 [2021-11-22 18:13:09] root: INFO: Starting Flye 2.9-b1768 |
2 [2021-06-30 16:00:39] root: DEBUG: Cmd: /usr/local/bin/flye --pacbio-raw ./input_0.fastq.gz ./input_1.fastq.gz ./input_2.fastq.gz ./input_3.fastq.gz ./input_4.fastq.gz ./input_5.fastq.gz ./input_6.fastq.gz -o out_dir -t 1 -i 0 | 2 [2021-11-22 18:13:09] root: DEBUG: Cmd: /usr/local/bin/flye --pacbio-raw ./input_0.fastq.gz ./input_1.fastq.gz ./input_2.fastq.gz ./input_3.fastq.gz ./input_4.fastq.gz ./input_5.fastq.gz ./input_6.fastq.gz -o out_dir -t 1 -i 0 |
3 [2021-06-30 16:00:39] root: DEBUG: Python version: 3.9.2 | packaged by conda-forge | (default, Feb 21 2021, 05:02:46) | 3 [2021-11-22 18:13:09] root: DEBUG: Python version: 3.9.6 | packaged by conda-forge | (default, Jul 11 2021, 03:39:48) |
4 [GCC 9.3.0] | 4 [GCC 9.3.0] |
5 [2021-06-30 16:00:39] root: INFO: >>>STAGE: configure | 5 [2021-11-22 18:13:09] root: INFO: >>>STAGE: configure |
6 [2021-06-30 16:00:39] root: INFO: Configuring run | 6 [2021-11-22 18:13:09] root: INFO: Configuring run |
7 [2021-06-30 16:00:39] root: INFO: Total read length: 7249289 | 7 [2021-11-22 18:13:10] root: INFO: Total read length: 7249289 |
8 [2021-06-30 16:00:39] root: INFO: Reads N50/N90: 11150 / 5790 | 8 [2021-11-22 18:13:10] root: INFO: Reads N50/N90: 11150 / 5790 |
9 [2021-06-30 16:00:39] root: INFO: Minimum overlap set to 5000 | 9 [2021-11-22 18:13:10] root: INFO: Minimum overlap set to 6000 |
10 [2021-06-30 16:00:39] root: INFO: >>>STAGE: assembly | 10 [2021-11-22 18:13:10] root: INFO: >>>STAGE: assembly |
11 [2021-06-30 16:00:39] root: INFO: Assembling disjointigs | 11 [2021-11-22 18:13:10] root: INFO: Assembling disjointigs |
12 [2021-06-30 16:00:39] root: DEBUG: -----Begin assembly log------ | 12 [2021-11-22 18:13:10] root: DEBUG: -----Begin assembly log------ |
13 [2021-06-30 16:00:39] root: DEBUG: Running: flye-modules assemble --reads ./input_0.fastq.gz,./input_1.fastq.gz,./input_2.fastq.gz,./input_3.fastq.gz,./input_4.fastq.gz,./input_5.fastq.gz,./input_6.fastq.gz --out-asm /tmp/tmpicy_msib/job_working_directory/000/8/working/out_dir/00-assembly/draft_assembly.fasta --config /usr/local/lib/python3.9/site-packages/flye/config/bin_cfg/asm_raw_reads.cfg --log /tmp/tmpicy_msib/job_working_directory/000/8/working/out_dir/flye.log --threads 1 --min-ovlp 5000 | 13 [2021-11-22 18:13:10] root: DEBUG: Running: flye-modules assemble --reads /tmp/tmpakmcmxzn/job_working_directory/000/8/working/input_0.fastq.gz,/tmp/tmpakmcmxzn/job_working_directory/000/8/working/input_1.fastq.gz,/tmp/tmpakmcmxzn/job_working_directory/000/8/working/input_2.fastq.gz,/tmp/tmpakmcmxzn/job_working_directory/000/8/working/input_3.fastq.gz,/tmp/tmpakmcmxzn/job_working_directory/000/8/working/input_4.fastq.gz,/tmp/tmpakmcmxzn/job_working_directory/000/8/working/input_5.fastq.gz,/tmp/tmpakmcmxzn/job_working_directory/000/8/working/input_6.fastq.gz --out-asm /tmp/tmpakmcmxzn/job_working_directory/000/8/working/out_dir/00-assembly/draft_assembly.fasta --config /usr/local/lib/python3.9/site-packages/flye/config/bin_cfg/asm_raw_reads.cfg --log /tmp/tmpakmcmxzn/job_working_directory/000/8/working/out_dir/flye.log --threads 1 --min-ovlp 6000 |
14 [2021-06-30 16:00:39] DEBUG: Build date: Mar 27 2021 19:08:40 | 14 [2021-11-22 18:13:10] DEBUG: Build date: Aug 22 2021 04:46:17 |
15 [2021-06-30 16:00:39] DEBUG: Total RAM: 15 Gb | 15 [2021-11-22 18:13:10] DEBUG: Total RAM: 15 Gb |
16 [2021-06-30 16:00:39] DEBUG: Available RAM: 11 Gb | 16 [2021-11-22 18:13:10] DEBUG: Available RAM: 9 Gb |
17 [2021-06-30 16:00:39] DEBUG: Total CPUs: 8 | 17 [2021-11-22 18:13:10] DEBUG: Total CPUs: 8 |
18 [2021-06-30 16:00:39] DEBUG: Loading /usr/local/lib/python3.9/site-packages/flye/config/bin_cfg/asm_raw_reads.cfg | 18 [2021-11-22 18:13:10] DEBUG: Loading /usr/local/lib/python3.9/site-packages/flye/config/bin_cfg/asm_raw_reads.cfg |
19 [2021-06-30 16:00:39] DEBUG: Loading /usr/local/lib/python3.9/site-packages/flye/config/bin_cfg/asm_defaults.cfg | 19 [2021-11-22 18:13:10] DEBUG: Loading /usr/local/lib/python3.9/site-packages/flye/config/bin_cfg/asm_defaults.cfg |
20 [2021-06-30 16:00:39] DEBUG: big_genome_threshold=29000000 | 20 [2021-11-22 18:13:10] DEBUG: big_genome_threshold=29000000 |
21 [2021-06-30 16:00:39] DEBUG: meta_read_filter_kmer_freq=100 | 21 [2021-11-22 18:13:10] DEBUG: meta_read_filter_kmer_freq=100 |
22 [2021-06-30 16:00:39] DEBUG: max_coverage_drop_rate=5 | 22 [2021-11-22 18:13:10] DEBUG: chain_large_gap_penalty=2 |
23 [2021-06-30 16:00:39] DEBUG: max_extensions_drop_rate=5 | 23 [2021-11-22 18:13:10] DEBUG: chain_small_gap_penalty=0.5 |
24 [2021-06-30 16:00:39] DEBUG: chimera_window=100 | 24 [2021-11-22 18:13:10] DEBUG: chain_gap_jump_threshold=100 |
25 [2021-06-30 16:00:39] DEBUG: min_reads_in_disjointig=4 | 25 [2021-11-22 18:13:10] DEBUG: max_coverage_drop_rate=5 |
26 [2021-06-30 16:00:39] DEBUG: max_inner_reads=10 | 26 [2021-11-22 18:13:10] DEBUG: max_extensions_drop_rate=5 |
27 [2021-06-30 16:00:39] DEBUG: max_inner_fraction=0.25 | 27 [2021-11-22 18:13:10] DEBUG: chimera_window=100 |
28 [2021-06-30 16:00:39] DEBUG: max_separation=500 | 28 [2021-11-22 18:13:10] DEBUG: chimera_overhang=1000 |
29 [2021-06-30 16:00:39] DEBUG: unique_edge_length=50000 | 29 [2021-11-22 18:13:10] DEBUG: min_reads_in_disjointig=4 |
30 [2021-06-30 16:00:39] DEBUG: min_repeat_res_support=0.51 | 30 [2021-11-22 18:13:10] DEBUG: max_inner_reads=10 |
31 [2021-06-30 16:00:39] DEBUG: out_paths_ratio=5 | 31 [2021-11-22 18:13:10] DEBUG: max_inner_fraction=0.25 |
32 [2021-06-30 16:00:39] DEBUG: graph_cov_drop_rate=5 | 32 [2021-11-22 18:13:10] DEBUG: max_separation=500 |
33 [2021-06-30 16:00:39] DEBUG: coverage_estimate_window=100 | 33 [2021-11-22 18:13:10] DEBUG: unique_edge_length=50000 |
34 [2021-06-30 16:00:39] DEBUG: max_bubble_length=50000 | 34 [2021-11-22 18:13:10] DEBUG: min_repeat_res_support=0.51 |
35 [2021-06-30 16:00:39] DEBUG: loop_coverage_rate=1.5 | 35 [2021-11-22 18:13:10] DEBUG: out_paths_ratio=5 |
36 [2021-06-30 16:00:39] DEBUG: repeat_edge_cov_mult=1.75 | 36 [2021-11-22 18:13:10] DEBUG: graph_cov_drop_rate=5 |
37 [2021-06-30 16:00:39] DEBUG: weak_detach_rate=5 | 37 [2021-11-22 18:13:10] DEBUG: coverage_estimate_window=100 |
38 [2021-06-30 16:00:39] DEBUG: tip_coverage_rate=2 | 38 [2021-11-22 18:13:10] DEBUG: max_bubble_length=50000 |
39 [2021-06-30 16:00:39] DEBUG: tip_length_rate=2 | 39 [2021-11-22 18:13:10] DEBUG: loop_coverage_rate=1.5 |
40 [2021-06-30 16:00:39] DEBUG: low_cutoff_warning=1 | 40 [2021-11-22 18:13:10] DEBUG: repeat_edge_cov_mult=1.75 |
41 [2021-06-30 16:00:39] DEBUG: hard_min_coverage_rate=10 | 41 [2021-11-22 18:13:10] DEBUG: weak_detach_rate=5 |
