MEGAHIT v1.1.3 --- [Thu Mar 28 11:36:58 2019] Start assembly. Number of CPU threads 28 --- --- [Thu Mar 28 11:36:58 2019] Available memory: 269759385600, used: 242783447040 --- [Thu Mar 28 11:36:58 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_2_S4_L002_R1_001_val_1_val_1_val_1.fq.gz,/gscratch/srlab/sam/data/metagenomics/P_generosa/Library_Geoduck_MG_2_S4_L002_R2_001_val_2_val_2_val_2.fq.gz): pe, 160288380 reads, 131 max length' b' [utils.h : 126] Real: 158.9316\tuser: 144.6860\tsys: 13.1894\tmaxrss: 154148' --- [Thu Mar 28 11:39:37 2019] k list: 21,29,39,59,79,99,119,141 --- --- [Thu Mar 28 11:39:37 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: 5784606792' b' [read_lib_functions-inl.h : 260] After reading, sizeof seq_package: 5784606792' b' [cx1_kmer_count.cpp : 136] 160288380 reads, 131 max read length' b' [cx1.h : 457] Preparing data... Done. Time elapsed: 22.4029' 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: 8260340184, 236463117696' b' [cx1_kmer_count.cpp : 356] 1952470110, 18769156 8260340184 236463117696' b' [cx1_kmer_count.cpp : 363] Memory for reads: 5925303688' b' [cx1_kmer_count.cpp : 364] max # lv.1 items = 1952470110' b' [cx1.h : 480] Preparing partitions and initialing global data... Done. Time elapsed: 8.3865' b' [cx1.h : 486] Start main loop...' b' [cx1.h : 515] Lv1 scanning from bucket 0 to 197' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 7.9799' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 10.6295' b' [cx1.h : 515] Lv1 scanning from bucket 197 to 1217' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 8.5723' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 24.5412' b' [cx1.h : 515] Lv1 scanning from bucket 1217 to 3385' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 8.8322' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 28.9411' b' [cx1.h : 515] Lv1 scanning from bucket 3385 to 6998' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 9.1909' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 29.7186' b' [cx1.h : 515] Lv1 scanning from bucket 6998 to 12474' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 9.4607' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 29.1943' b' [cx1.h : 515] Lv1 scanning from bucket 12474 to 20527' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 9.6885' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 28.6982' b' [cx1.h : 515] Lv1 scanning from bucket 20527 to 32647' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 10.0240' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 28.5929' b' [cx1.h : 515] Lv1 scanning from bucket 32647 to 55251' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 10.3590' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 29.2319' b' [cx1.h : 515] Lv1 scanning from bucket 55251 to 65536' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 7.8190' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 4.5454' b' [cx1.h : 607] Main loop done. Time elapsed: 296.0212' b' [cx1.h : 613] Postprocessing...' b' [cx1_kmer_count.cpp : 860] Total number of candidate reads: 6647761(22134431)' b' [cx1_kmer_count.cpp : 871] Total number of solid edges: 1419750820' b' [cx1.h : 621] Postprocess done. Time elapsed: 4.2417' b' [utils.h : 126] Real: 331.0703\tuser: 8377.5372\tsys: 30.0862\tmaxrss: 15183804' --- [Thu Mar 28 11:45:09 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: 1419750820' b' [cx1_seq2sdbg.cpp : 434] Bases to reserve: 39043147550, number contigs: 0, number multiplicity: 1774688525' b' [cx1_seq2sdbg.cpp : 440] Before reading, sizeof seq_package: 9760786896, multiplicity vector: 1774688525' b' [cx1_seq2sdbg.cpp : 455] Adding mercy edges...' b' [cx1_seq2sdbg.cpp : 373] Number of reads: 6647761, Number of mercy edges: 90920974' b' [cx1_seq2sdbg.cpp : 462] Done. Time elapsed: 89.1886' b' [cx1_seq2sdbg.cpp : 529] After reading, sizeof seq_package: 9760786896, multiplicity vector: 1774688525' b' [cx1.h : 457] Preparing data... Done. Time elapsed: 508.9200' b' [cx1.h : 464] Preparing partitions and initialing global data...' b' [cx1_seq2sdbg.cpp : 740] Memory for sequence: 13041777228' b' [cx1_seq2sdbg.cpp : 741] max # lv.1 items = 1208537435' b' [cx1.h : 480] Preparing partitions and initialing global data... Done. Time elapsed: 3.4958' b' [cx1.h : 486] Start main loop...' b' [cx1.h : 515] Lv1 scanning from bucket 0 to 1003' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 3.0864' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 10.6622' b' [cx1.h : 515] Lv1 scanning from bucket 1003 to 3819' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 3.1519' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 12.7792' b' [cx1.h : 515] Lv1 scanning from bucket 3819 to 8477' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 3.1984' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 13.2797' b' [cx1.h : 515] Lv1 scanning from bucket 8477 to 15121' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 3.2256' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 13.2409' b' [cx1.h : 515] Lv1 scanning from bucket 15121 to 24051' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 3.3137' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 13.7149' b' [cx1.h : 515] Lv1 scanning from bucket 24051 to 35708' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 3.4741' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 14.0193' b' [cx1.h : 515] Lv1 scanning from bucket 35708 to 51320' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 3.5889' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 14.3381' b' [cx1.h : 515] Lv1 scanning from bucket 51320 to 65536' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 3.0506' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 8.9679' b' [cx1.h : 607] Main loop done. Time elapsed: 127.0929' 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] 25584080 899152980 596318347 594571456 901517823 19783240 7819836 7652857 20100562' b' [cx1_seq2sdbg.cpp :1151] Total number of edges: 3072501181' b' [cx1_seq2sdbg.cpp :1152] Total number of ONEs: 2991560606' b' [cx1_seq2sdbg.cpp :1153] Total number of $v edges: 25584080' b' [cx1.h : 621] Postprocess done. Time elapsed: 0.0448' b' [utils.h : 126] Real: 639.5856\tuser: 5626.8688\tsys: 55.2482\tmaxrss: 16105540' --- [Thu Mar 28 11:55:49 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: 189.198944' b' [assembler.cpp : 152] Number of Edges: 3072501181; 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: 2089604; time elapsed: 9.8325' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 4; Accumulated tips removed: 6475543; time elapsed: 11.8131' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 8; Accumulated tips removed: 11220763; time elapsed: 16.6673' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 16; Accumulated tips removed: 17593786; time elapsed: 27.3798' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 32; Accumulated tips removed: 23776817; time elapsed: 41.4406' b' [assembly_algorithms.cpp : 170] Removing tips with length less than 42; Accumulated tips removed: 25858852; time elapsed: 43.9846' b' [assembler.cpp : 179] Tips removal done! Time elapsed(sec): 151.229600' b' [assembler.cpp : 188] unitig graph size: 63011656, time for building: 341.359963' b' [assembler.cpp : 211] Number of bubbles removed: 2570220, Time elapsed(sec): 23.261973' b' [assembler.cpp : 225] Number of complex bubbles removed: 318988, Time elapsed(sec): 16.992489' b' [assembler.cpp : 243] Number unitigs disconnected: 15177248, time: 26.219574' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 97417, time: 7.068179' b' [assembler.cpp : 200] Tips removed: 98471, time: 17.398027' b' [assembler.cpp : 211] Number of