[2025-08-18 20:58:09] root: INFO: Starting Flye 2.9.6-b1802 [2025-08-18 20:58:09] root: DEBUG: Cmd: /home/pabloati/miniforge3/envs/pablo_course/bin/flye --nano-raw results/bsubtilis/filtered/bsubtilis_long_reads_filtered.fastq -t 8 -o results/bsubtilis/assembly --genome-size 4300000 [2025-08-18 20:58:09] root: DEBUG: Python version: 3.12.11 | packaged by conda-forge | (main, Jun 4 2025, 14:45:31) [GCC 13.3.0] [2025-08-18 20:58:09] root: INFO: >>>STAGE: configure [2025-08-18 20:58:09] root: INFO: Configuring run [2025-08-18 20:58:10] root: INFO: Total read length: 265762798 [2025-08-18 20:58:10] root: INFO: Input genome size: 4300000 [2025-08-18 20:58:10] root: INFO: Estimated coverage: 61 [2025-08-18 20:58:10] root: INFO: Reads N50/N90: 7600 / 2639 [2025-08-18 20:58:10] root: INFO: Minimum overlap set to 3000 [2025-08-18 20:58:10] root: INFO: >>>STAGE: assembly [2025-08-18 20:58:10] root: INFO: Assembling disjointigs [2025-08-18 20:58:10] root: DEBUG: -----Begin assembly log------ [2025-08-18 20:58:10] root: DEBUG: Running: flye-modules assemble --reads /media/pabloati/HDD/pablo/macourse/results/bsubtilis/filtered/bsubtilis_long_reads_filtered.fastq --out-asm /media/pabloati/HDD/pablo/macourse/results/bsubtilis/assembly/00-assembly/draft_assembly.fasta --config /home/pabloati/miniforge3/envs/pablo_course/lib/python3.12/site-packages/flye/config/bin_cfg/asm_raw_reads.cfg --log /media/pabloati/HDD/pablo/macourse/results/bsubtilis/assembly/flye.log --threads 8 --genome-size 4300000 --min-ovlp 3000 [2025-08-18 20:58:10] DEBUG: Build date: May 4 2025 23:17:52 [2025-08-18 20:58:10] DEBUG: Total RAM: 31 Gb [2025-08-18 20:58:10] DEBUG: Available RAM: 29 Gb [2025-08-18 20:58:10] DEBUG: Total CPUs: 8 [2025-08-18 20:58:10] DEBUG: Loading /home/pabloati/miniforge3/envs/pablo_course/lib/python3.12/site-packages/flye/config/bin_cfg/asm_raw_reads.cfg [2025-08-18 20:58:10] DEBUG: Loading /home/pabloati/miniforge3/envs/pablo_course/lib/python3.12/site-packages/flye/config/bin_cfg/asm_defaults.cfg [2025-08-18 20:58:10] DEBUG: big_genome_threshold=29000000 [2025-08-18 20:58:10] DEBUG: meta_read_filter_kmer_freq=100 [2025-08-18 20:58:10] DEBUG: chain_large_gap_penalty=2 [2025-08-18 20:58:10] DEBUG: chain_small_gap_penalty=0.5 [2025-08-18 20:58:10] DEBUG: chain_gap_jump_threshold=100 [2025-08-18 20:58:10] DEBUG: max_jump_gap=500 [2025-08-18 20:58:10] DEBUG: max_coverage_drop_rate=5 [2025-08-18 20:58:10] DEBUG: max_extensions_drop_rate=5 [2025-08-18 20:58:10] DEBUG: chimera_window=100 [2025-08-18 20:58:10] DEBUG: chimera_overhang=1000 [2025-08-18 20:58:10] DEBUG: min_reads_in_disjointig=4 [2025-08-18 20:58:10] DEBUG: max_inner_reads=10 [2025-08-18 20:58:10] DEBUG: max_inner_fraction=0.25 [2025-08-18 20:58:10] DEBUG: aggressive_dup_filter=1 [2025-08-18 20:58:10] DEBUG: max_separation=500 [2025-08-18 20:58:10] DEBUG: unique_edge_length=50000 [2025-08-18 20:58:10] DEBUG: min_repeat_res_support=0.51 [2025-08-18 20:58:10] DEBUG: out_paths_ratio=5 [2025-08-18 20:58:10] DEBUG: graph_cov_drop_rate=5 [2025-08-18 20:58:10] DEBUG: coverage_estimate_window=100 [2025-08-18 20:58:10] DEBUG: max_bubble_length=50000 [2025-08-18 20:58:10] DEBUG: loop_coverage_rate=1.5 [2025-08-18 20:58:10] DEBUG: repeat_edge_cov_mult=1.75 [2025-08-18 20:58:10] DEBUG: weak_detach_rate=5 [2025-08-18 20:58:10] DEBUG: tip_coverage_rate=2 [2025-08-18 20:58:10] DEBUG: tip_length_rate=2 [2025-08-18 20:58:10] DEBUG: output_gfa_before_rr=1 [2025-08-18 20:58:10] DEBUG: remove_alt_edges=0 [2025-08-18 20:58:10] DEBUG: low_cutoff_warning=1 [2025-08-18 20:58:10] DEBUG: kmer_size=17 [2025-08-18 20:58:10] DEBUG: use_minimizers=0 [2025-08-18 20:58:10] DEBUG: reads_base_alignment=0 [2025-08-18 20:58:10] DEBUG: meta_read_top_kmer_rate=0.40 [2025-08-18 20:58:10] DEBUG: maximum_jump=1500 [2025-08-18 20:58:10] DEBUG: maximum_overhang=1500 [2025-08-18 20:58:10] DEBUG: repeat_kmer_rate=100 [2025-08-18 20:58:10] DEBUG: