Mercurial > repos > bgruening > flye
diff test-data/result1.log @ 12:3e4f8642c77e draft default tip
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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--- a/test-data/result1.log Mon Mar 18 12:44:09 2024 +0000 +++ b/test-data/result1.log Mon Aug 26 13:54:31 2024 +0000 @@ -1,95 +1,97 @@ -[2021-11-22 18:13:09] root: INFO: Starting Flye 2.9-b1768 -[2021-11-22 18:13:09] 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 -[2021-11-22 18:13:09] root: DEBUG: Python version: 3.9.6 | packaged by conda-forge | (default, Jul 11 2021, 03:39:48) -[GCC 9.3.0] -[2021-11-22 18:13:09] root: INFO: >>>STAGE: configure -[2021-11-22 18:13:09] root: INFO: Configuring run -[2021-11-22 18:13:10] root: INFO: Total read length: 7249289 -[2021-11-22 18:13:10] root: INFO: Reads N50/N90: 11150 / 5790 -[2021-11-22 18:13:10] root: INFO: Minimum overlap set to 6000 -[2021-11-22 18:13:10] root: INFO: >>>STAGE: assembly -[2021-11-22 18:13:10] root: INFO: Assembling disjointigs -[2021-11-22 18:13:10] root: DEBUG: -----Begin assembly log------ -[2021-11-22 18:13:10] root: DEBUG: Running: flye-modules assemble --reads /tmp/tmpakmcmxzn/job_working_directory/000/8/working/input_0.fastq.gz,/tmp/tmpakmcmxzn/job_working_directory/000/8/working/input_1.fastq.gz,/tmp/tmpakmcmxzn/job_working_directory/000/8/working/input_2.fastq.gz,/tmp/tmpakmcmxzn/job_working_directory/000/8/working/input_3.fastq.gz,/tmp/tmpakmcmxzn/job_working_directory/000/8/working/input_4.fastq.gz,/tmp/tmpakmcmxzn/job_working_directory/000/8/working/input_5.fastq.gz,/tmp/tmpakmcmxzn/job_working_directory/000/8/working/input_6.fastq.gz --out-asm /tmp/tmpakmcmxzn/job_working_directory/000/8/working/out_dir/00-assembly/draft_assembly.fasta --config /usr/local/lib/python3.9/site-packages/flye/config/bin_cfg/asm_raw_reads.cfg --log /tmp/tmpakmcmxzn/job_working_directory/000/8/working/out_dir/flye.log --threads 1 --min-ovlp 6000 -[2021-11-22 18:13:10] DEBUG: Build date: Aug 22 2021 04:46:17 -[2021-11-22 18:13:10] DEBUG: Total RAM: 15 Gb -[2021-11-22 18:13:10] DEBUG: Available RAM: 9 Gb -[2021-11-22 18:13:10] DEBUG: Total CPUs: 8 -[2021-11-22 18:13:10] DEBUG: Loading /usr/local/lib/python3.9/site-packages/flye/config/bin_cfg/asm_raw_reads.cfg -[2021-11-22 18:13:10] DEBUG: Loading /usr/local/lib/python3.9/site-packages/flye/config/bin_cfg/asm_defaults.cfg -[2021-11-22 18:13:10] DEBUG: big_genome_threshold=29000000 -[2021-11-22 18:13:10] DEBUG: meta_read_filter_kmer_freq=100 -[2021-11-22 18:13:10] DEBUG: chain_large_gap_penalty=2 -[2021-11-22 18:13:10] DEBUG: chain_small_gap_penalty=0.5 -[2021-11-22 18:13:10] DEBUG: chain_gap_jump_threshold=100 -[2021-11-22 18:13:10] DEBUG: max_coverage_drop_rate=5 -[2021-11-22 18:13:10] DEBUG: max_extensions_drop_rate=5 -[2021-11-22 18:13:10] DEBUG: chimera_window=100 -[2021-11-22 18:13:10] DEBUG: chimera_overhang=1000 -[2021-11-22 18:13:10] DEBUG: min_reads_in_disjointig=4 -[2021-11-22 18:13:10] DEBUG: max_inner_reads=10 -[2021-11-22 18:13:10] DEBUG: max_inner_fraction=0.25 -[2021-11-22 18:13:10] DEBUG: max_separation=500 -[2021-11-22 18:13:10] DEBUG: unique_edge_length=50000 -[2021-11-22 18:13:10] DEBUG: min_repeat_res_support=0.51 -[2021-11-22 18:13:10] DEBUG: out_paths_ratio=5 -[2021-11-22 18:13:10] DEBUG: graph_cov_drop_rate=5 -[2021-11-22 18:13:10] DEBUG: coverage_estimate_window=100 -[2021-11-22 18:13:10] DEBUG: max_bubble_length=50000 -[2021-11-22 18:13:10] DEBUG: loop_coverage_rate=1.5 -[2021-11-22 18:13:10] DEBUG: repeat_edge_cov_mult=1.75 -[2021-11-22 18:13:10] DEBUG: weak_detach_rate=5 -[2021-11-22 18:13:10] DEBUG: tip_coverage_rate=2 -[2021-11-22 18:13:10] DEBUG: tip_length_rate=2 -[2021-11-22 18:13:10] DEBUG: output_gfa_before_rr=0 -[2021-11-22 18:13:10] DEBUG: low_cutoff_warning=1 -[2021-11-22 18:13:10] DEBUG: kmer_size=17 -[2021-11-22 18:13:10] DEBUG: use_minimizers=0 -[2021-11-22 18:13:10] DEBUG: reads_base_alignment=0 -[2021-11-22 18:13:10] DEBUG: meta_read_top_kmer_rate=0.40 -[2021-11-22 18:13:10] DEBUG: maximum_jump=1500 -[2021-11-22 18:13:10] DEBUG: maximum_overhang=1500 -[2021-11-22 18:13:10] DEBUG: repeat_kmer_rate=100 -[2021-11-22 18:13:10] DEBUG: assemble_ovlp_divergence=0.10 -[2021-11-22 18:13:10] DEBUG: assemble_divergence_relative=1 -[2021-11-22 18:13:10] DEBUG: repeat_graph_ovlp_divergence=0.08 -[2021-11-22 18:13:10] DEBUG: read_align_ovlp_divergence=0.25 -[2021-11-22 18:13:10] DEBUG: hpc_scoring_on=0 -[2021-11-22 18:13:10] DEBUG: add_unassembled_reads=0 -[2021-11-22 18:13:10] DEBUG: extend_contigs_with_repeats=0 -[2021-11-22 18:13:10] DEBUG: min_read_cov_cutoff=3 -[2021-11-22 18:13:10] DEBUG: short_tip_length=20000 -[2021-11-22 18:13:10] DEBUG: long_tip_length=100000 -[2021-11-22 18:13:10] DEBUG: Running with k-mer size: 17 -[2021-11-22 18:13:10] DEBUG: Running with minimum overlap 6000 -[2021-11-22 18:13:10] DEBUG: Metagenome mode: N -[2021-11-22 18:13:10] DEBUG: Short mode: N -[2021-11-22 18:13:10] INFO: Reading sequences -[2021-11-22 18:13:10] DEBUG: Building positional index -[2021-11-22 18:13:10] DEBUG: Total sequence: 6471580 bp -[2021-11-22 18:13:12] INFO: Counting k-mers: -[2021-11-22 18:13:13] DEBUG: Updating k-mer histogram -[2021-11-22 18:13:56] DEBUG: Hash size: 29 -[2021-11-22 18:13:56] DEBUG: Total k-mers 5958598 -[2021-11-22 18:13:56] INFO: Filling index table (1/2) -[2021-11-22 18:13:59] DEBUG: Mean k-mer frequency: 2.57396 -[2021-11-22 18:13:59] DEBUG: Repetitive k-mer frequency: 257 -[2021-11-22 18:13:59] DEBUG: Filtered 0 repetitive k-mers (0) -[2021-11-22 18:13:59] INFO: Filling index table (2/2) -[2021-11-22 18:14:01] DEBUG: Sorting k-mer index -[2021-11-22 18:14:01] DEBUG: Selected k-mers: 319695 -[2021-11-22 18:14:01] DEBUG: Index size: 822885 -[2021-11-22 18:14:01] DEBUG: Mean k-mer index frequency: 2.57397 -[2021-11-22 18:14:01] DEBUG: Peak RAM usage: 8 Gb -[2021-11-22 18:14:01] DEBUG: Estimating k-mer identity bias -[2021-11-22 18:14:05] DEBUG: Initial divergence estimate : 0.237684 -[2021-11-22 18:14:05] DEBUG: Relative threshold: Y -[2021-11-22 18:14:05] DEBUG: Max divergence threshold set to 0.337684 -[2021-11-22 18:14:05] INFO: Extending reads -[2021-11-22 18:14:05] DEBUG: Estimating overlap coverage -[2021-11-22 18:14:07] INFO: Overlap-based coverage: 10 -[2021-11-22 18:14:07] INFO: Median overlap divergence: 0.235584 -[2021-11-22 18:14:07] DEBUG: Sequence divergence distribution: +[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: | * | | * | @@ -116,7 +118,7 @@ Q25 = 0.22, Q50 = 0.24, Q75 = 0.25 -[2021-11-22 18:14:08] DEBUG: Assembled disjointig 1 +[2024-08-19 09:45:00] DEBUG: Assembled disjointig 1 With 83 reads Start read: +S1_395 At position: 40 @@ -128,8 +130,8 @@ Min overlap len: 4225 Inner reads: 0 Length: 434635 -[2021-11-22 18:14:08] DEBUG: Inner: 1024 covered: 1014 total: 1152 -[2021-11-22 18:14:08] DEBUG: Assembled disjointig 2 +[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 @@ -141,173 +143,178 @@ Min overlap len: 7703 Inner reads: 0 Length: 34343 -[2021-11-22 18:14:08] DEBUG: Inner: 1040 covered: 1056 total: 1152 -[2021-11-22 18:14:08] INFO: Assembled 2 disjointigs -[2021-11-22 18:14:08] INFO: Generating sequence -[2021-11-22 18:14:08] DEBUG: Building positional index -[2021-11-22 18:14:08] DEBUG: Total sequence: 470346 bp -[2021-11-22 18:14:08] DEBUG: Mean k-mer frequency: 1.00134 -[2021-11-22 18:14:08] DEBUG: Repetitive k-mer frequency: 100 -[2021-11-22 18:14:08] DEBUG: Filtered 0 repetitive k-mers (0) -[2021-11-22 18:14:08] DEBUG: Sorting k-mer index -[2021-11-22 18:14:08] DEBUG: Selected k-mers: 469680 -[2021-11-22 18:14:08] DEBUG: K-mer index size: 470312 -[2021-11-22 18:14:08] DEBUG: Mean k-mer frequency: 1.00135 -[2021-11-22 18:14:08] DEBUG: Minimizer rate: 1.00007 -[2021-11-22 18:14:08] INFO: Filtering contained disjointigs -[2021-11-22 18:14:09] DEBUG: Computing transitive closure for overlaps -[2021-11-22 18:14:09] DEBUG: Found 0 overlaps -[2021-11-22 18:14:09] DEBUG: Left 0 overlaps after filtering -[2021-11-22 18:14:09] INFO: Contained seqs: 0 -[2021-11-22 18:14:09] DEBUG: Writing FASTA -[2021-11-22 18:14:09] DEBUG: Peak RAM usage: 8 Gb +[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------------ -[2021-11-22 18:14:09] root: DEBUG: Disjointigs length: 470346, N50: 436173 -[2021-11-22 18:14:09] root: INFO: >>>STAGE: consensus -[2021-11-22 18:14:09] root: INFO: Running Minimap2 -[2021-11-22 18:14:14] root: INFO: Computing consensus -[2021-11-22 18:14:23] root: INFO: Alignment error rate: 0.197031 -[2021-11-22 18:14:23] root: INFO: >>>STAGE: repeat -[2021-11-22 18:14:23] root: INFO: Building and resolving repeat graph -[2021-11-22 18:14:23] root: DEBUG: -----Begin repeat analyser log------ -[2021-11-22 18:14:23] root: DEBUG: Running: flye-modules repeat --disjointigs /tmp/tmpakmcmxzn/job_working_directory/000/8/working/out_dir/10-consensus/consensus.fasta --reads /tmp/tmpakmcmxzn/job_working_directory/000/8/working/input_0.fastq.gz,/tmp/tmpakmcmxzn/job_working_directory/000/8/working/input_1.fastq.gz,/tmp/tmpakmcmxzn/job_working_directory/000/8/working/input_2.fastq.gz,/tmp/tmpakmcmxzn/job_working_directory/000/8/working/input_3.fastq.gz,/tmp/tmpakmcmxzn/job_working_directory/000/8/working/input_4.fastq.gz,/tmp/tmpakmcmxzn/job_working_directory/000/8/working/input_5.fastq.gz,/tmp/tmpakmcmxzn/job_working_directory/000/8/working/input_6.fastq.gz --out-dir /tmp/tmpakmcmxzn/job_working_directory/000/8/working/out_dir/20-repeat --config /usr/local/lib/python3.9/site-packages/flye/config/bin_cfg/asm_raw_reads.cfg --log /tmp/tmpakmcmxzn/job_working_directory/000/8/working/out_dir/flye.log --threads 1 --min-ovlp 6000 -[2021-11-22 18:14:23] DEBUG: Build date: Aug 22 2021 04:47:01 -[2021-11-22 18:14:23] DEBUG: Total RAM: 15 Gb -[2021-11-22 18:14:23] DEBUG: Available RAM: 9 Gb -[2021-11-22 18:14:23] DEBUG: Total CPUs: 8 -[2021-11-22 18:14:23] DEBUG: Loading /usr/local/lib/python3.9/site-packages/flye/config/bin_cfg/asm_raw_reads.cfg -[2021-11-22 18:14:23] DEBUG: Loading /usr/local/lib/python3.9/site-packages/flye/config/bin_cfg/asm_defaults.cfg -[2021-11-22 18:14:23] DEBUG: big_genome_threshold=29000000 -[2021-11-22 18:14:23] DEBUG: meta_read_filter_kmer_freq=100 -[2021-11-22 18:14:23] DEBUG: chain_large_gap_penalty=2 -[2021-11-22 18:14:23] DEBUG: chain_small_gap_penalty=0.5 -[2021-11-22 18:14:23] DEBUG: chain_gap_jump_threshold=100 -[2021-11-22 18:14:23] DEBUG: max_coverage_drop_rate=5 -[2021-11-22 18:14:23] DEBUG: max_extensions_drop_rate=5 -[2021-11-22 18:14:23] DEBUG: chimera_window=100 -[2021-11-22 18:14:23] DEBUG: chimera_overhang=1000 -[2021-11-22 18:14:23] DEBUG: min_reads_in_disjointig=4 -[2021-11-22 18:14:23] DEBUG: max_inner_reads=10 -[2021-11-22 18:14:23] DEBUG: max_inner_fraction=0.25 -[2021-11-22 18:14:23] DEBUG: max_separation=500 -[2021-11-22 18:14:23] DEBUG: unique_edge_length=50000 -[2021-11-22 18:14:23] DEBUG: min_repeat_res_support=0.51 -[2021-11-22 18:14:23] DEBUG: out_paths_ratio=5 -[2021-11-22 18:14:23] DEBUG: graph_cov_drop_rate=5 -[2021-11-22 18:14:23] DEBUG: coverage_estimate_window=100 -[2021-11-22 18:14:23] DEBUG: max_bubble_length=50000 -[2021-11-22 18:14:23] DEBUG: loop_coverage_rate=1.5 -[2021-11-22 18:14:23] DEBUG: repeat_edge_cov_mult=1.75 -[2021-11-22 18:14:23] DEBUG: weak_detach_rate=5 -[2021-11-22 18:14:23] DEBUG: tip_coverage_rate=2 -[2021-11-22 18:14:23] DEBUG: tip_length_rate=2 -[2021-11-22 18:14:23] DEBUG: output_gfa_before_rr=0 -[2021-11-22 18:14:23] DEBUG: low_cutoff_warning=1 -[2021-11-22 18:14:23] DEBUG: kmer_size=17 -[2021-11-22 18:14:23] DEBUG: use_minimizers=0 -[2021-11-22 18:14:23] DEBUG: reads_base_alignment=0 -[2021-11-22 18:14:23] DEBUG: meta_read_top_kmer_rate=0.40 -[2021-11-22 18:14:23] DEBUG: maximum_jump=1500 -[2021-11-22 18:14:23] DEBUG: maximum_overhang=1500 -[2021-11-22 18:14:23] DEBUG: repeat_kmer_rate=100 -[2021-11-22 18:14:23] DEBUG: assemble_ovlp_divergence=0.10 -[2021-11-22 18:14:23] DEBUG: assemble_divergence_relative=1 -[2021-11-22 18:14:23] DEBUG: repeat_graph_ovlp_divergence=0.08 -[2021-11-22 18:14:23] DEBUG: read_align_ovlp_divergence=0.25 -[2021-11-22 18:14:23] DEBUG: hpc_scoring_on=0 -[2021-11-22 18:14:23] DEBUG: add_unassembled_reads=0 -[2021-11-22 18:14:23] DEBUG: extend_contigs_with_repeats=0 -[2021-11-22 18:14:23] DEBUG: min_read_cov_cutoff=3 -[2021-11-22 18:14:23] DEBUG: short_tip_length=20000 -[2021-11-22 18:14:23] DEBUG: long_tip_length=100000 -[2021-11-22 18:14:23] DEBUG: Running with k-mer size: 17 -[2021-11-22 18:14:23] DEBUG: Selected minimum overlap 6000 -[2021-11-22 18:14:23] DEBUG: Metagenome mode: N -[2021-11-22 18:14:23] INFO: Parsing disjointigs -[2021-11-22 18:14:23] DEBUG: Building positional index -[2021-11-22 18:14:23] DEBUG: Total sequence: 452437 bp -[2021-11-22 18:14:23] INFO: Building repeat graph -[2021-11-22 18:14:24] DEBUG: Mean k-mer frequency: 1.05543 -[2021-11-22 