42 [2021-06-30 16:00:39] DEBUG: kmer_size=17 | 42 [2021-11-22 18:13:10] DEBUG: tip_coverage_rate=2 |
43 [2021-06-30 16:00:39] DEBUG: use_minimizers=0 | 43 [2021-11-22 18:13:10] DEBUG: tip_length_rate=2 |
44 [2021-06-30 16:00:39] DEBUG: reads_base_alignment=0 | 44 [2021-11-22 18:13:10] DEBUG: output_gfa_before_rr=0 |
45 [2021-06-30 16:00:39] DEBUG: assemble_kmer_sample=1 | 45 [2021-11-22 18:13:10] DEBUG: low_cutoff_warning=1 |
46 [2021-06-30 16:00:39] DEBUG: repeat_graph_kmer_sample=1 | 46 [2021-11-22 18:13:10] DEBUG: kmer_size=17 |
47 [2021-06-30 16:00:39] DEBUG: read_align_kmer_sample=1 | 47 [2021-11-22 18:13:10] DEBUG: use_minimizers=0 |
48 [2021-06-30 16:00:39] DEBUG: meta_read_top_kmer_rate=0.40 | 48 [2021-11-22 18:13:10] DEBUG: reads_base_alignment=0 |
49 [2021-06-30 16:00:39] DEBUG: maximum_jump=1500 | 49 [2021-11-22 18:13:10] DEBUG: meta_read_top_kmer_rate=0.40 |
50 [2021-06-30 16:00:39] DEBUG: maximum_overhang=1500 | 50 [2021-11-22 18:13:10] DEBUG: maximum_jump=1500 |
51 [2021-06-30 16:00:39] DEBUG: repeat_kmer_rate=100 | 51 [2021-11-22 18:13:10] DEBUG: maximum_overhang=1500 |
52 [2021-06-30 16:00:39] DEBUG: assemble_ovlp_divergence=0.10 | 52 [2021-11-22 18:13:10] DEBUG: repeat_kmer_rate=100 |
53 [2021-06-30 16:00:39] DEBUG: assemble_divergence_relative=1 | 53 [2021-11-22 18:13:10] DEBUG: assemble_ovlp_divergence=0.10 |
54 [2021-06-30 16:00:39] DEBUG: repeat_graph_ovlp_divergence=0.08 | 54 [2021-11-22 18:13:10] DEBUG: assemble_divergence_relative=1 |
55 [2021-06-30 16:00:39] DEBUG: read_align_ovlp_divergence=0.25 | 55 [2021-11-22 18:13:10] DEBUG: repeat_graph_ovlp_divergence=0.08 |
56 [2021-06-30 16:00:39] DEBUG: hpc_scoring_on=0 | 56 [2021-11-22 18:13:10] DEBUG: read_align_ovlp_divergence=0.25 |
57 [2021-06-30 16:00:39] DEBUG: add_unassembled_reads=0 | 57 [2021-11-22 18:13:10] DEBUG: hpc_scoring_on=0 |
58 [2021-06-30 16:00:39] DEBUG: extend_contigs_with_repeats=0 | 58 [2021-11-22 18:13:10] DEBUG: add_unassembled_reads=0 |
59 [2021-06-30 16:00:39] DEBUG: min_read_cov_cutoff=3 | 59 [2021-11-22 18:13:10] DEBUG: extend_contigs_with_repeats=0 |
60 [2021-06-30 16:00:39] DEBUG: short_tip_length=20000 | 60 [2021-11-22 18:13:10] DEBUG: min_read_cov_cutoff=3 |
61 [2021-06-30 16:00:39] DEBUG: long_tip_length=100000 | 61 [2021-11-22 18:13:10] DEBUG: short_tip_length=20000 |
62 [2021-06-30 16:00:39] DEBUG: Running with k-mer size: 17 | 62 [2021-11-22 18:13:10] DEBUG: long_tip_length=100000 |
63 [2021-06-30 16:00:39] DEBUG: Running with minimum overlap 5000 | 63 [2021-11-22 18:13:10] DEBUG: Running with k-mer size: 17 |
64 [2021-06-30 16:00:39] DEBUG: Metagenome mode: N | 64 [2021-11-22 18:13:10] DEBUG: Running with minimum overlap 6000 |
65 [2021-06-30 16:00:39] INFO: Reading sequences | 65 [2021-11-22 18:13:10] DEBUG: Metagenome mode: N |
66 [2021-06-30 16:00:39] DEBUG: Building positional index | 66 [2021-11-22 18:13:10] DEBUG: Short mode: N |
67 [2021-06-30 16:00:39] DEBUG: Total sequence: 6702247 bp | 67 [2021-11-22 18:13:10] INFO: Reading sequences |
68 [2021-06-30 16:00:42] INFO: Counting k-mers: | 68 [2021-11-22 18:13:10] DEBUG: Building positional index |
69 [2021-06-30 16:00:42] DEBUG: Updating k-mer histogram | 69 [2021-11-22 18:13:10] DEBUG: Total sequence: 6471580 bp |
70 [2021-06-30 16:01:29] DEBUG: Hash size: 32 | 70 [2021-11-22 18:13:12] INFO: Counting k-mers: |
71 [2021-06-30 16:01:29] DEBUG: Total k-mers 6159182 | 71 [2021-11-22 18:13:13] DEBUG: Updating k-mer histogram |
72 [2021-06-30 16:01:29] INFO: Filling index table (1/2) | 72 [2021-11-22 18:13:56] DEBUG: Hash size: 29 |
73 [2021-06-30 16:01:32] DEBUG: Mean k-mer frequency: 2.59564 | 73 [2021-11-22 18:13:56] DEBUG: Total k-mers 5958598 |
74 [2021-06-30 16:01:32] DEBUG: Repetitive k-mer frequency: 259 | 74 [2021-11-22 18:13:56] INFO: Filling index table (1/2) |
75 [2021-06-30 16:01:32] DEBUG: Filtered 0 repetitive k-mers (0) | 75 [2021-11-22 18:13:59] DEBUG: Mean k-mer frequency: 2.57396 |
76 [2021-06-30 16:01:32] INFO: Filling index table (2/2) | 76 [2021-11-22 18:13:59] DEBUG: Repetitive k-mer frequency: 257 |
77 [2021-06-30 16:01:35] DEBUG: Sorting k-mer index | 77 [2021-11-22 18:13:59] DEBUG: Filtered 0 repetitive k-mers (0) |
78 [2021-06-30 16:01:35] DEBUG: Selected k-mers: 333758 | 78 [2021-11-22 18:13:59] INFO: Filling index table (2/2) |
79 [2021-06-30 16:01:35] DEBUG: Index size: 866317 | 79 [2021-11-22 18:14:01] DEBUG: Sorting k-mer index |
80 [2021-06-30 16:01:35] DEBUG: Mean k-mer index frequency: 2.59564 | 80 [2021-11-22 18:14:01] DEBUG: Selected k-mers: 319695 |
81 [2021-06-30 16:01:35] DEBUG: Peak RAM usage: 8 Gb | 81 [2021-11-22 18:14:01] DEBUG: Index size: 822885 |
82 [2021-06-30 16:01:35] DEBUG: Estimating k-mer identity bias | 82 [2021-11-22 18:14:01] DEBUG: Mean k-mer index frequency: 2.57397 |
83 [2021-06-30 16:01:39] DEBUG: Initial divergence estimate : 0.235584 | 83 [2021-11-22 18:14:01] DEBUG: Peak RAM usage: 8 Gb |
84 [2021-06-30 16:01:39] DEBUG: Relative threshold: Y | 84 [2021-11-22 18:14:01] DEBUG: Estimating k-mer identity bias |
85 [2021-06-30 16:01:39] DEBUG: Max divergence threshold set to 0.335584 | 85 [2021-11-22 18:14:05] DEBUG: Initial divergence estimate : 0.237684 |
86 [2021-06-30 16:01:39] INFO: Extending reads | 86 [2021-11-22 18:14:05] DEBUG: Relative threshold: Y |
87 [2021-06-30 16:01:39] DEBUG: Estimating overlap coverage | 87 [2021-11-22 18:14:05] DEBUG: Max divergence threshold set to 0.337684 |
88 [2021-06-30 16:01:42] INFO: Overlap-based coverage: 11 | 88 [2021-11-22 18:14:05] INFO: Extending reads |
89 [2021-06-30 16:01:42] INFO: Median overlap divergence: 0.235584 | 89 [2021-11-22 18:14:05] DEBUG: Estimating overlap coverage |
90 [2021-06-30 16:01:42] DEBUG: Sequence divergence distribution: | 90 [2021-11-22 18:14:07] INFO: Overlap-based coverage: 10 |
91 [2021-11-22 18:14:07] INFO: Median overlap divergence: 0.235584 | |
92 [2021-11-22 18:14:07] DEBUG: Sequence divergence distribution: | |
91 | 93 |
92 | * | | 94 | * | |
93 | * | | 95 | * | |
94 | * *** | | 96 | *** | |
95 | * *** | | 97 | * *** | |
96 | ****** | | 98 | ****** | |
97 | ******* | | 99 | ******* | |
98 | ******* | | 100 | ******* | |
99 | ******** | | 101 | ******** | |
101 | ********* | | 103 | ********* | |
102 | ********* | | 104 | ********* | |
103 | ********* | | 105 | ********* | |
104 | ********** | | 106 | ********** | |
105 | ************ | | 107 | ************ | |
106 | ************* | | 108 | ************ | |
107 | ************** | | 109 | ************** | |
108 | ************** | | 110 | ************** | |
109 | **************** | | 111 | **************** | |
