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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
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12
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
1 [2024-08-19 09:44:19] root: INFO: Starting Flye 2.9.4-b1799
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
2 [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
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
3 [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]
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
4 [2024-08-19 09:44:19] root: INFO: >>>STAGE: configure
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
5 [2024-08-19 09:44:19] root: INFO: Configuring run
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
6 [2024-08-19 09:44:19] root: INFO: Total read length: 7249289
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
7 [2024-08-19 09:44:19] root: INFO: Reads N50/N90: 11150 / 5790
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
8 [2024-08-19 09:44:19] root: INFO: Minimum overlap set to 6000
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
9 [2024-08-19 09:44:19] root: INFO: >>>STAGE: assembly
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
10 [2024-08-19 09:44:19] root: INFO: Assembling disjointigs
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
11 [2024-08-19 09:44:19] root: DEBUG: -----Begin assembly log------
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
12 [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
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
13 [2024-08-19 09:44:19] DEBUG: Build date: Jul 26 2024 16:36:15
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
14 [2024-08-19 09:44:19] DEBUG: Total RAM: 31 Gb
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
15 [2024-08-19 09:44:19] DEBUG: Available RAM: 21 Gb
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
16 [2024-08-19 09:44:19] DEBUG: Total CPUs: 12
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
17 [2024-08-19 09:44:19] DEBUG: Loading /usr/local/lib/python3.11/site-packages/flye/config/bin_cfg/asm_raw_reads.cfg
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
18 [2024-08-19 09:44:19] DEBUG: Loading /usr/local/lib/python3.11/site-packages/flye/config/bin_cfg/asm_defaults.cfg
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
19 [2024-08-19 09:44:19] DEBUG: big_genome_threshold=29000000
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
20 [2024-08-19 09:44:19] DEBUG: meta_read_filter_kmer_freq=100
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
21 [2024-08-19 09:44:19] DEBUG: chain_large_gap_penalty=2
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
22 [2024-08-19 09:44:19] DEBUG: chain_small_gap_penalty=0.5
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
23 [2024-08-19 09:44:19] DEBUG: chain_gap_jump_threshold=100
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
24 [2024-08-19 09:44:19] DEBUG: max_jump_gap=500
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
25 [2024-08-19 09:44:19] DEBUG: max_coverage_drop_rate=5
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
26 [2024-08-19 09:44:19] DEBUG: max_extensions_drop_rate=5
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
27 [2024-08-19 09:44:19] DEBUG: chimera_window=100
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
28 [2024-08-19 09:44:19] DEBUG: chimera_overhang=1000
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
29 [2024-08-19 09:44:19] DEBUG: min_reads_in_disjointig=4
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
30 [2024-08-19 09:44:19] DEBUG: max_inner_reads=10
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
31 [2024-08-19 09:44:19] DEBUG: max_inner_fraction=0.25
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
32 [2024-08-19 09:44:19] DEBUG: aggressive_dup_filter=1
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
33 [2024-08-19 09:44:19] DEBUG: max_separation=500
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
34 [2024-08-19 09:44:19] DEBUG: unique_edge_length=50000
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
35 [2024-08-19 09:44:19] DEBUG: min_repeat_res_support=0.51
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
36 [2024-08-19 09:44:19] DEBUG: out_paths_ratio=5
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
37 [2024-08-19 09:44:19] DEBUG: graph_cov_drop_rate=5
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
38 [2024-08-19 09:44:19] DEBUG: coverage_estimate_window=100
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
39 [2024-08-19 09:44:19] DEBUG: max_bubble_length=50000
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
40 [2024-08-19 09:44:19] DEBUG: loop_coverage_rate=1.5
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
41 [2024-08-19 09:44:19] DEBUG: repeat_edge_cov_mult=1.75
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
42 [2024-08-19 09:44:19] DEBUG: weak_detach_rate=5
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
43 [2024-08-19 09:44:19] DEBUG: tip_coverage_rate=2
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
44 [2024-08-19 09:44:19] DEBUG: tip_length_rate=2
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
45 [2024-08-19 09:44:19] DEBUG: output_gfa_before_rr=1
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
46 [2024-08-19 09:44:19] DEBUG: remove_alt_edges=0
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
47 [2024-08-19 09:44:19] DEBUG: low_cutoff_warning=1
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
48 [2024-08-19 09:44:19] DEBUG: kmer_size=17
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
49 [2024-08-19 09:44:19] DEBUG: use_minimizers=0
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
50 [2024-08-19 09:44:19] DEBUG: reads_base_alignment=0
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
51 [2024-08-19 09:44:19] DEBUG: meta_read_top_kmer_rate=0.40
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
52 [2024-08-19 09:44:19] DEBUG: maximum_jump=1500
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
53 [2024-08-19 09:44:19] DEBUG: maximum_overhang=1500
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
54 [2024-08-19 09:44:19] DEBUG: repeat_kmer_rate=100
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
55 [2024-08-19 09:44:19] DEBUG: assemble_ovlp_divergence=0.10
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
56 [2024-08-19 09:44:19] DEBUG: assemble_divergence_relative=1
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
57 [2024-08-19 09:44:19] DEBUG: repeat_graph_ovlp_divergence=0.08
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
58 [2024-08-19 09:44:19] DEBUG: read_align_ovlp_divergence=0.25
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
59 [2024-08-19 09:44:19] DEBUG: hpc_scoring_on=0
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
