[2024-08-27 13:42:20] root: INFO: Starting Flye 2.9.3-b1797 [2024-08-27 13:42:20] root: DEBUG: Cmd: /data/tools/Flye/bin/flye --nano-hq output_7.fasta -o tmp_7 [2024-08-27 13:42:20] root: DEBUG: Python version: 3.8.10 (default, Nov 22 2023, 10:22:35) [GCC 9.4.0] [2024-08-27 13:42:20] root: INFO: >>>STAGE: configure [2024-08-27 13:42:20] root: INFO: Configuring run [2024-08-27 13:42:20] root: INFO: Total read length: 117213 [2024-08-27 13:42:20] root: INFO: Reads N50/N90: 8239 / 4347 [2024-08-27 13:42:20] root: INFO: Minimum overlap set to 4000 [2024-08-27 13:42:20] root: INFO: >>>STAGE: assembly [2024-08-27 13:42:20] root: INFO: Assembling disjointigs [2024-08-27 13:42:20] root: DEBUG: -----Begin assembly log------ [2024-08-27 13:42:20] root: DEBUG: Running: flye-modules assemble --reads /home/prom/Documents/Programmes/pandora_lib_assembler/output_7.fasta --out-asm /home/prom/Documents/Programmes/pandora_lib_assembler/tmp_7/00-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_7/flye.log --threads 1 --min-ovlp 4000 [2024-08-27 13:42:20] DEBUG: Build date: May 16 2023 00:48:26 [2024-08-27 13:42:20] DEBUG: Total RAM: 503 Gb [2024-08-27 13:42:20] DEBUG: Available RAM: 420 Gb [2024-08-27 13:42:20] DEBUG: Total CPUs: 160 [2024-08-27 13:42:20] DEBUG: Loading /data/tools/Flye/flye/config/bin_cfg/asm_nano_hq.cfg [2024-08-27 13:42:20] DEBUG: Loading /data/tools/Flye/flye/config/bin_cfg/asm_defaults.cfg [2024-08-27 13:42:20] DEBUG: big_genome_threshold=29000000 [2024-08-27 13:42:20] DEBUG: meta_read_filter_kmer_freq=100 [2024-08-27 13:42:20] DEBUG: chain_large_gap_penalty=2 [2024-08-27 13:42:20] DEBUG: chain_small_gap_penalty=0.5 [2024-08-27 13:42:20] DEBUG: chain_gap_jump_threshold=100 [2024-08-27 13:42:20] DEBUG: max_jump_gap=500 [2024-08-27 13:42:20] DEBUG: max_coverage_drop_rate=5 [2024-08-27 13:42:20] DEBUG: max_extensions_drop_rate=5 [2024-08-27 13:42:20] DEBUG: chimera_window=100 [2024-08-27 13:42:20] DEBUG: chimera_overhang=1000 [2024-08-27 13:42:20] DEBUG: min_reads_in_disjointig=4 [2024-08-27 13:42:20] DEBUG: max_inner_reads=10 [2024-08-27 13:42:20] DEBUG: max_inner_fraction=0.25 [2024-08-27 13:42:20] DEBUG: aggressive_dup_filter=1 [2024-08-27 13:42:20] DEBUG: max_separation=500 [2024-08-27 13:42:20] DEBUG: unique_edge_length=50000 [2024-08-27 13:42:20] DEBUG: min_repeat_res_support=0.51 [2024-08-27 13:42:20] DEBUG: out_paths_ratio=5 [2024-08-27 13:42:20] DEBUG: graph_cov_drop_rate=5 [2024-08-27 13:42:20] DEBUG: coverage_estimate_window=100 [2024-08-27 13:42:20] DEBUG: max_bubble_length=50000 [2024-08-27 13:42:20] DEBUG: loop_coverage_rate=1.5 [2024-08-27 13:42:20] DEBUG: repeat_edge_cov_mult=1.75 [2024-08-27 13:42:20] DEBUG: weak_detach_rate=5 [2024-08-27 13:42:20] DEBUG: tip_coverage_rate=2 [2024-08-27 13:42:20] DEBUG: tip_length_rate=2 [2024-08-27 13:42:20] DEBUG: output_gfa_before_rr=1 [2024-08-27 13:42:20] DEBUG: remove_alt_edges=0 [2024-08-27 13:42:20] DEBUG: low_cutoff_warning=0 [2024-08-27 13:42:20] DEBUG: kmer_size=17 [2024-08-27 13:42:20] DEBUG: use_minimizers=1 [2024-08-27 13:42:20] DEBUG: minimizer_window=10 [2024-08-27 13:42:20] DEBUG: reads_base_alignment=1 [2024-08-27 13:42:20] DEBUG: meta_read_top_kmer_rate=0.75 [2024-08-27 13:42:20] DEBUG: maximum_jump=1500 [2024-08-27 13:42:20] DEBUG: maximum_overhang=1500 [2024-08-27 13:42:20] DEBUG: repeat_kmer_rate=100 [2024-08-27 13:42:20] DEBUG: assemble_ovlp_divergence=0.05 [2024-08-27 13:42:20] DEBUG: assemble_divergence_relative=1 [2024-08-27 13:42:20] DEBUG: repeat_graph_ovlp_divergence=0.05 [2024-08-27 13:42:20] DEBUG: read_align_ovlp_divergence=0.10 [2024-08-27 13:42:20] DEBUG: hpc_scoring_on=1 [2024-08-27 13:42:20] DEBUG: add_unassembled_reads=0 [2024-08-27 13:42:20] DEBUG: extend_contigs_with_repeats=0 [2024-08-27 13:42:20] DEBUG: min_read_cov_cutoff=3 [2024-08-27 13:42:20] DEBUG: short_tip_length=20000 [2024-08-27 13:42:20] DEBUG: long_tip_length=100000 [2024-08-27 13:42:20] DEBUG: Running with k-mer size: 17 [2024-08-27 13:42:20] DEBUG: Running with minimum overlap 4000 [2024-08-27 13:42:20] DEBUG: Metagenome mode: N [2024-08-27 13:42:20] DEBUG: Short mode: N [2024-08-27 13:42:20] INFO: Reading sequences [2024-08-27 13:42:20] DEBUG: Building positional index [2024-08-27 13:42:20] DEBUG: Total sequence: 113554 bp [2024-08-27 13:42:20] INFO: Building minimizer index [2024-08-27 13:42:20] INFO: Pre-calculating index storage [2024-08-27 13:42:20] DEBUG: Mean k-mer frequency: 3.72347 [2024-08-27 13:42:20] DEBUG: Repetitive k-mer frequency: 372 [2024-08-27 13:42:20] DEBUG: Filtered 0 repetitive k-mers (0) [2024-08-27 13:42:20] INFO: Filling index [2024-08-27 13:42:20] DEBUG: Sorting k-mer index [2024-08-27 13:42:20] DEBUG: Selected k-mers: 5492 [2024-08-27 13:42:20] DEBUG: K-mer index size: 20453 [2024-08-27 13:42:20] DEBUG: Mean k-mer frequency: 3.72414 [2024-08-27 13:42:20] DEBUG: Minimizer rate: 5.55195 [2024-08-27 13:42:20] DEBUG: Peak RAM usage: 0 Gb [2024-08-27 13:42:20] DEBUG: Estimating k-mer identity bias [2024-08-27 15:43:17] DEBUG: Initial divergence estimate : 0.0111658 [2024-08-27 15:43:17] DEBUG: Relative threshold: Y [2024-08-27 15:43:17] DEBUG: Max divergence threshold set to 0.0611658 [2024-08-27 15:43:17] INFO: Extending reads [2024-08-27 15:43:17] DEBUG: Estimating overlap coverage [2024-08-27 15:44:44] INFO: Overlap-based coverage: 9 [2024-08-27 15:44:44] INFO: Median overlap divergence: 0.0122304 [2024-08-27 15:44:44] DEBUG: Sequence divergence distribution: | * | | * | | * | | * | | * | | * | | * | | * | | * | | * | | ** | | ** | | ** | |**** | |**** | |**** | |***** | |***** | |***** | |***** | ---------------------------------------------------------------------------------------------------- 0% 5% 10% 15% 20% 25% 30% 35% 40% 45% Q25 = 0.0094, Q50 = 0.012, Q75 = 0.015 [2024-08-27 15:44:44] DEBUG: Assembled disjointig 1 With 6 reads Start read: +56bbfd4a-0d1d-4d97-b307-7626be446ce8 At position: 4 leftTip: 1 rightTip: 1 Suspicious: 4 Short ext: 1 Mean extensions: 2 Avg overlap len: 5205 Min overlap len: 3173 Inner reads: 0 Length: 20431 [2024-08-27 15:44:44] DEBUG: Inner: 24 covered: 28 total: 28 [2024-08-27 15:46:08] INFO: Assembled 1 disjointigs [2024-08-27 15:46:08] INFO: Generating sequence [2024-08-27 15:46:08] DEBUG: Building positional index [2024-08-27 15:46:08] DEBUG: Total sequence: 20417 bp [2024-08-27 15:46:08] DEBUG: Mean k-mer frequency: 1.00241 [2024-08-27 15:46:08] DEBUG: Repetitive k-mer frequency: 100 [2024-08-27 15:46:08] DEBUG: Filtered 0 repetitive k-mers (0) [2024-08-27 15:46:09] DEBUG: Sorting k-mer index [2024-08-27 15:46:09] DEBUG: Selected k-mers: 3738 [2024-08-27 15:46:09] DEBUG: K-mer index size: 3748 [2024-08-27 15:46:09] DEBUG: Mean k-mer frequency: 1.00268 [2024-08-27 15:46:09] DEBUG: Minimizer rate: 5.44744 [2024-08-27 15:46:09] INFO: Filtering contained disjointigs [2024-08-27 15:46:09] DEBUG: Computing transitive closure for overlaps [2024-08-27 15:46:09] DEBUG: Found 0 overlaps [2024-08-27 15:46:09] DEBUG: Left 0 overlaps after filtering [2024-08-27 15:46:09] INFO: Contained seqs: 0 [2024-08-27 15:46:09] DEBUG: Writing FASTA [2024-08-27 15:46:09] DEBUG: Peak RAM usage: 0 Gb -----------End assembly log------------ [2024-08-27 15:46:09] root: DEBUG: Disjointigs length: 20417, N50: 20417 [2024-08-27 15:46:09] root: INFO: >>>STAGE: consensus [2024-08-27 15:46:09] root: INFO: Running Minimap2 [2024-08-27 15:46:09] root: INFO: Computing consensus [2024-08-27 15:46:09] root: INFO: Alignment error rate: 0.008460 [2024-08-27 15:46:09] root: INFO: >>>STAGE: repeat [2024-08-27 15:46:09] root: INFO: Building and resolving repeat graph [2024-08-27 15:46:09] root: DEBUG: -----Begin repeat analyser log------ [2024-08-27 15:46:09] root: DEBUG: Running: flye-modules repeat --disjointigs /home/prom/Documents/Programmes/pandora_lib_assembler/tmp_7/10-consensus/consensus.fasta --reads /home/prom/Documents/Programmes/pandora_lib_assembler/output_7.fasta --out-dir /home/prom/Documents/Programmes/pandora_lib_assembler/tmp_7/20-repeat --config /data/tools/Flye/flye/config/bin_cfg/asm_nano_hq.cfg --log /home/prom/Documents/Programmes/pandora_lib_assembler/tmp_7/flye.log --threads 1 --min-ovlp 4000 [2024-08-27 15:46:09] DEBUG: Build date: May 16 2023 00:48:44 [2024-08-27 15:46:09] DEBUG: Total RAM: 503 Gb [2024-08-27 15:46:09] DEBUG: Available RAM: 420 Gb [2024-08-27 15:46:09] DEBUG: Total CPUs: 160 [2024-08-27 15:46:09] DEBUG: Loading /data/tools/Flye/flye/config/bin_cfg/asm_nano_hq.cfg [2024-08-27 15:46:09] DEBUG: Loading /data/tools/Flye/flye/config/bin_cfg/asm_defaults.cfg [2024-08-27 15:46:09] DEBUG: big_genome_threshold=29000000 [2024-08-27 15:46:09] DEBUG: meta_read_filter_kmer_freq=100 [2024-08-27 15:46:09] DEBUG: chain_large_gap_penalty=2 [2024-08-27 15:46:09] DEBUG: chain_small_gap_penalty=0.5 [2024-08-27 15:46:09] DEBUG: chain_gap_jump_threshold=100 [2024-08-27 15:46:09] DEBUG: max_jump_gap=500 [2024-08-27 15:46:09] DEBUG: max_coverage_drop_rate=5 [2024-08-27 15:46:09] DEBUG: max_extensions_drop_rate=5 [2024-08-27 15:46:09] DEBUG: chimera_window=100 [2024-08-27 15:46:09] DEBUG: chimera_overhang=1000 [2024-08-27 15:46:09] DEBUG: min_reads_in_disjointig=4 [2024-08-27 15:46:09] DEBUG: max_inner_reads=10 [2024-08-27 15:46:09] DEBUG: max_inner_fraction=0.25 [2024-08-27 15:46:09] DEBUG: aggressive_dup_filter=1 [2024-08-27 15:46:09] DEBUG: max_separation=500 [2024-08-27 15:46:09] DEBUG: unique_edge_length=50000 [2024-08-27 15:46:09] DEBUG: min_repeat_res_support=0.51 [2024-08-27 15:46:09] DEBUG: out_paths_ratio=5 [2024-08-27 15:46:09] DEBUG: graph_cov_drop_rate=5 [2024-08-27 15:46:09] DEBUG: coverage_estimate_window=100 [2024-08-27 15:46:09] DEBUG: max_bubble_length=50000 [2024-08-27 15:46:09] DEBUG: loop_coverage_rate=1.5 [2024-08-27 15:46:09] DEBUG: repeat_edge_cov_mult=1.75 [2024-08-27 15:46:09] DEBUG: weak_detach_rate=5 [2024-08-27 15:46:09] DEBUG: tip_coverage_rate=2 [2024-08-27 15:46:09] DEBUG: tip_length_rate=2 [2024-08-27 15:46:09] DEBUG: output_gfa_before_rr=1 [2024-08-27 15:46:09] DEBUG: remove_alt_edges=0 [2024-08-27 15:46:09] DEBUG: low_cutoff_warning=0 [2024-08-27 15:46:09] DEBUG: kmer_size=17 [2024-08-27 15:46:09] DEBUG: use_minimizers=1 [2024-08-27 15:46:09] DEBUG: minimizer_window=10 [2024-08-27 15:46:09] DEBUG: reads_base_alignment=1 [2024-08-27 15:46:09] DEBUG: meta_read_top_kmer_rate=0.75 [2024-08-27 15:46:09] DEBUG: maximum_jump=1500 [2024-08-27 15:46:09] DEBUG: maximum_overhang=1500 [2024-08-27 15:46:09] DEBUG: repeat_kmer_rate=100 [2024-08-27 15:46:09] DEBUG: assemble_ovlp_divergence=0.05 [2024-08-27 15:46:09] DEBUG: assemble_divergence_relative=1 [2024-08-27 15:46:09] DEBUG: repeat_graph_ovlp_divergence=0.05 [2024-08-27 15:46:09] DEBUG: read_align_ovlp_divergence=0.10 [2024-08-27 15:46:09] DEBUG: hpc_scoring_on=1 [2024-08-27 15:46:09] DEBUG: add_unassembled_reads=0 [2024-08-27 15:46:09] DEBUG: extend_contigs_with_repeats=0 [2024-08-27 15:46:09] DEBUG: min_read_cov_cutoff=3 [2024-08-27 15:46:09] DEBUG: short_tip_length=20000 [2024-08-27 15:46:09] DEBUG: long_tip_length=100000 [2024-08-27 15:46:09] DEBUG: Running with k-mer size: 17 [2024-08-27 15:46:09] DEBUG: Selected minimum overlap 4000 [2024-08-27 15:46:09] DEBUG: Metagenome mode: N [2024-08-27 15:46:09] INFO: Parsing disjointigs [2024-08-27 15:46:09] DEBUG: Building positional index [2024-08-27 15:46:09] DEBUG: Total sequence: 20438 bp [2024-08-27 15:46:09] INFO: Building repeat graph [2024-08-27 15:46:09] DEBUG: Mean k-mer frequency: 1.00242 [2024-08-27 15:46:09] DEBUG: Repetitive k-mer frequency: 100 [2024-08-27 15:46:09] DEBUG: Filtered 0 repetitive k-mers (0) [2024-08-27 15:46:09] DEBUG: Sorting k-mer index [2024-08-27 15:46:09] DEBUG: Selected k-mers: 3721 [2024-08-27 15:46:09] DEBUG: K-mer index size: 3731 [2024-08-27 15:46:09] DEBUG: Mean k-mer frequency: 1.00269 [2024-08-27 15:46:09] DEBUG: Minimizer rate: 5.47789 [2024-08-27 15:46:09] DEBUG: Computing transitive closure for overlaps [2024-08-27 15:46:09] DEBUG: Found 0 overlaps [2024-08-27 15:46:09] DEBUG: Left 0 overlaps after filtering [2024-08-27 15:46:09] INFO: Median overlap divergence: 0 [2024-08-27 15:46:09] DEBUG: Sequence divergence distribution: | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | ---------------------------------------------------------------------------------------------------- 0% 5% 10% 15% 20% 25% 30% 35% 40% 45% Q25 = 0, Q50 = 0, Q75 = 0 [2024-08-27 15:46:09] DEBUG: Computing gluepoints [2024-08-27 15:46:09] DEBUG: Added 0 gluepoint