[2019-09-06 08:49:43] root: INFO: Starting Flye 2.4-release [2019-09-06 08:49:43] root: DEBUG: Cmd: /usr/local/bin/flye --nano-raw output.sickle.fastq --out-dir output.flye --threads 8 --genome-size 10M [2019-09-06 08:49:43] root: INFO: >>>STAGE: configure [2019-09-06 08:49:43] root: INFO: Configuring run [2019-09-06 08:49:43] root: DEBUG: Total sequence length: 70608891 [2019-09-06 08:49:43] root: INFO: Input genome size: 10000000 [2019-09-06 08:49:43] root: INFO: Estimated coverage: 7 [2019-09-06 08:49:43] root: INFO: Reads N50/N90: 25366 / 5928 [2019-09-06 08:49:43] root: INFO: Minimum overlap set to 5000 [2019-09-06 08:49:43] root: INFO: Selected k-mer size: 15 [2019-09-06 08:49:43] root: INFO: >>>STAGE: assembly [2019-09-06 08:49:43] root: INFO: Assembling reads [2019-09-06 08:49:43] root: DEBUG: -----Begin assembly log------ [2019-09-06 08:49:43] root: DEBUG: Running: flye-assemble -l /data/user2/work/81/output.flye/flye.log -t 8 -v 5000 -k 15 output.sickle.fastq /data/user2/work/81/output.flye/00-assembly/draft_assembly.fasta 10000000 /usr/local/lib/python2.7/site-packages/flye/config/bin_cfg/asm_raw_reads.cfg [2019-09-06 08:49:43] DEBUG: Build date: Jan 15 2019 02:45:44 [2019-09-06 08:49:43] DEBUG: Total RAM: 204 Gb [2019-09-06 08:49:43] DEBUG: Available RAM: 198 Gb [2019-09-06 08:49:43] DEBUG: Total CPUs: 32 [2019-09-06 08:49:43] DEBUG: Parameters: [2019-09-06 08:49:43] DEBUG: big_genome_threshold=50000000 [2019-09-06 08:49:43] DEBUG: low_cutoff_warning=1 [2019-09-06 08:49:43] DEBUG: hard_min_coverage_rate=10 [2019-09-06 08:49:43] DEBUG: assemble_kmer_sample=1 [2019-09-06 08:49:43] DEBUG: repeat_graph_kmer_sample=1 [2019-09-06 08:49:43] DEBUG: read_align_kmer_sample=1 [2019-09-06 08:49:43] DEBUG: maximum_jump=1500 [2019-09-06 08:49:43] DEBUG: maximum_overhang=1500 [2019-09-06 08:49:43] DEBUG: repeat_kmer_rate=100 [2019-09-06 08:49:43] DEBUG: assemble_ovlp_divergence=0.30 [2019-09-06 08:49:43] DEBUG: repeat_graph_ovlp_divergence=0.15 [2019-09-06 08:49:43] DEBUG: repeat_graph_ovlp_end_adjust=0.00 [2019-09-06 08:49:43] DEBUG: read_align_ovlp_divergence=0.25 [2019-09-06 08:49:43] DEBUG: max_coverage_drop_rate=5 [2019-09-06 08:49:43] DEBUG: chimera_window=100 [2019-09-06 08:49:43] DEBUG: min_reads_in_contig=4 [2019-09-06 08:49:43] DEBUG: max_inner_reads=10 [2019-09-06 08:49:43] DEBUG: max_inner_fraction=0.25 [2019-09-06 08:49:43] DEBUG: add_unassembled_reads=0 [2019-09-06 08:49:43] DEBUG: max_separation=500 [2019-09-06 08:49:43] DEBUG: tip_length_threshold=20000 [2019-09-06 08:49:43] DEBUG: unique_edge_length=50000 [2019-09-06 08:49:43] DEBUG: min_repeat_res_support=0.51 [2019-09-06 08:49:43] DEBUG: out_paths_ratio=5 [2019-09-06 08:49:43] DEBUG: graph_cov_drop_rate=10 [2019-09-06 08:49:43] DEBUG: coverage_estimate_window=100 [2019-09-06 08:49:43] DEBUG: extend_contigs_with_repeats=1 [2019-09-06 08:49:43] DEBUG: Running with k-mer size: 15 [2019-09-06 08:49:43] DEBUG: Running with minimum overlap 5000 [2019-09-06 08:49:43] DEBUG: Metagenome mode: N [2019-09-06 08:49:43] INFO: Reading sequences [2019-09-06 08:49:43] DEBUG: Building positional index [2019-09-06 08:49:43] DEBUG: Total sequence: 70608891 bp [2019-09-06 08:49:43] DEBUG: Expected read coverage: 7 [2019-09-06 08:49:43] INFO: Generating solid k-mer index [2019-09-06 08:49:43] DEBUG: Hard threshold set to 2 [2019-09-06 08:49:43] DEBUG: Started kmer counting [2019-09-06 08:50:01] INFO: Counting kmers (1/2): [2019-09-06 08:50:02] INFO: Counting kmers (2/2): [2019-09-06 08:50:06] WARNING: Unable to separate erroneous k-mers from solid k-mers. Possible reasons: (1) Incorrect expected assembly size parameter (2) Highly uneven coverage of the assembly (3) Running with error-corrected reads in raw reads mode Assembly will continue, but results might not be optimal [2019-09-06 08:50:06] DEBUG: Estimated minimum kmer coverage: 2 [2019-09-06 08:50:06] DEBUG: Filtered 0 erroneous k-mers [2019-09-06 08:50:06] DEBUG: Repetetive k-mer frequency: 457 [2019-09-06 08:50:06] DEBUG: Filtered 69 repetitive kmers (7.69183e-06) [2019-09-06 08:50:06] INFO: Filling index table [2019-09-06 08:50:06] DEBUG: Sampling rate: 1 [2019-09-06 08:50:06] DEBUG: Solid kmers: 8970489 [2019-09-06 08:50:06] DEBUG: Kmer index size: 40921857 [2019-09-06 08:50:06] DEBUG: Mean k-mer frequency: 4.56183 [2019-09-06 08:50:11] DEBUG: Sorting k-mer index [2019-09-06 08:50:11] DEBUG: Peak RAM usage: 1 Gb [2019-09-06 08:50:11] INFO: Extending reads [2019-09-06 08:50:11] DEBUG: Estimating overlap coverage [2019-09-06 08:50:53] INFO: Overlap-based coverage: 11 [2019-09-06 08:50:53] INFO: Median overlap divergence: 0.119044 [2019-09-06 08:50:53] DEBUG: Sequence divergence distribution: | *** | **** | ***** | ***** | ****** | ****** | ******* | ******* | ******* | ******* | ******* | ******** | ********* | ********** | ********** | ************ | ************ | ************* | *************** | ********************** ---------------------------------------------------------------------------------------------------- 0% 5% 10% 15% 20% 25% 30% 35% 40% 45% Q25 = 0.11, Q50 = 0.12, Q75 = 0.13 [2019-09-06 08:50:55] DEBUG: Assembled contig 1 With 7 reads Start read: +a0d562ee-5c32-4285-8428-2dde75e6d4b2 At position: 5 leftTip: 1 rightTip: 0 Suspicios: 1 Mean extensions: 17 Avg overlap len: 20251 Min overlap len: 5067 Inner reads: 0 Length: 28722 [2019-09-06 08:50:55] DEBUG: Ovlp index size: 16922 [2019-09-06 08:50:55] DEBUG: Inner: 134 covered: 184 total: 6758 [2019-09-06 08:50:55] DEBUG: Assembled contig 2 With 5 reads Start read: +14d90d20-4de7-44ef-922e-59eb1fd35b0e At position: 3 leftTip: 1 rightTip: 0 Suspicios: 1 Mean extensions: 23 Avg overlap len: 12419 Min overlap len: 6804 Inner reads: 0 Length: 25951 [2019-09-06 08:50:55] DEBUG: Ovlp index size: 17281 [2019-09-06 08:50:55] DEBUG: Inner: 200 covered: 306 total: 6758 [2019-09-06 08:50:56] DEBUG: Discarded contig with 7 reads and 2 inner overlaps [2019-09-06 08:50:59] DEBUG: Assembled contig 3 With 158 reads Start read: +133b8587-a044-4ef0-b1fb-641064b744a3 At position: 1 leftTip: 1 rightTip: 0 Suspicios: 1 Mean extensions: 6 Avg overlap len: 41690 Min overlap len: 10235 Inner reads: 0 Length: 4483926 [2019-09-06 08:50:59] DEBUG: Ovlp index size: 20184 [2019-09-06 08:50:59] DEBUG: Inner: 3508 covered: 3714 total: 6758 [2019-09-06 08:50:59] DEBUG: Discarded contig with 153 reads and 151 inner overlaps [2019-09-06 08:50:59] DEBUG: Discarded contig with 157 reads and 154 inner overlaps [2019-09-06 08:50:59] DEBUG: Discarded contig with 51 reads and 45 inner overlaps [2019-09-06 08:50:59] DEBUG: Discarded contig with 120 reads and 118 inner overlaps [2019-09-06 08:50:59] DEBUG: Discarded contig with 84 reads and 82 inner overlaps [2019-09-06 08:50:59] DEBUG: Discarded contig with 159 reads and 155 inner overlaps [2019-09-06 08:50:59] DEBUG: Discarded contig with 118 reads and 116 inner overlaps [2019-09-06 08:50:59] DEBUG: Assembled contig 4 With 5 reads Start read: +e6844ecb-8675-46de-b5a8-557f6be33ae5 At position: 3 leftTip: 0 rightTip: 0 Suspicios: 0 Mean extensions: 25 Avg overlap len: 9423 Min overlap len: 6370 Inner reads: 0 Length: 24023 [2019-09-06 08:50:59] DEBUG: Ovlp index size: 20454 [2019-09-06 08:50:59] DEBUG: Inner: 3542 covered: 3800 total: 6758 [2019-09-06 08:51:00] DEBUG: Assembled contig 5 With 5 reads Start read: +11ea8b0c-35d4-44d8-a7cc-9bf1b5cfa581 At position: 3 leftTip: 0 rightTip: 0 Suspicios: 0 Mean extensions: 28 Avg overlap len: 9568 Min overlap len: 5211 Inner reads: 0 Length: 30356 [2019-09-06 08:51:00] DEBUG: Ovlp index size: 20763 [2019-09-06 08:51:00] DEBUG: Inner: 3574 covered: 3854 total: 6758 [2019-09-06 08:51:00] DEBUG: Assembled contig 6 With 6 reads Start read: +f0db5748-63f8-41c7-bbbe-8157fdb27856 At position: 3 leftTip: 0 rightTip: 0 Suspicios: 0 Mean extensions: 20 Avg overlap len: 18019 Min overlap len: 9025 Inner reads: 1 Length: 29904 [2019-09-06 08:51:00] DEBUG: Ovlp index size: 21042 [2019-09-06 08:51:00] DEBUG: Inner: 3610 covered: 3884 total: 6758 [2019-09-06 08:51:00] DEBUG: Assembled contig 7 With 4 reads Start read: +6d52e1e6-3714-4b18-9cb1-ff4e26279c22 At position: 3 leftTip: 0 rightTip: 0 Suspicios: 0 Mean extensions: 21 Avg overlap len: 12396 Min overlap len: 12361 Inner reads: 0 Length: 31985 [2019-09-06 08:51:00] DEBUG: Ovlp index size: 21077 [2019-09-06 08:51:00] DEBUG: Inner: 3620 covered: 3892 total: 6758 [2019-09-06 08:51:00] DEBUG: Assembled contig 8 With 5 reads Start read: +7cc82689-0bd2-4353-9ff0-efffde736062 