Mercurial > repos > bgruening > flye
diff test-data/result1.log @ 8:2522110f3cb4 draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
| author | bgruening |
|---|---|
| date | Tue, 23 Nov 2021 08:34:56 +0000 |
| parents | 28898f6f2352 |
| children | 7066276883d6 |
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--- a/test-data/result1.log Wed Jun 30 20:02:16 2021 +0000 +++ b/test-data/result1.log Tue Nov 23 08:34:56 2021 +0000 @@ -1,97 +1,99 @@ -[2021-06-30 16:00:39] root: INFO: Starting Flye 2.8.3-b1695 -[2021-06-30 16:00:39] 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 -[2021-06-30 16:00:39] root: DEBUG: Python version: 3.9.2 | packaged by conda-forge | (default, Feb 21 2021, 05:02:46) +[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] -[2021-06-30 16:00:39] root: INFO: >>>STAGE: configure -[2021-06-30 16:00:39] root: INFO: Configuring run -[2021-06-30 16:00:39] root: INFO: Total read length: 7249289 -[2021-06-30 16:00:39] root: INFO: Reads N50/N90: 11150 / 5790 -[2021-06-30 16:00:39] root: INFO: Minimum overlap set to 5000 -[2021-06-30 16:00:39] root: INFO: >>>STAGE: assembly -[2021-06-30 16:00:39] root: INFO: Assembling disjointigs -[2021-06-30 16:00:39] root: DEBUG: -----Begin assembly log------ -[2021-06-30 16:00:39] root: DEBUG: Running: flye-modules assemble --reads ./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 --out-asm /tmp/tmpicy_msib/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/tmpicy_msib/job_working_directory/000/8/working/out_dir/flye.log --threads 1 --min-ovlp 5000 -[2021-06-30 16:00:39] DEBUG: Build date: Mar 27 2021 19:08:40 -[2021-06-30 16:00:39] DEBUG: Total RAM: 15 Gb -[2021-06-30 16:00:39] DEBUG: Available RAM: 11 Gb -[2021-06-30 16:00:39] DEBUG: Total CPUs: 8 -[2021-06-30 16:00:39] DEBUG: Loading /usr/local/lib/python3.9/site-packages/flye/config/bin_cfg/asm_raw_reads.cfg -[2021-06-30 16:00:39] DEBUG: Loading /usr/local/lib/python3.9/site-packages/flye/config/bin_cfg/asm_defaults.cfg -[2021-06-30 16:00:39] DEBUG: big_genome_threshold=29000000 -[2021-06-30 16:00:39] DEBUG: meta_read_filter_kmer_freq=100 -[2021-06-30 16:00:39] DEBUG: max_coverage_drop_rate=5 -[2021-06-30 16:00:39] DEBUG: max_extensions_drop_rate=5 -[2021-06-30 16:00:39] DEBUG: chimera_window=100 -[2021-06-30 16:00:39] DEBUG: min_reads_in_disjointig=4 -[2021-06-30 16:00:39] DEBUG: max_inner_reads=10 -[2021-06-30 16:00:39] DEBUG: max_inner_fraction=0.25 -[2021-06-30 16:00:39] DEBUG: max_separation=500 -[2021-06-30 16:00:39] DEBUG: unique_edge_length=50000 -[2021-06-30 16:00:39] DEBUG: min_repeat_res_support=0.51 -[2021-06-30 16:00:39] DEBUG: out_paths_ratio=5 -[2021-06-30 16:00:39] DEBUG: graph_cov_drop_rate=5 -[2021-06-30 16:00:39] DEBUG: coverage_estimate_window=100 -[2021-06-30 16:00:39] DEBUG: max_bubble_length=50000 -[2021-06-30 16:00:39] DEBUG: loop_coverage_rate=1.5 -[2021-06-30 16:00:39] DEBUG: repeat_edge_cov_mult=1.75 -[2021-06-30 16:00:39] DEBUG: weak_detach_rate=5 -[2021-06-30 16:00:39] DEBUG: tip_coverage_rate=2 -[2021-06-30 16:00:39] DEBUG: tip_length_rate=2 -[2021-06-30 16:00:39] DEBUG: low_cutoff_warning=1 -[2021-06-30 16:00:39] DEBUG: hard_min_coverage_rate=10 -[2021-06-30 16:00:39] DEBUG: kmer_size=17 -[2021-06-30 16:00:39] DEBUG: use_minimizers=0 -[2021-06-30 16:00:39] DEBUG: reads_base_alignment=0 -[2021-06-30 16:00:39] DEBUG: assemble_kmer_sample=1 -[2021-06-30 16:00:39] DEBUG: repeat_graph_kmer_sample=1 -[2021-06-30 16:00:39] DEBUG: read_align_kmer_sample=1 -[2021-06-30 16:00:39] DEBUG: meta_read_top_kmer_rate=0.40 -[2021-06-30 16:00:39] DEBUG: maximum_jump=1500 -[2021-06-30 16:00:39] DEBUG: maximum_overhang=1500 -[2021-06-30 16:00:39] DEBUG: repeat_kmer_rate=100 -[2021-06-30 16:00:39] DEBUG: assemble_ovlp_divergence=0.10 -[2021-06-30 16:00:39] DEBUG: assemble_divergence_relative=1 -[2021-06-30 16:00:39] DEBUG: repeat_graph_ovlp_divergence=0.08 -[2021-06-30 16:00:39] DEBUG: read_align_ovlp_divergence=0.25 -[2021-06-30 16:00:39] DEBUG: hpc_scoring_on=0 -[2021-06-30 16:00:39] DEBUG: add_unassembled_reads=0 -[2021-06-30 16:00:39] DEBUG: extend_contigs_with_repeats=0 -[2021-06-30 16:00:39] DEBUG: min_read_cov_cutoff=3 -[2021-06-30 16:00:39] DEBUG: short_tip_length=20000 -[2021-06-30 16:00:39] DEBUG: long_tip_length=100000 -[2021-06-30 16:00:39] DEBUG: Running with k-mer size: 17 -[2021-06-30 16:00:39] DEBUG: Running with minimum overlap 5000 -[2021-06-30 16:00:39] DEBUG: Metagenome mode: N -[2021-06-30 16:00:39] INFO: Reading sequences -[2021-06-30 16:00:39] DEBUG: Building positional index -[2021-06-30 16:00:39] DEBUG: Total sequence: 6702247 bp -[2021-06-30 16:00:42] INFO: Counting k-mers: -[2021-06-30 16:00:42] DEBUG: Updating k-mer histogram -[2021-06-30 16:01:29] DEBUG: Hash size: 32 -[2021-06-30 16:01:29] DEBUG: Total k-mers 6159182 -[2021-06-30 16:01:29] INFO: Filling index table (1/2) -[2021-06-30 16:01:32] DEBUG: Mean k-mer frequency: 2.59564 -[2021-06-30 16:01:32] DEBUG: Repetitive k-mer frequency: 259 -[2021-06-30 16:01:32] DEBUG: Filtered 0 repetitive k-mers (0) -[2021-06-30 16:01:32] INFO: Filling index table (2/2) -[2021-06-30 16:01:35] DEBUG: Sorting k-mer index -[2021-06-30 16:01:35] DEBUG: Selected k-mers: 333758 -[2021-06-30 16:01:35] DEBUG: Index size: 866317 -[2021-06-30 16:01:35] DEBUG: Mean k-mer index frequency: 2.59564 -[2021-06-30 16:01:35] DEBUG: Peak RAM usage: 8 Gb -[2021-06-30 16:01:35] DEBUG: Estimating k-mer identity bias -[2021-06-30 16:01:39] DEBUG: Initial divergence estimate : 0.235584 -[2021-06-30 16:01:39] DEBUG: Relative threshold: Y -[2021-06-30 16:01:39] DEBUG: Max divergence threshold set to 0.335584 -[2021-06-30 16:01:39] INFO: Extending reads -[2021-06-30 16:01:39] DEBUG: Estimating overlap coverage -[2021-06-30 16:01:42] INFO: Overlap-based coverage: 11 -[2021-06-30 16:01:42] INFO: Median overlap divergence: 0.235584 -[2021-06-30 16:01:42] DEBUG: Sequence divergence distribution: +[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: | * | | * | - | * *** | + | *** | | * *** | | ****** | | ******* | @@ -103,7 +105,7 @@ | ********* | | ********** | | ************ | - | ************* | + | ************ | | ************** | | ************** | | **************** | @@ -114,327 +116,361 @@ Q25 = 0.22, Q50 = 0.24, Q75 = 0.25 -[2021-06-30 16:01:42] DEBUG: Assembled disjointig 1 - With 86 reads - Start read: +S1_371 - At position: 35 +[2021-11-22 18:14:08] DEBUG: Assembled disjointig 1 + With 83 reads + Start read: +S1_395 + At position: 40 leftTip: 1 rightTip: 1 - Suspicious: 3 - Short ext: 2 + Suspicious: 5 + Short ext: 3 Mean extensions: 9 - Avg overlap len: 10074 - Min overlap len: 2570 + Avg overlap len: 10043 + 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 + 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: 433999 -[2021-06-30 16:01:42] DEBUG: Inner: 1040 covered: 1110 total: 1236 -[2021-06-30 16:01:42] INFO: Assembled 1 disjointigs -[2021-06-30 16:01:42] INFO: Generating sequence -[2021-06-30 16:01:43] DEBUG: Writing FASTA -[2021-06-30 16:01:43] DEBUG: Peak RAM usage: 8 Gb + 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 -----------End assembly log------------ -[2021-06-30 16:01:43] root: DEBUG: Disjointigs length: 434844, N50: 434844 -[2021-06-30 16:01:43] root: INFO: >>>STAGE: consensus -[2021-06-30 16:01:43] root: INFO: Running Minimap2 -[2021-06-30 16:01:48] root: INFO: Computing consensus -[2021-06-30 16:01:57] root: INFO: Alignment error rate: 0.196236 -[2021-06-30 16:01:57] root: INFO: >>>STAGE: repeat -[2021-06-30 16:01:57] root: INFO: Building and resolving repeat graph -[2021-06-30 16:01:57] root: DEBUG: -----Begin repeat analyser log------ -[2021-06-30 16:01:57] root: DEBUG: Running: flye-modules repeat --disjointigs /tmp/tmpicy_msib/job_working_directory/000/8/working/out_dir/10-consensus/consensus.fasta --reads ./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 --out-dir /tmp/tmpicy_msib/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/tmpicy_msib/job_working_directory/000/8/working/out_dir/flye.log --threads 1 --min-ovlp 5000 -[2021-06-30 16:01:57] DEBUG: Build date: Mar 27 2021 19:09:05 -[2021-06-30 16:01:57] DEBUG: Total RAM: 15 Gb -[2021-06-30 16:01:57] DEBUG: Available RAM: 11 Gb -[2021-06-30 16:01:57] DEBUG: Total CPUs: 8 -[2021-06-30 16:01:57] DEBUG: Loading /usr/local/lib/python3.9/site-packages/flye/config/bin_cfg/asm_raw_reads.cfg -[2021-06-30 16:01:57] DEBUG: Loading /usr/local/lib/python3.9/site-packages/flye/config/bin_cfg/asm_defaults.cfg -[2021-06-30 16:01:57] DEBUG: big_genome_threshold=29000000 -[2021-06-30 16:01:57] DEBUG: meta_read_filter_kmer_freq=100 -[2021-06-30 16:01:57] DEBUG: max_coverage_drop_rate=5 -[2021-06-30 16:01:57] DEBUG: max_extensions_drop_rate=5 -[2021-06-30 16:01:57] DEBUG: chimera_window=100 -[2021-06-30 16:01:57] DEBUG: min_reads_in_disjointig=4 -[2021-06-30 16:01:57] DEBUG: max_inner_reads=10 -[2021-06-30 16:01:57] DEBUG: max_inner_fraction=0.25 -[2021-06-30 16:01:57] DEBUG: max_separation=500 -[2021-06-30 16:01:57] DEBUG: unique_edge_length=50000 -[2021-06-30 16:01:57] DEBUG: min_repeat_res_support=0.51 -[2021-06-30 16:01:57] DEBUG: out_paths_ratio=5 -[2021-06-30 16:01:57] DEBUG: graph_cov_drop_rate=5 -[2021-06-30 16:01:57] DEBUG: coverage_estimate_window=100 -[2021-06-30 16:01:57] DEBUG: max_bubble_length=50000 -[2021-06-30 16:01:57] DEBUG: loop_coverage_rate=1.5 -[2021-06-30 16:01:57] DEBUG: repeat_edge_cov_mult=1.75 -[2021-06-30 16:01:57] DEBUG: weak_detach_rate=5 -[2021-06-30 16:01:57] DEBUG: tip_coverage_rate=2 -[2021-06-30 16:01:57] DEBUG: tip_length_rate=2 -[2021-06-30 16:01:57] DEBUG: low_cutoff_warning=1 -[2021-06-30 16:01:57] DEBUG: hard_min_coverage_rate=10 -[2021-06-30 16:01:57] DEBUG: kmer_size=17 -[2021-06-30 16:01:57] DEBUG: use_minimizers=0 -[2021-06-30 16:01:57] DEBUG: reads_base_alignment=0 -[2021-06-30 16:01:57] DEBUG: assemble_kmer_sample=1 -[2021-06-30 16:01:57] DEBUG: repeat_graph_kmer_sample=1 -[2021-06-30 16:01:57] DEBUG: read_align_kmer_sample=1 -[2021-06-30 16:01:57] DEBUG: meta_read_top_kmer_rate=0.40 -[2021-06-30 16:01:57] DEBUG: maximum_jump=1500 -[2021-06-30 16:01:57] DEBUG: maximum_overhang=1500 -[2021-06-30 16:01:57] DEBUG: repeat_kmer_rate=100 -[2021-06-30 16:01:57] DEBUG: assemble_ovlp_divergence=0.10 -[2021-06-30 16:01:57] DEBUG: assemble_divergence_relative=1 -[2021-06-30 16:01:57] DEBUG: repeat_graph_ovlp_divergence=0.08 -[2021-06-30 16:01:57] DEBUG: read_align_ovlp_divergence=0.25 -[2021-06-30 16:01:57] DEBUG: hpc_scoring_on=0 -[2021-06-30 16:01:57] DEBUG: add_unassembled_reads=0 -[2021-06-30 16:01:57] DEBUG: extend_contigs_with_repeats=0 -[2021-06-30 16:01:57] DEBUG: min_read_cov_cutoff=3 -[2021-06-30 16:01:57] DEBUG: short_tip_length=20000 -[2021-06-30 16:01:57] DEBUG: long_tip_length=100000 -[2021-06-30 16:01:57] DEBUG: Running with k-mer size: 17 -[2021-06-30 16:01:57] DEBUG: Selected minimum overlap 5000 -[2021-06-30 16:01:57] DEBUG: Metagenome mode: N -[2021-06-30 16:01:57] INFO: Parsing disjointigs -[2021-06-30 16:01:57] DEBUG: Building positional index -[2021-06-30 16:01:57] DEBUG: Total sequence: 418806 bp -[2021-06-30 16:01:57] INFO: Building repeat graph -[2021-06-30 16:01:57] DEBUG: Mean k-mer frequency: 1.00896 -[2021-06-30 16:01:57] DEBUG: Repetitive k-mer frequency: 100 -[2021-06-30 16:01:57] DEBUG: Filtered 0 repetitive k-mers (0) -[2021-06-30 16:01:57] DEBUG: Sorting k-mer index -[2021-06-30 16:01:57] DEBUG: Selected k-mers: 415069 -[2021-06-30 16:01:57] DEBUG: K-mer index size: 418789 -[2021-06-30 16:01:57] DEBUG: Mean k-mer frequency: 1.00896 -[2021-06-30 16:01:57] DEBUG: Minimizer rate: 1.00004 -[2021-06-30 16:01:58] DEBUG: Computing transitive closure for overlaps -[2021-06-30 16:01:58] DEBUG: Found 0 overlaps -[2021-06-30 16:01:58] DEBUG: Left 0 overlaps after filtering -[2021-06-30 16:01:58] INFO: Median overlap divergence: 0 -[2021-06-30 16:01:58] DEBUG: Sequence