Mercurial > repos > kkonganti > cfsan_flye
diff test-data/result1.log @ 0:96bb0635f0a0
"planemo upload"
| author | kkonganti |
|---|---|
| date | Fri, 24 Jun 2022 14:18:37 -0400 |
| parents | |
| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/result1.log Fri Jun 24 14:18:37 2022 -0400 @@ -0,0 +1,476 @@ +[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: + + | * | + | * | + | *** | + | * *** | + | ****** | + | ******* | + | ******* | + | ******** | + | ******** | + | ********* | + | ********* | + | ********* | + | ********** | + | ************ | + | ************ | + | ************** | + | ************** | + | **************** | + | * ***************** * | + | * ** ************************ | * * + ---------------------------------------------------------------------------------------------------- + 0% 5% 10% 15% 20% 25% 30% 35% 40% 45% + + Q25 = 0.22, Q50 = 0.24, Q75 = 0.25 + +[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: 5 + Short ext: 3 + Mean extensions: 9 + 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: 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------------ +[2021-11-22 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 = 0.034, Q50 = 0.034, Q75 = 0.034 + +[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 + +[2021-11-22 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------------ +[2021-11-22 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------------ +[2021-11-22 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: 419576 + Fragments: 1 + Fragments N50: 419576 + Largest frg: 419576 + 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