Mercurial > repos > bgruening > flye
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
| author | bgruening |
|---|---|
| date | Mon, 26 Aug 2024 13:54:31 +0000 |
| parents | 276f5d8712d5 |
| children |
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[2024-08-19 09:44:19] root: INFO: Starting Flye 2.9.4-b1799 [2024-08-19 09:44:19] root: DEBUG: Cmd: /usr/local/bin/flye --pacbio-raw ./input_0.fastq.gz ./input_1.fastq.gz ./input_2.fastq.gz ./input_3.fastq.gz ./input_4.fastq.gz ./input_5.fastq.gz ./input_6.fastq.gz -o out_dir -t 1 -i 0 [2024-08-19 09:44:19] root: DEBUG: Python version: 3.11.9 | packaged by conda-forge | (main, Apr 19 2024, 18:36:13) [GCC 12.3.0] [2024-08-19 09:44:19] root: INFO: >>>STAGE: configure [2024-08-19 09:44:19] root: INFO: Configuring run [2024-08-19 09:44:19] root: INFO: Total read length: 7249289 [2024-08-19 09:44:19] root: INFO: Reads N50/N90: 11150 / 5790 [2024-08-19 09:44:19] root: INFO: Minimum overlap set to 6000 [2024-08-19 09:44:19] root: INFO: >>>STAGE: assembly [2024-08-19 09:44:19] root: INFO: Assembling disjointigs [2024-08-19 09:44:19] root: DEBUG: -----Begin assembly log------ [2024-08-19 09:44:19] root: DEBUG: Running: flye-modules assemble --reads /tmp/tmpmmr8wbsp/job_working_directory/000/8/working/input_0.fastq.gz,/tmp/tmpmmr8wbsp/job_working_directory/000/8/working/input_1.fastq.gz,/tmp/tmpmmr8wbsp/job_working_directory/000/8/working/input_2.fastq.gz,/tmp/tmpmmr8wbsp/job_working_directory/000/8/working/input_3.fastq.gz,/tmp/tmpmmr8wbsp/job_working_directory/000/8/working/input_4.fastq.gz,/tmp/tmpmmr8wbsp/job_working_directory/000/8/working/input_5.fastq.gz,/tmp/tmpmmr8wbsp/job_working_directory/000/8/working/input_6.fastq.gz --out-asm /tmp/tmpmmr8wbsp/job_working_directory/000/8/working/out_dir/00-assembly/draft_assembly.fasta --config /usr/local/lib/python3.11/site-packages/flye/config/bin_cfg/asm_raw_reads.cfg --log /tmp/tmpmmr8wbsp/job_working_directory/000/8/working/out_dir/flye.log --threads 1 --min-ovlp 6000 [2024-08-19 09:44:19] DEBUG: Build date: Jul 26 2024 16:36:15 [2024-08-19 09:44:19] DEBUG: Total RAM: 31 Gb [2024-08-19 09:44:19] DEBUG: Available RAM: 21 Gb [2024-08-19 09:44:19] DEBUG: Total CPUs: 12 [2024-08-19 09:44:19] DEBUG: Loading /usr/local/lib/python3.11/site-packages/flye/config/bin_cfg/asm_raw_reads.cfg [2024-08-19 09:44:19] DEBUG: Loading /usr/local/lib/python3.11/site-packages/flye/config/bin_cfg/asm_defaults.cfg [2024-08-19 09:44:19] DEBUG: big_genome_threshold=29000000 [2024-08-19 09:44:19] DEBUG: meta_read_filter_kmer_freq=100 [2024-08-19 09:44:19] DEBUG: chain_large_gap_penalty=2 [2024-08-19 09:44:19] DEBUG: chain_small_gap_penalty=0.5 [2024-08-19 09:44:19] DEBUG: chain_gap_jump_threshold=100 [2024-08-19 09:44:19] DEBUG: max_jump_gap=500 [2024-08-19 09:44:19] DEBUG: max_coverage_drop_rate=5 [2024-08-19 09:44:19] DEBUG: max_extensions_drop_rate=5 [2024-08-19 09:44:19] DEBUG: chimera_window=100 [2024-08-19 09:44:19] DEBUG: chimera_overhang=1000 [2024-08-19 09:44:19] DEBUG: min_reads_in_disjointig=4 [2024-08-19 09:44:19] DEBUG: max_inner_reads=10 [2024-08-19 09:44:19] DEBUG: max_inner_fraction=0.25 [2024-08-19 09:44:19] DEBUG: aggressive_dup_filter=1 [2024-08-19 09:44:19] DEBUG: max_separation=500 [2024-08-19 09:44:19] DEBUG: unique_edge_length=50000 [2024-08-19 09:44:19] DEBUG: min_repeat_res_support=0.51 [2024-08-19 09:44:19] DEBUG: out_paths_ratio=5 [2024-08-19 09:44:19] DEBUG: graph_cov_drop_rate=5 [2024-08-19 09:44:19] DEBUG: coverage_estimate_window=100 [2024-08-19 09:44:19] DEBUG: max_bubble_length=50000 [2024-08-19 09:44:19] DEBUG: loop_coverage_rate=1.5 [2024-08-19 09:44:19] DEBUG: repeat_edge_cov_mult=1.75 [2024-08-19 09:44:19] DEBUG: weak_detach_rate=5 [2024-08-19 09:44:19] DEBUG: tip_coverage_rate=2 [2024-08-19 09:44:19] DEBUG: tip_length_rate=2 [2024-08-19 09:44:19] DEBUG: output_gfa_before_rr=1 [2024-08-19 09:44:19] DEBUG: remove_alt_edges=0 [2024-08-19 09:44:19] DEBUG: low_cutoff_warning=1 [2024-08-19 09:44:19] DEBUG: kmer_size=17 [2024-08-19 09:44:19] DEBUG: use_minimizers=0 [2024-08-19 09:44:19] DEBUG: reads_base_alignment=0 [2024-08-19 09:44:19] DEBUG: meta_read_top_kmer_rate=0.40 [2024-08-19 09:44:19] DEBUG: maximum_jump=1500 [2024-08-19 09:44:19] DEBUG: maximum_overhang=1500 [2024-08-19 09:44:19] DEBUG: repeat_kmer_rate=100 [2024-08-19 09:44:19] DEBUG: assemble_ovlp_divergence=0.10 [2024-08-19 09:44:19] DEBUG: assemble_divergence_relative=1 [2024-08-19 09:44:19] DEBUG: repeat_graph_ovlp_divergence=0.08 [2024-08-19 09:44:19] DEBUG: read_align_ovlp_divergence=0.25 [2024-08-19 09:44:19] DEBUG: hpc_scoring_on=0 [2024-08-19 09:44:19] DEBUG: add_unassembled_reads=0 [2024-08-19 09:44:19] DEBUG: extend_contigs_with_repeats=0 [2024-08-19 09:44:19] DEBUG: min_read_cov_cutoff=3 [2024-08-19 09:44:19] DEBUG: short_tip_length=20000 [2024-08-19 09:44:19] DEBUG: long_tip_length=100000 [2024-08-19 09:44:19] DEBUG: Running with k-mer size: 17 [2024-08-19 09:44:19] DEBUG: Running with minimum overlap 6000 [2024-08-19 09:44:19] DEBUG: Metagenome mode: N [2024-08-19 09:44:19] DEBUG: Short mode: N [2024-08-19 09:44:19] INFO: Reading sequences [2024-08-19 09:44:19] DEBUG: Building positional index [2024-08-19 09:44:19] DEBUG: Total sequence: 6471580 bp [2024-08-19 09:44:21] INFO: Counting k-mers: [2024-08-19 09:44:22] DEBUG: Updating k-mer histogram [2024-08-19 09:44:52] DEBUG: Hash size: 29 [2024-08-19 09:44:52] DEBUG: Total k-mers 5958598 [2024-08-19 09:44:52] INFO: Filling index table (1/2) [2024-08-19 09:44:54] DEBUG: Mean k-mer frequency: 2.57396 [2024-08-19 09:44:54] DEBUG: Repetitive k-mer frequency: 257 [2024-08-19 09:44:54] DEBUG: Filtered 0 repetitive k-mers (0) [2024-08-19 09:44:54] INFO: Filling index table (2/2) [2024-08-19 09:44:56] DEBUG: Sorting k-mer index [2024-08-19 09:44:56] DEBUG: Selected k-mers: 319695 [2024-08-19 09:44:56] DEBUG: Index size: 822885 [2024-08-19 09:44:56] DEBUG: Mean k-mer index frequency: 2.57397 [2024-08-19 09:44:56] DEBUG: Peak RAM usage: 8 Gb [2024-08-19 09:44:56] DEBUG: Estimating k-mer identity bias [2024-08-19 09:44:58] DEBUG: Initial divergence estimate : 0.237684 [2024-08-19 09:44:58] DEBUG: Relative threshold: Y [2024-08-19 09:44:58] DEBUG: Max divergence threshold set to 0.337684 [2024-08-19 09:44:58] INFO: Extending reads [2024-08-19 09:44:58] DEBUG: Estimating overlap coverage [2024-08-19 09:45:00] INFO: Overlap-based coverage: 10 [2024-08-19 09:45:00] INFO: Median overlap divergence: 0.235584 [2024-08-19 09:45:00] DEBUG: Sequence divergence distribution: | * | | * | | *** | | * *** | | ****** | | ******* | | ******* | | ******** | | ******** | | ********* | | ********* | | ********* | | ********** | | ************ | | ************ | | ************** | | ************** | | **************** | | * ***************** * | | * ** ************************ | * * ---------------------------------------------------------------------------------------------------- 0% 5% 10% 15% 20% 25% 30% 35% 40% 45% Q25 = 0.22, Q50 = 0.24, Q75 = 0.25 [2024-08-19 09:45:00] DEBUG: Assembled disjointig 1 With 83 reads Start read: +S1_395 At position: 40 leftTip: 1 rightTip: 1 Suspicious: 5 Short ext: 3 Mean extensions: 9 Avg overlap len: 10043 Min overlap len: 4225 Inner reads: 0 Length: 434635 [2024-08-19 09:45:00] DEBUG: Inner: 1024 covered: 1014 total: 1152 [2024-08-19 09:45:00] DEBUG: Assembled disjointig 2 With 6 reads Start read: +S1_921 At position: 4 leftTip: 0 rightTip: 0 Suspicious: 0 Short ext: 0 Mean extensions: 4 Avg overlap len: 8689 Min overlap len: 7703 Inner reads: 0 Length: 34343 [2024-08-19 09:45:00] DEBUG: Inner: 1040 covered: 1056 total: 1152 [2024-08-19 09:45:00] INFO: Assembled 2 disjointigs [2024-08-19 09:45:00] INFO: Generating sequence [2024-08-19 09:45:00] DEBUG: Building positional index [2024-08-19 09:45:00] DEBUG: Total sequence: 470346 bp [2024-08-19 09:45:00] DEBUG: Mean k-mer frequency: 1.00134 [2024-08-19 09:45:00] DEBUG: Repetitive k-mer frequency: 100 [2024-08-19 09:45:00] DEBUG: Filtered 0 repetitive k-mers (0) [2024-08-19 09:45:00] DEBUG: Sorting k-mer index [2024-08-19 09:45:00] DEBUG: Selected k-mers: 469680 [2024-08-19 09:45:00] DEBUG: K-mer index size: 470312 [2024-08-19 09:45:00] DEBUG: Mean k-mer frequency: 1.00135 [2024-08-19 09:45:00] DEBUG: Minimizer rate: 1.00007 [2024-08-19 09:45:00] INFO: Filtering contained disjointigs [2024-08-19 09:45:00] DEBUG: Computing transitive closure for overlaps [2024-08-19 09:45:00] DEBUG: Found 0 overlaps [2024-08-19 09:45:00] DEBUG: Left 0 overlaps after filtering [2024-08-19 09:45:00] INFO: Contained seqs: 0 [2024-08-19 09:45:00] DEBUG: Writing FASTA [2024-08-19 09:45:00] DEBUG: Peak RAM usage: 8 Gb -----------End assembly log------------ [2024-08-19 09:45:00] root: DEBUG: Disjointigs length: 470346, N50: 436173 [2024-08-19 09:45:00] root: INFO: >>>STAGE: consensus [2024-08-19 09:45:00] root: INFO: Running Minimap2 [2024-08-19 09:45:04] root: INFO: Computing consensus [2024-08-19 09:45:08] root: INFO: Alignment error rate: 0.196554 [2024-08-19 09:45:08] root: INFO: >>>STAGE: repeat [2024-08-19 09:45:08] root: INFO: Building and resolving repeat graph [2024-08-19 09:45:08] root: DEBUG: -----Begin repeat analyser log------ [2024-08-19 09:45:08] root: DEBUG: Running: flye-modules repeat --disjointigs /tmp/tmpmmr8wbsp/job_working_directory/000/8/working/out_dir/10-consensus/consensus.fasta --reads /tmp/tmpmmr8wbsp/job_working_directory/000/8/working/input_0.fastq.gz,/tmp/tmpmmr8wbsp/job_working_directory/000/8/working/input_1.fastq.gz,/tmp/tmpmmr8wbsp/job_working_directory/000/8/working/input_2.fastq.gz,/tmp/tmpmmr8wbsp/job_working_directory/000/8/working/input_3.fastq.gz,/tmp/tmpmmr8wbsp/job_working_directory/000/8/working/input_4.fastq.gz,/tmp/tmpmmr8wbsp/job_working_directory/000/8/working/input_5.fastq.gz,/tmp/tmpmmr8wbsp/job_working_directory/000/8/working/input_6.fastq.gz --out-dir /tmp/tmpmmr8wbsp/job_working_directory/000/8/working/out_dir/20-repeat --config /usr/local/lib/python3.11/site-packages/flye/config/bin_cfg/asm_raw_reads.cfg --log /tmp/tmpmmr8wbsp/job_working_directory/000/8/working/out_dir/flye.log --threads 1 --min-ovlp 6000 [2024-08-19 09:45:08] DEBUG: Build