60 [2024-08-19 09:44:19] DEBUG: add_unassembled_reads=0
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
61 [2024-08-19 09:44:19] DEBUG: extend_contigs_with_repeats=0
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
62 [2024-08-19 09:44:19] DEBUG: min_read_cov_cutoff=3
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
63 [2024-08-19 09:44:19] DEBUG: short_tip_length=20000
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
64 [2024-08-19 09:44:19] DEBUG: long_tip_length=100000
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
65 [2024-08-19 09:44:19] DEBUG: Running with k-mer size: 17
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
66 [2024-08-19 09:44:19] DEBUG: Running with minimum overlap 6000
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
67 [2024-08-19 09:44:19] DEBUG: Metagenome mode: N
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
68 [2024-08-19 09:44:19] DEBUG: Short mode: N
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
69 [2024-08-19 09:44:19] INFO: Reading sequences
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
70 [2024-08-19 09:44:19] DEBUG: Building positional index
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
71 [2024-08-19 09:44:19] DEBUG: Total sequence: 6471580 bp
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
72 [2024-08-19 09:44:21] INFO: Counting k-mers:
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
73 [2024-08-19 09:44:22] DEBUG: Updating k-mer histogram
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
74 [2024-08-19 09:44:52] DEBUG: Hash size: 29
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
75 [2024-08-19 09:44:52] DEBUG: Total k-mers 5958598
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
76 [2024-08-19 09:44:52] INFO: Filling index table (1/2)
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
77 [2024-08-19 09:44:54] DEBUG: Mean k-mer frequency: 2.57396
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
78 [2024-08-19 09:44:54] DEBUG: Repetitive k-mer frequency: 257
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
79 [2024-08-19 09:44:54] DEBUG: Filtered 0 repetitive k-mers (0)
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
80 [2024-08-19 09:44:54] INFO: Filling index table (2/2)
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
81 [2024-08-19 09:44:56] DEBUG: Sorting k-mer index
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
82 [2024-08-19 09:44:56] DEBUG: Selected k-mers: 319695
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
83 [2024-08-19 09:44:56] DEBUG: Index size: 822885
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
84 [2024-08-19 09:44:56] DEBUG: Mean k-mer index frequency: 2.57397
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
85 [2024-08-19 09:44:56] DEBUG: Peak RAM usage: 8 Gb
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
86 [2024-08-19 09:44:56] DEBUG: Estimating k-mer identity bias
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
87 [2024-08-19 09:44:58] DEBUG: Initial divergence estimate : 0.237684
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
88 [2024-08-19 09:44:58] DEBUG: Relative threshold: Y
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
89 [2024-08-19 09:44:58] DEBUG: Max divergence threshold set to 0.337684
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
90 [2024-08-19 09:44:58] INFO: Extending reads
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
91 [2024-08-19 09:44:58] DEBUG: Estimating overlap coverage
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
92 [2024-08-19 09:45:00] INFO: Overlap-based coverage: 10
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
93 [2024-08-19 09:45:00] INFO: Median overlap divergence: 0.235584
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
94 [2024-08-19 09:45:00] DEBUG: Sequence divergence distribution:
8
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents:
diff changeset
95
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents:
diff changeset
96 | * |
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents:
diff changeset
97 | * |
9
276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 8
diff changeset
98 | *** |
8
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents:
diff changeset
99 | * *** |
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents:
diff changeset
100 | ****** |
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents:
diff changeset
101 | ******* |
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents:
diff changeset
102 | ******* |
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents:
diff changeset
103 | ******** |
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents:
diff changeset
104 | ******** |
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents:
diff changeset
105 | ********* |
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents:
diff changeset
106 | ********* |
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents:
diff changeset
107 | ********* |
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents:
diff changeset
108 | ********** |
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents:
diff changeset
109 | ************ |
9
276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 8
diff changeset
110 | ************ |
8
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents:
diff changeset
111 | ************** |
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents:
diff changeset
112 | ************** |
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents:
diff changeset
113 | **************** |
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents:
diff changeset
114 | * ***************** * |
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents:
diff changeset
115 | * ** ************************ | * *
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents:
diff changeset
116 ----------------------------------------------------------------------------------------------------
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents:
diff changeset
117 0% 5% 10% 15% 20% 25% 30% 35% 40% 45%
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents:
diff changeset
118
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents:
diff changeset
119 Q25 = 0.22, Q50 = 0.24, Q75 = 0.25
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents:
diff changeset
120
12
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
121 [2024-08-19 09:45:00] DEBUG: Assembled disjointig 1
9
276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 8
diff changeset
122 With 83 reads
276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 8
diff changeset
123 Start read: +S1_395
276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 8
diff changeset
124 At position: 40
8
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents:
diff changeset
125 leftTip: 1 rightTip: 1
9