At position: 4 leftTip: 0 rightTip: 0 Suspicios: 0 Mean extensions: 18 Avg overlap len: 21331 Min overlap len: 20216 Inner reads: 0 Length: 36707 [2019-09-06 08:51:00] DEBUG: Ovlp index size: 21146 [2019-09-06 08:51:00] DEBUG: Inner: 3630 covered: 3900 total: 6758 [2019-09-06 08:51:00] DEBUG: Assembled contig 9 With 5 reads Start read: +20369a65-ce6d-4799-9835-0694e5ee7c0a At position: 3 leftTip: 0 rightTip: 0 Suspicios: 0 Mean extensions: 20 Avg overlap len: 18326 Min overlap len: 15295 Inner reads: 1 Length: 29345 [2019-09-06 08:51:00] DEBUG: Ovlp index size: 21250 [2019-09-06 08:51:00] DEBUG: Inner: 3640 covered: 3920 total: 6758 [2019-09-06 08:51:00] DEBUG: Assembled contig 10 With 5 reads Start read: +482cfdfd-1308-4ded-924c-f5fe6b0b83cb At position: 3 leftTip: 0 rightTip: 0 Suspicios: 0 Mean extensions: 28 Avg overlap len: 15829 Min overlap len: 8516 Inner reads: 1 Length: 23668 [2019-09-06 08:51:00] DEBUG: Ovlp index size: 21319 [2019-09-06 08:51:00] DEBUG: Inner: 3656 covered: 3936 total: 6758 [2019-09-06 08:51:00] DEBUG: Discarded contig with 5 reads and 2 inner overlaps [2019-09-06 08:51:01] DEBUG: Assembled contig 11 With 5 reads Start read: +4ebab051-1b6c-4ee3-9222-0c637f977677 At position: 3 leftTip: 0 rightTip: 0 Suspicios: 0 Mean extensions: 26 Avg overlap len: 14641 Min overlap len: 5678 Inner reads: 0 Length: 30917 [2019-09-06 08:51:01] DEBUG: Ovlp index size: 21823 [2019-09-06 08:51:01] DEBUG: Inner: 3670 covered: 3986 total: 6758 [2019-09-06 08:51:01] DEBUG: Assembled contig 12 With 4 reads Start read: +4493d8e8-f6f9-40f8-897e-119a816babc3 At position: 3 leftTip: 0 rightTip: 0 Suspicios: 0 Mean extensions: 24 Avg overlap len: 6024 Min overlap len: 6024 Inner reads: 0 Length: 14073 [2019-09-06 08:51:01] DEBUG: Ovlp index size: 21927 [2019-09-06 08:51:01] DEBUG: Inner: 3692 covered: 4022 total: 6758 [2019-09-06 08:51:01] DEBUG: Assembled contig 13 With 4 reads Start read: +fe77f683-0a8d-4316-9efa-0b9acdd2f7a5 At position: 3 leftTip: 0 rightTip: 0 Suspicios: 0 Mean extensions: 26 Avg overlap len: 7139 Min overlap len: 7080 Inner reads: 0 Length: 28451 [2019-09-06 08:51:01] DEBUG: Ovlp index size: 22801 [2019-09-06 08:51:01] DEBUG: Inner: 3700 covered: 4072 total: 6758 [2019-09-06 08:51:02] DEBUG: Assembled contig 14 With 5 reads Start read: +d0f089ed-e4f7-4980-b91a-4d13d051d4b2 At position: 4 leftTip: 0 rightTip: 0 Suspicios: 1 Mean extensions: 26 Avg overlap len: 10645 Min overlap len: 8736 Inner reads: 0 Length: 17591 [2019-09-06 08:51:02] DEBUG: Ovlp index size: 23304 [2019-09-06 08:51:02] DEBUG: Inner: 3728 covered: 4110 total: 6758 [2019-09-06 08:51:02] DEBUG: Assembled contig 15 With 6 reads Start read: +3ce26322-83e7-4ade-8c97-8aa32c7eb704 At position: 5 leftTip: 0 rightTip: 1 Suspicios: 1 Mean extensions: 22 Avg overlap len: 13371 Min overlap len: 5670 Inner reads: 1 Length: 28706 [2019-09-06 08:51:02] DEBUG: Ovlp index size: 23339 [2019-09-06 08:51:02] DEBUG: Inner: 3804 covered: 4200 total: 6758 [2019-09-06 08:51:02] DEBUG: Assembled contig 16 With 4 reads Start read: +b8ea1799-2b38-4ed0-a373-3499fa788124 At position: 3 leftTip: 0 rightTip: 0 Suspicios: 0 Mean extensions: 26 Avg overlap len: 9030 Min overlap len: 9029 Inner reads: 1 Length: 38720 [2019-09-06 08:51:02] DEBUG: Ovlp index size: 23443 [2019-09-06 08:51:02] DEBUG: Inner: 3808 covered: 4216 total: 6758 [2019-09-06 08:51:02] DEBUG: Assembled contig 17 With 5 reads Start read: +cfdeb67c-7123-4e5c-9604-042f042bc799 At position: 2 leftTip: 1 rightTip: 0 Suspicios: 1 Mean extensions: 26 Avg overlap len: 11537 Min overlap len: 5397 Inner reads: 0 Length: 23706 [2019-09-06 08:51:02] DEBUG: Ovlp index size: 23557 [2019-09-06 08:51:02] DEBUG: Inner: 3848 covered: 4292 total: 6758 [2019-09-06 08:51:02] DEBUG: Assembled contig 18 With 4 reads Start read: +0aabcff8-fc60-467a-a6d0-f2e8836b02c2 At position: 3 leftTip: 0 rightTip: 0 Suspicios: 0 Mean extensions: 7 Avg overlap len: 10340 Min overlap len: 10340 Inner reads: 0 Length: 54103 [2019-09-06 08:51:02] DEBUG: Ovlp index size: 23614 [2019-09-06 08:51:02] DEBUG: Inner: 3886 covered: 4352 total: 6758 [2019-09-06 08:51:03] DEBUG: Assembled contig 19 With 6 reads Start read: +d9c784fd-6ff6-4006-ac9c-73bfd35ddba7 At