18:14:24] DEBUG: Repetitive k-mer frequency: 105 -[2021-11-22 18:14:24] DEBUG: Filtered 0 repetitive k-mers (0) -[2021-11-22 18:14:24] DEBUG: Sorting k-mer index -[2021-11-22 18:14:24] DEBUG: Selected k-mers: 428642 -[2021-11-22 18:14:24] DEBUG: K-mer index size: 452403 -[2021-11-22 18:14:24] DEBUG: Mean k-mer frequency: 1.05543 -[2021-11-22 18:14:24] DEBUG: Minimizer rate: 1.00008 -[2021-11-22 18:14:24] DEBUG: Computing transitive closure for overlaps -[2021-11-22 18:14:24] DEBUG: Found 10 overlaps -[2021-11-22 18:14:24] DEBUG: Left 4 overlaps after filtering -[2021-11-22 18:14:24] INFO: Median overlap divergence: 0.0343169 -[2021-11-22 18:14:24] DEBUG: Sequence divergence distribution: +[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 = 0.034, Q50 = 0.034, Q75 = 0.034 + Q25 = 0.083, Q50 = 0.083, Q75 = 0.083 -[2021-11-22 18:14:24] DEBUG: Computing gluepoints -[2021-11-22 18:14:24] DEBUG: Added 0 gluepoint projections -[2021-11-22 18:14:24] DEBUG: Created 12 gluepoints -[2021-11-22 18:14:24] DEBUG: Artificial loops removed: 0 left, 0 right, 0 both -[2021-11-22 18:14:24] DEBUG: Initializing edges -[2021-11-22 18:14:24] DEBUG: Edges length checksum: 2261029433 -[2021-11-22 18:14:24] DEBUG: Filtered 0 singleton segments -[2021-11-22 18:14:24] DEBUG: Removed 0 simple and 0 double chimeric junctions -[2021-11-22 18:14:24] DEBUG: Collapsed 2 edges -[2021-11-22 18:14:24] DEBUG: * 4 +disjointig_1 0 419576 419576 -[2021-11-22 18:14:24] DEBUG: Total edges: 4 -[2021-11-22 18:14:24] INFO: Parsing reads -[2021-11-22 18:14:24] DEBUG: Building positional index -[2021-11-22 18:14:24] DEBUG: Total sequence: 7249289 bp -[2021-11-22 18:14:24] DEBUG: Building positional index -[2021-11-22 18:14:24] DEBUG: Total sequence: 419576 bp -[2021-11-22 18:14:24] INFO: Aligning reads to the graph -[2021-11-22 18:14:24] DEBUG: Mean k-mer frequency: 1.00888 -[2021-11-22 18:14:24] DEBUG: Repetitive k-mer frequency: 100 -[2021-11-22 18:14:24] DEBUG: Filtered 0 repetitive k-mers (0) -[2021-11-22 18:14:24] DEBUG: Sorting k-mer index -[2021-11-22 18:14:24] DEBUG: Selected k-mers: 415865 -[2021-11-22 18:14:24] DEBUG: K-mer index size: 419559 -[2021-11-22 18:14:24] DEBUG: Mean k-mer frequency: 1.00888 -[2021-11-22 18:14:24] DEBUG: Minimizer rate: 1.00004 -[2021-11-22 18:14:26] DEBUG: Total reads : 576 -[2021-11-22 18:14:26] DEBUG: Read with aligned parts : 566 -[2021-11-22 18:14:26] DEBUG: Aligned in one piece : 566 -[2021-11-22 18:14:26] INFO: Aligned read sequence: 6321188 / 6471580 (0.976761) -[2021-11-22 18:14:26] INFO: Median overlap divergence: 0.129819 -[2021-11-22 18:14:26] DEBUG: Sequence divergence distribution: +[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: | * | | ** | - | ** | | *** | | *** | | *** | + | *** * | | ***** | | ***** | | ***** | - | ***** | + | ****** | | ****** | | ******* | | ******* | @@ -315,162 +322,185 @@ | ********* | | ********* | | ********** | - | ************ | - | *************** | - | **************** | + | ************ * | + | ************ * | + | * **************** | ---------------------------------------------------------------------------------------------------- 0% 5% 10% 15% 20% 25% 30% 35% 40% 45% Q25 = 0.12, Q50 = 