276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 8
diff changeset
126 Suspicious: 5
276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 8
diff changeset
127 Short ext: 3
8
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents:
diff changeset
128 Mean extensions: 9
9
276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 8
diff changeset
129 Avg overlap len: 10043
276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 8
diff changeset
130 Min overlap len: 4225
276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 8
diff changeset
131 Inner reads: 0
276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 8
diff changeset
132 Length: 434635
12
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
133 [2024-08-19 09:45:00] DEBUG: Inner: 1024 covered: 1014 total: 1152
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
134 [2024-08-19 09:45:00] DEBUG: Assembled disjointig 2
9
276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 8
diff changeset
135 With 6 reads
276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 8
diff changeset
136 Start read: +S1_921
276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 8
diff changeset
137 At position: 4
276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 8
diff changeset
138 leftTip: 0 rightTip: 0
276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 8
diff changeset
139 Suspicious: 0
276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 8
diff changeset
140 Short ext: 0
276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 8
diff changeset
141 Mean extensions: 4
276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 8
diff changeset
142 Avg overlap len: 8689
276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 8
diff changeset
143 Min overlap len: 7703
8
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents:
diff changeset
144 Inner reads: 0
9
276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 8
diff changeset
145 Length: 34343
12
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
146 [2024-08-19 09:45:00] DEBUG: Inner: 1040 covered: 1056 total: 1152
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
147 [2024-08-19 09:45:00] INFO: Assembled 2 disjointigs
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
148 [2024-08-19 09:45:00] INFO: Generating sequence
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
149 [2024-08-19 09:45:00] DEBUG: Building positional index
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
150 [2024-08-19 09:45:00] DEBUG: Total sequence: 470346 bp
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
151 [2024-08-19 09:45:00] DEBUG: Mean k-mer frequency: 1.00134
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
152 [2024-08-19 09:45:00] DEBUG: Repetitive k-mer frequency: 100
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
153 [2024-08-19 09:45:00] DEBUG: Filtered 0 repetitive k-mers (0)
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
154 [2024-08-19 09:45:00] DEBUG: Sorting k-mer index
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
155 [2024-08-19 09:45:00] DEBUG: Selected k-mers: 469680
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
156 [2024-08-19 09:45:00] DEBUG: K-mer index size: 470312
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
157 [2024-08-19 09:45:00] DEBUG: Mean k-mer frequency: 1.00135
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
158 [2024-08-19 09:45:00] DEBUG: Minimizer rate: 1.00007
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
159 [2024-08-19 09:45:00] INFO: Filtering contained disjointigs
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
160 [2024-08-19 09:45:00] DEBUG: Computing transitive closure for overlaps
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
161 [2024-08-19 09:45:00] DEBUG: Found 0 overlaps
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
162 [2024-08-19 09:45:00] DEBUG: Left 0 overlaps after filtering
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
163 [2024-08-19 09:45:00] INFO: Contained seqs: 0
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
164 [2024-08-19 09:45:00] DEBUG: Writing FASTA
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
165 [2024-08-19 09:45:00] DEBUG: Peak RAM usage: 8 Gb
8
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents:
diff changeset
166 -----------End assembly log------------
12
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
167 [2024-08-19 09:45:00] root: DEBUG: Disjointigs length: 470346, N50: 436173
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
168 [2024-08-19 09:45:00] root: INFO: >>>STAGE: consensus
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
169 [2024-08-19 09:45:00] root: INFO: Running Minimap2
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
170 [2024-08-19 09:45:04] root: INFO: Computing consensus
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
171 [2024-08-19 09:45:08] root: INFO: Alignment error rate: 0.196554
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
172 [2024-08-19 09:45:08] root: INFO: >>>STAGE: repeat
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
173 [2024-08-19 09:45:08] root: INFO: Building and resolving repeat graph
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
174 [2024-08-19 09:45:08] root: DEBUG: -----Begin repeat analyser log------
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
175 [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
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
176 [2024-08-19 09:45:08] DEBUG: Build date: Jul 26 2024 16:36:40
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
177 [2024-08-19 09:45:08] DEBUG: Total RAM: 31 Gb
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
178 [2024-08-19 09:45:08] DEBUG: Available RAM: 21 Gb
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
179 [2024-08-19 09:45:08] DEBUG: Total CPUs: 12
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
180 [2024-08-19 09:45:08] DEBUG: Loading /usr/local/lib/python3.11/site-packages/flye/config/bin_cfg/asm_raw_reads.cfg
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
181 [2024-08-19 09:45:08] DEBUG: Loading /usr/local/lib/python3.11/site-packages/flye/config/bin_cfg/asm_defaults.cfg
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
182 [2024-08-19 09:45:08] DEBUG: big_genome_threshold=29000000
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
183 [2024-08-19 09:45:08] DEBUG: meta_read_filter_kmer_freq=100
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
184 [2024-08-19 09:45:08] DEBUG: chain_large_gap_penalty=2
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
185 [2024-08-19 09:45:08] DEBUG: chain_small_gap_penalty=0.5
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
186 [2024-08-19 09:45:08] DEBUG: chain_gap_jump_threshold=100
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
187 [2024-08-19 09:45:08] DEBUG: max_jump_gap=500
