diff test-data/result1.log @ 12:3e4f8642c77e draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
author bgruening
date Mon, 26 Aug 2024 13:54:31 +0000
parents 276f5d8712d5
children
line wrap: on
line diff
--- a/test-data/result1.log	Mon Mar 18 12:44:09 2024 +0000
+++ b/test-data/result1.log	Mon Aug 26 13:54:31 2024 +0000
@@ -1,95 +1,97 @@
-[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: 
+[2024-08-19 09:44:19] root: INFO: Starting Flye 2.9.4-b1799
+[2024-08-19 09:44:19] 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
+[2024-08-19 09:44:19] root: DEBUG: Python version: 3.11.9 | packaged by conda-forge | (main, Apr 19 2024, 18:36:13) [GCC 12.3.0]
+[2024-08-19 09:44:19] root: INFO: >>>STAGE: configure
+[2024-08-19 09:44:19] root: INFO: Configuring run
+[2024-08-19 09:44:19] root: INFO: Total read length: 7249289
+[2024-08-19 09:44:19] root: INFO: Reads N50/N90: 11150 / 5790
+[2024-08-19 09:44:19] root: INFO: Minimum overlap set to 6000
+[2024-08-19 09:44:19] root: INFO: >>>STAGE: assembly
+[2024-08-19 09:44:19] root: INFO: Assembling disjointigs
+[2024-08-19 09:44:19] root: DEBUG: -----Begin assembly log------
+[2024-08-19 09:44:19] root: DEBUG: Running: flye-modules assemble --reads /tmp/tmpmmr8wbsp/job_working_directory/000/8/working/input_0.fastq.gz,/tmp/tmpmmr8wbsp/job_working_directory/000/8/working/input_1.fastq.gz,/tmp/tmpmmr8wbsp/job_working_directory/000/8/working/input_2.fastq.gz,/tmp/tmpmmr8wbsp/job_working_directory/000/8/working/input_3.fastq.gz,/tmp/tmpmmr8wbsp/job_working_directory/000/8/working/input_4.fastq.gz,/tmp/tmpmmr8wbsp/job_working_directory/000/8/working/input_5.fastq.gz,/tmp/tmpmmr8wbsp/job_working_directory/000/8/working/input_6.fastq.gz --out-asm /tmp/tmpmmr8wbsp/job_working_directory/000/8/working/out_dir/00-assembly/draft_assembly.fasta --config /usr/local/lib/python3.11/site-packages/flye/config/bin_cfg/asm_raw_reads.cfg --log /tmp/tmpmmr8wbsp/job_working_directory/000/8/working/out_dir/flye.log --threads 1 --min-ovlp 6000
+[2024-08-19 09:44:19] DEBUG: Build date: Jul 26 2024 16:36:15
+[2024-08-19 09:44:19] DEBUG: Total RAM: 31 Gb
+[2024-08-19 09:44:19] DEBUG: Available RAM: 21 Gb
+[2024-08-19 09:44:19] DEBUG: Total CPUs: 12
+[2024-08-19 09:44:19] DEBUG: Loading /usr/local/lib/python3.11/site-packages/flye/config/bin_cfg/asm_raw_reads.cfg
+[2024-08-19 09:44:19] DEBUG: Loading /usr/local/lib/python3.11/site-packages/flye/config/bin_cfg/asm_defaults.cfg
+[2024-08-19 09:44:19] DEBUG: 	big_genome_threshold=29000000
+[2024-08-19 09:44:19] DEBUG: 	meta_read_filter_kmer_freq=100
+[2024-08-19 09:44:19] DEBUG: 	chain_large_gap_penalty=2
+[2024-08-19 09:44:19] DEBUG: 	chain_small_gap_penalty=0.5
+[2024-08-19 09:44:19] DEBUG: 	chain_gap_jump_threshold=100
+[2024-08-19 09:44:19] DEBUG: 	max_jump_gap=500
+[2024-08-19 09:44:19] DEBUG: 	max_coverage_drop_rate=5
+[2024-08-19 09:44:19] DEBUG: 	max_extensions_drop_rate=5
+[2024-08-19 09:44:19] DEBUG: 	chimera_window=100
+[2024-08-19 09:44:19] DEBUG: 	chimera_overhang=1000
+[2024-08-19 09:44:19] DEBUG: 	min_reads_in_disjointig=4
+[2024-08-19 09:44:19] DEBUG: 	max_inner_reads=10
+[2024-08-19 09:44:19] DEBUG: 	max_inner_fraction=0.25
+[2024-08-19 09:44:19] DEBUG: 	aggressive_dup_filter=1
+[2024-08-19 09:44:19] DEBUG: 	max_separation=500
+[2024-08-19 09:44:19] DEBUG: 	unique_edge_length=50000
+[2024-08-19 09:44:19] DEBUG: 	min_repeat_res_support=0.51
+[2024-08-19 09:44:19] DEBUG: 	out_paths_ratio=5
+[2024-08-19 09:44:19] DEBUG: 	graph_cov_drop_rate=5
+[2024-08-19 09:44:19] DEBUG: 	coverage_estimate_window=100
+[2024-08-19 09:44:19] DEBUG: 	max_bubble_length=50000
+[2024-08-19 09:44:19] DEBUG: 	loop_coverage_rate=1.5
+[2024-08-19 09:44:19] DEBUG: 	repeat_edge_cov_mult=1.75
+[2024-08-19 09:44:19] DEBUG: 	weak_detach_rate=5
+[2024-08-19 09:44:19] DEBUG: 	tip_coverage_rate=2
+[2024-08-19 09:44:19] DEBUG: 	tip_length_rate=2
+[2024-08-19 09:44:19] DEBUG: 	output_gfa_before_rr=1
+[2024-08-19 09:44:19] DEBUG: 	remove_alt_edges=0
+[2024-08-19 09:44:19] DEBUG: 	low_cutoff_warning=1
+[2024-08-19 09:44:19] DEBUG: 	kmer_size=17
+[2024-08-19 09:44:19] DEBUG: 	use_minimizers=0
+[2024-08-19 09:44:19] DEBUG: 	reads_base_alignment=0
+[2024-08-19 09:44:19] DEBUG: 	meta_read_top_kmer_rate=0.40
+[2024-08-19 09:44:19] DEBUG: 	maximum_jump=1500
+[2024-08-19 09:44:19] DEBUG: 	maximum_overhang=1500