110 | * ***************** * | | 112 | * ***************** * | |
111 | * ** ************************ | * * | 113 | * ** ************************ | * * |
112 ---------------------------------------------------------------------------------------------------- | 114 ---------------------------------------------------------------------------------------------------- |
113 0% 5% 10% 15% 20% 25% 30% 35% 40% 45% | 115 0% 5% 10% 15% 20% 25% 30% 35% 40% 45% |
114 | 116 |
115 Q25 = 0.22, Q50 = 0.24, Q75 = 0.25 | 117 Q25 = 0.22, Q50 = 0.24, Q75 = 0.25 |
116 | 118 |
117 [2021-06-30 16:01:42] DEBUG: Assembled disjointig 1 | 119 [2021-11-22 18:14:08] DEBUG: Assembled disjointig 1 |
118 With 86 reads | 120 With 83 reads |
119 Start read: +S1_371 | 121 Start read: +S1_395 |
120 At position: 35 | 122 At position: 40 |
121 leftTip: 1 rightTip: 1 | 123 leftTip: 1 rightTip: 1 |
122 Suspicious: 3 | 124 Suspicious: 5 |
123 Short ext: 2 | 125 Short ext: 3 |
124 Mean extensions: 9 | 126 Mean extensions: 9 |
125 Avg overlap len: 10074 | 127 Avg overlap len: 10043 |
126 Min overlap len: 2570 | 128 Min overlap len: 4225 |
127 Inner reads: 0 | 129 Inner reads: 0 |
128 Length: 433999 | 130 Length: 434635 |
129 [2021-06-30 16:01:42] DEBUG: Inner: 1040 covered: 1110 total: 1236 | 131 [2021-11-22 18:14:08] DEBUG: Inner: 1024 covered: 1014 total: 1152 |
130 [2021-06-30 16:01:42] INFO: Assembled 1 disjointigs | 132 [2021-11-22 18:14:08] DEBUG: Assembled disjointig 2 |
131 [2021-06-30 16:01:42] INFO: Generating sequence | 133 With 6 reads |
132 [2021-06-30 16:01:43] DEBUG: Writing FASTA | 134 Start read: +S1_921 |
133 [2021-06-30 16:01:43] DEBUG: Peak RAM usage: 8 Gb | 135 At position: 4 |
136 leftTip: 0 rightTip: 0 | |
137 Suspicious: 0 | |
138 Short ext: 0 | |
139 Mean extensions: 4 | |
140 Avg overlap len: 8689 | |
141 Min overlap len: 7703 | |
142 Inner reads: 0 | |
143 Length: 34343 | |
144 [2021-11-22 18:14:08] DEBUG: Inner: 1040 covered: 1056 total: 1152 | |
145 [2021-11-22 18:14:08] INFO: Assembled 2 disjointigs | |
146 [2021-11-22 18:14:08] INFO: Generating sequence | |
147 [2021-11-22 18:14:08] DEBUG: Building positional index | |
148 [2021-11-22 18:14:08] DEBUG: Total sequence: 470346 bp | |
149 [2021-11-22 18:14:08] DEBUG: Mean k-mer frequency: 1.00134 | |
150 [2021-11-22 18:14:08] DEBUG: Repetitive k-mer frequency: 100 | |
151 [2021-11-22 18:14:08] DEBUG: Filtered 0 repetitive k-mers (0) | |
152 [2021-11-22 18:14:08] DEBUG: Sorting k-mer index | |
153 [2021-11-22 18:14:08] DEBUG: Selected k-mers: 469680 | |
154 [2021-11-22 18:14:08] DEBUG: K-mer index size: 470312 | |
155 [2021-11-22 18:14:08] DEBUG: Mean k-mer frequency: 1.00135 | |
156 [2021-11-22 18:14:08] DEBUG: Minimizer rate: 1.00007 | |
157 [2021-11-22 18:14:08] INFO: Filtering contained disjointigs | |
158 [2021-11-22 18:14:09] DEBUG: Computing transitive closure for overlaps | |
159 [2021-11-22 18:14:09] DEBUG: Found 0 overlaps | |
160 [2021-11-22 18:14:09] DEBUG: Left 0 overlaps after filtering | |
161 [2021-11-22 18:14:09] INFO: Contained seqs: 0 | |
162 [2021-11-22 18:14:09] DEBUG: Writing FASTA | |
163 [2021-11-22 18:14:09] DEBUG: Peak RAM usage: 8 Gb | |
134 -----------End assembly log------------ | 164 -----------End assembly log------------ |
135 [2021-06-30 16:01:43] root: DEBUG: Disjointigs length: 434844, N50: 434844 | 165 [2021-11-22 18:14:09] root: DEBUG: Disjointigs length: 470346, N50: 436173 |
136 [2021-06-30 16:01:43] root: INFO: >>>STAGE: consensus | 166 [2021-11-22 18:14:09] root: INFO: >>>STAGE: consensus |
137 [2021-06-30 16:01:43] root: INFO: Running Minimap2 | 167 [2021-11-22 18:14:09] root: INFO: Running Minimap2 |
138 [2021-06-30 16:01:48] root: INFO: Computing consensus | 168 [2021-11-22 18:14:14] root: INFO: Computing consensus |
139 [2021-06-30 16:01:57] root: INFO: Alignment error rate: 0.196236 | 169 [2021-11-22 18:14:23] root: INFO: Alignment error rate: 0.197031 |
140 [2021-06-30 16:01:57] root: INFO: >>>STAGE: repeat | 170 [2021-11-22 18:14:23] root: INFO: >>>STAGE: repeat |
141 [2021-06-30 16:01:57] root: INFO: Building and resolving repeat graph | 171 [2021-11-22 18:14:23] root: INFO: Building and resolving repeat graph |
142 [2021-06-30 16:01:57] root: DEBUG: -----Begin repeat analyser log------ | 172 [2021-11-22 18:14:23] root: DEBUG: -----Begin repeat analyser log------ |
143 [2021-06-30 16:01:57] root: DEBUG: Running: flye-modules repeat --disjointigs /tmp/tmpicy_msib/job_working_directory/000/8/working/out_dir/10-consensus/consensus.fasta --reads ./input_0.fastq.gz,./input_1.fastq.gz,./input_2.fastq.gz,./input_3.fastq.gz,./input_4.fastq.gz,./input_5.fastq.gz,./input_6.fastq.gz --out-dir /tmp/tmpicy_msib/job_working_directory/000/8/working/out_dir/20-repeat --config /usr/local/lib/python3.9/site-packages/flye/config/bin_cfg/asm_raw_reads.cfg --log /tmp/tmpicy_msib/job_working_directory/000/8/working/out_dir/flye.log --threads 1 --min-ovlp 5000 | 173 [2021-11-22 18:14:23] root: DEBUG: Running: flye-modules repeat --disjointigs /tmp/tmpakmcmxzn/job_working_directory/000/8/working/out_dir/10-consensus/consensus.fasta --reads /tmp/tmpakmcmxzn/job_working_directory/000/8/working/input_0.fastq.gz,/tmp/tmpakmcmxzn/job_working_directory/000/8/working/input_1.fastq.gz,/tmp/tmpakmcmxzn/job_working_directory/000/8/working/input_2.fastq.gz,/tmp/tmpakmcmxzn/job_working_directory/000/8/working/input_3.fastq.gz,/tmp/tmpakmcmxzn/job_working_directory/000/8/working/input_4.fastq.gz,/tmp/tmpakmcmxzn/job_working_directory/000/8/working/input_5.fastq.gz,/tmp/tmpakmcmxzn/job_working_directory/000/8/working/input_6.fastq.gz --out-dir /tmp/tmpakmcmxzn/job_working_directory/000/8/working/out_dir/20-repeat --config /usr/local/lib/python3.9/site-packages/flye/config/bin_cfg/asm_raw_reads.cfg --log /tmp/tmpakmcmxzn/job_working_directory/000/8/working/out_dir/flye.log --threads 1 --min-ovlp 6000 |
144 [2021-06-30 16:01:57] DEBUG: Build date: Mar 27 2021 19:09:05 | 174 [2021-11-22 18:14:23] DEBUG: Build date: Aug 22 2021 04:47:01 |
145 [2021-06-30 16:01:57] DEBUG: Total RAM: 15 Gb | 175 [2021-11-22 18:14:23] DEBUG: Total RAM: 15 Gb |
146 [2021-06-30 16:01:57] DEBUG: Available RAM: 11 Gb | 176 [2021-11-22 18:14:23] DEBUG: Available RAM: 9 Gb |
147 [2021-06-30 16:01:57] DEBUG: Total CPUs: 8 | 177 [2021-11-22 18:14:23] DEBUG: Total CPUs: 8 |
148 [2021-06-30 16:01:57] DEBUG: Loading /usr/local/lib/python3.9/site-packages/flye/config/bin_cfg/asm_raw_reads.cfg | 178 [2021-11-22 18:14:23] DEBUG: Loading /usr/local/lib/python3.9/site-packages/flye/config/bin_cfg/asm_raw_reads.cfg |