date: Jul 26 2024 16:36:40 [2024-08-19 09:45:08] DEBUG: Total RAM: 31 Gb [2024-08-19 09:45:08] DEBUG: Available RAM: 21 Gb [2024-08-19 09:45:08] DEBUG: Total CPUs: 12 [2024-08-19 09:45:08] DEBUG: Loading /usr/local/lib/python3.11/site-packages/flye/config/bin_cfg/asm_raw_reads.cfg [2024-08-19 09:45:08] DEBUG: Loading /usr/local/lib/python3.11/site-packages/flye/config/bin_cfg/asm_defaults.cfg [2024-08-19 09:45:08] DEBUG: big_genome_threshold=29000000 [2024-08-19 09:45:08] DEBUG: meta_read_filter_kmer_freq=100 [2024-08-19 09:45:08] DEBUG: chain_large_gap_penalty=2 [2024-08-19 09:45:08] DEBUG: chain_small_gap_penalty=0.5 [2024-08-19 09:45:08] DEBUG: chain_gap_jump_threshold=100 [2024-08-19 09:45:08] DEBUG: max_jump_gap=500 [2024-08-19 09:45:08] DEBUG: max_coverage_drop_rate=5 [2024-08-19 09:45:08] DEBUG: max_extensions_drop_rate=5 [2024-08-19 09:45:08] DEBUG: chimera_window=100 [2024-08-19 09:45:08] DEBUG: chimera_overhang=1000 [2024-08-19 09:45:08] DEBUG: min_reads_in_disjointig=4 [2024-08-19 09:45:08] DEBUG: max_inner_reads=10 [2024-08-19 09:45:08] DEBUG: max_inner_fraction=0.25 [2024-08-19 09:45:08] DEBUG: aggressive_dup_filter=1 [2024-08-19 09:45:08] DEBUG: max_separation=500 [2024-08-19 09:45:08] DEBUG: unique_edge_length=50000 [2024-08-19 09:45:08] DEBUG: min_repeat_res_support=0.51 [2024-08-19 09:45:08] DEBUG: out_paths_ratio=5 [2024-08-19 09:45:08] DEBUG: graph_cov_drop_rate=5 [2024-08-19 09:45:08] DEBUG: coverage_estimate_window=100 [2024-08-19 09:45:08] DEBUG: max_bubble_length=50000 [2024-08-19 09:45:08] DEBUG: loop_coverage_rate=1.5 [2024-08-19 09:45:08] DEBUG: repeat_edge_cov_mult=1.75 [2024-08-19 09:45:08] DEBUG: weak_detach_rate=5 [2024-08-19 09:45:08] DEBUG: tip_coverage_rate=2 [2024-08-19 09:45:08] DEBUG: tip_length_rate=2 [2024-08-19 09:45:08] DEBUG: output_gfa_before_rr=1 [2024-08-19 09:45:08] DEBUG: remove_alt_edges=0 [2024-08-19 09:45:08] DEBUG: low_cutoff_warning=1 [2024-08-19 09:45:08] DEBUG: kmer_size=17 [2024-08-19 09:45:08] DEBUG: use_minimizers=0 [2024-08-19 09:45:08] DEBUG: reads_base_alignment=0 [2024-08-19 09:45:08] DEBUG: meta_read_top_kmer_rate=0.40 [2024-08-19 09:45:08] DEBUG: maximum_jump=1500 [2024-08-19 09:45:08] DEBUG: maximum_overhang=1500 [2024-08-19 09:45:08] DEBUG: repeat_kmer_rate=100 [2024-08-19 09:45:08] DEBUG: assemble_ovlp_divergence=0.10 [2024-08-19 09:45:08] DEBUG: assemble_divergence_relative=1 [2024-08-19 09:45:08] DEBUG: repeat_graph_ovlp_divergence=0.08 [2024-08-19 09:45:08] DEBUG: read_align_ovlp_divergence=0.25 [2024-08-19 09:45:08] DEBUG: hpc_scoring_on=0 [2024-08-19 09:45:08] DEBUG: add_unassembled_reads=0 [2024-08-19 09:45:08] DEBUG: extend_contigs_with_repeats=0 [2024-08-19 09:45:08] DEBUG: min_read_cov_cutoff=3 [2024-08-19 09:45:08] DEBUG: short_tip_length=20000 [2024-08-19 09:45:08] DEBUG: long_tip_length=100000 [2024-08-19 09:45:08] DEBUG: Running with k-mer size: 17 [2024-08-19 09:45:08] DEBUG: Selected minimum overlap 6000 [2024-08-19 09:45:08] DEBUG: Metagenome mode: N [2024-08-19 09:45:08] INFO: Parsing disjointigs [2024-08-19 09:45:08] DEBUG: Building positional index [2024-08-19 09:45:08] DEBUG: Total sequence: 452901 bp [2024-08-19 09:45:08] INFO: Building repeat graph [2024-08-19 09:45:08] DEBUG: Mean k-mer frequency: 1.03014 [2024-08-19 09:45:08] DEBUG: Repetitive k-mer frequency: 103 [2024-08-19 09:45:08] DEBUG: Filtered 0 repetitive k-mers (0) [2024-08-19 