[2019-12-07 18:44:24] root: INFO: Running Flye 2.3.7-release [2019-12-07 18:44:24] root: DEBUG: Cmd: /usr/local/tools/_conda/envs/__flye@2.3.7/bin/flye --subassemblies ./input_0.fastq.gz -o out_dir -g 5m -t 20 -i 0 [2019-12-07 18:44:24] root: INFO: Configuring run [2019-12-07 18:44:25] root: DEBUG: Total sequence length: 19553060 [2019-12-07 18:44:25] root: INFO: Input genome size: 5000000 [2019-12-07 18:44:25] root: INFO: Estimated coverage: 3 [2019-12-07 18:44:25] root: WARNING: Expected read coverage is 3, the assembly is not guaranteed to be optimal in this setting. Are you sure that the genome size was entered correctly? [2019-12-07 18:44:25] root: INFO: Reads N50/N90: 4887515 / 4887515 [2019-12-07 18:44:25] root: INFO: Minimum overlap set to 1000 [2019-12-07 18:44:25] root: INFO: Selected k-mer size: 31 [2019-12-07 18:44:25] root: INFO: Assembling reads [2019-12-07 18:44:25] root: DEBUG: -----Begin assembly log------ [2019-12-07 18:44:25] root: DEBUG: Running: flye-assemble -l /data/dnb02/galaxy_db/job_working_directory/006/490/6490684/working/out_dir/flye.log -t 20 -v 1000 -k 31 ./input_0.fastq.gz /data/dnb02/galaxy_db/job_working_directory/006/490/6490684/working/out_dir/0-assembly/draft_assembly.fasta 5000000 /usr/local/tools/_conda/envs/__flye@2.3.7/lib/python2.7/site-packages/flye/config/bin_cfg/asm_subasm.cfg [2019-12-07 18:44:25] DEBUG: Build date: Nov 15 2018 20:00:50 [2019-12-07 18:44:25] DEBUG: Total RAM: 984 Gb [2019-12-07 18:44:25] DEBUG: Total CPUs: 40 [2019-12-07 18:44:25] DEBUG: Parameters: [2019-12-07 18:44:25] DEBUG: big_genome_threshold=50000000 [2019-12-07 18:44:25] DEBUG: low_cutoff_warning=0 [2019-12-07 18:44:25] DEBUG: hard_min_coverage_rate=50 [2019-12-07 18:44:25] DEBUG: assemble_kmer_sample=2 [2019-12-07 18:44:25] DEBUG: repeat_graph_kmer_sample=2 [2019-12-07 18:44:25] DEBUG: read_align_kmer_sample=2 [2019-12-07 18:44:25] DEBUG: maximum_jump=500 [2019-12-07 18:44:25] DEBUG: maximum_overhang=100 [2019-12-07 18:44:25] DEBUG: repeat_kmer_rate=100 [2019-12-07 18:44:25] DEBUG: assemble_ovlp_ident=0.02 [2019-12-07 18:44:25] DEBUG: repeat_graph_ovlp_ident=0.02 [2019-12-07 18:44:25] DEBUG: repeat_graph_ovlp_end_adjust=0 [2019-12-07 18:44:25] DEBUG: read_align_ovlp_ident=0.02 [2019-12-07 18:44:25] DEBUG: max_coverage_drop_rate=10 [2019-12-07 18:44:25] DEBUG: chimera_window=100 [2019-12-07 18:44:25] DEBUG: min_reads_in_contig=4 [2019-12-07 18:44:25] DEBUG: max_inner_reads=10 [2019-12-07 18:44:25] DEBUG: max_inner_fraction=0.25 [2019-12-07 18:44:25] DEBUG: add_unassembled_reads=1 [2019-12-07 18:44:25] DEBUG: max_separation=500 [2019-12-07 18:44:25] DEBUG: tip_length_threshold=1000 [2019-12-07 18:44:25] DEBUG: unique_edge_length=50000 [2019-12-07 18:44:25] DEBUG: min_repeat_res_support=0.51 [2019-12-07 18:44:25] DEBUG: out_paths_ratio=5 [2019-12-07 18:44:25] DEBUG: graph_cov_drop_rate=10 [2019-12-07 18:44:25] DEBUG: coverage_estimate_window=100 [2019-12-07 18:44:25] DEBUG: extend_contigs_with_repeats=0 [2019-12-07 18:44:25] DEBUG: Running with k-mer size: 31 [2019-12-07 18:44:25] INFO: Reading sequences [2019-12-07 18:44:26] DEBUG: Total sequence: 19553060 bp [2019-12-07 18:44:26] DEBUG: Running with minimum overlap 1000 [2019-12-07 18:44:26] DEBUG: Expected read coverage: 3 [2019-12-07 18:44:26] INFO: Generating solid k-mer index [2019-12-07 18:44:26] DEBUG: Hard threshold set to 2 [2019-12-07 18:44:26] DEBUG: Started kmer counting [2019-12-07 18:44:52] INFO: Counting kmers (1/2): [2019-12-07 18:44:54] INFO: Counting kmers (2/2): [2019-12-07 18:44:59] DEBUG: Estimated minimum kmer coverage: 2 [2019-12-07 18:44:59] DEBUG: Filtered 0 erroneous k-mers [2019-12-07 18:44:59] DEBUG: Repetetive k-mer frequency: 259 [2019-12-07 18:44:59] DEBUG: Filtered 0 repetitive kmers (0) [2019-12-07 18:44:59] INFO: Filling index table [2019-12-07 18:44:59] DEBUG: Sampling rate: 2 [2019-12-07 18:44:59] DEBUG: Solid kmers: 3306599 [2019-12-07 18:44:59] DEBUG: Kmer index size: 8596183 [2019-12-07 18:44:59] DEBUG: Mean k-mer frequency: 2.59971 [2019-12-07 18:45:04] DEBUG: Sorting k-mer index [2019-12-07 18:45:04] DEBUG: Peak RAM usage: 1 Gb [2019-12-07 18:45:04] INFO: Extending reads [2019-12-07 18:45:04] DEBUG: Estimating overlap coverage [2019-12-07 18:46:19] INFO: Overlap-based coverage: 3 [2019-12-07 18:46:19] INFO: Median overlap divergence: 0.00414035 [2019-12-07 18:46:19] DEBUG: Sequence divergence distribution: |* |* |* |* |* |* |* |* |* |* |* |* |* |* |* |* |* |* |* |* ---------------------------------------------------------------------------------------------------- 0% 5% 10% 15% 20% 25% 30% 35% 40% 45% Q25 = 0.0041, Q50 = 0.0041, Q75 = 0.0041 [2019-12-07 18:46:37] INFO: Added 1 singleton reads [2019-12-07 18:46:37] INFO: Assembled 1 draft contigs [2019-12-07 18:46:37] INFO: Generating contig sequences [2019-12-07 18:46:37] DEBUG: Writing FASTA [2019-12-07 18:46:37] DEBUG: Peak RAM usage: 1 Gb -----------End assembly log------------ [2019-12-07 18:46:37] root: INFO: Performing repeat analysis [2019-12-07 18:46:37] root: DEBUG: -----Begin repeat analyser log------ [2019-12-07 18:46:37] root: DEBUG: Running: flye-repeat -l /data/dnb02/galaxy_db/job_working_directory/006/490/6490684/working/out_dir/flye.log -t 20 -v 1000 -k 31 /data/dnb02/galaxy_db/job_working_directory/006/490/6490684/working/out_dir/0-assembly/draft_assembly.fasta ./input_0.fastq.gz /data/dnb02/galaxy_db/job_working_directory/006/490/6490684/working/out_dir/2-repeat 5000000 /usr/local/tools/_conda/envs/__flye@2.3.7/lib/python2.7/site-packages/flye/config/bin_cfg/asm_subasm.cfg [2019-12-07 18:46:37] DEBUG: Build date: Nov 15 2018 19:59:41 [2019-12-07 18:46:38] DEBUG: Parameters: [2019-12-07 18:46:38] DEBUG: big_genome_threshold=50000000 [2019-12-07 18:46:38] DEBUG: low_cutoff_warning=0 [2019-12-07 18:46:38] DEBUG: hard_min_coverage_rate=50 [2019-12-07 18:46:38] DEBUG: assemble_kmer_sample=2 [2019-12-07 18:46:38] DEBUG: repeat_graph_kmer_sample=2 [2019-12-07 18:46:38] DEBUG: read_align_kmer_sample=2 [2019-12-07 18:46:38] DEBUG: maximum_jump=500 [2019-12-07 18:46:38] DEBUG: maximum_overhang=100 [2019-12-07 18:46:38] DEBUG: repeat_kmer_rate=100 [2019-12-07 18:46:38] DEBUG: assemble_ovlp_ident=0.02 [2019-12-07 18:46:38] DEBUG: repeat_graph_ovlp_ident=0.02 [2019-12-07 18:46:38] DEBUG: repeat_graph_ovlp_end_adjust=0 [2019-12-07 18:46:38] DEBUG: read_align_ovlp_ident=0.02 [2019-12-07 18:46:38] DEBUG: max_coverage_drop_rate=10 [2019-12-07 18:46:38] DEBUG: chimera_window=100 [2019-12-07 18:46:38] DEBUG: min_reads_in_contig=4 [2019-12-07 18:46:38] DEBUG: max_inner_reads=10 [2019-12-07 18:46:38] DEBUG: max_inner_fraction=0.25 [2019-12-07 18:46:38] DEBUG: add_unassembled_reads=1 [2019-12-07 18:46:38] DEBUG: max_separation=500 [2019-12-07 18:46:38] DEBUG: tip_length_threshold=1000 [2019-12-07 18:46:38] DEBUG: unique_edge_length=50000 [2019-12-07 18:46:38] DEBUG: min_repeat_res_support=0.51 [2019-12-07 18:46:38] DEBUG: out_paths_ratio=5 [2019-12-07 18:46:38] DEBUG: graph_cov_drop_rate=10 [2019-12-07 18:46:38] DEBUG: coverage_estimate_window=100 [2019-12-07 18:46:38] DEBUG: extend_contigs_with_repeats=0 [2019-12-07 18:46:38] DEBUG: Running with k-mer size: 31 [2019-12-07 18:46:38] INFO: Reading sequences [2019-12-07 18:46:38] DEBUG: Total sequence: 19553060 bp [2019-12-07 18:46:38] DEBUG: Total sequence: 4887515 bp [2019-12-07 18:46:38] DEBUG: Selected minimum overlap 1000 [2019-12-07 18:46:38] INFO: Building repeat graph [2019-12-07 18:46:38] DEBUG: Hard threshold set to 1 [2019-12-07 18:46:38] DEBUG: Started kmer counting [2019-12-07 18:47:14] DEBUG: Repetetive k-mer frequency: 101 [2019-12-07 18:47:14] DEBUG: Filtered 0 repetitive kmers (0) [2019-12-07 18:47:14] DEBUG: Sampling rate: 2 [2019-12-07 18:47:14] DEBUG: Solid kmers: 24276 [2019-12-07 18:47:14] DEBUG: Kmer index size: 66608 [2019-12-07 18:47:14] DEBUG: Mean k-mer frequency: 2.74378 [2019-12-07 18:47:15] DEBUG: Sorting k-mer index [2019-12-07 18:47:20] DEBUG: Computing transitive closure for overlaps [2019-12-07 18:47:20] DEBUG: Found 410 overlaps [2019-12-07 18:47:20] DEBUG: Left 172 overlaps after filtering [2019-12-07 18:47:20] INFO: Median overlap divergence: 0.024349 [2019-12-07 18:47:20] DEBUG: Sequence divergence distribution: |* |* |* |* |* |* |* |* |* |* |* |* |* * |* * |* * * * |* * * * |* *** * * |******* *** * * * |******* *** ** * * |******* *** ** * * ---------------------------------------------------------------------------------------------------- 0% 5% 10% 15% 20% 25% 30% 35% 40% 45% Q25 = 0.004, Q50 = 0.024, Q75 = 0.049 [2019-12-07 18:47:20] DEBUG: Computing gluepoints [2019-12-07 18:47:20] DEBUG: Added 0 gluepoint projections [2019-12-07 18:47:20] DEBUG: Created 140 gluepoints [2019-12-07 18:47:20] DEBUG: Tandems removed: 0 left, 0 right, 0 both [2019-12-07 18:47:20] DEBUG: Initializing edges [2019-12-07 18:47:20] DEBUG: Filtered 0 singleton segments [2019-12-07 18:47:20] DEBUG: * 31 +read_1 0 242233 242233 [2019-12-07 18:47:20] DEBUG: -37 +read_1 242233 243525 1292 [2019-12-07 18:47:20] DEBUG: * -34 +read_1 243525 404716 161191 [2019-12-07 18:47:20] DEBUG: 36 +read_1 404716 409962 5246 [2019-12-07 18:47:20] DEBUG: * -32 +read_1 409962 440839 30877 [2019-12-07 18:47:20] DEBUG: 30 +read_1 440839 441899 1060 [2019-12-07 18:47:20] DEBUG: * 28 +read_1 441899 446184 4285 [2019-12-07 18:47:20] DEBUG: 24 +read_1 446184 451437 5253 [2019-12-07 18:47:20] DEBUG: * 26 +read_1 451437 495046 43609 [2019-12-07 