Mercurial > repos > bgruening > flye
annotate test-data/result1.log @ 12:3e4f8642c77e draft default tip
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
author | bgruening |
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date | Mon, 26 Aug 2024 13:54:31 +0000 |
parents | 276f5d8712d5 |
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rev | line source |
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12
3e4f8642c77e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents:
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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
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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
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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
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changeset
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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
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changeset
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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
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changeset
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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
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9
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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
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changeset
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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
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changeset
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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
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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
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changeset
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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:
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changeset
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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
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changeset
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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
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changeset
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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
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changeset
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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
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changeset
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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
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changeset
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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
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changeset
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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
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changeset
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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
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changeset
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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
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changeset
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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
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changeset
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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
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changeset
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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
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changeset
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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
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changeset
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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
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changeset
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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
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changeset
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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
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changeset
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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
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changeset
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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
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changeset
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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
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changeset
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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
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changeset
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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
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changeset
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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
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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
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changeset
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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
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changeset
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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
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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
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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
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changeset
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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
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changeset
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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
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changeset
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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
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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
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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
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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
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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
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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
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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
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changeset
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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
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changeset
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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
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changeset
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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
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changeset
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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
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changeset
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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
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changeset
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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
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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
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changeset
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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
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changeset
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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
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changeset
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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
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changeset
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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
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changeset
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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
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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
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changeset
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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:
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changeset
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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:
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changeset
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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:
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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:
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changeset
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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
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changeset
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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
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503 Scaffolds: 0 |
9
276f5d8712d5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents:
8
diff
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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
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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 |