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