149 [2021-06-30 16:01:57] DEBUG: Loading /usr/local/lib/python3.9/site-packages/flye/config/bin_cfg/asm_defaults.cfg | 179 [2021-11-22 18:14:23] DEBUG: Loading /usr/local/lib/python3.9/site-packages/flye/config/bin_cfg/asm_defaults.cfg |
150 [2021-06-30 16:01:57] DEBUG: big_genome_threshold=29000000 | 180 [2021-11-22 18:14:23] DEBUG: big_genome_threshold=29000000 |
151 [2021-06-30 16:01:57] DEBUG: meta_read_filter_kmer_freq=100 | 181 [2021-11-22 18:14:23] DEBUG: meta_read_filter_kmer_freq=100 |
152 [2021-06-30 16:01:57] DEBUG: max_coverage_drop_rate=5 | 182 [2021-11-22 18:14:23] DEBUG: chain_large_gap_penalty=2 |
153 [2021-06-30 16:01:57] DEBUG: max_extensions_drop_rate=5 | 183 [2021-11-22 18:14:23] DEBUG: chain_small_gap_penalty=0.5 |
154 [2021-06-30 16:01:57] DEBUG: chimera_window=100 | 184 [2021-11-22 18:14:23] DEBUG: chain_gap_jump_threshold=100 |
155 [2021-06-30 16:01:57] DEBUG: min_reads_in_disjointig=4 | 185 [2021-11-22 18:14:23] DEBUG: max_coverage_drop_rate=5 |
156 [2021-06-30 16:01:57] DEBUG: max_inner_reads=10 | 186 [2021-11-22 18:14:23] DEBUG: max_extensions_drop_rate=5 |
157 [2021-06-30 16:01:57] DEBUG: max_inner_fraction=0.25 | 187 [2021-11-22 18:14:23] DEBUG: chimera_window=100 |
158 [2021-06-30 16:01:57] DEBUG: max_separation=500 | 188 [2021-11-22 18:14:23] DEBUG: chimera_overhang=1000 |
159 [2021-06-30 16:01:57] DEBUG: unique_edge_length=50000 | 189 [2021-11-22 18:14:23] DEBUG: min_reads_in_disjointig=4 |
160 [2021-06-30 16:01:57] DEBUG: min_repeat_res_support=0.51 | 190 [2021-11-22 18:14:23] DEBUG: max_inner_reads=10 |
161 [2021-06-30 16:01:57] DEBUG: out_paths_ratio=5 | 191 [2021-11-22 18:14:23] DEBUG: max_inner_fraction=0.25 |
162 [2021-06-30 16:01:57] DEBUG: graph_cov_drop_rate=5 | 192 [2021-11-22 18:14:23] DEBUG: max_separation=500 |
163 [2021-06-30 16:01:57] DEBUG: coverage_estimate_window=100 | 193 [2021-11-22 18:14:23] DEBUG: unique_edge_length=50000 |
164 [2021-06-30 16:01:57] DEBUG: max_bubble_length=50000 | 194 [2021-11-22 18:14:23] DEBUG: min_repeat_res_support=0.51 |
165 [2021-06-30 16:01:57] DEBUG: loop_coverage_rate=1.5 | 195 [2021-11-22 18:14:23] DEBUG: out_paths_ratio=5 |
166 [2021-06-30 16:01:57] DEBUG: repeat_edge_cov_mult=1.75 | 196 [2021-11-22 18:14:23] DEBUG: graph_cov_drop_rate=5 |
167 [2021-06-30 16:01:57] DEBUG: weak_detach_rate=5 | 197 [2021-11-22 18:14:23] DEBUG: coverage_estimate_window=100 |
168 [2021-06-30 16:01:57] DEBUG: tip_coverage_rate=2 | 198 [2021-11-22 18:14:23] DEBUG: max_bubble_length=50000 |
169 [2021-06-30 16:01:57] DEBUG: tip_length_rate=2 | 199 [2021-11-22 18:14:23] DEBUG: loop_coverage_rate=1.5 |
170 [2021-06-30 16:01:57] DEBUG: low_cutoff_warning=1 | 200 [2021-11-22 18:14:23] DEBUG: repeat_edge_cov_mult=1.75 |
171 [2021-06-30 16:01:57] DEBUG: hard_min_coverage_rate=10 | 201 [2021-11-22 18:14:23] DEBUG: weak_detach_rate=5 |
172 [2021-06-30 16:01:57] DEBUG: kmer_size=17 | 202 [2021-11-22 18:14:23] DEBUG: tip_coverage_rate=2 |
173 [2021-06-30 16:01:57] DEBUG: use_minimizers=0 | 203 [2021-11-22 18:14:23] DEBUG: tip_length_rate=2 |
174 [2021-06-30 16:01:57] DEBUG: reads_base_alignment=0 | 204 [2021-11-22 18:14:23] DEBUG: output_gfa_before_rr=0 |
175 [2021-06-30 16:01:57] DEBUG: assemble_kmer_sample=1 | 205 [2021-11-22 18:14:23] DEBUG: low_cutoff_warning=1 |
176 [2021-06-30 16:01:57] DEBUG: repeat_graph_kmer_sample=1 | 206 [2021-11-22 18:14:23] DEBUG: kmer_size=17 |
177 [2021-06-30 16:01:57] DEBUG: read_align_kmer_sample=1 | 207 [2021-11-22 18:14:23] DEBUG: use_minimizers=0 |
178 [2021-06-30 16:01:57] DEBUG: meta_read_top_kmer_rate=0.40 | 208 [2021-11-22 18:14:23] DEBUG: reads_base_alignment=0 |
179 [2021-06-30 16:01:57] DEBUG: maximum_jump=1500 | 209 [2021-11-22 18:14:23] DEBUG: meta_read_top_kmer_rate=0.40 |
180 [2021-06-30 16:01:57] DEBUG: maximum_overhang=1500 | 210 [2021-11-22 18:14:23] DEBUG: maximum_jump=1500 |
181 [2021-06-30 16:01:57] DEBUG: repeat_kmer_rate=100 | 211 [2021-11-22 18:14:23] DEBUG: maximum_overhang=1500 |
182 [2021-06-30 16:01:57] DEBUG: assemble_ovlp_divergence=0.10 | 212 [2021-11-22 18:14:23] DEBUG: repeat_kmer_rate=100 |
183 [2021-06-30 16:01:57] DEBUG: assemble_divergence_relative=1 | 213 [2021-11-22 18:14:23] DEBUG: assemble_ovlp_divergence=0.10 |
184 [2021-06-30 16:01:57] DEBUG: repeat_graph_ovlp_divergence=0.08 | 214 [2021-11-22 18:14:23] DEBUG: assemble_divergence_relative=1 |
185 [2021-06-30 16:01:57] DEBUG: read_align_ovlp_divergence=0.25 | 215 [2021-11-22 18:14:23] DEBUG: repeat_graph_ovlp_divergence=0.08 |
186 [2021-06-30 16:01:57] DEBUG: hpc_scoring_on=0 | 216 [2021-11-22 18:14:23] DEBUG: read_align_ovlp_divergence=0.25 |
187 [2021-06-30 16:01:57] DEBUG: add_unassembled_reads=0 | 217 [2021-11-22 18:14:23] DEBUG: hpc_scoring_on=0 |
188 [2021-06-30 16:01:57] DEBUG: extend_contigs_with_repeats=0 | 218 [2021-11-22 18:14:23] DEBUG: add_unassembled_reads=0 |
189 [2021-06-30 16:01:57] DEBUG: min_read_cov_cutoff=3 | 219 [2021-11-22 18:14:23] DEBUG: extend_contigs_with_repeats=0 |
190 [2021-06-30 16:01:57] DEBUG: short_tip_length=20000 | 220 [2021-11-22 18:14:23] DEBUG: min_read_cov_cutoff=3 |
191 [2021-06-30 16:01:57] DEBUG: long_tip_length=100000 | 221 [2021-11-22 18:14:23] DEBUG: short_tip_length=20000 |
192 [2021-06-30 16:01:57] DEBUG: Running with k-mer size: 17 | 222 [2021-11-22 18:14:23] DEBUG: long_tip_length=100000 |
193 [2021-06-30 16:01:57] DEBUG: Selected minimum overlap 5000 | 223 [2021-11-22 18:14:23] DEBUG: Running with k-mer size: 17 |
194 [2021-06-30 16:01:57] DEBUG: Metagenome mode: N | 224 [2021-11-22 18:14:23] DEBUG: Selected minimum overlap 6000 |
195 [2021-06-30 16:01:57] INFO: Parsing disjointigs | 225 [2021-11-22 18:14:23] DEBUG: Metagenome mode: N |
196 [2021-06-30 16:01:57] DEBUG: Building positional index | 226 [2021-11-22 18:14:23] INFO: Parsing disjointigs |
197 [2021-06-30 16:01:57] DEBUG: Total sequence: 418806 bp | 227 [2021-11-22 18:14:23] DEBUG: Building positional index |
198 [2021-06-30 16:01:57] INFO: Building repeat graph | 228 [2021-11-22 18:14:23] DEBUG: Total sequence: 452437 bp |
199 [2021-06-30 16:01:57] DEBUG: Mean k-mer frequency: 1.00896 | 229 [2021-11-22 18:14:23] INFO: Building repeat graph |
200 [2021-06-30 16:01:57] DEBUG: Repetitive k-mer frequency: 100 | 230 [2021-11-22 18:14:24] DEBUG: Mean k-mer frequency: 1.05543 |
201 [2021-06-30 16:01:57] DEBUG: Filtered 0 repetitive k-mers (0) | 231 [2021-11-22 18:14:24] DEBUG: Repetitive k-mer frequency: 105 |
202 [2021-06-30 16:01:57] DEBUG: Sorting k-mer index | 232 [2021-11-22 18:14:24] DEBUG: Filtered 0 repetitive k-mers (0) |
203 [2021-06-30 16:01:57] DEBUG: Selected k-mers: 415069 | 233 [2021-11-22 18:14:24] DEBUG: Sorting k-mer index |
