Mercurial > repos > bgruening > flye
diff test-data/result1.log @ 8:e27815e82dd4 draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
| author | bgruening |
|---|---|
| date | Wed, 30 Jun 2021 20:02:51 +0000 |
| parents | |
| children | 276f5d8712d5 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/result1.log Wed Jun 30 20:02:51 2021 +0000 @@ -0,0 +1,440 @@ +[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) +[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: + + | * | + | * | + | * *** | + | * *** | + | ****** | + | ******* | + | ******* | + | ******** | + | ******** | + | ********* | + | ********* | + | ********* | + | ********** | + | ************ | + | ************* | + | ************** | + | ************** | + | **************** | + | * ***************** * | + | * ** ************************ | * * + ---------------------------------------------------------------------------------------------------- + 0% 5% 10% 15% 20% 25% 30% 35% 40% 45% + + 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 + leftTip: 1 rightTip: 1 + Suspicious: 3 + Short ext: 2 + Mean extensions: 9 + Avg overlap len: 10074 + Min overlap len: 2570 + 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 +-----------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: + + | | + | | + | | + | | + | | + | | + | | + | | + | | + | | + | | + | | + | | + | | + | | + | | + | | + | | + | | + | | + ---------------------------------------------------------------------------------------------------- + 0% 5% 10% 15% 20% 25% 30% 35% 40% 45% + + Q25 = 0, Q50 = 0, Q75 = 0 + +[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: + + | * | + | * | + | ** | + | ** | + | ** | + | *** | + | *** * | + | *** * | + | ***** | + | ***** | + | ****** | + | ******* | + | ******* | + | ******** | + | ********* | + | ********* | + | ********** | + | *********** | + | ************ * | + | ***************** | + ---------------------------------------------------------------------------------------------------- + 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 +-----------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 +-----------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: + + Total length: 418805 + Fragments: 1 + Fragments N50: 418805 + Largest frg: 418805 + Scaffolds: 0 + Mean coverage: 15 + +[2021-06-30 16:02:01] root: INFO: Final assembly: /tmp/tmpicy_msib/job_working_directory/000/8/working/out_dir/assembly.fasta