+[2024-08-19 09:44:19] DEBUG: 	repeat_kmer_rate=100
+[2024-08-19 09:44:19] DEBUG: 	assemble_ovlp_divergence=0.10
+[2024-08-19 09:44:19] DEBUG: 	assemble_divergence_relative=1
+[2024-08-19 09:44:19] DEBUG: 	repeat_graph_ovlp_divergence=0.08
+[2024-08-19 09:44:19] DEBUG: 	read_align_ovlp_divergence=0.25
+[2024-08-19 09:44:19] DEBUG: 	hpc_scoring_on=0
+[2024-08-19 09:44:19] DEBUG: 	add_unassembled_reads=0
+[2024-08-19 09:44:19] DEBUG: 	extend_contigs_with_repeats=0
+[2024-08-19 09:44:19] DEBUG: 	min_read_cov_cutoff=3
+[2024-08-19 09:44:19] DEBUG: 	short_tip_length=20000
+[2024-08-19 09:44:19] DEBUG: 	long_tip_length=100000
+[2024-08-19 09:44:19] DEBUG: Running with k-mer size: 17
+[2024-08-19 09:44:19] DEBUG: Running with minimum overlap 6000
+[2024-08-19 09:44:19] DEBUG: Metagenome mode: N
+[2024-08-19 09:44:19] DEBUG: Short mode: N
+[2024-08-19 09:44:19] INFO: Reading sequences
+[2024-08-19 09:44:19] DEBUG: Building positional index
+[2024-08-19 09:44:19] DEBUG: Total sequence: 6471580 bp
+[2024-08-19 09:44:21] INFO: Counting k-mers:
+[2024-08-19 09:44:22] DEBUG: Updating k-mer histogram
+[2024-08-19 09:44:52] DEBUG: Hash size: 29
+[2024-08-19 09:44:52] DEBUG: Total k-mers 5958598
+[2024-08-19 09:44:52] INFO: Filling index table (1/2)
+[2024-08-19 09:44:54] DEBUG: Mean k-mer frequency: 2.57396
+[2024-08-19 09:44:54] DEBUG: Repetitive k-mer frequency: 257
+[2024-08-19 09:44:54] DEBUG: Filtered 0 repetitive k-mers (0)
+[2024-08-19 09:44:54] INFO: Filling index table (2/2)
+[2024-08-19 09:44:56] DEBUG: Sorting k-mer index
+[2024-08-19 09:44:56] DEBUG: Selected k-mers: 319695
+[2024-08-19 09:44:56] DEBUG: Index size: 822885
+[2024-08-19 09:44:56] DEBUG: Mean k-mer index frequency: 2.57397
+[2024-08-19 09:44:56] DEBUG: Peak RAM usage: 8 Gb
+[2024-08-19 09:44:56] DEBUG: Estimating k-mer identity bias
+[2024-08-19 09:44:58] DEBUG: Initial divergence estimate : 0.237684
+[2024-08-19 09:44:58] DEBUG: Relative threshold: Y
+[2024-08-19 09:44:58] DEBUG: Max divergence threshold set to 0.337684
+[2024-08-19 09:44:58] INFO: Extending reads
+[2024-08-19 09:44:58] DEBUG: Estimating overlap coverage
+[2024-08-19 09:45:00] INFO: Overlap-based coverage: 10
+[2024-08-19 09:45:00] INFO: Median overlap divergence: 0.235584
+[2024-08-19 09:45:00] DEBUG: Sequence divergence distribution: 
 
     |                                              *                    |                                
     |                                              *                    |                                
@@ -116,7 +118,7 @@
 
     Q25 = 0.22, Q50 = 0.24, Q75 = 0.25
 
-[2021-11-22 18:14:08] DEBUG: Assembled disjointig 1
+[2024-08-19 09:45:00] DEBUG: Assembled disjointig 1
 	With 83 reads
 	Start read: +S1_395
 	At position: 40
@@ -128,8 +130,8 @@
 	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
+[2024-08-19 09:45:00] DEBUG: Inner: 1024 covered: 1014 total: 1152
+[2024-08-19 09:45:00] DEBUG: Assembled disjointig 2
 	With 6 reads
 	Start read: +S1_921
 	At position: 4
@@ -141,173 +143,178 @@
 	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
+[2024-08-19 09:45:00] DEBUG: Inner: 1040 covered: 1056 total: 1152
+[2024-08-19 09:45:00] INFO: Assembled 2 disjointigs
+[2024-08-19 09:45:00] INFO: Generating sequence
+[2024-08-19 09:45:00] DEBUG: Building positional index
+[2024-08-19 09:45:00] DEBUG: Total sequence: 470346 bp
+[2024-08-19 09:45:00] DEBUG: Mean k-mer frequency: 1.00134
+[2024-08-19 09:45:00] DEBUG: Repetitive k-mer frequency: 100
+[2024-08-19 09:45:00] DEBUG: Filtered 0 repetitive k-mers (0)
+[2024-08-19 09:45:00] DEBUG: Sorting k-mer index
+[2024-08-19 09:45:00] DEBUG: Selected k-mers: 469680
+[2024-08-19 09:45:00] DEBUG: K-mer index size: 470312
+[2024-08-19 09:45:00] DEBUG: Mean k-mer frequency: 1.00135
+[2024-08-19 09:45:00] DEBUG: Minimizer rate: 1.00007
+[2024-08-19 09:45:00] INFO: Filtering contained disjointigs
+[2024-08-19 09:45:00] DEBUG: Computing transitive closure for overlaps
+[2024-08-19 09:45:00] DEBUG: Found 0 overlaps
+[2024-08-19 09:45:00] DEBUG: Left 0 overlaps after filtering
+[2024-08-19 09:45:00] INFO: Contained seqs: 0
+[2024-08-19 09:45:00] DEBUG: Writing FASTA
+[2024-08-19 09:45:00] 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: 
+[2024-08-19 09:45:00] root: DEBUG: Disjointigs length: 470346, N50: 436173
