MEGAHIT v1.1.3 --- [Thu Mar 28 22:53:07 2019] Start assembly. Number of CPU threads 28 --- --- [Thu Mar 28 22:53:07 2019] Available memory: 269759385600, used: 242783447040 --- [Thu Mar 28 22:53:07 2019] Converting reads to binaries --- /gscratch/srlab/programs/megahit_v1.1.4_LINUX_CPUONLY_x86_64-bin/megahit_asm_core buildlib ./megahit_out/tmp/reads.lib ./megahit_out/tmp/reads.lib b' [read_lib_functions-inl.h : 209] Lib 0 (/gscratch/srlab/sam/data/metagenomics/P_generosa/Library_Geoduck_MG_6_S5_L002_R1_001_val_1_val_1_val_1.fq.gz,/gscratch/srlab/sam/data/metagenomics/P_generosa/Library_Geoduck_MG_6_S5_L002_R2_001_val_2_val_2_val_2.fq.gz): pe, 143722488 reads, 131 max length' b' [utils.h : 126] Real: 144.0256\tuser: 130.9582\tsys: 12.1357\tmaxrss: 153956' --- [Thu Mar 28 22:55:31 2019] k list: 21,29,39,59,79,99,119,141 --- --- [Thu Mar 28 22:55:31 2019] Extracting solid (k+1)-mers for k = 21 --- cmd: /gscratch/srlab/programs/megahit_v1.1.4_LINUX_CPUONLY_x86_64-bin/megahit_sdbg_build count -k 21 -m 2 --host_mem 242783447040 --mem_flag 1 --gpu_mem 0 --output_prefix ./megahit_out/tmp/k21/21 --num_cpu_threads 28 --num_output_threads 9 --read_lib_file ./megahit_out/tmp/reads.lib b' [sdbg_builder.cpp : 112] Host memory to be used: 242783447040' b' [sdbg_builder.cpp : 113] Number CPU threads: 28' b' [cx1.h : 450] Preparing data...' b' [read_lib_functions-inl.h : 256] Before reading, sizeof seq_package: 5214492324' b' [read_lib_functions-inl.h : 260] After reading, sizeof seq_package: 5214492324' b' [cx1_kmer_count.cpp : 136] 143722488 reads, 131 max read length' b' [cx1.h : 457] Preparing data... Done. Time elapsed: 20.3637' 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: 7469177256, 237080038556' b' [cx1_kmer_count.cpp : 356] 1765465482, 16971472 7469177256 237080038556' b' [cx1_kmer_count.cpp : 363] Memory for reads: 5341514612' b' [cx1_kmer_count.cpp : 364] max # lv.1 items = 1765465482' b' [cx1.h : 480] Preparing partitions and initialing global data... Done. Time elapsed: 7.6120' b' [cx1.h : 486] Start main loop...' b' [cx1.h : 515] Lv1 scanning from bucket 0 to 245' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 7.3143' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 10.9084' b' [cx1.h : 515] Lv1 scanning from bucket 245 to 1362' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 7.8574' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 22.5410' b' [cx1.h : 515] Lv1 scanning from bucket 1362 to 3608' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 8.0540' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 25.6976' b' [cx1.h : 515] Lv1 scanning from bucket 3608 to 7238' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 8.2777' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 26.2799' b' [cx1.h : 515] Lv1 scanning from bucket 7238 to 12677' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 8.5310' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 25.8360' b' [cx1.h : 515] Lv1 scanning from bucket 12677 to 20669' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 8.7939' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 25.2671' b' [cx1.h : 515] Lv1 scanning from bucket 20669 to 32918' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 9.0514' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 25.4174' b' [cx1.h : 515] Lv1 scanning from bucket 32918 to 57930' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 9.5382' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 26.0483' b' [cx1.h : 515] Lv1 scanning from bucket 57930 to 65536' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 6.9575' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 2.3930' b' [cx1.h : 607] Main loop done. Time elapsed: 264.7657' b' [cx1.h : 613] Postprocessing...' b' [cx1_kmer_count.cpp : 860] Total number of candidate reads: 4266396(14673018)' b' [cx1_kmer_count.cpp : 871] Total number of solid edges: 1062898789' b' [cx1.h : 621] Postprocess done. Time elapsed: 2.8930' b' [utils.h : 126] Real: 295.6503\tuser: 7488.1171\tsys: 27.0742\tmaxrss: 13711748' --- [Thu Mar 28 23:00:27 2019] Building graph for k = 21 --- /gscratch/srlab/programs/megahit_v1.1.4_LINUX_CPUONLY_x86_64-bin/megahit_sdbg_build seq2sdbg --host_mem 242783447040 --mem_flag 1 --gpu_mem 0 --output_prefix ./megahit_out/tmp/k21/21 --num_cpu_threads 28 -k 21 --kmer_from 0 --num_edge_files 9 --input_prefix ./megahit_out/tmp/k21/21 --need_mercy b' [sdbg_builder.cpp : 339] Host memory to be used: 242783447040' b' [sdbg_builder.cpp : 340] Number CPU threads: 28' b' [cx1.h : 450] Preparing data...' b' [cx1_seq2sdbg.cpp : 394] Number edges: 1062898789' b' [cx1_seq2sdbg.cpp : 434] Bases to reserve: 29229716692, number contigs: 0, number multiplicity: 1328623486' b' [cx1_seq2sdbg.cpp : 440] Before reading, sizeof seq_package: 7307429184, multiplicity vector: 1328623486' b' [cx1_seq2sdbg.cpp : 455] Adding mercy edges...' b' [cx1_seq2sdbg.cpp : 373] Number of reads: 4266396, Number of mercy edges: 59329031' b' [cx1_seq2sdbg.cpp : 462] Done. Time elapsed: 52.5170' b' [cx1_seq2sdbg.cpp : 529] After reading, sizeof seq_package: 7307429184, multiplicity vector: 1328623486' b' [cx1.h : 457] Preparing data... Done. Time elapsed: 207.0939' b' [cx1.h : 464] Preparing partitions and initialing global data...' b' [cx1_seq2sdbg.cpp : 740] Memory for sequence: 9744767760' b' [cx1_seq2sdbg.cpp : 741] max # lv.1 items = 897782256' b' [cx1.h : 480] Preparing partitions and initialing global data... Done. Time elapsed: 2.3361' b' [cx1.h : 486] Start main loop...' b' [cx1.h : 515] Lv1 scanning from bucket 0 to 930' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 2.1338' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 7.7447' b' [cx1.h : 515] Lv1 scanning from bucket 930 to 3537' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 2.1955' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 9.1692' b' [cx1.h : 515] Lv1 scanning from bucket 3537 to 7808' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 2.2361' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 9.4708' b' [cx1.h : 515] Lv1 scanning from bucket 7808 to 13930' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 2.2616' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 9.6352' b' [cx1.h : 515] Lv1 scanning from bucket 13930 to 22286' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 2.3170' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 10.1077' b' [cx1.h : 515] Lv1 scanning from bucket 22286 to 33577' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 2.3924' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 10.5906' b' [cx1.h : 515] Lv1 scanning from bucket 33577 to 49465' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 2.5172' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 10.6363' b' [cx1.h : 515] Lv1 scanning from bucket 49465 to 65536' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 2.2271' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 6.9416' b' [cx1.h : 607] Main loop done. Time elapsed: 92.5778' 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] 17659773 682507395 428437243 427120540 684281150 14501933 5308048 5225269 14726327' b' [cx1_seq2sdbg.cpp :1151] Total number of edges: 2279767678' b' [cx1_seq2sdbg.cpp :1152] Total number of ONEs: 2222346328' b' [cx1_seq2sdbg.cpp :1153] Total number of $v edges: 17659773' b' [cx1.h : 621] Postprocess done. Time elapsed: 0.0409' b' [utils.h : 126] Real: 302.0739\tuser: 3779.1088\tsys: 35.7732\tmaxrss: 12477396' --- [Thu Mar 28 23:05:30 2019] Assembling contigs from SdBG for k = 21 --- cmd: /gscratch/srlab/programs/megahit_v1.1.4_LINUX_CPUONLY_x86_64-bin/megahit_asm_core assemble -s ./megahit_out/tmp/k21/21 -o ./megahit_out/intermediate_contigs/k21 -t 28 --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_out/tmp/k21/21 Done. Time elapsed: 128.582691' b' [assembler.cpp : 152] Number of Edges: 2279767678; K value: 21' b' [assembler.cpp : 162] Number of CPU threads: 28' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 2; Accumulated tips removed: 1358082; time elapsed: 6.9784' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 4; Accumulated tips removed: 4492720; time elapsed: 8.4359' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 8; Accumulated tips removed: 8038855; time elapsed: 11.8113' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 16; Accumulated tips removed: 12841001; time elapsed: 18.9171' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 32; Accumulated tips removed: 17204044; time elapsed: 28.1329' b' [assembly_algorithms.cpp : 170] Removing tips with length less than 42; Accumulated tips removed: 18536911; time elapsed: 30.0091' b' [assembler.cpp : 179] Tips removal done! Time elapsed(sec): 104.369269' b' [assembler.cpp : 188] unitig graph size: 46176819, time for building: 227.473154' b' [assembler.cpp : 211] Number of bubbles removed: 2208263, Time elapsed(sec): 18.505311' b' [assembler.cpp : 225] Number of complex bubbles removed: 285890, Time elapsed(sec): 12.549896' b' [assembler.cpp : 243] Number unitigs disconnected: 10426362, time: 16.674130' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 96443, time: 7.529383' b' [assembler.cpp : 200] Tips removed: 59435, time: 12.275504' b' [assembler.cpp : 211] Number of bubbles removed: 83442, Time elapsed(sec): 5.112563' b' [assembler.cpp : 225] Number of complex bubbles removed: 