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
188 [2024-08-19 09:45:08] DEBUG: max_coverage_drop_rate=5
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
189 [2024-08-19 09:45:08] DEBUG: max_extensions_drop_rate=5
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
190 [2024-08-19 09:45:08] DEBUG: chimera_window=100
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
191 [2024-08-19 09:45:08] DEBUG: chimera_overhang=1000
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
192 [2024-08-19 09:45:08] DEBUG: min_reads_in_disjointig=4
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
193 [2024-08-19 09:45:08] DEBUG: max_inner_reads=10
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
194 [2024-08-19 09:45:08] DEBUG: max_inner_fraction=0.25
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
195 [2024-08-19 09:45:08] DEBUG: aggressive_dup_filter=1
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
196 [2024-08-19 09:45:08] DEBUG: max_separation=500
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
197 [2024-08-19 09:45:08] DEBUG: unique_edge_length=50000
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
198 [2024-08-19 09:45:08] DEBUG: min_repeat_res_support=0.51
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
199 [2024-08-19 09:45:08] DEBUG: out_paths_ratio=5
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
200 [2024-08-19 09:45:08] DEBUG: graph_cov_drop_rate=5
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
201 [2024-08-19 09:45:08] DEBUG: coverage_estimate_window=100
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
202 [2024-08-19 09:45:08] DEBUG: max_bubble_length=50000
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
203 [2024-08-19 09:45:08] DEBUG: loop_coverage_rate=1.5
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
204 [2024-08-19 09:45:08] DEBUG: repeat_edge_cov_mult=1.75
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
205 [2024-08-19 09:45:08] DEBUG: weak_detach_rate=5
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
206 [2024-08-19 09:45:08] DEBUG: tip_coverage_rate=2
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
207 [2024-08-19 09:45:08] DEBUG: tip_length_rate=2
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
208 [2024-08-19 09:45:08] DEBUG: output_gfa_before_rr=1
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
209 [2024-08-19 09:45:08] DEBUG: remove_alt_edges=0
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
210 [2024-08-19 09:45:08] DEBUG: low_cutoff_warning=1
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
211 [2024-08-19 09:45:08] DEBUG: kmer_size=17
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
212 [2024-08-19 09:45:08] DEBUG: use_minimizers=0
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
213 [2024-08-19 09:45:08] DEBUG: reads_base_alignment=0
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
214 [2024-08-19 09:45:08] DEBUG: meta_read_top_kmer_rate=0.40
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
215 [2024-08-19 09:45:08] DEBUG: maximum_jump=1500
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
216 [2024-08-19 09:45:08] DEBUG: maximum_overhang=1500
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
217 [2024-08-19 09:45:08] DEBUG: repeat_kmer_rate=100
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
218 [2024-08-19 09:45:08] DEBUG: assemble_ovlp_divergence=0.10
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
219 [2024-08-19 09:45:08] DEBUG: assemble_divergence_relative=1
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
220 [2024-08-19 09:45:08] DEBUG: repeat_graph_ovlp_divergence=0.08
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
221 [2024-08-19 09:45:08] DEBUG: read_align_ovlp_divergence=0.25
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
222 [2024-08-19 09:45:08] DEBUG: hpc_scoring_on=0
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
223 [2024-08-19 09:45:08] DEBUG: add_unassembled_reads=0
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
224 [2024-08-19 09:45:08] DEBUG: extend_contigs_with_repeats=0
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
225 [2024-08-19 09:45:08] DEBUG: min_read_cov_cutoff=3
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
226 [2024-08-19 09:45:08] DEBUG: short_tip_length=20000
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
227 [2024-08-19 09:45:08] DEBUG: long_tip_length=100000
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
228 [2024-08-19 09:45:08] DEBUG: Running with k-mer size: 17
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
229 [2024-08-19 09:45:08] DEBUG: Selected minimum overlap 6000
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
230 [2024-08-19 09:45:08] DEBUG: Metagenome mode: N
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
231 [2024-08-19 09:45:08] INFO: Parsing disjointigs
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
232 [2024-08-19 09:45:08] DEBUG: Building positional index
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
233 [2024-08-19 09:45:08] DEBUG: Total sequence: 452901 bp
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
234 [2024-08-19 09:45:08] INFO: Building repeat graph
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
235 [2024-08-19 09:45:08] DEBUG: Mean k-mer frequency: 1.03014
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
236 [2024-08-19 09:45:08] DEBUG: Repetitive k-mer frequency: 103
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
237 [2024-08-19 09:45:08] DEBUG: Filtered 0 repetitive k-mers (0)
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
238 [2024-08-19 09:45:08] DEBUG: Sorting k-mer index
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
239 [2024-08-19 09:45:08] DEBUG: Selected k-mers: 439615
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
240 [2024-08-19 09:45:08] DEBUG: K-mer index size: 452867
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
241 [2024-08-19 09:45:08] DEBUG: Mean k-mer frequency: 1.03014
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
242 [2024-08-19 09:45:08] DEBUG: Minimizer rate: 1.00008
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
243 [2024-08-19 09:45:10] DEBUG: Computing transitive closure for overlaps
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
244 [2024-08-19 09:45:10] DEBUG: Found 10 overlaps
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
245 [2024-08-19 09:45:10] DEBUG: Left 4 overlaps after filtering
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
246 [2024-08-19 09:45:10] INFO: Median overlap divergence: 0.083035
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
247 [2024-08-19 09:45:10] DEBUG: Sequence divergence distribution:
8
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents:
diff changeset
248
12
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