+[2024-08-19 09:45:00] root: INFO: >>>STAGE: consensus
+[2024-08-19 09:45:00] root: INFO: Running Minimap2
+[2024-08-19 09:45:04] root: INFO: Computing consensus
+[2024-08-19 09:45:08] root: INFO: Alignment error rate: 0.196554
+[2024-08-19 09:45:08] root: INFO: >>>STAGE: repeat
+[2024-08-19 09:45:08] root: INFO: Building and resolving repeat graph
+[2024-08-19 09:45:08] root: DEBUG: -----Begin repeat analyser log------
+[2024-08-19 09:45:08] root: DEBUG: Running: flye-modules repeat --disjointigs /tmp/tmpmmr8wbsp/job_working_directory/000/8/working/out_dir/10-consensus/consensus.fasta --reads /tmp/tmpmmr8wbsp/job_working_directory/000/8/working/input_0.fastq.gz,/tmp/tmpmmr8wbsp/job_working_directory/000/8/working/input_1.fastq.gz,/tmp/tmpmmr8wbsp/job_working_directory/000/8/working/input_2.fastq.gz,/tmp/tmpmmr8wbsp/job_working_directory/000/8/working/input_3.fastq.gz,/tmp/tmpmmr8wbsp/job_working_directory/000/8/working/input_4.fastq.gz,/tmp/tmpmmr8wbsp/job_working_directory/000/8/working/input_5.fastq.gz,/tmp/tmpmmr8wbsp/job_working_directory/000/8/working/input_6.fastq.gz --out-dir /tmp/tmpmmr8wbsp/job_working_directory/000/8/working/out_dir/20-repeat --config /usr/local/lib/python3.11/site-packages/flye/config/bin_cfg/asm_raw_reads.cfg --log /tmp/tmpmmr8wbsp/job_working_directory/000/8/working/out_dir/flye.log --threads 1 --min-ovlp 6000
+[2024-08-19 09:45:08] DEBUG: Build date: Jul 26 2024 16:36:40
+[2024-08-19 09:45:08] DEBUG: Total RAM: 31 Gb
+[2024-08-19 09:45:08] DEBUG: Available RAM: 21 Gb
+[2024-08-19 09:45:08] DEBUG: Total CPUs: 12
+[2024-08-19 09:45:08] DEBUG: Loading /usr/local/lib/python3.11/site-packages/flye/config/bin_cfg/asm_raw_reads.cfg
+[2024-08-19 09:45:08] DEBUG: Loading /usr/local/lib/python3.11/site-packages/flye/config/bin_cfg/asm_defaults.cfg
+[2024-08-19 09:45:08] DEBUG: 	big_genome_threshold=29000000
+[2024-08-19 09:45:08] DEBUG: 	meta_read_filter_kmer_freq=100
+[2024-08-19 09:45:08] DEBUG: 	chain_large_gap_penalty=2
+[2024-08-19 09:45:08] DEBUG: 	chain_small_gap_penalty=0.5
+[2024-08-19 09:45:08] DEBUG: 	chain_gap_jump_threshold=100
+[2024-08-19 09:45:08] DEBUG: 	max_jump_gap=500
+[2024-08-19 09:45:08] DEBUG: 	max_coverage_drop_rate=5
+[2024-08-19 09:45:08] DEBUG: 	max_extensions_drop_rate=5
+[2024-08-19 09:45:08] DEBUG: 	chimera_window=100
+[2024-08-19 09:45:08] DEBUG: 	chimera_overhang=1000
+[2024-08-19 09:45:08] DEBUG: 	min_reads_in_disjointig=4
+[2024-08-19 09:45:08] DEBUG: 	max_inner_reads=10
+[2024-08-19 09:45:08] DEBUG: 	max_inner_fraction=0.25
+[2024-08-19 09:45:08] DEBUG: 	aggressive_dup_filter=1
+[2024-08-19 09:45:08] DEBUG: 	max_separation=500
+[2024-08-19 09:45:08] DEBUG: 	unique_edge_length=50000
+[2024-08-19 09:45:08] DEBUG: 	min_repeat_res_support=0.51
+[2024-08-19 09:45:08] DEBUG: 	out_paths_ratio=5
+[2024-08-19 09:45:08] DEBUG: 	graph_cov_drop_rate=5
+[2024-08-19 09:45:08] DEBUG: 	coverage_estimate_window=100
+[2024-08-19 09:45:08] DEBUG: 	max_bubble_length=50000
+[2024-08-19 09:45:08] DEBUG: 	loop_coverage_rate=1.5
+[2024-08-19 09:45:08] DEBUG: 	repeat_edge_cov_mult=1.75
+[2024-08-19 09:45:08] DEBUG: 	weak_detach_rate=5
+[2024-08-19 09:45:08] DEBUG: 	tip_coverage_rate=2
+[2024-08-19 09:45:08] DEBUG: 	tip_length_rate=2
+[2024-08-19 09:45:08] DEBUG: 	output_gfa_before_rr=1
+[2024-08-19 09:45:08] DEBUG: 	remove_alt_edges=0
+[2024-08-19 09:45:08] DEBUG: 	low_cutoff_warning=1
+[2024-08-19 09:45:08] DEBUG: 	kmer_size=17
+[2024-08-19 09:45:08] DEBUG: 	use_minimizers=0
+[2024-08-19 09:45:08] DEBUG: 	reads_base_alignment=0
+[2024-08-19 09:45:08] DEBUG: 	meta_read_top_kmer_rate=0.40
+[2024-08-19 09:45:08] DEBUG: 	maximum_jump=1500
+[2024-08-19 09:45:08] DEBUG: 	maximum_overhang=1500
+[2024-08-19 09:45:08] DEBUG: 	repeat_kmer_rate=100
+[2024-08-19 09:45:08] DEBUG: 	assemble_ovlp_divergence=0.10
+[2024-08-19 09:45:08] DEBUG: 	assemble_divergence_relative=1
+[2024-08-19 09:45:08] DEBUG: 	repeat_graph_ovlp_divergence=0.08
+[2024-08-19 09:45:08] DEBUG: 	read_align_ovlp_divergence=0.25
+[2024-08-19 09:45:08] DEBUG: 	hpc_scoring_on=0
+[2024-08-19 09:45:08] DEBUG: 	add_unassembled_reads=0
+[2024-08-19 09:45:08] DEBUG: 	extend_contigs_with_repeats=0
+[2024-08-19 09:45:08] DEBUG: 	min_read_cov_cutoff=3
+[2024-08-19 09:45:08] DEBUG: 	short_tip_length=20000