88768, Time elapsed(sec): 8.856711' b' [assembler.cpp : 243] Number unitigs disconnected: 1490803, time: 8.678619' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 72, time: 7.281590' b' [assembler.cpp : 200] Tips removed: 1314219, time: 12.600233' b' [assembler.cpp : 211] Number of bubbles removed: 92095, Time elapsed(sec): 4.783002' b' [assembler.cpp : 225] Number of complex bubbles removed: 11164, Time elapsed(sec): 8.476052' b' [assembler.cpp : 243] Number unitigs disconnected: 14854, time: 7.559809' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 3, time: 7.266351' b' [assembler.cpp : 200] Tips removed: 4539, time: 11.311785' b' [assembler.cpp : 211] Number of bubbles removed: 450, Time elapsed(sec): 4.337124' b' [assembler.cpp : 225] Number of complex bubbles removed: 238, Time elapsed(sec): 8.391654' b' [assembler.cpp : 243] Number unitigs disconnected: 366, time: 7.475047' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 1, time: 7.153508' b' [assembler.cpp : 200] Tips removed: 140, time: 11.097362' b' [assembler.cpp : 211] Number of bubbles removed: 0, Time elapsed(sec): 4.342810' b' [assembler.cpp : 225] Number of complex bubbles removed: 7, Time elapsed(sec): 8.334366' b' [assembler.cpp : 243] Number unitigs disconnected: 9, time: 7.542008' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 0, time: 5.505635' b' [assembler.cpp : 132] Total length: 1634523417, N50: 64, Mean: 49, number of contigs: 33049598' b' [assembler.cpp : 133] Maximum length: 10934' b' [assembler.cpp : 290] Time to output: 58.111875' b' [assembler.cpp : 317] Number of local low depth unitigs removed: 1384571, complex bubbles removed: 94542, time: 618.692062' b' [assembler.cpp : 132] Total length: 1231592778, N50: 50, Mean: 45, number of contigs: 26877114' b' [assembler.cpp : 133] Maximum length: 11969' b' [utils.h : 126] Real: 1383.1438\tuser: 33565.8499\tsys: 39.2228\tmaxrss: 8184768' --- [Thu Mar 28 23:28:34 2019] Local assembling k = 21 --- cmd: /gscratch/srlab/programs/megahit_v1.1.4_LINUX_CPUONLY_x86_64-bin/megahit_asm_core local -c ./megahit_out/intermediate_contigs/k21.contigs.fa -l ./megahit_out/tmp/reads.lib -t 28 -o ./megahit_out/intermediate_contigs/k21.local.fa --kmax 29 b' [local_assembler.cpp : 89] Number of contigs: 650649, Mapper size: 25554280' b' [read_lib_functions-inl.h : 256] Before reading, sizeof seq_package: 5214492324' b' [read_lib_functions-inl.h : 260] After reading, sizeof seq_package: 5214492324' b' [local_assembler.cpp : 330] Lib 0, insert size: 240.90 sd: 87.99' b' [local_assembler.cpp : 462] Lib 0: total 143722488 reads, aligned 36119482, added 18372552 reads for local assembly' b' [utils.h : 126] Real: 298.7891\tuser: 7746.7448\tsys: 12.7996\tmaxrss: 6888640' --- [Thu Mar 28 23:33:32 2019] Extracting iterative edges from k = 21 to 29 --- cmd: /gscratch/srlab/programs/megahit_v1.1.4_LINUX_CPUONLY_x86_64-bin/megahit_asm_core iterate -c ./megahit_out/intermediate_contigs/k21.contigs.fa -b ./megahit_out/intermediate_contigs/k21.bubble_seq.fa -t 28 -k 21 -s 8 -o ./megahit_out/tmp/k29/29 -r ./megahit_out/tmp/reads.lib.bin -f binary b' [iterate_edges.cpp : 570] Number of crusial kmers: 6981230' b' [iterate_edges.cpp : 570] Number of crusial kmers: 61720087' b' [iterate_edges.cpp : 443] Processed: 67108864, aligned: 47593879. Iterative edges: 189085017' b' [iterate_edges.cpp : 443] Processed: 134217728, aligned: 95268494. Iterative edges: 238434166' b' [iterate_edges.cpp : 447] Total: 143722488, aligned: 102089551. Iterative edges: 242853041' b' [iterate_edges.cpp : 451] Writing iterative edges...' b' [utils.h : 126] Real: 322.9844\tuser: 8034.0081\tsys: 11.1149\tmaxrss: 7727692' --- [Thu Mar 28 23:38:55 2019] Building graph for k = 29 --- /gscratch/srlab/programs/megahit_v1.1.4_LINUX_CPUONLY_x86_64-bin/megahit_sdbg_build seq2sdbg --host_mem 242783447040 --mem_flag 1 --gpu_mem 0 --output_prefix ./megahit_out/tmp/k29/29 --num_cpu_threads 28 -k 29 --kmer_from 21 --num_edge_files 1 --input_prefix ./megahit_out/tmp/k29/29 --addi_contig ./megahit_out/intermediate_contigs/k21.addi.fa --local_contig ./megahit_out/intermediate_contigs/k21.local.fa --contig ./megahit_out/intermediate_contigs/k21.contigs.fa --bubble ./megahit_out/intermediate_contigs/k21.bubble_seq.fa b' [sdbg_builder.cpp : 339] Host memory to be used: 242783447040' b' [sdbg_builder.cpp : 340] Number CPU threads: 28' b' [cx1.h : 450] Preparing data...' b' [cx1_seq2sdbg.cpp : 394] Number edges: 242853041' b' [cx1_seq2sdbg.cpp : 434] Bases to reserve: 10511797966, number contigs: 61164969, number multiplicity: 304018010' b' [cx1_seq2sdbg.cpp : 440] Before reading, sizeof seq_package: 3117269252, multiplicity vector: 304018010' b' [cx1_seq2sdbg.cpp : 529] After reading, sizeof seq_package: 3117269252, multiplicity vector: 304018010' b' [cx1.h : 457] Preparing data... Done. Time elapsed: 23.9912' b' [cx1.h : 464] Preparing partitions and initialing global data...' b' [cx1_seq2sdbg.cpp : 740] Memory for sequence: 3724513022' b' [cx1_seq2sdbg.cpp : 741] max # lv.1 items = 572306345' b' [cx1.h : 480] Preparing partitions and initialing global data... Done. Time elapsed: 7.8866' b' [cx1.h : 486] Start main loop...' b' [cx1.h : 515] Lv1 scanning from bucket 0 to 768' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 5.9952' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 7.0872' b' [cx1.h : 515] Lv1 scanning from bucket 768 to 3248' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 7.2338' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 9.1190' b' [cx1.h : 515] Lv1 scanning from bucket 3248 to 7418' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 8.0741' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 9.4324' b' [cx1.h : 515] Lv1 scanning from bucket 7418 to 13424' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 9.1272' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 10.2534' b' [cx1.h : 515] Lv1 scanning from bucket 13424 to 21609' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 9.5063' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 10.4622' b' [cx1.h : 515] Lv1 scanning from bucket 21609 to 32641' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 9.9798' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 10.4420' b' [cx1.h : 515] Lv1 scanning from bucket 32641 to 48117' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 10.1361' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 11.3953' b' [cx1.h : 515] Lv1 scanning from bucket 48117 to 65536' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 8.1990' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 8.1163' b' [cx1.h : 607] Main loop done. Time elapsed: 144.5605' 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] 15087652 604030557 378775849 378503967 604570727 3445110 2641128 1917006 3804708' b' [cx1_seq2sdbg.cpp :1151] Total number of edges: 1992776704' b' [cx1_seq2sdbg.cpp :1152] Total number of ONEs: 1965881100' b' [cx1_seq2sdbg.cpp :1153] Total number of $v edges: 15087652' b' [cx1.h : 621] Postprocess done. Time elapsed: 0.0395' b' [utils.h : 126] Real: 176.4868\tuser: 2388.1014\tsys: 18.0727\tmaxrss: 5429952' --- [Thu Mar 28 23:41:52 2019] Assembling contigs from SdBG for k = 29 --- cmd: /gscratch/srlab/programs/megahit_v1.1.4_LINUX_CPUONLY_x86_64-bin/megahit_asm_core assemble -s ./megahit_out/tmp/k29/29 -o ./megahit_out/intermediate_contigs/k29 -t 28 --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_out/tmp/k29/29 Done. Time elapsed: 117.601717' b' [assembler.cpp : 152] Number of Edges: 1992776704; K value: 29' b' [assembler.cpp : 162] Number of CPU threads: 28' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 2; Accumulated tips removed: 434606; time elapsed: 6.2226' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 4; Accumulated tips removed: 1534673; time elapsed: 7.6711' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 8; Accumulated tips removed: 2696562; time elapsed: 11.0333' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 16; Accumulated tips removed: 4662123; time elapsed: 18.4422' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 32; Accumulated tips removed: 8340581; time elapsed: 32.1416' b' [assembly_algorithms.cpp : 170] Removing tips with length less than 58; Accumulated tips removed: 11465490; time elapsed: 43.2398' b' [assembler.cpp : 179] Tips removal done! Time elapsed(sec): 118.825472' b' [assembler.cpp : 188] unitig graph size: 16011539, time for building: 127.439053' b' [assembler.cpp : 211] Number of bubbles removed: 1629995, Time elapsed(sec): 18.570571' b' [assembler.cpp : 225] Number of complex bubbles removed: 293168, Time elapsed(sec): 7.336393' b' [assembler.cpp : 243] Number unitigs disconnected: 266446, time: 2.899942' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 22751, time: 2.782461' b' [assembler.cpp : 200] Tips removed: 16444, time: 4.314494' b' [assembler.cpp : 211] Number of bubbles removed: 26336, Time elapsed(sec): 2.348166' b' [assembler.cpp : 225] Number of complex bubbles removed: 10440, Time elapsed(sec): 3.172808' b' [assembler.cpp : 243] Number unitigs disconnected: 27696, time: 2.727451' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 129, time: 2.881069' b' [assembler.cpp : 200] Tips removed: 11137, time: 4.183128' b' [assembler.cpp : 211] Number of bubbles removed: 3383, Time elapsed(sec): 1.750657' b' [assembler.cpp : 