249 | *
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
250 | *
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
251 | *
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
252 | *
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
253 | *
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
254 | *
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
255 | *
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
256 | *
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
257 | *
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
258 | *
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
259 | *
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
260 | *
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
261 | *
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
262 | *
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
263 | *
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
264 | *
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
265 | *
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
266 | *
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
267 | *
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
268 | *
8
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents:
diff changeset
269 ----------------------------------------------------------------------------------------------------
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents:
diff changeset
270 0% 5% 10% 15% 20% 25% 30% 35% 40% 45%
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents:
diff changeset
271
12
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
272 Q25 = 0.083, Q50 = 0.083, Q75 = 0.083
8
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents:
diff changeset
273
12
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
274 [2024-08-19 09:45:10] DEBUG: Computing gluepoints
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
275 [2024-08-19 09:45:10] DEBUG: Added 0 gluepoint projections
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
276 [2024-08-19 09:45:10] DEBUG: Created 14 gluepoints
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
277 [2024-08-19 09:45:10] DEBUG: Artificial loops removed: 0 left, 0 right, 0 both
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
278 [2024-08-19 09:45:10] DEBUG: Initializing edges
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
279 [2024-08-19 09:45:10] DEBUG: Edges length checksum: 2641675703
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
280 [2024-08-19 09:45:10] DEBUG: Filtered 0 singleton segments
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
281 [2024-08-19 09:45:10] DEBUG: Removed 0 simple and 0 double chimeric junctions
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
282 [2024-08-19 09:45:10] DEBUG: Collapsed 1 edges
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
283 [2024-08-19 09:45:10] DEBUG: * 1 +disjointig_1 0 370783 370783
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
284 [2024-08-19 09:45:10] DEBUG: * 5 +disjointig_1 370783 419825 49042
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
285 [2024-08-19 09:45:10] DEBUG: * -3 +disjointig_2 0 26527 26527
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
286 [2024-08-19 09:45:10] DEBUG: Total edges: 5
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
287 [2024-08-19 09:45:10] INFO: Parsing reads
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
288 [2024-08-19 09:45:10] DEBUG: Building positional index
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
289 [2024-08-19 09:45:10] DEBUG: Total sequence: 7249289 bp
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
290 [2024-08-19 09:45:10] DEBUG: Building positional index
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
291 [2024-08-19 09:45:10] DEBUG: Total sequence: 446352 bp
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
292 [2024-08-19 09:45:10] INFO: Aligning reads to the graph
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
293 [2024-08-19 09:45:10] DEBUG: Mean k-mer frequency: 1.02577
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
294 [2024-08-19 09:45:10] DEBUG: Repetitive k-mer frequency: 102
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
295 [2024-08-19 09:45:10] DEBUG: Filtered 0 repetitive k-mers (0)
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
296 [2024-08-19 09:45:10] DEBUG: Sorting k-mer index
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
297 [2024-08-19 09:45:10] DEBUG: Selected k-mers: 435087
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
298 [2024-08-19 09:45:10] DEBUG: K-mer index size: 446301
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
299 [2024-08-19 09:45:10] DEBUG: Mean k-mer frequency: 1.02577
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
300 [2024-08-19 09:45:10] DEBUG: Minimizer rate: 1.00011
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
301 [2024-08-19 09:45:11] DEBUG: Total reads : 576
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
302 [2024-08-19 09:45:11] DEBUG: Read with aligned parts : 566
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
303 [2024-08-19 09:45:11] DEBUG: Aligned in one piece : 566
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
304 [2024-08-19 09:45:11] INFO: Aligned read sequence: 6321543 / 6471580 (0.976816)
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
305 [2024-08-19 09:45:11] INFO: Median overlap divergence: 0.12965
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
306 [2024-08-19 09:45:11] DEBUG: Sequence divergence distribution:
8
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents:
diff changeset
307
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents:
diff changeset
308 | * |
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents:
diff changeset
309 | ** |
9
276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 8
diff changeset
310 | *** |
276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 8
diff changeset
311 | *** |
8
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents:
diff changeset
312 | *** |
12
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
313 | *** * |
9
276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 8
diff changeset
314 | ***** |
276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 8
diff changeset
315 | ***** |
8
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents:
diff changeset
316 | ***** |
12
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
317 | ****** |
8
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents:
diff changeset
318 | ****** |
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents:
diff changeset
319 | ******* |
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents:
diff changeset
320 | ******* |
9
276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 8
diff changeset
321 | ******** |
8