bubbles removed: 81951, Time elapsed(sec): 7.057938' b' [assembler.cpp : 225] Number of complex bubbles removed: 155757, Time elapsed(sec): 12.787751' b' [assembler.cpp : 243] Number unitigs disconnected: 1484293, time: 9.264543' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 89, time: 6.798696' b' [assembler.cpp : 200] Tips removed: 1255004, time: 17.544691' b' [assembler.cpp : 211] Number of bubbles removed: 76099, Time elapsed(sec): 6.874080' b' [assembler.cpp : 225] Number of complex bubbles removed: 11492, Time elapsed(sec): 12.383333' b' [assembler.cpp : 243] Number unitigs disconnected: 15417, time: 7.966921' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 5, time: 6.703315' b' [assembler.cpp : 200] Tips removed: 4540, time: 16.090542' b' [assembler.cpp : 211] Number of bubbles removed: 408, Time elapsed(sec): 6.292937' b' [assembler.cpp : 225] Number of complex bubbles removed: 269, Time elapsed(sec): 12.270664' b' [assembler.cpp : 243] Number unitigs disconnected: 409, time: 7.966004' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 1, time: 6.774104' b' [assembler.cpp : 200] Tips removed: 117, time: 16.033812' b' [assembler.cpp : 211] Number of bubbles removed: 6, Time elapsed(sec): 6.307931' b' [assembler.cpp : 225] Number of complex bubbles removed: 7, Time elapsed(sec): 12.440076' b' [assembler.cpp : 243] Number unitigs disconnected: 13, time: 8.002736' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 0, time: 4.329473' b' [assembler.cpp : 132] Total length: 2279385534, N50: 63, Mean: 47, number of contigs: 47767096' b' [assembler.cpp : 133] Maximum length: 12523' b' [assembler.cpp : 290] Time to output: 85.400277' b' [assembler.cpp : 317] Number of local low depth unitigs removed: 1678475, complex bubbles removed: 92861, time: 609.205370' b' [assembler.cpp : 132] Total length: 1715838091, N50: 46, Mean: 43, number of contigs: 39726684' b' [assembler.cpp : 133] Maximum length: 12523' b' [utils.h : 126] Real: 1695.1109\tuser: 39691.2815\tsys: 47.2677\tmaxrss: 10207636' --- [Thu Mar 28 12:24:05 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: 820447, Mapper size: 29292226' b' [read_lib_functions-inl.h : 256] Before reading, sizeof seq_package: 5784606792' b' [read_lib_functions-inl.h : 260] After reading, sizeof seq_package: 5784606792' b' [local_assembler.cpp : 330] Lib 0, insert size: 243.60 sd: 88.83' b' [local_assembler.cpp : 462] Lib 0: total 160288380 reads, aligned 35924293, added 18453815 reads for local assembly' b' [utils.h : 126] Real: 324.5682\tuser: 8262.0760\tsys: 15.3328\tmaxrss: 7769520' --- [Thu Mar 28 12:29:30 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: 8549558' b' [iterate_edges.cpp : 570] Number of crusial kmers: 86322709' b' [iterate_edges.cpp : 443] Processed: 67108864, aligned: 46159376. Iterative edges: 228568765' b' [iterate_edges.cpp : 443] Processed: 134217728, aligned: 92356659. Iterative edges: 300835994' b' [iterate_edges.cpp : 447] Total: 160288380, aligned: 110415051. Iterative edges: 318381107' b' [iterate_edges.cpp : 451] Writing iterative edges...' b' [utils.h : 126] Real: 326.1969\tuser: 7852.2864\tsys: 13.9625\tmaxrss: 11041228' --- [Thu Mar 28 12:34:56 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: 318381107' b' [cx1_seq2sdbg.cpp : 434] Bases to reserve: 13831500915, number contigs: 88348553, number multiplicity: 406729660' b' [cx1_seq2sdbg.cpp : 440] Before reading, sizeof seq_package: 4164663664, multiplicity vector: 406729660' b' [cx1_seq2sdbg.cpp : 529] After reading, sizeof seq_package: 4164663664, multiplicity vector: 406729660' b' [cx1.h : 457] Preparing data... Done. Time elapsed: 33.2299' b' [cx1.h : 464] Preparing partitions and initialing global data...' b' [cx1_seq2sdbg.cpp : 740] Memory for sequence: 4959281548' b' [cx1_seq2sdbg.cpp : 741] max # lv.1 items = 718679068' b' [cx1.h : 480] Preparing partitions and initialing global data... Done. Time elapsed: 9.0551' b' [cx1.h : 486] Start main loop...' b' [cx1.h : 515] Lv1 scanning from bucket 0 to 723' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 6.9556' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 8.7589' b' [cx1.h : 515] Lv1 scanning from bucket 723 to 3184' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 8.6779' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 11.5270' b' [cx1.h : 515] Lv1 scanning from bucket 3184 to 7476' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 9.2890' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 12.3208' b' [cx1.h : 515] Lv1 scanning from bucket 7476 to 13744' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 11.2161' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 12.7710' b' [cx1.h : 515] Lv1 scanning from bucket 13744 to 22304' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 10.7854' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 13.3109' b' [cx1.h : 515] Lv1 scanning from bucket 22304 to 33667' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 11.3923' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 13.8349' b' [cx1.h : 515] Lv1 scanning from bucket 33667 to 49054' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 13.0103' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 14.2193' b' [cx1.h : 515] Lv1 scanning from bucket 49054 to 65536' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 10.4091' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 10.2520' b' [cx1.h : 607] Main loop done. Time elapsed: 178.7318' 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] 23088820 792065519 525184951 524458924 793111214 4329146 3298100 2495368 4716189' b' [cx1_seq2sdbg.cpp :1151] Total number of edges: 2672748231' b' [cx1_seq2sdbg.cpp :1152] Total number of ONEs: 2634820608' b' [cx1_seq2sdbg.cpp :1153] Total number of $v edges: 23088820' b' [cx1.h : 621] Postprocess done. Time elapsed: 0.0425' b' [utils.h : 126] Real: 221.0707\tuser: 3042.0791\tsys: 22.9776\tmaxrss: 6933688' --- [Thu Mar 28 12:38:37 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: 158.326817' b' [assembler.cpp : 152] Number of Edges: 2672748231; 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: 785454; time elapsed: 8.8694' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 4; Accumulated tips removed: 2618883; time elapsed: 10.9814' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 8; Accumulated tips removed: 4534586; time elapsed: 15.9638' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 16; Accumulated tips removed: 7388510; time elapsed: 26.5657' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 32; Accumulated tips removed: 12453345; time elapsed: 46.0498' b' [assembly_algorithms.cpp : 170] Removing tips with length less than 58; Accumulated tips removed: 17203746; time elapsed: 63.5400' b' [assembler.cpp : 179] Tips removal done! Time elapsed(sec): 172.067490' b' [assembler.cpp : 188] unitig graph size: 20377980, time for building: 184.816518' b' [assembler.cpp : 211] Number of bubbles removed: 1904244, Time elapsed(sec): 20.723258' b' [assembler.cpp : 225] Number of complex bubbles removed: 329930, Time elapsed(sec): 8.306721' b' [assembler.cpp : 243] Number unitigs disconnected: 323145, time: 3.148403' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 20345, time: 2.502677' b' [assembler.cpp : 200] Tips removed: 27899, time: 5.170355' b' [assembler.cpp : 211] Number of bubbles removed: 23893, Time elapsed(sec): 2.531857' b' [assembler.cpp : 225] Number of complex bubbles removed: 11447, Time elapsed(sec): 3.757023' b' [assembler.cpp : 243] Number unitigs disconnected: 36025, time: 2.881709' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 131, time: 2.491893' b' [assembler.cpp : 200] Tips removed: 