divergence distribution: +[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: - | | - | | - | | - | | - | | - | | - | | - | | - | | - | | - | | - | | - | | - | | - | | - | | - | | - | | - | | - | | + | * | + | * | + | * | + | * | + | * | + | * | + | * | + | * | + | * | + | * | + | * | + | * | + | * | + | * | + | * | + | * | + | * | + | * | + | * | + | * | ---------------------------------------------------------------------------------------------------- 0% 5% 10% 15% 20% 25% 30% 35% 40% 45% - Q25 = 0, Q50 = 0, Q75 = 0 + Q25 = 0.034, Q50 = 0.034, Q75 = 0.034 -[2021-06-30 16:01:58] DEBUG: Computing gluepoints -[2021-06-30 16:01:58] DEBUG: Added 0 gluepoint projections -[2021-06-30 16:01:58] DEBUG: Created 4 gluepoints -[2021-06-30 16:01:58] DEBUG: Artificial loops removed: 0 left, 0 right, 0 both -[2021-06-30 16:01:58] DEBUG: Initializing edges -[2021-06-30 16:01:58] DEBUG: Edges length checksum: 18446744073013520505 -[2021-06-30 16:01:58] DEBUG: Filtered 0 singleton segments -[2021-06-30 16:01:58] DEBUG: Removed 0 simple and 0 double chimeric junctions -[2021-06-30 16:01:58] DEBUG: Collapsed 0 edges -[2021-06-30 16:01:58] DEBUG: * 1 +disjointig_1 0 418805 418805 -[2021-06-30 16:01:58] DEBUG: Total edges: 1 -[2021-06-30 16:01:58] INFO: Parsing reads -[2021-06-30 16:01:58] DEBUG: Building positional index -[2021-06-30 16:01:58] DEBUG: Total sequence: 7249289 bp -[2021-06-30 16:01:58] DEBUG: Building positional index -[2021-06-30 16:01:58] DEBUG: Total sequence: 418805 bp -[2021-06-30 16:01:58] INFO: Aligning reads to the graph -[2021-06-30 16:01:58] DEBUG: Mean k-mer frequency: 1.00896 -[2021-06-30 16:01:58] DEBUG: Repetitive k-mer frequency: 100 -[2021-06-30 16:01:58] DEBUG: Filtered 0 repetitive k-mers (0) -[2021-06-30 16:01:58] DEBUG: Sorting k-mer index -[2021-06-30 16:01:58] DEBUG: Selected k-mers: 415068 -[2021-06-30 16:01:58] DEBUG: K-mer index size: 418788 -[2021-06-30 16:01:58] DEBUG: Mean k-mer frequency: 1.00896 -[2021-06-30 16:01:58] DEBUG: Minimizer rate: 1.00004 -[2021-06-30 16:02:00] DEBUG: Total reads : 618 -[2021-06-30 16:02:00] DEBUG: Read with aligned parts : 610 -[2021-06-30 16:02:00] DEBUG: Aligned in one piece : 610 -[2021-06-30 16:02:00] INFO: Aligned read sequence: 6562529 / 6702247 (0.979154) -[2021-06-30 16:02:00] INFO: Median overlap divergence: 0.129507 -[2021-06-30 16:02:00] DEBUG: Sequence divergence distribution: +[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: | * | - | * | | ** | | ** | - | ** | + | *** | + | *** | | *** | - | *** * | - | *** * | + | ***** | + | ***** | | ***** | | ***** | | ****** | | ******* | | ******* | - | ******** | + | ******** | | ********* | | ********* | | ********** | - | *********** | - | ************ * | - | ***************** | + | ************ | + | *************** | + | **************** | ---------------------------------------------------------------------------------------------------- 0% 5% 10% 15% 20% 25% 30% 35% 40% 