[2024-08-27 13:40:10] root: INFO: Starting Flye 2.9.3-b1797 [2024-08-27 13:40:10] root: DEBUG: Cmd: /data/tools/Flye/bin/flye --nano-hq output_0.fasta -o tmp/ [2024-08-27 13:40:10] root: DEBUG: Python version: 3.8.10 (default, Nov 22 2023, 10:22:35) [GCC 9.4.0] [2024-08-27 13:40:10] root: INFO: >>>STAGE: configure [2024-08-27 13:40:10] root: INFO: Configuring run [2024-08-27 13:40:10] root: INFO: Total read length: 126075 [2024-08-27 13:40:10] root: INFO: Reads N50/N90: 10216 / 4807 [2024-08-27 13:40:10] root: INFO: Minimum overlap set to 5000 [2024-08-27 13:40:10] root: INFO: >>>STAGE: assembly [2024-08-27 13:40:10] root: INFO: Assembling disjointigs [2024-08-27 13:40:10] root: DEBUG: -----Begin assembly log------ [2024-08-27 13:40:10] root: DEBUG: Running: flye-modules assemble --reads /home/prom/Documents/Programmes/pandora_lib_assembler/output_0.fasta --out-asm /home/prom/Documents/Programmes/pandora_lib_assembler/tmp/00-assembly/draft_assembly.fasta --config /data/tools/Flye/flye/config/bin_cfg/asm_nano_hq.cfg --log /home/prom/Documents/Programmes/pandora_lib_assembler/tmp/flye.log --threads 1 --min-ovlp 5000 [2024-08-27 13:40:10] DEBUG: Build date: May 16 2023 00:48:26 [2024-08-27 13:40:10] DEBUG: Total RAM: 503 Gb [2024-08-27 13:40:10] DEBUG: Available RAM: 421 Gb [2024-08-27 13:40:10] DEBUG: Total CPUs: 160 [2024-08-27 13:40:10] DEBUG: Loading /data/tools/Flye/flye/config/bin_cfg/asm_nano_hq.cfg [2024-08-27 13:40:10] DEBUG: Loading /data/tools/Flye/flye/config/bin_cfg/asm_defaults.cfg [2024-08-27 13:40:10] DEBUG: big_genome_threshold=29000000 [2024-08-27 13:40:10] DEBUG: meta_read_filter_kmer_freq=100 [2024-08-27 13:40:10] DEBUG: chain_large_gap_penalty=2 [2024-08-27 13:40:10] DEBUG: chain_small_gap_penalty=0.5 [2024-08-27 13:40:10] DEBUG: chain_gap_jump_threshold=100 [2024-08-27 13:40:10] DEBUG: max_jump_gap=500 [2024-08-27 13:40:10] DEBUG: max_coverage_drop_rate=5 [2024-08-27 13:40:10] DEBUG: max_extensions_drop_rate=5 [2024-08-27 13:40:10] DEBUG: chimera_window=100 [2024-08-27 13:40:10] DEBUG: chimera_overhang=1000 [2024-08-27 13:40:10] DEBUG: min_reads_in_disjointig=4 [2024-08-27 13:40:10] DEBUG: max_inner_reads=10 [2024-08-27 13:40:10] DEBUG: max_inner_fraction=0.25 [2024-08-27 13:40:10] DEBUG: aggressive_dup_filter=1 [2024-08-27 13:40:10] DEBUG: max_separation=500 [2024-08-27 13:40:10] DEBUG: unique_edge_length=50000 [2024-08-27 13:40:10] DEBUG: min_repeat_res_support=0.51 [2024-08-27 13:40:10] DEBUG: out_paths_ratio=5 [2024-08-27 13:40:10] DEBUG: graph_cov_drop_rate=5 [2024-08-27 13:40:10] DEBUG: coverage_estimate_window=100 [2024-08-27 13:40:10] DEBUG: max_bubble_length=50000 [2024-08-27 13:40:10] DEBUG: loop_coverage_rate=1.5 [2024-08-27 13:40:10] DEBUG: repeat_edge_cov_mult=1.75 [2024-08-27 13:40:10] DEBUG: weak_detach_rate=5 [2024-08-27 13:40:10] DEBUG: tip_coverage_rate=2 [2024-08-27 13:40:10] DEBUG: tip_length_rate=2 [2024-08-27 13:40:10] DEBUG: output_gfa_before_rr=1 [2024-08-27 13:40:10] DEBUG: remove_alt_edges=0 [2024-08-27 13:40:10] DEBUG: low_cutoff_warning=0 [2024-08-27 13:40:10] DEBUG: kmer_size=17 [2024-08-27 13:40:10] DEBUG: use_minimizers=1 [2024-08-27 13:40:10] DEBUG: minimizer_window=10 [2024-08-27 13:40:10] DEBUG: reads_base_alignment=1 [2024-08-27 13:40:10] DEBUG: meta_read_top_kmer_rate=0.75 [2024-08-27 13:40:10] DEBUG: maximum_jump=1500 [2024-08-27 13:40:10] DEBUG: maximum_overhang=1500 [2024-08-27 13:40:10] DEBUG: repeat_kmer_rate=100 [2024-08-27 13:40:10] DEBUG: assemble_ovlp_divergence=0.05 [2024-08-27 13:40:10] DEBUG: assemble_divergence_relative=1 [2024-08-27 13:40:10] DEBUG: repeat_graph_ovlp_divergence=0.05 [2024-08-27 13:40:10] DEBUG: read_align_ovlp_divergence=0.10 [2024-08-27 13:40:10] DEBUG: hpc_scoring_on=1 [2024-08-27 13:40:10] DEBUG: add_unassembled_reads=0 [2024-08-27 13:40:10] DEBUG: extend_contigs_with_repeats=0 [2024-08-27 13:40:10] DEBUG: min_read_cov_cutoff=3 [2024-08-27 13:40:10] DEBUG: short_tip_length=20000 [2024-08-27 13:40:10] DEBUG: long_tip_length=100000 [2024-08-27 13:40:10] DEBUG: Running with k-mer size: 17 [2024-08-27 13:40:10] DEBUG: Running with minimum overlap 5000 [2024-08-27 13:40:10] DEBUG: Metagenome mode: N [2024-08-27 13:40:10] DEBUG: Short mode: N [2024-08-27 13:40:10] INFO: Reading sequences [2024-08-27 13:40:10] DEBUG: Building positional index [2024-08-27 13:40:10] DEBUG: Total sequence: 108918 bp [2024-08-27 13:40:10] INFO: Building minimizer index [2024-08-27 13:40:10] INFO: Pre-calculating index storage [2024-08-27 13:40:10] DEBUG: Mean k-mer frequency: 2.77281 [2024-08-27 13:40:10] DEBUG: Repetitive k-mer frequency: 277 [2024-08-27 13:40:10] DEBUG: Filtered 0 repetitive k-mers (0) [2024-08-27 13:40:10] INFO: Filling index [2024-08-27 13:40:11] DEBUG: Sorting k-mer index [2024-08-27 13:40:11] DEBUG: Selected k-mers: 7068 [2024-08-27 13:40:11] DEBUG: K-mer index size: 19601 [2024-08-27 13:40:11] DEBUG: Mean k-mer frequency: 2.7732 [2024-08-27 13:40:11] DEBUG: Minimizer rate: 5.55676 [2024-08-27 13:40:11] DEBUG: Peak RAM usage: 0 Gb [2024-08-27 13:40:11] DEBUG: Estimating k-mer identity bias [2024-08-27 15:59:40] DEBUG: Initial divergence estimate : 0.0122304 [2024-08-27 15:59:40] DEBUG: Relative threshold: Y [2024-08-27 15:59:40] DEBUG: Max divergence threshold set to 0.0622304 [2024-08-27 15:59:40] INFO: Extending reads [2024-08-27 15:59:40] DEBUG: Estimating overlap coverage [2024-08-27 16:01:06] INFO: Overlap-based coverage: 6 [2024-08-27 16:01:06] INFO: Median overlap divergence: 0.0127758 [2024-08-27 16:01:06] DEBUG: Sequence divergence distribution: | * | | * | | * | | * | | * | | * | | * | | * | | ** | | ** | | ** | | ** | | ** | | ** | | ** | | ** | | ***** * | | ***** * | | ***** * | | ***** * | ---------------------------------------------------------------------------------------------------- 0% 5% 10% 15% 20% 25% 30% 35% 40% 45% Q25 = 0.011, Q50 = 0.013, Q75 = 0.021 [2024-08-27 16:01:06] DEBUG: Assembled disjointig 1 With 3 reads Start read: +0373698d-ca92-426c-809f-c0a1ec63921a At position: 2 leftTip: 1 rightTip: 1 Suspicious: 2 Short ext: 0 Mean extensions: 1 Avg overlap len: 7924 Min overlap len: 6534 Inner reads: 0 Length: 25544 [2024-08-27 16:01:06] DEBUG: Inner: 18 covered: 18 total: 22 [2024-08-27 16:02:30] INFO: Assembled 1 disjointigs [2024-08-27 16:02:30] INFO: Generating sequence [2024-08-27 16:02:30] DEBUG: Building positional index [2024-08-27 16:02:30] DEBUG: Total sequence: 25548 bp [2024-08-27 16:02:30] DEBUG: Mean k-mer frequency: 1.00279 [2024-08-27 16:02:30] DEBUG: Repetitive k-mer frequency: 100 [2024-08-27 16:02:30] DEBUG: Filtered 0 repetitive k-mers (0) [2024-08-27 16:02:30] DEBUG: Sorting k-mer index [2024-08-27 16:02:30] DEBUG: Selected k-mers: 4653 [2024-08-27 16:02:30] DEBUG: K-mer index size: 4667 [2024-08-27 16:02:30] DEBUG: Mean k-mer frequency: 1.00301 [2024-08-27 16:02:30] DEBUG: Minimizer rate: 5.47418 [2024-08-27 16:02:30] INFO: Filtering contained disjointigs [2024-08-27 16:02:30] DEBUG: Computing transitive closure for overlaps [2024-08-27 16:02:30] DEBUG: Found 0 overlaps [2024-08-27 16:02:30] DEBUG: Left 0 overlaps after filtering [2024-08-27 16:02:30] INFO: Contained seqs: 0 [2024-08-27 16:02:30] DEBUG: Writing FASTA [2024-08-27 16:02:30] DEBUG: Peak RAM usage: 0 Gb -----------End assembly log------------ [2024-08-27 16:02:30] root: DEBUG: Disjointigs length: 25548, N50: 25548 [2024-08-27 16:02:30] root: INFO: >>>STAGE: consensus [2024-08-27 16:02:30] root: INFO: Running Minimap2 [2024-08-27 16:02:30] root: INFO: Computing consensus [2024-08-27 16:02:30] root: INFO: Alignment error rate: 0.014393 [2024-08-27 16:02:30] root: INFO: >>>STAGE: repeat [2024-08-27 16:02:30] root: INFO: Building and resolving repeat graph [2024-08-27 16:02:30] root: DEBUG: -----Begin repeat analyser log------ [2024-08-27 16:02:30] root: DEBUG: Running: flye-modules repeat --disjointigs /home/prom/Documents/Programmes/pandora_lib_assembler/tmp/10-consensus/consensus.fasta --reads /home/prom/Documents/Programmes/pandora_lib_assembler/output_0.fasta --out-dir /home/prom/Documents/Programmes/pandora_lib_assembler/tmp/20-repeat --config /data/tools/Flye/flye/config/bin_cfg/asm_nano_hq.cfg --log /home/prom/Documents/Programmes/pandora_lib_assembler/tmp/flye.log --threads 1 --min-ovlp 5000 [2024-08-27 16:02:30] DEBUG: Build date: May 16 2023 00:48:44 [2024-08-27 16:02:30] DEBUG: Total RAM: 503 Gb [2024-08-27 16:02:30] DEBUG: Available RAM: 421 Gb [2024-08-27 16:02:30] DEBUG: Total CPUs: 160 [2024-08-27 16:02:30] DEBUG: Loading /data/tools/Flye/flye/config/bin_cfg/asm_nano_hq.cfg [2024-08-27 16:02:30] DEBUG: Loading /data/tools/Flye/flye/config/bin_cfg/asm_defaults.cfg [2024-08-27 16:02:30] DEBUG: big_genome_threshold=29000000 [2024-08-27 16:02:30] DEBUG: meta_read_filter_kmer_freq=100 [2024-08-27 16:02:30] DEBUG: chain_large_gap_penalty=2 [2024-08-27 16:02:30] DEBUG: chain_small_gap_penalty=0.5 [2024-08-27 16:02:30] DEBUG: chain_gap_jump_threshold=100 [2024-08-27 16:02:30] DEBUG: max_jump_gap=500 [2024-08-27 16:02:30] DEBUG: max_coverage_drop_rate=5 [2024-08-27 16:02:30] DEBUG: max_extensions_drop_rate=5 [2024-08-27 16:02:30] DEBUG: chimera_window=100 [2024-08-27 16:02:30] DEBUG: chimera_overhang=1000 [2024-08-27 16:02:30] DEBUG: min_reads_in_disjointig=4 [2024-08-27 16:02:30] DEBUG: max_inner_reads=10 [2024-08-27 16:02:30] DEBUG: max_inner_fraction=0.25 [2024-08-27 16:02:30] DEBUG: aggressive_dup_filter=1 [2024-08-27 16:02:30] DEBUG: max_separation=500 [2024-08-27 16:02:30] DEBUG: unique_edge_length=50000 [2024-08-27 16:02:30] DEBUG: min_repeat_res_support=0.51 [2024-08-27 16:02:30] DEBUG: out_paths_ratio=5 [2024-08-27 16:02:30] DEBUG: graph_cov_drop_rate=5 [2024-08-27 16:02:30] DEBUG: coverage_estimate_window=100 [2024-08-27 16:02:30] DEBUG: max_bubble_length=50000 [2024-08-27 16:02:30] DEBUG: loop_coverage_rate=1.5 [2024-08-27 16:02:30] DEBUG: repeat_edge_cov_mult=1.75 [2024-08-27 16:02:30] DEBUG: weak_detach_rate=5 [2024-08-27 16:02:30] DEBUG: tip_coverage_rate=2 [2024-08-27 16:02:30] DEBUG: tip_length_rate=2 [2024-08-27 16:02:30] DEBUG: output_gfa_before_rr=1 [2024-08-27 16:02:30] DEBUG: remove_alt_edges=0 [2024-08-27 16:02:30] DEBUG: low_cutoff_warning=0 [2024-08-27 16:02:30] DEBUG: kmer_size=17 [2024-08-27 16:02:30] DEBUG: use_minimizers=1 [2024-08-27 16:02:30] DEBUG: minimizer_window=10 [2024-08-27 16:02:30] DEBUG: reads_base_alignment=1 [2024-08-27 16:02:30] DEBUG: meta_read_top_kmer_rate=0.75 [2024-08-27 16:02:30] DEBUG: maximum_jump=1500 [2024-08-27 16:02:30] DEBUG: maximum_overhang=1500 [2024-08-27 16:02:30] DEBUG: repeat_kmer_rate=100 [2024-08-27 16:02:30] DEBUG: assemble_ovlp_divergence=0.05 [2024-08-27 16:02:30] DEBUG: assemble_divergence_relative=1 [2024-08-27 16:02:30] DEBUG: repeat_graph_ovlp_divergence=0.05 [2024-08-27 16:02:30] DEBUG: read_align_ovlp_divergence=0.10 [2024-08-27 16:02:30] DEBUG: hpc_scoring_on=1 [2024-08-27 16:02:30] DEBUG: add_unassembled_reads=0 [2024-08-27 16:02:30] DEBUG: extend_contigs_with_repeats=0 [2024-08-27 16:02:30] DEBUG: min_read_cov_cutoff=3 [2024-08-27 16:02:30] DEBUG: short_tip_length=20000 [2024-08-27 16:02:30] DEBUG: long_tip_length=100000 [2024-08-27 16:02:30] DEBUG: Running with k-mer size: 17 [2024-08-27 16:02:30] DEBUG: Selected minimum overlap 5000 [2024-08-27 16:02:30] DEBUG: Metagenome mode: N [2024-08-27 16:02:30] INFO: Parsing disjointigs [2024-08-27 16:02:30] DEBUG: Building positional index [2024-08-27 16:02:30] DEBUG: Total sequence: 25572 bp [2024-08-27 16:02:30] INFO: Building repeat graph [2024-08-27 16:02:30] DEBUG: Mean k-mer frequency: 1.00259 [2024-08-27 16:02:30] DEBUG: Repetitive k-mer frequency: 100 [2024-08-27 16:02:30] DEBUG: Filtered 0 repetitive k-mers (0) [2024-08-27 16:02:30] DEBUG: Sorting k-mer index [2024-08-27 16:02:30] DEBUG: Selected k-mers: 4639 [2024-08-27 16:02:30] DEBUG: K-mer index size: 4652 [2024-08-27 16:02:30] DEBUG: Mean k-mer frequency: 1.0028 [2024-08-27 16:02:30] DEBUG: Minimizer rate: 5.49699 [2024-08-27 16:02:31] DEBUG: Computing transitive closure for overlaps [2024-08-27 16:02:31] DEBUG: Found 0 overlaps [2024-08-27 16:02:31] DEBUG: Left 0 overlaps after filtering [2024-08-27 16:02:31] INFO: Median overlap divergence: 0 [2024-08-27 16:02:31] DEBUG: Sequence divergence distribution: | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | ---------------------------------------------------------------------------------------------------- 0% 5% 10% 15% 20% 25% 30% 35% 40% 45% Q25 = 0, Q50 = 0, Q75 = 0 [2024-08-27 16:02:31] DEBUG: Computing gluepoints [2024-08-27 16:02:31] DEBUG: Added 0 gluepoint projections [2024-08-27 16:02:31] DEBUG: Created 4 gluepoints [2024-08-27 16:02:31] DEBUG: Artificial loops removed: 0 left, 0 right, 0 both [2024-08-27 16:02:31] DEBUG: Initializing edges [2024-08-27 16:02:31] DEBUG: Edges length checksum: 653876041 [2024-08-27 16:02:31] DEBUG: Filtered 0 singleton segments [2024-08-27 16:02:31] DEBUG: Removed 0 simple and 0 double chimeric junctions [2024-08-27 16:02:31] DEBUG: Collapsed 0 edges [2024-08-27 16:02:31] DEBUG: * 1 +disjointig_1 0 25571 25571 [2024-08-27 16:02:31] DEBUG: Total edges: 1 [2024-08-27 16:02:31] INFO: Parsing reads [2024-08-27 16:02:31] DEBUG: Building positional index [2024-08-27 16:02:31] DEBUG: Total sequence: 126075 bp [2024-08-27 16:02:31] DEBUG: Building positional index [2024-08-27 16:02:31] DEBUG: Total sequence: 25571 bp [2024-08-27 16:02:31] INFO: Aligning reads to the graph [2024-08-27 