09:45:08] DEBUG: Sorting k-mer index [2024-08-19 09:45:08] DEBUG: Selected k-mers: 439615 [2024-08-19 09:45:08] DEBUG: K-mer index size: 452867 [2024-08-19 09:45:08] DEBUG: Mean k-mer frequency: 1.03014 [2024-08-19 09:45:08] DEBUG: Minimizer rate: 1.00008 [2024-08-19 09:45:10] DEBUG: Computing transitive closure for overlaps [2024-08-19 09:45:10] DEBUG: Found 10 overlaps [2024-08-19 09:45:10] DEBUG: Left 4 overlaps after filtering [2024-08-19 09:45:10] INFO: Median overlap divergence: 0.083035 [2024-08-19 09:45:10] DEBUG: Sequence divergence distribution: | * | * | * | * | * | * | * | * | * | * | * | * | * | * | * | * | * | * | * | * ---------------------------------------------------------------------------------------------------- 0% 5% 10% 15% 20% 25% 30% 35% 40% 45% Q25 = 0.083, Q50 = 0.083, Q75 = 0.083 [2024-08-19 09:45:10] DEBUG: Computing gluepoints [2024-08-19 09:45:10] DEBUG: Added 0 gluepoint projections [2024-08-19 09:45:10] DEBUG: Created 14 gluepoints [2024-08-19 09:45:10] DEBUG: Artificial loops removed: 0 left, 0 right, 0 both [2024-08-19 09:45:10] DEBUG: Initializing edges [2024-08-19 09:45:10] DEBUG: Edges length checksum: 2641675703 [2024-08-19 09:45:10] DEBUG: Filtered 0 singleton segments [2024-08-19 09:45:10] DEBUG: Removed 0 simple and 0 double chimeric junctions [2024-08-19 09:45:10] DEBUG: Collapsed 1 edges [2024-08-19 09:45:10] DEBUG: * 1 +disjointig_1 0 370783 370783 [2024-08-19 09:45:10] DEBUG: * 5 +disjointig_1 370783 419825 49042 [2024-08-19 09:45:10] DEBUG: * -3 +disjointig_2 0 26527 26527 [2024-08-19 09:45:10] DEBUG: Total edges: 5 [2024-08-19 09:45:10] INFO: Parsing reads [2024-08-19 09:45:10] DEBUG: Building positional index [2024-08-19 09:45:10] DEBUG: Total sequence: 7249289 bp [2024-08-19 09:45:10] DEBUG: Building positional index [2024-08-19 09:45:10] DEBUG: Total sequence: 446352 bp [2024-08-19 09:45:10] INFO: Aligning reads to the graph [2024-08-19 09:45:10] DEBUG: Mean k-mer frequency: 1.02577 [2024-08-19 09:45:10] DEBUG: Repetitive k-mer frequency: 102 [2024-08-19 09:45:10] DEBUG: Filtered 0 repetitive k-mers (0) [2024-08-19 09:45:10] DEBUG: Sorting k-mer index [2024-08-19 09:45:10] DEBUG: Selected k-mers: 435087 [2024-08-19 09:45:10] DEBUG: K-mer index size: 446301 [2024-08-19 09:45:10] DEBUG: Mean k-mer frequency: 1.02577 [2024-08-19 09:45:10] DEBUG: Minimizer rate: 1.00011 [2024-08-19 09:45:11] DEBUG: Total reads : 576 [2024-08-19 09:45:11] DEBUG: Read with aligned parts : 566 [2024-08-19 09:45:11] DEBUG: Aligned in one piece : 566 [2024-08-19 09:45:11] INFO: Aligned read sequence: 6321543 / 6471580 (0.976816) [2024-08-19 09:45:11] INFO: Median overlap divergence: 0.12965 [2024-08-19 09:45:11] DEBUG: Sequence divergence distribution: | * | | ** | | *** | | *** | | *** | | *** * | | ***** | | ***** | | ***** | | ****** | | ****** | | ******* | | ******* | | ******** | | ********* | | ********* | | ********** | | ************ * | | ************ * | | * **************** | ---------------------------------------------------------------------------------------------------- 0% 5% 10% 15% 20% 25% 30% 35% 40% 45% Q25 = 0.12, Q50 = 0.13, Q75 = 0.14 [2024-08-19 09:45:11] INFO: Mean edge coverage: 13 [2024-08-19 09:45:11] DEBUG: 1 len:370783 cov:15 mult:1.15385 [2024-08-19 09:45:11] DEBUG: -1 len:370783 cov:15 mult:1.15385 [2024-08-19 09:45:11] DEBUG: 3 len:26527 cov:7 mult:0.538462 [2024-08-19 09:45:11] DEBUG: -3 len:26527 cov:7 mult:0.538462 [2024-08-19 09:45:11] DEBUG: 5 len:49042 cov:12 mult:0.923077 [2024-08-19 09:45:11] DEBUG: -5 len:49042 cov:12 mult:0.923077 [2024-08-19 09:45:11] DEBUG: Unique coverage threshold 26 [2024-08-19 09:45:11] INFO: Simplifying the graph [2024-08-19 09:45:11] DEBUG: Read coverage cutoff: 3 [2024-08-19 09:45:11] DEBUG: [SIMPL] Removed 0 paths with low coverage [2024-08-19 09:45:11] DEBUG: [SIMPL] Masked 0 heterozygous loops [2024-08-19 09:45:11] DEBUG: [SIMPL] Masked 0 simple bubbles [2024-08-19 09:45:11] DEBUG: Finding repeats [2024-08-19 09:45:11] DEBUG: Read coverage cutoff: 3 [2024-08-19 09:45:11] DEBUG: Repeat detection iteration 1 [2024-08-19 09:45:11] DEBUG: Starting -5 aln:7 [2024-08-19 09:45:11] DEBUG: T -1 num:2 flank:9812 span:40 [2024-08-19 09:45:11] DEBUG: T 3 num:5 flank:5809 span:11 [2024-08-19 09:45:11] DEBUG: Mult: 5 49042 12 (1,0) [2024-08-19 09:45:11] DEBUG: Writing Dot [2024-08-19 09:45:11] DEBUG: Writing FASTA [2024-08-19 09:45:11] DEBUG: Writing Gfa [2024-08-19 09:45:11] DEBUG: [SIMPL] == Iteration 1 == [2024-08-19 09:45:11] DEBUG: Splitting nodes [2024-08-19 09:45:11] DEBUG: [SIMPL] Split 0 nodes [2024-08-19 09:45:11] DEBUG: [SIMPL] Clipped 0 short and 0 long tips [2024-08-19 09:45:11] DEBUG: [SIMPL] Masked 0 heterozygous loops [2024-08-19 09:45:11] DEBUG: [SIMPL] Masked 0 simple bubbles [2024-08-19 09:45:11] DEBUG: Finding repeats [2024-08-19 09:45:11] DEBUG: Read coverage cutoff: 3 [2024-08-19 09:45:11] DEBUG: Repeat detection iteration 1 [2024-08-19 09:45:11] DEBUG: Starting -5 aln:7 [2024-08-19 09:45:11] DEBUG: T -1 num:2 flank:9812 span:40 [2024-08-19 09:45:11] DEBUG: T 3 num:5 flank:5809 span:11 [2024-08-19 09:45:11] DEBUG: Mult: 5 49042 12 (1,0) [2024-08-19 09:45:11] DEBUG: Total unique edges: 2 [2024-08-19 09:45:11] DEBUG: [SIMPL] Resolved repeats: 0 [2024-08-19 09:45:11] DEBUG: RR links: 0 [2024-08-19 09:45:11] DEBUG: Unresolved: 0 [2024-08-19 09:45:11] DEBUG: Removed 0 simple and 0 double chimeric junctions [2024-08-19 09:45:11] DEBUG: [SIMPL] Collapsed 0 haplotypes [2024-08-19 09:45:11] DEBUG: [SIMPL] Resolved 0 simple repeats [2024-08-19 09:45:11] DEBUG: Read coverage cutoff: 3 [2024-08-19 09:45:11] DEBUG: [SIMPL] Removed 0 paths with low coverage [2024-08-19 09:45:11] DEBUG: Finding repeats [2024-08-19 09:45:11] DEBUG: Read coverage cutoff: 3 [2024-08-19 09:45:11] DEBUG: Repeat detection iteration 1 [2024-08-19 09:45:11] DEBUG: Starting -5 aln:7 [2024-08-19 09:45:11] DEBUG: T -1 num:2 flank:9812 span:40 [2024-08-19 09:45:11] DEBUG: T 3 num:5 flank:5809 span:11 [2024-08-19 09:45:11] DEBUG: Mult: 5 49042 12 (1,0) [2024-08-19 09:45:11] DEBUG: Writing Dot [2024-08-19 09:45:11] DEBUG: Writing FASTA [2024-08-19 09:45:11] DEBUG: Peak RAM usage: 0 Gb -----------End assembly log------------ [2024-08-19 09:45:11] root: INFO: >>>STAGE: contigger [2024-08-19 09:45:11] root: INFO: Generating contigs [2024-08-19 09:45:11] root: DEBUG: -----Begin contigger analyser log------ [2024-08-19 09:45:11] root: DEBUG: Running: flye-modules contigger --graph-edges /tmp/tmpmmr8wbsp/job_working_directory/000/8/working/out_dir/20-repeat/repeat_graph_edges.fasta --reads /tmp/tmpmmr8wbsp/job_working_directory/000/8/working/input_0.fastq.gz,/tmp/tmpmmr8wbsp/job_working_directory/000/8/working/input_1.fastq.gz,/tmp/tmpmmr8wbsp/job_working_directory/000/8/working/input_2.fastq.gz,/tmp/tmpmmr8wbsp/job_working_directory/000/8/working/input_3.fastq.gz,/tmp/tmpmmr8wbsp/job_working_directory/000/8/working/input_4.fastq.gz,/tmp/tmpmmr8wbsp/job_working_directory/000/8/working/input_5.fastq.gz,/tmp/tmpmmr8wbsp/job_working_directory/000/8/working/input_6.fastq.gz --out-dir /tmp/tmpmmr8wbsp/job_working_directory/000/8/working/out_dir/30-contigger --config /usr/local/lib/python3.11/site-packages/flye/config/bin_cfg/asm_raw_reads.cfg --repeat-graph /tmp/tmpmmr8wbsp/job_working_directory/000/8/working/out_dir/20-repeat/repeat_graph_dump --graph-aln /tmp/tmpmmr8wbsp/job_working_directory/000/8/working/out_dir/20-repeat/read_alignment_dump --log /tmp/tmpmmr8wbsp/job_working_directory/000/8/working/out_dir/flye.log --threads 1 --min-ovlp 6000 [2024-08-19 09:45:11] DEBUG: Build date: Jul 26 2024 16:37:08 [2024-08-19 09:45:11] DEBUG: Total RAM: 31 Gb [2024-08-19 09:45:11] DEBUG: Available RAM: 21 Gb [2024-08-19 09:45:11] DEBUG: Total CPUs: 12 [2024-08-19 09:45:11] DEBUG: Loading /usr/local/lib/python3.11/site-packages/flye/config/bin_cfg/asm_raw_reads.cfg [2024-08-19 09:45:11] DEBUG: Loading /usr/local/lib/python3.11/site-packages/flye/config/bin_cfg/asm_defaults.cfg [2024-08-19 09:45:11] DEBUG: big_genome_threshold=29000000 [2024-08-19 09:45:11] DEBUG: meta_read_filter_kmer_freq=100 [2024-08-19 09:45:11] DEBUG: chain_large_gap_penalty=2 [2024-08-19 09:45:11] DEBUG: chain_small_gap_penalty=0.5 [2024-08-19 09:45:11] DEBUG: chain_gap_jump_threshold=100 [2024-08-19 09:45:11] DEBUG: max_jump_gap=500 [2024-08-19 09:45:11] DEBUG: max_coverage_drop_rate=5 [2024-08-19 09:45:11] DEBUG: max_extensions_drop_rate=5 [2024-08-19 09:45:11] DEBUG: chimera_window=100 [2024-08-19 09:45:11] DEBUG: chimera_overhang=1000 [2024-08-19 09:45:11] DEBUG: min_reads_in_disjointig=4 [2024-08-19 09:45:11] DEBUG: max_inner_reads=10 [2024-08-19 09:45:11] DEBUG: max_inner_fraction=0.25 [2024-08-19 09:45:11] DEBUG: aggressive_dup_filter=1 [2024-08-19 09:45:11] DEBUG: max_separation=500 [2024-08-19 09:45:11] DEBUG: unique_edge_length=50000 [2024-08-19 09:45:11] DEBUG: min_repeat_res_support=0.51 [2024-08-19 09:45:11] DEBUG: out_paths_ratio=5 [2024-08-19 09:45:11] DEBUG: graph_cov_drop_rate=5 [2024-08-19 09:45:11] DEBUG: coverage_estimate_window=100 [2024-08-19 09:45:11] DEBUG: max_bubble_length=50000 [2024-08-19 09:45:11] DEBUG: loop_coverage_rate=1.5 [2024-08-19 09:45:11] DEBUG: repeat_edge_cov_mult=1.75 [2024-08-19 09:45:11] DEBUG: weak_detach_rate=5 [2024-08-19 09:45:11] DEBUG: tip_coverage_rate=2 [2024-08-19 09:45:11] DEBUG: tip_length_rate=2 [2024-08-19 09:45:11] DEBUG: output_gfa_before_rr=1 [2024-08-19 09:45:11] DEBUG: remove_alt_edges=0 [2024-08-19 09:45:11] DEBUG: low_cutoff_warning=1 [2024-08-19 09:45:11] DEBUG: kmer_size=17 [2024-08-19 09:45:11] DEBUG: use_minimizers=0 [2024-08-19 09:45:11] DEBUG: reads_base_alignment=0 [2024-08-19 09:45:11] DEBUG: meta_read_top_kmer_rate=0.40 [2024-08-19 09:45:11] DEBUG: maximum_jump=1500 [2024-08-19 09:45:11] DEBUG: maximum_overhang=1500 [2024-08-19 09:45:11] DEBUG: repeat_kmer_rate=100 [2024-08-19 09:45:11] DEBUG: assemble_ovlp_divergence=0.10 [2024-08-19 09:45:11] DEBUG: assemble_divergence_relative=1 [2024-08-19 09:45:11] DEBUG: repeat_graph_ovlp_divergence=0.08 [2024-08-19 09:45:11] DEBUG: read_align_ovlp_divergence=0.25 [2024-08-19 09:45:11] DEBUG: hpc_scoring_on=0 [2024-08-19 