204 [2021-06-30 16:01:57] DEBUG: K-mer index size: 418789 | 234 [2021-11-22 18:14:24] DEBUG: Selected k-mers: 428642 |
205 [2021-06-30 16:01:57] DEBUG: Mean k-mer frequency: 1.00896 | 235 [2021-11-22 18:14:24] DEBUG: K-mer index size: 452403 |
206 [2021-06-30 16:01:57] DEBUG: Minimizer rate: 1.00004 | 236 [2021-11-22 18:14:24] DEBUG: Mean k-mer frequency: 1.05543 |
207 [2021-06-30 16:01:58] DEBUG: Computing transitive closure for overlaps | 237 [2021-11-22 18:14:24] DEBUG: Minimizer rate: 1.00008 |
208 [2021-06-30 16:01:58] DEBUG: Found 0 overlaps | 238 [2021-11-22 18:14:24] DEBUG: Computing transitive closure for overlaps |
209 [2021-06-30 16:01:58] DEBUG: Left 0 overlaps after filtering | 239 [2021-11-22 18:14:24] DEBUG: Found 10 overlaps |
210 [2021-06-30 16:01:58] INFO: Median overlap divergence: 0 | 240 [2021-11-22 18:14:24] DEBUG: Left 4 overlaps after filtering |
211 [2021-06-30 16:01:58] DEBUG: Sequence divergence distribution: | 241 [2021-11-22 18:14:24] INFO: Median overlap divergence: 0.0343169 |
212 | 242 [2021-11-22 18:14:24] DEBUG: Sequence divergence distribution: |
213 | | | 243 |
214 | | | 244 | * | |
215 | | | 245 | * | |
216 | | | 246 | * | |
217 | | | 247 | * | |
218 | | | 248 | * | |
219 | | | 249 | * | |
220 | | | 250 | * | |
221 | | | 251 | * | |
222 | | | 252 | * | |
223 | | | 253 | * | |
224 | | | 254 | * | |
225 | | | 255 | * | |
226 | | | 256 | * | |
227 | | | 257 | * | |
228 | | | 258 | * | |
229 | | | 259 | * | |
230 | | | 260 | * | |
231 | | | 261 | * | |
232 | | | 262 | * | |
263 | * | | |
233 ---------------------------------------------------------------------------------------------------- | 264 ---------------------------------------------------------------------------------------------------- |
234 0% 5% 10% 15% 20% 25% 30% 35% 40% 45% | 265 0% 5% 10% 15% 20% 25% 30% 35% 40% 45% |
235 | 266 |
236 Q25 = 0, Q50 = 0, Q75 = 0 | 267 Q25 = 0.034, Q50 = 0.034, Q75 = 0.034 |
237 | 268 |
238 [2021-06-30 16:01:58] DEBUG: Computing gluepoints | 269 [2021-11-22 18:14:24] DEBUG: Computing gluepoints |
239 [2021-06-30 16:01:58] DEBUG: Added 0 gluepoint projections | 270 [2021-11-22 18:14:24] DEBUG: Added 0 gluepoint projections |
240 [2021-06-30 16:01:58] DEBUG: Created 4 gluepoints | 271 [2021-11-22 18:14:24] DEBUG: Created 12 gluepoints |
241 [2021-06-30 16:01:58] DEBUG: Artificial loops removed: 0 left, 0 right, 0 both | 272 [2021-11-22 18:14:24] DEBUG: Artificial loops removed: 0 left, 0 right, 0 both |
242 [2021-06-30 16:01:58] DEBUG: Initializing edges | 273 [2021-11-22 18:14:24] DEBUG: Initializing edges |
243 [2021-06-30 16:01:58] DEBUG: Edges length checksum: 18446744073013520505 | 274 [2021-11-22 18:14:24] DEBUG: Edges length checksum: 2261029433 |
244 [2021-06-30 16:01:58] DEBUG: Filtered 0 singleton segments | 275 [2021-11-22 18:14:24] DEBUG: Filtered 0 singleton segments |
245 [2021-06-30 16:01:58] DEBUG: Removed 0 simple and 0 double chimeric junctions | 276 [2021-11-22 18:14:24] DEBUG: Removed 0 simple and 0 double chimeric junctions |
246 [2021-06-30 16:01:58] DEBUG: Collapsed 0 edges | 277 [2021-11-22 18:14:24] DEBUG: Collapsed 2 edges |
247 [2021-06-30 16:01:58] DEBUG: * 1 +disjointig_1 0 418805 418805 | 278 [2021-11-22 18:14:24] DEBUG: * 4 +disjointig_1 0 419576 419576 |
248 [2021-06-30 16:01:58] DEBUG: Total edges: 1 | 279 [2021-11-22 18:14:24] DEBUG: Total edges: 4 |
249 [2021-06-30 16:01:58] INFO: Parsing reads | 280 [2021-11-22 18:14:24] INFO: Parsing reads |
250 [2021-06-30 16:01:58] DEBUG: Building positional index | 281 [2021-11-22 18:14:24] DEBUG: Building positional index |
251 [2021-06-30 16:01:58] DEBUG: Total sequence: 7249289 bp | 282 [2021-11-22 18:14:24] DEBUG: Total sequence: 7249289 bp |
252 [2021-06-30 16:01:58] DEBUG: Building positional index | 283 [2021-11-22 18:14:24] DEBUG: Building positional index |
253 [2021-06-30 16:01:58] DEBUG: Total sequence: 418805 bp | 284 [2021-11-22 18:14:24] DEBUG: Total sequence: 419576 bp |
254 [2021-06-30 16:01:58] INFO: Aligning reads to the graph | 285 [2021-11-22 18:14:24] INFO: Aligning reads to the graph |
255 [2021-06-30 16:01:58] DEBUG: Mean k-mer frequency: 1.00896 | 286 [2021-11-22 18:14:24] DEBUG: Mean k-mer frequency: 1.00888 |
256 [2021-06-30 16:01:58] DEBUG: Repetitive k-mer frequency: 100 | 287 [2021-11-22 18:14:24] DEBUG: Repetitive k-mer frequency: 100 |
257 [2021-06-30 16:01:58] DEBUG: Filtered 0 repetitive k-mers (0) | 288 [2021-11-22 18:14:24] DEBUG: Filtered 0 repetitive k-mers (0) |
258 [2021-06-30 16:01:58] DEBUG: Sorting k-mer index | 289 [2021-11-22 18:14:24] DEBUG: Sorting k-mer index |
259 [2021-06-30 16:01:58] DEBUG: Selected k-mers: 415068 | 290 [2021-11-22 18:14:24] DEBUG: Selected k-mers: 415865 |
260 [2021-06-30 16:01:58] DEBUG: K-mer index size: 418788 | 291 [2021-11-22 18:14:24] DEBUG: K-mer index size: 419559 |
261 [2021-06-30 16:01:58] DEBUG: Mean k-mer frequency: 1.00896 | 292 [2021-11-22 18:14:24] DEBUG: Mean k-mer frequency: 1.00888 |
262 [2021-06-30 16:01:58] DEBUG: Minimizer rate: 1.00004 | 293 [2021-11-22 18:14:24] DEBUG: Minimizer rate: 1.00004 |
263 [2021-06-30 16:02:00] DEBUG: Total reads : 618 | 294 [2021-11-22 18:14:26] DEBUG: Total reads : 576 |
264 [2021-06-30 16:02:00] DEBUG: Read with aligned parts : 610 | 295 [2021-11-22 18:14:26] DEBUG: Read with aligned parts : 566 |
265 [2021-06-30 16:02:00] DEBUG: Aligned in one piece : 610 | 296 [2021-11-22 18:14:26] DEBUG: Aligned in one piece : 566 |
266 [2021-06-30 16:02:00] INFO: Aligned read sequence: 6562529 / 6702247 (0.979154) | 297 [2021-11-22 18:14:26] INFO: Aligned read sequence: 6321188 / 6471580 (0.976761) |
267 [2021-06-30 16:02:00] INFO: Median overlap divergence: 0.129507 | 298 [2021-11-22 18:14:26] INFO: Median overlap divergence: 0.129819 |
268 [2021-06-30 16:02:00] DEBUG: Sequence divergence distribution: | 299 [2021-11-22 18:14:26] DEBUG: Sequence divergence distribution: |
269 | 300 |
270 | * | | |
271 | * | | 301 | * | |
272 | ** | | 302 | ** | |
273 | ** | | 303 | ** | |
274 | ** | | |
275 | *** | | 304 | *** | |
276 | *** * | | 305 | *** | |
277 | *** * | | 306 | *** | |
307 | ***** | | |
308 | ***** | | |
278 | ***** | | 309 | ***** | |
279 | ***** | | 310 | ***** | |
280 | ****** | | 311 | ****** | |
281 | ******* | | 312 | ******* | |
282 | ******* | | 313 | ******* | |
283 | ******** | | 314 | ******** | |
284 | ********* | | 315 | ********* | |
285 | ********* | | 316 | ********* | |
286 | ********** | | 317 | ********** | |
287 | *********** | | 318 | ************ | |
288 | ************ * | | 319 | *************** | |
289 | ***************** | | 320 | **************** | |