position: 3 leftTip: 0 rightTip: 0 Suspicios: 0 Mean extensions: 7 Avg overlap len: 9418 Min overlap len: 8019 Inner reads: 0 Length: 51655 [2019-09-06 08:51:03] DEBUG: Ovlp index size: 23698 [2019-09-06 08:51:03] DEBUG: Inner: 3900 covered: 4444 total: 6758 [2019-09-06 08:51:03] DEBUG: Assembled contig 20 With 4 reads Start read: +c37a0cff-9773-4403-a5c1-c912c6f35fea At position: 3 leftTip: 0 rightTip: 0 Suspicios: 0 Mean extensions: 12 Avg overlap len: 15932 Min overlap len: 15862 Inner reads: 0 Length: 49610 [2019-09-06 08:51:03] DEBUG: Ovlp index size: 23758 [2019-09-06 08:51:03] DEBUG: Inner: 3940 covered: 4520 total: 6758 [2019-09-06 08:51:03] DEBUG: Assembled contig 21 With 5 reads Start read: +4977c39d-555a-4a85-8b70-38829db052b0 At position: 2 leftTip: 1 rightTip: 0 Suspicios: 0 Mean extensions: 6 Avg overlap len: 19750 Min overlap len: 9487 Inner reads: 0 Length: 60418 [2019-09-06 08:51:03] DEBUG: Ovlp index size: 23786 [2019-09-06 08:51:03] DEBUG: Inner: 3998 covered: 4590 total: 6758 [2019-09-06 08:51:04] DEBUG: Assembled contig 22 With 4 reads Start read: +6865c6d7-be26-4031-88ab-4518c4d94f93 At position: 1 leftTip: 1 rightTip: 0 Suspicios: 0 Mean extensions: 4 Avg overlap len: 9637 Min overlap len: 5428 Inner reads: 0 Length: 85367 [2019-09-06 08:51:04] DEBUG: Ovlp index size: 23906 [2019-09-06 08:51:04] DEBUG: Inner: 4012 covered: 4698 total: 6758 [2019-09-06 08:51:04] DEBUG: Assembled contig 23 With 7 reads Start read: +1a9fdae7-07e8-4b75-8ef9-d016b0597d95 At position: 6 leftTip: 0 rightTip: 0 Suspicios: 0 Mean extensions: 10 Avg overlap len: 11026 Min overlap len: 7396 Inner reads: 0 Length: 73085 [2019-09-06 08:51:04] DEBUG: Ovlp index size: 23948 [2019-09-06 08:51:04] DEBUG: Inner: 4064 covered: 4762 total: 6758 [2019-09-06 08:51:04] DEBUG: Assembled contig 24 With 4 reads Start read: +35dcc79a-914a-453d-8f14-42875fab6925 At position: 3 leftTip: 0 rightTip: 0 Suspicios: 0 Mean extensions: 6 Avg overlap len: 7457 Min overlap len: 7047 Inner reads: 0 Length: 104933 [2019-09-06 08:51:04] DEBUG: Ovlp index size: 23983 [2019-09-06 08:51:04] DEBUG: Inner: 4090 covered: 4832 total: 6758 [2019-09-06 08:51:05] DEBUG: Assembled contig 25 With 6 reads Start read: +1a46171a-bacb-48c6-a9e2-0fa10d3d8db9 At position: 4 leftTip: 0 rightTip: 0 Suspicios: 0 Mean extensions: 7 Avg overlap len: 10583 Min overlap len: 6808 Inner reads: 0 Length: 120944 [2019-09-06 08:51:05] DEBUG: Ovlp index size: 24048 [2019-09-06 08:51:05] DEBUG: Inner: 4112 covered: 5032 total: 6758 [2019-09-06 08:51:07] DEBUG: Assembled contig 26 With 4 reads Start read: +bfa69060-045c-43f6-b563-ae018c194b91 At position: 3 leftTip: 0 rightTip: 0 Suspicios: 0 Mean extensions: 9 Avg overlap len: 16093 Min overlap len: 11581 Inner reads: 0 Length: 243754 [2019-09-06 08:51:07] DEBUG: Ovlp index size: 24179 [2019-09-06 08:51:07] DEBUG: Inner: 4158 covered: 5412 total: 6758 [2019-09-06 08:51:14] INFO: Assembled 26 draft contigs [2019-09-06 08:51:14] INFO: Generating contig sequences [2019-09-06 08:51:53] DEBUG: Writing FASTA [2019-09-06 08:51:53] DEBUG: Peak RAM usage: 2 Gb -----------End assembly log------------ [2019-09-06 08:51:54] root: INFO: >>>STAGE: consensus [2019-09-06 08:51:54] root: INFO: Running Minimap2 [2019-09-06 08:52:06] root: INFO: Computing consensus [2019-09-06 08:53:34] root: INFO: Alignment error rate: 0.17155453639 [2019-09-06 08:53:34] root: INFO: >>>STAGE: repeat [2019-09-06 08:53:34] root: INFO: Building and resolving repeat graph [2019-09-06 08:53:34] root: DEBUG: -----Begin repeat analyser log------ [2019-09-06 08:53:34] root: DEBUG: Running: flye-repeat -l /data/user2/work/81/output.flye/flye.log -t 8 -v 5000 -k 15 /data/user2/work/81/output.flye/10-consensus/consensus.fasta output.sickle.fastq /data/user2/work/81/output.flye/20-repeat /usr/local/lib/python2.7/site-packages/flye/config/bin_cfg/asm_raw_reads.cfg [2019-09-06 08:53:34] DEBUG: Build date: Jan 15 2019 02:45:24 [2019-09-06 08:53:34] DEBUG: Total RAM: 204 Gb [2019-09-06 08:53:34] DEBUG: Available RAM: 199 Gb [2019-09-06 08:53:34] DEBUG: Total CPUs: 32 [2019-09-06 08:53:34] DEBUG: Parameters: [2019-09-06 08:53:34] DEBUG: big_genome_threshold=50000000 [2019-09-06 08:53:34] DEBUG: low_cutoff_warning=1 [2019-09-06 