+[2024-08-19 09:45:08] DEBUG: 	long_tip_length=100000
+[2024-08-19 09:45:08] DEBUG: Running with k-mer size: 17
+[2024-08-19 09:45:08] DEBUG: Selected minimum overlap 6000
+[2024-08-19 09:45:08] DEBUG: Metagenome mode: N
+[2024-08-19 09:45:08] INFO: Parsing disjointigs
+[2024-08-19 09:45:08] DEBUG: Building positional index
+[2024-08-19 09:45:08] DEBUG: Total sequence: 452901 bp
+[2024-08-19 09:45:08] INFO: Building repeat graph
+[2024-08-19 09:45:08] DEBUG: Mean k-mer frequency: 1.03014
+[2024-08-19 09:45:08] DEBUG: Repetitive k-mer frequency: 103
+[2024-08-19 09:45:08] DEBUG: Filtered 0 repetitive k-mers (0)
+[2024-08-19 09:45:08] DEBUG: Sorting k-mer index
+[2024-08-19 09:45:08] DEBUG: Selected k-mers: 439615
+[2024-08-19 09:45:08] DEBUG: K-mer index size: 452867
+[2024-08-19 09:45:08] DEBUG: Mean k-mer frequency: 1.03014
+[2024-08-19 09:45:08] DEBUG: Minimizer rate: 1.00008
+[2024-08-19 09:45:10] DEBUG: Computing transitive closure for overlaps
+[2024-08-19 09:45:10] DEBUG: Found 10 overlaps
+[2024-08-19 09:45:10] DEBUG: Left 4 overlaps after filtering
+[2024-08-19 09:45:10] INFO: Median overlap divergence: 0.083035
+[2024-08-19 09:45:10] DEBUG: Sequence divergence distribution: 
 
-    |      *         |                                                                                   
-    |      *         |                                                                                   
-    |      *         |                                                                                   
-    |      *         |                                                                                   
-    |      *         |                                                                                   
-    |      *         |                                                                                   
-    |      *         |                                                                                   
-    |      *         |                                                                                   
-    |      *         |                                                                                   
-    |      *         |                                                                                   
-    |      *         |                                                                                   
-    |      *         |                                                                                   
-    |      *         |                                                                                   
-    |      *         |                                                                                   
-    |      *         |                                                                                   
-    |      *         |                                                                                   
-    |      *         |                                                                                   
-    |      *         |                                                                                   
-    |      *         |                                                                                   
-    |      *         |                                                                                   
+    |                *                                                                                   
+    |                *                                                                                   
+    |                *                                                                                   
+    |                *                                                                                   
+    |                *                                                                                   
+    |                *                                                                                   
+    |                *                                                                                   
+    |                *                                                                                   
+    |                *                                                                                   