290 ---------------------------------------------------------------------------------------------------- | 321 ---------------------------------------------------------------------------------------------------- |
291 0% 5% 10% 15% 20% 25% 30% 35% 40% 45% | 322 0% 5% 10% 15% 20% 25% 30% 35% 40% 45% |
292 | 323 |
293 Q25 = 0.12, Q50 = 0.13, Q75 = 0.14 | 324 Q25 = 0.12, Q50 = 0.13, Q75 = 0.14 |
294 | 325 |
295 [2021-06-30 16:02:00] INFO: Mean edge coverage: 14 | 326 [2021-11-22 18:14:27] INFO: Mean edge coverage: 14 |
296 [2021-06-30 16:02:00] DEBUG: 1 len:418805 cov:15 mult:1.07143 | 327 [2021-11-22 18:14:27] DEBUG: 4 len:419576 cov:14 mult:1 |
297 [2021-06-30 16:02:00] DEBUG: -1 len:418805 cov:15 mult:1.07143 | 328 [2021-11-22 18:14:27] DEBUG: -4 len:419576 cov:14 mult:1 |
298 [2021-06-30 16:02:00] DEBUG: Unique coverage threshold 26 | 329 [2021-11-22 18:14:27] DEBUG: Unique coverage threshold 24 |
299 [2021-06-30 16:02:00] INFO: Simplifying the graph | 330 [2021-11-22 18:14:27] INFO: Simplifying the graph |
300 [2021-06-30 16:02:00] DEBUG: Read coverage cutoff: 3 | 331 [2021-11-22 18:14:27] DEBUG: Read coverage cutoff: 3 |
301 [2021-06-30 16:02:00] DEBUG: [SIMPL] Removed 0 paths with low coverage | 332 [2021-11-22 18:14:27] DEBUG: [SIMPL] Removed 0 paths with low coverage |
302 [2021-06-30 16:02:00] DEBUG: Finding repeats | 333 [2021-11-22 18:14:27] DEBUG: [SIMPL] Masked 0 heterozygous loops |
303 [2021-06-30 16:02:00] DEBUG: Read coverage cutoff: 3 | 334 [2021-11-22 18:14:27] DEBUG: [SIMPL] Masked 0 simple bubbles |
304 [2021-06-30 16:02:00] DEBUG: Repeat detection iteration 1 | 335 [2021-11-22 18:14:27] DEBUG: Finding repeats |
305 [2021-06-30 16:02:00] DEBUG: Writing Dot | 336 [2021-11-22 18:14:27] DEBUG: Read coverage cutoff: 3 |
306 [2021-06-30 16:02:00] DEBUG: Writing FASTA | 337 [2021-11-22 18:14:27] DEBUG: Repeat detection iteration 1 |
307 [2021-06-30 16:02:00] DEBUG: [SIMPL] == Iteration 1 == | 338 [2021-11-22 18:14:27] DEBUG: Writing Dot |
308 [2021-06-30 16:02:00] DEBUG: Splitting nodes | 339 [2021-11-22 18:14:27] DEBUG: Writing FASTA |
309 [2021-06-30 16:02:00] DEBUG: [SIMPL] Split 0 nodes | 340 [2021-11-22 18:14:27] DEBUG: [SIMPL] == Iteration 1 == |
310 [2021-06-30 16:02:00] DEBUG: [SIMPL] Clipped 0 short and 0 long tips | 341 [2021-11-22 18:14:27] DEBUG: Splitting nodes |
311 [2021-06-30 16:02:00] DEBUG: [SIMPL] Masked 0 heterozygous loops | 342 [2021-11-22 18:14:27] DEBUG: [SIMPL] Split 0 nodes |
312 [2021-06-30 16:02:00] DEBUG: [SIMPL] Masked 0 simple bubbles | 343 [2021-11-22 18:14:27] DEBUG: [SIMPL] Clipped 0 short and 0 long tips |
313 [2021-06-30 16:02:00] DEBUG: Finding repeats | 344 [2021-11-22 18:14:27] DEBUG: [SIMPL] Masked 0 heterozygous loops |
314 [2021-06-30 16:02:00] DEBUG: Read coverage cutoff: 3 | 345 [2021-11-22 18:14:27] DEBUG: [SIMPL] Masked 0 simple bubbles |
315 [2021-06-30 16:02:00] DEBUG: Repeat detection iteration 1 | 346 [2021-11-22 18:14:27] DEBUG: Finding repeats |
316 [2021-06-30 16:02:00] DEBUG: Total unique edges: 1 | 347 [2021-11-22 18:14:27] DEBUG: Read coverage cutoff: 3 |
317 [2021-06-30 16:02:00] DEBUG: [SIMPL] Resolved repeats: 0 | 348 [2021-11-22 18:14:27] DEBUG: Repeat detection iteration 1 |
318 [2021-06-30 16:02:00] DEBUG: RR links: 0 | 349 [2021-11-22 18:14:27] DEBUG: Total unique edges: 1 |
319 [2021-06-30 16:02:00] DEBUG: Unresolved: 0 | 350 [2021-11-22 18:14:27] DEBUG: [SIMPL] Resolved repeats: 0 |
320 [2021-06-30 16:02:00] DEBUG: Removed 0 simple and 0 double chimeric junctions | 351 [2021-11-22 18:14:27] DEBUG: RR links: 0 |
321 [2021-06-30 16:02:00] DEBUG: [SIMPL] Collapsed 0 haplotypes | 352 [2021-11-22 18:14:27] DEBUG: Unresolved: 0 |
322 [2021-06-30 16:02:00] DEBUG: [SIMPL] Resolved 0 simple repeats | 353 [2021-11-22 18:14:27] DEBUG: Removed 0 simple and 0 double chimeric junctions |
323 [2021-06-30 16:02:00] DEBUG: Read coverage cutoff: 3 | 354 [2021-11-22 18:14:27] DEBUG: [SIMPL] Collapsed 0 haplotypes |
324 [2021-06-30 16:02:00] DEBUG: [SIMPL] Removed 0 paths with low coverage | 355 [2021-11-22 18:14:27] DEBUG: [SIMPL] Resolved 0 simple repeats |
325 [2021-06-30 16:02:00] DEBUG: Finding repeats | 356 [2021-11-22 18:14:27] DEBUG: Read coverage cutoff: 3 |
326 [2021-06-30 16:02:00] DEBUG: Read coverage cutoff: 3 | 357 [2021-11-22 18:14:27] DEBUG: [SIMPL] Removed 0 paths with low coverage |
327 [2021-06-30 16:02:00] DEBUG: Repeat detection iteration 1 | 358 [2021-11-22 18:14:27] DEBUG: Finding repeats |
328 [2021-06-30 16:02:00] DEBUG: Writing Dot | 359 [2021-11-22 18:14:27] DEBUG: Read coverage cutoff: 3 |
329 [2021-06-30 16:02:00] DEBUG: Writing FASTA | 360 [2021-11-22 18:14:27] DEBUG: Repeat detection iteration 1 |
330 [2021-06-30 16:02:00] DEBUG: Peak RAM usage: 0 Gb | 361 [2021-11-22 18:14:27] DEBUG: Writing Dot |
362 [2021-11-22 18:14:27] DEBUG: Writing FASTA | |
363 [2021-11-22 18:14:27] DEBUG: Peak RAM usage: 0 Gb | |
331 -----------End assembly log------------ | 364 -----------End assembly log------------ |
332 [2021-06-30 16:02:00] root: INFO: >>>STAGE: contigger | 365 [2021-11-22 18:14:27] root: INFO: >>>STAGE: contigger |
333 [2021-06-30 16:02:00] root: INFO: Generating contigs | 366 [2021-11-22 18:14:27] root: INFO: Generating contigs |
334 [2021-06-30 16:02:00] root: DEBUG: -----Begin contigger analyser log------ | 367 [2021-11-22 18:14:27] root: DEBUG: -----Begin contigger analyser log------ |
335 [2021-06-30 16:02:00] root: DEBUG: Running: flye-modules contigger --graph-edges /tmp/tmpicy_msib/job_working_directory/000/8/working/out_dir/20-repeat/repeat_graph_edges.fasta --reads ./input_0.fastq.gz,./input_1.fastq.gz,./input_2.fastq.gz,./input_3.fastq.gz,./input_4.fastq.gz,./input_5.fastq.gz,./input_6.fastq.gz --out-dir /tmp/tmpicy_msib/job_working_directory/000/8/working/out_dir/30-contigger --config /usr/local/lib/python3.9/site-packages/flye/config/bin_cfg/asm_raw_reads.cfg --repeat-graph /tmp/tmpicy_msib/job_working_directory/000/8/working/out_dir/20-repeat/repeat_graph_dump --graph-aln /tmp/tmpicy_msib/job_working_directory/000/8/working/out_dir/20-repeat/read_alignment_dump --log /tmp/tmpicy_msib/job_working_directory/000/8/working/out_dir/flye.log --threads 1 --min-ovlp 5000 | 368 [2021-11-22 18:14:27] root: DEBUG: Running: flye-modules contigger --graph-edges /tmp/tmpakmcmxzn/job_working_directory/000/8/working/out_dir/20-repeat/repeat_graph_edges.fasta --reads /tmp/tmpakmcmxzn/job_working_directory/000/8/working/input_0.fastq.gz,/tmp/tmpakmcmxzn/job_working_directory/000/8/working/input_1.fastq.gz,/tmp/tmpakmcmxzn/job_working_directory/000/8/working/input_2.fastq.gz,/tmp/tmpakmcmxzn/job_working_directory/000/8/working/input_3.fastq.gz,/tmp/tmpakmcmxzn/job_working_directory/000/8/working/input_4.fastq.gz,/tmp/tmpakmcmxzn/job_working_directory/000/8/working/input_5.fastq.gz,/tmp/tmpakmcmxzn/job_working_directory/000/8/working/input_6.fastq.gz --out-dir /tmp/tmpakmcmxzn/job_working_directory/000/8/working/out_dir/30-contigger --config /usr/local/lib/python3.9/site-packages/flye/config/bin_cfg/asm_raw_reads.cfg --repeat-graph /tmp/tmpakmcmxzn/job_working_directory/000/8/working/out_dir/20-repeat/repeat_graph_dump --graph-aln /tmp/tmpakmcmxzn/job_working_directory/000/8/working/out_dir/20-repeat/read_alignment_dump --log /tmp/tmpakmcmxzn/job_working_directory/000/8/working/out_dir/flye.log --threads 1 --min-ovlp 6000 |