45% Q25 = 0.12, Q50 = 0.13, Q75 = 0.14 -[2021-06-30 16:02:00] INFO: Mean edge coverage: 14 -[2021-06-30 16:02:00] DEBUG: 1 len:418805 cov:15 mult:1.07143 -[2021-06-30 16:02:00] DEBUG: -1 len:418805 cov:15 mult:1.07143 -[2021-06-30 16:02:00] DEBUG: Unique coverage threshold 26 -[2021-06-30 16:02:00] INFO: Simplifying the graph -[2021-06-30 16:02:00] DEBUG: Read coverage cutoff: 3 -[2021-06-30 16:02:00] DEBUG: [SIMPL] Removed 0 paths with low coverage -[2021-06-30 16:02:00] DEBUG: Finding repeats -[2021-06-30 16:02:00] DEBUG: Read coverage cutoff: 3 -[2021-06-30 16:02:00] DEBUG: Repeat detection iteration 1 -[2021-06-30 16:02:00] DEBUG: Writing Dot -[2021-06-30 16:02:00] DEBUG: Writing FASTA -[2021-06-30 16:02:00] DEBUG: [SIMPL] == Iteration 1 == -[2021-06-30 16:02:00] DEBUG: Splitting nodes -[2021-06-30 16:02:00] DEBUG: [SIMPL] Split 0 nodes -[2021-06-30 16:02:00] DEBUG: [SIMPL] Clipped 0 short and 0 long tips -[2021-06-30 16:02:00] DEBUG: [SIMPL] Masked 0 heterozygous loops -[2021-06-30 16:02:00] DEBUG: [SIMPL] Masked 0 simple bubbles -[2021-06-30 16:02:00] DEBUG: Finding repeats -[2021-06-30 16:02:00] DEBUG: Read coverage cutoff: 3 -[2021-06-30 16:02:00] DEBUG: Repeat detection iteration 1 -[2021-06-30 16:02:00] DEBUG: Total unique edges: 1 -[2021-06-30 16:02:00] DEBUG: [SIMPL] Resolved repeats: 0 -[2021-06-30 16:02:00] DEBUG: RR links: 0 -[2021-06-30 16:02:00] DEBUG: Unresolved: 0 -[2021-06-30 16:02:00] DEBUG: Removed 0 simple and 0 double chimeric junctions -[2021-06-30 16:02:00] DEBUG: [SIMPL] Collapsed 0 haplotypes -[2021-06-30 16:02:00] DEBUG: [SIMPL] Resolved 0 simple repeats -[2021-06-30 16:02:00] DEBUG: Read coverage cutoff: 3 -[2021-06-30 16:02:00] DEBUG: [SIMPL] Removed 0 paths with low coverage -[2021-06-30 16:02:00] DEBUG: Finding repeats -[2021-06-30 16:02:00] DEBUG: Read coverage cutoff: 3 -[2021-06-30 16:02:00] DEBUG: Repeat detection iteration 1 -[2021-06-30 16:02:00] DEBUG: Writing Dot -[2021-06-30 16:02:00] DEBUG: Writing FASTA -[2021-06-30 16:02:00] DEBUG: Peak RAM usage: 0 Gb +[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 -----------End assembly log------------ -[2021-06-30 16:02:00] root: INFO: >>>STAGE: contigger -[2021-06-30 16:02:00] root: INFO: Generating contigs -[2021-06-30 16:02:00] root: DEBUG: -----Begin contigger analyser log------ -[2021-06-30 16:02:00] root: DEBUG: Running: flye-modules contigger --graph-edges /tmp/tmpicy_msib/job_working_directory/000/8/working/out_dir/20-repeat/repeat_graph_edges.fasta --reads ./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 --out-dir /tmp/tmpicy_msib/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/tmpicy_msib/job_working_directory/000/8/working/out_dir/20-repeat/repeat_graph_dump --graph-aln /tmp/tmpicy_msib/job_working_directory/000/8/working/out_dir/20-repeat/read_alignment_dump --log /tmp/tmpicy_msib/job_working_directory/000/8/working/out_dir/flye.log --threads 1 --min-ovlp 5000 -[2021-06-30 16:02:00] DEBUG: Build date: Mar 27 2021 19:09:32 -[2021-06-30 16:02:00] DEBUG: Total RAM: 15 Gb -[2021-06-30 16:02:00] DEBUG: Available RAM: 11 Gb -[2021-06-30 16:02:00] DEBUG: Total CPUs: 8 -[2021-06-30 16:02:00] DEBUG: Loading /usr/local/lib/python3.9/site-packages/flye/config/bin_cfg/asm_raw_reads.cfg -[2021-06-30 16:02:00] DEBUG: Loading /usr/local/lib/python3.9/site-packages/flye/config/bin_cfg/asm_defaults.cfg -[2021-06-30 16:02:00] DEBUG: big_genome_threshold=29000000 -[2021-06-30 16:02:00] DEBUG: meta_read_filter_kmer_freq=100 -[2021-06-30 16:02:00] DEBUG: max_coverage_drop_rate=5 -[2021-06-30 16:02:00] DEBUG: max_extensions_drop_rate=5 -[2021-06-30 16:02:00] DEBUG: chimera_window=100 -[2021-06-30 16:02:00] DEBUG: min_reads_in_disjointig=4 -[2021-06-30 16:02:00] DEBUG: max_inner_reads=10 -[2021-06-30 16:02:00] DEBUG: max_inner_fraction=0.25 -[2021-06-30 16:02:00] DEBUG: max_separation=500 -[2021-06-30 16:02:00] DEBUG: unique_edge_length=50000 -[2021-06-30 16:02:00] DEBUG: min_repeat_res_support=0.51 -[2021-06-30 16:02:00] DEBUG: out_paths_ratio=5 -[2021-06-30 16:02:00] DEBUG: graph_cov_drop_rate=5 -[2021-06-30 16:02:00] DEBUG: coverage_estimate_window=100 -[2021-06-30 16:02:00] DEBUG: max_bubble_length=50000 -[2021-06-30 16:02:00] DEBUG: loop_coverage_rate=1.5 -[2021-06-30 16:02:00] DEBUG: repeat_edge_cov_mult=1.75 -[2021-06-30 16:02:00] DEBUG: weak_detach_rate=5 -[2021-06-30 16:02:00] DEBUG: tip_coverage_rate=2 -[2021-06-30 16:02:00] DEBUG: tip_length_rate=2 -[2021-06-30 16:02:00] DEBUG: low_cutoff_warning=1 -[2021-06-30 16:02:00] DEBUG: hard_min_coverage_rate=10 -[2021-06-30 16:02:00] DEBUG: kmer_size=17 -[2021-06-30 16:02:00] DEBUG: use_minimizers=0 -[2021-06-30 16:02:00] DEBUG: reads_base_alignment=0 -[2021-06-30 16:02:00] DEBUG: assemble_kmer_sample=1 -[2021-06-30 16:02:00] DEBUG: repeat_graph_kmer_sample=1 -[2021-06-30 16:02:00] DEBUG: read_align_kmer_sample=1 -[2021-06-30 16:02:00] DEBUG: meta_read_top_kmer_rate=0.40 -[2021-06-30 16:02:00] DEBUG: maximum_jump=1500 -[2021-06-30 16:02:00] DEBUG: maximum_overhang=1500 -[2021-06-30 16:02:00] DEBUG: repeat_kmer_rate=100 -[2021-06-30 16:02:00] DEBUG: assemble_ovlp_divergence=0.10 -[2021-06-30 16:02:00] DEBUG: assemble_divergence_relative=1 -[2021-06-30 16:02:00] DEBUG: repeat_graph_ovlp_divergence=0.08 -[2021-06-30 16:02:00] DEBUG: read_align_ovlp_divergence=0.25 -[2021-06-30 16:02:00] DEBUG: hpc_scoring_on=0 -[2021-06-30 16:02:00] DEBUG: add_unassembled_reads=0 -[2021-06-30 16:02:00] DEBUG: extend_contigs_with_repeats=0 -[2021-06-30 16:02:00] DEBUG: min_read_cov_cutoff=3 -[2021-06-30 16:02:00] DEBUG: short_tip_length=20000 -[2021-06-30 16:02:00] DEBUG: long_tip_length=100000 -[2021-06-30 16:02:00] DEBUG: Running with k-mer size: 17 -[2021-06-30 16:02:00] DEBUG: Selected minimum overlap 5000 -[2021-06-30 16:02:00] INFO: Reading sequences -[2021-06-30 16:02:01] DEBUG: Building positional index -[2021-06-30 16:02:01] DEBUG: Total sequence: 7249289 bp -[2021-06-30 