12313, time: 5.164248' b' [assembler.cpp : 211] Number of bubbles removed: 3091, Time elapsed(sec): 2.150216' b' [assembler.cpp : 225] Number of complex bubbles removed: 1270, Time elapsed(sec): 3.603634' b' [assembler.cpp : 243] Number unitigs disconnected: 3286, time: 2.814718' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 17, time: 2.468864' b' [assembler.cpp : 200] Tips removed: 291, time: 5.117419' b' [assembler.cpp : 211] Number of bubbles removed: 37, Time elapsed(sec): 1.986672' b' [assembler.cpp : 225] Number of complex bubbles removed: 54, Time elapsed(sec): 3.586021' b' [assembler.cpp : 243] Number unitigs disconnected: 420, time: 2.808265' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 1, time: 2.487564' b' [assembler.cpp : 200] Tips removed: 24, time: 5.198014' b' [assembler.cpp : 211] Number of bubbles removed: 2, Time elapsed(sec): 2.004599' b' [assembler.cpp : 225] Number of complex bubbles removed: 1, Time elapsed(sec): 3.586382' b' [assembler.cpp : 243] Number unitigs disconnected: 87, time: 2.821739' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 0, time: 1.599354' b' [assembler.cpp : 132] Total length: 1558257497, N50: 128, Mean: 96, number of contigs: 16187361' b' [assembler.cpp : 133] Maximum length: 48724' b' [assembler.cpp : 290] Time to output: 46.876987' b' [assembler.cpp : 317] Number of local low depth unitigs removed: 260816, complex bubbles removed: 28904, time: 186.900801' b' [assembler.cpp : 132] Total length: 738608720, N50: 80, Mean: 70, number of contigs: 10403380' b' [assembler.cpp : 133] Maximum length: 48724' b' [utils.h : 126] Real: 868.3511\tuser: 18693.1002\tsys: 32.0147\tmaxrss: 7467456' --- [Thu Mar 28 12:53:06 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: 1190670, Mapper size: 54082472' b' [read_lib_functions-inl.h : 256] Before reading, sizeof seq_package: 5784606792' b' [read_lib_functions-inl.h : 260] After reading, sizeof seq_package: 5784606792' b' [local_assembler.cpp : 330] Lib 0, insert size: 258.64 sd: 98.19' b' [local_assembler.cpp : 462] Lib 0: total 160288380 reads, aligned 61043586, added 21730890 reads for local assembly' b' [utils.h : 126] Real: 411.3659\tuser: 10776.7931\tsys: 16.8023\tmaxrss: 9055152' --- [Thu Mar 28 12:59:58 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: 6608489' b' [iterate_edges.cpp : 570] Number of crusial kmers: 27281800' b' [iterate_edges.cpp : 443] Processed: 67108864, aligned: 32163057. Iterative edges: 108799982' b' [iterate_edges.cpp : 443] Processed: 134217728, aligned: 64361031. Iterative edges: 138171066' b' [iterate_edges.cpp : 447] Total: 160288380, aligned: 77008465. Iterative edges: 145181996' b' [iterate_edges.cpp : 451] Writing iterative edges...' b' [utils.h : 126] Real: 298.3982\tuser: 7216.9340\tsys: 10.8093\tmaxrss: 5773032' --- [Thu Mar 28 13:04:56 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: 145181996' b' [cx1_seq2sdbg.cpp : 434] Bases to reserve: 8452082916, number contigs: 28353472, number multiplicity: 173535468' b' [cx1_seq2sdbg.cpp : 440] Before reading, sizeof seq_package: 2339848516, multiplicity vector: 173535468' b' [cx1_seq2sdbg.cpp : 529] After reading, sizeof seq_package: 2339848516, multiplicity vector: 173535468' b' [cx1.h : 457] Preparing data... Done. Time elapsed: 19.5544' b' [cx1.h : 464] Preparing partitions and initialing global data...' b' [cx1_seq2sdbg.cpp : 740] Memory for sequence: 2732363960' b' [cx1_seq2sdbg.cpp : 741] max # lv.1 items = 621782901' b' [cx1.h : 480] Preparing partitions and initialing global data... Done. Time elapsed: 9.0573' b' [cx1.h : 486] Start main loop...' b' [cx1.h : 515] Lv1 scanning from bucket 0 to 955' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 7.2586' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 8.5255' b' [cx1.h : 515] Lv1 scanning from bucket 955 to 3744' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 8.7809' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 10.5663' b' [cx1.h : 515] Lv1 scanning from bucket 3744 to 8303' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 10.3836' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 10.9492' b' [cx1.h : 515] Lv1 scanning from bucket 8303 to 14786' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 10.5250' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 11.5126' b' [cx1.h : 515] Lv1 scanning from bucket 14786 to 23510' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 11.1611' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 12.2094' b' [cx1.h : 515] Lv1 scanning from bucket 23510 to 35009' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 10.9064' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 12.7911' b' [cx1.h : 515] Lv1 scanning from bucket 35009 to 50638' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 11.0446' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 13.2118' b' [cx1.h : 515] Lv1 scanning from bucket 50638 to 65536' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 8.9492' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 8.1532' b' [cx1.h : 607] Main loop done. Time elapsed: 166.9297' 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] 14294593 678347598 455369320 454600414 679237154 2432561 1209759 1195966 2442056' b' [cx1_seq2sdbg.cpp :1151] Total number of edges: 2289129421' b' [cx1_seq2sdbg.cpp :1152] Total number of ONEs: 2267554486' b' [cx1_seq2sdbg.cpp :1153] Total number of $v edges: 14294593' b' [cx1.h : 621] Postprocess done. Time elapsed: 0.0393' b' [utils.h : 126] Real: 195.5886\tuser: 2710.9153\tsys: 17.1262\tmaxrss: 5172620' --- [Thu Mar 28 13:08:12 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: 140.285628' b' [assembler.cpp : 152] Number of Edges: 2289129421; 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: 137634; time elapsed: 6.8800' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 4; Accumulated tips removed: 649196; time elapsed: 8.2406' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 8; Accumulated tips removed: 1246049; time elapsed: 11.4668' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 16; Accumulated tips removed: 1974757; time elapsed: 19.5730' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 32; Accumulated tips removed: 3003678; time elapsed: 34.6415' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 64; Accumulated tips removed: 6778318; time elapsed: 58.5003' b' [assembly_algorithms.cpp : 170] Removing tips with length less than 78; Accumulated tips removed: 8813003; time elapsed: 56.0525' b' [assembler.cpp : 179] Tips removal done! Time elapsed(sec): 195.438336' b' [assembler.cpp : 188] unitig graph size: 11914169, time for building: 143.966312' b' [assembler.cpp : 211] Number of bubbles removed: 1325781, Time elapsed(sec): 20.133282' b' [assembler.cpp : 225] Number of complex bubbles removed: 223362, Time elapsed(sec): 6.837028' b' [assembler.cpp : 243] Number unitigs disconnected: 170002, time: 1.808995' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 46835, time: 1.636846' b' [assembler.cpp : 200] Tips removed: 24291, time: 3.600605' b' [assembler.cpp : 211] Number of bubbles removed: 26004, Time elapsed(sec): 1.868746' b' [assembler.cpp : 225] Number of complex bubbles removed: 12673, Time elapsed(sec): 2.163859' b' [assembler.cpp : 243] Number unitigs disconnected: 14069, time: 1.668586' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 212, time: 1.537706' b' [assembler.cpp : 200] Tips removed: 6661, time: 3.462679' b' [assembler.cpp : 211] Number of bubbles removed: 1811, Time elapsed(sec): 1.139383' b' [assembler.cpp : 225] Number of complex bubbles removed: 1218, Time elapsed(sec): 1.829202' b' [assembler.cpp : 243] Number unitigs disconnected: 