08:53:34] DEBUG: hard_min_coverage_rate=10 [2019-09-06 08:53:34] DEBUG: assemble_kmer_sample=1 [2019-09-06 08:53:34] DEBUG: repeat_graph_kmer_sample=1 [2019-09-06 08:53:34] DEBUG: read_align_kmer_sample=1 [2019-09-06 08:53:34] DEBUG: maximum_jump=1500 [2019-09-06 08:53:34] DEBUG: maximum_overhang=1500 [2019-09-06 08:53:34] DEBUG: repeat_kmer_rate=100 [2019-09-06 08:53:34] DEBUG: assemble_ovlp_divergence=0.30 [2019-09-06 08:53:34] DEBUG: repeat_graph_ovlp_divergence=0.15 [2019-09-06 08:53:34] DEBUG: repeat_graph_ovlp_end_adjust=0.00 [2019-09-06 08:53:34] DEBUG: read_align_ovlp_divergence=0.25 [2019-09-06 08:53:34] DEBUG: max_coverage_drop_rate=5 [2019-09-06 08:53:34] DEBUG: chimera_window=100 [2019-09-06 08:53:34] DEBUG: min_reads_in_contig=4 [2019-09-06 08:53:34] DEBUG: max_inner_reads=10 [2019-09-06 08:53:34] DEBUG: max_inner_fraction=0.25 [2019-09-06 08:53:34] DEBUG: add_unassembled_reads=0 [2019-09-06 08:53:34] DEBUG: max_separation=500 [2019-09-06 08:53:34] DEBUG: tip_length_threshold=20000 [2019-09-06 08:53:34] DEBUG: unique_edge_length=50000 [2019-09-06 08:53:34] DEBUG: min_repeat_res_support=0.51 [2019-09-06 08:53:34] DEBUG: out_paths_ratio=5 [2019-09-06 08:53:34] DEBUG: graph_cov_drop_rate=10 [2019-09-06 08:53:34] DEBUG: coverage_estimate_window=100 [2019-09-06 08:53:34] DEBUG: extend_contigs_with_repeats=1 [2019-09-06 08:53:34] DEBUG: Running with k-mer size: 15 [2019-09-06 08:53:34] DEBUG: Selected minimum overlap 5000 [2019-09-06 08:53:34] DEBUG: Metagenome mode: N [2019-09-06 08:53:34] INFO: Reading sequences [2019-09-06 08:53:34] DEBUG: Building positional index [2019-09-06 08:53:34] DEBUG: Total sequence: 70608891 bp [2019-09-06 08:53:34] DEBUG: Building positional index [2019-09-06 08:53:34] DEBUG: Total sequence: 5640253 bp [2019-09-06 08:53:34] INFO: Building repeat graph [2019-09-06 08:53:35] DEBUG: Hard threshold set to 1 [2019-09-06 08:53:35] DEBUG: Started kmer counting [2019-09-06 08:53:56] DEBUG: Repetetive k-mer frequency: 115 [2019-09-06 08:53:56] DEBUG: Filtered 0 repetitive kmers (0) [2019-09-06 08:53:56] DEBUG: Sampling rate: 1 [2019-09-06 08:53:56] DEBUG: Solid kmers: 452219 [2019-09-06 08:53:56] DEBUG: Kmer index size: 1196613 [2019-09-06 08:53:56] DEBUG: Mean k-mer frequency: 2.64609 [2019-09-06 08:53:57] DEBUG: Sorting k-mer index [2019-09-06 08:54:06] DEBUG: Computing transitive closure for overlaps [2019-09-06 08:54:06] DEBUG: Found 1212 overlaps [2019-09-06 08:54:06] DEBUG: Left 496 overlaps after filtering [2019-09-06 08:54:06] INFO: Median overlap divergence: 0.119365 [2019-09-06 08:54:06] DEBUG: Sequence divergence distribution: | * | * | * ** * | * ** * | * ** * | * *** * | * *** * | * *** * | * * *** * * * | * * *** * * * | * * *** * * * | *** ******* ** * | *** ******* ** * | *** ******* ** * | * *** ******* *** * * * * | * *** ******* *** * * * * | * *** ******* *** * * * * | * *********** *** ** * ** * * * * ** | * *********** *** ** * ** * * * * ** | * *********** *** ** * ** * * * * ** ---------------------------------------------------------------------------------------------------- 0% 5% 10% 15% 20% 25% 30% 35% 40% 45% Q25 = 0.097, Q50 = 0.12, Q75 = 0.15 [2019-09-06 08:54:06] DEBUG: Computing gluepoints [2019-09-06 08:54:06] DEBUG: Added 10 gluepoint projections [2019-09-06 08:54:06] DEBUG: Added 8 gluepoint projections [2019-09-06 08:54:06] DEBUG: Added 0 gluepoint projections [2019-09-06 08:54:06] DEBUG: Created 580 gluepoints [2019-09-06 08:54:06] DEBUG: Tandems removed: 17 left, 17 right, 0 both [2019-09-06 08:54:06] DEBUG: Initializing edges [2019-09-06 08:54:06] DEBUG: Filtered 0 singleton segments [2019-09-06 08:54:06] DEBUG: Removed 0 simple and 0 double chimeric junctions [2019-09-06 08:54:06] DEBUG: Collapsed 35 edges [2019-09-06 08:54:06] DEBUG: Collapsed 0 bulges [2019-09-06 08:54:06] DEBUG: Collapsed 0 edges [2019-09-06 08:54:06] DEBUG: -48 +contig_8 23020 23595 575 [2019-09-06 08:54:06] DEBUG: -47 +contig_8 23595 24301 706 [2019-09-06 08:54:06] DEBUG: -48 +contig_9 11847 12493 646 [2019-09-06 08:54:06] DEBUG: -47 +contig_9 12493 13125 632 [2019-09-06 08:54:06] DEBUG: * -21 +contig_21 0 59998 59998 [2019-09-06 08:54:06] DEBUG: -54 +contig_1 9 19760 19751 [2019-09-06 08:54:06] DEBUG: 47 +contig_1 19760 