+    |                *                                                                                   
+    |                *                                                                                   
+    |                *                                                                                   
+    |                *                                                                                   
+    |                *                                                                                   
+    |                *                                                                                   
+    |                *                                                                                   
+    |                *                                                                                   
+    |                *                                                                                   
+    |                *                                                                                   
+    |                *                                                                                   
     ----------------------------------------------------------------------------------------------------
     0%        5%        10%       15%       20%       25%       30%       35%       40%       45%       
 
-    Q25 = 0.034, Q50 = 0.034, Q75 = 0.034
+    Q25 = 0.083, Q50 = 0.083, Q75 = 0.083
 
-[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: 
+[2024-08-19 09:45:10] DEBUG: Computing gluepoints
+[2024-08-19 09:45:10] DEBUG: Added 0 gluepoint projections
+[2024-08-19 09:45:10] DEBUG: Created 14 gluepoints
+[2024-08-19 09:45:10] DEBUG: Artificial loops removed: 0 left, 0 right, 0 both
+[2024-08-19 09:45:10] DEBUG: Initializing edges
+[2024-08-19 09:45:10] DEBUG: Edges length checksum: 2641675703
+[2024-08-19 09:45:10] DEBUG: Filtered 0 singleton segments
+[2024-08-19 09:45:10] DEBUG: Removed 0 simple and 0 double chimeric junctions
+[2024-08-19 09:45:10] DEBUG: Collapsed 1 edges
+[2024-08-19 09:45:10] DEBUG: *	1	+disjointig_1	0	370783	370783	
+[2024-08-19 09:45:10] DEBUG: *	5	+disjointig_1	370783	419825	49042	
+[2024-08-19 09:45:10] DEBUG: *	-3	+disjointig_2	0	26527	26527	
+[2024-08-19 09:45:10] DEBUG: Total edges: 5
+[2024-08-19 09:45:10] INFO: Parsing reads
+[2024-08-19 09:45:10] DEBUG: Building positional index
+[2024-08-19 09:45:10] DEBUG: Total sequence: 7249289 bp
+[2024-08-19 09:45:10] DEBUG: Building positional index
+[2024-08-19 09:45:10] DEBUG: Total sequence: 446352 bp
+[2024-08-19 09:45:10] INFO: Aligning reads to the graph
+[2024-08-19 09:45:10] DEBUG: Mean k-mer frequency: 1.02577
+[2024-08-19 09:45:10] DEBUG: Repetitive k-mer frequency: 102
+[2024-08-19 09:45:10] DEBUG: Filtered 0 repetitive k-mers (0)
+[2024-08-19 09:45:10] DEBUG: Sorting k-mer index
+[2024-08-19 09:45:10] DEBUG: Selected k-mers: 435087
+[2024-08-19 09:45:10] DEBUG: K-mer index size: 446301
+[2024-08-19 09:45:10] DEBUG: Mean k-mer frequency: 1.02577
+[2024-08-19 09:45:10] DEBUG: Minimizer rate: 1.00011
+[2024-08-19 09:45:11] DEBUG: Total reads : 576
+[2024-08-19 09:45:11] DEBUG: Read with aligned parts : 566
+[2024-08-19 09:45:11] DEBUG: Aligned in one piece : 566
+[2024-08-19 09:45:11] INFO: Aligned read sequence: 6321543 / 6471580 (0.976816)
+[2024-08-19 09:45:11] INFO: Median overlap divergence: 0.12965
+[2024-08-19 09:45:11] DEBUG: Sequence divergence distribution: 
 
     |                        *                         |                                                 
     |                        **                        |                                                 
-    |                        **                        |                                                 
     |                       ***                        |                                                 
     |                       ***                        |                                                 
     |                       ***                        |                                                 
+    |                       *** *                      |                                                 
     |                       *****                      |                                                 