projections [2024-08-27 15:46:09] DEBUG: Created 4 gluepoints [2024-08-27 15:46:09] DEBUG: Artificial loops removed: 0 left, 0 right, 0 both [2024-08-27 15:46:09] DEBUG: Initializing edges [2024-08-27 15:46:09] DEBUG: Edges length checksum: 417670969 [2024-08-27 15:46:09] DEBUG: Filtered 0 singleton segments [2024-08-27 15:46:09] DEBUG: Removed 0 simple and 0 double chimeric junctions [2024-08-27 15:46:09] DEBUG: Collapsed 0 edges [2024-08-27 15:46:09] DEBUG: * 1 +disjointig_1 0 20437 20437 [2024-08-27 15:46:09] DEBUG: Total edges: 1 [2024-08-27 15:46:09] INFO: Parsing reads [2024-08-27 15:46:09] DEBUG: Building positional index [2024-08-27 15:46:09] DEBUG: Total sequence: 117213 bp [2024-08-27 15:46:09] DEBUG: Building positional index [2024-08-27 15:46:09] DEBUG: Total sequence: 20437 bp [2024-08-27 15:46:09] INFO: Aligning reads to the graph [2024-08-27 15:46:09] DEBUG: Mean k-mer frequency: 1.00242 [2024-08-27 15:46:09] DEBUG: Repetitive k-mer frequency: 100 [2024-08-27 15:46:09] DEBUG: Filtered 0 repetitive k-mers (0) [2024-08-27 15:46:09] DEBUG: Sorting k-mer index [2024-08-27 15:46:09] DEBUG: Selected k-mers: 3721 [2024-08-27 15:46:09] DEBUG: K-mer index size: 3731 [2024-08-27 15:46:09] DEBUG: Mean k-mer frequency: 1.00269 [2024-08-27 15:46:09] DEBUG: Minimizer rate: 5.47762 [2024-08-27 15:46:09] DEBUG: Total reads : 14 [2024-08-27 15:46:09] DEBUG: Read with aligned parts : 14 [2024-08-27 15:46:09] DEBUG: Aligned in one piece : 14 [2024-08-27 15:46:09] INFO: Aligned read sequence: 107454 / 113554 (0.946281) [2024-08-27 15:46:09] INFO: Median overlap divergence: 0.00542122 [2024-08-27 15:46:09] DEBUG: Sequence divergence distribution: |** | |** | |** | |** | |** | |** | |** | |** | |** | |** | |** | |** | |** | |** | |** | |** | |**** | |**** | |**** | |**** | ---------------------------------------------------------------------------------------------------- 0% 5% 10% 15% 20% 25% 30% 35% 40% 45% Q25 = 0.0031, Q50 = 0.0054, Q75 = 0.0061 [2024-08-27 15:46:09] INFO: Mean edge coverage: 5 [2024-08-27 15:46:09] DEBUG: 1 len:20437 cov:3 mult:0.6 [2024-08-27 15:46:09] DEBUG: -1 len:20437 cov:3 mult:0.6 [2024-08-27 15:46:09] DEBUG: Unique coverage threshold 5 [2024-08-27 15:46:09] INFO: Simplifying the graph [2024-08-27 15:46:09] DEBUG: Read coverage cutoff: 3 [2024-08-27 15:46:09] DEBUG: [SIMPL] Removed 0 paths with low coverage [2024-08-27 15:46:09] DEBUG: [SIMPL] Masked 0 heterozygous loops [2024-08-27 15:46:09] DEBUG: [SIMPL] Masked 0 simple bubbles [2024-08-27 15:46:09] DEBUG: Finding repeats [2024-08-27 15:46:09] DEBUG: Read coverage cutoff: 3 [2024-08-27 15:46:09] DEBUG: Repeat detection iteration 1 [2024-08-27 15:46:09] DEBUG: Writing Dot [2024-08-27 15:46:09] DEBUG: Writing FASTA [2024-08-27 15:46:09] DEBUG: Writing Gfa [2024-08-27 15:46:09] DEBUG: [SIMPL] == Iteration 1 == [2024-08-27 15:46:09] DEBUG: Splitting nodes [2024-08-27 15:46:09] DEBUG: [SIMPL] Split 0 nodes [2024-08-27 15:46:09] DEBUG: [SIMPL] Clipped 0 short and 0 long tips [2024-08-27 15:46:09] DEBUG: [SIMPL] Masked 0 heterozygous loops [2024-08-27 15:46:09] DEBUG: [SIMPL] Masked 0 