20392 632 [2019-09-06 08:54:06] DEBUG: 48 +contig_1 20392 21033 641 [2019-09-06 08:54:06] DEBUG: * -18 +contig_22 20915 84129 63214 [2019-09-06 08:54:06] DEBUG: -48 +contig_16 20344 20984 640 [2019-09-06 08:54:06] DEBUG: -47 +contig_16 20984 21630 646 [2019-09-06 08:54:06] DEBUG: 47 +contig_5 6958 7591 633 [2019-09-06 08:54:06] DEBUG: 48 +contig_5 7591 8218 627 [2019-09-06 08:54:06] DEBUG: * 55 +contig_2 88 25677 25589 [2019-09-06 08:54:06] DEBUG: -48 +contig_10 11076 11728 652 [2019-09-06 08:54:06] DEBUG: -47 +contig_10 11728 12348 620 [2019-09-06 08:54:06] DEBUG: * 57 +contig_3 10842 468847 458005 [2019-09-06 08:54:06] DEBUG: * -22 +contig_3 468847 593263 124416 [2019-09-06 08:54:06] DEBUG: -11 +contig_3 593263 598331 5068 [2019-09-06 08:54:06] DEBUG: * 53 +contig_3 598331 2932015 2333684 [2019-09-06 08:54:06] DEBUG: 11 +contig_3 2932015 2937087 5072 [2019-09-06 08:54:06] DEBUG: * 10 +contig_3 2937087 3599490 662403 [2019-09-06 08:54:06] DEBUG: 11 +contig_3 3599490 3604659 5169 [2019-09-06 08:54:06] DEBUG: * -51 +contig_3 3604659 4095904 491245 [2019-09-06 08:54:06] DEBUG: -11 +contig_3 4095904 4100984 5080 [2019-09-06 08:54:06] DEBUG: * -9 +contig_3 4100984 4185467 84483 [2019-09-06 08:54:06] DEBUG: -11 +contig_3 4185467 4190525 5058 [2019-09-06 08:54:06] DEBUG: * -8 +contig_3 4190525 4310790 120265 [2019-09-06 08:54:06] DEBUG: -11 +contig_3 4310790 4315896 5106 [2019-09-06 08:54:06] DEBUG: * -7 +contig_3 4315896 4350444 34548 [2019-09-06 08:54:06] DEBUG: -11 +contig_3 4350444 4355475 5031 [2019-09-06 08:54:06] DEBUG: * -56 +contig_3 4355475 4381377 25902 [2019-09-06 08:54:06] DEBUG: * -46 +contig_3 4381377 4386554 5177 [2019-09-06 08:54:06] DEBUG: 47 +contig_11 11281 11921 640 [2019-09-06 08:54:06] DEBUG: 48 +contig_11 11921 12560 639 [2019-09-06 08:54:06] DEBUG: -47 +contig_15 80 783 703 [2019-09-06 08:54:06] DEBUG: 54 +contig_15 783 20162 19379 [2019-09-06 08:54:06] DEBUG: 47 +contig_7 17917 18545 628 [2019-09-06 08:54:06] DEBUG: 48 +contig_7 18545 19154 609 [2019-09-06 08:54:06] DEBUG: 48 +contig_4 94 741 647 [2019-09-06 08:54:06] DEBUG: -48 +contig_6 14436 15073 637 [2019-09-06 08:54:06] DEBUG: -47 +contig_6 15073 15685 612 [2019-09-06 08:54:06] DEBUG: Total edges: 57 [2019-09-06 08:54:06] DEBUG: Building positional index [2019-09-06 08:54:06] DEBUG: Total sequence: 4576408 bp [2019-09-06 08:54:06] INFO: Aligning reads to the graph [2019-09-06 08:54:06] DEBUG: Hard threshold set to 1 [2019-09-06 08:54:06] DEBUG: Started kmer counting [2019-09-06 08:54:26] DEBUG: Repetetive k-mer frequency: 104 [2019-09-06 08:54:26] DEBUG: Filtered 0 repetitive kmers (0) [2019-09-06 08:54:26] DEBUG: Sampling rate: 1 [2019-09-06 08:54:26] DEBUG: Solid kmers: 4397852 [2019-09-06 08:54:26] DEBUG: Kmer index size: 4575778 [2019-09-06 08:54:26] DEBUG: Mean k-mer frequency: 1.04046 [2019-09-06 08:54:28] DEBUG: Sorting k-mer index [2019-09-06 08:54:37] DEBUG: Total reads : 3379 [2019-09-06 08:54:37] DEBUG: Read with aligned parts : 3330 [2019-09-06 08:54:37] DEBUG: Aligned in one piece : 3301 [2019-09-06 08:54:37] INFO: Aligned read sequence: 64646194 / 65381103 (0.98876) [2019-09-06 08:54:37] INFO: Median overlap divergence: 0.0813888 [2019-09-06 08:54:37] DEBUG: Sequence divergence distribution: | ** | ** | *** | *** | *** | **** | **** | ***** | ***** | ***** | ******* | ******* | ******* | ******** | ******** | ********* | ********** | *********** | ************* | * ********************************************************************************** ---------------------------------------------------------------------------------------------------- 0% 5% 10% 15% 20% 25% 30% 35% 40% 45% Q25 = 0.072, Q50 = 0.081, Q75 = 0.096 [2019-09-06 08:54:38] INFO: Mean edge coverage: 14 [2019-09-06 08:54:38] DEBUG: -56 len:25902 cov:7 mult:0.5 [2019-09-06 08:54:38] DEBUG: 56 len:25902 cov:7 mult:0.5 [2019-09-06 08:54:38] DEBUG: -55 len:25589 cov:293 mult:20.9286 [2019-09-06 08:54:38] DEBUG: 55 len:25589 cov:293 mult:20.9286 [2019-09-06 08:54:38] DEBUG: 54 len:19565 cov:224 mult:16 [2019-09-06 08:54:38] DEBUG: -51 len:491245 cov:12 mult:0.857143 [2019-09-06 08:54:38] DEBUG: -22 len:124416 cov:11 mult:0.785714 [2019-09-06 08:54:38] DEBUG: -54 len:19565 cov:224 mult:16 [2019-09-06 