18:47:20] DEBUG: -19 +read_1 495046 498632 3586 [2019-12-07 18:47:20] DEBUG: * 16 +read_1 498632 586370 87738 [2019-12-07 18:47:20] DEBUG: 24 +read_1 586370 591623 5253 [2019-12-07 18:47:20] DEBUG: * 44 +read_1 591623 686542 94919 [2019-12-07 18:47:20] DEBUG: 36 +read_1 686542 691704 5162 [2019-12-07 18:47:20] DEBUG: * 45 +read_1 691704 877168 185464 [2019-12-07 18:47:20] DEBUG: -19 +read_1 877168 880814 3646 [2019-12-07 18:47:20] DEBUG: * -43 +read_1 880814 974938 94124 [2019-12-07 18:47:20] DEBUG: -35 +read_1 974938 976184 1246 [2019-12-07 18:47:20] DEBUG: * 46 +read_1 976184 1168493 192309 [2019-12-07 18:47:20] DEBUG: -30 +read_1 1168493 1169553 1060 [2019-12-07 18:47:20] DEBUG: * -38 +read_1 1169553 1195705 26152 [2019-12-07 18:47:20] DEBUG: -24 +read_1 1195705 1200959 5254 [2019-12-07 18:47:20] DEBUG: * -22 +read_1 1200959 1570260 369301 [2019-12-07 18:47:20] DEBUG: 37 +read_1 1570260 1571552 1292 [2019-12-07 18:47:20] DEBUG: * -42 +read_1 1571552 1865961 294409 [2019-12-07 18:47:20] DEBUG: -25 +read_1 1865961 1867214 1253 [2019-12-07 18:47:20] DEBUG: * -47 +read_1 1867214 1897410 30196 [2019-12-07 18:47:20] DEBUG: -36 +read_1 1897410 1902647 5237 [2019-12-07 18:47:20] DEBUG: * 33 +read_1 1902647 2163193 260546 [2019-12-07 18:47:20] DEBUG: 37 +read_1 2163193 2164485 1292 [2019-12-07 18:47:20] DEBUG: * 29 +read_1 2164485 2519094 354609 [2019-12-07 18:47:20] DEBUG: -20 +read_1 2519094 2520299 1205 [2019-12-07 18:47:20] DEBUG: * -15 +read_1 2520299 2659979 139680 [2019-12-07 18:47:20] DEBUG: -14 +read_1 2659979 2661653 1674 [2019-12-07 18:47:20] DEBUG: * -13 +read_1 2661653 2837273 175620 [2019-12-07 18:47:20] DEBUG: -14 +read_1 2837273 2838952 1679 [2019-12-07 18:47:20] DEBUG: * -12 +read_1 2838952 3218538 379586 [2019-12-07 18:47:20] DEBUG: -35 +read_1 3218538 3219784 1246 [2019-12-07 18:47:20] DEBUG: * -41 +read_1 3219784 3264858 45074 [2019-12-07 18:47:20] DEBUG: 20 +read_1 3264858 3266123 1265 [2019-12-07 18:47:20] DEBUG: * -11 +read_1 3266123 3297801 31678 [2019-12-07 18:47:20] DEBUG: 14 +read_1 3297801 3299506 1705 [2019-12-07 18:47:20] DEBUG: * 18 +read_1 3299506 3361536 62030 [2019-12-07 18:47:20] DEBUG: -17 +read_1 3361536 3362721 1185 [2019-12-07 18:47:20] DEBUG: * -10 +read_1 3362721 3708793 346072 [2019-12-07 18:47:20] DEBUG: -25 +read_1 3708793 3710046 1253 [2019-12-07 18:47:20] DEBUG: * -9 +read_1 3710046 3945970 235924 [2019-12-07 18:47:20] DEBUG: -37 +read_1 3945970 3947262 1292 [2019-12-07 18:47:20] DEBUG: * 8 +read_1 3947262 4068520 121258 [2019-12-07 18:47:20] DEBUG: -40 +read_1 4068520 4069530 1010 [2019-12-07 18:47:20] DEBUG: * -39 +read_1 4069530 4070391 861 [2019-12-07 18:47:20] DEBUG: -40 +read_1 4070391 4071401 1010 [2019-12-07 18:47:20] DEBUG: * 7 +read_1 4071401 4212979 141578 [2019-12-07 18:47:20] DEBUG: -6 +read_1 4212979 4215458 2479 [2019-12-07 18:47:20] DEBUG: * -5 +read_1 4215458 4216551 1093 [2019-12-07 18:47:20] DEBUG: -6 +read_1 4216551 4219030 2479 [2019-12-07 18:47:20] DEBUG: * 4 +read_1 4219030 4220306 1276 [2019-12-07 18:47:20] DEBUG: -20 +read_1 4220306 4221511 1205 [2019-12-07 18:47:20] DEBUG: * -3 +read_1 4221511 4235007 13496 [2019-12-07 