MEGAHIT v1.1.2 --- [Sat Dec 11 12:43:52 2021] Start assembly. Number of CPU threads 4 --- --- [Sat Dec 11 12:43:52 2021] Available memory: 1081385017344, used: 973246515609 --- [Sat Dec 11 12:43:53 2021] Converting reads to binaries --- /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/conda/anaconda3/envs/de_novo_example/bin/megahit_asm_core buildlib megahit_default_assembly/tmp/reads.lib megahit_default_assembly/tmp/reads.lib b' [read_lib_functions-inl.h : 209] Lib 0 (BCep_R1_QCd_err_cor.fastq.gz,BCep_R2_QCd_err_cor.fastq.gz): pe, 2969452 reads, 140 max length' b' [utils.h : 126] Real: 5.1948\tuser: 3.9757\tsys: 0.5482\tmaxrss: 163724' --- [Sat Dec 11 12:43:58 2021] k list: 21,29,39,59,79,99,119,141 --- --- [Sat Dec 11 12:43:58 2021] Extracting solid (k+1)-mers for k = 21 --- cmd: /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/conda/anaconda3/envs/de_novo_example/bin/megahit_sdbg_build count -k 21 -m 2 --host_mem 973246515609 --mem_flag 1 --gpu_mem 0 --output_prefix megahit_default_assembly/tmp/k21/21 --num_cpu_threads 4 --num_output_threads 1 --read_lib_file megahit_default_assembly/tmp/reads.lib b' [sdbg_builder.cpp : 112] Host memory to be used: 973246515609' b' [sdbg_builder.cpp : 113] Number CPU threads: 4' b' [cx1.h : 450] Preparing data...' b' [read_lib_functions-inl.h : 256] Before reading, sizeof seq_package: 127686404' b' [read_lib_functions-inl.h : 260] After reading, sizeof seq_package: 127686404' b' [cx1_kmer_count.cpp : 136] 2969452 reads, 140 max read length' b' [cx1.h : 457] Preparing data... Done. Time elapsed: 0.5507' b' [cx1.h : 464] Preparing partitions and initialing global data...' b' [cx1_kmer_count.cpp : 227] 2 words per substring, 2 words per edge' b' [cx1_kmer_count.cpp : 322] Set: 195950356, 973098108101' b' [cx1_kmer_count.cpp : 356] 47115283, 312051 195950356 973098108101' b' [cx1_kmer_count.cpp : 363] Memory for reads: 130934268' b' [cx1_kmer_count.cpp : 364] max # lv.1 items = 47115283' b' [cx1.h : 480] Preparing partitions and initialing global data... Done. Time elapsed: 1.1701' b' [cx1.h : 486] Start main loop...' b' [cx1.h : 515] Lv1 scanning from bucket 0 to 362' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 1.6129' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 2.7048' b' [cx1.h : 515] Lv1 scanning from bucket 362 to 1135' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 1.5796' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 3.7593' b' [cx1.h : 515] Lv1 scanning from bucket 1135 to 2451' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 1.6297' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 4.0423' b' [cx1.h : 515] Lv1 scanning from bucket 2451 to 4592' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 1.6410' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 4.2702' b' [cx1.h : 515] Lv1 scanning from bucket 4592 to 8065' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 1.6796' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 4.3423' b' [cx1.h : 515] Lv1 scanning from bucket 8065 to 14221' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 1.7507' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 4.3331' b' [cx1.h : 515] Lv1 scanning from bucket 14221 to 28966' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 1.8104' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 3.9718' b' [cx1.h : 515] Lv1 scanning from bucket 28966 to 65536' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 1.5866' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 2.2400' b' [cx1.h : 607] Main loop done. Time elapsed: 42.9553' b' [cx1.h : 613] Postprocessing...' b' [cx1_kmer_count.cpp : 860] Total number of candidate reads: 735(3299)' b' [cx1_kmer_count.cpp : 871] Total number of solid edges: 8787628' b' [cx1.h : 621] Postprocess done. Time elapsed: 0.1551' b' [utils.h : 126] Real: 44.8551\tuser: 170.7475\tsys: 5.3365\tmaxrss: 356372' --- [Sat Dec 11 12:44:43 2021] Building graph for k = 21 --- /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/conda/anaconda3/envs/de_novo_example/bin/megahit_sdbg_build seq2sdbg --host_mem 973246515609 --mem_flag 1 --gpu_mem 0 --output_prefix megahit_default_assembly/tmp/k21/21 --num_cpu_threads 4 -k 21 --kmer_from 0 --num_edge_files 1 --input_prefix megahit_default_assembly/tmp/k21/21 --need_mercy b' [sdbg_builder.cpp : 339] Host memory to be used: 973246515609' b' [sdbg_builder.cpp : 340] Number CPU threads: 4' b' [cx1.h : 450] Preparing data...' b' [cx1_seq2sdbg.cpp : 394] Number edges: 8787628' b' [cx1_seq2sdbg.cpp : 434] Bases to reserve: 241659770, number contigs: 0, number multiplicity: 10984535' b' [cx1_seq2sdbg.cpp : 440] Before reading, sizeof seq_package: 60414952, multiplicity vector: 10984535' b' [cx1_seq2sdbg.cpp : 455] Adding mercy edges...' b' [cx1_seq2sdbg.cpp : 373] Number of reads: 735, Number of mercy edges: 5052' b' [cx1_seq2sdbg.cpp : 462] Done. Time elapsed: 0.2913' b' [cx1_seq2sdbg.cpp : 529] After reading, sizeof seq_package: 60414952, multiplicity vector: 10984535' b' [cx1.h : 457] Preparing data... Done. Time elapsed: 1.0383' b' [cx1.h : 464] Preparing partitions and initialing global data...' b' [cx1_seq2sdbg.cpp : 740] Memory for sequence: 79511584' b' [cx1_seq2sdbg.cpp : 741] max # lv.1 items = 7034144' b' [cx1.h : 480] Preparing partitions and initialing global data... Done. Time elapsed: 0.1378' b' [cx1.h : 486] Start main loop...' b' [cx1.h : 515] Lv1 scanning from bucket 0 to 447' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 0.1269' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 0.4076' b' [cx1.h : 515] Lv1 scanning from bucket 447 to 1439' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 0.1183' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 0.4562' b' [cx1.h : 515] Lv1 scanning from bucket 1439 to 3130' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 0.1208' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 0.4469' b' [cx1.h : 515] Lv1 scanning from bucket 3130 to 5843' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 0.1535' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 0.4366' b' [cx1.h : 515] Lv1 scanning from bucket 5843 to 10232' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 0.1266' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 0.5011' b' [cx1.h : 515] Lv1 scanning from bucket 10232 to 17823' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 0.2064' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 0.5432' b' [cx1.h : 515] Lv1 scanning from bucket 17823 to 34455' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 0.1374' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 0.5245' b' [cx1.h : 515] Lv1 scanning from bucket 34455 to 65536' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 0.1200' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 0.2430' b' [cx1.h : 607] Main loop done. Time elapsed: 4.6704' b' [cx1.h : 613] Postprocessing...' b' [cx1_seq2sdbg.cpp :1139] Number of $ A C G T A- C- G- T-:' b' [cx1_seq2sdbg.cpp :1142] 11444 2895615 5876566 5868415 2897940 9332 19471 19863 9446' b' [cx1_seq2sdbg.cpp :1151] Total number of edges: 17608092' b' [cx1_seq2sdbg.cpp :1152] Total number of ONEs: 17538536' b' [cx1_seq2sdbg.cpp :1153] Total number of $v edges: 11444' b' [cx1.h : 621] Postprocess done. Time elapsed: 0.1068' b' [utils.h : 126] Real: 5.9669\tuser: 19.0902\tsys: 0.8876\tmaxrss: 330384' --- [Sat Dec 11 12:44:49 2021] Assembling contigs from SdBG for k = 21 --- cmd: /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/conda/anaconda3/envs/de_novo_example/bin/megahit_asm_core assemble -s megahit_default_assembly/tmp/k21/21 -o megahit_default_assembly/intermediate_contigs/k21 -t 4 --min_standalone 300.0 --prune_level 2 --merge_len 20 --merge_similar 0.95 --low_local_ratio 0.2 --min_depth 2 --bubble_level 2 --max_tip_len -1 --careful_bubble b' [assembler.cpp : 148] Loading succinct de Bruijn graph: megahit_default_assembly/tmp/k21/21 Done. Time elapsed: 0.668383' b' [assembler.cpp : 152] Number of Edges: 17608092; K value: 21' b' [assembler.cpp : 162] Number of CPU threads: 4' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 2; Accumulated tips removed: 2830; time elapsed: 0.3164' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 4; Accumulated tips removed: 7754; time elapsed: 0.3261' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 8; Accumulated tips removed: 12980; time elapsed: 0.3372' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 16; Accumulated tips removed: 18604; time elapsed: 0.3526' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 32; Accumulated tips removed: 21192; time elapsed: 0.3271' b' [assembly_algorithms.cpp : 170] Removing tips with length less than 42; Accumulated tips removed: 21250; time elapsed: 0.3168' b' [assembler.cpp : 179] Tips removal done! Time elapsed(sec): 1.977948' b' [assembler.cpp : 188] unitig graph size: 67961, time for building: 4.277845' b' [assembler.cpp : 211] Number of bubbles removed: 11543, Time elapsed(sec): 0.098289' b' [assembler.cpp : 225] Number of complex bubbles removed: 484, Time elapsed(sec): 0.093724' b' [assembler.cpp : 243] Number unitigs disconnected: 20349, time: 0.042208' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 156, time: 0.017856' b' [assembler.cpp : 200] Tips removed: 72, time: 0.049047' b' [assembler.cpp : 211] Number of bubbles removed: 132, Time elapsed(sec): 0.020023' b' [assembler.cpp : 225] Number of complex bubbles removed: 46, Time elapsed(sec): 0.068001' b' [assembler.cpp : 243] Number unitigs disconnected: 7738, time: 0.030494' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 5, time: 0.014455' b' [assembler.cpp : 200] Tips removed: 7111, time: 0.056996' b' [assembler.cpp : 211] Number of bubbles removed: 146, Time elapsed(sec): 0.017141' b' [assembler.cpp : 225] Number of complex bubbles removed: 7, Time elapsed(sec): 0.069356' b' [assembler.cpp : 243] Number unitigs disconnected: 81, time: 0.015620' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 0, time: 0.006300' b' [assembler.cpp : 200] Tips removed: 46, time: 0.032068' b' [assembler.cpp : 211] Number of bubbles removed: 0, Time elapsed(sec): 0.011133' b' [assembler.cpp : 225] Number of complex bubbles removed: 0, Time elapsed(sec): 0.067485' b' [assembler.cpp : 243] Number unitigs disconnected: 2, time: 0.015422' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 0, time: 0.006203' b' [assembler.cpp : 200] Tips removed: 2, time: 0.031462' b' [assembler.cpp : 211] Number of bubbles removed: 0, Time elapsed(sec): 0.019059' b' [assembler.cpp : 225] Number of complex bubbles removed: 0, Time elapsed(sec): 0.074783' b' [assembler.cpp : 243] Number unitigs disconnected: 0, time: 0.016899' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 0, time: 0.006851' b' [assembler.cpp : 132] Total length: 8953118, N50: 1372, Mean: 376, number of contigs: 23755' b' [assembler.cpp : 133] Maximum length: 24729' b' [assembler.cpp : 290] Time to output: 1.124398' b' [assembler.cpp : 317] Number of local low depth unitigs removed: 956, complex bubbles removed: 7, time: 0.541559' b' [assembler.cpp : 132] Total length: 8884750, N50: 1431, Mean: 414, number of contigs: 21429' b' [assembler.cpp : 133] Maximum length: 24729' b' [utils.h : 126] Real: 10.4685\tuser: 36.9987\tsys: 0.5057\tmaxrss: 48008' --- [Sat Dec 11 12:44:59 2021] Local assembling k = 21 --- cmd: /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/conda/anaconda3/envs/de_novo_example/bin/megahit_asm_core local -c megahit_default_assembly/intermediate_contigs/k21.contigs.fa -l megahit_default_assembly/tmp/reads.lib -t 4 -o megahit_default_assembly/intermediate_contigs/k21.local.fa --kmax 29 b' [local_assembler.cpp : 89] Number of contigs: 8002, Mapper size: 987358' b' [read_lib_functions-inl.h : 256] Before reading, sizeof seq_package: 127686404' b' [read_lib_functions-inl.h : 260] After reading, sizeof seq_package: 127686404' b' [local_assembler.cpp : 330] Lib 0, insert size: 359.03 sd: 104.40' b' [local_assembler.cpp : 462] Lib 0: total 2969452 reads, aligned 2775293, added 883930 reads for local assembly' b' [utils.h : 126] Real: 39.4895\tuser: 152.2800\tsys: 0.9567\tmaxrss: 171280' --- [Sat Dec 11 12:45:39 2021] Extracting iterative edges from k = 21 to 29 --- cmd: /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/conda/anaconda3/envs/de_novo_example/bin/megahit_asm_core iterate -c megahit_default_assembly/intermediate_contigs/k21.contigs.fa -b megahit_default_assembly/intermediate_contigs/k21.bubble_seq.fa -t 4 -k 21 -s 8 -o megahit_default_assembly/tmp/k29/29 -r megahit_default_assembly/tmp/reads.lib.bin -f binary b' [iterate_edges.cpp : 570] Number of crusial kmers: 3870' b' [iterate_edges.cpp : 570] Number of crusial kmers: 48067' b' [iterate_edges.cpp : 447] Total: 2969452, aligned: 515673. Iterative edges: 225760' b' [iterate_edges.cpp : 451] Writing iterative edges...' b' [utils.h : 126] Real: 20.3373\tuser: 59.5399\tsys: 0.3222\tmaxrss: 166612' --- [Sat Dec 11 12:45:59 2021] Building graph for k = 29 --- /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/conda/anaconda3/envs/de_novo_example/bin/megahit_sdbg_build seq2sdbg --host_mem 973246515609 --mem_flag 1 --gpu_mem 0 --output_prefix megahit_default_assembly/tmp/k29/29 --num_cpu_threads 4 -k 29 --kmer_from 21 --num_edge_files 1 --input_prefix megahit_default_assembly/tmp/k29/29 --addi_contig megahit_default_assembly/intermediate_contigs/k21.addi.fa --local_contig megahit_default_assembly/intermediate_contigs/k21.local.fa --contig megahit_default_assembly/intermediate_contigs/k21.contigs.fa --bubble megahit_default_assembly/intermediate_contigs/k21.bubble_seq.fa b' [sdbg_builder.cpp : 339] Host memory to be used: 973246515609' b' [sdbg_builder.cpp : 340] Number CPU threads: 4' b' [cx1.h : 450] Preparing data...' b' [cx1_seq2sdbg.cpp : 394] Number edges: 225760' b' [cx1_seq2sdbg.cpp : 434] Bases to reserve: 40369247, number contigs: 66928, number multiplicity: 292688' b' [cx1_seq2sdbg.cpp : 440] Before reading, sizeof seq_package: 10627744, multiplicity vector: 292688' b' [cx1_seq2sdbg.cpp : 529] After reading, sizeof seq_package: 10627744, multiplicity vector: 292688' b' [cx1.h : 457] Preparing data... Done. Time elapsed: 0.1110' b' [cx1.h : 464] Preparing partitions and initialing global data...' b' [cx1_seq2sdbg.cpp : 740] Memory for sequence: 11412514' b' [cx1_seq2sdbg.cpp : 741] max # lv.1 items = 6660914' b' [cx1.h : 480] Preparing partitions and initialing global data... Done. Time elapsed: 0.1857' b' [cx1.h : 486] Start main loop...' b' [cx1.h : 515] Lv1 scanning from bucket 0 to 405' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 0.2803' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 0.3055' b' [cx1.h : 515] Lv1 scanning from bucket 405 to 1306' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 0.2886' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 0.3726' b' [cx1.h : 515] Lv1 scanning from bucket 1306 to 2832' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 0.2978' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 0.4260' b' [cx1.h : 515] Lv1 scanning from bucket 2832 to 5298' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 0.3111' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 0.4034' b' [cx1.h : 515] Lv1 scanning from bucket 5298 to 9317' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 0.3128' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 0.3969' b' [cx1.h : 515] Lv1 scanning from bucket 9317 to 16357' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 0.3299' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 0.4640' b' [cx1.h : 515] Lv1 scanning from bucket 16357 to 32330' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 0.3249' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 0.4342' b' [cx1.h : 515] Lv1 scanning from bucket 32330 to 65536' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 0.2468' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 0.1946' b' [cx1.h : 607] Main loop done. Time elapsed: 5.3898' b' [cx1.h : 613] Postprocessing...' b' [cx1_seq2sdbg.cpp :1139] Number of $ A C G T A- C- G- T-:' b' [cx1_seq2sdbg.cpp :1142] 3699 2832759 5675564 5675811 2833002 1245 2497 2370 1229' b' [cx1_seq2sdbg.cpp :1151] Total number of edges: 17028176' b' [cx1_seq2sdbg.cpp :1152] Total number of ONEs: 17017136' b' [cx1_seq2sdbg.cpp :1153] Total number of $v edges: 3699' b' [cx1.h : 621] Postprocess done. Time elapsed: 0.0927' b' [utils.h : 126] Real: 5.7818\tuser: 14.6828\tsys: 0.1286\tmaxrss: 55044' --- [Sat Dec 11 12:46:05 2021] Assembling contigs from SdBG for k = 29 --- cmd: /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/conda/anaconda3/envs/de_novo_example/bin/megahit_asm_core assemble -s megahit_default_assembly/tmp/k29/29 -o megahit_default_assembly/intermediate_contigs/k29 -t 4 --min_standalone 300.0 --prune_level 2 --merge_len 20 --merge_similar 0.95 --low_local_ratio 0.2 --min_depth 2 --bubble_level 2 --max_tip_len -1 --careful_bubble b' [assembler.cpp : 148] Loading succinct de Bruijn graph: megahit_default_assembly/tmp/k29/29 Done. Time elapsed: 0.645961' b' [assembler.cpp : 152] Number of Edges: 17028176; K value: 29' b' [assembler.cpp : 162] Number of CPU threads: 4' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 2; Accumulated tips removed: 1210; time elapsed: 0.2976' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 4; Accumulated tips removed: 2034; time elapsed: 0.3028' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 8; Accumulated tips removed: 2800; time elapsed: 0.3084' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 16; Accumulated tips removed: 4320; time elapsed: 0.3251' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 