1340, time: 1.651603' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 13, time: 1.532933' b' [assembler.cpp : 200] Tips removed: 159, time: 3.486890' b' [assembler.cpp : 211] Number of bubbles removed: 12, Time elapsed(sec): 1.073884' b' [assembler.cpp : 225] Number of complex bubbles removed: 32, Time elapsed(sec): 1.789054' b' [assembler.cpp : 243] Number unitigs disconnected: 349, time: 1.659789' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 1, time: 1.526012' b' [assembler.cpp : 200] Tips removed: 13, time: 3.417369' b' [assembler.cpp : 211] Number of bubbles removed: 0, Time elapsed(sec): 1.052626' b' [assembler.cpp : 225] Number of complex bubbles removed: 4, Time elapsed(sec): 1.769404' b' [assembler.cpp : 243] Number unitigs disconnected: 75, time: 1.645287' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 0, time: 1.035559' b' [assembler.cpp : 132] Total length: 1260311839, N50: 169, Mean: 140, number of contigs: 8945388' b' [assembler.cpp : 133] Maximum length: 91209' b' [assembler.cpp : 290] Time to output: 37.794960' b' [assembler.cpp : 317] Number of local low depth unitigs removed: 61640, complex bubbles removed: 8492, time: 127.879641' b' [assembler.cpp : 132] Total length: 540106054, N50: 123, Mean: 104, number of contigs: 5177699' b' [assembler.cpp : 133] Maximum length: 91209' b' [utils.h : 126] Real: 729.9105\tuser: 15402.7229\tsys: 27.0472\tmaxrss: 5791012' --- [Thu Mar 28 13:20:23 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: 1246124, Mapper size: 63492219' b' [read_lib_functions-inl.h : 256] Before reading, sizeof seq_package: 5784606792' b' [read_lib_functions-inl.h : 260] After reading, sizeof seq_package: 5784606792' b' [local_assembler.cpp : 330] Lib 0, insert size: 263.03 sd: 101.02' b' [local_assembler.cpp : 462] Lib 0: total 160288380 reads, aligned 74097143, added 24989909 reads for local assembly' b' [utils.h : 126] Real: 630.7040\tuser: 16907.1366\tsys: 16.7471\tmaxrss: 9440912' --- [Thu Mar 28 13:30:53 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: 4395499' b' [iterate_edges.cpp : 570] Number of crusial kmers: 14165786' b' [iterate_edges.cpp : 443] Processed: 67108864, aligned: 21878932. Iterative edges: 101683539' b' [iterate_edges.cpp : 443] Processed: 134217728, aligned: 43694963. Iterative edges: 134476451' b' [iterate_edges.cpp : 447] Total: 160288380, aligned: 52377989. Iterative edges: 142846496' b' [iterate_edges.cpp : 451] Writing iterative edges...' b' [utils.h : 126] Real: 268.6810\tuser: 6308.1698\tsys: 11.5052\tmaxrss: 5944356' --- [Thu Mar 28 13:35:22 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: 142846496' b' [cx1_seq2sdbg.cpp : 434] Bases to reserve: 10820250926, number contigs: 15768873, number multiplicity: 158615369' b' [cx1_seq2sdbg.cpp : 440] Before reading, sizeof seq_package: 2831213724, multiplicity vector: 158615369' b' [cx1_seq2sdbg.cpp : 529] After reading, sizeof seq_package: 5536276456, multiplicity vector: 158615369' b' [cx1.h : 457] Preparing data... Done. Time elapsed: 20.1033' b' [cx1.h : 464] Preparing partitions and initialing global data...' b' [cx1_seq2sdbg.cpp : 740] Memory for sequence: 5928862832' b' [cx1_seq2sdbg.cpp : 741] max # lv.1 items = 555791621' b' [cx1.h : 480] Preparing partitions and initialing global data... Done. Time elapsed: 9.1624' b' [cx1.h : 486] Start main loop...' b' [cx1.h : 515] Lv1 scanning from bucket 0 to 836' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 7.7405' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 7.1776' b' [cx1.h : 515] Lv1 scanning from bucket 836 to 3444' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 9.7671' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 9.1283' b' [cx1.h : 515] Lv1 scanning from bucket 3444 to 7788' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 10.5824' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 9.6997' b' [cx1.h : 515] Lv1 scanning from bucket 7788 to 14036' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 11.4031' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 9.9375' b' [cx1.h : 515] Lv1 scanning from bucket 14036 to 22542' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 12.1060' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 10.4292' b' [cx1.h : 515] Lv1 scanning from bucket 22542 to 33907' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 12.7256' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 11.2581' b' [cx1.h : 515] Lv1 scanning from bucket 33907 to 49542' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 12.1428' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 11.5182' b' [cx1.h : 515] Lv1 scanning from bucket 49542 to 65536' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 9.1706' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 7.6044' b' [cx1.h : 607] Main loop done. Time elapsed: 162.3922' 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] 10287152 564726194 376715034 376259480 565418184 1100291 861272 650097 1205869' b' [cx1_seq2sdbg.cpp :1151] Total number of edges: 1897223573' b' [cx1_seq2sdbg.cpp :1152] Total number of ONEs: 1883118892' b' [cx1_seq2sdbg.cpp :1153] Total number of $v edges: 10287152' b' [cx1.h : 621] Postprocess done. Time elapsed: 0.0379' b' [utils.h : 126] Real: 191.7051\tuser: 2353.4777\tsys: 20.6406\tmaxrss: 5674508' --- [Thu Mar 28 13:38:34 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: 117.461385' b' [assembler.cpp : 152] Number of Edges: 1897223573; 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: 71378; time elapsed: 5.5456' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 4; Accumulated tips removed: 283347; time elapsed: 6.5091' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 8; Accumulated tips removed: 619844; time elapsed: 8.8727' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 16; Accumulated tips removed: 1169504; time elapsed: 14.7685' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 32; Accumulated tips removed: 1802092; time elapsed: 25.5650' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 64; Accumulated tips removed: 4345398; time elapsed: 44.2659' b' [assembly_algorithms.cpp : 170] Removing tips with length less than 118; Accumulated tips removed: 9181636; time elapsed: 46.6511' b' [assembler.cpp : 179] Tips removal done! Time elapsed(sec): 152.246341' b' [assembler.cpp : 188] unitig graph size: 4902640, time for building: 106.255093' b' [assembler.cpp : 211] Number of bubbles removed: 589059, Time elapsed(sec): 13.805318' b' [assembler.cpp : 225] Number of complex bubbles removed: 124997, Time elapsed(sec): 5.364321' b' [assembler.cpp : 243] Number unitigs disconnected: 199508, time: 0.866141' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 75715, time: 0.839845' b' [assembler.cpp : 200] Tips removed: 4872, time: 1.349665' b' [assembler.cpp : 211] Number of bubbles removed: 25107, Time elapsed(sec): 1.517659' b' [assembler.cpp : 225] Number of complex bubbles removed: 15217, Time elapsed(sec): 1.496915' b' [assembler.cpp : 243] Number unitigs disconnected: 10586, time: 0.717911' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 546, time: 0.648180' b' [assembler.cpp : 200] Tips removed: 5437, time: 1.310241' b' [assembler.cpp : 211] Number of bubbles removed: 1039, Time elapsed(sec): 0.530631' b' [assembler.cpp : 225] Number of complex bubbles removed: 1140, Time elapsed(sec): 0.818192' b' [assembler.cpp : 243] Number unitigs disconnected: 406, time: 0.710909' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 27, time: 0.651870' b' [assembler.cpp : 200] Tips removed: 66, time: 1.294729' b' [assembler.cpp : 211] Number of bubbles removed: 8, Time elapsed(sec): 0.407066' b' [assembler.cpp : 225] Number