Mercurial > repos > bgruening > flye
view test-data/result1.log @ 9:276f5d8712d5 draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
| author | bgruening |
|---|---|
| date | Tue, 23 Nov 2021 08:35:32 +0000 |
| parents | e27815e82dd4 |
| children |
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[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