     |                       *****                      |                                                 
     |                       *****                      |                                                 
-    |                       *****                      |                                                 
+    |                       ******                     |                                                 
     |                       ******                     |                                                 
     |                       *******                    |                                                 
     |                       *******                    |                                                 
@@ -315,162 +322,185 @@
     |                      *********                   |                                                 
     |                      *********                   |                                                 
     |                      **********                  |                                                 
-    |                     ************                 |                                                 
-    |                     ***************              |                                                 
-    |                    ****************              |                                                 
+    |                     ************ *               |                                                 
+    |                     ************ *               |                                                 
+    |             *      ****************              |                                                 
     ----------------------------------------------------------------------------------------------------
     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
+[2024-08-19 09:45:11] INFO: Mean edge coverage: 13
+[2024-08-19 09:45:11] DEBUG: 1	len:370783	cov:15	mult:1.15385
+[2024-08-19 09:45:11] DEBUG: -1	len:370783	cov:15	mult:1.15385
+[2024-08-19 09:45:11] DEBUG: 3	len:26527	cov:7	mult:0.538462
+[2024-08-19 09:45:11] DEBUG: -3	len:26527	cov:7	mult:0.538462
+[2024-08-19 09:45:11] DEBUG: 5	len:49042	cov:12	mult:0.923077
+[2024-08-19 09:45:11] DEBUG: -5	len:49042	cov:12	mult:0.923077
+[2024-08-19 09:45:11] DEBUG: Unique coverage threshold 26
+[2024-08-19 09:45:11] INFO: Simplifying the graph
+[2024-08-19 09:45:11] DEBUG: Read coverage cutoff: 3
+[2024-08-19 09:45:11] DEBUG: [SIMPL] Removed 0 paths with low coverage
+[2024-08-19 09:45:11] DEBUG: [SIMPL] Masked 0 heterozygous loops
+[2024-08-19 09:45:11] DEBUG: [SIMPL] Masked 0 simple bubbles
+[2024-08-19 09:45:11] DEBUG: Finding repeats
+[2024-08-19 09:45:11] DEBUG: Read coverage cutoff: 3
+[2024-08-19 09:45:11] DEBUG: Repeat detection iteration 1
+[2024-08-19 09:45:11] DEBUG: Starting -5 aln:7
+[2024-08-19 09:45:11] DEBUG: 	    T -1	num:2	flank:9812	span:40
+[2024-08-19 09:45:11] DEBUG: 	    T 3	num:5	flank:5809	span:11
+[2024-08-19 09:45:11] DEBUG: Mult: 5	49042	12	 (1,0)
+[2024-08-19 09:45:11] DEBUG: Writing Dot
+[2024-08-19 09:45:11] DEBUG: Writing FASTA
+[2024-08-19 09:45:11] DEBUG: Writing Gfa
+[2024-08-19 09:45:11] DEBUG: [SIMPL] == Iteration 1 ==
+[2024-08-19 09:45:11] DEBUG: Splitting nodes
+[2024-08-19 09:45:11] DEBUG: [SIMPL] Split 0 nodes
+[2024-08-19 09:45:11] DEBUG: [SIMPL] Clipped 0 short and 0 long tips
+[2024-08-19 09:45:11] DEBUG: [SIMPL] Masked 0 heterozygous loops
+[2024-08-19 09:45:11] DEBUG: [SIMPL] Masked 0 simple bubbles
+[2024-08-19 09:45:11] DEBUG: Finding repeats
+[2024-08-19 09:45:11] DEBUG: Read coverage cutoff: 3
+[2024-08-19 09:45:11] DEBUG: Repeat detection iteration 1
+[2024-08-19 09:45:11] DEBUG: Starting -5 aln:7
+[2024-08-19 09:45:11] DEBUG: 	    T -1	num:2	flank:9812	span:40
+[2024-08-19 09:45:11] DEBUG: 	    T 3	num:5	flank:5809	span:11
+[2024-08-19 09:45:11] DEBUG: Mult: 5	49042	12	 (1,0)
+[2024-08-19 09:45:11] DEBUG: Total unique edges: 2
+[2024-08-19 09:45:11] DEBUG: [SIMPL] Resolved repeats: 0
+[2024-08-19 09:45:11] DEBUG: RR links: 0
+[2024-08-19 09:45:11] DEBUG: Unresolved: 0
+[2024-08-19 09:45:11] DEBUG: Removed 0 simple and 0 double chimeric junctions
+[2024-08-19 09:45:11] DEBUG: [SIMPL] Collapsed 0 haplotypes