16:02:31] DEBUG: Mean k-mer frequency: 1.00259 [2024-08-27 16:02:31] DEBUG: Repetitive k-mer frequency: 100 [2024-08-27 16:02:31] DEBUG: Filtered 0 repetitive k-mers (0) [2024-08-27 16:02:31] DEBUG: Sorting k-mer index [2024-08-27 16:02:31] DEBUG: Selected k-mers: 4638 [2024-08-27 16:02:31] DEBUG: K-mer index size: 4651 [2024-08-27 16:02:31] DEBUG: Mean k-mer frequency: 1.0028 [2024-08-27 16:02:31] DEBUG: Minimizer rate: 5.49796 [2024-08-27 16:02:31] DEBUG: Total reads : 11 [2024-08-27 16:02:31] DEBUG: Read with aligned parts : 11 [2024-08-27 16:02:31] DEBUG: Aligned in one piece : 11 [2024-08-27 16:02:31] INFO: Aligned read sequence: 100440 / 108918 (0.922162) [2024-08-27 16:02:31] INFO: Median overlap divergence: 0.00583172 [2024-08-27 16:02:31] DEBUG: Sequence divergence distribution: | * | | * | | * | | * | | * | | * | | * | | * | | * | | * | | * | | * | | * | |*** | |*** | |*** | |**** | |**** | |**** | |**** | ---------------------------------------------------------------------------------------------------- 0% 5% 10% 15% 20% 25% 30% 35% 40% 45% Q25 = 0.005, Q50 = 0.0058, Q75 = 0.011 [2024-08-27 16:02:31] INFO: Mean edge coverage: 3 [2024-08-27 16:02:31] DEBUG: 1 len:25571 cov:2 mult:0.666667 [2024-08-27 16:02:31] DEBUG: -1 len:25571 cov:2 mult:0.666667 [2024-08-27 16:02:31] DEBUG: Unique coverage threshold 3 [2024-08-27 16:02:31] INFO: Simplifying the graph [2024-08-27 16:02:31] DEBUG: Read coverage cutoff: 3 [2024-08-27 16:02:31] DEBUG: [SIMPL] Removed 1 paths with low coverage [2024-08-27 16:02:31] DEBUG: [SIMPL] Masked 0 heterozygous loops [2024-08-27 16:02:31] DEBUG: [SIMPL] Masked 0 simple bubbles [2024-08-27 16:02:31] DEBUG: Finding repeats [2024-08-27 16:02:31] DEBUG: Read coverage cutoff: 3 [2024-08-27 16:02:31] DEBUG: Repeat detection iteration 1 [2024-08-27 16:02:31] DEBUG: Writing Dot [2024-08-27 16:02:31] DEBUG: Writing FASTA [2024-08-27 16:02:31] DEBUG: Writing Gfa [2024-08-27 16:02:31] DEBUG: [SIMPL] == Iteration 1 == [2024-08-27 16:02:31] DEBUG: Splitting nodes [2024-08-27 16:02:31] DEBUG: [SIMPL] Split 0 nodes [2024-08-27 16:02:31] DEBUG: [SIMPL] Clipped 0 short and 0 long tips [2024-08-27 16:02:31] DEBUG: [SIMPL] Masked 0 heterozygous loops [2024-08-27 16:02:31] DEBUG: [SIMPL] Masked 0 simple bubbles [2024-08-27 16:02:31] DEBUG: Finding repeats [2024-08-27 16:02:31] DEBUG: Read coverage cutoff: 3 [2024-08-27 16:02:31] DEBUG: Repeat detection iteration 1 [2024-08-27 16:02:31] DEBUG: Total unique edges: 0 [2024-08-27 16:02:31] DEBUG: [SIMPL] Resolved repeats: 0 [2024-08-27 16:02:31] DEBUG: RR links: 0 [2024-08-27 16:02:31] DEBUG: Unresolved: 0 [2024-08-27 16:02:31] DEBUG: Removed 0 simple and 0 double chimeric