of complex bubbles removed: 16, Time elapsed(sec): 0.756345' b' [assembler.cpp : 243] Number unitigs disconnected: 56, time: 0.703206' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 4, time: 0.642768' b' [assembler.cpp : 200] Tips removed: 2, time: 1.304136' b' [assembler.cpp : 211] Number of bubbles removed: 0, Time elapsed(sec): 0.401018' b' [assembler.cpp : 225] Number of complex bubbles removed: 1, Time elapsed(sec): 0.771535' b' [assembler.cpp : 243] Number unitigs disconnected: 10, time: 0.706509' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 0, time: 0.451122' b' [assembler.cpp : 132] Total length: 835397782, N50: 346, Mean: 254, number of contigs: 3282120' b' [assembler.cpp : 133] Maximum length: 159653' b' [assembler.cpp : 290] Time to output: 25.120567' b' [assembler.cpp : 317] Number of local low depth unitigs removed: 17231, complex bubbles removed: 2346, time: 55.966016' b' [assembler.cpp : 132] Total length: 363564810, N50: 291, Mean: 191, number of contigs: 1901692' b' [assembler.cpp : 133] Maximum length: 159653' b' [utils.h : 126] Real: 505.7782\tuser: 10068.2631\tsys: 19.6474\tmaxrss: 4664244' --- [Thu Mar 28 13:47:00 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: 1314829, Mapper size: 72232061' b' [read_lib_functions-inl.h : 256] Before reading, sizeof seq_package: 5784606792' b' [read_lib_functions-inl.h : 260] After reading, sizeof seq_package: 5784606792' b' [local_assembler.cpp : 330] Lib 0, insert size: 266.57 sd: 103.49' b' [local_assembler.cpp : 462] Lib 0: total 160288380 reads, aligned 85397400, added 26990072 reads for local assembly' b' [utils.h : 126] Real: 752.1353\tuser: 20411.3924\tsys: 17.2713\tmaxrss: 10018296' --- [Thu Mar 28 13:59:32 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: 1976446' b' [iterate_edges.cpp : 570] Number of crusial kmers: 5485701' b' [iterate_edges.cpp : 443] Processed: 67108864, aligned: 11306435. Iterative edges: 37528034' b' [iterate_edges.cpp : 443] Processed: 134217728, aligned: 22447423. Iterative edges: 48280399' b' [iterate_edges.cpp : 447] Total: 160288380, aligned: 26975646. Iterative edges: 51009610' b' [iterate_edges.cpp : 451] Writing iterative edges...' b' [utils.h : 126] Real: 167.2136\tuser: 4048.5033\tsys: 6.5595\tmaxrss: 2407024' --- [Thu Mar 28 14:02:20 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: 51009610' b' [cx1_seq2sdbg.cpp : 434] Bases to reserve: 5831563559, number contigs: 6744034, number multiplicity: 57753644' b' [cx1_seq2sdbg.cpp : 440] Before reading, sizeof seq_package: 1511843172, multiplicity vector: 57753644' b' [cx1_seq2sdbg.cpp : 529] After reading, sizeof seq_package: 2969734064, multiplicity vector: 57753644' b' [cx1.h : 457] Preparing data... Done. Time elapsed: 11.4886' b' [cx1.h : 464] Preparing partitions and initialing global data...' b' [cx1_seq2sdbg.cpp : 740] Memory for sequence: 3128603816' b' [cx1_seq2sdbg.cpp : 741] max # lv.1 items = 413041330' b' [cx1.h : 480] Preparing partitions and initialing global data... Done. Time elapsed: 6.5840' b' [cx1.h : 486] Start main loop...' b' [cx1.h : 515] Lv1 scanning from bucket 0 to 700' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 5.7507' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 4.6738' b' [cx1.h : 515] Lv1 scanning from bucket 700 to 3074' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 6.6174' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 6.4909' b' [cx1.h : 515] Lv1 scanning from bucket 3074 to 7135' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 7.4947' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 6.9212' b' [cx1.h : 515] Lv1 scanning from bucket 7135 to 13064' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 8.9785' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 7.1034' b' [cx1.h : 515] Lv1 scanning from bucket 13064 to 21250' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 7.7505' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 7.7875' b' [cx1.h : 515] Lv1 scanning from bucket 21250 to 32381' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 8.5456' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 8.0865' b' [cx1.h : 515] Lv1 scanning from bucket 32381 to 47931' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 8.5053' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 8.1743' b' [cx1.h : 515] Lv1 scanning from bucket 47931 to 65536' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 6.9723' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 6.1391' b' [cx1.h : 607] Main loop done. Time elapsed: 115.9928' 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] 4242863 425807413 278416781 278179635 426193349 658878 347199 462076 601666' b' [cx1_seq2sdbg.cpp :1151] Total number of edges: 1414909860' b' [cx1_seq2sdbg.cpp :1152] Total number of ONEs: 1408597178' b' [cx1_seq2sdbg.cpp :1153] Total number of $v edges: 4242863' b' [cx1.h : 621] Postprocess done. Time elapsed: 0.0373' b' [utils.h : 126] Real: 134.1078\tuser: 1698.0637\tsys: 12.2598\tmaxrss: 3421700' --- [Thu Mar 28 14:04:34 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: 68.844620' b' [assembler.cpp : 152] Number of Edges: 1414909860; 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: 34330; time elapsed: 3.9785' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 4; Accumulated tips removed: 131078; time elapsed: 4.2975' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 8; Accumulated tips removed: 286580; time elapsed: 5.3140' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 16; Accumulated tips removed: 559865; time elapsed: 7.7877' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 32; Accumulated tips removed: 871788; time elapsed: 12.1606' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 64; Accumulated tips removed: 1559573; time elapsed: 19.8725' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 128; Accumulated tips removed: 2924542; time elapsed: 29.6387' b' [assembly_algorithms.cpp : 170] Removing tips with length less than 158; Accumulated tips removed: 3472108; time elapsed: 27.5916' b' [assembler.cpp : 179] Tips removal done! Time elapsed(sec): 110.695047' b' [assembler.cpp : 188] unitig graph size: 2684607, time for building: 80.303322' b' [assembler.cpp : 211] Number of bubbles removed: 284287, Time elapsed(sec): 10.633769' b' [assembler.cpp : 225] Number of complex bubbles removed: 67088, Time elapsed(sec): 4.508619' b' [assembler.cpp : 243] Number unitigs disconnected: 220419, time: 0.512092' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 83859, time: 0.535871' b' [assembler.cpp : 200] Tips removed: 3111, time: 0.855593' b' [assembler.cpp : 211] Number of bubbles removed: 19414, Time elapsed(sec): 1.220217' b' [assembler.cpp : 225] Number of complex bubbles removed: 13515, Time elapsed(sec): 1.329565' b' [assembler.cpp : 243] Number unitigs disconnected: 10025, time: 0.303831' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 1261, time: 0.282560' b' [assembler.cpp : 200] Tips removed: 6269, time: 0.818464' b' [assembler.cpp : 211] Number of bubbles removed: 601, Time elapsed(sec): 0.240789' b' [assembler.cpp : 225] Number of complex bubbles removed: 867, Time elapsed(sec): 0.496547' b' [assembler.cpp : 243] Number unitigs disconnected: 391, time: 0.286505' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 148, time: 0.268741' b' [assembler.cpp : 200] Tips removed: 154, time: 0.831415' b' [assembler.cpp : 211] Number of bubbles removed: 6, Time elapsed(sec): 0.206533' b' [assembler.cpp : 225] Number of complex bubbles removed: 22, Time elapsed(sec): 0.417263' b' [assembler.cpp : 243] Number unitigs disconnected: 22, time: 0.286814' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 