16:02:01] DEBUG: Flipped 0 -[2021-06-30 16:02:01] DEBUG: UPath 1: 1 -[2021-06-30 16:02:01] DEBUG: Final graph contiain 1 egdes -[2021-06-30 16:02:01] DEBUG: Extending contigs into repeats -[2021-06-30 16:02:01] DEBUG: Covered 0 repetitive contigs -[2021-06-30 16:02:01] INFO: Generated 1 contigs -[2021-06-30 16:02:01] DEBUG: Writing FASTA -[2021-06-30 16:02:01] DEBUG: Generating scaffold connections -[2021-06-30 16:02:01] INFO: Added 0 scaffold connections -[2021-06-30 16:02:01] DEBUG: Writing Dot -[2021-06-30 16:02:01] DEBUG: Writing FASTA -[2021-06-30 16:02:01] DEBUG: Writing Gfa -[2021-06-30 16:02:01] DEBUG: Peak RAM usage: 0 Gb +[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 -----------End assembly log------------ -[2021-06-30 16:02:01] root: INFO: >>>STAGE: finalize -[2021-06-30 16:02:01] root: DEBUG: ---Output dir contents:---- -[2021-06-30 16:02:01] root: DEBUG: out_dir/ -[2021-06-30 16:02:01] root: DEBUG: 367.0 B assembly_graph.gv -[2021-06-30 16:02:01] root: DEBUG: 415.0 K assembly.fasta -[2021-06-30 16:02:01] root: DEBUG: 92.0 B params.json -[2021-06-30 16:02:01] root: DEBUG: 26.0 K flye.log -[2021-06-30 16:02:01] root: DEBUG: 409.0 K assembly_graph.gfa -[2021-06-30 16:02:01] root: DEBUG: 10-consensus/ -[2021-06-30 16:02:01] root: DEBUG: 415.0 K consensus.fasta -[2021-06-30 16:02:01] root: DEBUG: 37.0 B chunks.fasta.fai -[2021-06-30 16:02:01] root: DEBUG: 30-contigger/ -[2021-06-30 16:02:01] root: DEBUG: 409.0 K graph_final.gfa -[2021-06-30 16:02:01] root: DEBUG: 0.0 B scaffolds_links.txt -[2021-06-30 16:02:01] root: DEBUG: 111.0 B contigs_stats.txt -[2021-06-30 16:02:01] root: DEBUG: 367.0 B graph_final.gv -[2021-06-30 16:02:01] root: DEBUG: 414.0 K graph_final.fasta -[2021-06-30 16:02:01] root: DEBUG: 414.0 K contigs.fasta -[2021-06-30 16:02:01] root: DEBUG: 00-assembly/ -[2021-06-30 16:02:01] root: DEBUG: 429.0 K draft_assembly.fasta -[2021-06-30 16:02:01] root: DEBUG: 20-repeat/ -[2021-06-30 16:02:01] root: DEBUG: 414.0 K graph_before_rr.fasta -[2021-06-30 16:02:01] root: DEBUG: 183.0 B repeat_graph_dump -[2021-06-30 16:02:01] root: DEBUG: 367.0 B graph_before_rr.gv -[2021-06-30 16:02:01] root: DEBUG: 367.0 B graph_after_rr.gv -[2021-06-30 16:02:01] root: DEBUG: 414.0 K repeat_graph_edges.fasta -[2021-06-30 16:02:01] root: DEBUG: 129.0 K read_alignment_dump -[2021-06-30 16:02:01] root: DEBUG: -------------------------- -[2021-06-30 16:02:01] root: INFO: Assembly statistics: +[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: - Total length: 418805 + Total length: 419576 Fragments: 1 - Fragments N50: 418805 - Largest frg: 418805 + Fragments N50: 419576 + Largest frg: 419576 Scaffolds: 0 - Mean coverage: 15 + Mean coverage: 14 -[2021-06-30 16:02:01] root: INFO: Final assembly: /tmp/tmpicy_msib/job_working_directory/000/8/working/out_dir/assembly.fasta +[2021-11-22 18:14:27] root: INFO: Final assembly: /tmp/tmpakmcmxzn/job_working_directory/000/8/working/out_dir/assembly.fasta