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents:
diff changeset
322 | ********* |
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents:
diff changeset
323 | ********* |
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents:
diff changeset
324 | ********** |
12
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
325 | ************ * |
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
326 | ************ * |
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
327 | * **************** |
8
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents:
diff changeset
328 ----------------------------------------------------------------------------------------------------
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents:
diff changeset
329 0% 5% 10% 15% 20% 25% 30% 35% 40% 45%
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents:
diff changeset
330
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents:
diff changeset
331 Q25 = 0.12, Q50 = 0.13, Q75 = 0.14
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents:
diff changeset
332
12
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
333 [2024-08-19 09:45:11] INFO: Mean edge coverage: 13
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
334 [2024-08-19 09:45:11] DEBUG: 1 len:370783 cov:15 mult:1.15385
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
335 [2024-08-19 09:45:11] DEBUG: -1 len:370783 cov:15 mult:1.15385
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
336 [2024-08-19 09:45:11] DEBUG: 3 len:26527 cov:7 mult:0.538462
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
337 [2024-08-19 09:45:11] DEBUG: -3 len:26527 cov:7 mult:0.538462
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
338 [2024-08-19 09:45:11] DEBUG: 5 len:49042 cov:12 mult:0.923077
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
339 [2024-08-19 09:45:11] DEBUG: -5 len:49042 cov:12 mult:0.923077
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
340 [2024-08-19 09:45:11] DEBUG: Unique coverage threshold 26
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
341 [2024-08-19 09:45:11] INFO: Simplifying the graph
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
342 [2024-08-19 09:45:11] DEBUG: Read coverage cutoff: 3
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
343 [2024-08-19 09:45:11] DEBUG: [SIMPL] Removed 0 paths with low coverage
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
344 [2024-08-19 09:45:11] DEBUG: [SIMPL] Masked 0 heterozygous loops
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
345 [2024-08-19 09:45:11] DEBUG: [SIMPL] Masked 0 simple bubbles
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
346 [2024-08-19 09:45:11] DEBUG: Finding repeats
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
347 [2024-08-19 09:45:11] DEBUG: Read coverage cutoff: 3
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
348 [2024-08-19 09:45:11] DEBUG: Repeat detection iteration 1
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
349 [2024-08-19 09:45:11] DEBUG: Starting -5 aln:7
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
350 [2024-08-19 09:45:11] DEBUG: T -1 num:2 flank:9812 span:40
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
351 [2024-08-19 09:45:11] DEBUG: T 3 num:5 flank:5809 span:11
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
352 [2024-08-19 09:45:11] DEBUG: Mult: 5 49042 12 (1,0)
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
353 [2024-08-19 09:45:11] DEBUG: Writing Dot
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
354 [2024-08-19 09:45:11] DEBUG: Writing FASTA
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
355 [2024-08-19 09:45:11] DEBUG: Writing Gfa
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
356 [2024-08-19 09:45:11] DEBUG: [SIMPL] == Iteration 1 ==
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
357 [2024-08-19 09:45:11] DEBUG: Splitting nodes
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
358 [2024-08-19 09:45:11] DEBUG: [SIMPL] Split 0 nodes
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
359 [2024-08-19 09:45:11] DEBUG: [SIMPL] Clipped 0 short and 0 long tips
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
360 [2024-08-19 09:45:11] DEBUG: [SIMPL] Masked 0 heterozygous loops
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
361 [2024-08-19 09:45:11] DEBUG: [SIMPL] Masked 0 simple bubbles
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
362 [2024-08-19 09:45:11] DEBUG: Finding repeats
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
363 [2024-08-19 09:45:11] DEBUG: Read coverage cutoff: 3
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
364 [2024-08-19 09:45:11] DEBUG: Repeat detection iteration 1
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
365 [2024-08-19 09:45:11] DEBUG: Starting -5 aln:7
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
366 [2024-08-19 09:45:11] DEBUG: T -1 num:2 flank:9812 span:40
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
367 [2024-08-19 09:45:11] DEBUG: T 3 num:5 flank:5809 span:11
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
368 [2024-08-19 09:45:11] DEBUG: Mult: 5 49042 12 (1,0)
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
369 [2024-08-19 09:45:11] DEBUG: Total unique edges: 2
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
370 [2024-08-19 09:45:11] DEBUG: [SIMPL] Resolved repeats: 0
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
371 [2024-08-19 09:45:11] DEBUG: RR links: 0
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
372 [2024-08-19 09:45:11] DEBUG: Unresolved: 0
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
373 [2024-08-19 09:45:11] DEBUG: Removed 0 simple and 0 double chimeric junctions
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
374 [2024-08-19 09:45:11] DEBUG: [SIMPL] Collapsed 0 haplotypes
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
375 [2024-08-19 09:45:11] DEBUG: [SIMPL] Resolved 0 simple repeats
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
376 [2024-08-19 09:45:11] DEBUG: Read coverage cutoff: 3
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
377 [2024-08-19 09:45:11] DEBUG: [SIMPL] Removed 0 paths with low coverage
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
378 [2024-08-19 09:45:11] DEBUG: Finding repeats
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
379 [2024-08-19 09:45:11] DEBUG: Read coverage cutoff: 3
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
380 [2024-08-19 09:45:11] DEBUG: Repeat detection iteration 1
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
381 [2024-08-19 09:45:11] DEBUG: Starting -5 aln:7
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
382 [2024-08-19 09:45:11] DEBUG: T -1 num:2 flank:9812 span:40
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
383 [2024-08-19 09:45:11] DEBUG: T 3 num:5 flank:5809 span:11