10, time: 0.268416' b' [assembler.cpp : 200] Tips removed: 8, time: 0.819365' b' [assembler.cpp : 211] Number of bubbles removed: 0, Time elapsed(sec): 0.199909' b' [assembler.cpp : 225] Number of complex bubbles removed: 0, Time elapsed(sec): 0.423061' b' [assembler.cpp : 243] Number unitigs disconnected: 3, time: 0.287347' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 0, time: 0.164508' b' [assembler.cpp : 132] Total length: 679663726, N50: 550, Mean: 407, number of contigs: 1666994' b' [assembler.cpp : 133] Maximum length: 281270' b' [assembler.cpp : 290] Time to output: 21.724651' b' [assembler.cpp : 317] Number of local low depth unitigs removed: 10404, complex bubbles removed: 1051, time: 19.410869' b' [assembler.cpp : 132] Total length: 272099095, N50: 659, Mean: 324, number of contigs: 838582' b' [assembler.cpp : 133] Maximum length: 281270' b' [utils.h : 126] Real: 335.4627\tuser: 6861.9748\tsys: 13.7544\tmaxrss: 3392128' --- [Thu Mar 28 14:10:10 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: 1059726, Mapper size: 71173021' b' [read_lib_functions-inl.h : 256] Before reading, sizeof seq_package: 5784606792' b' [read_lib_functions-inl.h : 260] After reading, sizeof seq_package: 5784606792' b' [local_assembler.cpp : 330] Lib 0, insert size: 272.20 sd: 106.13' b' [local_assembler.cpp : 462] Lib 0: total 160288380 reads, aligned 82556958, added 19645171 reads for local assembly' b' [utils.h : 126] Real: 581.4222\tuser: 15645.3692\tsys: 14.5895\tmaxrss: 9606288' --- [Thu Mar 28 14:19:51 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: 954908' b' [iterate_edges.cpp : 570] Number of crusial kmers: 2444920' b' [iterate_edges.cpp : 443] Processed: 67108864, aligned: 5008050. Iterative edges: 14950879' b' [iterate_edges.cpp : 443] Processed: 134217728, aligned: 9920552. Iterative edges: 19686528' b' [iterate_edges.cpp : 447] Total: 160288380, aligned: 11943498. Iterative edges: 20927572' b' [iterate_edges.cpp : 451] Writing iterative edges...' b' [utils.h : 126] Real: 100.9590\tuser: 2413.9118\tsys: 4.8089\tmaxrss: 1425952' --- [Thu Mar 28 14:21:32 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: 20927572' b' [cx1_seq2sdbg.cpp : 434] Bases to reserve: 3452845613, number contigs: 3358015, number multiplicity: 24285587' b' [cx1_seq2sdbg.cpp : 440] Before reading, sizeof seq_package: 890075532, multiplicity vector: 24285587' b' [cx1_seq2sdbg.cpp : 529] After reading, sizeof seq_package: 1753286936, multiplicity vector: 24285587' b' [cx1.h : 457] Preparing data... Done. Time elapsed: 7.6477' b' [cx1.h : 464] Preparing partitions and initialing global data...' b' [cx1_seq2sdbg.cpp : 740] Memory for sequence: 1829276638' b' [cx1_seq2sdbg.cpp : 741] max # lv.1 items = 331316402' b' [cx1.h : 480] Preparing partitions and initialing global data... Done. Time elapsed: 3.7240' b' [cx1.h : 486] Start main loop...' b' [cx1.h : 515] Lv1 scanning from bucket 0 to 597' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 3.0464' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 3.4188' b' [cx1.h : 515] Lv1 scanning from bucket 597 to 2788' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 3.7378' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 5.1457' b' [cx1.h : 515] Lv1 scanning from bucket 2788 to 6653' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 4.3360' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 5.4783' b' [cx1.h : 515] Lv1 scanning from bucket 6653 to 12363' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 4.4147' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 6.0081' b' [cx1.h : 515] Lv1 scanning from bucket 12363 to 20329' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 4.6758' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 6.3530' b' [cx1.h : 515] Lv1 scanning from bucket 20329 to 31266' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 4.5850' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 6.3997' b' [cx1.h : 515] Lv1 scanning from bucket 31266 to 46650' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 4.7286' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 6.7697' b' [cx1.h : 515] Lv1 scanning from bucket 46650 to 65536' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 3.9882' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 5.4355' b' [cx1.h : 607] Main loop done. Time elapsed: 78.5223' 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] 2581081 358062456 232393612 232250342 358342310 359115 172066 171839 359765' b' [cx1_seq2sdbg.cpp :1151] Total number of edges: 1184692586' b' [cx1_seq2sdbg.cpp :1152] Total number of ONEs: 1181048720' b' [cx1_seq2sdbg.cpp :1153] Total number of $v edges: 2581081' b' [cx1.h : 621] Postprocess done. Time elapsed: 0.0881' b' [utils.h : 126] Real: 89.9872\tuser: 1369.1796\tsys: 9.6022\tmaxrss: 2437568' --- [Thu Mar 28 14:23:02 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: 41.315989' b' [assembler.cpp : 152] Number of Edges: 1184692586; 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: 20592; time elapsed: 3.3543' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 4; Accumulated tips removed: 76549; time elapsed: 3.4408' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 8; Accumulated tips removed: 173457; time elapsed: 4.0776' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 16; Accumulated tips removed: 343252; time elapsed: 5.5312' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 32; Accumulated tips removed: 531002; time elapsed: 8.0878' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 64; Accumulated tips removed: 789318; time elapsed: 13.0641' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 128; Accumulated tips removed: 1276059; time elapsed: 21.5328' b' [assembly_algorithms.cpp : 170] Removing tips with length less than 198; Accumulated tips removed: 1870021; time elapsed: 26.1647' b' [assembler.cpp : 179] Tips removal done! Time elapsed(sec): 85.298301' b' [assembler.cpp : 188] unitig graph size: 1484646, time for building: 69.885174' b' [assembler.cpp : 211] Number of bubbles removed: 129203, Time elapsed(sec): 7.580332' b' [assembler.cpp : 225] Number of complex bubbles removed: 31825, Time elapsed(sec): 3.305945' b' [assembler.cpp : 243] Number unitigs disconnected: 127913, time: 0.288182' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 47659, time: 0.361235' b' [assembler.cpp : 200] Tips removed: 1667, time: 0.458796' b' [assembler.cpp : 211] Number of bubbles removed: 8491, Time elapsed(sec): 0.650840' b' [assembler.cpp : 225] Number of complex bubbles removed: 7951, Time elapsed(sec): 0.985679' b' [assembler.cpp : 243] Number unitigs disconnected: 5165, time: 0.169355' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 715, time: 0.179350' b' [assembler.cpp : 200] Tips removed: 3008, time: 0.470432' b' [assembler.cpp : 211] Number of bubbles removed: 242, Time elapsed(sec): 0.127275' b' [assembler.cpp : 225] Number of complex bubbles removed: 492, Time elapsed(sec): 0.371095' b' [assembler.cpp : 243] Number unitigs disconnected: 232, time: 0.168874' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 94, time: 0.175800' b' [assembler.cpp : 200] Tips removed: 97, time: 0.438064' b' [assembler.cpp : 211] Number of bubbles removed: 4, Time elapsed(sec): 0.140708' b' [assembler.cpp : 225] Number of complex bubbles removed: 17, Time elapsed(sec): 0.269575' b' [assembler.cpp : 243] Number unitigs disconnected: 19, time: 0.164069' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 15, time: 0.175941' b' [assembler.cpp : 200] Tips removed: 10, time: 0.436541' b' [assembler.cpp : 211] Number of bubbles removed: 0, Time elapsed(sec): 0.105689' b' [assembler.cpp : 225] Number