09:45:11] DEBUG: add_unassembled_reads=0 [2024-08-19 09:45:11] DEBUG: extend_contigs_with_repeats=0 [2024-08-19 09:45:11] DEBUG: min_read_cov_cutoff=3 [2024-08-19 09:45:11] DEBUG: short_tip_length=20000 [2024-08-19 09:45:11] DEBUG: long_tip_length=100000 [2024-08-19 09:45:11] DEBUG: Running with k-mer size: 17 [2024-08-19 09:45:11] DEBUG: Selected minimum overlap 6000 [2024-08-19 09:45:11] INFO: Reading sequences [2024-08-19 09:45:11] DEBUG: Building positional index [2024-08-19 09:45:11] DEBUG: Total sequence: 7249289 bp [2024-08-19 09:45:11] DEBUG: Flipped 0 [2024-08-19 09:45:11] DEBUG: UPath 1: 1 [2024-08-19 09:45:11] DEBUG: UPath 2: 3 [2024-08-19 09:45:11] DEBUG: UPath 3: 5 [2024-08-19 09:45:11] DEBUG: Final graph contains 3 egdes [2024-08-19 09:45:11] DEBUG: Extending contigs into repeats [2024-08-19 09:45:11] DEBUG: Covered 0 repetitive contigs [2024-08-19 09:45:11] INFO: Generated 3 contigs [2024-08-19 09:45:11] DEBUG: Writing FASTA [2024-08-19 09:45:11] DEBUG: Generating scaffold connections [2024-08-19 09:45:11] INFO: Added 0 scaffold connections [2024-08-19 09:45:11] DEBUG: Writing Dot [2024-08-19 09:45:11] DEBUG: Writing FASTA [2024-08-19 09:45:11] DEBUG: Writing Gfa [2024-08-19 09:45:11] DEBUG: Peak RAM usage: 0 Gb -----------End assembly log------------ [2024-08-19 09:45:11] root: INFO: >>>STAGE: finalize [2024-08-19 09:45:11] root: DEBUG: ---Output dir contents:---- [2024-08-19 09:45:11] root: DEBUG: out_dir/ [2024-08-19 09:45:11] root: DEBUG: 705.0 B assembly_graph.gv [2024-08-19 09:45:11] root: DEBUG: 464.0 K assembly.fasta [2024-08-19 09:45:11] root: DEBUG: 92.0 B params.json [2024-08-19 09:45:11] root: DEBUG: 30.0 K flye.log [2024-08-19 09:45:11] root: DEBUG: 436.0 K assembly_graph.gfa [2024-08-19 09:45:11] root: DEBUG: 30-contigger/ [2024-08-19 09:45:11] root: DEBUG: 462.0 K contigs.fasta [2024-08-19 09:45:11] root: DEBUG: 441.0 K graph_final.fasta [2024-08-19 09:45:11] root: DEBUG: 182.0 B contigs_stats.txt [2024-08-19 09:45:11] root: DEBUG: 436.0 K graph_final.gfa [2024-08-19 09:45:11] root: DEBUG: 0.0 B scaffolds_links.txt [2024-08-19 09:45:11] root: DEBUG: 705.0 B graph_final.gv [2024-08-19 09:45:11] root: DEBUG: 20-repeat/ [2024-08-19 09:45:11] root: DEBUG: 705.0 B graph_after_rr.gv [2024-08-19 09:45:11] root: DEBUG: 441.0 K repeat_graph_edges.fasta [2024-08-19 09:45:11] root: DEBUG: 441.0 K graph_before_rr.fasta [2024-08-19 09:45:11] root: DEBUG: 705.0 B graph_before_rr.gv [2024-08-19 09:45:11] root: DEBUG: 436.0 K graph_before_rr.gfa [2024-08-19 09:45:11] root: DEBUG: 564.0 B repeat_graph_dump [2024-08-19 09:45:11] root: DEBUG: 121.0 K read_alignment_dump [2024-08-19 09:45:11] root: DEBUG: 10-consensus/ [2024-08-19 09:45:11] root: DEBUG: 449.0 K consensus.fasta [2024-08-19 09:45:11] root: DEBUG: 3.0 K minimap.bam.bai [2024-08-19 09:45:11] root: DEBUG: 1.0 K minimap.stderr [2024-08-19 09:45:11] root: DEBUG: 00-assembly/ [2024-08-19 09:45:11] root: DEBUG: 465.0 K draft_assembly.fasta [2024-08-19 09:45:11] root: DEBUG: 61.0 B draft_assembly.fasta.fai [2024-08-19 09:45:11] root: DEBUG: -------------------------- [2024-08-19 09:45:11] root: INFO: Assembly statistics: Total length: 467534 Fragments: 3 Fragments N50: 382469 Largest frg: 382469 Scaffolds: 0 Mean coverage: 14 [2024-08-19 09:45:11] root: INFO: Final assembly: /tmp/tmpmmr8wbsp/job_working_directory/000/8/working/out_dir/assembly.fasta