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
384 [2024-08-19 09:45:11] DEBUG: Mult: 5 49042 12 (1,0)
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
385 [2024-08-19 09:45:11] DEBUG: Writing Dot
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
386 [2024-08-19 09:45:11] DEBUG: Writing FASTA
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
387 [2024-08-19 09:45:11] DEBUG: Peak RAM usage: 0 Gb
8
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents:
diff changeset
388 -----------End assembly log------------
12
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
389 [2024-08-19 09:45:11] root: INFO: >>>STAGE: contigger
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
390 [2024-08-19 09:45:11] root: INFO: Generating contigs
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
391 [2024-08-19 09:45:11] root: DEBUG: -----Begin contigger analyser log------
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
392 [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
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
393 [2024-08-19 09:45:11] DEBUG: Build date: Jul 26 2024 16:37:08
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
394 [2024-08-19 09:45:11] DEBUG: Total RAM: 31 Gb
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
395 [2024-08-19 09:45:11] DEBUG: Available RAM: 21 Gb
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
396 [2024-08-19 09:45:11] DEBUG: Total CPUs: 12
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
397 [2024-08-19 09:45:11] DEBUG: Loading /usr/local/lib/python3.11/site-packages/flye/config/bin_cfg/asm_raw_reads.cfg
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
398 [2024-08-19 09:45:11] DEBUG: Loading /usr/local/lib/python3.11/site-packages/flye/config/bin_cfg/asm_defaults.cfg
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
399 [2024-08-19 09:45:11] DEBUG: big_genome_threshold=29000000
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
400 [2024-08-19 09:45:11] DEBUG: meta_read_filter_kmer_freq=100
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
401 [2024-08-19 09:45:11] DEBUG: chain_large_gap_penalty=2
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
402 [2024-08-19 09:45:11] DEBUG: chain_small_gap_penalty=0.5
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
403 [2024-08-19 09:45:11] DEBUG: chain_gap_jump_threshold=100
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
404 [2024-08-19 09:45:11] DEBUG: max_jump_gap=500
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
405 [2024-08-19 09:45:11] DEBUG: max_coverage_drop_rate=5
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
406 [2024-08-19 09:45:11] DEBUG: max_extensions_drop_rate=5
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
407 [2024-08-19 09:45:11] DEBUG: chimera_window=100
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
408 [2024-08-19 09:45:11] DEBUG: chimera_overhang=1000
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
409 [2024-08-19 09:45:11] DEBUG: min_reads_in_disjointig=4
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
410 [2024-08-19 09:45:11] DEBUG: max_inner_reads=10
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
411 [2024-08-19 09:45:11] DEBUG: max_inner_fraction=0.25
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
412 [2024-08-19 09:45:11] DEBUG: aggressive_dup_filter=1
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
413 [2024-08-19 09:45:11] DEBUG: max_separation=500
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
414 [2024-08-19 09:45:11] DEBUG: unique_edge_length=50000
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
415 [2024-08-19 09:45:11] DEBUG: min_repeat_res_support=0.51
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
416 [2024-08-19 09:45:11] DEBUG: out_paths_ratio=5
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
417 [2024-08-19 09:45:11] DEBUG: graph_cov_drop_rate=5
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
418 [2024-08-19 09:45:11] DEBUG: coverage_estimate_window=100
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
419 [2024-08-19 09:45:11] DEBUG: max_bubble_length=50000
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
420 [2024-08-19 09:45:11] DEBUG: loop_coverage_rate=1.5
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
421 [2024-08-19 09:45:11] DEBUG: repeat_edge_cov_mult=1.75
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
422 [2024-08-19 09:45:11] DEBUG: weak_detach_rate=5
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
423 [2024-08-19 09:45:11] DEBUG: tip_coverage_rate=2
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
424 [2024-08-19 09:45:11] DEBUG: tip_length_rate=2
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
425 [2024-08-19 09:45:11] DEBUG: output_gfa_before_rr=1
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
426 [2024-08-19 09:45:11] DEBUG: remove_alt_edges=0
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
427 [2024-08-19 09:45:11] DEBUG: low_cutoff_warning=1
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
428 [2024-08-19 09:45:11] DEBUG: kmer_size=17
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
429 [2024-08-19 09:45:11] DEBUG: use_minimizers=0
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
430 [2024-08-19 09:45:11] DEBUG: reads_base_alignment=0
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
431 [2024-08-19 09:45:11] DEBUG: meta_read_top_kmer_rate=0.40
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
432 [2024-08-19 09:45:11] DEBUG: maximum_jump=1500
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
433 [2024-08-19 09:45:11] DEBUG: maximum_overhang=1500
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
434 [2024-08-19 09:45:11] DEBUG: repeat_kmer_rate=100
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
435 [2024-08-19 09:45:11] DEBUG: assemble_ovlp_divergence=0.10
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
436 [2024-08-19 09:45:11] DEBUG: assemble_divergence_relative=1
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
437 [2024-08-19 09:45:11] DEBUG: repeat_graph_ovlp_divergence=0.08
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
438 [2024-08-19 09:45:11] DEBUG: read_align_ovlp_divergence=0.25
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
439 [2024-08-19 09:45:11] DEBUG: hpc_scoring_on=0
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
440 [2024-08-19 09:45:11] DEBUG: add_unassembled_reads=0
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
441 [2024-08-19 09:45:11] DEBUG: extend_contigs_with_repeats=0
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
442 [2024-08-19 09:45:11] DEBUG: min_read_cov_cutoff=3
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
443 [2024-08-19 09:45:11] DEBUG: short_tip_length=20000
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
444 [2024-08-19 09:45:11] DEBUG: long_tip_length=100000