simple bubbles [2024-08-27 15:46:09] DEBUG: Finding repeats [2024-08-27 15:46:09] DEBUG: Read coverage cutoff: 3 [2024-08-27 15:46:09] DEBUG: Repeat detection iteration 1 [2024-08-27 15:46:09] DEBUG: Total unique edges: 1 [2024-08-27 15:46:09] DEBUG: [SIMPL] Resolved repeats: 0 [2024-08-27 15:46:09] DEBUG: RR links: 0 [2024-08-27 15:46:09] DEBUG: Unresolved: 0 [2024-08-27 15:46:09] DEBUG: Removed 0 simple and 0 double chimeric junctions [2024-08-27 15:46:09] DEBUG: [SIMPL] Collapsed 0 haplotypes [2024-08-27 15:46:09] DEBUG: [SIMPL] Resolved 0 simple repeats [2024-08-27 15:46:09] DEBUG: Read coverage cutoff: 3 [2024-08-27 15:46:09] DEBUG: [SIMPL] Removed 0 paths with low coverage [2024-08-27 15:46:09] DEBUG: Finding repeats [2024-08-27 15:46:09] DEBUG: Read coverage cutoff: 3 [2024-08-27 15:46:09] DEBUG: Repeat detection iteration 1 [2024-08-27 15:46:09] DEBUG: Writing Dot [2024-08-27 15:46:09] DEBUG: Writing FASTA [2024-08-27 15:46:09] DEBUG: Peak RAM usage: 0 Gb -----------End assembly log------------ [2024-08-27 15:46:09] root: INFO: >>>STAGE: contigger [2024-08-27 15:46:09] root: INFO: Generating contigs [2024-08-27 15:46:09] root: DEBUG: -----Begin contigger analyser log------ [2024-08-27 15:46:09] root: DEBUG: Running: flye-modules contigger --graph-edges /home/prom/Documents/Programmes/pandora_lib_assembler/tmp_7/20-repeat/repeat_graph_edges.fasta --reads /home/prom/Documents/Programmes/pandora_lib_assembler/output_7.fasta --out-dir /home/prom/Documents/Programmes/pandora_lib_assembler/tmp_7/30-contigger --config /data/tools/Flye/flye/config/bin_cfg/asm_nano_hq.cfg --repeat-graph /home/prom/Documents/Programmes/pandora_lib_assembler/tmp_7/20-repeat/repeat_graph_dump --graph-aln /home/prom/Documents/Programmes/pandora_lib_assembler/tmp_7/20-repeat/read_alignment_dump --log /home/prom/Documents/Programmes/pandora_lib_assembler/tmp_7/flye.log --threads 1 --min-ovlp 4000 [2024-08-27 15:46:09] DEBUG: Build date: May 16 2023 00:48:47 [2024-08-27 15:46:09] DEBUG: Total RAM: 503 Gb [2024-08-27 15:46:09] DEBUG: Available RAM: 420 Gb [2024-08-27 15:46:09] DEBUG: Total CPUs: 160 [2024-08-27 15:46:09] DEBUG: Loading /data/tools/Flye/flye/config/bin_cfg/asm_nano_hq.cfg [2024-08-27 15:46:09] DEBUG: Loading /data/tools/Flye/flye/config/bin_cfg/asm_defaults.cfg [2024-08-27 15:46:09] DEBUG: big_genome_threshold=29000000 [2024-08-27 15:46:09] DEBUG: meta_read_filter_kmer_freq=100 [2024-08-27 15:46:09] DEBUG: chain_large_gap_penalty=2 [2024-08-27 15:46:09] DEBUG: chain_small_gap_penalty=0.5 [2024-08-27 15:46:09] DEBUG: chain_gap_jump_threshold=100 [2024-08-27 15:46:09] DEBUG: max_jump_gap=500 [2024-08-27 15:46:09] DEBUG: max_coverage_drop_rate=5 [2024-08-27 15:46:09] DEBUG: max_extensions_drop_rate=5 [2024-08-27 15:46:09] DEBUG: chimera_window=100 [2024-08-27 15:46:09] DEBUG: chimera_overhang=1000 [2024-08-27 15:46:09] DEBUG: min_reads_in_disjointig=4 [2024-08-27 15:46:09] DEBUG: max_inner_reads=10 [2024-08-27 15:46:09] DEBUG: max_inner_fraction=0.25 [2024-08-27 15:46:09] DEBUG: aggressive_dup_filter=1 [2024-08-27 15:46:09] DEBUG: max_separation=500 [2024-08-27 