0.13, Q75 = 0.14 -[2021-11-22 18:14:27] INFO: Mean edge coverage: 14 -[2021-11-22 18:14:27] DEBUG: 4 len:419576 cov:14 mult:1 -[2021-11-22 18:14:27] DEBUG: -4 len:419576 cov:14 mult:1 -[2021-11-22 18:14:27] DEBUG: Unique coverage threshold 24 -[2021-11-22 18:14:27] INFO: Simplifying the graph -[2021-11-22 18:14:27] DEBUG: Read coverage cutoff: 3 -[2021-11-22 18:14:27] DEBUG: [SIMPL] Removed 0 paths with low coverage -[2021-11-22 18:14:27] DEBUG: [SIMPL] Masked 0 heterozygous loops -[2021-11-22 18:14:27] DEBUG: [SIMPL] Masked 0 simple bubbles -[2021-11-22 18:14:27] DEBUG: Finding repeats -[2021-11-22 18:14:27] DEBUG: Read coverage cutoff: 3 -[2021-11-22 18:14:27] DEBUG: Repeat detection iteration 1 -[2021-11-22 18:14:27] DEBUG: Writing Dot -[2021-11-22 18:14:27] DEBUG: Writing FASTA -[2021-11-22 18:14:27] DEBUG: [SIMPL] == Iteration 1 == -[2021-11-22 18:14:27] DEBUG: Splitting nodes -[2021-11-22 18:14:27] DEBUG: [SIMPL] Split 0 nodes -[2021-11-22 18:14:27] DEBUG: [SIMPL] Clipped 0 short and 0 long tips -[2021-11-22 18:14:27] DEBUG: [SIMPL] Masked 0 heterozygous loops -[2021-11-22 18:14:27] DEBUG: [SIMPL] Masked 0 simple bubbles -[2021-11-22 18:14:27] DEBUG: Finding repeats -[2021-11-22 18:14:27] DEBUG: Read coverage cutoff: 3 -[2021-11-22 18:14:27] DEBUG: Repeat detection iteration 1 -[2021-11-22 18:14:27] DEBUG: Total unique edges: 1 -[2021-11-22 18:14:27] DEBUG: [SIMPL] Resolved repeats: 0 -[2021-11-22 18:14:27] DEBUG: RR links: 0 -[2021-11-22 18:14:27] DEBUG: Unresolved: 0 -[2021-11-22 18:14:27] DEBUG: Removed 0 simple and 0 double chimeric junctions -[2021-11-22 18:14:27] DEBUG: [SIMPL] Collapsed 0 haplotypes -[2021-11-22 18:14:27] DEBUG: [SIMPL] Resolved 0 simple repeats -[2021-11-22 18:14:27] DEBUG: Read coverage cutoff: 3 -[2021-11-22 18:14:27] DEBUG: [SIMPL] Removed 0 paths with low coverage -[2021-11-22 18:14:27] DEBUG: Finding repeats -[2021-11-22 18:14:27] DEBUG: Read coverage cutoff: 3 -[2021-11-22 18:14:27] DEBUG: Repeat detection iteration 1 -[2021-11-22 18:14:27] DEBUG: Writing Dot -[2021-11-22 18:14:27] DEBUG: Writing FASTA -[2021-11-22 18:14:27] DEBUG: Peak RAM usage: 0 Gb +[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------------ -[2021-11-22 18:14:27] root: INFO: >>>STAGE: contigger -[2021-11-22 18:14:27] root: INFO: Generating contigs -[2021-11-22 18:14:27] root: DEBUG: -----Begin contigger analyser log------ -[2021-11-22 18:14:27] root: DEBUG: Running: flye-modules contigger --graph-edges /tmp/tmpakmcmxzn/job_working_directory/000/8/working/out_dir/20-repeat/repeat_graph_edges.fasta --reads /tmp/tmpakmcmxzn/job_working_directory/000/8/working/input_0.fastq.gz,/tmp/tmpakmcmxzn/job_working_directory/000/8/working/input_1.fastq.gz,/tmp/tmpakmcmxzn/job_working_directory/000/8/working/input_2.fastq.gz,/tmp/tmpakmcmxzn/job_working_directory/000/8/working/input_3.fastq.gz,/tmp/tmpakmcmxzn/job_working_directory/000/8/working/input_4.fastq.gz,/tmp/tmpakmcmxzn/job_working_directory/000/8/working/input_5.fastq.gz,/tmp/tmpakmcmxzn/job_working_directory/000/8/working/input_6.fastq.gz --out-dir /tmp/tmpakmcmxzn/job_working_directory/000/8/working/out_dir/30-contigger --config /usr/local/lib/python3.9/site-packages/flye/config/bin_cfg/asm_raw_reads.cfg --repeat-graph /tmp/tmpakmcmxzn/job_working_directory/000/8/working/out_dir/20-repeat/repeat_graph_dump --graph-aln /tmp/tmpakmcmxzn/job_working_directory/000/8/working/out_dir/20-repeat/read_alignment_dump --log /tmp/tmpakmcmxzn/job_working_directory/000/8/working/out_dir/flye.log --threads 1 --min-ovlp 6000 -[2021-11-22 18:14:27] DEBUG: Build date: Aug 22 2021 04:47:48 -[2021-11-22 18:14:27] DEBUG: Total RAM: 15 Gb -[2021-11-22 18:14:27] DEBUG: Available RAM: 9 Gb -[2021-11-22 18:14:27] DEBUG: Total CPUs: 8 -[2021-11-22 18:14:27] DEBUG: Loading /usr/local/lib/python3.9/site-packages/flye/config/bin_cfg/asm_raw_reads.cfg -[2021-11-22 18:14:27] DEBUG: Loading /usr/local/lib/python3.9/site-packages/flye/config/bin_cfg/asm_defaults.cfg -[2021-11-22 18:14:27] DEBUG: big_genome_threshold=29000000 -[2021-11-22 18:14:27] DEBUG: meta_read_filter_kmer_freq=100 -[2021-11-22 18:14:27] DEBUG: chain_large_gap_penalty=2 -[2021-11-22 18:14:27] DEBUG: chain_small_gap_penalty=0.5 -[2021-11-22 18:14:27] DEBUG: chain_gap_jump_threshold=100 -[2021-11-22 18:14:27] DEBUG: max_coverage_drop_rate=5 -[2021-11-22 18:14:27] DEBUG: max_extensions_drop_rate=5 -[2021-11-22 18:14:27] DEBUG: chimera_window=100 -[2021-11-22 18:14:27] DEBUG: chimera_overhang=1000 -[2021-11-22 18:14:27] DEBUG: min_reads_in_disjointig=4 -[2021-11-22 18:14:27] DEBUG: max_inner_reads=10 -[2021-11-22 18:14:27] DEBUG: max_inner_fraction=0.25 -[2021-11-22 18:14:27] DEBUG: max_separation=500 -[2021-11-22 18:14:27] DEBUG: unique_edge_length=50000 -[2021-11-22 18:14:27] DEBUG: min_repeat_res_support=0.51 -[2021-11-22 18:14:27] DEBUG: out_paths_ratio=5 -[2021-11-22 18:14:27] DEBUG: graph_cov_drop_rate=5 -[2021-11-22 18:14:27] DEBUG: coverage_estimate_window=100 -[2021-11-22 18:14:27] DEBUG: max_bubble_length=50000 -[2021-11-22 18:14:27] DEBUG: loop_coverage_rate=1.5 -[2021-11-22 18:14:27] DEBUG: repeat_edge_cov_mult=1.75 -[2021-11-22 18:14:27] DEBUG: weak_detach_rate=5 -[2021-11-22 18:14:27] DEBUG: tip_coverage_rate=2 -[2021-11-22 18:14:27] DEBUG: tip_length_rate=2 -[2021-11-22 18:14:27] DEBUG: output_gfa_before_rr=0 -[2021-11-22 18:14:27] DEBUG: low_cutoff_warning=1 -[2021-11-22 18:14:27] DEBUG: kmer_size=17 -[2021-11-22 18:14:27] DEBUG: use_minimizers=0 -[2021-11-22 18:14:27] DEBUG: reads_base_alignment=0 -[2021-11-22 18:14:27] DEBUG: meta_read_top_kmer_rate=0.40 -[2021-11-22 18:14:27] DEBUG: maximum_jump=1500 -[2021-11-22 18:14:27] DEBUG: maximum_overhang=1500 -[2021-11-22 18:14:27] DEBUG: repeat_kmer_rate=100 -[2021-11-22 18:14:27] DEBUG: assemble_ovlp_divergence=0.10 -[2021-11-22 18:14:27] DEBUG: assemble_divergence_relative=1 -[2021-11-22 18:14:27] DEBUG: repeat_graph_ovlp_divergence=0.08 -[2021-11-22 18:14:27] DEBUG: read_align_ovlp_divergence=0.25 -[2021-11-22 18:14:27] DEBUG: hpc_scoring_on=0 -[2021-11-22 18:14:27] DEBUG: add_unassembled_reads=0 -[2021-11-22 18:14:27] DEBUG: extend_contigs_with_repeats=0 -[2021-11-22 18:14:27] DEBUG: min_read_cov_cutoff=3 -[2021-11-22 18:14:27] DEBUG: short_tip_length=20000 -[2021-11-22 18:14:27] DEBUG: long_tip_length=100000 -[2021-11-22 18:14:27] DEBUG: Running with k-mer size: 17 -[2021-11-22 18:14:27] DEBUG: Selected minimum overlap 