[2024-08-27 13:44:29] root: INFO: Starting Flye 2.9.3-b1797 [2024-08-27 13:44:29] root: DEBUG: Cmd: /data/tools/Flye/bin/flye --nano-hq output_15.fasta -o tmp_15/ [2024-08-27 13:44:29] root: DEBUG: Python version: 3.8.10 (default, Nov 22 2023, 10:22:35) [GCC 9.4.0] [2024-08-27 13:44:29] root: INFO: >>>STAGE: configure [2024-08-27 13:44:29] root: INFO: Configuring run [2024-08-27 13:44:29] root: INFO: Total read length: 122990 [2024-08-27 13:44:29] root: INFO: Reads N50/N90: 9776 / 4347 [2024-08-27 13:44:29] root: INFO: Minimum overlap set to 4000 [2024-08-27 13:44:29] root: INFO: >>>STAGE: assembly [2024-08-27 13:44:29] root: INFO: Assembling disjointigs [2024-08-27 13:44:29] root: DEBUG: -----Begin assembly log------ [2024-08-27 13:44:29] root: DEBUG: Running: flye-modules assemble --reads /home/prom/Documents/Programmes/pandora_lib_assembler/output_15.fasta --out-asm /home/prom/Documents/Programmes/pandora_lib_assembler/tmp_15/00-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_15/flye.log --threads 1 --min-ovlp 4000 [2024-08-27 13:44:29] DEBUG: Build date: May 16 2023 00:48:26 [2024-08-27 13:44:29] DEBUG: Total RAM: 503 Gb [2024-08-27 13:44:29] DEBUG: Available RAM: 419 Gb [2024-08-27 13:44:29] DEBUG: Total CPUs: 160 [2024-08-27 13:44:29] DEBUG: Loading /data/tools/Flye/flye/config/bin_cfg/asm_nano_hq.cfg [2024-08-27 13:44:29] DEBUG: Loading /data/tools/Flye/flye/config/bin_cfg/asm_defaults.cfg [2024-08-27 13:44:29] DEBUG: big_genome_threshold=29000000 [2024-08-27 13:44:29] DEBUG: meta_read_filter_kmer_freq=100 [2024-08-27 13:44:29] DEBUG: chain_large_gap_penalty=2 [2024-08-27 13:44:29] DEBUG: chain_small_gap_penalty=0.5 [2024-08-27 13:44:29] DEBUG: chain_gap_jump_threshold=100 [2024-08-27 13:44:29] DEBUG: max_jump_gap=500 [2024-08-27 13:44:29] DEBUG: max_coverage_drop_rate=5 [2024-08-27 13:44:29] DEBUG: max_extensions_drop_rate=5 [2024-08-27 13:44:29] DEBUG: chimera_window=100 [2024-08-27 13:44:29] DEBUG: chimera_overhang=1000 [2024-08-27 13:44:29] DEBUG: min_reads_in_disjointig=4 [2024-08-27 13:44:29] DEBUG: max_inner_reads=10 [2024-08-27 13:44:29] DEBUG: max_inner_fraction=0.25 [2024-08-27 13:44:29] DEBUG: aggressive_dup_filter=1 [2024-08-27 13:44:29] DEBUG: max_separation=500 [2024-08-27 13:44:29] DEBUG: unique_edge_length=50000 [2024-08-27 13:44:29] DEBUG: min_repeat_res_support=0.51 [2024-08-27 13:44:29] DEBUG: out_paths_ratio=5 [2024-08-27 13:44:29] DEBUG: graph_cov_drop_rate=5 [2024-08-27 13:44:29] DEBUG: coverage_estimate_window=100 [2024-08-27 13:44:29] DEBUG: max_bubble_length=50000 [2024-08-27 13:44:29] DEBUG: loop_coverage_rate=1.5 [2024-08-27 13:44:29] DEBUG: repeat_edge_cov_mult=1.75 [2024-08-27 