336 [2021-06-30 16:02:00] DEBUG: Build date: Mar 27 2021 19:09:32 | 369 [2021-11-22 18:14:27] DEBUG: Build date: Aug 22 2021 04:47:48 |
337 [2021-06-30 16:02:00] DEBUG: Total RAM: 15 Gb | 370 [2021-11-22 18:14:27] DEBUG: Total RAM: 15 Gb |
338 [2021-06-30 16:02:00] DEBUG: Available RAM: 11 Gb | 371 [2021-11-22 18:14:27] DEBUG: Available RAM: 9 Gb |
339 [2021-06-30 16:02:00] DEBUG: Total CPUs: 8 | 372 [2021-11-22 18:14:27] DEBUG: Total CPUs: 8 |
340 [2021-06-30 16:02:00] DEBUG: Loading /usr/local/lib/python3.9/site-packages/flye/config/bin_cfg/asm_raw_reads.cfg | 373 [2021-11-22 18:14:27] DEBUG: Loading /usr/local/lib/python3.9/site-packages/flye/config/bin_cfg/asm_raw_reads.cfg |
341 [2021-06-30 16:02:00] DEBUG: Loading /usr/local/lib/python3.9/site-packages/flye/config/bin_cfg/asm_defaults.cfg | 374 [2021-11-22 18:14:27] DEBUG: Loading /usr/local/lib/python3.9/site-packages/flye/config/bin_cfg/asm_defaults.cfg |
342 [2021-06-30 16:02:00] DEBUG: big_genome_threshold=29000000 | 375 [2021-11-22 18:14:27] DEBUG: big_genome_threshold=29000000 |
343 [2021-06-30 16:02:00] DEBUG: meta_read_filter_kmer_freq=100 | 376 [2021-11-22 18:14:27] DEBUG: meta_read_filter_kmer_freq=100 |
344 [2021-06-30 16:02:00] DEBUG: max_coverage_drop_rate=5 | 377 [2021-11-22 18:14:27] DEBUG: chain_large_gap_penalty=2 |
345 [2021-06-30 16:02:00] DEBUG: max_extensions_drop_rate=5 | 378 [2021-11-22 18:14:27] DEBUG: chain_small_gap_penalty=0.5 |
346 [2021-06-30 16:02:00] DEBUG: chimera_window=100 | 379 [2021-11-22 18:14:27] DEBUG: chain_gap_jump_threshold=100 |
347 [2021-06-30 16:02:00] DEBUG: min_reads_in_disjointig=4 | 380 [2021-11-22 18:14:27] DEBUG: max_coverage_drop_rate=5 |
348 [2021-06-30 16:02:00] DEBUG: max_inner_reads=10 | 381 [2021-11-22 18:14:27] DEBUG: max_extensions_drop_rate=5 |
349 [2021-06-30 16:02:00] DEBUG: max_inner_fraction=0.25 | 382 [2021-11-22 18:14:27] DEBUG: chimera_window=100 |
350 [2021-06-30 16:02:00] DEBUG: max_separation=500 | 383 [2021-11-22 18:14:27] DEBUG: chimera_overhang=1000 |
351 [2021-06-30 16:02:00] DEBUG: unique_edge_length=50000 | 384 [2021-11-22 18:14:27] DEBUG: min_reads_in_disjointig=4 |
352 [2021-06-30 16:02:00] DEBUG: min_repeat_res_support=0.51 | 385 [2021-11-22 18:14:27] DEBUG: max_inner_reads=10 |
353 [2021-06-30 16:02:00] DEBUG: out_paths_ratio=5 | 386 [2021-11-22 18:14:27] DEBUG: max_inner_fraction=0.25 |
354 [2021-06-30 16:02:00] DEBUG: graph_cov_drop_rate=5 | 387 [2021-11-22 18:14:27] DEBUG: max_separation=500 |
355 [2021-06-30 16:02:00] DEBUG: coverage_estimate_window=100 | 388 [2021-11-22 18:14:27] DEBUG: unique_edge_length=50000 |
356 [2021-06-30 16:02:00] DEBUG: max_bubble_length=50000 | 389 [2021-11-22 18:14:27] DEBUG: min_repeat_res_support=0.51 |
357 [2021-06-30 16:02:00] DEBUG: loop_coverage_rate=1.5 | 390 [2021-11-22 18:14:27] DEBUG: out_paths_ratio=5 |
358 [2021-06-30 16:02:00] DEBUG: repeat_edge_cov_mult=1.75 | 391 [2021-11-22 18:14:27] DEBUG: graph_cov_drop_rate=5 |
359 [2021-06-30 16:02:00] DEBUG: weak_detach_rate=5 | 392 [2021-11-22 18:14:27] DEBUG: coverage_estimate_window=100 |
360 [2021-06-30 16:02:00] DEBUG: tip_coverage_rate=2 | 393 [2021-11-22 18:14:27] DEBUG: max_bubble_length=50000 |
361 [2021-06-30 16:02:00] DEBUG: tip_length_rate=2 | 394 [2021-11-22 18:14:27] DEBUG: loop_coverage_rate=1.5 |
362 [2021-06-30 16:02:00] DEBUG: low_cutoff_warning=1 | 395 [2021-11-22 18:14:27] DEBUG: repeat_edge_cov_mult=1.75 |
363 [2021-06-30 16:02:00] DEBUG: hard_min_coverage_rate=10 | 396 [2021-11-22 18:14:27] DEBUG: weak_detach_rate=5 |
364 [2021-06-30 16:02:00] DEBUG: kmer_size=17 | 397 [2021-11-22 18:14:27] DEBUG: tip_coverage_rate=2 |
365 [2021-06-30 16:02:00] DEBUG: use_minimizers=0 | 398 [2021-11-22 18:14:27] DEBUG: tip_length_rate=2 |
366 [2021-06-30 16:02:00] DEBUG: reads_base_alignment=0 | 399 [2021-11-22 18:14:27] DEBUG: output_gfa_before_rr=0 |
367 [2021-06-30 16:02:00] DEBUG: assemble_kmer_sample=1 | 400 [2021-11-22 18:14:27] DEBUG: low_cutoff_warning=1 |
368 [2021-06-30 16:02:00] DEBUG: repeat_graph_kmer_sample=1 | 401 [2021-11-22 18:14:27] DEBUG: kmer_size=17 |
369 [2021-06-30 16:02:00] DEBUG: read_align_kmer_sample=1 | 402 [2021-11-22 18:14:27] DEBUG: use_minimizers=0 |
370 [2021-06-30 16:02:00] DEBUG: meta_read_top_kmer_rate=0.40 | 403 [2021-11-22 18:14:27] DEBUG: reads_base_alignment=0 |
371 [2021-06-30 16:02:00] DEBUG: maximum_jump=1500 | 404 [2021-11-22 18:14:27] DEBUG: meta_read_top_kmer_rate=0.40 |
372 [2021-06-30 16:02:00] DEBUG: maximum_overhang=1500 | 405 [2021-11-22 18:14:27] DEBUG: maximum_jump=1500 |
373 [2021-06-30 16:02:00] DEBUG: repeat_kmer_rate=100 | 406 [2021-11-22 18:14:27] DEBUG: maximum_overhang=1500 |
374 [2021-06-30 16:02:00] DEBUG: assemble_ovlp_divergence=0.10 | 407 [2021-11-22 18:14:27] DEBUG: repeat_kmer_rate=100 |
375 [2021-06-30 16:02:00] DEBUG: assemble_divergence_relative=1 | 408 [2021-11-22 18:14:27] DEBUG: assemble_ovlp_divergence=0.10 |
376 [2021-06-30 16:02:00] DEBUG: repeat_graph_ovlp_divergence=0.08 | 409 [2021-11-22 18:14:27] DEBUG: assemble_divergence_relative=1 |
377 [2021-06-30 16:02:00] DEBUG: read_align_ovlp_divergence=0.25 | 410 [2021-11-22 18:14:27] DEBUG: repeat_graph_ovlp_divergence=0.08 |
378 [2021-06-30 16:02:00] DEBUG: hpc_scoring_on=0 | 411 [2021-11-22 18:14:27] DEBUG: read_align_ovlp_divergence=0.25 |
379 [2021-06-30 16:02:00] DEBUG: add_unassembled_reads=0 | 412 [2021-11-22 18:14:27] DEBUG: hpc_scoring_on=0 |
380 [2021-06-30 16:02:00] DEBUG: extend_contigs_with_repeats=0 | 413 [2021-11-22 18:14:27] DEBUG: add_unassembled_reads=0 |
381 [2021-06-30 16:02:00] DEBUG: min_read_cov_cutoff=3 | 414 [2021-11-22 18:14:27] DEBUG: extend_contigs_with_repeats=0 |
382 [2021-06-30 16:02:00] DEBUG: short_tip_length=20000 | 415 [2021-11-22 18:14:27] DEBUG: min_read_cov_cutoff=3 |
383 [2021-06-30 16:02:00] DEBUG: long_tip_length=100000 | 416 [2021-11-22 18:14:27] DEBUG: short_tip_length=20000 |