32; Accumulated tips removed: 5324; time elapsed: 0.3091' b' [assembly_algorithms.cpp : 170] Removing tips with length less than 58; Accumulated tips removed: 5550; time elapsed: 0.3050' b' [assembler.cpp : 179] Tips removal done! Time elapsed(sec): 1.849344' b' [assembler.cpp : 188] unitig graph size: 7895, time for building: 3.518937' b' [assembler.cpp : 211] Number of bubbles removed: 1372, Time elapsed(sec): 0.756039' b' [assembler.cpp : 225] Number of complex bubbles removed: 293, Time elapsed(sec): 0.086195' b' [assembler.cpp : 243] Number unitigs disconnected: 288, time: 0.002801' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 135, time: 0.002690' b' [assembler.cpp : 200] Tips removed: 0, time: 0.004965' b' [assembler.cpp : 211] Number of bubbles removed: 6, Time elapsed(sec): 0.042807' b' [assembler.cpp : 225] Number of complex bubbles removed: 8, Time elapsed(sec): 0.039792' b' [assembler.cpp : 243] Number unitigs disconnected: 2, time: 0.002663' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 0, time: 0.001191' b' [assembler.cpp : 200] Tips removed: 0, time: 0.005857' b' [assembler.cpp : 211] Number of bubbles removed: 0, Time elapsed(sec): 0.002136' b' [assembler.cpp : 225] Number of complex bubbles removed: 0, Time elapsed(sec): 0.040448' b' [assembler.cpp : 243] Number unitigs disconnected: 0, time: 0.002498' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 0, time: 0.001173' b' [assembler.cpp : 132] Total length: 8593107, N50: 13852, Mean: 1889, number of contigs: 4548' b' [assembler.cpp : 133] Maximum length: 73092' b' [assembler.cpp : 290] Time to output: 1.038103' b' [assembler.cpp : 317] Number of local low depth unitigs removed: 16, complex bubbles removed: 5, time: 0.088700' b' [assembler.cpp : 132] Total length: 8534392, N50: 13868, Mean: 1925, number of contigs: 4433' b' [assembler.cpp : 133] Maximum length: 73092' b' [utils.h : 126] Real: 9.3126\tuser: 31.7720\tsys: 0.4391\tmaxrss: 44552' --- [Sat Dec 11 12:46:14 2021] Local assembling k = 29 --- cmd: /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/conda/anaconda3/envs/de_novo_example/bin/megahit_asm_core local -c megahit_default_assembly/intermediate_contigs/k29.contigs.fa -l megahit_default_assembly/tmp/reads.lib -t 4 -o megahit_default_assembly/intermediate_contigs/k29.local.fa --kmax 39 b' [local_assembler.cpp : 89] Number of contigs: 1516, Mapper size: 1043139' b' [read_lib_functions-inl.h : 256] Before reading, sizeof seq_package: 127686404' b' [read_lib_functions-inl.h : 260] After reading, sizeof seq_package: 127686404' b' [local_assembler.cpp : 330] Lib 0, insert size: 373.18 sd: 107.22' b' [local_assembler.cpp : 462] Lib 0: total 2969452 reads, aligned 2918061, added 159850 reads for local assembly' b' [utils.h : 126] Real: 27.9629\tuser: 106.3312\tsys: 0.4439\tmaxrss: 161888' --- [Sat Dec 11 12:46:42 2021] Extracting iterative edges from k = 29 to 39 --- cmd: /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/conda/anaconda3/envs/de_novo_example/bin/megahit_asm_core iterate -c megahit_default_assembly/intermediate_contigs/k29.contigs.fa -b megahit_default_assembly/intermediate_contigs/k29.bubble_seq.fa -t 4 -k 29 -s 10 -o megahit_default_assembly/tmp/k39/39 -r megahit_default_assembly/tmp/reads.lib.bin -f binary b' [iterate_edges.cpp : 570] Number of crusial kmers: 3957' b' [iterate_edges.cpp : 570] Number of crusial kmers: 11937' b' [iterate_edges.cpp : 447] Total: 2969452, aligned: 127407. Iterative edges: 72680' b' [iterate_edges.cpp : 451] Writing iterative edges...' b' [utils.h : 126] Real: 19.9342\tuser: 57.4050\tsys: 0.5546\tmaxrss: 164504' --- [Sat Dec 11 12:47:02 2021] Building graph for k = 39 --- /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/conda/anaconda3/envs/de_novo_example/bin/megahit_sdbg_build seq2sdbg --host_mem 973246515609 --mem_flag 1 --gpu_mem 0 --output_prefix megahit_default_assembly/tmp/k39/39 --num_cpu_threads 4 -k 39 --kmer_from 29 --num_edge_files 1 --input_prefix megahit_default_assembly/tmp/k39/39 --addi_contig megahit_default_assembly/intermediate_contigs/k29.addi.fa --local_contig megahit_default_assembly/intermediate_contigs/k29.local.fa --contig megahit_default_assembly/intermediate_contigs/k29.contigs.fa --bubble megahit_default_assembly/intermediate_contigs/k29.bubble_seq.fa b' [sdbg_builder.cpp : 339] Host memory to be used: 973246515609' b' [sdbg_builder.cpp : 340] Number CPU threads: 4' b' [cx1.h : 450] Preparing data...' b' [cx1_seq2sdbg.cpp : 394] Number edges: 72680' b' [cx1_seq2sdbg.cpp : 434] Bases to reserve: 29104883, number contigs: 16892, number multiplicity: 89572' b' [cx1_seq2sdbg.cpp : 440] Before reading, sizeof seq_package: 7411368, multiplicity vector: 89572' b' [cx1_seq2sdbg.cpp : 529] After reading, sizeof seq_package: 7411368, multiplicity vector: 89572' b' [cx1.h : 457] Preparing data... Done. Time elapsed: 0.0729' b' [cx1.h : 464] Preparing partitions and initialing global data...' b' [cx1_seq2sdbg.cpp : 740] Memory for sequence: 7740250' b' [cx1_seq2sdbg.cpp : 741] max # lv.1 items = 4691500' b' [cx1.h : 480] Preparing partitions and initialing global data... Done. Time elapsed: 0.1504' b' [cx1.h : 486] Start main loop...' b' [cx1.h : 515] Lv1 scanning from bucket 0 to 449' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 0.1966' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 0.2730' b' [cx1.h : 515] Lv1 scanning from bucket 449 to 1442' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 0.2049' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 0.3744' b' [cx1.h : 515] Lv1 scanning from bucket 1442 to 3117' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 0.2141' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 0.3450' b' [cx1.h : 515] Lv1 scanning from bucket 3117 to 5793' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 0.2221' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 0.3770' b' [cx1.h : 515] Lv1 scanning from bucket 5793 to 10112' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 0.2328' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 0.3888' b' [cx1.h : 515] Lv1 scanning from bucket 10112 to 17581' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 0.2294' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 0.3377' b' [cx1.h : 515] Lv1 scanning from bucket 17581 to 34062' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 0.2354' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 0.3865' b' [cx1.h : 515] Lv1 scanning from bucket 34062 to 65536' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 0.1675' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 0.1495' b' [cx1.h : 607] Main loop done. Time elapsed: 4.3353' b' [cx1.h : 613] Postprocessing...' b' [cx1_seq2sdbg.cpp :1139] Number of $ A C G T A- C- G- T-:' b' [cx1_seq2sdbg.cpp :1142] 505 2829921 5663085 5663202 2830330 456 1153 1117 449' b' [cx1_seq2sdbg.cpp :1151] Total number of edges: 16990218' b' [cx1_seq2sdbg.cpp :1152] Total number of ONEs: 16986538' b' [cx1_seq2sdbg.cpp :1153] Total number of $v edges: 505' b' [cx1.h : 621] Postprocess done. Time elapsed: 0.1083' b' [utils.h : 126] Real: 4.6687\tuser: 12.4019\tsys: 0.1247\tmaxrss: 43424' --- [Sat Dec 11 12:47:07 2021] Assembling contigs from SdBG for k = 39 --- cmd: /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/conda/anaconda3/envs/de_novo_example/bin/megahit_asm_core assemble -s megahit_default_assembly/tmp/k39/39 -o megahit_default_assembly/intermediate_contigs/k39 -t 4 --min_standalone 300.0 --prune_level 2 --merge_len 20 --merge_similar 0.95 --low_local_ratio 0.2 --min_depth 2 --bubble_level 2 --max_tip_len -1 --careful_bubble b' [assembler.cpp : 148] Loading succinct de Bruijn graph: megahit_default_assembly/tmp/k39/39 Done. Time elapsed: 0.635935' b' [assembler.cpp : 152] Number of Edges: 16990218; K value: 39' b' [assembler.cpp : 162] Number of CPU threads: 4' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 2; Accumulated tips removed: 80; time elapsed: 0.2943' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 4; Accumulated tips removed: 180; time elapsed: 0.2945' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 8; Accumulated tips removed: 309; time elapsed: 0.2965' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 16; Accumulated tips removed: 417; time elapsed: 0.3139' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 32; Accumulated tips removed: 499; time elapsed: 0.3031' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 64; Accumulated tips removed: 645; time elapsed: 0.3013' b' [assembly_algorithms.cpp : 170] Removing tips with length less than 78; Accumulated tips removed: 677; time elapsed: 0.3002' b' [assembler.cpp : 179] Tips removal done! Time elapsed(sec): 2.105157' b' [assembler.cpp : 188] unitig graph size: 4331, time for building: 3.453885' b' [assembler.cpp : 211] Number of bubbles removed: 852, Time elapsed(sec): 1.514259' b' [assembler.cpp : 225] Number of complex bubbles removed: 177, Time elapsed(sec): 0.144841' b' [assembler.cpp : 243] Number unitigs disconnected: 96, time: 0.001077' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 42, time: 0.001152' b' [assembler.cpp : 200] Tips removed: 1, time: 0.003370' b' [assembler.cpp : 211] Number of bubbles removed: 2, Time elapsed(sec): 0.002522' b' [assembler.cpp : 225] Number of complex bubbles removed: 12, Time elapsed(sec): 0.024543' b' [assembler.cpp : 243] Number unitigs disconnected: 1, time: 0.000965' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 0, time: 0.000372' b' [assembler.cpp : 200] Tips removed: 1, time: 0.002912' b' [assembler.cpp : 211] Number of bubbles removed: 0, Time elapsed(sec): 0.000881' b' [assembler.cpp : 225] Number of complex bubbles removed: 0, Time elapsed(sec): 0.023070' b' [assembler.cpp : 243] Number unitigs disconnected: 0, time: 0.000964' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 0, time: 0.000369' b' [assembler.cpp : 132] Total length: 8548912, N50: 28977, Mean: 3623, number of contigs: 2359' b' [assembler.cpp : 133] Maximum length: 109341' b' [assembler.cpp : 290] Time to output: 0.988141' b' [assembler.cpp : 317] Number of local low depth unitigs removed: 1, complex bubbles removed: 0, time: 0.036165' b' [assembler.cpp : 132] Total length: 8464055, N50: 28848, Mean: 3629, number of contigs: 2332' b' [assembler.cpp : 133] Maximum length: 109341' b' [utils.h : 126] Real: 9.9122\tuser: 33.3955\tsys: 0.4390\tmaxrss: 44508' --- [Sat Dec 11 12:47:17 2021] Local assembling k = 39 --- cmd: /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/conda/anaconda3/envs/de_novo_example/bin/megahit_asm_core local -c megahit_default_assembly/intermediate_contigs/k39.contigs.fa -l megahit_default_assembly/tmp/reads.lib -t 4 -o megahit_default_assembly/intermediate_contigs/k39.local.fa --kmax 59 b' [local_assembler.cpp : 89] Number of contigs: 854, Mapper size: 1050942' b' [read_lib_functions-inl.h : 256] Before reading, sizeof seq_package: 127686404' b' [read_lib_functions-inl.h : 260] After reading, sizeof seq_package: 127686404' b' [local_assembler.cpp : 330] Lib 0, insert size: 374.49 sd: 107.34' b' [local_assembler.cpp : 462] Lib 0: total 2969452 reads, aligned 2919425, added 79983 reads for local assembly' b' [utils.h : 126] Real: 21.0725\tuser: 81.7372\tsys: 0.4379\tmaxrss: 165408' --- [Sat Dec 11 12:47:38 2021] Extracting iterative edges from k = 39 to 59 --- cmd: /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/conda/anaconda3/envs/de_novo_example/bin/megahit_asm_core iterate -c megahit_default_assembly/intermediate_contigs/k39.contigs.fa -b megahit_default_assembly/intermediate_contigs/k39.bubble_seq.fa -t 4 -k 39 -s 20 -o megahit_default_assembly/tmp/k59/59 -r megahit_default_assembly/tmp/reads.lib.bin -f binary b' [iterate_edges.cpp : 570] Number of crusial kmers: 2936' b' [iterate_edges.cpp : 570] Number of crusial kmers: 6928' b' [iterate_edges.cpp : 447] Total: 2969452, aligned: 72635. Iterative edges: 81567' b' [iterate_edges.cpp : 451] Writing iterative edges...' b' [utils.h : 126] Real: 17.8430\tuser: 51.3760\tsys: 0.3412\tmaxrss: 164300' --- [Sat Dec 11 12:47:56 2021] Building graph for k = 59 --- /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/conda/anaconda3/envs/de_novo_example/bin/megahit_sdbg_build seq2sdbg --host_mem 973246515609 --mem_flag 1 --gpu_mem 0 --output_prefix megahit_default_assembly/tmp/k59/59 --num_cpu_threads 4 -k 59 --kmer_from 39 --num_edge_files 1 --input_prefix megahit_default_assembly/tmp/k59/59 --addi_contig megahit_default_assembly/intermediate_contigs/k39.addi.fa --local_contig megahit_default_assembly/intermediate_contigs/k39.local.fa --contig megahit_default_assembly/intermediate_contigs/k39.contigs.fa --bubble megahit_default_assembly/intermediate_contigs/k39.bubble_seq.fa b' [sdbg_builder.cpp : 339] Host memory to be used: 973246515609' b' [sdbg_builder.cpp : 340] Number CPU threads: 4' b' [cx1.h : 450] Preparing data...' b' [cx1_seq2sdbg.cpp : 394] Number edges: 81567' b' [cx1_seq2sdbg.cpp : 434] Bases to reserve: 34844315, number contigs: 9856, number multiplicity: 91423' b' [cx1_seq2sdbg.cpp : 440] Before reading, sizeof seq_package: 8789936, multiplicity vector: 91423' b' [cx1_seq2sdbg.cpp : 529] After reading, sizeof seq_package: 8789936, multiplicity vector: 91423' b' [cx1.h : 457] Preparing data... Done. Time elapsed: 0.0804' b' [cx1.h : 464] Preparing partitions and initialing global data...' b' [cx1_seq2sdbg.cpp : 740] Memory for sequence: 9172418' b' [cx1_seq2sdbg.cpp : 741] max # lv.1 items = 5706255' b' [cx1.h : 480] Preparing partitions and initialing global data... Done. Time elapsed: 0.2155' b' [cx1.h : 486] Start main loop...' b' [cx1.h : 515] Lv1 scanning from bucket 0 to 433' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 0.2383' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 0.2766' b' [cx1.h : 515] Lv1 scanning from bucket 433 to 1411' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 0.2538' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 0.3460' b' [cx1.h : 515] Lv1 scanning from bucket 1411 to 3073' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 0.2609' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 0.3782' b' [cx1.h : 515] Lv1 scanning from bucket 3073 to 5743' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 0.2738' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 0.3565' b' [cx1.h : 515] Lv1 scanning from bucket 5743 to 10068' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 0.2785' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 0.3857' b' [cx1.h : 515] Lv1 scanning from bucket 10068 to 17581' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 0.2857' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 0.4420' b' [cx1.h : 515] Lv1 scanning from bucket 17581 to 34233' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 0.2961' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 0.3938' b' [cx1.h : 515] Lv1 scanning from bucket 34233 to 65536' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 0.2104' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 0.1878' b' [cx1.h : 607] Main loop done. Time elapsed: 4.8646' b' [cx1.h : 613] Postprocessing...' b' [cx1_seq2sdbg.cpp :1139] Number of $ A C G T A- C- G- T-:' b' [cx1_seq2sdbg.cpp :1142] 453 2834505 5673510 5673837 2835058 308 657 594 319' b' [cx1_seq2sdbg.cpp :1151] Total number of edges: 17019241' b' [cx1_seq2sdbg.cpp :1152] Total number of ONEs: 17016910' b' [cx1_seq2sdbg.cpp :1153] Total number of $v edges: 453' b' [cx1.h : 621] Postprocess done. Time elapsed: 0.1004' b' [utils.h : 126] Real: 5.2628\tuser: 13.4006\tsys: 0.1228\tmaxrss: 49164' --- [Sat Dec 11 12:48:01 2021] Assembling contigs from SdBG for k = 59 --- cmd: /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/conda/anaconda3/envs/de_novo_example/bin/megahit_asm_core assemble -s megahit_default_assembly/tmp/k59/59 -o megahit_default_assembly/intermediate_contigs/k59 -t 4 --min_standalone 300.0 --prune_level 2 --merge_len 20 --merge_similar 0.95 --low_local_ratio 0.2 --min_depth 2 --bubble_level 2 --max_tip_len -1 --careful_bubble b' [assembler.cpp : 148] Loading succinct de Bruijn graph: megahit_default_assembly/tmp/k59/59 Done. Time elapsed: 0.641057' b' [assembler.cpp : 152] Number of Edges: 17019241; K value: 59' b' [assembler.cpp : 162] Number of CPU threads: 4' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 2; Accumulated tips removed: 18; time elapsed: 0.2990' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 4; Accumulated tips removed: 69; time elapsed: 0.2959' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 8; Accumulated tips removed: 130; time elapsed: 0.3065' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 16; Accumulated tips removed: 253; time elapsed: 0.3326' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 32; Accumulated tips removed: 365; time elapsed: 0.3080' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 64; Accumulated tips removed: 597; time elapsed: 0.3036' b' [assembly_algorithms.cpp : 170] Removing tips with length less than 118; Accumulated tips removed: 649; time elapsed: 0.3021' b' [assembler.cpp : 179] Tips removal done! Time elapsed(sec): 2.149312' b' [assembler.cpp : 188] unitig graph size: 2411, time for building: 3.320726' b' [assembler.cpp : 211] Number of bubbles removed: 562, Time elapsed(sec): 1.869661' b' [assembler.cpp : 225] Number of complex bubbles removed: 110, Time elapsed(sec): 0.206245' b' [assembler.cpp : 243] Number unitigs disconnected: 106, time: 0.000543' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 52, time: 0.000752' b' [assembler.cpp : 200] Tips removed: 0, time: 0.001161' b' [assembler.cpp : 211] Number of bubbles removed: 6, Time elapsed(sec): 0.002816' b' [assembler.cpp : 225] Number of complex bubbles removed: 7, Time elapsed(sec): 0.031925' b' [assembler.cpp : 243] Number unitigs disconnected: 2, time: 0.000407' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 0, time: 0.000132' b' [assembler.cpp : 200] Tips removed: 1, time: 0.001134' b' [assembler.cpp : 211] Number of bubbles removed: 0, Time elapsed(sec): 0.000319' b' [assembler.cpp : 225] Number of complex bubbles removed: 0, Time elapsed(sec): 0.018332' b' [assembler.cpp : 243] Number unitigs disconnected: 0, time: 0.000402' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 0, time: 0.000125' b' [assembler.cpp : 132] Total length: 8530213, N50: 57420, Mean: 8062, number of contigs: 1058' b' [assembler.cpp : 133] Maximum length: 314414' b' [assembler.cpp : 290] Time to output: 1.130858' b' [assembler.cpp : 317] Number of local low depth unitigs removed: 0, complex bubbles removed: 0, time: 0.022125' b' [assembler.cpp : 132] Total length: 8269570, N50: 57447, Mean: 7905, number of contigs: 1046' b' [assembler.cpp : 133] Maximum length: 314414' b' [utils.h : 126] Real: 10.4874\tuser: 33.8615\tsys: 0.4050\tmaxrss: 44560' --- [Sat Dec 11 12:48:12 2021] Local assembling k = 59 --- cmd: /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/conda/anaconda3/envs/de_novo_example/bin/megahit_asm_core local -c megahit_default_assembly/intermediate_contigs/k59.contigs.fa -l megahit_default_assembly/tmp/reads.lib -t 4 -o megahit_default_assembly/intermediate_contigs/k59.local.fa --kmax 79 b' [local_assembler.cpp : 89] Number of contigs: 484, Mapper size: 1056698' b' [read_lib_functions-inl.h : 256] Before reading, sizeof seq_package: 127686404' b' [read_lib_functions-inl.h : 260] After reading, sizeof seq_package: 127686404' b' [local_assembler.cpp : 330] Lib 0, insert size: 375.00 sd: 107.44' b' [local_assembler.cpp : 462] Lib 0: total 2969452 reads, aligned 2912861, added 39798 reads for local assembly' b' [utils.h : 126] Real: 21.3508\tuser: 81.0685\tsys: 0.4499\tmaxrss: 164700' --- [Sat Dec 11 12:48:33 2021] Extracting iterative edges from k = 59 to 79 --- cmd: /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/conda/anaconda3/envs/de_novo_example/bin/megahit_asm_core iterate -c megahit_default_assembly/intermediate_contigs/k59.contigs.fa -b megahit_default_assembly/intermediate_contigs/k59.bubble_seq.fa -t 4 -k 59 -s 20 -o megahit_default_assembly/tmp/k79/79 -r megahit_default_assembly/tmp/reads.lib.bin -f binary b' [iterate_edges.cpp : 570] Number of crusial kmers: 1872' b' [iterate_edges.cpp : 570] Number of crusial kmers: 3618' b' [iterate_edges.cpp : 447] Total: 2969452, aligned: 38170. Iterative edges: 40129' b' [iterate_edges.cpp : 451] Writing iterative edges...' b' [utils.h : 126] Real: 13.8862\tuser: 38.9231\tsys: 0.3372\tmaxrss: 164316' --- [Sat Dec 11 12:48:47 2021] Building graph for k = 79 --- /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/conda/anaconda3/envs/de_novo_example/bin/megahit_sdbg_build seq2sdbg --host_mem 973246515609 --mem_flag 1 --gpu_mem 0 --output_prefix megahit_default_assembly/tmp/k79/79 --num_cpu_threads 4 -k 79 --kmer_from 59 --num_edge_files 1 --input_prefix megahit_default_assembly/tmp/k79/79 --addi_contig megahit_default_assembly/intermediate_contigs/k59.addi.fa --local_contig megahit_default_assembly/intermediate_contigs/k59.local.fa --contig megahit_default_assembly/intermediate_contigs/k59.contigs.fa --bubble megahit_default_assembly/intermediate_contigs/k59.bubble_seq.fa b' [sdbg_builder.cpp : 339] Host memory to be used: 973246515609' b' [sdbg_builder.cpp : 340] Number CPU threads: 4' b' [cx1.h : 450] Preparing data...' b' [cx1_seq2sdbg.cpp : 394] Number edges: 40129' b' [cx1_seq2sdbg.cpp : 434] Bases to reserve: 35831590, number contigs: 5295, number multiplicity: 45424' b' [cx1_seq2sdbg.cpp : 440] Before reading, sizeof seq_package: 9000268, multiplicity vector: 45424' b' [cx1_seq2sdbg.cpp : 529] After reading, sizeof seq_package: 9000268, multiplicity vector: 45424' b' [cx1.h : 457] Preparing data... Done. Time elapsed: 0.0875' b' [cx1.h : 464] Preparing partitions and initialing global data...' b' [cx1_seq2sdbg.cpp : 740] Memory for sequence: 9305670' b' [cx1_seq2sdbg.cpp : 741] max # lv.1 items = 6508618' b' [cx1.h : 480] Preparing partitions and initialing global data... Done. Time elapsed: 0.1841' b' [cx1.h : 486] Start main loop...' b' [cx1.h : 515] Lv1 scanning from bucket 0 to 423' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 0.2774' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 0.3935' b' [cx1.h : 515] Lv1 scanning from bucket 423 to 1393' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 0.2872' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 0.3059' b' [cx1.h : 515] Lv1 scanning from bucket 1393 to 3047' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 0.2997' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 0.3005' b' [cx1.h : 515] Lv1 scanning from bucket 3047 to 5713' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 0.3146' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 0.3692' b' [cx1.h : 515] Lv1 scanning from bucket 5713 to 10042' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 0.3211' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 0.4034' b' [cx1.h : 515] Lv1 scanning from bucket 10042 to 17585' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 0.3290' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 0.3820' b' [cx1.h : 515] Lv1 scanning from bucket 17585 to 34395' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 0.3338' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 0.3980' b' [cx1.h : 515] Lv1 scanning from bucket 34395 to 65536' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 0.2403' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 0.1603' b' [cx1.h : 607] Main loop done. Time elapsed: 5.1166' b' [cx1.h : 613] Postprocessing...' b' [cx1_seq2sdbg.cpp :1139] Number of $ A C G T A- C- G- T-:' b' [cx1_seq2sdbg.cpp :1142] 343 2835360 5674692 5674794 2835534 227 389 362 166' b' [cx1_seq2sdbg.cpp :1151] Total number of edges: 17021867' b' [cx1_seq2sdbg.cpp :1152] Total number of ONEs: 17020380' b' [cx1_seq2sdbg.cpp :1153] Total number of $v edges: 343' b' [cx1.h : 621] Postprocess done. Time elapsed: 0.1262' b' [utils.h : 126] Real: 5.5174\tuser: 13.4480\tsys: 0.1276\tmaxrss: 52892' --- [Sat Dec 11 12:48:53 2021] Assembling contigs from SdBG for k = 79 --- cmd: /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/conda/anaconda3/envs/de_novo_example/bin/megahit_asm_core assemble -s megahit_default_assembly/tmp/k79/79 -o megahit_default_assembly/intermediate_contigs/k79 -t 4 --min_standalone 300.0 --prune_level 2 --merge_len 20 --merge_similar 0.95 --low_local_ratio 0.2 --min_depth 2 --bubble_level 2 --max_tip_len -1 --careful_bubble b' [assembler.cpp : 148] Loading succinct de Bruijn graph: megahit_default_assembly/tmp/k79/79 Done. Time elapsed: 0.675854' b' [assembler.cpp : 152] Number of Edges: 17021867; K value: 79' b' [assembler.cpp : 162] Number of CPU threads: 4' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 2; Accumulated tips removed: 2; time elapsed: 0.2954' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 4; Accumulated tips removed: 22; time elapsed: 0.2979' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 8; Accumulated tips removed: 46; time elapsed: 0.2967' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 16; Accumulated tips removed: 94; time elapsed: 0.3079' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 32; Accumulated tips removed: 162; time elapsed: 0.3000' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 64; Accumulated tips removed: 268; time elapsed: 0.3014' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 128; Accumulated tips removed: 456; time elapsed: 0.3041' b' [assembly_algorithms.cpp : 170] Removing tips with length less than 158; Accumulated tips removed: 462; time elapsed: 0.3451' b' [assembler.cpp : 179] Tips removal done! Time elapsed(sec): 2.450023' b' [assembler.cpp : 188] unitig graph size: 1435, time for building: 3.254293' b' [assembler.cpp : 211] Number of bubbles removed: 342, Time elapsed(sec): 2.006392' b' [assembler.cpp : 225] Number of complex bubbles removed: 64, Time elapsed(sec): 0.222521' b' [assembler.cpp : 243] Number unitigs disconnected: 76, time: 0.000324' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 32, time: 0.000626' b' [assembler.cpp : 200] Tips removed: 0, time: 0.000844' b' [assembler.cpp : 211] Number of bubbles removed: 2, Time elapsed(sec): 0.001110' b' [assembler.cpp : 225] Number of complex bubbles removed: 8, Time elapsed(sec): 0.016974' b' [assembler.cpp : 243] Number unitigs disconnected: 3, time: 0.000222' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 