13:44:29] DEBUG: weak_detach_rate=5 [2024-08-27 13:44:29] DEBUG: tip_coverage_rate=2 [2024-08-27 13:44:29] DEBUG: tip_length_rate=2 [2024-08-27 13:44:29] DEBUG: output_gfa_before_rr=1 [2024-08-27 13:44:29] DEBUG: remove_alt_edges=0 [2024-08-27 13:44:29] DEBUG: low_cutoff_warning=0 [2024-08-27 13:44:29] DEBUG: kmer_size=17 [2024-08-27 13:44:29] DEBUG: use_minimizers=1 [2024-08-27 13:44:29] DEBUG: minimizer_window=10 [2024-08-27 13:44:29] DEBUG: reads_base_alignment=1 [2024-08-27 13:44:29] DEBUG: meta_read_top_kmer_rate=0.75 [2024-08-27 13:44:29] DEBUG: maximum_jump=1500 [2024-08-27 13:44:29] DEBUG: maximum_overhang=1500 [2024-08-27 13:44:29] DEBUG: repeat_kmer_rate=100 [2024-08-27 13:44:29] DEBUG: assemble_ovlp_divergence=0.05 [2024-08-27 13:44:29] DEBUG: assemble_divergence_relative=1 [2024-08-27 13:44:29] DEBUG: repeat_graph_ovlp_divergence=0.05 [2024-08-27 13:44:29] DEBUG: read_align_ovlp_divergence=0.10 [2024-08-27 13:44:29] DEBUG: hpc_scoring_on=1 [2024-08-27 13:44:29] DEBUG: add_unassembled_reads=0 [2024-08-27 13:44:29] DEBUG: extend_contigs_with_repeats=0 [2024-08-27 13:44:29] DEBUG: min_read_cov_cutoff=3 [2024-08-27 13:44:29] DEBUG: short_tip_length=20000 [2024-08-27 13:44:29] DEBUG: long_tip_length=100000 [2024-08-27 13:44:29] DEBUG: Running with k-mer size: 17 [2024-08-27 13:44:29] DEBUG: Running with minimum overlap 4000 [2024-08-27 13:44:29] DEBUG: Metagenome mode: N [2024-08-27 13:44:29] DEBUG: Short mode: N [2024-08-27 13:44:29] INFO: Reading sequences [2024-08-27 13:44:29] DEBUG: Building positional index [2024-08-27 13:44:29] DEBUG: Total sequence: 119331 bp [2024-08-27 13:44:29] INFO: Building minimizer index [2024-08-27 13:44:29] INFO: Pre-calculating index storage [2024-08-27 13:44:29] DEBUG: Mean k-mer frequency: 3.00615 [2024-08-27 13:44:29] DEBUG: Repetitive k-mer frequency: 300 [2024-08-27 13:44:29] DEBUG: Filtered 0 repetitive k-mers (0) [2024-08-27 13:44:29] INFO: Filling index [2024-08-27 13:44:29] DEBUG: Sorting k-mer index [2024-08-27 13:44:29] DEBUG: Selected k-mers: 7158 [2024-08-27 13:44:29] DEBUG: K-mer index size: 21521 [2024-08-27 13:44:29] DEBUG: Mean k-mer frequency: 3.00657 [2024-08-27 13:44:29] DEBUG: Minimizer rate: 5.54486 [2024-08-27 13:44:29] DEBUG: Peak RAM usage: 0 Gb [2024-08-27 13:44:29] DEBUG: Estimating k-mer identity bias [2024-08-27 15:36:51] DEBUG: Initial divergence estimate : 0.0134247 [2024-08-27 15:36:51] DEBUG: Relative threshold: Y [2024-08-27 15:36:51] DEBUG: Max divergence threshold set to 0.0634247 [2024-08-27 15:36:51] INFO: Extending reads [2024-08-27 15:36:51] DEBUG: Estimating overlap coverage [2024-08-27 15:38:22] INFO: Overlap-based coverage: 8 [2024-08-27 15:38:22] INFO: Median overlap divergence: 0.0138662 [2024-08-27 15:38:22] DEBUG: Sequence divergence distribution: | * | | * | | * | | * | | * | | * | | * | | * | | * | | * | | * | | * | | * | | * | | * | |* * * | |* * * | |* **** * | |* **** * | |* **** * | ---------------------------------------------------------------------------------------------------- 0% 5% 10% 15% 20% 25% 30% 35% 40% 45% Q25 = 0.011, Q50 = 0.014, Q75 = 0.021 [2024-08-27 15:38:22] DEBUG: Assembled disjointig 1 With 5 reads Start read: +9fcbc387-8503-4055-9cbd-0e55b2c4f656 At position: 4 leftTip: 1 rightTip: 1 Suspicious: 3 Short ext: 0 Mean extensions: 1 Avg overlap len: 7924 Min overlap len: 6178 Inner reads: 0 Length: 25562 [2024-08-27 15:38:22] DEBUG: Inner: 24 covered: 28 total: 28 [2024-08-27 15:39:48] INFO: Assembled 1 disjointigs [2024-08-27 15:39:48] INFO: Generating sequence [2024-08-27 15:39:48] DEBUG: Building positional index [2024-08-27 15:39:48] DEBUG: Total sequence: 25551 bp [2024-08-27 15:39:48] DEBUG: Mean k-mer frequency: 1.0028 [2024-08-27 15:39:48] DEBUG: Repetitive k-mer frequency: 100 [2024-08-27 15:39:48] DEBUG: Filtered 0 repetitive k-mers (0) [2024-08-27 15:39:48] DEBUG: Sorting k-mer index [2024-08-27 15:39:48] DEBUG: Selected k-mers: 4649 [2024-08-27 15:39:48] DEBUG: K-mer index size: 4663 [2024-08-27 15:39:48] DEBUG: Mean k-mer frequency: 1.00301 [2024-08-27 15:39:48] DEBUG: Minimizer rate: 5.47952 [2024-08-27 15:39:48] INFO: Filtering contained disjointigs [2024-08-27 15:39:48] DEBUG: Computing transitive closure for overlaps [2024-08-27 15:39:48] DEBUG: Found 0 overlaps [2024-08-27 15:39:48] DEBUG: Left 0 overlaps after filtering [2024-08-27 15:39:48] INFO: Contained seqs: 0 [2024-08-27 15:39:48] DEBUG: Writing FASTA [2024-08-27 15:39:48] DEBUG: Peak RAM usage: 0 Gb -----------End assembly log------------ [2024-08-27 15:39:48] root: DEBUG: Disjointigs length: 25551, N50: 25551 [2024-08-27 15:39:48] root: INFO: >>>STAGE: consensus [2024-08-27 15:39:48] root: INFO: Running Minimap2 [2024-08-27 15:39:48] root: INFO: Computing consensus [2024-08-27 15:39:49] root: INFO: Alignment error rate: 0.011591 [2024-08-27 15:39:49] root: INFO: >>>STAGE: repeat [2024-08-27 15:39:49] root: INFO: Building and resolving repeat graph [2024-08-27 15:39:49] root: DEBUG: -----Begin repeat analyser log------ [2024-08-27 15:39:49] root: DEBUG: Running: flye-modules repeat --disjointigs /home/prom/Documents/Programmes/pandora_lib_assembler/tmp_15/10-consensus/consensus.fasta --reads /home/prom/Documents/Programmes/pandora_lib_assembler/output_15.fasta --out-dir /home/prom/Documents/Programmes/pandora_lib_assembler/tmp_15/20-repeat --config /data/tools/Flye/flye/config/bin_cfg/asm_nano_hq.cfg --log /home/prom/Documents/Programmes/pandora_lib_assembler/tmp_15/flye.log --threads 1 --min-ovlp 4000 [2024-08-27 15:39:49] DEBUG: Build date: May 16 2023 00:48:44 [2024-08-27 15:39:49] DEBUG: Total RAM: 503 Gb [2024-08-27 15:39:49] DEBUG: Available RAM: 420 Gb [2024-08-27 15:39:49] DEBUG: Total CPUs: 160 [2024-08-27 15:39:49] DEBUG: Loading /data/tools/Flye/flye/config/bin_cfg/asm_nano_hq.cfg [2024-08-27 15:39:49] DEBUG: Loading /data/tools/Flye/flye/config/bin_cfg/asm_defaults.cfg [2024-08-27 15:39:49] DEBUG: big_genome_threshold=29000000 [2024-08-27 15:39:49] DEBUG: meta_read_filter_kmer_freq=100 [2024-08-27 15:39:49] DEBUG: chain_large_gap_penalty=2 [2024-08-27 15:39:49] DEBUG: chain_small_gap_penalty=0.5 [2024-08-27 15:39:49] DEBUG: chain_gap_jump_threshold=100 [2024-08-27 15:39:49] DEBUG: max_jump_gap=500 [2024-08-27 15:39:49] DEBUG: max_coverage_drop_rate=5 [2024-08-27 15:39:49] DEBUG: max_extensions_drop_rate=5 [2024-08-27 15:39:49] DEBUG: chimera_window=100 [2024-08-27 15:39:49] DEBUG: chimera_overhang=1000 [2024-08-27 15:39:49] DEBUG: min_reads_in_disjointig=4 [2024-08-27 15:39:49] DEBUG: max_inner_reads=10 [2024-08-27 15:39:49] DEBUG: max_inner_fraction=0.25 [2024-08-27 15:39:49] DEBUG: aggressive_dup_filter=1 [2024-08-27 15:39:49] DEBUG: max_separation=500 [2024-08-27 15:39:49] DEBUG: unique_edge_length=50000 [2024-08-27 15:39:49] DEBUG: min_repeat_res_support=0.51 [2024-08-27 15:39:49] DEBUG: out_paths_ratio=5 [2024-08-27 15:39:49] DEBUG: graph_cov_drop_rate=5 [2024-08-27 15:39:49] DEBUG: coverage_estimate_window=100 [2024-08-27 15:39:49] DEBUG: max_bubble_length=50000 [2024-08-27 15:39:49] DEBUG: loop_coverage_rate=1.5 [2024-08-27 15:39:49] DEBUG: repeat_edge_cov_mult=1.75 [2024-08-27 15:39:49] DEBUG: weak_detach_rate=5 [2024-08-27 15:39:49] DEBUG: tip_coverage_rate=2 [2024-08-27 15:39:49] DEBUG: tip_length_rate=2 [2024-08-27 15:39:49] DEBUG: output_gfa_before_rr=1 [2024-08-27 15:39:49] DEBUG: remove_alt_edges=0 [2024-08-27 15:39:49] DEBUG: low_cutoff_warning=0 [2024-08-27 15:39:49] DEBUG: kmer_size=17 [2024-08-27 15:39:49] DEBUG: use_minimizers=1 [2024-08-27 15:39:49] DEBUG: minimizer_window=10 [2024-08-27 15:39:49] DEBUG: reads_base_alignment=1 [2024-08-27 15:39:49] DEBUG: meta_read_top_kmer_rate=0.75 [2024-08-27 15:39:49] DEBUG: maximum_jump=1500 [2024-08-27 15:39:49] DEBUG: maximum_overhang=1500 [2024-08-27 15:39:49] DEBUG: repeat_kmer_rate=100 [2024-08-27 15:39:49] DEBUG: assemble_ovlp_divergence=0.05 [2024-08-27 15:39:49] DEBUG: assemble_divergence_relative=1 [2024-08-27 15:39:49] DEBUG: repeat_graph_ovlp_divergence=0.05 [2024-08-27 15:39:49] DEBUG: read_align_ovlp_divergence=0.10 [2024-08-27 15:39:49] DEBUG: hpc_scoring_on=1 [2024-08-27 15:39:49] DEBUG: add_unassembled_reads=0 [2024-08-27 15:39:49] DEBUG: extend_contigs_with_repeats=0 [2024-08-27 15:39:49] DEBUG: min_read_cov_cutoff=3 [2024-08-27 15:39:49] DEBUG: short_tip_length=20000 [2024-08-27 15:39:49] DEBUG: long_tip_length=100000 [2024-08-27 15:39:49] DEBUG: Running with k-mer size: 17 [2024-08-27 15:39:49] DEBUG: Selected minimum overlap 4000 [2024-08-27 15:39:49] DEBUG: Metagenome mode: N [2024-08-27 15:39:49] INFO: Parsing disjointigs [2024-08-27 15:39:49] DEBUG: Building positional index [2024-08-27 15:39:49] DEBUG: Total sequence: 25575 bp [2024-08-27 15:39:49] INFO: Building repeat graph [2024-08-27 15:39:49] DEBUG: Mean k-mer frequency: 1.00259 [2024-08-27 15:39:49] DEBUG: Repetitive k-mer frequency: 100 [2024-08-27 15:39:49] DEBUG: Filtered 0 repetitive k-mers (0) [2024-08-27 15:39:49] DEBUG: Sorting k-mer index [2024-08-27 15:39:49] DEBUG: Selected k-mers: 4638 [2024-08-27 15:39:49] DEBUG: K-mer index size: 4651 [2024-08-27 15:39:49] DEBUG: Mean k-mer frequency: 1.0028 [2024-08-27 15:39:49] DEBUG: Minimizer rate: 5.49882 [2024-08-27 15:39:49] DEBUG: Computing transitive closure for overlaps [2024-08-27 15:39:49] DEBUG: Found 0 overlaps [2024-08-27 15:39:49] DEBUG: Left 0 overlaps after filtering [2024-08-27 15:39:49] INFO: Median overlap divergence: 0 [2024-08-27 15:39:49] DEBUG: Sequence divergence distribution: | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | ---------------------------------------------------------------------------------------------------- 0% 5% 10% 15% 20% 25% 30% 35% 40% 45% Q25 = 0, Q50 = 0, Q75 = 0 [2024-08-27 15:39:49] DEBUG: Computing gluepoints [2024-08-27 15:39:49] DEBUG: Added 0 gluepoint projections [2024-08-27 15:39:49] DEBUG: Created 4 gluepoints [2024-08-27 15:39:49] DEBUG: Artificial loops removed: 0 left, 0 right, 0 both [2024-08-27 15:39:49] DEBUG: Initializing edges [2024-08-27 15:39:49] DEBUG: Edges length checksum: 654029476 [2024-08-27 15:39:49] DEBUG: Filtered 0 singleton segments [2024-08-27 15:39:49] DEBUG: Removed 0 simple and 0 double chimeric junctions [2024-08-27 15:39:49] DEBUG: Collapsed 0 edges [2024-08-27 15:39:49] DEBUG: * 1 +disjointig_1 0 25574 25574 [2024-08-27 15:39:49] DEBUG: Total edges: 1 [2024-08-27 15:39:49] INFO: Parsing reads [2024-08-27 15:39:49] DEBUG: Building positional index [2024-08-27 15:39:49] DEBUG: Total sequence: 122990 bp [2024-08-27 15:39:49] DEBUG: Building positional index [2024-08-27 15:39:49] DEBUG: Total sequence: 25574 bp [2024-08-27 15:39:49] INFO: Aligning reads to the graph [2024-08-27 15:39:49] DEBUG: Mean k-mer frequency: 