15:46:09] DEBUG: unique_edge_length=50000 [2024-08-27 15:46:09] DEBUG: min_repeat_res_support=0.51 [2024-08-27 15:46:09] DEBUG: out_paths_ratio=5 [2024-08-27 15:46:09] DEBUG: graph_cov_drop_rate=5 [2024-08-27 15:46:09] DEBUG: coverage_estimate_window=100 [2024-08-27 15:46:09] DEBUG: max_bubble_length=50000 [2024-08-27 15:46:09] DEBUG: loop_coverage_rate=1.5 [2024-08-27 15:46:09] DEBUG: repeat_edge_cov_mult=1.75 [2024-08-27 15:46:09] DEBUG: weak_detach_rate=5 [2024-08-27 15:46:09] DEBUG: tip_coverage_rate=2 [2024-08-27 15:46:09] DEBUG: tip_length_rate=2 [2024-08-27 15:46:09] DEBUG: output_gfa_before_rr=1 [2024-08-27 15:46:09] DEBUG: remove_alt_edges=0 [2024-08-27 15:46:09] DEBUG: low_cutoff_warning=0 [2024-08-27 15:46:09] DEBUG: kmer_size=17 [2024-08-27 15:46:09] DEBUG: use_minimizers=1 [2024-08-27 15:46:09] DEBUG: minimizer_window=10 [2024-08-27 15:46:09] DEBUG: reads_base_alignment=1 [2024-08-27 15:46:09] DEBUG: meta_read_top_kmer_rate=0.75 [2024-08-27 15:46:09] DEBUG: maximum_jump=1500 [2024-08-27 15:46:09] DEBUG: maximum_overhang=1500 [2024-08-27 15:46:09] DEBUG: repeat_kmer_rate=100 [2024-08-27 15:46:09] DEBUG: assemble_ovlp_divergence=0.05 [2024-08-27 15:46:09] DEBUG: assemble_divergence_relative=1 [2024-08-27 15:46:09] DEBUG: repeat_graph_ovlp_divergence=0.05 [2024-08-27 15:46:09] DEBUG: read_align_ovlp_divergence=0.10 [2024-08-27 15:46:09] DEBUG: hpc_scoring_on=1 [2024-08-27 15:46:09] DEBUG: add_unassembled_reads=0 [2024-08-27 15:46:09] DEBUG: extend_contigs_with_repeats=0 [2024-08-27 15:46:09] DEBUG: min_read_cov_cutoff=3 [2024-08-27 15:46:09] DEBUG: short_tip_length=20000 [2024-08-27 15:46:09] DEBUG: long_tip_length=100000 [2024-08-27 15:46:09] DEBUG: Running with k-mer size: 17 [2024-08-27 15:46:09] DEBUG: Selected minimum overlap 4000 [2024-08-27 15:46:09] INFO: Reading sequences [2024-08-27 15:46:09] DEBUG: Building positional index [2024-08-27 15:46:09] DEBUG: Total sequence: 117213 bp [2024-08-27 15:46:09] DEBUG: Flipped 0 [2024-08-27 15:46:09] DEBUG: UPath 1: 1 [2024-08-27 15:46:09] DEBUG: Final graph contains 1 egdes [2024-08-27 15:46:09] DEBUG: Extending contigs into repeats [2024-08-27 15:46:09] DEBUG: Covered 0 repetitive contigs [2024-08-27 15:46:09] INFO: Generated 1 contigs [2024-08-27 15:46:09] DEBUG: Writing FASTA [2024-08-27 15:46:09] DEBUG: Generating scaffold connections [2024-08-27 15:46:09] INFO: Added 0 scaffold connections [2024-08-27 15:46:09] DEBUG: Writing Dot [2024-08-27 15:46:09] DEBUG: Writing FASTA [2024-08-27 15:46:09] DEBUG: Writing Gfa [2024-08-27 15:46:09] DEBUG: Peak RAM usage: 0 Gb -----------End assembly log------------ [2024-08-27 15:46:09] root: INFO: >>>STAGE: polishing [2024-08-27 15:46:09] root: INFO: Polishing genome (1/1) [2024-08-27 15:46:09] root: INFO: Running minimap2 [2024-08-27 15:46:09] root: INFO: Separating alignment into bubbles [2024-08-27 15:46:10] root: DEBUG: Generated 1204 bubbles [2024-08-27 15:46:10] root: DEBUG: Split 0 long bubbles [2024-08-27 15:46:10] root: DEBUG: Skipped 0 empty bubbles [2024-08-27 15:46:10] root: DEBUG: Skipped 0 bubbles with long branches [2024-08-27 15:46:10] root: INFO: Alignment error rate: 0.007978 [2024-08-27 15:46:10] root: INFO: Correcting bubbles [2024-08-27 15:46:10] root: DEBUG: Mean contig coverage: 3, selected threshold: 3 [2024-08-27 15:46:10] root: DEBUG: Filtered 0 contigs of total length 0 [2024-08-27 15:46:10] root: DEBUG: Generating polished GFA [2024-08-27 15:46:10] root: DEBUG: 0 sequences remained unpolished [2024-08-27 15:46:10] root: INFO: >>>STAGE: finalize [2024-08-27 15:46:10] root: DEBUG: ---Output dir contents:---- [2024-08-27 15:46:10] root: DEBUG: tmp_7/ [2024-08-27 15:46:10] root: DEBUG: 363.0 B assembly_graph.gv [2024-08-27 15:46:10] root: DEBUG: 28.0 K flye.log [2024-08-27 15:46:10] root: DEBUG: 20.0 K assembly_graph.gfa [2024-08-27 15:46:10] root: DEBUG: 20.0 K assembly.fasta [2024-08-27 15:46:10] root: DEBUG: 92.0 B params.json [2024-08-27 15:46:10] root: DEBUG: 10-consensus/ [2024-08-27 15:46:10] root: DEBUG: 902.0 B minimap.stderr [2024-08-27 15:46:10] root: DEBUG: 104.0 B minimap.bam.bai [2024-08-27 15:46:10] root: DEBUG: 20.0 K consensus.fasta [2024-08-27 15:46:10] root: DEBUG: 00-assembly/ [2024-08-27 15:46:10] root: DEBUG: 28.0 B draft_assembly.fasta.fai [2024-08-27 15:46:10] root: DEBUG: 20.0 K draft_assembly.fasta [2024-08-27 15:46:10] root: DEBUG: 30-contigger/ [2024-08-27 15:46:10] root: DEBUG: 24.0 B contigs.fasta.fai [2024-08-27 15:46:10] root: DEBUG: 0.0 B scaffolds_links.txt [2024-08-27 15:46:10] root: DEBUG: 20.0 K graph_final.gfa [2024-08-27 15:46:10] root: DEBUG: 20.0 K graph_final.fasta [2024-08-27 15:46:10] root: DEBUG: 109.0 B contigs_stats.txt [2024-08-27 15:46:10] root: DEBUG: 363.0 B graph_final.gv [2024-08-27 15:46:10] root: DEBUG: 20.0 K contigs.fasta [2024-08-27 15:46:10] root: DEBUG: 20-repeat/ [2024-08-27 15:46:10] root: DEBUG: 3.0 K read_alignment_dump [2024-08-27 15:46:10] root: DEBUG: 363.0 B graph_before_rr.gv [2024-08-27 15:46:10] root: DEBUG: 20.0 K graph_before_rr.fasta [2024-08-27 15:46:10] root: DEBUG: 173.0 B repeat_graph_dump [2024-08-27 15:46:10] root: DEBUG: 363.0 B graph_after_rr.gv [2024-08-27 15:46:10] root: DEBUG: 19.0 K graph_before_rr.gfa [2024-08-27 15:46:10] root: DEBUG: 20.0 K repeat_graph_edges.fasta [2024-08-27 15:46:10] root: DEBUG: 40-polishing/ [2024-08-27 15:46:10] root: DEBUG: 20.0 K filtered_contigs.fasta [2024-08-27 15:46:10] root: DEBUG: 926.0 B minimap.stderr [2024-08-27 15:46:10] root: DEBUG: 24.0 B filtered_contigs.fasta.fai [2024-08-27 15:46:10] root: DEBUG: 43.0 B contigs_stats.txt [2024-08-27 15:46:10] root: DEBUG: 104.0 B minimap_1.bam.bai [2024-08-27 15:46:10] root: DEBUG: 104.0 B edges_aln.bam.bai [2024-08-27 15:46:10] root: DEBUG: 20.0 K polished_edges.gfa [2024-08-27 15:46:10] root: DEBUG: 5.0 K base_coverage.bed.gz [2024-08-27 15:46:10] root: DEBUG: 43.0 B filtered_stats.txt [2024-08-27 15:46:10] root: DEBUG: -------------------------- [2024-08-27 15:46:10] root: INFO: Assembly statistics: Total length: 20439 Fragments: 1 Fragments N50: 20439 Largest frg: 20439 Scaffolds: 0 Mean coverage: 3 [2024-08-27 15:46:10] root: INFO: Final assembly: /home/prom/Documents/Programmes/pandora_lib_assembler/tmp_7/assembly.fasta