384 [2021-06-30 16:02:00] DEBUG: Running with k-mer size: 17 | 417 [2021-11-22 18:14:27] DEBUG: long_tip_length=100000 |
385 [2021-06-30 16:02:00] DEBUG: Selected minimum overlap 5000 | 418 [2021-11-22 18:14:27] DEBUG: Running with k-mer size: 17 |
386 [2021-06-30 16:02:00] INFO: Reading sequences | 419 [2021-11-22 18:14:27] DEBUG: Selected minimum overlap 6000 |
387 [2021-06-30 16:02:01] DEBUG: Building positional index | 420 [2021-11-22 18:14:27] INFO: Reading sequences |
388 [2021-06-30 16:02:01] DEBUG: Total sequence: 7249289 bp | 421 [2021-11-22 18:14:27] DEBUG: Building positional index |
389 [2021-06-30 16:02:01] DEBUG: Flipped 0 | 422 [2021-11-22 18:14:27] DEBUG: Total sequence: 7249289 bp |
390 [2021-06-30 16:02:01] DEBUG: UPath 1: 1 | 423 [2021-11-22 18:14:27] DEBUG: Flipped 0 |
391 [2021-06-30 16:02:01] DEBUG: Final graph contiain 1 egdes | 424 [2021-11-22 18:14:27] DEBUG: UPath 1: 4 |
392 [2021-06-30 16:02:01] DEBUG: Extending contigs into repeats | 425 [2021-11-22 18:14:27] DEBUG: Final graph contains 1 egdes |
393 [2021-06-30 16:02:01] DEBUG: Covered 0 repetitive contigs | 426 [2021-11-22 18:14:27] DEBUG: Extending contigs into repeats |
394 [2021-06-30 16:02:01] INFO: Generated 1 contigs | 427 [2021-11-22 18:14:27] DEBUG: Covered 0 repetitive contigs |
395 [2021-06-30 16:02:01] DEBUG: Writing FASTA | 428 [2021-11-22 18:14:27] INFO: Generated 1 contigs |
396 [2021-06-30 16:02:01] DEBUG: Generating scaffold connections | 429 [2021-11-22 18:14:27] DEBUG: Writing FASTA |
397 [2021-06-30 16:02:01] INFO: Added 0 scaffold connections | 430 [2021-11-22 18:14:27] DEBUG: Generating scaffold connections |
398 [2021-06-30 16:02:01] DEBUG: Writing Dot | 431 [2021-11-22 18:14:27] INFO: Added 0 scaffold connections |
399 [2021-06-30 16:02:01] DEBUG: Writing FASTA | 432 [2021-11-22 18:14:27] DEBUG: Writing Dot |
400 [2021-06-30 16:02:01] DEBUG: Writing Gfa | 433 [2021-11-22 18:14:27] DEBUG: Writing FASTA |
401 [2021-06-30 16:02:01] DEBUG: Peak RAM usage: 0 Gb | 434 [2021-11-22 18:14:27] DEBUG: Writing Gfa |
435 [2021-11-22 18:14:27] DEBUG: Peak RAM usage: 0 Gb | |
402 -----------End assembly log------------ | 436 -----------End assembly log------------ |
403 [2021-06-30 16:02:01] root: INFO: >>>STAGE: finalize | 437 [2021-11-22 18:14:27] root: INFO: >>>STAGE: finalize |
404 [2021-06-30 16:02:01] root: DEBUG: ---Output dir contents:---- | 438 [2021-11-22 18:14:27] root: DEBUG: ---Output dir contents:---- |
405 [2021-06-30 16:02:01] root: DEBUG: out_dir/ | 439 [2021-11-22 18:14:27] root: DEBUG: out_dir/ |
406 [2021-06-30 16:02:01] root: DEBUG: 367.0 B assembly_graph.gv | 440 [2021-11-22 18:14:27] root: DEBUG: 367.0 B assembly_graph.gv |
407 [2021-06-30 16:02:01] root: DEBUG: 415.0 K assembly.fasta | 441 [2021-11-22 18:14:27] root: DEBUG: 416.0 K assembly.fasta |
408 [2021-06-30 16:02:01] root: DEBUG: 92.0 B params.json | 442 [2021-11-22 18:14:27] root: DEBUG: 92.0 B params.json |
409 [2021-06-30 16:02:01] root: DEBUG: 26.0 K flye.log | 443 [2021-11-22 18:14:27] root: DEBUG: 28.0 K flye.log |
410 [2021-06-30 16:02:01] root: DEBUG: 409.0 K assembly_graph.gfa | 444 [2021-11-22 18:14:27] root: DEBUG: 409.0 K assembly_graph.gfa |
411 [2021-06-30 16:02:01] root: DEBUG: 10-consensus/ | 445 [2021-11-22 18:14:27] root: DEBUG: 10-consensus/ |
412 [2021-06-30 16:02:01] root: DEBUG: 415.0 K consensus.fasta | 446 [2021-11-22 18:14:27] root: DEBUG: 1.0 K minimap.stderr |
413 [2021-06-30 16:02:01] root: DEBUG: 37.0 B chunks.fasta.fai | 447 [2021-11-22 18:14:27] root: DEBUG: 449.0 K consensus.fasta |
414 [2021-06-30 16:02:01] root: DEBUG: 30-contigger/ | 448 [2021-11-22 18:14:27] root: DEBUG: 3.0 K minimap.bam.bai |
415 [2021-06-30 16:02:01] root: DEBUG: 409.0 K graph_final.gfa | 449 [2021-11-22 18:14:27] root: DEBUG: 30-contigger/ |
416 [2021-06-30 16:02:01] root: DEBUG: 0.0 B scaffolds_links.txt | 450 [2021-11-22 18:14:27] root: DEBUG: 409.0 K graph_final.gfa |
417 [2021-06-30 16:02:01] root: DEBUG: 111.0 B contigs_stats.txt | 451 [2021-11-22 18:14:27] root: DEBUG: 0.0 B scaffolds_links.txt |
418 [2021-06-30 16:02:01] root: DEBUG: 367.0 B graph_final.gv | 452 [2021-11-22 18:14:27] root: DEBUG: 111.0 B contigs_stats.txt |
419 [2021-06-30 16:02:01] root: DEBUG: 414.0 K graph_final.fasta | 453 [2021-11-22 18:14:27] root: DEBUG: 367.0 B graph_final.gv |
420 [2021-06-30 16:02:01] root: DEBUG: 414.0 K contigs.fasta | 454 [2021-11-22 18:14:27] root: DEBUG: 414.0 K graph_final.fasta |
421 [2021-06-30 16:02:01] root: DEBUG: 00-assembly/ | 455 [2021-11-22 18:14:27] root: DEBUG: 414.0 K contigs.fasta |
422 [2021-06-30 16:02:01] root: DEBUG: 429.0 K draft_assembly.fasta | 456 [2021-11-22 18:14:27] root: DEBUG: 00-assembly/ |
423 [2021-06-30 16:02:01] root: DEBUG: 20-repeat/ | 457 [2021-11-22 18:14:27] root: DEBUG: 61.0 B draft_assembly.fasta.fai |
424 [2021-06-30 16:02:01] root: DEBUG: 414.0 K graph_before_rr.fasta | 458 [2021-11-22 18:14:27] root: DEBUG: 465.0 K draft_assembly.fasta |
425 [2021-06-30 16:02:01] root: DEBUG: 183.0 B repeat_graph_dump | 459 [2021-11-22 18:14:27] root: DEBUG: 20-repeat/ |
426 [2021-06-30 16:02:01] root: DEBUG: 367.0 B graph_before_rr.gv | 460 [2021-11-22 18:14:27] root: DEBUG: 414.0 K graph_before_rr.fasta |
427 [2021-06-30 16:02:01] root: DEBUG: 367.0 B graph_after_rr.gv | 461 [2021-11-22 18:14:27] root: DEBUG: 183.0 B repeat_graph_dump |
428 [2021-06-30 16:02:01] root: DEBUG: 414.0 K repeat_graph_edges.fasta | 462 [2021-11-22 18:14:27] root: DEBUG: 367.0 B graph_before_rr.gv |
429 [2021-06-30 16:02:01] root: DEBUG: 129.0 K read_alignment_dump | 463 [2021-11-22 18:14:27] root: DEBUG: 367.0 B graph_after_rr.gv |
430 [2021-06-30 16:02:01] root: DEBUG: -------------------------- | 464 [2021-11-22 18:14:27] root: DEBUG: 414.0 K repeat_graph_edges.fasta |
431 [2021-06-30 16:02:01] root: INFO: Assembly statistics: | 465 [2021-11-22 18:14:27] root: DEBUG: 119.0 K read_alignment_dump |
432 | 466 [2021-11-22 18:14:27] root: DEBUG: -------------------------- |
433 Total length: 418805 | 467 [2021-11-22 18:14:27] root: INFO: Assembly statistics: |
468 | |
469 Total length: 419576 | |
434 Fragments: 1 | 470 Fragments: 1 |
435 Fragments N50: 418805 | 471 Fragments N50: 419576 |
436 Largest frg: 418805 | 472 Largest frg: 419576 |
437 Scaffolds: 0 | 473 Scaffolds: 0 |
438 Mean coverage: 15 | 474 Mean coverage: 14 |
439 | 475 |
440 [2021-06-30 16:02:01] root: INFO: Final assembly: /tmp/tmpicy_msib/job_working_directory/000/8/working/out_dir/assembly.fasta | 476 [2021-11-22 18:14:27] root: INFO: Final assembly: /tmp/tmpakmcmxzn/job_working_directory/000/8/working/out_dir/assembly.fasta |