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 3e4f8642c77e
line wrap: on
line source

[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