0, time: 0.000069' b' [assembler.cpp : 200] Tips removed: 3, time: 0.000684' b' [assembler.cpp : 211] Number of bubbles removed: 0, Time elapsed(sec): 0.000164' b' [assembler.cpp : 225] Number of complex bubbles removed: 0, Time elapsed(sec): 0.013553' b' [assembler.cpp : 243] Number unitigs disconnected: 0, time: 0.000214' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 0, time: 0.000070' b' [assembler.cpp : 132] Total length: 8519711, N50: 92361, Mean: 14294, number of contigs: 596' b' [assembler.cpp : 133] Maximum length: 539126' b' [assembler.cpp : 290] Time to output: 1.054820' b' [assembler.cpp : 317] Number of local low depth unitigs removed: 2, complex bubbles removed: 0, time: 0.021031' b' [assembler.cpp : 132] Total length: 7366162, N50: 84322, Mean: 12923, number of contigs: 570' b' [assembler.cpp : 133] Maximum length: 268466' b' [utils.h : 126] Real: 10.6243\tuser: 34.1070\tsys: 0.4280\tmaxrss: 44560' --- [Sat Dec 11 12:49:03 2021] Local assembling k = 79 --- cmd: /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/conda/anaconda3/envs/de_novo_example/bin/megahit_asm_core local -c megahit_default_assembly/intermediate_contigs/k79.contigs.fa -l megahit_default_assembly/tmp/reads.lib -t 4 -o megahit_default_assembly/intermediate_contigs/k79.local.fa --kmax 99 b' [local_assembler.cpp : 89] Number of contigs: 353, Mapper size: 1058581' b' [read_lib_functions-inl.h : 256] Before reading, sizeof seq_package: 127686404' b' [read_lib_functions-inl.h : 260] After reading, sizeof seq_package: 127686404' b' [local_assembler.cpp : 330] Lib 0, insert size: 375.10 sd: 107.43' b' [local_assembler.cpp : 462] Lib 0: total 2969452 reads, aligned 2909809, added 25757 reads for local assembly' b' [utils.h : 126] Real: 21.0512\tuser: 77.6921\tsys: 0.5806\tmaxrss: 164612' --- [Sat Dec 11 12:49:24 2021] Extracting iterative edges from k = 79 to 99 --- cmd: /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/conda/anaconda3/envs/de_novo_example/bin/megahit_asm_core iterate -c megahit_default_assembly/intermediate_contigs/k79.contigs.fa -b megahit_default_assembly/intermediate_contigs/k79.bubble_seq.fa -t 4 -k 79 -s 20 -o megahit_default_assembly/tmp/k99/99 -r megahit_default_assembly/tmp/reads.lib.bin -f binary b' [iterate_edges.cpp : 570] Number of crusial kmers: 1151' b' [iterate_edges.cpp : 570] Number of crusial kmers: 2105' b' [iterate_edges.cpp : 447] Total: 2969452, aligned: 19435. Iterative edges: 22327' b' [iterate_edges.cpp : 451] Writing iterative edges...' b' [utils.h : 126] Real: 12.2705\tuser: 35.1381\tsys: 0.3989\tmaxrss: 164436' --- [Sat Dec 11 12:49:37 2021] Building graph for k = 99 --- /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/conda/anaconda3/envs/de_novo_example/bin/megahit_sdbg_build seq2sdbg --host_mem 973246515609 --mem_flag 1 --gpu_mem 0 --output_prefix megahit_default_assembly/tmp/k99/99 --num_cpu_threads 4 -k 99 --kmer_from 79 --num_edge_files 1 --input_prefix megahit_default_assembly/tmp/k99/99 --addi_contig megahit_default_assembly/intermediate_contigs/k79.addi.fa --local_contig megahit_default_assembly/intermediate_contigs/k79.local.fa --contig megahit_default_assembly/intermediate_contigs/k79.contigs.fa --bubble megahit_default_assembly/intermediate_contigs/k79.bubble_seq.fa b' [sdbg_builder.cpp : 339] Host memory to be used: 973246515609' b' [sdbg_builder.cpp : 340] Number CPU threads: 4' b' [cx1.h : 450] Preparing data...' b' [cx1_seq2sdbg.cpp : 394] Number edges: 22327' b' [cx1_seq2sdbg.cpp : 434] Bases to reserve: 33145525, number contigs: 3198, number multiplicity: 25525' b' [cx1_seq2sdbg.cpp : 440] Before reading, sizeof seq_package: 8311976, multiplicity vector: 25525' b' [cx1_seq2sdbg.cpp : 529] After reading, sizeof seq_package: 8311976, multiplicity vector: 25525' b' [cx1.h : 457] Preparing data... Done. Time elapsed: 0.0897' b' [cx1.h : 464] Preparing partitions and initialing global data...' b' [cx1_seq2sdbg.cpp : 740] Memory for sequence: 8572420' b' [cx1_seq2sdbg.cpp : 741] max # lv.1 items = 6552970' b' [cx1.h : 480] Preparing partitions and initialing global data... Done. Time elapsed: 0.1869' b' [cx1.h : 486] Start main loop...' b' [cx1.h : 515] Lv1 scanning from bucket 0 to 417' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 0.2786' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 0.3790' b' [cx1.h : 515] Lv1 scanning from bucket 417 to 1389' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 0.3302' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 0.4371' b' [cx1.h : 515] Lv1 scanning from bucket 1389 to 3053' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 0.3057' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 0.4629' b' [cx1.h : 515] Lv1 scanning from bucket 3053 to 5738' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 0.3109' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 0.3581' b' [cx1.h : 515] Lv1 scanning from bucket 5738 to 10106' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 0.3216' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 0.4184' b' [cx1.h : 515] Lv1 scanning from bucket 10106 to 17714' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 0.3303' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 0.3862' b' [cx1.h : 515] Lv1 scanning from bucket 17714 to 34665' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 0.3439' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 0.4675' b' [cx1.h : 515] Lv1 scanning from bucket 34665 to 65536' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 0.2437' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 0.1988' b' [cx1.h : 607] Main loop done. Time elapsed: 5.5737' b' [cx1.h : 613] Postprocessing...' b' [cx1_seq2sdbg.cpp :1139] Number of $ A C G T A- C- G- T-:' b' [cx1_seq2sdbg.cpp :1142] 311 2834663 5671147 5671183 2834883 100 232 240 100' b' [cx1_seq2sdbg.cpp :1151] Total number of edges: 17012859' b' [cx1_seq2sdbg.cpp :1152] Total number of ONEs: 17011876' b' [cx1_seq2sdbg.cpp :1153] Total number of $v edges: 311' b' [cx1.h : 621] Postprocess done. Time elapsed: 0.1470' b' [utils.h : 126] Real: 6.0005\tuser: 15.0652\tsys: 0.1436\tmaxrss: 53940' --- [Sat Dec 11 12:49:43 2021] Assembling contigs from SdBG for k = 99 --- cmd: /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/conda/anaconda3/envs/de_novo_example/bin/megahit_asm_core assemble -s megahit_default_assembly/tmp/k99/99 -o megahit_default_assembly/intermediate_contigs/k99 -t 4 --min_standalone 300.0 --prune_level 2 --merge_len 20 --merge_similar 0.95 --low_local_ratio 0.2 --min_depth 2 --bubble_level 2 --max_tip_len -1 --careful_bubble b' [assembler.cpp : 148] Loading succinct de Bruijn graph: megahit_default_assembly/tmp/k99/99 Done. Time elapsed: 0.667054' b' [assembler.cpp : 152] Number of Edges: 17012859; K value: 99' b' [assembler.cpp : 162] Number of CPU threads: 4' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 2; Accumulated tips removed: 2; time elapsed: 0.2975' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 4; Accumulated tips removed: 24; time elapsed: 0.2982' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 8; Accumulated tips removed: 50; time elapsed: 0.2979' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 16; Accumulated tips removed: 82; time elapsed: 0.3334' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 32; Accumulated tips removed: 122; time elapsed: 0.3017' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 64; Accumulated tips removed: 160; time elapsed: 0.3044' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 128; Accumulated tips removed: 370; time elapsed: 0.3094' b' [assembly_algorithms.cpp : 170] Removing tips with length less than 198; Accumulated tips removed: 378; time elapsed: 0.3120' b' [assembler.cpp : 179] Tips removal done! Time elapsed(sec): 2.456149' b' [assembler.cpp : 188] unitig graph size: 807, time for building: 3.843987' b' [assembler.cpp : 211] Number of bubbles removed: 146, Time elapsed(sec): 1.683625' b' [assembler.cpp : 225] Number of complex bubbles removed: 37, Time elapsed(sec): 0.149471' b' [assembler.cpp : 243] Number unitigs disconnected: 46, time: 0.000378' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 20, time: 0.000517' b' [assembler.cpp : 200] Tips removed: 2, time: 0.000713' b' [assembler.cpp : 211] Number of bubbles removed: 2, Time elapsed(sec): 0.000649' b' [assembler.cpp : 225] Number of complex bubbles removed: 3, Time elapsed(sec): 0.014612' b' [assembler.cpp : 243] Number unitigs disconnected: 0, time: 0.000199' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 0, time: 0.000061' b' [assembler.cpp : 200] Tips removed: 0, time: 0.000583' b' [assembler.cpp : 211] Number of bubbles removed: 0, Time elapsed(sec): 0.000131' b' [assembler.cpp : 225] Number of complex bubbles removed: 0, Time elapsed(sec): 0.014221' b' [assembler.cpp : 