+[2024-08-19 09:45:11] DEBUG: [SIMPL] Resolved 0 simple repeats
+[2024-08-19 09:45:11] DEBUG: Read coverage cutoff: 3
+[2024-08-19 09:45:11] DEBUG: [SIMPL] Removed 0 paths with low coverage
+[2024-08-19 09:45:11] DEBUG: Finding repeats
+[2024-08-19 09:45:11] DEBUG: Read coverage cutoff: 3
+[2024-08-19 09:45:11] DEBUG: Repeat detection iteration 1
+[2024-08-19 09:45:11] DEBUG: Starting -5 aln:7
+[2024-08-19 09:45:11] DEBUG: 	    T -1	num:2	flank:9812	span:40
+[2024-08-19 09:45:11] DEBUG: 	    T 3	num:5	flank:5809	span:11
+[2024-08-19 09:45:11] DEBUG: Mult: 5	49042	12	 (1,0)
+[2024-08-19 09:45:11] DEBUG: Writing Dot
+[2024-08-19 09:45:11] DEBUG: Writing FASTA
+[2024-08-19 09:45:11] 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
+[2024-08-19 09:45:11] root: INFO: >>>STAGE: contigger
+[2024-08-19 09:45:11] root: INFO: Generating contigs
+[2024-08-19 09:45:11] root: DEBUG: -----Begin contigger analyser log------
+[2024-08-19 09:45:11] root: DEBUG: Running: flye-modules contigger --graph-edges /tmp/tmpmmr8wbsp/job_working_directory/000/8/working/out_dir/20-repeat/repeat_graph_edges.fasta --reads /tmp/tmpmmr8wbsp/job_working_directory/000/8/working/input_0.fastq.gz,/tmp/tmpmmr8wbsp/job_working_directory/000/8/working/input_1.fastq.gz,/tmp/tmpmmr8wbsp/job_working_directory/000/8/working/input_2.fastq.gz,/tmp/tmpmmr8wbsp/job_working_directory/000/8/working/input_3.fastq.gz,/tmp/tmpmmr8wbsp/job_working_directory/000/8/working/input_4.fastq.gz,/tmp/tmpmmr8wbsp/job_working_directory/000/8/working/input_5.fastq.gz,/tmp/tmpmmr8wbsp/job_working_directory/000/8/working/input_6.fastq.gz --out-dir /tmp/tmpmmr8wbsp/job_working_directory/000/8/working/out_dir/30-contigger --config /usr/local/lib/python3.11/site-packages/flye/config/bin_cfg/asm_raw_reads.cfg --repeat-graph /tmp/tmpmmr8wbsp/job_working_directory/000/8/working/out_dir/20-repeat/repeat_graph_dump --graph-aln /tmp/tmpmmr8wbsp/job_working_directory/000/8/working/out_dir/20-repeat/read_alignment_dump --log /tmp/tmpmmr8wbsp/job_working_directory/000/8/working/out_dir/flye.log --threads 1 --min-ovlp 6000
+[2024-08-19 09:45:11] DEBUG: Build date: Jul 26 2024 16:37:08
+[2024-08-19 09:45:11] DEBUG: Total RAM: 31 Gb
+[2024-08-19 09:45:11] DEBUG: Available RAM: 21 Gb
+[2024-08-19 09:45:11] DEBUG: Total CPUs: 12
+[2024-08-19 09:45:11] DEBUG: Loading /usr/local/lib/python3.11/site-packages/flye/config/bin_cfg/asm_raw_reads.cfg
+[2024-08-19 09:45:11] DEBUG: Loading /usr/local/lib/python3.11/site-packages/flye/config/bin_cfg/asm_defaults.cfg
+[2024-08-19 09:45:11] DEBUG: 	big_genome_threshold=29000000
+[2024-08-19 09:45:11] DEBUG: 	meta_read_filter_kmer_freq=100
+[2024-08-19 09:45:11] DEBUG: 	chain_large_gap_penalty=2
+[2024-08-19 09:45:11] DEBUG: 	chain_small_gap_penalty=0.5
+[2024-08-19 09:45:11] DEBUG: 	chain_gap_jump_threshold=100
+[2024-08-19 09:45:11] DEBUG: 	max_jump_gap=500
+[2024-08-19 09:45:11] DEBUG: 	max_coverage_drop_rate=5
+[2024-08-19 09:45:11] DEBUG: 	max_extensions_drop_rate=5
+[2024-08-19 09:45:11] DEBUG: 	chimera_window=100
+[2024-08-19 09:45:11] DEBUG: 	chimera_overhang=1000
+[2024-08-19 09:45:11] DEBUG: 	min_reads_in_disjointig=4
+[2024-08-19 09:45:11] DEBUG: 	max_inner_reads=10
+[2024-08-19 09:45:11] DEBUG: 	max_inner_fraction=0.25
+[2024-08-19 09:45:11] DEBUG: 	aggressive_dup_filter=1
+[2024-08-19 09:45:11] DEBUG: 	max_separation=500
+[2024-08-19 09:45:11] DEBUG: 	unique_edge_length=50000
+[2024-08-19 09:45:11] DEBUG: 	min_repeat_res_support=0.51
+[2024-08-19 09:45:11] DEBUG: 	out_paths_ratio=5
+[2024-08-19 09:45:11] DEBUG: 	graph_cov_drop_rate=5
+[2024-08-19 09:45:11] DEBUG: 	coverage_estimate_window=100
+[2024-08-19 09:45:11] DEBUG: 	max_bubble_length=50000
+[2024-08-19 09:45:11] DEBUG: 	loop_coverage_rate=1.5
+[2024-08-19 09:45:11] DEBUG: 	repeat_edge_cov_mult=1.75
+[2024-08-19 09:45:11] DEBUG: 	weak_detach_rate=5
+[2024-08-19 09:45:11] DEBUG: 	tip_coverage_rate=2
+[2024-08-19 09:45:11] DEBUG: 	tip_length_rate=2
+[2024-08-19 09:45:11] DEBUG: 	output_gfa_before_rr=1
+[2024-08-19 09:45:11] DEBUG: 	remove_alt_edges=0
+[2024-08-19 09:45:11] DEBUG: 	low_cutoff_warning=1
+[2024-08-19 09:45:11] DEBUG: 	kmer_size=17
+[2024-08-19 09:45:11] DEBUG: 	use_minimizers=0
+[2024-08-19 09:45:11] DEBUG: 	reads_base_alignment=0
+[2024-08-19 09:45:11] DEBUG: 	meta_read_top_kmer_rate=0.40