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
445 [2024-08-19 09:45:11] DEBUG: Running with k-mer size: 17
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
446 [2024-08-19 09:45:11] DEBUG: Selected minimum overlap 6000
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
447 [2024-08-19 09:45:11] INFO: Reading sequences
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
448 [2024-08-19 09:45:11] DEBUG: Building positional index
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
449 [2024-08-19 09:45:11] DEBUG: Total sequence: 7249289 bp
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
450 [2024-08-19 09:45:11] DEBUG: Flipped 0
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
451 [2024-08-19 09:45:11] DEBUG: UPath 1: 1
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
452 [2024-08-19 09:45:11] DEBUG: UPath 2: 3
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
453 [2024-08-19 09:45:11] DEBUG: UPath 3: 5
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
454 [2024-08-19 09:45:11] DEBUG: Final graph contains 3 egdes
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
455 [2024-08-19 09:45:11] DEBUG: Extending contigs into repeats
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
456 [2024-08-19 09:45:11] DEBUG: Covered 0 repetitive contigs
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
457 [2024-08-19 09:45:11] INFO: Generated 3 contigs
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
458 [2024-08-19 09:45:11] DEBUG: Writing FASTA
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
459 [2024-08-19 09:45:11] DEBUG: Generating scaffold connections
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
460 [2024-08-19 09:45:11] INFO: Added 0 scaffold connections
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
461 [2024-08-19 09:45:11] DEBUG: Writing Dot
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
462 [2024-08-19 09:45:11] DEBUG: Writing FASTA
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
463 [2024-08-19 09:45:11] DEBUG: Writing Gfa
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
464 [2024-08-19 09:45:11] DEBUG: Peak RAM usage: 0 Gb
8
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents:
diff changeset
465 -----------End assembly log------------
12
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
466 [2024-08-19 09:45:11] root: INFO: >>>STAGE: finalize
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
467 [2024-08-19 09:45:11] root: DEBUG: ---Output dir contents:----
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
468 [2024-08-19 09:45:11] root: DEBUG: out_dir/
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
469 [2024-08-19 09:45:11] root: DEBUG: 705.0 B assembly_graph.gv
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
470 [2024-08-19 09:45:11] root: DEBUG: 464.0 K assembly.fasta
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
471 [2024-08-19 09:45:11] root: DEBUG: 92.0 B params.json
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
472 [2024-08-19 09:45:11] root: DEBUG: 30.0 K flye.log
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
473 [2024-08-19 09:45:11] root: DEBUG: 436.0 K assembly_graph.gfa
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
474 [2024-08-19 09:45:11] root: DEBUG: 30-contigger/
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
475 [2024-08-19 09:45:11] root: DEBUG: 462.0 K contigs.fasta
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
476 [2024-08-19 09:45:11] root: DEBUG: 441.0 K graph_final.fasta
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
477 [2024-08-19 09:45:11] root: DEBUG: 182.0 B contigs_stats.txt
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
478 [2024-08-19 09:45:11] root: DEBUG: 436.0 K graph_final.gfa
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
479 [2024-08-19 09:45:11] root: DEBUG: 0.0 B scaffolds_links.txt
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
480 [2024-08-19 09:45:11] root: DEBUG: 705.0 B graph_final.gv
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
481 [2024-08-19 09:45:11] root: DEBUG: 20-repeat/
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
482 [2024-08-19 09:45:11] root: DEBUG: 705.0 B graph_after_rr.gv
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
483 [2024-08-19 09:45:11] root: DEBUG: 441.0 K repeat_graph_edges.fasta
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
484 [2024-08-19 09:45:11] root: DEBUG: 441.0 K graph_before_rr.fasta
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
485 [2024-08-19 09:45:11] root: DEBUG: 705.0 B graph_before_rr.gv
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
486 [2024-08-19 09:45:11] root: DEBUG: 436.0 K graph_before_rr.gfa
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
487 [2024-08-19 09:45:11] root: DEBUG: 564.0 B repeat_graph_dump
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
488 [2024-08-19 09:45:11] root: DEBUG: 121.0 K read_alignment_dump
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
489 [2024-08-19 09:45:11] root: DEBUG: 10-consensus/
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
490 [2024-08-19 09:45:11] root: DEBUG: 449.0 K consensus.fasta
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
491 [2024-08-19 09:45:11] root: DEBUG: 3.0 K minimap.bam.bai
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
492 [2024-08-19 09:45:11] root: DEBUG: 1.0 K minimap.stderr
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
493 [2024-08-19 09:45:11] root: DEBUG: 00-assembly/
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
494 [2024-08-19 09:45:11] root: DEBUG: 465.0 K draft_assembly.fasta
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
495 [2024-08-19 09:45:11] root: DEBUG: 61.0 B draft_assembly.fasta.fai
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
496 [2024-08-19 09:45:11] root: DEBUG: --------------------------
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
497 [2024-08-19 09:45:11] root: INFO: Assembly statistics:
8
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents:
diff changeset
498
12
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
499 Total length: 467534
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
500 Fragments: 3
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
501 Fragments N50: 382469
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
502 Largest frg: 382469
8
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents:
diff changeset
503 Scaffolds: 0
9
276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 8
diff changeset
504 Mean coverage: 14
8
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents:
diff changeset
505
12
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
506 [2024-08-19 09:45:11] root: INFO: Final assembly: /tmp/tmpmmr8wbsp/job_working_directory/000/8/working/out_dir/assembly.fasta