243] Number unitigs disconnected: 0, time: 0.000189' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 0, time: 0.000063' b' [assembler.cpp : 132] Total length: 8517912, N50: 115349, Mean: 21564, number of contigs: 395' b' [assembler.cpp : 133] Maximum length: 539126' b' [assembler.cpp : 290] Time to output: 1.138849' b' [assembler.cpp : 317] Number of local low depth unitigs removed: 0, complex bubbles removed: 0, time: 0.016430' b' [assembler.cpp : 132] Total length: 7208337, N50: 108097, Mean: 19377, number of contigs: 372' b' [assembler.cpp : 133] Maximum length: 295894' b' [utils.h : 126] Real: 10.8979\tuser: 34.6758\tsys: 0.4618\tmaxrss: 44508' --- [Sat Dec 11 12:49:54 2021] Local assembling k = 99 --- cmd: /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/conda/anaconda3/envs/de_novo_example/bin/megahit_asm_core local -c megahit_default_assembly/intermediate_contigs/k99.contigs.fa -l megahit_default_assembly/tmp/reads.lib -t 4 -o megahit_default_assembly/intermediate_contigs/k99.local.fa --kmax 119 b' [local_assembler.cpp : 89] Number of contigs: 284, Mapper size: 1060499' b' [read_lib_functions-inl.h : 256] Before reading, sizeof seq_package: 127686404' b' [read_lib_functions-inl.h : 260] After reading, sizeof seq_package: 127686404' b' [local_assembler.cpp : 330] Lib 0, insert size: 375.15 sd: 107.45' b' [local_assembler.cpp : 462] Lib 0: total 2969452 reads, aligned 2902196, added 18676 reads for local assembly' b' [utils.h : 126] Real: 20.2212\tuser: 78.3660\tsys: 0.4409\tmaxrss: 164392' --- [Sat Dec 11 12:50:14 2021] Extracting iterative edges from k = 99 to 119 --- cmd: /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/conda/anaconda3/envs/de_novo_example/bin/megahit_asm_core iterate -c megahit_default_assembly/intermediate_contigs/k99.contigs.fa -b megahit_default_assembly/intermediate_contigs/k99.bubble_seq.fa -t 4 -k 99 -s 20 -o megahit_default_assembly/tmp/k119/119 -r megahit_default_assembly/tmp/reads.lib.bin -f binary b' [iterate_edges.cpp : 570] Number of crusial kmers: 568' b' [iterate_edges.cpp : 570] Number of crusial kmers: 1187' b' [iterate_edges.cpp : 447] Total: 2969452, aligned: 8431. Iterative edges: 12122' b' [iterate_edges.cpp : 451] Writing iterative edges...' b' [utils.h : 126] Real: 8.7826\tuser: 24.8378\tsys: 0.4659\tmaxrss: 164168' --- [Sat Dec 11 12:50:23 2021] Building graph for k = 119 --- /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/conda/anaconda3/envs/de_novo_example/bin/megahit_sdbg_build seq2sdbg --host_mem 973246515609 --mem_flag 1 --gpu_mem 0 --output_prefix megahit_default_assembly/tmp/k119/119 --num_cpu_threads 4 -k 119 --kmer_from 99 --num_edge_files 1 --input_prefix megahit_default_assembly/tmp/k119/119 --addi_contig megahit_default_assembly/intermediate_contigs/k99.addi.fa --local_contig megahit_default_assembly/intermediate_contigs/k99.local.fa --contig megahit_default_assembly/intermediate_contigs/k99.contigs.fa --bubble megahit_default_assembly/intermediate_contigs/k99.bubble_seq.fa b' [sdbg_builder.cpp : 339] Host memory to be used: 973246515609' b' [sdbg_builder.cpp : 340] Number CPU threads: 4' b' [cx1.h : 450] Preparing data...' b' [cx1_seq2sdbg.cpp : 394] Number edges: 12122' b' [cx1_seq2sdbg.cpp : 434] Bases to reserve: 26941645, number contigs: 1877, number multiplicity: 13999' b' [cx1_seq2sdbg.cpp : 440] Before reading, sizeof seq_package: 6750436, multiplicity vector: 13999' b' [cx1_seq2sdbg.cpp : 529] After reading, sizeof seq_package: 6750436, multiplicity vector: 13999' b' [cx1.h : 457] Preparing data... Done. Time elapsed: 0.0714' b' [cx1.h : 464] Preparing partitions and initialing global data...' b' [cx1_seq2sdbg.cpp : 740] Memory for sequence: 6941932' b' [cx1_seq2sdbg.cpp : 741] max # lv.1 items = 5185766' b' [cx1.h : 480] Preparing partitions and initialing global data... Done. Time elapsed: 0.1555' b' [cx1.h : 486] Start main loop...' b' [cx1.h : 515] Lv1 scanning from bucket 0 to 400' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 0.2179' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 0.3769' b' [cx1.h : 515] Lv1 scanning from bucket 400 to 1360' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 0.2322' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 0.3876' b' [cx1.h : 515] Lv1 scanning from bucket 1360 to 3015' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 0.2386' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 0.4133' b' [cx1.h : 515] Lv1 scanning from bucket 3015 to 5700' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 0.2533' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 0.3940' b' [cx1.h : 515] Lv1 scanning from bucket 5700 to 10076' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 0.2544' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 0.4447' b' [cx1.h : 515] Lv1 scanning from bucket 10076 to 17728' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 0.2628' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 0.3357' b' [cx1.h : 515] Lv1 scanning from bucket 17728 to 34904' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 0.2721' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 0.4504' b' [cx1.h : 515] Lv1 scanning from bucket 34904 to 65536' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 0.1841' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 0.1796' b' [cx1.h : 607] Main loop done. Time elapsed: 4.8982' b' [cx1.h : 613] Postprocessing...' b' [cx1_seq2sdbg.cpp :1139] Number of $ A C G T A- C- G- T-:' b' [cx1_seq2sdbg.cpp :1142] 258 2832695 5664815 5665041 2832895 76 110 111 66' b' [cx1_seq2sdbg.cpp :1151] Total number of edges: 16996067' b' [cx1_seq2sdbg.cpp :1152] Total number of ONEs: 16995446' b' [cx1_seq2sdbg.cpp :1153] Total number of $v edges: 258' b' [cx1.h : 621] Postprocess done. Time elapsed: 0.1011' b' [utils.h : 126] Real: 5.2281\tuser: 13.9864\tsys: 0.1118\tmaxrss: 47208' --- [Sat Dec 11 12:50:28 2021] Assembling contigs from SdBG for k = 119 --- cmd: /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/conda/anaconda3/envs/de_novo_example/bin/megahit_asm_core assemble -s megahit_default_assembly/tmp/k119/119 -o megahit_default_assembly/intermediate_contigs/k119 -t 4 --min_standalone 300.0 --prune_level 2 --merge_len 20 --merge_similar 0.95 --low_local_ratio 0.2 --min_depth 2 --bubble_level 2 --max_tip_len 182.0 --careful_bubble b' [assembler.cpp : 148] Loading succinct de Bruijn graph: megahit_default_assembly/tmp/k119/119 Done. Time elapsed: 0.653545' b' [assembler.cpp : 152] Number of Edges: 16996067; K value: 119' b' [assembler.cpp : 162] Number of CPU threads: 4' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 2; Accumulated tips removed: 0; time elapsed: 0.2949' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 4; Accumulated tips removed: 10; time elapsed: 0.2965' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 8; Accumulated tips removed: 28; time elapsed: 0.2956' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 16; Accumulated tips removed: 58; time elapsed: 0.3154' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 32; Accumulated tips removed: 74; time elapsed: 0.2980' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 64; Accumulated tips removed: 86; time elapsed: 0.3001' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 128; Accumulated tips removed: 204; time elapsed: 0.3045' b' [assembly_algorithms.cpp : 170] Removing tips with length less than 182; Accumulated tips removed: 210; time elapsed: 0.3051' b' [assembler.cpp : 179] Tips removal done! Time elapsed(sec): 2.411700' b' [assembler.cpp : 188] unitig graph size: 495, time for building: 3.426079' b' [assembler.cpp : 211] Number of bubbles removed: 46, Time elapsed(sec): 0.018337' b' [assembler.cpp : 225] Number of complex bubbles removed: 21, Time elapsed(sec): 0.120953' b' [assembler.cpp : 243] Number unitigs disconnected: 32, time: 0.000301' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 15, time: 0.000646' b' [assembler.cpp : 200] Tips removed: 0, time: 0.000491' b' [assembler.cpp : 211] Number of bubbles removed: 0, Time elapsed(sec): 0.000135' b' [assembler.cpp : 225] Number of complex bubbles removed: 4, Time elapsed(sec): 0.025091' b' [assembler.cpp : 243] Number unitigs disconnected: 1, time: 0.000187' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 1, time: 0.000124' b' [assembler.cpp : 200] Tips removed: 0, time: 0.000453' b' [assembler.cpp : 211] Number of bubbles removed: 0, Time elapsed(sec): 0.000108' b' [assembler.cpp : 225] Number of complex bubbles removed: 0, Time elapsed(sec): 0.023493' b' [assembler.cpp : 243] Number unitigs disconnected: 0, time: 0.000166' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 0, time: 0.000041' b' [assembler.cpp : 132] Total length: 8517266, N50: 117434, Mean: 28017, number of contigs: 304' b' [assembler.cpp : 133] Maximum length: 