+[2024-08-19 09:45:11] DEBUG: 	maximum_jump=1500
+[2024-08-19 09:45:11] DEBUG: 	maximum_overhang=1500
+[2024-08-19 09:45:11] DEBUG: 	repeat_kmer_rate=100
+[2024-08-19 09:45:11] DEBUG: 	assemble_ovlp_divergence=0.10
+[2024-08-19 09:45:11] DEBUG: 	assemble_divergence_relative=1
+[2024-08-19 09:45:11] DEBUG: 	repeat_graph_ovlp_divergence=0.08
+[2024-08-19 09:45:11] DEBUG: 	read_align_ovlp_divergence=0.25
+[2024-08-19 09:45:11] DEBUG: 	hpc_scoring_on=0
+[2024-08-19 09:45:11] DEBUG: 	add_unassembled_reads=0
+[2024-08-19 09:45:11] DEBUG: 	extend_contigs_with_repeats=0
+[2024-08-19 09:45:11] DEBUG: 	min_read_cov_cutoff=3
+[2024-08-19 09:45:11] DEBUG: 	short_tip_length=20000
+[2024-08-19 09:45:11] DEBUG: 	long_tip_length=100000
+[2024-08-19 09:45:11] DEBUG: Running with k-mer size: 17
+[2024-08-19 09:45:11] DEBUG: Selected minimum overlap 6000
+[2024-08-19 09:45:11] INFO: Reading sequences
+[2024-08-19 09:45:11] DEBUG: Building positional index
+[2024-08-19 09:45:11] DEBUG: Total sequence: 7249289 bp
+[2024-08-19 09:45:11] DEBUG: Flipped 0
+[2024-08-19 09:45:11] DEBUG: UPath 1: 1
+[2024-08-19 09:45:11] DEBUG: UPath 2: 3
+[2024-08-19 09:45:11] DEBUG: UPath 3: 5
+[2024-08-19 09:45:11] DEBUG: Final graph contains 3 egdes
+[2024-08-19 09:45:11] DEBUG: Extending contigs into repeats
+[2024-08-19 09:45:11] DEBUG: Covered 0 repetitive contigs
+[2024-08-19 09:45:11] INFO: Generated 3 contigs
+[2024-08-19 09:45:11] DEBUG: Writing FASTA
+[2024-08-19 09:45:11] DEBUG: Generating scaffold connections
+[2024-08-19 09:45:11] INFO: Added 0 scaffold connections
+[2024-08-19 09:45:11] DEBUG: Writing Dot
+[2024-08-19 09:45:11] DEBUG: Writing FASTA
+[2024-08-19 09:45:11] DEBUG: Writing Gfa
+[2024-08-19 09:45:11] 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:
+[2024-08-19 09:45:11] root: INFO: >>>STAGE: finalize
+[2024-08-19 09:45:11] root: DEBUG: ---Output dir contents:----
+[2024-08-19 09:45:11] root: DEBUG: out_dir/
+[2024-08-19 09:45:11] root: DEBUG:     705.0 B     assembly_graph.gv
+[2024-08-19 09:45:11] root: DEBUG:     464.0 K     assembly.fasta
+[2024-08-19 09:45:11] root: DEBUG:     92.0 B      params.json
+[2024-08-19 09:45:11] root: DEBUG:     30.0 K      flye.log
+[2024-08-19 09:45:11] root: DEBUG:     436.0 K     assembly_graph.gfa
+[2024-08-19 09:45:11] root: DEBUG:     30-contigger/
+[2024-08-19 09:45:11] root: DEBUG:         462.0 K     contigs.fasta
+[2024-08-19 09:45:11] root: DEBUG:         441.0 K     graph_final.fasta
+[2024-08-19 09:45:11] root: DEBUG:         182.0 B     contigs_stats.txt
+[2024-08-19 09:45:11] root: DEBUG:         436.0 K     graph_final.gfa
+[2024-08-19 09:45:11] root: DEBUG:         0.0 B       scaffolds_links.txt
+[2024-08-19 09:45:11] root: DEBUG:         705.0 B     graph_final.gv
+[2024-08-19 09:45:11] root: DEBUG:     20-repeat/
+[2024-08-19 09:45:11] root: DEBUG:         705.0 B     graph_after_rr.gv
+[2024-08-19 09:45:11] root: DEBUG:         441.0 K     repeat_graph_edges.fasta
+[2024-08-19 09:45:11] root: DEBUG:         441.0 K     graph_before_rr.fasta
+[2024-08-19 09:45:11] root: DEBUG:         705.0 B     graph_before_rr.gv
+[2024-08-19 09:45:11] root: DEBUG:         436.0 K     graph_before_rr.gfa
+[2024-08-19 09:45:11] root: DEBUG:         564.0 B     repeat_graph_dump
+[2024-08-19 09:45:11] root: DEBUG:         121.0 K     read_alignment_dump
+[2024-08-19 09:45:11] root: DEBUG:     10-consensus/
+[2024-08-19 09:45:11] root: DEBUG:         449.0 K     consensus.fasta
+[2024-08-19 09:45:11] root: DEBUG:         3.0 K       minimap.bam.bai
+[2024-08-19 09:45:11] root: DEBUG:         1.0 K       minimap.stderr
+[2024-08-19 09:45:11] root: DEBUG:     00-assembly/
+[2024-08-19 09:45:11] root: DEBUG:         465.0 K     draft_assembly.fasta
+[2024-08-19 09:45:11] root: DEBUG:         61.0 B      draft_assembly.fasta.fai
+[2024-08-19 09:45:11] root: DEBUG: --------------------------
+[2024-08-19 09:45:11] root: INFO: Assembly statistics:
 
-	Total length:	419576
-	Fragments:	1
-	Fragments N50:	419576
-	Largest frg:	419576
+	Total length:	467534
+	Fragments:	3
+	Fragments N50:	382469
+	Largest frg:	382469
 	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
+[2024-08-19 09:45:11] root: INFO: Final assembly: /tmp/tmpmmr8wbsp/job_working_directory/000/8/working/out_dir/assembly.fasta