1.00259 [2024-08-27 15:39:49] DEBUG: Repetitive k-mer frequency: 100 [2024-08-27 15:39:49] DEBUG: Filtered 0 repetitive k-mers (0) [2024-08-27 15:39:49] DEBUG: Sorting k-mer index [2024-08-27 15:39:49] DEBUG: Selected k-mers: 4637 [2024-08-27 15:39:49] DEBUG: K-mer index size: 4650 [2024-08-27 15:39:49] DEBUG: Mean k-mer frequency: 1.0028 [2024-08-27 15:39:49] DEBUG: Minimizer rate: 5.49978 [2024-08-27 15:39:49] DEBUG: Total reads : 14 [2024-08-27 15:39:49] DEBUG: Read with aligned parts : 14 [2024-08-27 15:39:49] DEBUG: Aligned in one piece : 14 [2024-08-27 15:39:49] INFO: Aligned read sequence: 110567 / 119331 (0.926557) [2024-08-27 15:39:49] INFO: Median overlap divergence: 0.00582945 [2024-08-27 15:39:49] DEBUG: Sequence divergence distribution: | * | | * | | * | | * | | * | | * | | * | | * | |** | |** | |** | |** | |** | |** | |*** | |*** | |*** | |**** | |**** | |**** | ---------------------------------------------------------------------------------------------------- 0% 5% 10% 15% 20% 25% 30% 35% 40% 45% Q25 = 0.0048, Q50 = 0.0058, Q75 = 0.0093 [2024-08-27 15:39:49] INFO: Mean edge coverage: 4 [2024-08-27 15:39:49] DEBUG: 1 len:25574 cov:2 mult:0.5 [2024-08-27 15:39:49] DEBUG: -1 len:25574 cov:2 mult:0.5 [2024-08-27 15:39:49] DEBUG: Unique coverage threshold 3 [2024-08-27 15:39:49] INFO: Simplifying the graph [2024-08-27 15:39:49] DEBUG: Read coverage cutoff: 3 [2024-08-27 15:39:49] DEBUG: [SIMPL] Removed 1 paths with low coverage [2024-08-27 15:39:49] DEBUG: [SIMPL] Masked 0 heterozygous loops [2024-08-27 15:39:49] DEBUG: [SIMPL] Masked 0 simple bubbles [2024-08-27 15:39:49] DEBUG: Finding repeats [2024-08-27 15:39:49] DEBUG: Read coverage cutoff: 3 [2024-08-27 15:39:49] DEBUG: Repeat detection iteration 1 [2024-08-27 15:39:49] DEBUG: Writing Dot [2024-08-27 15:39:49] DEBUG: Writing FASTA [2024-08-27 15:39:49] DEBUG: Writing Gfa [2024-08-27 15:39:49] DEBUG: [SIMPL] == Iteration 1 == [2024-08-27 15:39:49] DEBUG: Splitting nodes [2024-08-27 15:39:49] DEBUG: [SIMPL] Split 0 nodes [2024-08-27 15:39:49] DEBUG: [SIMPL] Clipped 0 short and 0 long tips [2024-08-27 15:39:49] DEBUG: [SIMPL] Masked 0 heterozygous loops [2024-08-27 15:39:49] DEBUG: [SIMPL] Masked 0 simple bubbles [2024-08-27 15:39:49] DEBUG: Finding repeats [2024-08-27 15:39:49] DEBUG: Read coverage cutoff: 3 [2024-08-27 15:39:49] DEBUG: Repeat detection iteration 1 [2024-08-27 15:39:49] DEBUG: Total unique edges: 0 [2024-08-27 15:39:49] DEBUG: [SIMPL] Resolved repeats: 0 [2024-08-27 15:39:49] DEBUG: RR links: 0 [2024-08-27 15:39:49] DEBUG: Unresolved: 0 [2024-08-27 15:39:49] DEBUG: Removed 0 simple and 0 double chimeric junctions [2024-08-27 15:39:49] DEBUG: [SIMPL] Collapsed 0 haplotypes [2024-08-27 15:39:49] DEBUG: [SIMPL] Resolved 0 simple repeats [2024-08-27 15:39:49] DEBUG: Read coverage cutoff: 3 [2024-08-27 15:39:49] DEBUG: [SIMPL] Removed 0 paths with low coverage [2024-08-27 15:39:49] DEBUG: Finding repeats [2024-08-27 15:39:49] DEBUG: Read coverage cutoff: 3 [2024-08-27 15:39:49] DEBUG: Repeat detection iteration 1 [2024-08-27 15:39:49] DEBUG: Writing Dot [2024-08-27 15:39:49] DEBUG: Writing FASTA [2024-08-27 15:39:49] DEBUG: Peak RAM usage: 0 Gb -----------End assembly log------------ [2024-08-27 15:39:49] root: INFO: >>>STAGE: contigger [2024-08-27 15:39:49] root: INFO: Generating contigs [2024-08-27 15:39:49] root: DEBUG: -----Begin contigger analyser log------ [2024-08-27 15:39:49] root: DEBUG: Running: flye-modules contigger --graph-edges /home/prom/Documents/Programmes/pandora_lib_assembler/tmp_15/20-repeat/repeat_graph_edges.fasta --reads /home/prom/Documents/Programmes/pandora_lib_assembler/output_15.fasta --out-dir /home/prom/Documents/Programmes/pandora_lib_assembler/tmp_15/30-contigger --config /data/tools/Flye/flye/config/bin_cfg/asm_nano_hq.cfg --repeat-graph /home/prom/Documents/Programmes/pandora_lib_assembler/tmp_15/20-repeat/repeat_graph_dump --graph-aln /home/prom/Documents/Programmes/pandora_lib_assembler/tmp_15/20-repeat/read_alignment_dump --log /home/prom/Documents/Programmes/pandora_lib_assembler/tmp_15/flye.log --threads 1 --min-ovlp 4000 [2024-08-27 15:39:49] DEBUG: Build date: May 16 2023 00:48:47 [2024-08-27 15:39:49] DEBUG: Total RAM: 503 Gb [2024-08-27 15:39:49] DEBUG: Available RAM: 420 Gb [2024-08-27 15:39:49] DEBUG: Total CPUs: 160 [2024-08-27 15:39:49] DEBUG: Loading /data/tools/Flye/flye/config/bin_cfg/asm_nano_hq.cfg [2024-08-27 15:39:49] DEBUG: Loading /data/tools/Flye/flye/config/bin_cfg/asm_defaults.cfg [2024-08-27 15:39:49] DEBUG: big_genome_threshold=29000000 [2024-08-27 15:39:49] DEBUG: meta_read_filter_kmer_freq=100 [2024-08-27 15:39:49] DEBUG: chain_large_gap_penalty=2 [2024-08-27 15:39:49] DEBUG: chain_small_gap_penalty=0.5 [2024-08-27 15:39:49] DEBUG: chain_gap_jump_threshold=100 [2024-08-27 15:39:49] DEBUG: max_jump_gap=500 [2024-08-27 15:39:49] DEBUG: max_coverage_drop_rate=5 [2024-08-27 15:39:49] DEBUG: max_extensions_drop_rate=5 [2024-08-27 15:39:49] DEBUG: chimera_window=100 [2024-08-27 15:39:49] DEBUG: chimera_overhang=1000 [2024-08-27 15:39:49] DEBUG: min_reads_in_disjointig=4 [2024-08-27 15:39:49] DEBUG: max_inner_reads=10 [2024-08-27 15:39:49] DEBUG: max_inner_fraction=0.25 [2024-08-27 15:39:49] DEBUG: aggressive_dup_filter=1 [2024-08-27 15:39:49] DEBUG: max_separation=500 [2024-08-27 15:39:49] DEBUG: unique_edge_length=50000 [2024-08-27 15:39:49] DEBUG: min_repeat_res_support=0.51 [2024-08-27 15:39:49] DEBUG: out_paths_ratio=5 [2024-08-27 15:39:49] DEBUG: graph_cov_drop_rate=5 [2024-08-27 15:39:49] DEBUG: coverage_estimate_window=100 [2024-08-27 15:39:49] DEBUG: max_bubble_length=50000 [2024-08-27 15:39:49] DEBUG: loop_coverage_rate=1.5 [2024-08-27 15:39:49] DEBUG: repeat_edge_cov_mult=1.75 [2024-08-27 15:39:49] DEBUG: weak_detach_rate=5 [2024-08-27 15:39:49] DEBUG: tip_coverage_rate=2 [2024-08-27 15:39:49] DEBUG: tip_length_rate=2 [2024-08-27 15:39:49] DEBUG: output_gfa_before_rr=1 [2024-08-27 15:39:49] DEBUG: remove_alt_edges=0 [2024-08-27 15:39:49] DEBUG: low_cutoff_warning=0 [2024-08-27 15:39:49] DEBUG: kmer_size=17 [2024-08-27 15:39:49] DEBUG: use_minimizers=1 [2024-08-27 15:39:49] DEBUG: minimizer_window=10 [2024-08-27 15:39:49] DEBUG: reads_base_alignment=1 [2024-08-27 15:39:49] DEBUG: meta_read_top_kmer_rate=0.75 [2024-08-27 15:39:49] DEBUG: maximum_jump=1500 [2024-08-27 15:39:49] DEBUG: maximum_overhang=1500 [2024-08-27 15:39:49] DEBUG: repeat_kmer_rate=100 [2024-08-27 15:39:49] DEBUG: assemble_ovlp_divergence=0.05 [2024-08-27 15:39:49] DEBUG: assemble_divergence_relative=1 [2024-08-27 15:39:49] DEBUG: repeat_graph_ovlp_divergence=0.05 [2024-08-27 15:39:49] DEBUG: read_align_ovlp_divergence=0.10 [2024-08-27 15:39:49] DEBUG: hpc_scoring_on=1 [2024-08-27 15:39:49] DEBUG: add_unassembled_reads=0 [2024-08-27 15:39:49] DEBUG: extend_contigs_with_repeats=0 [2024-08-27 15:39:49] DEBUG: min_read_cov_cutoff=3 [2024-08-27 15:39:49] DEBUG: short_tip_length=20000 [2024-08-27 15:39:49] DEBUG: long_tip_length=100000 [2024-08-27 15:39:49] DEBUG: Running with k-mer size: 17 [2024-08-27 15:39:49] DEBUG: Selected minimum overlap 4000 [2024-08-27 15:39:49] INFO: Reading sequences [2024-08-27 15:39:49] DEBUG: Building positional index [2024-08-27 15:39:49] DEBUG: Total sequence: 122990 bp [2024-08-27 15:39:49] DEBUG: Flipped 0 [2024-08-27 15:39:49] DEBUG: Final graph contains 0 egdes [2024-08-27 15:39:49] DEBUG: Extending contigs into repeats [2024-08-27 15:39:49] DEBUG: Covered 0 repetitive contigs [2024-08-27 15:39:49] INFO: Generated 0 contigs [2024-08-27 15:39:49] DEBUG: Writing FASTA [2024-08-27 15:39:49] DEBUG: Generating scaffold connections [2024-08-27 15:39:49] INFO: Added 0 scaffold connections [2024-08-27 15:39:49] DEBUG: Writing Dot [2024-08-27 15:39:49] DEBUG: Writing FASTA [2024-08-27 15:39:49] DEBUG: Writing Gfa [2024-08-27 15:39:49] DEBUG: Peak RAM usage: 0 Gb -----------End assembly log------------ [2024-08-27 15:39:49] root: ERROR: No contigs were assembled - pipeline stopped [2024-08-27 15:39:49] root: ERROR: Pipeline aborted