539126' b' [assembler.cpp : 290] Time to output: 1.097282' b' [assembler.cpp : 317] Number of local low depth unitigs removed: 0, complex bubbles removed: 0, time: 0.023462' b' [assembler.cpp : 132] Total length: 7175782, N50: 117434, Mean: 25905, number of contigs: 277' b' [assembler.cpp : 133] Maximum length: 295919' b' [utils.h : 126] Real: 8.7678\tuser: 30.1579\tsys: 0.4241\tmaxrss: 44472' --- [Sat Dec 11 12:50:37 2021] Local assembling k = 119 --- cmd: /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/conda/anaconda3/envs/de_novo_example/bin/megahit_asm_core local -c megahit_default_assembly/intermediate_contigs/k119.contigs.fa -l megahit_default_assembly/tmp/reads.lib -t 4 -o megahit_default_assembly/intermediate_contigs/k119.local.fa --kmax 141 b' [local_assembler.cpp : 89] Number of contigs: 249, Mapper size: 1060811' b' [read_lib_functions-inl.h : 256] Before reading, sizeof seq_package: 127686404' b' [read_lib_functions-inl.h : 260] After reading, sizeof seq_package: 127686404' b' [local_assembler.cpp : 330] Lib 0, insert size: 375.17 sd: 107.45' b' [local_assembler.cpp : 462] Lib 0: total 2969452 reads, aligned 2900028, added 16950 reads for local assembly' b' [utils.h : 126] Real: 20.8268\tuser: 80.8901\tsys: 0.4220\tmaxrss: 164296' --- [Sat Dec 11 12:50:58 2021] Extracting iterative edges from k = 119 to 141 --- cmd: /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/conda/anaconda3/envs/de_novo_example/bin/megahit_asm_core iterate -c megahit_default_assembly/intermediate_contigs/k119.contigs.fa -b megahit_default_assembly/intermediate_contigs/k119.bubble_seq.fa -t 4 -k 119 -s 22 -o megahit_default_assembly/tmp/k141/141 -r megahit_default_assembly/tmp/reads.lib.bin -f binary b' [iterate_edges.cpp : 570] Number of crusial kmers: 224' b' [iterate_edges.cpp : 570] Number of crusial kmers: 713' b' [iterate_edges.cpp : 447] Total: 2969452, aligned: 0. Iterative edges: 0' b' [utils.h : 126] Real: 0.5584\tuser: 0.4264\tsys: 0.2733\tmaxrss: 164160' --- [Sat Dec 11 12:50:58 2021] Building graph for k = 141 --- /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/conda/anaconda3/envs/de_novo_example/bin/megahit_sdbg_build seq2sdbg --host_mem 973246515609 --mem_flag 1 --gpu_mem 0 --output_prefix megahit_default_assembly/tmp/k141/141 --num_cpu_threads 4 -k 141 --kmer_from 119 --num_edge_files 1 --addi_contig megahit_default_assembly/intermediate_contigs/k119.addi.fa --local_contig megahit_default_assembly/intermediate_contigs/k119.local.fa --contig megahit_default_assembly/intermediate_contigs/k119.contigs.fa --bubble megahit_default_assembly/intermediate_contigs/k119.bubble_seq.fa b' [sdbg_builder.cpp : 339] Host memory to be used: 973246515609' b' [sdbg_builder.cpp : 340] Number CPU threads: 4' b' [cx1.h : 450] Preparing data...' b' [cx1_seq2sdbg.cpp : 434] Bases to reserve: 15045873, number contigs: 1205, number multiplicity: 1205' b' [cx1_seq2sdbg.cpp : 440] Before reading, sizeof seq_package: 3771120, multiplicity vector: 1205' b' [cx1_seq2sdbg.cpp : 529] After reading, sizeof seq_package: 3771120, multiplicity vector: 1205' b' [cx1.h : 457] Preparing data... Done. Time elapsed: 0.0327' b' [cx1.h : 464] Preparing partitions and initialing global data...' b' [cx1_seq2sdbg.cpp : 740] Memory for sequence: 3844858' b' [cx1_seq2sdbg.cpp : 741] max # lv.1 items = 2421185' b' [cx1.h : 480] Preparing partitions and initialing global data... Done. Time elapsed: 0.0793' b' [cx1.h : 486] Start main loop...' b' [cx1.h : 515] Lv1 scanning from bucket 0 to 411' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 0.0758' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 0.3220' b' [cx1.h : 515] Lv1 scanning from bucket 411 to 1407' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 0.0811' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 0.3214' b' [cx1.h : 515] Lv1 scanning from bucket 1407 to 3129' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 0.0844' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 0.3991' b' [cx1.h : 515] Lv1 scanning from bucket 3129 to 5914' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 0.0883' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 0.5296' b' [cx1.h : 515] Lv1 scanning from bucket 5914 to 10446' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 0.0887' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 0.4112' b' [cx1.h : 515] Lv1 scanning from bucket 10446 to 18328' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 0.0895' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 0.4832' b' [cx1.h : 515] Lv1 scanning from bucket 18328 to 35876' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 0.0922' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 0.4364' b' [cx1.h : 515] Lv1 scanning from bucket 35876 to 65536' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 0.0642' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 0.1896' b' [cx1.h : 607] Main loop done. Time elapsed: 3.7571' b' [cx1.h : 613] Postprocessing...' b' [cx1_seq2sdbg.cpp :1139] Number of $ A C G T A- C- G- T-:' b' [cx1_seq2sdbg.cpp :1142] 210 2831510 5660971 5661447 2831490 29 70 90 38' b' [cx1_seq2sdbg.cpp :1151] Total number of edges: 16985855' b' [cx1_seq2sdbg.cpp :1152] Total number of ONEs: 16985418' b' [cx1_seq2sdbg.cpp :1153] Total number of $v edges: 210' b' [cx1.h : 621] Postprocess done. Time elapsed: 0.1188' b' [utils.h : 126] Real: 3.9900\tuser: 13.3355\tsys: 0.0967\tmaxrss: 32340' --- [Sat Dec 11 12:51:02 2021] Assembling contigs from SdBG for k = 141 --- cmd: /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/conda/anaconda3/envs/de_novo_example/bin/megahit_asm_core assemble -s megahit_default_assembly/tmp/k141/141 -o megahit_default_assembly/intermediate_contigs/k141 -t 4 --min_standalone 300.0 --prune_level 2 --merge_len 20 --merge_similar 0.95 --low_local_ratio 0.2 --min_depth 2 --bubble_level 2 --max_tip_len 160.0 --is_final_round b' [assembler.cpp : 148] Loading succinct de Bruijn graph: megahit_default_assembly/tmp/k141/141 Done. Time elapsed: 0.648847' b' [assembler.cpp : 152] Number of Edges: 16985855; K value: 141' b' [assembler.cpp : 162] Number of CPU threads: 4' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 2; Accumulated tips removed: 2; time elapsed: 0.2946' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 4; Accumulated tips removed: 10; time elapsed: 0.2973' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 8; Accumulated tips removed: 12; time elapsed: 0.3015' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 16; Accumulated tips removed: 24; time elapsed: 0.3106' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 32; Accumulated tips removed: 34; time elapsed: 0.2966' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 64; Accumulated tips removed: 50; time elapsed: 0.3070' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 128; Accumulated tips removed: 103; time elapsed: 0.3094' b' [assembly_algorithms.cpp : 170] Removing tips with length less than 160; Accumulated tips removed: 113; time elapsed: 0.3187' b' [assembler.cpp : 179] Tips removal done! Time elapsed(sec): 2.437604' b' [assembler.cpp : 188] unitig graph size: 349, time for building: 3.690789' b' [assembler.cpp : 211] Number of bubbles removed: 16, Time elapsed(sec): 0.000881' b' [assembler.cpp : 225] Number of complex bubbles removed: 8, Time elapsed(sec): 0.009893' b' [assembler.cpp : 243] Number unitigs disconnected: 55, time: 0.000238' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 24, time: 0.000477' b' [assembler.cpp : 200] Tips removed: 1, time: 0.000395' b' [assembler.cpp : 211] Number of bubbles removed: 0, Time elapsed(sec): 0.000080' b' [assembler.cpp : 225] Number of complex bubbles removed: 4, Time elapsed(sec): 0.008650' b' [assembler.cpp : 243] Number unitigs disconnected: 3, time: 0.000131' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 1, time: 0.000073' b' [assembler.cpp : 200] Tips removed: 0, time: 0.000364' b' [assembler.cpp : 211] Number of bubbles removed: 0, Time elapsed(sec): 0.000070' b' [assembler.cpp : 225] Number of complex bubbles removed: 0, Time elapsed(sec): 0.007728' b' [assembler.cpp : 243] Number unitigs disconnected: 0, time: 0.000108' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 0, time: 0.000027' b' [assembler.cpp : 317] Number of local low depth unitigs removed: 0, complex bubbles removed: 0, time: 0.008292' b' [assembler.cpp : 132] Total length: 8513975, N50: 144335, Mean: 39599, number of contigs: 215' b' [assembler.cpp : 133] Maximum length: 539126' b' [utils.h : 126] Real: 8.0895\tuser: 27.3527\tsys: 0.4460\tmaxrss: 44496' --- [Sat Dec 11 12:51:10 2021] Merging to output final contigs --- --- [STAT] 200 contigs, total 8511587 bp, min 201 bp, max 539126 bp, avg 42558 bp, N50 144335 bp --- [Sat Dec 11 12:51:11 2021] ALL DONE. Time elapsed: 438.487427 seconds ---