assemble_ovlp_divergence=0.10 [2025-08-18 20:58:10] DEBUG: assemble_divergence_relative=1 [2025-08-18 20:58:10] DEBUG: repeat_graph_ovlp_divergence=0.08 [2025-08-18 20:58:10] DEBUG: read_align_ovlp_divergence=0.25 [2025-08-18 20:58:10] DEBUG: hpc_scoring_on=0 [2025-08-18 20:58:10] DEBUG: add_unassembled_reads=0 [2025-08-18 20:58:10] DEBUG: extend_contigs_with_repeats=0 [2025-08-18 20:58:10] DEBUG: min_read_cov_cutoff=3 [2025-08-18 20:58:10] DEBUG: short_tip_length=20000 [2025-08-18 20:58:10] DEBUG: long_tip_length=100000 [2025-08-18 20:58:10] DEBUG: Running with k-mer size: 17 [2025-08-18 20:58:10] DEBUG: Running with minimum overlap 3000 [2025-08-18 20:58:10] DEBUG: Metagenome mode: N [2025-08-18 20:58:10] DEBUG: Short mode: N [2025-08-18 20:58:10] INFO: Reading sequences [2025-08-18 20:58:10] DEBUG: Building positional index [2025-08-18 20:58:10] DEBUG: Total sequence: 231394655 bp [2025-08-18 20:58:15] INFO: Counting k-mers: [2025-08-18 20:58:28] DEBUG: Updating k-mer histogram [2025-08-18 20:59:19] DEBUG: Hash size: 4248291 [2025-08-18 20:59:19] DEBUG: Total k-mers 28720935 [2025-08-18 20:59:19] INFO: Filling index table (1/2) [2025-08-18 20:59:42] DEBUG: Mean k-mer frequency: 32.3271 [2025-08-18 20:59:42] DEBUG: Repetitive k-mer frequency: 3232 [2025-08-18 20:59:42] DEBUG: Filtered 1584784 repetitive k-mers (0.015858) [2025-08-18 20:59:42] INFO: Filling index table (2/2) [2025-08-18 21:00:06] DEBUG: Sorting k-mer index [2025-08-18 21:00:07] DEBUG: Selected k-mers: 3271430 [2025-08-18 21:00:07] DEBUG: Index size: 98526294 [2025-08-18 21:00:07] DEBUG: Mean k-mer index frequency: 30.1172 [2025-08-18 21:00:07] DEBUG: Peak RAM usage: 8 Gb [2025-08-18 21:00:07] DEBUG: Estimating k-mer identity bias [2025-08-18 21:00:14] DEBUG: Initial divergence estimate : 0.0422661 [2025-08-18 21:00:14] DEBUG: Relative threshold: Y [2025-08-18 21:00:14] DEBUG: Max divergence threshold set to 0.142266 [2025-08-18 21:00:14] INFO: Extending reads [2025-08-18 21:00:14] DEBUG: Estimating overlap coverage [2025-08-18 21:00:51] INFO: Overlap-based coverage: 48 [2025-08-18 21:00:51] INFO: Median overlap divergence: 0.0428845 [2025-08-18 21:00:51] DEBUG: Sequence divergence distribution: | * | | * | | * * | | ** *** | | ****** | | ****** | | ******* | | ******** | | ******** | | ******** | | ********* | | ********** | | ********** | | ********** | | ************ | | ************ * | | ************** | | ************** | | **************** | | *********************** **|*** ---------------------------------------------------------------------------------------------------- 0% 5% 10% 15% 20% 25% 30% 35% 40% 45% Q25 = 0.03, Q50 = 0.043, Q75 = 0.055 [2025-08-18 21:00:56] DEBUG: Assembled disjointig 1 With 23 reads Start read: +c06aedd9-66bb-4104-9fa0-43092905ad3a At position: 19 leftTip: 0 rightTip: 0 Suspicious: 2 Short ext: 2 Mean extensions: 57 Avg overlap len: 13214 Min overlap len: 2889 Inner reads: 0 Length: 107033 [2025-08-18 21:00:56] DEBUG: Inner: 2152 covered: 2046 total: 62362 [2025-08-18 21:01:17] DEBUG: Assembled disjointig 2 With 750 reads Start read: +2275334c-980e-49b2-a335-fd23b146e457 At position: 746 leftTip: 0 rightTip: 0 Suspicious: 9 Short ext: 4 Mean extensions: 30 Avg overlap len: 13754 Min overlap len: 1794 Inner reads: 0 Length: 4242987 [2025-08-18 21:01:17] DEBUG: Inner: 59426 covered: 58598 total: 62362 [2025-08-18 21:01:17] DEBUG: Discarded disjointig with 772 reads and 743 inner overlaps [2025-08-18 21:01:17] DEBUG: Discarded disjointig with 366 reads and 330 inner overlaps [2025-08-18 21:01:17] DEBUG: Discarded disjointig with 664 reads and 609 inner overlaps [2025-08-18 21:01:17] DEBUG: Discarded disjointig with 676 reads and 637 inner overlaps [2025-08-18 21:01:17] DEBUG: Discarded disjointig with 571 reads and 512 inner overlaps [2025-08-18 21:01:17] DEBUG: Discarded disjointig with 387 reads and 346 inner overlaps [2025-08-18 21:01:17] DEBUG: Discarded disjointig with 699 reads and 670 inner overlaps [2025-08-18 21:01:38] INFO: Assembled 2 disjointigs [2025-08-18 21:01:38] INFO: Generating sequence [2025-08-18 21:01:38] DEBUG: Building positional index [2025-08-18 21:01:38] DEBUG: Total sequence: 4349983 bp [2025-08-18 21:01:41] DEBUG: Mean k-mer frequency: 1.0238 [2025-08-18 21:01:41] DEBUG: Repetitive k-mer frequency: 102 [2025-08-18 21:01:41] DEBUG: Filtered 0 repetitive k-mers (0) [2025-08-18 21:01:42] DEBUG: Sorting k-mer index [2025-08-18 21:01:42] DEBUG: Selected k-mers: 4248839 [2025-08-18 21:01:42] DEBUG: K-mer index size: 4349949 [2025-08-18 21:01:42] DEBUG: Mean k-mer frequency: 1.0238 [2025-08-18 21:01:42] DEBUG: Minimizer rate: 1.00001 [2025-08-18 21:01:42] INFO: Filtering contained disjointigs [2025-08-18 21:01:44] DEBUG: Computing transitive closure for overlaps [2025-08-18 21:01:44] DEBUG: Found 8 overlaps [2025-08-18 21:01:44] DEBUG: Left 8 overlaps after filtering [2025-08-18 21:01:44] INFO: Contained seqs: 0 [2025-08-18 21:01:44] DEBUG: Writing FASTA [2025-08-18 21:01:44] DEBUG: Peak RAM usage: 8 Gb -----------End assembly log------------ [2025-08-18 21:01:45] root: DEBUG: Disjointigs length: 4349983, N50: 4242940 [2025-08-18 21:01:45] root: INFO: >>>STAGE: consensus [2025-08-18 21:01:45] root: INFO: Running Minimap2 [2025-08-18 21:02:40] root: INFO: Computing consensus [2025-08-18 21:03:14] root: INFO: Alignment error rate: 0.036488 [2025-08-18 21:03:14] root: INFO: >>>STAGE: repeat [2025-08-18 21:03:14] root: INFO: Building and resolving repeat graph [2025-08-18 21:03:14] root: DEBUG: -----Begin repeat analyser log------ [2025-08-18 21:03:14] root: DEBUG: Running: flye-modules repeat --disjointigs /media/pabloati/HDD/pablo/macourse/results/bsubtilis/assembly/10-consensus/consensus.fasta --reads /media/pabloati/HDD/pablo/macourse/results/bsubtilis/filtered/bsubtilis_long_reads_filtered.fastq --out-dir /media/pabloati/HDD/pablo/macourse/results/bsubtilis/assembly/20-repeat --config /home/pabloati/miniforge3/envs/pablo_course/lib/python3.12/site-packages/flye/config/bin_cfg/asm_raw_reads.cfg --log /media/pabloati/HDD/pablo/macourse/results/bsubtilis/assembly/flye.log --threads 8 --min-ovlp 3000 [2025-08-18 21:03:14] DEBUG: Build date: May 4 2025 23:18:08 [2025-08-18 21:03:14] DEBUG: Total RAM: 31 Gb [2025-08-18 21:03:14] DEBUG: Available RAM: 29 Gb [2025-08-18 21:03:14] DEBUG: Total CPUs: 8 [2025-08-18 21:03:14] DEBUG: Loading /home/pabloati/miniforge3/envs/pablo_course/lib/python3.12/site-packages/flye/config/bin_cfg/asm_raw_reads.cfg [2025-08-18 21:03:14] DEBUG: Loading /home/pabloati/miniforge3/envs/pablo_course/lib/python3.12/site-packages/flye/config/bin_cfg/asm_defaults.cfg [2025-08-18 21:03:14] DEBUG: big_genome_threshold=29000000 [2025-08-18 21:03:14] DEBUG: meta_read_filter_kmer_freq=100 [2025-08-18 21:03:14] DEBUG: chain_large_gap_penalty=2 [2025-08-18 21:03:14] DEBUG: chain_small_gap_penalty=0.5 [2025-08-18 21:03:14] DEBUG: chain_gap_jump_threshold=100 [2025-08-18 21:03:14] DEBUG: max_jump_gap=500 [2025-08-18 21:03:14] DEBUG: max_coverage_drop_rate=5 [2025-08-18 21:03:14] DEBUG: max_extensions_drop_rate=5 [2025-08-18 21:03:14] DEBUG: chimera_window=100 [2025-08-18 21:03:14] DEBUG: chimera_overhang=1000 [2025-08-18 21:03:14] DEBUG: min_reads_in_disjointig=4 [2025-08-18 21:03:14] DEBUG: max_inner_reads=10 [2025-08-18 21:03:14] DEBUG: max_inner_fraction=0.25 [2025-08-18 21:03:14] DEBUG: aggressive_dup_filter=1 [2025-08-18 21:03:14] DEBUG: max_separation=500 [2025-08-18 21:03:14] DEBUG: unique_edge_length=50000 [2025-08-18 21:03:14] DEBUG: min_repeat_res_support=0.51 [2025-08-18 21:03:14] DEBUG: out_paths_ratio=5 [2025-08-18 21:03:14] DEBUG: graph_cov_drop_rate=5 [2025-08-18 21:03:14] DEBUG: coverage_estimate_window=100 [2025-08-18 21:03:14] DEBUG: max_bubble_length=50000 [2025-08-18 21:03:14] DEBUG: loop_coverage_rate=1.5 [2025-08-18 21:03:14] DEBUG: repeat_edge_cov_mult=1.75 [2025-08-18 21:03:14] DEBUG: weak_detach_rate=5 [2025-08-18 21:03:14] DEBUG: tip_coverage_rate=2 [2025-08-18 21:03:14] DEBUG: tip_length_rate=2 [2025-08-18 21:03:14] DEBUG: output_gfa_before_rr=1 [2025-08-18 21:03:14] DEBUG: remove_alt_edges=0 [2025-08-18 21:03:14] DEBUG: low_cutoff_warning=1 [2025-08-18 21:03:14] DEBUG: kmer_size=17 [2025-08-18 21:03:14] DEBUG: use_minimizers=0 [2025-08-18 21:03:14] DEBUG: reads_base_alignment=0 [2025-08-18 21:03:14] DEBUG: meta_read_top_kmer_rate=0.40 [2025-08-18 21:03:14] DEBUG: maximum_jump=1500 [2025-08-18 21:03:14] DEBUG: maximum_overhang=1500 [2025-08-18 21:03:14] DEBUG: repeat_kmer_rate=100 [2025-08-18 21:03:14] DEBUG: assemble_ovlp_divergence=0.10 [2025-08-18 21:03:14] DEBUG: assemble_divergence_relative=1 [2025-08-18 21:03:14] DEBUG: repeat_graph_ovlp_divergence=0.08 [2025-08-18 21:03:14] DEBUG: read_align_ovlp_divergence=0.25 [2025-08-18 21:03:14] DEBUG: hpc_scoring_on=0 [2025-08-18 21:03:14] DEBUG: add_unassembled_reads=0 [2025-08-18 21:03:14] DEBUG: extend_contigs_with_repeats=0 [2025-08-18 21:03:14] DEBUG: min_read_cov_cutoff=3 [2025-08-18 21:03:14] DEBUG: short_tip_length=20000 [2025-08-18 21:03:14] DEBUG: long_tip_length=100000 [2025-08-18 21:03:14] DEBUG: Running with k-mer size: 17 [2025-08-18 21:03:14] DEBUG: Selected minimum overlap 3000 [2025-08-18 21:03:14] DEBUG: Metagenome mode: N [2025-08-18 21:03:14] INFO: Parsing disjointigs [2025-08-18 21:03:14] DEBUG: Building positional index [2025-08-18 21:03:14] DEBUG: Total sequence: 4357637 bp [2025-08-18 21:03:14] INFO: Building repeat graph [2025-08-18 21:03:16] DEBUG: Mean k-mer frequency: 1.02876 [2025-08-18 21:03:16] DEBUG: Repetitive k-mer frequency: 102 [2025-08-18 21:03:16] DEBUG: Filtered 0 repetitive k-mers (0) [2025-08-18 21:03:17] DEBUG: Sorting k-mer index [2025-08-18 21:03:18] DEBUG: Selected k-mers: 4235775 [2025-08-18 21:03:18] DEBUG: K-mer index size: 4357603 [2025-08-18 21:03:18] DEBUG: Mean k-mer frequency: 1.02876 [2025-08-18 21:03:18] DEBUG: Minimizer rate: 1.00001 [2025-08-18 21:03:20] DEBUG: Computing transitive closure for overlaps [2025-08-18 21:03:20] DEBUG: Found 480 overlaps [2025-08-18 21:03:20] DEBUG: Left 220 overlaps after filtering [2025-08-18 21:03:20] INFO: Median overlap divergence: 0.0286428 [2025-08-18 21:03:20] DEBUG: Sequence divergence distribution: |* | |* | |* | |* | |* | |* * | |* * | |* * | |* * | |* * | |* * | * * |* * | * * |* * | * * |* * | * * |* * | * * |* ***** | * * |* ***** | * * |* ***** | * * |* ***** | * * |* ***** | * * ---------------------------------------------------------------------------------------------------- 0% 5% 10% 15% 20% 25% 30% 35% 40% 45% Q25 = 0.00072, Q50 = 0.029, Q75 = 0.25 [2025-08-18 21:03:20] DEBUG: Computing gluepoints [2025-08-18 21:03:20] DEBUG: Added 0 gluepoint projections [2025-08-18 21:03:20] DEBUG: Created 58 gluepoints [2025-08-18 21:03:20] DEBUG: Artificial loops removed: 0 left, 0 right, 0 both [2025-08-18 21:03:20] DEBUG: Initializing edges [2025-08-18 21:03:20] DEBUG: Edges length checksum: 1149651167 [2025-08-18 21:03:20] DEBUG: Filtered 0 singleton segments [2025-08-18 21:03:20] DEBUG: Removed 0 simple and 0 double chimeric junctions [2025-08-18 21:03:20] DEBUG: Collapsed 2 edges [2025-08-18 21:03:20] DEBUG: * 13 +disjointig_1 23060 107275 84215 [2025-08-18 21:03:20] DEBUG: 3 +disjointig_2 147 1129 982 [2025-08-18 21:03:20] DEBUG: 4 +disjointig_2 1129 6032 4903 [2025-08-18 21:03:20] DEBUG: * 14 +disjointig_2 6032 65623 59591 [2025-08-18 21:03:20] DEBUG: 4 +disjointig_2 65623 70523 4900 [2025-08-18 21:03:20] DEBUG: 3 +disjointig_2 70523 71236 713 [2025-08-18 21:03:20] DEBUG: 4 +disjointig_2 71236 81141 9905 [2025-08-18 21:03:20] DEBUG: * 5 +disjointig_2 81141 540078 458937 [2025-08-18 21:03:20] DEBUG: 4 +disjointig_2 540078 545052 4974 [2025-08-18 21:03:20] DEBUG: * 6 +disjointig_2 545052 851336 306284 [2025-08-18 21:03:20] DEBUG: 4 +disjointig_2 851336 856358 5022 [2025-08-18 21:03:20] DEBUG: * 9 +disjointig_2 856358 3077692 2221334 [2025-08-18 21:03:20] DEBUG: -3 +disjointig_2 3077692 3078543 851 [2025-08-18 21:03:20] DEBUG: -4 +disjointig_2 3078543 3083519 4976 [2025-08-18 21:03:20] DEBUG: * 11 +disjointig_2 3083519 4129992 1046473 [2025-08-18 21:03:20] DEBUG: 4 +disjointig_2 4129992 4135138 5146 [2025-08-18 21:03:20] DEBUG: * 7 +disjointig_2 4135138 4150524 15386 [2025-08-18 21:03:20] DEBUG: 4 +disjointig_2 4150524 4155683 5159 [2025-08-18 21:03:20] DEBUG: * 8 +disjointig_2 4155683 4210771 55088 [2025-08-18 21:03:20] DEBUG: 4 +disjointig_2 4210771 4215652 4881 [2025-08-18 21:03:20] DEBUG: 3 +disjointig_2 4215652 4216632 980 [2025-08-18 21:03:20] DEBUG: 4 +disjointig_2 4216632 4221535 4903 [2025-08-18 21:03:20] DEBUG: Total edges: 14 [2025-08-18 21:03:20] INFO: Parsing reads [2025-08-18 21:03:21] DEBUG: Building positional index [2025-08-18 21:03:21] DEBUG: Total sequence: 265762798 bp [2025-08-18 21:03:21] DEBUG: Building positional index [2025-08-18 21:03:21] DEBUG: Total sequence: 4305603 bp [2025-08-18 21:03:21] INFO: Aligning reads to the graph [2025-08-18 21:03:22] DEBUG: Mean k-mer frequency: 1.01654 [2025-08-18 21:03:22] DEBUG: Repetitive k-mer frequency: 101 [2025-08-18 21:03:22] DEBUG: Filtered 0 repetitive k-mers (0) [2025-08-18 21:03:23] DEBUG: Sorting k-mer index [2025-08-18 21:03:23] DEBUG: Selected k-mers: 4235162 [2025-08-18 21:03:23] DEBUG: K-mer index size: 4305212 [2025-08-18 21:03:23] DEBUG: Mean k-mer frequency: 1.01654 [2025-08-18 21:03:23] DEBUG: Minimizer rate: 1.00009 [2025-08-18 21:03:50] DEBUG: Total reads : 31181 [2025-08-18 21:03:50] DEBUG: Read with aligned parts : 30235 [2025-08-18 21:03:50] DEBUG: Aligned in one piece : 30162 [2025-08-18 21:03:50] INFO: Aligned read sequence: 223886985 / 231394655 (0.967555) [2025-08-18 21:03:50] INFO: Median overlap divergence: 0.00641191 [2025-08-18 21:03:50] DEBUG: Sequence divergence distribution: | * | | * | | * | | * | | * | | * | | * | | * | |** | |** | |** | |** | |** | |** | |** | |*** | |*** | |*** | |**** | |************ ** * * ** | * ---------------------------------------------------------------------------------------------------- 0% 5% 10% 15% 20% 25% 30% 35% 40% 45% Q25 = 0.0047, Q50 = 0.0064, Q75 = 0.0091 [2025-08-18 21:03:50] INFO: Mean edge coverage: 52 [2025-08-18 21:03:50] DEBUG: 3 len:881 cov:182 mult:3.5 [2025-08-18 21:03:50] DEBUG: -3 len:881 cov:182 mult:3.5 [2025-08-18 21:03:50] DEBUG: 4 len:4979 cov:561 mult:10.7885 [2025-08-18 21:03:50] DEBUG: -4 len:4979 cov:561 mult:10.7885 [2025-08-18 21:03:50] DEBUG: 5 len:458937 cov:61 mult:1.17308 [2025-08-18 21:03:50] DEBUG: -5 len:458937 cov:61 mult:1.17308 [2025-08-18 21:03:50] DEBUG: 6 len:306284 cov:54 mult:1.03846 [2025-08-18 21:03:50] DEBUG: -6 len:306284 cov:54 mult:1.03846 [2025-08-18 21:03:50] DEBUG: 7 len:15386 cov:53 mult:1.01923 [2025-08-18 21:03:50] DEBUG: -7 len:15386 cov:53 mult:1.01923 [2025-08-18 21:03:50] DEBUG: 8 len:55088 cov:68 mult:1.30769 [2025-08-18 21:03:50] DEBUG: -8 len:55088 cov:68 mult:1.30769 [2025-08-18 21:03:50] DEBUG: 9 len:2221334 cov:44 mult:0.846154 [2025-08-18 21:03:50] DEBUG: -9 len:2221334 cov:44 mult:0.846154 [2025-08-18 21:03:50] DEBUG: 11 len:1046473 cov:58 mult:1.11538 [2025-08-18 21:03:50] DEBUG: -11 len:1046473 cov:58 mult:1.11538 [2025-08-18 21:03:50] DEBUG: 13 len:84215 cov:91 mult:1.75 [2025-08-18 21:03:50] DEBUG: -13 len:84215 cov:91 mult:1.75 [2025-08-18 21:03:50] DEBUG: 14 len:59591 cov:62 mult:1.19231 [2025-08-18 21:03:50] DEBUG: -14 len:59591 cov:62 mult:1.19231 [2025-08-18 21:03:50] DEBUG: Unique coverage threshold 108 [2025-08-18 21:03:50] INFO: Simplifying the graph [2025-08-18 21:03:50] DEBUG: Read coverage cutoff: 10 [2025-08-18 21:03:50] DEBUG: [SIMPL] Removed 0 paths with low coverage [2025-08-18 21:03:50] DEBUG: [SIMPL] Masked 0 heterozygous loops [2025-08-18 21:03:50] DEBUG: [SIMPL] Masked 0 simple bubbles [2025-08-18 21:03:50] DEBUG: Finding repeats [2025-08-18 21:03:50] DEBUG: Read coverage cutoff: 10 [2025-08-18 21:03:50] DEBUG: High-cov: 3 881 182 [2025-08-18 21:03:50] DEBUG: Short-loop: 3 [2025-08-18 21:03:50] DEBUG: High-cov: 4 4979 561 [2025-08-18 21:03:50] DEBUG: Short-loop: 4 [2025-08-18 21:03:50] DEBUG: Repeat detection iteration 1 [2025-08-18 21:03:50] DEBUG: Writing Dot [2025-08-18 21:03:50] DEBUG: Writing FASTA [2025-08-18 21:03:50] DEBUG: Writing Gfa [2025-08-18 21:03:50] DEBUG: [SIMPL] == Iteration 1 == [2025-08-18 21:03:50] DEBUG: Splitting nodes [2025-08-18 21:03:50] DEBUG: [SIMPL] Split 0 nodes [2025-08-18 21:03:50] DEBUG: [SIMPL] Clipped 0 short and 0 long tips [2025-08-18 21:03:50] DEBUG: [SIMPL] Masked 0 heterozygous loops [2025-08-18 21:03:50] DEBUG: [SIMPL] Masked 0 simple bubbles [2025-08-18 21:03:50] DEBUG: Finding repeats [2025-08-18 21:03:50] DEBUG: Read coverage cutoff: 10 [2025-08-18 21:03:50] DEBUG: High-cov: 3 881 182 [2025-08-18 21:03:50] DEBUG: Short-loop: 3 [2025-08-18 21:03:50] DEBUG: High-cov: 4 4979 561 [2025-08-18 21:03:50] DEBUG: Short-loop: 4 [2025-08-18 21:03:50] DEBUG: Repeat detection iteration 1 [2025-08-18 21:03:50] DEBUG: Total unique edges: 8 [2025-08-18 21:03:50] DEBUG: Connection -14 -8 5 1 [2025-08-18 21:03:50] DEBUG: Connection -8 -7 9 1 [2025-08-18 21:03:50] DEBUG: Connection -6 -5 23 1 [2025-08-18 21:03:50] DEBUG: Connection 14 5 3 1 [2025-08-18 21:03:50] DEBUG: Connection -11 -9 10 1 [2025-08-18 21:03:50] DEBUG: Connection -7 -11 16 1 [2025-08-18 21:03:50] DEBUG: Connection 6 9 13 1 [2025-08-18 21:03:50] DEBUG: [SIMPL] Resolved repeats: 7 [2025-08-18 21:03:50] DEBUG: RR links: 158 [2025-08-18 21:03:50] DEBUG: Unresolved: 0 [2025-08-18 21:03:50] DEBUG: Removed 0 simple and 0 double chimeric junctions [2025-08-18 21:03:50] DEBUG: [SIMPL] == Iteration 2 == [2025-08-18 21:03:50] DEBUG: Splitting nodes [2025-08-18 21:03:50] DEBUG: [SIMPL] Split 0 nodes [2025-08-18 21:03:50] DEBUG: [SIMPL] Clipped 0 short and 0 long tips [2025-08-18 21:03:50] DEBUG: [SIMPL] Masked 0 heterozygous loops [2025-08-18 21:03:50] DEBUG: [SIMPL] Masked 0 simple bubbles [2025-08-18 21:03:50] DEBUG: Finding repeats [2025-08-18 21:03:50] DEBUG: Read coverage cutoff: 10 [2025-08-18 21:03:50] DEBUG: Repeat detection iteration 1 [2025-08-18 21:03:50] DEBUG: Total unique edges: 15 [2025-08-18 21:03:50] DEBUG: [SIMPL] Resolved repeats: 0 [2025-08-18 21:03:50] DEBUG: RR links: 0 [2025-08-18 21:03:50] DEBUG: Unresolved: 0 [2025-08-18 21:03:50] DEBUG: Removed 0 simple and 0 double chimeric junctions [2025-08-18 21:03:50] DEBUG: [SIMPL] Collapsed 0 haplotypes [2025-08-18 21:03:50] DEBUG: [SIMPL] Resolved 0 simple repeats [2025-08-18 21:03:50] DEBUG: Read coverage cutoff: 10 [2025-08-18 21:03:50] DEBUG: [SIMPL] Removed 0 paths with low coverage [2025-08-18 21:03:50] DEBUG: Finding repeats [2025-08-18 21:03:50] DEBUG: Read coverage cutoff: 10 [2025-08-18 21:03:50] DEBUG: Repeat detection iteration 1 [2025-08-18 21:03:50] DEBUG: Writing Dot [2025-08-18 21:03:50] DEBUG: Writing FASTA [2025-08-18 21:03:50] DEBUG: Peak RAM usage: 0 Gb -----------End assembly log------------ [2025-08-18 21:03:50] root: INFO: >>>STAGE: contigger [2025-08-18 21:03:50] root: INFO: Generating contigs [2025-08-18 21:03:50] root: DEBUG: -----Begin contigger analyser log------ [2025-08-18 21:03:50] root: DEBUG: Running: flye-modules contigger --graph-edges /media/pabloati/HDD/pablo/macourse/results/bsubtilis/assembly/20-repeat/repeat_graph_edges.fasta --reads /media/pabloati/HDD/pablo/macourse/results/bsubtilis/filtered/bsubtilis_long_reads_filtered.fastq --out-dir /media/pabloati/HDD/pablo/macourse/results/bsubtilis/assembly/30-contigger --config /home/pabloati/miniforge3/envs/pablo_course/lib/python3.12/site-packages/flye/config/bin_cfg/asm_raw_reads.cfg --repeat-graph /media/pabloati/HDD/pablo/macourse/results/bsubtilis/assembly/20-repeat/repeat_graph_dump --graph-aln /media/pabloati/HDD/pablo/macourse/results/bsubtilis/assembly/20-repeat/read_alignment_dump --log /media/pabloati/HDD/pablo/macourse/results/bsubtilis/assembly/flye.log --threads 8 --min-ovlp 3000 [2025-08-18 21:03:50] DEBUG: Build date: May 4 2025 23:18:25 [2025-08-18 21:03:50] DEBUG: Total RAM: 31 Gb [2025-08-18 21:03:50] DEBUG: Available RAM: 29 Gb [2025-08-18 21:03:50] DEBUG: Total CPUs: 8 [2025-08-18 21:03:50] DEBUG: Loading /home/pabloati/miniforge3/envs/pablo_course/lib/python3.12/site-packages/flye/config/bin_cfg/asm_raw_reads.cfg [2025-08-18 21:03:50] DEBUG: Loading /home/pabloati/miniforge3/envs/pablo_course/lib/python3.12/site-packages/flye/config/bin_cfg/asm_defaults.cfg [2025-08-18 21:03:50] DEBUG: big_genome_threshold=29000000 [2025-08-18 21:03:50] DEBUG: meta_read_filter_kmer_freq=100 [2025-08-18 21:03:50] DEBUG: chain_large_gap_penalty=2 [2025-08-18 21:03:50] DEBUG: chain_small_gap_penalty=0.5 [2025-08-18 21:03:50] DEBUG: chain_gap_jump_threshold=100 [2025-08-18 21:03:50] DEBUG: max_jump_gap=500 [2025-08-18 21:03:50] DEBUG: max_coverage_drop_rate=5 [2025-08-18 21:03:50] DEBUG: max_extensions_drop_rate=5 [2025-08-18 21:03:50] DEBUG: chimera_window=100 [2025-08-18 21:03:50] DEBUG: chimera_overhang=1000 [2025-08-18 21:03:50] DEBUG: min_reads_in_disjointig=4 [2025-08-18 21:03:50] DEBUG: max_inner_reads=10 [2025-08-18 21:03:50] DEBUG: max_inner_fraction=0.25 [2025-08-18 21:03:50] DEBUG: aggressive_dup_filter=1 [2025-08-18 21:03:50] DEBUG: max_separation=500 [2025-08-18 21:03:50] DEBUG: unique_edge_length=50000 [2025-08-18 21:03:50] DEBUG: min_repeat_res_support=0.51 [2025-08-18 21:03:50] DEBUG: out_paths_ratio=5 [2025-08-18 21:03:50] DEBUG: graph_cov_drop_rate=5 [2025-08-18 21:03:50] DEBUG: coverage_estimate_window=100 [2025-08-18 21:03:50] DEBUG: max_bubble_length=50000 [2025-08-18 21:03:50] DEBUG: loop_coverage_rate=1.5 [2025-08-18 21:03:50] DEBUG: repeat_edge_cov_mult=1.75 [2025-08-18 21:03:50] DEBUG: weak_detach_rate=5 [2025-08-18 21:03:50] DEBUG: tip_coverage_rate=2 [2025-08-18 21:03:50] DEBUG: tip_length_rate=2 [2025-08-18 21:03:50] DEBUG: output_gfa_before_rr=1 [2025-08-18 21:03:50] DEBUG: remove_alt_edges=0 [2025-08-18 21:03:50] DEBUG: low_cutoff_warning=1 [2025-08-18 21:03:50] DEBUG: kmer_size=17 [2025-08-18 21:03:50] DEBUG: use_minimizers=0 [2025-08-18 21:03:50] DEBUG: reads_base_alignment=0 [2025-08-18 21:03:50] DEBUG: meta_read_top_kmer_rate=0.40 [2025-08-18 21:03:50] DEBUG: maximum_jump=1500 [2025-08-18 21:03:50] DEBUG: maximum_overhang=1500 [2025-08-18 21:03:50] DEBUG: repeat_kmer_rate=100 [2025-08-18 21:03:50] DEBUG: assemble_ovlp_divergence=0.10 [2025-08-18 21:03:50] DEBUG: assemble_divergence_relative=1 [2025-08-18 21:03:50] DEBUG: repeat_graph_ovlp_divergence=0.08 [2025-08-18 21:03:50] DEBUG: read_align_ovlp_divergence=0.25 [2025-08-18 21:03:50] DEBUG: hpc_scoring_on=0 [2025-08-18 21:03:50] DEBUG: add_unassembled_reads=0 [2025-08-18 21:03:50] DEBUG: extend_contigs_with_repeats=0 [2025-08-18 21:03:50] DEBUG: min_read_cov_cutoff=3 [2025-08-18 21:03:50] DEBUG: short_tip_length=20000 [2025-08-18 21:03:50] DEBUG: long_tip_length=100000 [2025-08-18 21:03:50] DEBUG: Running with k-mer size: 17 [2025-08-18 21:03:50] DEBUG: Selected minimum overlap 3000 [2025-08-18 21:03:50] INFO: Reading sequences [2025-08-18 21:03:51] DEBUG: Building positional index [2025-08-18 21:03:51] DEBUG: Total sequence: 265762798 bp [2025-08-18 21:03:51] DEBUG: Flipped 0 [2025-08-18 21:03:51] DEBUG: UPath 1: 17 -> 6 -> 21 -> 9 -> -19 -> 11 -> 20 -> 7 -> -16 -> 8 -> 15 -> 14 -> -18 -> 5 [2025-08-18 21:03:51] DEBUG: UPath 2: 13 [2025-08-18 21:03:51] DEBUG: Final graph contains 2 egdes [2025-08-18 21:03:51] DEBUG: Extending contigs into repeats [2025-08-18 21:03:51] DEBUG: Covered 0 repetitive contigs [2025-08-18 21:03:51] INFO: Generated 2 contigs [2025-08-18 21:03:51] DEBUG: Writing FASTA [2025-08-18 21:03:51] DEBUG: Generating scaffold connections [2025-08-18 21:03:51] INFO: Added 0 scaffold connections [2025-08-18 21:03:51] DEBUG: Writing Dot [2025-08-18 21:03:51] DEBUG: Writing FASTA [2025-08-18 21:03:51] DEBUG: Writing Gfa [2025-08-18 21:03:51] DEBUG: Peak RAM usage: 0 Gb -----------End assembly log------------ [2025-08-18 21:03:51] root: INFO: >>>STAGE: polishing [2025-08-18 21:03:51] root: INFO: Polishing genome (1/1) [2025-08-18 21:03:51] root: INFO: Running minimap2 [2025-08-18 21:04:15] root: INFO: Separating alignment into bubbles [2025-08-18 21:04:59] root: DEBUG: Generated 286149 bubbles [2025-08-18 21:04:59] root: DEBUG: Split 0 long bubbles [2025-08-18 21:04:59] root: DEBUG: Skipped 0 empty bubbles [2025-08-18 21:04:59] root: DEBUG: Skipped 0 bubbles with long branches [2025-08-18 21:04:59] root: INFO: Alignment error rate: 0.016517 [2025-08-18 21:04:59] root: INFO: Correcting bubbles [2025-08-18 21:05:37] root: DEBUG: Mean contig coverage: 59, selected threshold: 12 [2025-08-18 21:05:37] root: DEBUG: Filtered 0 contigs of total length 0 [2025-08-18 21:05:37] root: DEBUG: Generating polished GFA [2025-08-18 21:05:40] root: DEBUG: 0 sequences remained unpolished [2025-08-18 21:05:40] root: INFO: >>>STAGE: finalize [2025-08-18 21:05:40] root: DEBUG: ---Output dir contents:---- [2025-08-18 21:05:40] root: DEBUG: assembly/ [2025-08-18 21:05:40] root: DEBUG: 4.0 M assembly_graph.gfa [2025-08-18 21:05:40] root: DEBUG: 34.0 K flye.log [2025-08-18 21:05:40] root: DEBUG: 306.0 B assembly_graph.gv [2025-08-18 21:05:40] root: DEBUG: 92.0 B params.json [2025-08-18 21:05:40] root: DEBUG: 4.0 M assembly.fasta [2025-08-18 21:05:40] root: DEBUG: 20-repeat/ [2025-08-18 21:05:40] root: DEBUG: 4.0 M graph_before_rr.gfa [2025-08-18 21:05:40] root: DEBUG: 1.0 K graph_before_rr.gv [2025-08-18 21:05:40] root: DEBUG: 3.0 K repeat_graph_dump [2025-08-18 21:05:40] root: DEBUG: 4.0 M graph_before_rr.fasta [2025-08-18 21:05:40] root: DEBUG: 8.0 M read_alignment_dump [2025-08-18 21:05:40] root: DEBUG: 4.0 M repeat_graph_edges.fasta [2025-08-18 21:05:40] root: DEBUG: 1.0 K graph_after_rr.gv [2025-08-18 21:05:40] root: DEBUG: 30-contigger/ [2025-08-18 21:05:40] root: DEBUG: 145.0 B contigs_stats.txt [2025-08-18 21:05:40] root: DEBUG: 4.0 M contigs.fasta [2025-08-18 21:05:40] root: DEBUG: 4.0 M graph_final.fasta [2025-08-18 21:05:40] root: DEBUG: 306.0 B graph_final.gv [2025-08-18 21:05:40] root: DEBUG: 0.0 B scaffolds_links.txt [2025-08-18 21:05:40] root: DEBUG: 55.0 B contigs.fasta.fai [2025-08-18 21:05:40] root: DEBUG: 4.0 M graph_final.gfa [2025-08-18 21:05:40] root: DEBUG: 40-polishing/ [2025-08-18 21:05:40] root: DEBUG: 4.0 M polished_edges.gfa [2025-08-18 21:05:40] root: DEBUG: 65.0 B contigs_stats.txt [2025-08-18 21:05:40] root: DEBUG: 4.0 M filtered_contigs.fasta [2025-08-18 21:05:40] root: DEBUG: 65.0 B filtered_stats.txt [2025-08-18 21:05:40] root: DEBUG: 114.0 B edges_aln.bam.csi [2025-08-18 21:05:40] root: DEBUG: 55.0 B filtered_contigs.fasta.fai [2025-08-18 21:05:40] root: DEBUG: 44.0 K minimap_1.bam.csi [2025-08-18 21:05:40] root: DEBUG: 1.0 M base_coverage.bed.gz [2025-08-18 21:05:40] root: DEBUG: 928.0 B minimap.stderr [2025-08-18 21:05:40] root: DEBUG: 00-assembly/ [2025-08-18 21:05:40] root: DEBUG: 63.0 B draft_assembly.fasta.fai [2025-08-18 21:05:40] root: DEBUG: 4.0 M draft_assembly.fasta [2025-08-18 21:05:40] root: DEBUG: 10-consensus/ [2025-08-18 21:05:40] root: DEBUG: 1001.0 B minimap.stderr [2025-08-18 21:05:40] root: DEBUG: 4.0 M consensus.fasta [2025-08-18 21:05:40] root: DEBUG: 45.0 K minimap.bam.csi [2025-08-18 21:05:40] root: DEBUG: -------------------------- [2025-08-18 21:05:40] root: INFO: Assembly statistics: Total length: 4299847 Fragments: 2 Fragments N50: 4215632 Largest frg: 4215632 Scaffolds: 0 Mean coverage: 59 [2025-08-18 21:05:40] root: INFO: Final assembly: /media/pabloati/HDD/pablo/macourse/results/bsubtilis/assembly/assembly.fasta