08:54:38] DEBUG: -53 len:2333684 cov:12 mult:0.857143 [2019-09-06 08:54:38] DEBUG: -18 len:63214 cov:2 mult:0.142857 [2019-09-06 08:54:38] DEBUG: -7 len:34548 cov:8 mult:0.571429 [2019-09-06 08:54:38] DEBUG: -21 len:59998 cov:1 mult:0.0714286 [2019-09-06 08:54:38] DEBUG: 46 len:5177 cov:7 mult:0.5 [2019-09-06 08:54:38] DEBUG: 51 len:491245 cov:12 mult:0.857143 [2019-09-06 08:54:38] DEBUG: 10 len:662403 cov:12 mult:0.857143 [2019-09-06 08:54:38] DEBUG: 48 len:631 cov:283 mult:20.2143 [2019-09-06 08:54:38] DEBUG: 21 len:59998 cov:1 mult:0.0714286 [2019-09-06 08:54:38] DEBUG: 11 len:5083 cov:61 mult:4.35714 [2019-09-06 08:54:38] DEBUG: 18 len:63214 cov:2 mult:0.142857 [2019-09-06 08:54:38] DEBUG: -9 len:84483 cov:11 mult:0.785714 [2019-09-06 08:54:38] DEBUG: 57 len:458005 cov:13 mult:0.928571 [2019-09-06 08:54:38] DEBUG: -47 len:645 cov:273 mult:19.5 [2019-09-06 08:54:38] DEBUG: -10 len:662403 cov:12 mult:0.857143 [2019-09-06 08:54:38] DEBUG: -8 len:120265 cov:7 mult:0.5 [2019-09-06 08:54:38] DEBUG: 8 len:120265 cov:7 mult:0.5 [2019-09-06 08:54:38] DEBUG: -48 len:631 cov:283 mult:20.2143 [2019-09-06 08:54:38] DEBUG: 22 len:124416 cov:11 mult:0.785714 [2019-09-06 08:54:38] DEBUG: 47 len:645 cov:273 mult:19.5 [2019-09-06 08:54:38] DEBUG: -57 len:458005 cov:13 mult:0.928571 [2019-09-06 08:54:38] DEBUG: -11 len:5083 cov:61 mult:4.35714 [2019-09-06 08:54:38] DEBUG: 53 len:2333684 cov:12 mult:0.857143 [2019-09-06 08:54:38] DEBUG: 7 len:34548 cov:8 mult:0.571429 [2019-09-06 08:54:38] DEBUG: 9 len:84483 cov:11 mult:0.785714 [2019-09-06 08:54:38] DEBUG: -46 len:5177 cov:7 mult:0.5 [2019-09-06 08:54:38] DEBUG: Unique coverage threshold 21 [2019-09-06 08:54:38] DEBUG: Read coverage cutoff: 1 [2019-09-06 08:54:38] DEBUG: Low coverage: -21 1 [2019-09-06 08:54:38] DEBUG: Removed 1 unsupported edges [2019-09-06 08:54:38] DEBUG: 0 tips clipped [2019-09-06 08:54:38] DEBUG: Unrolled 1 heterozygous loops [2019-09-06 08:54:38] DEBUG: Removed 0 heterozygous loops [2019-09-06 08:54:38] DEBUG: Popped 0 heterozygous bulges [2019-09-06 08:54:38] INFO: Resolving repeats [2019-09-06 08:54:38] DEBUG: Finding repeats [2019-09-06 08:54:38] DEBUG: Cov: -55 25589 293 [2019-09-06 08:54:38] DEBUG: Cov: 54 19565 224 [2019-09-06 08:54:38] DEBUG: Cov: 48 631 283 [2019-09-06 08:54:38] DEBUG: Cov: 11 5083 61 [2019-09-06 08:54:38] DEBUG: Cov: -47 645 273 [2019-09-06 08:54:38] DEBUG: Repeat detection iteration 1 [2019-09-06 08:54:38] DEBUG: Writing Dot [2019-09-06 08:54:38] DEBUG: Writing FASTA [2019-09-06 08:54:38] DEBUG: Total unique edges: 11 [2019-09-06 08:54:38] DEBUG: Connection 56 7 5 0.909091 [2019-09-06 08:54:38] DEBUG: Connection -22 53 9 1 [2019-09-06 08:54:38] DEBUG: Connection 51 -10 3 1 [2019-09-06 08:54:38] DEBUG: Connection 7 8 4 1 [2019-09-06 08:54:38] DEBUG: Connection 53 10 6 1 [2019-09-06 08:54:38] DEBUG: Connection 8 9 6 1 [2019-09-06 08:54:38] DEBUG: Connection 57 -18 6 0.923077 [2019-09-06 08:54:38] DEBUG: Connection -51 -9 6 1 [2019-09-06 08:54:38] DEBUG: Resolved: 8 links: 94 [2019-09-06 08:54:38] DEBUG: Unresolved: 0 [2019-09-06 08:54:38] DEBUG: Finding repeats [2019-09-06 08:54:38] DEBUG: Cov: -55 25589 293 [2019-09-06 08:54:38] DEBUG: Cov: 54 19565 224 [2019-09-06 08:54:38] DEBUG: Cov: 48 631 283 [2019-09-06 08:54:38] DEBUG: Cov: -47 645 273 [2019-09-06 08:54:38] DEBUG: Repeat detection iteration 1 [2019-09-06 08:54:38] DEBUG: Total unique edges: 18 [2019-09-06 08:54:38] DEBUG: Resolved: 0 links: 0 [2019-09-06 08:54:38] DEBUG: Unresolved: 0 [2019-09-06 08:54:38] DEBUG: Removed 0 simple and 0 double chimeric junctions [2019-09-06 08:54:38] DEBUG: Writing Dot [2019-09-06 08:54:38] DEBUG: Writing FASTA [2019-09-06 08:54:38] DEBUG: Peak RAM usage: 9 Gb -----------End assembly log------------ [2019-09-06 08:54:38] root: INFO: >>>STAGE: trestle [2019-09-06 08:54:38] root: DEBUG: Finding unbridged repeats [2019-09-06 08:54:38] root: INFO: Simple unbridged repeats: 0 [2019-09-06 08:54:38] root: INFO: Resolved: 0 [2019-09-06 08:54:38] root: INFO: >>>STAGE: contigger [2019-09-06 08:54:38] root: INFO: Generating contigs [2019-09-06 08:54:38] root: DEBUG: -----Begin contigger analyser log------ [2019-09-06 08:54:38] root: DEBUG: Running: flye-contigger -l /data/user2/work/81/output.flye/flye.log -t 8 -v 5000 -k 15 /data/user2/work/81/output.flye/21-trestle/repeat_graph_edges.fasta output.sickle.fastq /data/user2/work/81/output.flye/30-contigger /usr/local/lib/python2.7/site-packages/flye/config/bin_cfg/asm_raw_reads.cfg /data/user2/work/81/output.flye/21-trestle/repeat_graph_dump /data/user2/work/81/output.flye/20-repeat/read_alignment_dump [2019-09-06 08:54:38] DEBUG: Build date: Jan 15 2019 02:45:52 [2019-09-06 08:54:38] DEBUG: Total RAM: 204 Gb [2019-09-06 08:54:38] DEBUG: Available RAM: 199 Gb [2019-09-06 08:54:38] DEBUG: Total CPUs: 32 [2019-09-06 08:54:38] DEBUG: Parameters: [2019-09-06 08:54:38] DEBUG: big_genome_threshold=50000000 [2019-09-06 08:54:38] DEBUG: low_cutoff_warning=1 [2019-09-06 08:54:38] DEBUG: hard_min_coverage_rate=10 [2019-09-06 08:54:38] DEBUG: assemble_kmer_sample=1 [2019-09-06 08:54:38] DEBUG: repeat_graph_kmer_sample=1 [2019-09-06 08:54:38] DEBUG: read_align_kmer_sample=1 [2019-09-06 08:54:38] DEBUG: maximum_jump=1500 [2019-09-06 08:54:38] DEBUG: maximum_overhang=1500 [2019-09-06 08:54:38] DEBUG: repeat_kmer_rate=100 [2019-09-06 08:54:38] DEBUG: assemble_ovlp_divergence=0.30 [2019-09-06 08:54:38] DEBUG: repeat_graph_ovlp_divergence=0.15 [2019-09-06 08:54:38] DEBUG: repeat_graph_ovlp_end_adjust=0.00 [2019-09-06 08:54:38] DEBUG: read_align_ovlp_divergence=0.25 [2019-09-06 08:54:38] DEBUG: max_coverage_drop_rate=5 [2019-09-06 08:54:38] DEBUG: chimera_window=100 [2019-09-06 08:54:38] DEBUG: min_reads_in_contig=4 [2019-09-06 08:54:38] DEBUG: max_inner_reads=10 [2019-09-06 08:54:38] DEBUG: max_inner_fraction=0.25 [2019-09-06 08:54:38] DEBUG: add_unassembled_reads=0 [2019-09-06 08:54:38] DEBUG: max_separation=500 [2019-09-06 08:54:38] DEBUG: tip_length_threshold=20000 [2019-09-06 08:54:38] DEBUG: unique_edge_length=50000 [2019-09-06 08:54:38] DEBUG: min_repeat_res_support=0.51 [2019-09-06 08:54:38] DEBUG: out_paths_ratio=5 [2019-09-06 08:54:38] DEBUG: graph_cov_drop_rate=10 [2019-09-06 08:54:38] DEBUG: coverage_estimate_window=100 [2019-09-06 08:54:38] DEBUG: extend_contigs_with_repeats=1 [2019-09-06 08:54:38] DEBUG: Running with k-mer size: 15 [2019-09-06 08:54:38] DEBUG: Selected minimum overlap 5000 [2019-09-06 08:54:38] INFO: Reading sequences [2019-09-06 08:54:38] DEBUG: Building positional index [2019-09-06 08:54:38] DEBUG: Total sequence: 70608891 bp [2019-09-06 08:54:38] DEBUG: UPath 1: -22 -> -59 -> 53 -> 62 -> 10 -> -60 -> -51 -> 65 -> -9 -> -63 -> -8 -> -61 -> -7 -> 58 -> -56 -> -46 -> 57 -> -18 [2019-09-06 08:54:38] DEBUG: UPath 2: -47 [2019-09-06 08:54:38] DEBUG: UPath 3: -48 [2019-09-06 08:54:38] DEBUG: UPath 4: -54 [2019-09-06 08:54:38] DEBUG: UPath 5: -55 [2019-09-06 08:54:38] DEBUG: Final graph contiain 5 egdes [2019-09-06 08:54:38] DEBUG: Extending contigs into repeats [2019-09-06 08:54:39] DEBUG: Covered 0 repetitive contigs [2019-09-06 08:54:39] INFO: Generated 5 contigs [2019-09-06 08:54:39] DEBUG: Writing FASTA [2019-09-06 08:54:39] DEBUG: Generating scaffold connections [2019-09-06 08:54:39] DEBUG: Writing Dot [2019-09-06 08:54:39] DEBUG: Writing FASTA [2019-09-06 08:54:39] DEBUG: Writing Gfa [2019-09-06 08:54:39] DEBUG: Peak RAM usage: 0 Gb -----------End assembly log------------ [2019-09-06 08:54:39] root: INFO: >>>STAGE: polishing [2019-09-06 08:54:39] root: INFO: Polishing genome (1/1) [2019-09-06 08:54:39] root: INFO: Running minimap2 [2019-09-06 08:54:45] root: INFO: Separating alignment into bubbles [2019-09-06 08:56:21] root: DEBUG: Generated 226116 bubbles [2019-09-06 08:56:21] root: DEBUG: Split 0 long bubbles [2019-09-06 08:56:21] root: DEBUG: Skipped 0 empty bubbles [2019-09-06 08:56:21] root: DEBUG: Skipped 0 bubbles with long branches [2019-09-06 08:56:21] root: INFO: Alignment error rate: 0.152418908582 [2019-09-06 08:56:21] root: INFO: Correcting bubbles [2019-09-06 08:57:41] root: DEBUG: Generating polished GFA [2019-09-06 08:57:45] root: DEBUG: 0 sequences remained unpolished [2019-09-06 08:57:45] root: INFO: >>>STAGE: finalize [2019-09-06 08:57:45] root: INFO: Assembly statistics: Total length: 4703774 Contigs: 5 Scaffolds: 5 Scaffolds N50: 4655002 Largest scf: 4655002 Mean coverage: 14 [2019-09-06 08:57:45] root: INFO: Final assembly: /data/user2/work/81/output.flye/scaffolds.fasta