of complex bubbles removed: 0, Time elapsed(sec): 0.264983' b' [assembler.cpp : 243] Number unitigs disconnected: 3, time: 0.164451' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 7, time: 0.176310' b' [assembler.cpp : 132] Total length: 590087503, N50: 767, Mean: 605, number of contigs: 974092' b' [assembler.cpp : 133] Maximum length: 281270' b' [assembler.cpp : 290] Time to output: 18.170623' b' [assembler.cpp : 317] Number of local low depth unitigs removed: 4613, complex bubbles removed: 494, time: 13.528731' b' [assembler.cpp : 132] Total length: 194820450, N50: 1515, Mean: 554, number of contigs: 351340' b' [assembler.cpp : 133] Maximum length: 281270' b' [utils.h : 126] Real: 251.8606\tuser: 5436.0392\tsys: 11.4059\tmaxrss: 2803760' --- [Thu Mar 28 14:27:15 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: 775915, Mapper size: 66631322' b' [read_lib_functions-inl.h : 256] Before reading, sizeof seq_package: 5784606792' b' [read_lib_functions-inl.h : 260] After reading, sizeof seq_package: 5784606792' b' [local_assembler.cpp : 330] Lib 0, insert size: 277.63 sd: 108.07' b' [local_assembler.cpp : 462] Lib 0: total 160288380 reads, aligned 77460610, added 11894602 reads for local assembly' b' [utils.h : 126] Real: 407.1754\tuser: 10816.0882\tsys: 12.7194\tmaxrss: 9079312' --- [Thu Mar 28 14:34:02 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: 410504' b' [iterate_edges.cpp : 570] Number of crusial kmers: 973031' b' [iterate_edges.cpp : 443] Processed: 67108864, aligned: 1458077. Iterative edges: 3566169' b' [iterate_edges.cpp : 443] Processed: 134217728, aligned: 2886386. Iterative edges: 5144971' b' [iterate_edges.cpp : 447] Total: 160288380, aligned: 3480434. Iterative edges: 5600246' b' [iterate_edges.cpp : 451] Writing iterative edges...' b' [utils.h : 126] Real: 55.4430\tuser: 1283.3780\tsys: 3.7152\tmaxrss: 732784' --- [Thu Mar 28 14:34:57 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: 5600246' b' [cx1_seq2sdbg.cpp : 434] Bases to reserve: 1647994896, number contigs: 1631123, number multiplicity: 7231369' b' [cx1_seq2sdbg.cpp : 440] Before reading, sizeof seq_package: 425047720, multiplicity vector: 7231369' b' [cx1_seq2sdbg.cpp : 529] After reading, sizeof seq_package: 850095440, multiplicity vector: 14462738' b' [cx1.h : 457] Preparing data... Done. Time elapsed: 5.3647' b' [cx1.h : 464] Preparing partitions and initialing global data...' b' [cx1_seq2sdbg.cpp : 740] Memory for sequence: 879410676' b' [cx1_seq2sdbg.cpp : 741] max # lv.1 items = 260359754' b' [cx1.h : 480] Preparing partitions and initialing global data... Done. Time elapsed: 2.1571' b' [cx1.h : 486] Start main loop...' b' [cx1.h : 515] Lv1 scanning from bucket 0 to 434' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 1.8693' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 2.5789' b' [cx1.h : 515] Lv1 scanning from bucket 434 to 2336' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 2.0436' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 4.3060' b' [cx1.h : 515] Lv1 scanning from bucket 2336 to 5925' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 2.3657' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 4.6214' b' [cx1.h : 515] Lv1 scanning from bucket 5925 to 11343' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 2.5140' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 4.9622' b' [cx1.h : 515] Lv1 scanning from bucket 11343 to 19018' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 2.6362' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 5.3180' b' [cx1.h : 515] Lv1 scanning from bucket 19018 to 29650' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 2.7550' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 5.5173' b' [cx1.h : 515] Lv1 scanning from bucket 29650 to 44629' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 2.6434' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 5.7573' b' [cx1.h : 515] Lv1 scanning from bucket 44629 to 65536' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 2.2720' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 5.3294' b' [cx1.h : 607] Main loop done. Time elapsed: 57.4906' 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] 1923246 311317887 202067109 201976314 311514760 123678 93183 70179 135363' b' [cx1_seq2sdbg.cpp :1151] Total number of edges: 1029221719' b' [cx1_seq2sdbg.cpp :1152] Total number of ONEs: 1026876070' b' [cx1_seq2sdbg.cpp :1153] Total number of $v edges: 1923246' b' [cx1.h : 621] Postprocess done. Time elapsed: 0.0322' b' [utils.h : 126] Real: 65.0469\tuser: 1169.4458\tsys: 7.7165\tmaxrss: 1693136' --- [Thu Mar 28 14:36:02 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: 20.717818' b' [assembler.cpp : 152] Number of Edges: 1029221719; 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: 17398; time elapsed: 2.9403' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 4; Accumulated tips removed: 63040; time elapsed: 2.9369' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 8; Accumulated tips removed: 148374; time elapsed: 3.4022' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 16; Accumulated tips removed: 324684; time elapsed: 4.3774' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 32; Accumulated tips removed: 420500; time elapsed: 6.2194' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 64; Accumulated tips removed: 540034; time elapsed: 9.7681' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 128; Accumulated tips removed: 807866; time elapsed: 15.8763' b' [assembly_algorithms.cpp : 170] Removing tips with length less than 182; Accumulated tips removed: 893621; time elapsed: 20.1141' b' [assembler.cpp : 179] Tips removal done! Time elapsed(sec): 65.675041' b' [assembler.cpp : 188] unitig graph size: 945456, time for building: 65.846176' b' [assembler.cpp : 211] Number of bubbles removed: 41578, Time elapsed(sec): 1.893685' b' [assembler.cpp : 225] Number of complex bubbles removed: 9150, Time elapsed(sec): 1.163641' b' [assembler.cpp : 243] Number unitigs disconnected: 43113, time: 0.183694' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 13999, time: 0.180365' b' [assembler.cpp : 200] Tips removed: 557, time: 0.324054' b' [assembler.cpp : 211] Number of bubbles removed: 1375, Time elapsed(sec): 0.272422' b' [assembler.cpp : 225] Number of complex bubbles removed: 2171, Time elapsed(sec): 0.593491' b' [assembler.cpp : 243] Number unitigs disconnected: 2143, time: 0.143582' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 153, time: 0.117114' b' [assembler.cpp : 200] Tips removed: 844, time: 0.320056' b' [assembler.cpp : 211] Number of bubbles removed: 86, Time elapsed(sec): 0.161914' b' [assembler.cpp : 225] Number of complex bubbles removed: 207, Time elapsed(sec): 0.257123' b' [assembler.cpp : 243] Number unitigs disconnected: 50, time: 0.142401' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 21, time: 0.117258' b' [assembler.cpp : 200] Tips removed: 10, time: 0.324900' b' [assembler.cpp : 211] Number of bubbles removed: 0, Time elapsed(sec): 0.080007' b' [assembler.cpp : 225] Number of complex bubbles removed: 6, Time elapsed(sec): 0.185456' b' [assembler.cpp : 243] Number unitigs disconnected: 0, time: 0.139980' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 1, time: 0.115041' b' [assembler.cpp : 200] Tips removed: 0, time: 0.316084' b' [assembler.cpp : 211] Number of bubbles removed: 0, Time elapsed(sec): 0.074520' b' [assembler.cpp : 225] Number of complex bubbles removed: 0, Time elapsed(sec): 0.183596' b' [assembler.cpp : 243] Number unitigs disconnected: 0, time: 0.139089' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 0, time: 0.071144' b' [assembler.cpp : 132] Total