225] Number of complex bubbles removed: 1214, Time elapsed(sec): 2.966060' b' [assembler.cpp : 243] Number unitigs disconnected: 1783, time: 2.717002' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 13, time: 2.858249' b' [assembler.cpp : 200] Tips removed: 185, time: 4.166041' b' [assembler.cpp : 211] Number of bubbles removed: 30, Time elapsed(sec): 1.589216' b' [assembler.cpp : 225] Number of complex bubbles removed: 32, Time elapsed(sec): 2.943213' b' [assembler.cpp : 243] Number unitigs disconnected: 191, time: 2.684832' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 0, time: 2.043274' b' [assembler.cpp : 200] Tips removed: 10, time: 4.189302' b' [assembler.cpp : 211] Number of bubbles removed: 2, Time elapsed(sec): 1.591799' b' [assembler.cpp : 225] Number of complex bubbles removed: 3, Time elapsed(sec): 2.942619' b' [assembler.cpp : 243] Number unitigs disconnected: 17, time: 2.772850' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 0, time: 2.066895' b' [assembler.cpp : 132] Total length: 1178555102, N50: 128, Mean: 95, number of contigs: 12381895' b' [assembler.cpp : 133] Maximum length: 112037' b' [assembler.cpp : 290] Time to output: 36.400453' b' [assembler.cpp : 317] Number of local low depth unitigs removed: 191948, complex bubbles removed: 25229, time: 185.937302' b' [assembler.cpp : 132] Total length: 637177184, N50: 86, Mean: 74, number of contigs: 8567425' b' [assembler.cpp : 133] Maximum length: 112037' b' [utils.h : 126] Real: 692.1515\tuser: 15130.5238\tsys: 27.2298\tmaxrss: 5212072' --- [Thu Mar 28 23:53:25 2019] Local assembling k = 29 --- cmd: /gscratch/srlab/programs/megahit_v1.1.4_LINUX_CPUONLY_x86_64-bin/megahit_asm_core local -c ./megahit_out/intermediate_contigs/k29.contigs.fa -l ./megahit_out/tmp/reads.lib -t 28 -o ./megahit_out/intermediate_contigs/k29.local.fa --kmax 39 b' [local_assembler.cpp : 89] Number of contigs: 876853, Mapper size: 43840774' b' [read_lib_functions-inl.h : 256] Before reading, sizeof seq_package: 5214492324' b' [read_lib_functions-inl.h : 260] After reading, sizeof seq_package: 5214492324' b' [local_assembler.cpp : 330] Lib 0, insert size: 255.79 sd: 97.59' b' [local_assembler.cpp : 462] Lib 0: total 143722488 reads, aligned 58813650, added 21131368 reads for local assembly' b' [utils.h : 126] Real: 359.3153\tuser: 9495.1462\tsys: 14.5790\tmaxrss: 7815996' --- [Thu Mar 28 23:59:24 2019] Extracting iterative edges from k = 29 to 39 --- cmd: /gscratch/srlab/programs/megahit_v1.1.4_LINUX_CPUONLY_x86_64-bin/megahit_asm_core iterate -c ./megahit_out/intermediate_contigs/k29.contigs.fa -b ./megahit_out/intermediate_contigs/k29.bubble_seq.fa -t 28 -k 29 -s 10 -o ./megahit_out/tmp/k39/39 -r ./megahit_out/tmp/reads.lib.bin -f binary b' [iterate_edges.cpp : 570] Number of crusial kmers: 5593614' b' [iterate_edges.cpp : 570] Number of crusial kmers: 22596843' b' [iterate_edges.cpp : 443] Processed: 67108864, aligned: 35740895. Iterative edges: 100597682' b' [iterate_edges.cpp : 443] Processed: 134217728, aligned: 71565627. Iterative edges: 123664460' b' [iterate_edges.cpp : 447] Total: 143722488, aligned: 76739027. Iterative edges: 125734327' b' [iterate_edges.cpp : 451] Writing iterative edges...' b' [utils.h : 126] Real: 244.7662\tuser: 6123.5914\tsys: 8.3026\tmaxrss: 4414980' --- [Fri Mar 29 00:03:29 2019] Building graph for k = 39 --- /gscratch/srlab/programs/megahit_v1.1.4_LINUX_CPUONLY_x86_64-bin/megahit_sdbg_build seq2sdbg --host_mem 242783447040 --mem_flag 1 --gpu_mem 0 --output_prefix ./megahit_out/tmp/k39/39 --num_cpu_threads 28 -k 39 --kmer_from 29 --num_edge_files 1 --input_prefix ./megahit_out/tmp/k39/39 --addi_contig ./megahit_out/intermediate_contigs/k29.addi.fa --local_contig ./megahit_out/intermediate_contigs/k29.local.fa --contig ./megahit_out/intermediate_contigs/k29.contigs.fa --bubble ./megahit_out/intermediate_contigs/k29.bubble_seq.fa b' [sdbg_builder.cpp : 339] Host memory to be used: 242783447040' b' [sdbg_builder.cpp : 340] Number CPU threads: 28' b' [cx1.h : 450] Preparing data...' b' [cx1_seq2sdbg.cpp : 394] Number edges: 125734327' b' [cx1_seq2sdbg.cpp : 434] Bases to reserve: 7338088315, number contigs: 23568402, number multiplicity: 149302729' b' [cx1_seq2sdbg.cpp : 440] Before reading, sizeof seq_package: 2023069304, multiplicity vector: 149302729' b' [cx1_seq2sdbg.cpp : 529] After reading, sizeof seq_package: 2023069304, multiplicity vector: 149302729' b' [cx1.h : 457] Preparing data... Done. Time elapsed: 16.2435' b' [cx1.h : 464] Preparing partitions and initialing global data...' b' [cx1_seq2sdbg.cpp : 740] Memory for sequence: 2359365532' b' [cx1_seq2sdbg.cpp : 741] max # lv.1 items = 515121843' b' [cx1.h : 480] Preparing partitions and initialing global data... Done. Time elapsed: 8.2324' b' [cx1.h : 486] Start main loop...' b' [cx1.h : 515] Lv1 scanning from bucket 0 to 983' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 7.0685' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 7.0647' b' [cx1.h : 515] Lv1 scanning from bucket 983 to 3772' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 8.8277' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 8.3053' b' [cx1.h : 515] Lv1 scanning from bucket 3772 to 8228' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 9.2611' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 9.0518' b' [cx1.h : 515] Lv1 scanning from bucket 8228 to 14490' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 9.0769' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 9.3957' b' [cx1.h : 515] Lv1 scanning from bucket 14490 to 22887' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 9.5444' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 9.9310' b' [cx1.h : 515] Lv1 scanning from bucket 22887 to 34085' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 10.8076' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 10.3202' b' [cx1.h : 515] Lv1 scanning from bucket 34085 to 49786' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 9.5797' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 10.2262' b' [cx1.h : 515] Lv1 scanning from bucket 49786 to 65536' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 8.1552' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 6.8087' b' [cx1.h : 607] Main loop done. Time elapsed: 143.4258' 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] 9571167 530367691 337795759 337305342 530930074 2126760 1047891 1043654 2133324' b' [cx1_seq2sdbg.cpp :1151] Total number of edges: 1752321662' b' [cx1_seq2sdbg.cpp :1152] Total number of ONEs: 1736398866' b' [cx1_seq2sdbg.cpp :1153] Total number of $v edges: 9571167' b' [cx1.h : 621] Postprocess done. Time elapsed: 0.0392' b' [utils.h : 126] Real: 167.9477\tuser: 2206.5606\tsys: 14.0555\tmaxrss: 4347656' --- [Fri Mar 29 00:06:17 2019] Assembling contigs from SdBG for k = 39 --- cmd: /gscratch/srlab/programs/megahit_v1.1.4_LINUX_CPUONLY_x86_64-bin/megahit_asm_core assemble -s ./megahit_out/tmp/k39/39 -o ./megahit_out/intermediate_contigs/k39 -t 28 --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_out/tmp/k39/39 Done. Time elapsed: 133.598549' b' [assembler.cpp : 152] Number of Edges: 1752321662; K value: 39' b' [assembler.cpp : 162] Number of CPU threads: 28' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 2; Accumulated tips removed: 85068; time elapsed: 5.0949' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 4; Accumulated tips removed: 431234; time elapsed: 5.9229' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 8; Accumulated tips removed: 854240; time elapsed: 8.1794' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 16; Accumulated tips removed: 1393162; time elapsed: 13.5964' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 32; Accumulated tips removed: 2170376; time elapsed: 23.7731' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 64; Accumulated tips removed: 4811661; time elapsed: 39.8438' b' [assembly_algorithms.cpp : 170] Removing tips with length less than 78; Accumulated tips removed: 6152726; time elapsed: 38.2166' b' [assembler.cpp : 179] Tips removal done! Time elapsed(sec): 134.694756' b' [assembler.cpp : 188] unitig graph size: 9833607, time for building: 102.185832' b' [assembler.cpp : 211] Number of bubbles removed: 1173264, Time elapsed(sec): 18.175686' b' [assembler.cpp : 225] Number of complex bubbles removed: 205993, Time elapsed(sec): 6.241131' b' [assembler.cpp : 243] Number unitigs disconnected: 145074, time: 1.239886' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 45400, time: 1.091631' b' [assembler.cpp : 200] Tips removed: 15709, time: 2.929114' b' [assembler.cpp : 211] Number of bubbles removed: 25535, Time elapsed(sec): 1.733880' b' [assembler.cpp : 225] Number of complex bubbles removed: 12434, Time elapsed(sec): 1.896787' b' [assembler.cpp : 243] Number unitigs disconnected: 9178, time: 1.138028' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 174, time: 1.005346' b' [assembler.cpp : 200] Tips removed: 5223, time: 2.852282' b' [assembler.cpp : 211] Number of bubbles removed: 1756, Time elapsed(sec): 1.055850' b' [assembler.cpp : 225] Number of complex bubbles removed: 1047, Time elapsed(sec): 1.536961' b' [assembler.cpp : 243] Number unitigs disconnected: 195, time: 1.125504' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 11, time: 0.998514' b' [assembler.cpp : 200] Tips removed: 51, time: 