junctions [2024-08-27 16:02:31] DEBUG: [SIMPL] Collapsed 0 haplotypes [2024-08-27 16:02:31] DEBUG: [SIMPL] Resolved 0 simple repeats [2024-08-27 16:02:31] DEBUG: Read coverage cutoff: 3 [2024-08-27 16:02:31] DEBUG: [SIMPL] Removed 0 paths with low coverage [2024-08-27 16:02:31] DEBUG: Finding repeats [2024-08-27 16:02:31] DEBUG: Read coverage cutoff: 3 [2024-08-27 16:02:31] DEBUG: Repeat detection iteration 1 [2024-08-27 16:02:31] DEBUG: Writing Dot [2024-08-27 16:02:31] DEBUG: Writing FASTA [2024-08-27 16:02:31] DEBUG: Peak RAM usage: 0 Gb -----------End assembly log------------ [2024-08-27 16:02:31] root: INFO: >>>STAGE: contigger [2024-08-27 16:02:31] root: INFO: Generating contigs [2024-08-27 16:02:31] root: DEBUG: -----Begin contigger analyser log------ [2024-08-27 16:02:31] root: DEBUG: Running: flye-modules contigger --graph-edges /home/prom/Documents/Programmes/pandora_lib_assembler/tmp/20-repeat/repeat_graph_edges.fasta --reads /home/prom/Documents/Programmes/pandora_lib_assembler/output_0.fasta --out-dir /home/prom/Documents/Programmes/pandora_lib_assembler/tmp/30-contigger --config /data/tools/Flye/flye/config/bin_cfg/asm_nano_hq.cfg --repeat-graph /home/prom/Documents/Programmes/pandora_lib_assembler/tmp/20-repeat/repeat_graph_dump --graph-aln /home/prom/Documents/Programmes/pandora_lib_assembler/tmp/20-repeat/read_alignment_dump --log /home/prom/Documents/Programmes/pandora_lib_assembler/tmp/flye.log --threads 1 --min-ovlp 5000 [2024-08-27 16:02:31] DEBUG: Build date: May 16 2023 00:48:47 [2024-08-27 16:02:31] DEBUG: Total RAM: 503 Gb [2024-08-27 16:02:31] DEBUG: Available RAM: 421 Gb [2024-08-27 16:02:31] DEBUG: Total CPUs: 160 [2024-08-27 16:02:31] DEBUG: Loading /data/tools/Flye/flye/config/bin_cfg/asm_nano_hq.cfg [2024-08-27 16:02:31] DEBUG: Loading /data/tools/Flye/flye/config/bin_cfg/asm_defaults.cfg [2024-08-27 16:02:31] DEBUG: big_genome_threshold=29000000 [2024-08-27 16:02:31] DEBUG: meta_read_filter_kmer_freq=100 [2024-08-27 16:02:31] DEBUG: chain_large_gap_penalty=2 [2024-08-27 16:02:31] DEBUG: chain_small_gap_penalty=0.5 [2024-08-27 16:02:31] DEBUG: chain_gap_jump_threshold=100 [2024-08-27 16:02:31] DEBUG: max_jump_gap=500 [2024-08-27 16:02:31] DEBUG: max_coverage_drop_rate=5 [2024-08-27 16:02:31] DEBUG: max_extensions_drop_rate=5 [2024-08-27 16:02:31] DEBUG: chimera_window=100 [2024-08-27 16:02:31] DEBUG: chimera_overhang=1000 [2024-08-27 16:02:31] DEBUG: min_reads_in_disjointig=4 [2024-08-27 16:02:31] DEBUG: max_inner_reads=10 [2024-08-27 16:02:31] DEBUG: max_inner_fraction=0.25 [2024-08-27 16:02:31] DEBUG: aggressive_dup_filter=1 [2024-08-27 16:02:31] DEBUG: max_separation=500 [2024-08-27 16:02:31] DEBUG: unique_edge_length=50000 [2024-08-27 16:02:31] DEBUG: min_repeat_res_support=0.51 [2024-08-27 16:02:31] DEBUG: out_paths_ratio=5 [2024-08-27 16:02:31] DEBUG: graph_cov_drop_rate=5 [2024-08-27 16:02:31] DEBUG: coverage_estimate_window=100 [2024-08-27 16:02:31] DEBUG: max_bubble_length=50000 [2024-08-27 16:02:31] DEBUG: loop_coverage_rate=1.5 [2024-08-27 16:02:31] DEBUG: repeat_edge_cov_mult=1.75 [2024-08-27 16:02:31] DEBUG: weak_detach_rate=5 [2024-08-27 16:02:31] DEBUG: tip_coverage_rate=2 [2024-08-27 16:02:31] DEBUG: tip_length_rate=2 [2024-08-27 16:02:31] DEBUG: output_gfa_before_rr=1 [2024-08-27 16:02:31] DEBUG: remove_alt_edges=0 [2024-08-27 16:02:31] DEBUG: low_cutoff_warning=0 [2024-08-27 16:02:31] DEBUG: kmer_size=17 [2024-08-27 16:02:31] DEBUG: use_minimizers=1 [2024-08-27 16:02:31] DEBUG: minimizer_window=10 [2024-08-27 16:02:31] DEBUG: reads_base_alignment=1 [2024-08-27 16:02:31] DEBUG: meta_read_top_kmer_rate=0.75 [2024-08-27 16:02:31] DEBUG: maximum_jump=1500 [2024-08-27 16:02:31] DEBUG: maximum_overhang=1500 [2024-08-27 16:02:31] DEBUG: repeat_kmer_rate=100 [2024-08-27 16:02:31] DEBUG: assemble_ovlp_divergence=0.05 [2024-08-27 16:02:31] DEBUG: assemble_divergence_relative=1 [2024-08-27 16:02:31] DEBUG: repeat_graph_ovlp_divergence=0.05 [2024-08-27 16:02:31] DEBUG: read_align_ovlp_divergence=0.10 [2024-08-27 16:02:31] DEBUG: hpc_scoring_on=1 [2024-08-27 16:02:31] DEBUG: add_unassembled_reads=0 [2024-08-27 16:02:31] DEBUG: extend_contigs_with_repeats=0 [2024-08-27 16:02:31] DEBUG: min_read_cov_cutoff=3 [2024-08-27 16:02:31] DEBUG: short_tip_length=20000 [2024-08-27 16:02:31] DEBUG: long_tip_length=100000 [2024-08-27 16:02:31] DEBUG: Running with k-mer size: 17 [2024-08-27 16:02:31] DEBUG: Selected minimum overlap 5000 [2024-08-27 16:02:31] INFO: Reading sequences [2024-08-27 16:02:31] DEBUG: Building positional index [2024-08-27 16:02:31] DEBUG: Total sequence: 126075 bp [2024-08-27 16:02:31] DEBUG: Flipped 0 [2024-08-27 16:02:31] DEBUG: Final graph contains 0 egdes [2024-08-27 16:02:31] DEBUG: Extending contigs into repeats [2024-08-27 16:02:31] DEBUG: Covered 0 repetitive contigs [2024-08-27 16:02:31] INFO: Generated 0 contigs [2024-08-27 16:02:31] DEBUG: Writing FASTA [2024-08-27 16:02:31] DEBUG: Generating scaffold connections [2024-08-27 16:02:31] INFO: Added 0 scaffold connections [2024-08-27 16:02:31] DEBUG: Writing Dot [2024-08-27 16:02:31] DEBUG: Writing FASTA [2024-08-27 16:02:31] DEBUG: Writing Gfa [2024-08-27 16:02:31] DEBUG: Peak RAM usage: 0 Gb -----------End assembly log------------ [2024-08-27 16:02:31] root: ERROR: No contigs were assembled - pipeline stopped [2024-08-27 16:02:31] root: ERROR: Pipeline aborted