18:47:20] DEBUG: -17 +read_1 4235007 4236192 1185 [2019-12-07 18:47:20] DEBUG: * -2 +read_1 4236192 4486962 250770 [2019-12-07 18:47:20] DEBUG: -37 +read_1 4486962 4488254 1292 [2019-12-07 18:47:20] DEBUG: * 21 +read_1 4488254 4656880 168626 [2019-12-07 18:47:20] DEBUG: 24 +read_1 4656880 4662134 5254 [2019-12-07 18:47:20] DEBUG: * -1 +read_1 4662134 4669672 7538 [2019-12-07 18:47:20] DEBUG: -37 +read_1 4669672 4670954 1282 [2019-12-07 18:47:20] DEBUG: * -27 +read_1 4670954 4826121 155167 [2019-12-07 18:47:20] DEBUG: 37 +read_1 4826121 4827413 1292 [2019-12-07 18:47:20] DEBUG: * -23 +read_1 4827413 4887514 60101 [2019-12-07 18:47:20] DEBUG: Total edges: 47 [2019-12-07 18:47:20] DEBUG: Removed 0 simple and 0 double chimeric junctions [2019-12-07 18:47:20] DEBUG: Removed 0 edges [2019-12-07 18:47:20] DEBUG: Added 0 edges [2019-12-07 18:47:20] DEBUG: Collapsed 0 bulges [2019-12-07 18:47:20] DEBUG: Removed 0 edges [2019-12-07 18:47:20] DEBUG: Added 0 edges [2019-12-07 18:47:20] INFO: Aligning reads to the graph [2019-12-07 18:47:20] DEBUG: Total sequence: 4887514 bp [2019-12-07 18:47:20] DEBUG: Hard threshold set to 1 [2019-12-07 18:47:20] DEBUG: Started kmer counting [2019-12-07 18:47:49] DEBUG: Repetetive k-mer frequency: 101 [2019-12-07 18:47:49] DEBUG: Filtered 0 repetitive kmers (0) [2019-12-07 18:47:49] DEBUG: Sampling rate: 2 [2019-12-07 18:47:49] DEBUG: Solid kmers: 2408678 [2019-12-07 18:47:49] DEBUG: Kmer index size: 2442935 [2019-12-07 18:47:49] DEBUG: Mean k-mer frequency: 1.01422 [2019-12-07 18:47:52] DEBUG: Sorting k-mer index [2019-12-07 18:48:05] DEBUG: Total reads : 4 [2019-12-07 18:48:05] DEBUG: Read with aligned parts : 4 [2019-12-07 18:48:05] DEBUG: Aligned in one piece : 0 [2019-12-07 18:48:05] INFO: Aligned read sequence: 19550730 / 19550060 (1.00003) [2019-12-07 18:48:05] INFO: Median overlap divergence: 0.000889574 [2019-12-07 18:48:05] DEBUG: Sequence divergence distribution: |* |* |* |* |* |* |* |* |* |* |* |* |* |* |* |* |* |* * * |* ** * * * |****** ***** ** ---------------------------------------------------------------------------------------------------- 0% 5% 10% 15% 20% 25% 30% 35% 40% 45% Q25 = 1.1e-05, Q50 = 0.00089, Q75 = 0.019 [2019-12-07 18:48:05] INFO: Mean edge coverage: 3 [2019-12-07 18:48:05] DEBUG: 47 len:30196 cov:4 mult:1.33333 [2019-12-07 18:48:05] DEBUG: -46 len:192309 cov:4 mult:1.33333 [2019-12-07 18:48:05] DEBUG: 46 len:192309 cov:4 mult:1.33333 [2019-12-07 18:48:05] DEBUG: -45 len:185464 cov:4 mult:1.33333 [2019-12-07 18:48:05] DEBUG: 45 len:185464 cov:4 mult:1.33333 [2019-12-07 18:48:05] DEBUG: 43 len:94124 cov:4 mult:1.33333 [2019-12-07 18:48:05] DEBUG: -42 len:294409 cov:4 mult:1.33333 [2019-12-07 18:48:05] DEBUG: 40 len:1010 cov:8 mult:2.66667 [2019-12-07 18:48:05] DEBUG: 39 len:861 cov:4 mult:1.33333 [2019-12-07 18:48:05] DEBUG: -37 len:1290 cov:28 mult:9.33333 [2019-12-07 18:48:05] DEBUG: 36 len:5215 cov:12 mult:4 [2019-12-07 18:48:05] DEBUG: -35 len:1246 cov:8 mult:2.66667 [2019-12-07 18:48:05] DEBUG: 35 len:1246 cov:8 mult:2.66667 [2019-12-07 18:48:05] DEBUG: 34 len:161191 cov:4 mult:1.33333 [2019-12-07 18:48:05] DEBUG: 32 len:30877 