2.809163' b' [assembler.cpp : 211] Number of bubbles removed: 10, Time elapsed(sec): 0.878737' b' [assembler.cpp : 225] Number of complex bubbles removed: 13, Time elapsed(sec): 1.501514' b' [assembler.cpp : 243] Number unitigs disconnected: 12, time: 1.121359' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 0, time: 0.597850' b' [assembler.cpp : 200] Tips removed: 1, time: 2.802234' b' [assembler.cpp : 211] Number of bubbles removed: 0, Time elapsed(sec): 0.880100' b' [assembler.cpp : 225] Number of complex bubbles removed: 0, Time elapsed(sec): 1.506547' b' [assembler.cpp : 243] Number unitigs disconnected: 2, time: 1.180564' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 0, time: 0.650061' b' [assembler.cpp : 132] Total length: 987119010, N50: 170, Mean: 137, number of contigs: 7180928' b' [assembler.cpp : 133] Maximum length: 268310' b' [assembler.cpp : 290] Time to output: 28.875484' b' [assembler.cpp : 317] Number of local low depth unitigs removed: 35606, complex bubbles removed: 6462, time: 81.550151' b' [assembler.cpp : 132] Total length: 505465736, N50: 126, Mean: 106, number of contigs: 4731887' b' [assembler.cpp : 133] Maximum length: 268310' b' [utils.h : 126] Real: 551.6731\tuser: 10994.1881\tsys: 22.3533\tmaxrss: 4709168' --- [Fri Mar 29 00:15:29 2019] Local assembling k = 39 --- cmd: /gscratch/srlab/programs/megahit_v1.1.4_LINUX_CPUONLY_x86_64-bin/megahit_asm_core local -c ./megahit_out/intermediate_contigs/k39.contigs.fa -l ./megahit_out/tmp/reads.lib -t 28 -o ./megahit_out/intermediate_contigs/k39.local.fa --kmax 59 b' [local_assembler.cpp : 89] Number of contigs: 913764, Mapper size: 51361117' b' [read_lib_functions-inl.h : 256] Before reading, sizeof seq_package: 5214492324' b' [read_lib_functions-inl.h : 260] After reading, sizeof seq_package: 5214492324' b' [local_assembler.cpp : 330] Lib 0, insert size: 260.31 sd: 100.49' b' [local_assembler.cpp : 462] Lib 0: total 143722488 reads, aligned 70458599, added 23399887 reads for local assembly' b' [utils.h : 126] Real: 537.0117\tuser: 14410.5271\tsys: 13.7539\tmaxrss: 8068844' --- [Fri Mar 29 00:24:26 2019] Extracting iterative edges from k = 39 to 59 --- cmd: /gscratch/srlab/programs/megahit_v1.1.4_LINUX_CPUONLY_x86_64-bin/megahit_asm_core iterate -c ./megahit_out/intermediate_contigs/k39.contigs.fa -b ./megahit_out/intermediate_contigs/k39.bubble_seq.fa -t 28 -k 39 -s 20 -o ./megahit_out/tmp/k59/59 -r ./megahit_out/tmp/reads.lib.bin -f binary b' [iterate_edges.cpp : 570] Number of crusial kmers: 3872942' b' [iterate_edges.cpp : 570] Number of crusial kmers: 12777253' b' [iterate_edges.cpp : 443] Processed: 67108864, aligned: 25573669. Iterative edges: 102061387' b' [iterate_edges.cpp : 443] Processed: 134217728, aligned: 51160060. Iterative edges: 130820447' b' [iterate_edges.cpp : 447] Total: 143722488, aligned: 54931027. Iterative edges: 133648004' b' [iterate_edges.cpp : 451] Writing iterative edges...' b' [utils.h : 126] Real: 218.0331\tuser: 5312.4847\tsys: 8.8156\tmaxrss: 4846228' --- [Fri Mar 29 00:28:04 2019] Building graph for k = 59 --- /gscratch/srlab/programs/megahit_v1.1.4_LINUX_CPUONLY_x86_64-bin/megahit_sdbg_build seq2sdbg --host_mem 242783447040 --mem_flag 1 --gpu_mem 0 --output_prefix ./megahit_out/tmp/k59/59 --num_cpu_threads 28 -k 59 --kmer_from 39 --num_edge_files 1 --input_prefix ./megahit_out/tmp/k59/59 --addi_contig ./megahit_out/intermediate_contigs/k39.addi.fa --local_contig ./megahit_out/intermediate_contigs/k39.local.fa --contig ./megahit_out/intermediate_contigs/k39.contigs.fa --bubble ./megahit_out/intermediate_contigs/k39.bubble_seq.fa b' [sdbg_builder.cpp : 339] Host memory to be used: 242783447040' b' [sdbg_builder.cpp : 340] Number CPU threads: 28' b' [cx1.h : 450] Preparing data...' b' [cx1_seq2sdbg.cpp : 394] Number edges: 133648004' b' [cx1_seq2sdbg.cpp : 434] Bases to reserve: 10153710391, number contigs: 14355045, number multiplicity: 148003049' b' [cx1_seq2sdbg.cpp : 440] Before reading, sizeof seq_package: 2653267968, multiplicity vector: 148003049' b' [cx1_seq2sdbg.cpp : 529] After reading, sizeof seq_package: 2653267968, multiplicity vector: 148003049' b' [cx1.h : 457] Preparing data... Done. Time elapsed: 16.3625' b' [cx1.h : 464] Preparing partitions and initialing global data...' b' [cx1_seq2sdbg.cpp : 740] Memory for sequence: 3016886342' b' [cx1_seq2sdbg.cpp : 741] max # lv.1 items = 496092775' b' [cx1.h : 480] Preparing partitions and initialing global data... Done. Time elapsed: 9.4625' b' [cx1.h : 486] Start main loop...' b' [cx1.h : 515] Lv1 scanning from bucket 0 to 914' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 8.2599' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 6.2473' b' [cx1.h : 515] Lv1 scanning from bucket 914 to 3638' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 9.9462' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 7.9221' b' [cx1.h : 515] Lv1 scanning from bucket 3638 to 8037' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 10.2832' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 8.1860' b' [cx1.h : 515] Lv1 scanning from bucket 8037 to 14238' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 11.7913' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 8.8790' b' [cx1.h : 515] Lv1 scanning from bucket 14238 to 22561' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 12.0196' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 8.9002' b' [cx1.h : 515] Lv1 scanning from bucket 22561 to 33673' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 11.9142' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 8.9544' b' [cx1.h : 515] Lv1 scanning from bucket 33673 to 49283' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 12.7737' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 9.5997' b' [cx1.h : 515] Lv1 scanning from bucket 49283 to 65536' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 9.4451' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 6.2030' b' [cx1.h : 607] Main loop done. Time elapsed: 151.3261' 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] 7251302 459992570 293202315 292936970 460461481 1031943 822030 606950 1138811' b' [cx1_seq2sdbg.cpp :1151] Total number of edges: 1517444372' b' [cx1_seq2sdbg.cpp :1152] Total number of ONEs: 1506593336' b' [cx1_seq2sdbg.cpp :1153] Total number of $v edges: 7251302' b' [cx1.h : 621] Postprocess done. Time elapsed: 0.0348' b' [utils.h : 126] Real: 177.1942\tuser: 2005.8162\tsys: 16.6167\tmaxrss: 4951568' --- [Fri Mar 29 00:31:02 2019] Assembling contigs from SdBG for k = 59 --- cmd: /gscratch/srlab/programs/megahit_v1.1.4_LINUX_CPUONLY_x86_64-bin/megahit_asm_core assemble -s ./megahit_out/tmp/k59/59 -o ./megahit_out/intermediate_contigs/k59 -t 28 --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_out/tmp/k59/59 Done. Time elapsed: 81.475996' b' [assembler.cpp : 152] Number of Edges: 1517444372; K value: 59' b' [assembler.cpp : 162] Number of CPU threads: 28' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 2; Accumulated tips removed: 54824; time elapsed: 4.4830' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 4; Accumulated tips removed: 225775; time elapsed: 4.9151' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 8; Accumulated tips removed: 505718; time elapsed: 6.6208' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 16; Accumulated tips removed: 980402; time elapsed: 10.7433' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 32; Accumulated tips removed: 1524431; time elapsed: 17.7383' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 64; Accumulated tips removed: 3514597; time elapsed: 30.3736' b' [assembly_algorithms.cpp : 170] Removing tips with length less than 118; Accumulated tips removed: 6791418; time elapsed: 32.6804' b' [assembler.cpp : 179] Tips removal done! Time elapsed(sec): 107.611295' b' [assembler.cpp : 188] unitig graph size: 4362278, time for building: 71.045437' b' [assembler.cpp : 211] Number of bubbles removed: 562765, Time elapsed(sec): 14.399988' b' [assembler.cpp : 225] Number of complex bubbles removed: 122919, Time elapsed(sec): 5.326773' b' [assembler.cpp : 243] Number unitigs disconnected: 182553, time: 0.599617' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 71550, time: 0.630885' b' [assembler.cpp : 200] Tips removed: 3446, time: 1.191997' b' [assembler.cpp : 211] Number of bubbles removed: 23893, Time elapsed(sec): 1.394699' b' [assembler.cpp : 225] Number of complex bubbles removed: 14378, Time elapsed(sec): 1.423492' b' [assembler.cpp : 243] Number unitigs disconnected: 8639, time: 0.502458' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 416, time: 0.451654' b' [assembler.cpp : 200] Tips removed: 4655, time: 1.160508' b' [assembler.cpp : 211] Number of bubbles removed: 960, Time elapsed(sec): 0.422079' b' [assembler.cpp : 225] Number of complex bubbles removed: 1003, Time elapsed(sec): 0.759130' b' [assembler.cpp : 243] Number unitigs disconnected: 148, time: 0.496636' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 27, time: 0.450104' b' [assembler.cpp : 200] Tips removed: 50, time: 1.149759' b' [assembler.cpp : 211] Number of bubbles removed: 6, Time elapsed(sec): 0.357672' b' [assembler.cpp : 225] Number of complex bubbles removed: 14, Time elapsed(sec): 0.705731' b' [assembler.cpp : 243] Number unitigs disconnected: 1, time: 