length: 576039517, N50: 881, Mean: 731, number of contigs: 787877' b' [assembler.cpp : 133] Maximum length: 282954' b' [assembler.cpp : 290] Time to output: 18.190308' b' [assembler.cpp : 317] Number of local low depth unitigs removed: 1169, complex bubbles removed: 120, time: 6.838039' b' [assembler.cpp : 132] Total length: 133370155, N50: 3294, Mean: 929, number of contigs: 143489' b' [assembler.cpp : 133] Maximum length: 282954' b' [utils.h : 126] Real: 189.3932\tuser: 4313.8927\tsys: 9.1549\tmaxrss: 2422944' --- [Thu Mar 28 14:39:12 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: 721595, Mapper size: 67179839' b' [read_lib_functions-inl.h : 256] Before reading, sizeof seq_package: 5784606792' b' [read_lib_functions-inl.h : 260] After reading, sizeof seq_package: 5784606792' b' [local_assembler.cpp : 330] Lib 0, insert size: 278.76 sd: 108.67' b' [local_assembler.cpp : 462] Lib 0: total 160288380 reads, aligned 74922184, added 8414778 reads for local assembly' b' [utils.h : 126] Real: 329.9759\tuser: 8621.5987\tsys: 11.0017\tmaxrss: 9012220' --- [Thu Mar 28 14:44:42 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: 80399' b' [iterate_edges.cpp : 570] Number of crusial kmers: 253830' 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: 160288380, aligned: 0. Iterative edges: 0' b' [utils.h : 126] Real: 14.8461\tuser: 21.3927\tsys: 2.8599\tmaxrss: 428448' --- [Thu Mar 28 14:44:57 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: 577471143, number contigs: 798822, number multiplicity: 798822' b' [cx1_seq2sdbg.cpp : 440] Before reading, sizeof seq_package: 150758372, multiplicity vector: 798822' b' [cx1_seq2sdbg.cpp : 529] After reading, sizeof seq_package: 301516744, multiplicity vector: 1597644' b' [cx1.h : 457] Preparing data... Done. Time elapsed: 3.1726' b' [cx1.h : 464] Preparing partitions and initialing global data...' b' [cx1_seq2sdbg.cpp : 740] Memory for sequence: 311031520' b' [cx1_seq2sdbg.cpp : 741] max # lv.1 items = 189134847' b' [cx1.h : 480] Preparing partitions and initialing global data... Done. Time elapsed: 0.6512' b' [cx1.h : 486] Start main loop...' b' [cx1.h : 515] Lv1 scanning from bucket 0 to 323' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 0.4752' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 1.6690' b' [cx1.h : 515] Lv1 scanning from bucket 323 to 1977' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 0.5050' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 3.0439' b' [cx1.h : 515] Lv1 scanning from bucket 1977 to 5354' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 0.5237' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 3.6046' b' [cx1.h : 515] Lv1 scanning from bucket 5354 to 10577' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 0.6006' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 3.8152' b' [cx1.h : 515] Lv1 scanning from bucket 10577 to 18062' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 0.6594' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 4.1859' b' [cx1.h : 515] Lv1 scanning from bucket 18062 to 28461' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 0.6553' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 4.1208' b' [cx1.h : 515] Lv1 scanning from bucket 28461 to 42981' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 0.6725' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 4.3620' b' [cx1.h : 515] Lv1 scanning from bucket 42981 to 65536' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 0.5969' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 4.3486' b' [cx1.h : 607] Main loop done. Time elapsed: 33.8396' 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] 1472033 293431938 190705713 190640451 293593148 54609 26990 26800 55187' b' [cx1_seq2sdbg.cpp :1151] Total number of edges: 970006869' b' [cx1_seq2sdbg.cpp :1152] Total number of ONEs: 968371250' b' [cx1_seq2sdbg.cpp :1153] Total number of $v edges: 1472033' b' [cx1.h : 621] Postprocess done. Time elapsed: 0.0388' b' [utils.h : 126] Real: 37.7040\tuser: 885.3246\tsys: 4.5554\tmaxrss: 1135368' --- [Thu Mar 28 14:45:35 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: 15.995216' b' [assembler.cpp : 152] Number of Edges: 970006869; 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: 2524; time elapsed: 2.6325' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 4; Accumulated tips removed: 8184; time elapsed: 2.7227' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 8; Accumulated tips removed: 18760; time elapsed: 3.0928' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 16; Accumulated tips removed: 38558; time elapsed: 3.9345' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 32; Accumulated tips removed: 73618; time elapsed: 5.6208' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 64; Accumulated tips removed: 128616; time elapsed: 8.9287' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 128; Accumulated tips removed: 206190; time elapsed: 14.9956' b' [assembly_algorithms.cpp : 170] Removing tips with length less than 160; Accumulated tips removed: 224471; time elapsed: 17.8712' b' [assembler.cpp : 179] Tips removal done! Time elapsed(sec): 59.836436' b' [assembler.cpp : 188] unitig graph size: 834893, time for building: 63.345992' b' [assembler.cpp : 211] Number of bubbles removed: 23327, Time elapsed(sec): 0.166354' b' [assembler.cpp : 225] Number of complex bubbles removed: 3726, Time elapsed(sec): 0.270064' b' [assembler.cpp : 243] Number unitigs disconnected: 22413, time: 0.173723' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 6043, time: 0.210510' b' [assembler.cpp : 200] Tips removed: 294, time: 0.285941' b' [assembler.cpp : 211] Number of bubbles removed: 174, Time elapsed(sec): 0.069715' b' [assembler.cpp : 225] Number of complex bubbles removed: 781, Time elapsed(sec): 0.180470' b' [assembler.cpp : 243] Number unitigs disconnected: 1291, time: 0.148037' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 82, time: 0.181586' b' [assembler.cpp : 200] Tips removed: 335, time: 0.284296' b' [assembler.cpp : 211] Number of bubbles removed: 22, Time elapsed(sec): 0.068649' b' [assembler.cpp : 225] Number of complex bubbles removed: 73, Time elapsed(sec): 0.151255' b' [assembler.cpp : 243] Number unitigs disconnected: 14, time: 0.155785' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 4, time: 0.181103' b' [assembler.cpp : 200] Tips removed: 2, time: 0.278116' b' [assembler.cpp : 211] Number of bubbles removed: 0, Time elapsed(sec): 0.068116' b' [assembler.cpp : 225] Number of complex bubbles removed: 1, Time elapsed(sec): 0.139897' b' [assembler.cpp : 243] Number unitigs disconnected: 0, time: 0.146352' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 2, time: 0.191271' b' [assembler.cpp : 200] Tips removed: 0, time: 0.277776' b' [assembler.cpp : 211] Number of bubbles removed: 0, Time elapsed(sec): 0.067540' b' [assembler.cpp : 225] Number of complex bubbles removed: 0, Time elapsed(sec): 0.143029' b' [assembler.cpp : 243] Number unitigs disconnected: 0, time: 0.146541' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 0, time: 0.140999' b' [assembler.cpp : 317] Number of local low depth unitigs removed: 398, complex bubbles removed: 18, time: 8.911331' b' [assembler.cpp : 132] Total length: 579884380, N50: 919, Mean: 767, number of contigs: 755929' b' [assembler.cpp : 133] Maximum length: 349741' b' [utils.h : 126] Real: 169.5346\tuser: 3972.7280\tsys: 7.5431\tmaxrss: 2208908' --- [Thu Mar 28 14:48:24 2019] Merging to output final contigs --- --- [STAT] 721044 contigs, total 573684951 bp, min 200 bp, max 349741 bp, avg 796 bp, N50 935 bp --- [Thu Mar 28 14:48:27 2019] ALL DONE. Time elapsed: 11488.527453 seconds ---