cov:4 mult:1.33333 [2019-12-07 18:48:05] DEBUG: 38 len:26152 cov:4 mult:1.33333 [2019-12-07 18:48:05] DEBUG: 31 len:242233 cov:4 mult:1.33333 [2019-12-07 18:48:05] DEBUG: 30 len:1060 cov:8 mult:2.66667 [2019-12-07 18:48:05] DEBUG: -29 len:354609 cov:4 mult:1.33333 [2019-12-07 18:48:05] DEBUG: 41 len:45074 cov:4 mult:1.33333 [2019-12-07 18:48:05] DEBUG: 29 len:354609 cov:4 mult:1.33333 [2019-12-07 18:48:05] DEBUG: -28 len:4285 cov:4 mult:1.33333 [2019-12-07 18:48:05] DEBUG: -38 len:26152 cov:4 mult:1.33333 [2019-12-07 18:48:05] DEBUG: 28 len:4285 cov:4 mult:1.33333 [2019-12-07 18:48:05] DEBUG: -36 len:5215 cov:12 mult:4 [2019-12-07 18:48:05] DEBUG: 27 len:155167 cov:4 mult:1.33333 [2019-12-07 18:48:05] DEBUG: -26 len:43609 cov:4 mult:1.33333 [2019-12-07 18:48:05] DEBUG: -33 len:260546 cov:4 mult:1.33333 [2019-12-07 18:48:05] DEBUG: -30 len:1060 cov:8 mult:2.66667 [2019-12-07 18:48:05] DEBUG: 26 len:43609 cov:4 mult:1.33333 [2019-12-07 18:48:05] DEBUG: -24 len:5253 cov:16 mult:5.33333 [2019-12-07 18:48:05] DEBUG: 24 len:5253 cov:16 mult:5.33333 [2019-12-07 18:48:05] DEBUG: -11 len:31678 cov:4 mult:1.33333 [2019-12-07 18:48:05] DEBUG: -10 len:346072 cov:4 mult:1.33333 [2019-12-07 18:48:05] DEBUG: 10 len:346072 cov:4 mult:1.33333 [2019-12-07 18:48:05] DEBUG: 9 len:235924 cov:4 mult:1.33333 [2019-12-07 18:48:05] DEBUG: -15 len:139680 cov:4 mult:1.33333 [2019-12-07 18:48:05] DEBUG: -25 len:1253 cov:8 mult:2.66667 [2019-12-07 18:48:05] DEBUG: 7 len:141578 cov:4 mult:1.33333 [2019-12-07 18:48:05] DEBUG: 33 len:260546 cov:4 mult:1.33333 [2019-12-07 18:48:05] DEBUG: -18 len:62030 cov:4 mult:1.33333 [2019-12-07 18:48:05] DEBUG: -9 len:235924 cov:4 mult:1.33333 [2019-12-07 18:48:05] DEBUG: -6 len:2479 cov:8 mult:2.66667 [2019-12-07 18:48:05] DEBUG: -20 len:1225 cov:12 mult:4 [2019-12-07 18:48:05] DEBUG: -19 len:3616 cov:8 mult:2.66667 [2019-12-07 18:48:05] DEBUG: 3 len:13496 cov:4 mult:1.33333 [2019-12-07 18:48:05] DEBUG: 15 len:139680 cov:4 mult:1.33333 [2019-12-07 18:48:05] DEBUG: 5 len:1093 cov:4 mult:1.33333 [2019-12-07 18:48:05] DEBUG: -40 len:1010 cov:8 mult:2.66667 [2019-12-07 18:48:05] DEBUG: -31 len:242233 cov:4 mult:1.33333 [2019-12-07 18:48:05] DEBUG: -8 len:121258 cov:4 mult:1.33333 [2019-12-07 18:48:05] DEBUG: 2 len:250770 cov:4 mult:1.33333 [2019-12-07 18:48:05] DEBUG: -3 len:13496 cov:4 mult:1.33333 [2019-12-07 18:48:05] DEBUG: -22 len:369301 cov:4 mult:1.33333 [2019-12-07 18:48:05] DEBUG: -27 len:155167 cov:4 mult:1.33333 [2019-12-07 18:48:05] DEBUG: -2 len:250770 cov:4 mult:1.33333 [2019-12-07 18:48:05] DEBUG: -41 len:45074 cov:4 mult:1.33333 [2019-12-07 18:48:05] DEBUG: 4 len:1276 cov:4 mult:1.33333 [2019-12-07 18:48:05] DEBUG: 37 len:1290 cov:28 mult:9.33333 [2019-12-07 18:48:05] DEBUG: -32 len:30877 cov:4 mult:1.33333 [2019-12-07 18:48:05] DEBUG: -17 len:1185 cov:8 mult:2.66667 [2019-12-07 18:48:05] DEBUG: 1 len:7538 cov:4 mult:1.33333 [2019-12-07 18:48:05] DEBUG: 14 len:1686 cov:12 mult:4 [2019-12-07 18:48:05] DEBUG: -39 len:861 cov:4 mult:1.33333 [2019-12-07 18:48:05] DEBUG: -23 len:60101 cov:4 mult:1.33333 [2019-12-07 18:48:05] DEBUG: -5 len:1093 cov:4 mult:1.33333 [2019-12-07 18:48:05] DEBUG: 20 len:1225 cov:12 mult:4 [2019-12-07 18:48:05] DEBUG: 12 len:379586 cov:4 mult:1.33333 [2019-12-07 18:48:05] DEBUG: -44 len:94919 cov:4 mult:1.33333 [2019-12-07 18:48:05] DEBUG: -12 len:379586 cov:4 mult:1.33333 [2019-12-07 18:48:05] DEBUG: -43 len:94124 cov:4 mult:1.33333 [2019-12-07 18:48:05] DEBUG: 8 len:121258 cov:4 mult:1.33333 [2019-12-07 18:48:05] DEBUG: 13 len:175620 cov:4 mult:1.33333 [2019-12-07 18:48:05] DEBUG: -34 len:161191 cov:4 mult:1.33333 [2019-12-07 18:48:05] DEBUG: 11 len:31678 cov:4 mult:1.33333 [2019-12-07 18:48:05] DEBUG: -13 len:175620 cov:4 mult:1.33333 [2019-12-07 18:48:05] DEBUG: 25 len:1253 cov:8 mult:2.66667 [2019-12-07 18:48:05] DEBUG: -4 len:1276 cov:4 mult:1.33333 [2019-12-07 18:48:05] DEBUG: -14 len:1686 cov:12 mult:4 [2019-12-07 18:48:05] DEBUG: 16 len:87738 cov:4 mult:1.33333 [2019-12-07 18:48:05] DEBUG: 19 len:3616 cov:8 mult:2.66667 [2019-12-07 18:48:05] DEBUG: 44 len:94919 cov:4 mult:1.33333 [2019-12-07 18:48:05] DEBUG: 6 len:2479 cov:8 mult:2.66667 [2019-12-07 18:48:05] DEBUG: -16 len:87738 cov:4 mult:1.33333 [2019-12-07 18:48:05] DEBUG: 42 len:294409 cov:4 mult:1.33333 [2019-12-07 18:48:05] DEBUG: -1 len:7538 cov:4 mult:1.33333 [2019-12-07 18:48:05] DEBUG: 18 len:62030 cov:4 mult:1.33333 [2019-12-07 18:48:05] DEBUG: 17 len:1185 cov:8 mult:2.66667 [2019-12-07 18:48:05] DEBUG: -7 len:141578 cov:4 mult:1.33333 [2019-12-07 18:48:05] DEBUG: 21 len:168626 cov:4 mult:1.33333 [2019-12-07 18:48:05] DEBUG: -21 len:168626 cov:4 mult:1.33333 [2019-12-07 18:48:05] DEBUG: -47 len:30196 cov:4 mult:1.33333 [2019-12-07 18:48:05] DEBUG: 22 len:369301 cov:4 mult:1.33333 [2019-12-07 18:48:05] DEBUG: 23 len:60101 cov:4 mult:1.33333 [2019-12-07 18:48:05] DEBUG: Unique coverage threshold 7 [2019-12-07 18:48:05] DEBUG: Read coverage cutoff: 0 [2019-12-07 18:48:05] DEBUG: Removed 0 unsupported edges [2019-12-07 18:48:05] DEBUG: 0 tips clipped [2019-12-07 18:48:05] DEBUG: Unrolled 0 heterozygous loops [2019-12-07 18:48:05] DEBUG: Removed 0 heterozygous loops [2019-12-07 18:48:05] DEBUG: Popped 0 heterozygous bulges [2019-12-07 18:48:05] INFO: Resolving repeats [2019-12-07 18:48:05] DEBUG: Finding repeats [2019-12-07 18:48:05] DEBUG: Cov: 40 1010 8 [2019-12-07 18:48:05] DEBUG: Cov: -37 1290 28 [2019-12-07 18:48:05] DEBUG: Cov: 36 5215 12 [2019-12-07 18:48:05] DEBUG: Cov: -35 1246 8 [2019-12-07 18:48:05] DEBUG: Cov: 30 1060 8 [2019-12-07 18:48:05] DEBUG: Cov: -24 5253 16 [2019-12-07 18:48:05] DEBUG: Cov: -25 1253 8 [2019-12-07 18:48:05] DEBUG: Cov: -6 2479 8 [2019-12-07 18:48:05] DEBUG: Cov: -20 1225 12 [2019-12-07 18:48:05] DEBUG: Cov: -19 3616 8 [2019-12-07 18:48:05] DEBUG: Cov: -17 1185 8 [2019-12-07 18:48:05] DEBUG: Cov: 14 1686 12 [2019-12-07 18:48:05] DEBUG: Writing Dot [2019-12-07 18:48:05] DEBUG: Writing FASTA [2019-12-07 18:48:06] DEBUG: Total unique edges: 35 [2019-12-07 18:48:06] DEBUG: Connection 38 -46 4 1 [2019-12-07 18:48:06] DEBUG: Connection -46 43 4 1 [2019-12-07 18:48:06] DEBUG: Connection 43 -45 4 1 [2019-12-07 18:48:06] DEBUG: Connection -45 -44 4 1 [2019-12-07 18:48:06] DEBUG: Connection -44 -16 4 1 [2019-12-07 18:48:06] DEBUG: Connection -16 -26 4 1 [2019-12-07 18:48:06] DEBUG: Connection -26 -28 4 1 [2019-12-07 18:48:06] DEBUG: Connection -28 32 4 1 [2019-12-07 18:48:06] DEBUG: Connection 32 34 4 1 [2019-12-07 18:48:06] DEBUG: Connection 34 -31 4 1 [2019-12-07 18:48:06] DEBUG: Connection 10 -18 4 1 [2019-12-07 18:48:06] DEBUG: Connection -18 11 4 1 [2019-12-07 18:48:06] DEBUG: Connection 11 41 4 1 [2019-12-07 18:48:06] DEBUG: Connection 41 12 4 1 [2019-12-07 18:48:06] DEBUG: Connection 12 13 4 1 [2019-12-07 18:48:06] DEBUG: Connection 13 15 4 1 [2019-12-07 18:48:06] DEBUG: Connection -22 -42 4 1 [2019-12-07 18:48:06] DEBUG: Connection -42 -47 4 1 [2019-12-07 18:48:06] DEBUG: Connection -47 33 4 1 [2019-12-07 18:48:06] DEBUG: Connection 33 29 4 1 [2019-12-07 18:48:06] DEBUG: Connection 29 -15 4 1 [2019-12-07 18:48:06] DEBUG: Connection -10 -9 4 1 [2019-12-07 18:48:06] DEBUG: Connection -9 8 4 1 [2019-12-07 18:48:06] DEBUG: Connection 8 -39 4 1 [2019-12-07 18:48:06] DEBUG: Connection -39 7 4 1 [2019-12-07 18:48:06] DEBUG: Connection 7 -5 4 1 [2019-12-07 18:48:06] DEBUG: Connection -5 4 4 1 [2019-12-07 18:48:06] DEBUG: Connection 4 -3 4 1 [2019-12-07 18:48:06] DEBUG: Connection -3 -2 4 1 [2019-12-07 18:48:06] DEBUG: Connection -2 21 4 1 [2019-12-07 18:48:06] DEBUG: Connection 21 -1 4 1 [2019-12-07 18:48:06] DEBUG: Connection -1 -27 4 1 [2019-12-07 18:48:06] DEBUG: Connection -27 -23 4 1 [2019-12-07 18:48:06] DEBUG: Resolved: 33 links: 280 [2019-12-07 18:48:06] DEBUG: Unresolved: 0 [2019-12-07 18:48:06] DEBUG: Finding repeats [2019-12-07 18:48:06] DEBUG: Total unique edges: 69 [2019-12-07 18:48:06] DEBUG: Resolved: 0 links: 16 [2019-12-07 18:48:06] DEBUG: Unresolved: 0 [2019-12-07 18:48:06] DEBUG: Removed 0 simple and 0 double chimeric junctions [2019-12-07 18:48:06] INFO: Generating contigs [2019-12-07 18:48:06] DEBUG: UPath 1: 31 -> -57 -> -34 -> -56 -> -32 -> -55 -> 28 -> -54 -> 26 -> -53 -> 16 -> -52 -> 44 -> -51 -> 45 -> -50 -> -43 -> -49 -> 46 -> -48 -> -38 -> -24 -> -22 -> -64 -> -42 -> -65 -> -47 -> -66 -> 33 -> -67 -> 29 -> -68 -> -15 -> -63 -> -13 -> -62 -> -12 -> -61 -> -41 -> 60 -> -11 -> -59 -> 18 -> -58 -> -10 -> -69 -> -9 -> -70 -> 8 -> -71 -> -39 -> -72 -> 7 -> -73 -> -5 -> -74 -> 4 -> -75 -> -3 -> -76 -> -2 -> -77 -> 21 -> -78 -> -1 -> -79 -> -27 -> -80 -> -23 [2019-12-07 18:48:06] DEBUG: Final graph contiain 1 egdes [2019-12-07 18:48:06] DEBUG: Extending contigs into repeats [2019-12-07 18:48:06] DEBUG: Covered 0 repetitive contigs [2019-12-07 18:48:06] INFO: Generated 1 contigs [2019-12-07 18:48:06] DEBUG: Writing FASTA [2019-12-07 18:48:06] DEBUG: Generating scaffold connections [2019-12-07 18:48:06] DEBUG: Writing Dot [2019-12-07 18:48:07] DEBUG: Writing FASTA [2019-12-07 18:48:07] DEBUG: Writing Gfa [2019-12-07 18:48:07] DEBUG: Peak RAM usage: 1 Gb -----------End assembly log------------ [2019-12-07 18:48:08] root: INFO: Assembly statistics: Total length: 4887514 Contigs: 1 Scaffolds: 1 Scaffolds N50: 4887514 Largest scf: 4887514 Mean coverage: 4 [2019-12-07 18:48:08] root: INFO: Final assembly: /data/dnb02/galaxy_db/job_working_directory/006/490/6490684/working/out_dir/scaffolds.fasta