0.494557' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 1, time: 0.450291' b' [assembler.cpp : 200] Tips removed: 0, time: 1.170241' b' [assembler.cpp : 211] Number of bubbles removed: 2, Time elapsed(sec): 0.359107' b' [assembler.cpp : 225] Number of complex bubbles removed: 0, Time elapsed(sec): 0.715379' b' [assembler.cpp : 243] Number unitigs disconnected: 0, time: 0.497748' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 0, time: 0.282573' b' [assembler.cpp : 132] Total length: 698045839, N50: 365, Mean: 247, number of contigs: 2814906' b' [assembler.cpp : 133] Maximum length: 474413' b' [assembler.cpp : 290] Time to output: 21.502323' b' [assembler.cpp : 317] Number of local low depth unitigs removed: 10826, complex bubbles removed: 1891, time: 33.778368' b' [assembler.cpp : 132] Total length: 364151655, N50: 302, Mean: 192, number of contigs: 1890819' b' [assembler.cpp : 133] Maximum length: 474413' b' [utils.h : 126] Real: 361.6996\tuser: 7264.5981\tsys: 15.1930\tmaxrss: 3831244' --- [Fri Mar 29 00:37:04 2019] Local assembling k = 59 --- cmd: /gscratch/srlab/programs/megahit_v1.1.4_LINUX_CPUONLY_x86_64-bin/megahit_asm_core local -c ./megahit_out/intermediate_contigs/k59.contigs.fa -l ./megahit_out/tmp/reads.lib -t 28 -o ./megahit_out/intermediate_contigs/k59.local.fa --kmax 79 b' [local_assembler.cpp : 89] Number of contigs: 971136, Mapper size: 59112316' b' [read_lib_functions-inl.h : 256] Before reading, sizeof seq_package: 5214492324' b' [read_lib_functions-inl.h : 260] After reading, sizeof seq_package: 5214492324' b' [local_assembler.cpp : 330] Lib 0, insert size: 263.60 sd: 103.21' b' [local_assembler.cpp : 462] Lib 0: total 143722488 reads, aligned 81150291, added 25524866 reads for local assembly' b' [utils.h : 126] Real: 653.8297\tuser: 17619.9895\tsys: 14.5686\tmaxrss: 8362176' --- [Fri Mar 29 00:47:58 2019] Extracting iterative edges from k = 59 to 79 --- cmd: /gscratch/srlab/programs/megahit_v1.1.4_LINUX_CPUONLY_x86_64-bin/megahit_asm_core iterate -c ./megahit_out/intermediate_contigs/k59.contigs.fa -b ./megahit_out/intermediate_contigs/k59.bubble_seq.fa -t 28 -k 59 -s 20 -o ./megahit_out/tmp/k79/79 -r ./megahit_out/tmp/reads.lib.bin -f binary b' [iterate_edges.cpp : 570] Number of crusial kmers: 1893295' b' [iterate_edges.cpp : 570] Number of crusial kmers: 5431500' b' [iterate_edges.cpp : 443] Processed: 67108864, aligned: 14049504. Iterative edges: 40659384' b' [iterate_edges.cpp : 443] Processed: 134217728, aligned: 27974156. Iterative edges: 50876090' b' [iterate_edges.cpp : 447] Total: 143722488, aligned: 30092769. Iterative edges: 51911545' b' [iterate_edges.cpp : 451] Writing iterative edges...' b' [utils.h : 126] Real: 148.2533\tuser: 3608.2631\tsys: 6.2427\tmaxrss: 2451840' --- [Fri Mar 29 00:50:26 2019] Building graph for k = 79 --- /gscratch/srlab/programs/megahit_v1.1.4_LINUX_CPUONLY_x86_64-bin/megahit_sdbg_build seq2sdbg --host_mem 242783447040 --mem_flag 1 --gpu_mem 0 --output_prefix ./megahit_out/tmp/k79/79 --num_cpu_threads 28 -k 79 --kmer_from 59 --num_edge_files 1 --input_prefix ./megahit_out/tmp/k79/79 --addi_contig ./megahit_out/intermediate_contigs/k59.addi.fa --local_contig ./megahit_out/intermediate_contigs/k59.local.fa --contig ./megahit_out/intermediate_contigs/k59.contigs.fa --bubble ./megahit_out/intermediate_contigs/k59.bubble_seq.fa b' [sdbg_builder.cpp : 339] Host memory to be used: 242783447040' b' [sdbg_builder.cpp : 340] Number CPU threads: 28' b' [cx1.h : 450] Preparing data...' b' [cx1_seq2sdbg.cpp : 394] Number edges: 51911545' b' [cx1_seq2sdbg.cpp : 434] Bases to reserve: 5862455167, number contigs: 6505452, number multiplicity: 58416997' b' [cx1_seq2sdbg.cpp : 440] Before reading, sizeof seq_package: 1517657416, multiplicity vector: 58416997' b' [cx1_seq2sdbg.cpp : 529] After reading, sizeof seq_package: 1517657416, multiplicity vector: 58416997' b' [cx1.h : 457] Preparing data... Done. Time elapsed: 9.6405' b' [cx1.h : 464] Preparing partitions and initialing global data...' b' [cx1_seq2sdbg.cpp : 740] Memory for sequence: 1676105718' b' [cx1_seq2sdbg.cpp : 741] max # lv.1 items = 379184108' b' [cx1.h : 480] Preparing partitions and initialing global data... Done. Time elapsed: 6.6290' b' [cx1.h : 486] Start main loop...' b' [cx1.h : 515] Lv1 scanning from bucket 0 to 840' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 6.0120' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 4.5237' b' [cx1.h : 515] Lv1 scanning from bucket 840 to 3476' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 6.9837' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 5.8691' b' [cx1.h : 515] Lv1 scanning from bucket 3476 to 7785' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 7.2444' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 6.2488' b' [cx1.h : 515] Lv1 scanning from bucket 7785 to 13887' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 8.3144' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 6.6088' b' [cx1.h : 515] Lv1 scanning from bucket 13887 to 22101' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 8.5318' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 6.8777' b' [cx1.h : 515] Lv1 scanning from bucket 22101 to 33105' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 8.8565' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 6.8213' b' [cx1.h : 515] Lv1 scanning from bucket 33105 to 48625' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 9.2029' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 7.1512' b' [cx1.h : 515] Lv1 scanning from bucket 48625 to 65536' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 6.9463' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 4.8317' b' [cx1.h : 607] Main loop done. Time elapsed: 111.0252' 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] 3231110 364522699 230531578 230367236 364797199 638921 336702 455535 580249' b' [cx1_seq2sdbg.cpp :1151] Total number of edges: 1195461229' b' [cx1_seq2sdbg.cpp :1152] Total number of ONEs: 1190218712' b' [cx1_seq2sdbg.cpp :1153] Total number of $v edges: 3231110' b' [cx1.h : 621] Postprocess done. Time elapsed: 0.0331' b' [utils.h : 126] Real: 127.3330\tuser: 1511.6679\tsys: 11.3641\tmaxrss: 3243616' --- [Fri Mar 29 00:52:34 2019] Assembling contigs from SdBG for k = 79 --- cmd: /gscratch/srlab/programs/megahit_v1.1.4_LINUX_CPUONLY_x86_64-bin/megahit_asm_core assemble -s ./megahit_out/tmp/k79/79 -o ./megahit_out/intermediate_contigs/k79 -t 28 --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_out/tmp/k79/79 Done. Time elapsed: 46.833848' b' [assembler.cpp : 152] Number of Edges: 1195461229; K value: 79' b' [assembler.cpp : 162] Number of CPU threads: 28' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 2; Accumulated tips removed: 29202; time elapsed: 3.3570' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 4; Accumulated tips removed: 115538; time elapsed: 3.5706' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 8; Accumulated tips removed: 257458; time elapsed: 4.3445' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 16; Accumulated tips removed: 511250; time elapsed: 6.1224' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 32; Accumulated tips removed: 797592; time elapsed: 9.2810' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 64; Accumulated tips removed: 1420347; time elapsed: 14.8211' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 128; Accumulated tips removed: 2485134; time elapsed: 21.6937' b' [assembly_algorithms.cpp : 170] Removing tips with length less than 158; Accumulated tips removed: 2870599; time elapsed: 19.7602' b' [assembler.cpp : 179] Tips removal done! Time elapsed(sec): 82.997183' b' [assembler.cpp : 188] unitig graph size: 2418288, time for building: 60.584564' b' [assembler.cpp : 211] Number of bubbles removed: 278088, Time elapsed(sec): 10.919462' b' [assembler.cpp : 225] Number of complex bubbles removed: 65784, Time elapsed(sec): 4.467941' b' [assembler.cpp : 243] Number unitigs disconnected: 208396, time: 0.436744' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 81617, time: 0.506915' b' [assembler.cpp : 200] Tips removed: 2639, time: 0.734498' b' [assembler.cpp : 211] Number of bubbles removed: 18584, Time elapsed(sec): 1.106501' b' [assembler.cpp : 225] Number of complex bubbles removed: 12545, Time elapsed(sec): 1.209679' b' [assembler.cpp : 243] Number unitigs disconnected: 8490, time: 0.277275' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 1020, time: 0.265060' b' [assembler.cpp : 200] Tips removed: 5415, time: 0.709500' b' [assembler.cpp : 211] Number of bubbles removed: 518, Time elapsed(sec): 0.222123' b' [assembler.cpp : 225] Number of complex bubbles removed: 827, Time elapsed(sec): 0.469448' b' [assembler.cpp : 243] Number unitigs disconnected: 198, time: 0.261465' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 87, time: 0.254928' b' [assembler.cpp : 200] Tips removed: 96, time: 0.674587' b' [assembler.cpp : 211] Number of bubbles removed: 6, Time elapsed(sec): 0.173968' b' [assembler.cpp : 225] Number of complex bubbles removed: 15, Time elapsed(sec): 0.407703' b' [assembler.cpp : 243] Number unitigs disconnected: 12, time: 0.262522' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 13, time: 0.254950' b' [assembler.cpp : 200] Tips removed: 5, time: 0.675542' b' [assembler.cpp : 211] Number of bubbles removed: 0, Time elapsed(sec): 