6000 -[2021-11-22 18:14:27] INFO: Reading sequences -[2021-11-22 18:14:27] DEBUG: Building positional index -[2021-11-22 18:14:27] DEBUG: Total sequence: 7249289 bp -[2021-11-22 18:14:27] DEBUG: Flipped 0 -[2021-11-22 18:14:27] DEBUG: UPath 1: 4 -[2021-11-22 18:14:27] DEBUG: Final graph contains 1 egdes -[2021-11-22 18:14:27] DEBUG: Extending contigs into repeats -[2021-11-22 18:14:27] DEBUG: Covered 0 repetitive contigs -[2021-11-22 18:14:27] INFO: Generated 1 contigs -[2021-11-22 18:14:27] DEBUG: Writing FASTA -[2021-11-22 18:14:27] DEBUG: Generating scaffold connections -[2021-11-22 18:14:27] INFO: Added 0 scaffold connections -[2021-11-22 18:14:27] DEBUG: Writing Dot -[2021-11-22 18:14:27] DEBUG: Writing FASTA -[2021-11-22 18:14:27] DEBUG: Writing Gfa -[2021-11-22 18:14:27] DEBUG: Peak RAM usage: 0 Gb +[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------------ -[2021-11-22 18:14:27] root: INFO: >>>STAGE: finalize -[2021-11-22 18:14:27] root: DEBUG: ---Output dir contents:---- -[2021-11-22 18:14:27] root: DEBUG: out_dir/ -[2021-11-22 18:14:27] root: DEBUG: 367.0 B assembly_graph.gv -[2021-11-22 18:14:27] root: DEBUG: 416.0 K assembly.fasta -[2021-11-22 18:14:27] root: DEBUG: 92.0 B params.json -[2021-11-22 18:14:27] root: DEBUG: 28.0 K flye.log -[2021-11-22 18:14:27] root: DEBUG: 409.0 K assembly_graph.gfa -[2021-11-22 18:14:27] root: DEBUG: 10-consensus/ -[2021-11-22 18:14:27] root: DEBUG: 1.0 K minimap.stderr -[2021-11-22 18:14:27] root: DEBUG: 449.0 K consensus.fasta -[2021-11-22 18:14:27] root: DEBUG: 3.0 K minimap.bam.bai -[2021-11-22 18:14:27] root: DEBUG: 30-contigger/ -[2021-11-22 18:14:27] root: DEBUG: 409.0 K graph_final.gfa -[2021-11-22 18:14:27] root: DEBUG: 0.0 B scaffolds_links.txt -[2021-11-22 18:14:27] root: DEBUG: 111.0 B contigs_stats.txt -[2021-11-22 18:14:27] root: DEBUG: 367.0 B graph_final.gv -[2021-11-22 18:14:27] root: DEBUG: 414.0 K graph_final.fasta -[2021-11-22 18:14:27] root: DEBUG: 414.0 K contigs.fasta -[2021-11-22 18:14:27] root: DEBUG: 00-assembly/ -[2021-11-22 18:14:27] root: DEBUG: 61.0 B draft_assembly.fasta.fai -[2021-11-22 18:14:27] root: DEBUG: 465.0 K draft_assembly.fasta -[2021-11-22 18:14:27] root: DEBUG: 20-repeat/ -[2021-11-22 18:14:27] root: DEBUG: 414.0 K graph_before_rr.fasta -[2021-11-22 18:14:27] root: DEBUG: 183.0 B repeat_graph_dump -[2021-11-22 18:14:27] root: DEBUG: 367.0 B graph_before_rr.gv -[2021-11-22 18:14:27] root: DEBUG: 367.0 B graph_after_rr.gv -[2021-11-22 18:14:27] root: DEBUG: 414.0 K repeat_graph_edges.fasta -[2021-11-22 18:14:27] root: DEBUG: 119.0 K read_alignment_dump -[2021-11-22 18:14:27] root: DEBUG: -------------------------- -[2021-11-22 18:14:27] root: INFO: Assembly statistics: +[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: 419576 - Fragments: 1 - Fragments N50: 419576 - Largest frg: 419576 + Total length: 467534 + Fragments: 3 + Fragments N50: 382469 + Largest frg: 382469 Scaffolds: 0 Mean coverage: 14 -[2021-11-22 18:14:27] root: INFO: Final assembly: /tmp/tmpakmcmxzn/job_working_directory/000/8/working/out_dir/assembly.fasta +[2024-08-19 09:45:11] root: INFO: Final assembly: /tmp/tmpmmr8wbsp/job_working_directory/000/8/working/out_dir/assembly.fasta