0.174355' b' [assembler.cpp : 225] Number of complex bubbles removed: 0, Time elapsed(sec): 0.410392' b' [assembler.cpp : 243] Number unitigs disconnected: 1, time: 0.263226' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 2, time: 0.254878' b' [assembler.cpp : 132] Total length: 582657313, N50: 602, Mean: 405, number of contigs: 1435848' b' [assembler.cpp : 133] Maximum length: 495089' b' [assembler.cpp : 290] Time to output: 18.344353' b' [assembler.cpp : 317] Number of local low depth unitigs removed: 7169, complex bubbles removed: 800, time: 23.154378' b' [assembler.cpp : 132] Total length: 274991057, N50: 674, Mean: 321, number of contigs: 856196' b' [assembler.cpp : 133] Maximum length: 495089' b' [utils.h : 126] Real: 265.6819\tuser: 5736.1363\tsys: 11.9709\tmaxrss: 2917620' --- [Fri Mar 29 00:57:00 2019] Local assembling k = 79 --- cmd: /gscratch/srlab/programs/megahit_v1.1.4_LINUX_CPUONLY_x86_64-bin/megahit_asm_core local -c ./megahit_out/intermediate_contigs/k79.contigs.fa -l ./megahit_out/tmp/reads.lib -t 28 -o ./megahit_out/intermediate_contigs/k79.local.fa --kmax 99 b' [local_assembler.cpp : 89] Number of contigs: 809168, Mapper size: 59725658' b' [read_lib_functions-inl.h : 256] Before reading, sizeof seq_package: 5214492324' b' [read_lib_functions-inl.h : 260] After reading, sizeof seq_package: 5214492324' b' [local_assembler.cpp : 330] Lib 0, insert size: 268.40 sd: 105.68' b' [local_assembler.cpp : 462] Lib 0: total 143722488 reads, aligned 80438377, added 20313037 reads for local assembly' b' [utils.h : 126] Real: 583.6925\tuser: 15816.7848\tsys: 13.3905\tmaxrss: 8132788' --- [Fri Mar 29 01:06:43 2019] Extracting iterative edges from k = 79 to 99 --- cmd: /gscratch/srlab/programs/megahit_v1.1.4_LINUX_CPUONLY_x86_64-bin/megahit_asm_core iterate -c ./megahit_out/intermediate_contigs/k79.contigs.fa -b ./megahit_out/intermediate_contigs/k79.bubble_seq.fa -t 28 -k 79 -s 20 -o ./megahit_out/tmp/k99/99 -r ./megahit_out/tmp/reads.lib.bin -f binary b' [iterate_edges.cpp : 570] Number of crusial kmers: 936406' b' [iterate_edges.cpp : 570] Number of crusial kmers: 2520353' b' [iterate_edges.cpp : 443] Processed: 67108864, aligned: 6454431. Iterative edges: 17306257' b' [iterate_edges.cpp : 443] Processed: 134217728, aligned: 12815743. Iterative edges: 22001026' b' [iterate_edges.cpp : 447] Total: 143722488, aligned: 13811983. Iterative edges: 22494959' b' [iterate_edges.cpp : 451] Writing iterative edges...' b' [utils.h : 126] Real: 94.4738\tuser: 2260.3071\tsys: 4.5190\tmaxrss: 1487152' --- [Fri Mar 29 01:08:18 2019] Building graph for k = 99 --- /gscratch/srlab/programs/megahit_v1.1.4_LINUX_CPUONLY_x86_64-bin/megahit_sdbg_build seq2sdbg --host_mem 242783447040 --mem_flag 1 --gpu_mem 0 --output_prefix ./megahit_out/tmp/k99/99 --num_cpu_threads 28 -k 99 --kmer_from 79 --num_edge_files 1 --input_prefix ./megahit_out/tmp/k99/99 --addi_contig ./megahit_out/intermediate_contigs/k79.addi.fa --local_contig ./megahit_out/intermediate_contigs/k79.local.fa --contig ./megahit_out/intermediate_contigs/k79.contigs.fa --bubble ./megahit_out/intermediate_contigs/k79.bubble_seq.fa b' [sdbg_builder.cpp : 339] Host memory to be used: 242783447040' b' [sdbg_builder.cpp : 340] Number CPU threads: 28' b' [cx1.h : 450] Preparing data...' b' [cx1_seq2sdbg.cpp : 394] Number edges: 22494959' b' [cx1_seq2sdbg.cpp : 434] Bases to reserve: 3587140552, number contigs: 3274232, number multiplicity: 25769191' b' [cx1_seq2sdbg.cpp : 440] Before reading, sizeof seq_package: 922979004, multiplicity vector: 25769191' b' [cx1_seq2sdbg.cpp : 529] After reading, sizeof seq_package: 1819764144, multiplicity vector: 25769191' b' [cx1.h : 457] Preparing data... Done. Time elapsed: 7.3772' b' [cx1.h : 464] Preparing partitions and initialing global data...' b' [cx1_seq2sdbg.cpp : 740] Memory for sequence: 1898352590' b' [cx1_seq2sdbg.cpp : 741] max # lv.1 items = 307591537' b' [cx1.h : 480] Preparing partitions and initialing global data... Done. Time elapsed: 4.2237' b' [cx1.h : 486] Start main loop...' b' [cx1.h : 515] Lv1 scanning from bucket 0 to 747' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 3.5172' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 3.3342' b' [cx1.h : 515] Lv1 scanning from bucket 747 to 3250' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 4.1587' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 4.6556' b' [cx1.h : 515] Lv1 scanning from bucket 3250 to 7424' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 4.9191' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 5.3373' b' [cx1.h : 515] Lv1 scanning from bucket 7424 to 13389' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 5.0993' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 5.5547' b' [cx1.h : 515] Lv1 scanning from bucket 13389 to 21474' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 5.7356' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 5.6479' b' [cx1.h : 515] Lv1 scanning from bucket 21474 to 32360' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 5.3194' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 5.4010' b' [cx1.h : 515] Lv1 scanning from bucket 32360 to 47772' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 5.7136' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 6.0593' b' [cx1.h : 515] Lv1 scanning from bucket 47772 to 65536' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 4.3883' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 4.1297' b' [cx1.h : 607] Main loop done. Time elapsed: 78.9720' 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] 2049786 315088247 198595089 198477010 315318530 364242 174074 173664 365725' b' [cx1_seq2sdbg.cpp :1151] Total number of edges: 1030606367' b' [cx1_seq2sdbg.cpp :1152] Total number of ONEs: 1027478876' b' [cx1_seq2sdbg.cpp :1153] Total number of $v edges: 2049786' b' [cx1.h : 621] Postprocess done. Time elapsed: 0.0326' b' [utils.h : 126] Real: 90.6091\tuser: 1230.7458\tsys: 8.0928\tmaxrss: 2345152' --- [Fri Mar 29 01:09:49 2019] Assembling contigs from SdBG for k = 99 --- cmd: /gscratch/srlab/programs/megahit_v1.1.4_LINUX_CPUONLY_x86_64-bin/megahit_asm_core assemble -s ./megahit_out/tmp/k99/99 -o ./megahit_out/intermediate_contigs/k99 -t 28 --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_out/tmp/k99/99 Done. Time elapsed: 21.449261' b' [assembler.cpp : 152] Number of Edges: 1030606367; K value: 99' b' [assembler.cpp : 162] Number of CPU threads: 28' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 2; Accumulated tips removed: 18460; time elapsed: 2.8302' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 4; Accumulated tips removed: 71558; time elapsed: 2.9540' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 8; Accumulated tips removed: 164492; time elapsed: 3.4709' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 16; Accumulated tips removed: 327890; time elapsed: 4.5304' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 32; Accumulated tips removed: 505729; time elapsed: 6.5712' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 64; Accumulated tips removed: 749779; time elapsed: 10.1951' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 128; Accumulated tips removed: 1214585; time elapsed: 16.3921' b' [assembly_algorithms.cpp : 170] Removing tips with length less than 198; Accumulated tips removed: 1643330; time elapsed: 19.2839' b' [assembler.cpp : 179] Tips removal done! Time elapsed(sec): 66.268720' b' [assembler.cpp : 188] unitig graph size: 1339259, time for building: 49.458748' b' [assembler.cpp : 211] Number of bubbles removed: 128446, Time elapsed(sec): 7.373455' b' [assembler.cpp : 225] Number of complex bubbles removed: 31069, Time elapsed(sec): 3.000001' b' [assembler.cpp : 243] Number unitigs disconnected: 140228, time: 0.295419' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 53998, time: 0.373652' b' [assembler.cpp : 200] Tips removed: 1685, time: 0.379642' b' [assembler.cpp : 211] Number of bubbles removed: 9763, Time elapsed(sec): 0.625868' b' [assembler.cpp : 225] Number of complex bubbles removed: 8275, Time elapsed(sec): 0.937501' b' [assembler.cpp : 243] Number unitigs disconnected: 4814, time: 0.171599' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 729, time: 0.185212' b' [assembler.cpp : 200] Tips removed: 2904, time: 0.379094' b' [assembler.cpp : 211] Number of bubbles removed: 262, Time elapsed(sec): 0.140239' b' [assembler.cpp : 225] Number of complex bubbles removed: 549, Time elapsed(sec): 0.321950' b' [assembler.cpp : 243] Number unitigs disconnected: 149, time: 0.167779' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 74, time: 0.183066' b' [assembler.cpp : 200] Tips removed: 70, time: 0.354606' b' [assembler.cpp : 211] Number of bubbles removed: 4, Time elapsed(sec): 0.088696' b' [assembler.cpp : 225] Number of complex bubbles removed: 4, Time elapsed(sec): 0.255804' b' [assembler.cpp : 243] Number unitigs disconnected: 10, time: 0.167967' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 12, time: 0.182541' b' [assembler.cpp : 200] Tips removed: 6, time: 0.365013' b' [assembler.cpp : 211] Number of bubbles removed: 0, Time elapsed(sec): 0.090901' b' [assembler.cpp : 225] Number of complex bubbles removed: 0, Time elapsed(sec): 0.259564' b' [assembler.cpp : 243] Number unitigs disconnected: 2, time: 0.168150' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 2, time: 0.181850' b' [assembler.cpp : 132] Total length: 511974914, N50: 890, Mean: 630, number of contigs: 811530' b' [assembler.cpp : 133] Maximum length: 570985' b' [assembler.cpp : 290] Time to output: 16.320317' b' [assembler.cpp : 317] Number of local low depth unitigs removed: 3833, complex bubbles removed: 439, time: 12.924120' b' [assembler.cpp : 132] Total length: 194808960, N50: 1504, Mean: 547, number of contigs: 355765' b' [assembler.cpp : 133] Maximum length: 570985' b' [utils.h : 126] Real: 189.5232\tuser: 4355.9507\tsys: 9.4580\tmaxrss: 2471596' --- [Fri Mar 29 01:12:58 2019] Local assembling k = 99 --- cmd: /gscratch/srlab/programs/megahit_v1.1.4_LINUX_CPUONLY_x86_64-bin/megahit_asm_core local -c ./megahit_out/intermediate_contigs/k99.contigs.fa -l ./megahit_out/tmp/reads.lib -t 28 -o ./megahit_out/intermediate_contigs/k99.local.fa --kmax 119 b' [local_assembler.cpp : 89] Number of contigs: 615018, Mapper size: 57485187' b' [read_lib_functions-inl.h : 256] Before reading, sizeof seq_package: 5214492324' b' [read_lib_functions-inl.h : 260] After reading, sizeof seq_package: 5214492324' b' [local_assembler.cpp : 330] Lib 0, insert size: 273.57 sd: 107.83' b' [local_assembler.cpp : 462] Lib 0: total 143722488 reads, aligned 74955007, added 12133418 reads for local assembly' b' [utils.h : 126] Real: 408.6063\tuser: 10915.9540\tsys: 11.6108\tmaxrss: 7771204' --- [Fri Mar 29 01:19:47 2019] Extracting iterative edges from k = 99 to 119 --- cmd: /gscratch/srlab/programs/megahit_v1.1.4_LINUX_CPUONLY_x86_64-bin/megahit_asm_core iterate -c ./megahit_out/intermediate_contigs/k99.contigs.fa -b ./megahit_out/intermediate_contigs/k99.bubble_seq.fa -t 28 -k 99 -s 20 -o ./megahit_out/tmp/k119/119 -r ./megahit_out/tmp/reads.lib.bin -f binary b' [iterate_edges.cpp : 570] Number of crusial kmers: 415863' b' [iterate_edges.cpp : 570] Number of crusial kmers: 1054294' b' [iterate_edges.cpp : 443] Processed: 67108864, aligned: 1988071. Iterative edges: 4629211' b' [iterate_edges.cpp : 443] Processed: 134217728, aligned: 3926520. Iterative edges: 6424111' b' [iterate_edges.cpp : 447] Total: 143722488, aligned: 4243227. Iterative edges: 6633496' b' [iterate_edges.cpp : 451] Writing iterative edges...' b' [utils.h : 126] Real: 44.9446\tuser: 1045.9367\tsys: 3.6112\tmaxrss: 756480' --- [Fri Mar 29 01:20:32 2019] Building graph for k = 119 --- /gscratch/srlab/programs/megahit_v1.1.4_LINUX_CPUONLY_x86_64-bin/megahit_sdbg_build seq2sdbg --host_mem 242783447040 --mem_flag 1 --gpu_mem 0 --output_prefix ./megahit_out/tmp/k119/119 --num_cpu_threads 28 -k 119 --kmer_from 99 --num_edge_files 1 --input_prefix ./megahit_out/tmp/k119/119 --addi_contig ./megahit_out/intermediate_contigs/k99.addi.fa --local_contig ./megahit_out/intermediate_contigs/k99.local.fa --contig ./megahit_out/intermediate_contigs/k99.contigs.fa --bubble ./megahit_out/intermediate_contigs/k99.bubble_seq.fa b' [sdbg_builder.cpp : 339] Host memory to be used: 242783447040' b' [sdbg_builder.cpp : 340] Number CPU threads: 28' b' [cx1.h : 450] Preparing data...' b' [cx1_seq2sdbg.cpp : 394] Number edges: 6633496' b' [cx1_seq2sdbg.cpp : 434] Bases to reserve: 1743877108, number contigs: 1572392, number multiplicity: 8205888' b' [cx1_seq2sdbg.cpp : 440] Before reading, sizeof seq_package: 448548424, multiplicity vector: 8205888' b' [cx1_seq2sdbg.cpp : 529] After reading, sizeof seq_package: 897096848, multiplicity vector: 16411776' b' [cx1.h : 457] Preparing data... Done. Time elapsed: 4.7979' b' [cx1.h : 464] Preparing partitions and initialing global data...' b' [cx1_seq2sdbg.cpp : 740] Memory for sequence: 928107388' b' [cx1_seq2sdbg.cpp : 741] max # lv.1 items = 239620975' b' [cx1.h : 480] Preparing partitions and initialing global data... Done. Time elapsed: 2.2754' b' [cx1.h : 486] Start main loop...' b' [cx1.h : 515] Lv1 scanning from bucket 0 to 571' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 1.7484' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 2.4348' b' [cx1.h : 515] Lv1 scanning from bucket 571 to 2789' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 1.9741' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 3.8070' b' [cx1.h : 515] Lv1 scanning from bucket 2789 to 6698' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 2.2020' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 4.3051' b' [cx1.h : 515] Lv1 scanning from bucket 6698 to 12404' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 2.4249' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 4.5651' b' [cx1.h : 515] Lv1 scanning from bucket 12404 to 20242' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 2.4257' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 4.6429' b' [cx1.h : 515] Lv1 scanning from bucket 20242 to 30879' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 2.8534' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 4.6849' b' [cx1.h : 515] Lv1 scanning from bucket 30879 to 45964' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 2.7052' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 4.7106' b' [cx1.h : 515] Lv1 scanning from bucket 45964 to 65536' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 2.4218' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 3.8445' b' [cx1.h : 607] Main loop done. Time elapsed: 51.7517' 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] 1623411 278587111 176175968 176108300 278746827 132760 99811 74404 146521' b' [cx1_seq2sdbg.cpp :1151] Total number of edges: 911695113' b' [cx1_seq2sdbg.cpp :1152] Total number of ONEs: 909618206' b' [cx1_seq2sdbg.cpp :1153] Total number of $v edges: 1623411' b' [cx1.h : 621] Postprocess done. Time elapsed: 0.0377' b' [utils.h : 126] Real: 58.8647\tuser: 1008.7793\tsys: 6.1605\tmaxrss: 1604040' --- [Fri Mar 29 01:21:31 2019] Assembling contigs from SdBG for k = 119 --- cmd: /gscratch/srlab/programs/megahit_v1.1.4_LINUX_CPUONLY_x86_64-bin/megahit_asm_core assemble -s ./megahit_out/tmp/k119/119 -o ./megahit_out/intermediate_contigs/k119 -t 28 --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_out/tmp/k119/119 Done. Time elapsed: 17.979685' b' [assembler.cpp : 152] Number of Edges: 911695113; K value: 119' b' [assembler.cpp : 162] Number of CPU threads: 28' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 2; Accumulated tips removed: 18234; time elapsed: 2.5037' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 4; Accumulated tips removed: 66698; time elapsed: 2.5761' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 8; Accumulated tips removed: 157600; time elapsed: 2.9659' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 16; Accumulated tips removed: 347678; time elapsed: 3.7892' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 32; Accumulated tips removed: 448346; time elapsed: 5.2884' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 64; Accumulated tips removed: 570712; time elapsed: 8.1857' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 128; Accumulated tips removed: 851762; time elapsed: 13.1041' b' [assembly_algorithms.cpp : 170] Removing tips with length less than 182; Accumulated tips removed: 930543; time elapsed: 15.8970' b' [assembler.cpp : 179] Tips removal done! Time elapsed(sec): 54.345465' b' [assembler.cpp : 188] unitig graph size: 774727, time for building: 45.746750' b' [assembler.cpp : 211] Number of bubbles removed: 42546, Time elapsed(sec): 1.684519' b' [assembler.cpp : 225] Number of complex bubbles removed: 9844, Time elapsed(sec): 0.996105' b' [assembler.cpp : 243] Number unitigs disconnected: 51439, time: 0.158446' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 17541, time: 0.170477' b' [assembler.cpp : 200] Tips removed: 620, time: 0.264168' b' [assembler.cpp : 211] Number of bubbles removed: 1929, Time elapsed(sec): 0.310500' b' [assembler.cpp : 225] Number of complex bubbles removed: 2819, Time elapsed(sec): 0.600870' b' [assembler.cpp : 243] Number unitigs disconnected: 2408, time: 0.117261' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 236, time: 0.097725' b' [assembler.cpp : 200] Tips removed: 984, time: 0.247295' b' [assembler.cpp : 211] Number of bubbles removed: 112, Time elapsed(sec): 0.115490' b' [assembler.cpp : 225] Number of complex bubbles removed: 275, Time elapsed(sec): 0.233213' b' [assembler.cpp : 243] Number unitigs disconnected: 57, time: 0.116550' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 18, time: 0.095225' b' [assembler.cpp : 200] Tips removed: 19, time: 0.241407' b' [assembler.cpp : 211] Number of bubbles removed: 0, Time elapsed(sec): 0.058238' b' [assembler.cpp : 225] Number of complex bubbles removed: 4, Time elapsed(sec): 0.183497' b' [assembler.cpp : 243] Number unitigs disconnected: 2, time: 0.119212' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 6, time: 0.095968' b' [assembler.cpp : 200] Tips removed: 2, time: 0.242500' b' [assembler.cpp : 211] Number of bubbles removed: 0, Time elapsed(sec): 0.058298' b' [assembler.cpp : 225] Number of complex bubbles removed: 0, Time elapsed(sec): 0.185430' b' [assembler.cpp : 243] Number unitigs disconnected: 0, time: 0.117807' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 0, time: 0.061859' b' [assembler.cpp : 132] Total length: 494117268, N50: 1096, Mean: 825, number of contigs: 598726' b' [assembler.cpp : 133] Maximum length: 571005' b' [assembler.cpp : 290] Time to output: 14.777106' b' [assembler.cpp : 317] Number of local low depth unitigs removed: 1122, complex bubbles removed: 125, time: 5.192462' b' [assembler.cpp : 132] Total length: 129875354, N50: 3576, Mean: 1115, number of contigs: 116469' b' [assembler.cpp : 133] Maximum length: 571005' b' [utils.h : 126] Real: 149.0867\tuser: 3390.7129\tsys: 7.9037\tmaxrss: 2170928' --- [Fri Mar 29 01:24:00 2019] Local assembling k = 119 --- cmd: /gscratch/srlab/programs/megahit_v1.1.4_LINUX_CPUONLY_x86_64-bin/megahit_asm_core local -c ./megahit_out/intermediate_contigs/k119.contigs.fa -l ./megahit_out/tmp/reads.lib -t 28 -o ./megahit_out/intermediate_contigs/k119.local.fa --kmax 141 b' [local_assembler.cpp : 89] Number of contigs: 565541, Mapper size: 58184194' b' [read_lib_functions-inl.h : 256] Before reading, sizeof seq_package: 5214492324' b' [read_lib_functions-inl.h : 260] After reading, sizeof seq_package: 5214492324' b' [local_assembler.cpp : 330] Lib 0, insert size: 275.77 sd: 108.99' b' [local_assembler.cpp : 462] Lib 0: total 143722488 reads, aligned 71928511, added 7769455 reads for local assembly' b' [utils.h : 126] Real: 319.4168\tuser: 8433.8222\tsys: 10.7434\tmaxrss: 7709440' --- [Fri Mar 29 01:29:20 2019] Extracting iterative edges from k = 119 to 141 --- cmd: /gscratch/srlab/programs/megahit_v1.1.4_LINUX_CPUONLY_x86_64-bin/megahit_asm_core iterate -c ./megahit_out/intermediate_contigs/k119.contigs.fa -b ./megahit_out/intermediate_contigs/k119.bubble_seq.fa -t 28 -k 119 -s 22 -o ./megahit_out/tmp/k141/141 -r ./megahit_out/tmp/reads.lib.bin -f binary b' [iterate_edges.cpp : 570] Number of crusial kmers: 89616' b' [iterate_edges.cpp : 570] Number of crusial kmers: 280028' b' [iterate_edges.cpp : 443] Processed: 67108864, aligned: 0. Iterative edges: 0' b' [iterate_edges.cpp : 443] Processed: 134217728, aligned: 0. Iterative edges: 0' b' [iterate_edges.cpp : 447] Total: 143722488, aligned: 0. Iterative edges: 0' b' [utils.h : 126] Real: 12.5634\tuser: 18.0415\tsys: 2.6068\tmaxrss: 434596' --- [Fri Mar 29 01:29:32 2019] Building graph for k = 141 --- /gscratch/srlab/programs/megahit_v1.1.4_LINUX_CPUONLY_x86_64-bin/megahit_sdbg_build seq2sdbg --host_mem 242783447040 --mem_flag 1 --gpu_mem 0 --output_prefix ./megahit_out/tmp/k141/141 --num_cpu_threads 28 -k 141 --kmer_from 119 --num_edge_files 1 --addi_contig ./megahit_out/intermediate_contigs/k119.addi.fa --local_contig ./megahit_out/intermediate_contigs/k119.local.fa --contig ./megahit_out/intermediate_contigs/k119.contigs.fa --bubble ./megahit_out/intermediate_contigs/k119.bubble_seq.fa b' [sdbg_builder.cpp : 339] Host memory to be used: 242783447040' b' [sdbg_builder.cpp : 340] Number CPU threads: 28' b' [cx1.h : 450] Preparing data...' b' [cx1_seq2sdbg.cpp : 434] Bases to reserve: 532619866, number contigs: 678515, number multiplicity: 678515' b' [cx1_seq2sdbg.cpp : 440] Before reading, sizeof seq_package: 138583096, multiplicity vector: 678515' b' [cx1_seq2sdbg.cpp : 529] After reading, sizeof seq_package: 277166192, multiplicity vector: 1357030' b' [cx1.h : 457] Preparing data... Done. Time elapsed: 2.7225' b' [cx1.h : 464] Preparing partitions and initialing global data...' b' [cx1_seq2sdbg.cpp : 740] Memory for sequence: 285234832' b' [cx1_seq2sdbg.cpp : 741] max # lv.1 items = 166535769' b' [cx1.h : 480] Preparing partitions and initialing global data... Done. Time elapsed: 0.5344' b' [cx1.h : 486] Start main loop...' b' [cx1.h : 515] Lv1 scanning from bucket 0 to 382' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 0.4011' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 1.5533' b' [cx1.h : 515] Lv1 scanning from bucket 382 to 2181' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 0.4444' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 2.6759' b' [cx1.h : 515] Lv1 scanning from bucket 2181 to 5644' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 0.4253' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 3.1562' b' [cx1.h : 515] Lv1 scanning from bucket 5644 to 10877' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 0.4655' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 3.6088' b' [cx1.h : 515] Lv1 scanning from bucket 10877 to 18242' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 0.4920' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 3.7232' b' [cx1.h : 515] Lv1 scanning from bucket 18242 to 28415' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 0.5245' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 3.9194' b' [cx1.h : 515] Lv1 scanning from bucket 28415 to 42914' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 0.5374' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 3.8514' b' [cx1.h : 515] Lv1 scanning from bucket 42914 to 65536' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 0.4801' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 3.8344' b' [cx1.h : 607] Main loop done. Time elapsed: 30.0939' 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] 1154513 262369411 166528301 166457438 262496118 59324 27929 28036 58601' b' [cx1_seq2sdbg.cpp :1151] Total number of edges: 859179671' b' [cx1_seq2sdbg.cpp :1152] Total number of ONEs: 857851268' b' [cx1_seq2sdbg.cpp :1153] Total number of $v edges: 1154513' b' [cx1.h : 621] Postprocess done. Time elapsed: 0.0347' b' [utils.h : 126] Real: 33.3872\tuser: 799.5179\tsys: 4.0845\tmaxrss: 1004636' --- [Fri Mar 29 01:30:06 2019] Assembling contigs from SdBG for k = 141 --- cmd: /gscratch/srlab/programs/megahit_v1.1.4_LINUX_CPUONLY_x86_64-bin/megahit_asm_core assemble -s ./megahit_out/tmp/k141/141 -o ./megahit_out/intermediate_contigs/k141 -t 28 --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_out/tmp/k141/141 Done. Time elapsed: 14.496849' b' [assembler.cpp : 152] Number of Edges: 859179671; K value: 141' b' [assembler.cpp : 162] Number of CPU threads: 28' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 2; Accumulated tips removed: 2358; time elapsed: 2.3555' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 4; Accumulated tips removed: 7846; time elapsed: 2.3736' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 8; Accumulated tips removed: 18104; time elapsed: 2.6908' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 16; Accumulated tips removed: 38152; time elapsed: 3.3993' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 32; Accumulated tips removed: 71862; time elapsed: 4.7798' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 64; Accumulated tips removed: 126244; time elapsed: 7.3925' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 128; Accumulated tips removed: 209609; time elapsed: 12.3447' b' [assembly_algorithms.cpp : 170] Removing tips with length less than 160; Accumulated tips removed: 230449; time elapsed: 14.4318' b' [assembler.cpp : 179] Tips removal done! Time elapsed(sec): 49.801374' b' [assembler.cpp : 188] unitig graph size: 653547, time for building: 44.556744' b' [assembler.cpp : 211] Number of bubbles removed: 24045, Time elapsed(sec): 0.148582' b' [assembler.cpp : 225] Number of complex bubbles removed: 3908, Time elapsed(sec): 0.240027' b' [assembler.cpp : 243] Number unitigs disconnected: 27527, time: 0.133145' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 7915, time: 0.121451' b' [assembler.cpp : 200] Tips removed: 389, time: 0.223482' b' [assembler.cpp : 211] Number of bubbles removed: 250, Time elapsed(sec): 0.054734' b' [assembler.cpp : 225] Number of complex bubbles removed: 937, Time elapsed(sec): 0.184037' b' [assembler.cpp : 243] Number unitigs disconnected: 1583, time: 0.108937' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 108, time: 0.086902' b' [assembler.cpp : 200] Tips removed: 353, time: 0.221995' b' [assembler.cpp : 211] Number of bubbles removed: 22, Time elapsed(sec): 0.052954' b' [assembler.cpp : 225] Number of complex bubbles removed: 86, Time elapsed(sec): 0.157421' b' [assembler.cpp : 243] Number unitigs disconnected: 30, time: 0.109145' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 3, time: 0.086691' b' [assembler.cpp : 200] Tips removed: 4, time: 0.219805' b' [assembler.cpp : 211] Number of bubbles removed: 0, Time elapsed(sec): 0.052548' b' [assembler.cpp : 225] Number of complex bubbles removed: 1, Time elapsed(sec): 0.146824' b' [assembler.cpp : 243] Number unitigs disconnected: 0, time: 0.108887' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 0, time: 0.054704' b' [assembler.cpp : 200] Tips removed: 0, time: 0.219789' b' [assembler.cpp : 211] Number of bubbles removed: 0, Time elapsed(sec): 0.053129' b' [assembler.cpp : 225] Number of complex bubbles removed: 0, Time elapsed(sec): 0.146384' b' [assembler.cpp : 243] Number unitigs disconnected: 0, time: 0.110154' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 0, time: 0.054782' b' [assembler.cpp : 317] Number of local low depth unitigs removed: 409, complex bubbles removed: 17, time: 3.897574' b' [assembler.cpp : 132] Total length: 497069312, N50: 1173, Mean: 879, number of contigs: 565145' b' [assembler.cpp : 133] Maximum length: 571027' b' [utils.h : 126] Real: 131.1652\tuser: 3013.2353\tsys: 6.8529\tmaxrss: 1968260' --- [Fri Mar 29 01:32:17 2019] Merging to output final contigs --- --- [STAT] 552969 contigs, total 494922369 bp, min 200 bp, max 571027 bp, avg 895 bp, N50 1183 bp --- [Fri Mar 29 01:32:19 2019] ALL DONE. Time elapsed: 9552.235692 seconds ---