MEGAHIT v1.1.3 --- [Fri Mar 29 02:03:00 2019] Start assembly. Number of CPU threads 28 --- --- [Fri Mar 29 02:03:00 2019] Available memory: 269759385600, used: 242783447040 --- [Fri Mar 29 02:03:01 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_7_S2_L002_R1_001_val_1_val_1_val_1.fq.gz,/gscratch/srlab/sam/data/metagenomics/P_generosa/Library_Geoduck_MG_7_S2_L002_R2_001_val_2_val_2_val_2.fq.gz): pe, 172333246 reads, 131 max length' b' [utils.h : 126] Real: 171.4013\tuser: 155.6499\tsys: 14.4252\tmaxrss: 154116' --- [Fri Mar 29 02:05:52 2019] k list: 21,29,39,59,79,99,119,141 --- --- [Fri Mar 29 02:05:52 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: 6222949328' b' [read_lib_functions-inl.h : 260] After reading, sizeof seq_package: 6222949328' b' [cx1_kmer_count.cpp : 136] 172333246 reads, 131 max read length' b' [cx1.h : 457] Preparing data... Done. Time elapsed: 24.1795' 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: 8889300888, 235989998444' b' [cx1_kmer_count.cpp : 356] 2101135566, 20198276 8889300888 235989998444' b' [cx1_kmer_count.cpp : 363] Memory for reads: 6374333208' b' [cx1_kmer_count.cpp : 364] max # lv.1 items = 2101135566' b' [cx1.h : 480] Preparing partitions and initialing global data... Done. Time elapsed: 9.2482' b' [cx1.h : 486] Start main loop...' b' [cx1.h : 515] Lv1 scanning from bucket 0 to 193' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 8.6388' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 11.5796' b' [cx1.h : 515] Lv1 scanning from bucket 193 to 1141' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 9.2999' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 25.9131' b' [cx1.h : 515] Lv1 scanning from bucket 1141 to 3132' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 9.5830' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 30.2323' b' [cx1.h : 515] Lv1 scanning from bucket 3132 to 6445' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 10.0501' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 31.8931' b' [cx1.h : 515] Lv1 scanning from bucket 6445 to 11521' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 10.2226' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 31.5244' b' [cx1.h : 515] Lv1 scanning from bucket 11521 to 19127' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 10.5247' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 30.8843' b' [cx1.h : 515] Lv1 scanning from bucket 19127 to 30932' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 10.8653' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 30.5059' b' [cx1.h : 515] Lv1 scanning from bucket 30932 to 53660' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 11.2404' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 30.5393' b' [cx1.h : 515] Lv1 scanning from bucket 53660 to 65536' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 8.4869' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 5.6117' b' [cx1.h : 607] Main loop done. Time elapsed: 317.5968' b' [cx1.h : 613] Postprocessing...' b' [cx1_kmer_count.cpp : 860] Total number of candidate reads: 5138677(16956159)' b' [cx1_kmer_count.cpp : 871] Total number of solid edges: 1256659786' b' [cx1.h : 621] Postprocess done. Time elapsed: 3.4853' b' [utils.h : 126] Real: 354.5288\tuser: 8998.0359\tsys: 27.8049\tmaxrss: 16330760' --- [Fri Mar 29 02:11:47 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: 1256659786' b' [cx1_seq2sdbg.cpp : 434] Bases to reserve: 34558144104, number contigs: 0, number multiplicity: 1570824732' b' [cx1_seq2sdbg.cpp : 440] Before reading, sizeof seq_package: 8639536036, multiplicity vector: 1570824732' b' [cx1_seq2sdbg.cpp : 455] Adding mercy edges...' b' [cx1_seq2sdbg.cpp : 373] Number of reads: 5138677, Number of mercy edges: 67951939' b' [cx1_seq2sdbg.cpp : 462] Done. Time elapsed: 56.6684' b' [cx1_seq2sdbg.cpp : 529] After reading, sizeof seq_package: 8639536036, multiplicity vector: 1570824732' b' [cx1.h : 457] Preparing data... Done. Time elapsed: 220.4563' b' [cx1.h : 464] Preparing partitions and initialing global data...' b' [cx1_seq2sdbg.cpp : 740] Memory for sequence: 11516427158' b' [cx1_seq2sdbg.cpp : 741] max # lv.1 items = 1059689380' b' [cx1.h : 480] Preparing partitions and initialing global data... Done. Time elapsed: 2.8036' b' [cx1.h : 486] Start main loop...' b' [cx1.h : 515] Lv1 scanning from bucket 0 to 865' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 2.5297' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 8.9765' b' [cx1.h : 515] Lv1 scanning from bucket 865 to 3350' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 2.6097' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 11.0209' b' [cx1.h : 515] Lv1 scanning from bucket 3350 to 7497' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 2.6406' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 10.9835' b' [cx1.h : 515] Lv1 scanning from bucket 7497 to 13531' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 2.6933' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 10.9662' b' [cx1.h : 515] Lv1 scanning from bucket 13531 to 21868' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 2.7475' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 11.3347' b' [cx1.h : 515] Lv1 scanning from bucket 21868 to 33193' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 2.9242' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 11.6837' b' [cx1.h : 515] Lv1 scanning from bucket 33193 to 49077' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 2.9835' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 11.8635' b' [cx1.h : 515] Lv1 scanning from bucket 49077 to 65536' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 2.6605' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 7.8508' b' [cx1.h : 607] Main loop done. Time elapsed: 106.4699' 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] 20566361 805405434 503596996 501956956 807521088 19041833 6488749 6381042 19390689' b' [cx1_seq2sdbg.cpp :1151] Total number of edges: 2690349148' b' [cx1_seq2sdbg.cpp :1152] Total number of ONEs: 2618480474' b' [cx1_seq2sdbg.cpp :1153] Total number of $v edges: 20566361' b' [cx1.h : 621] Postprocess done. Time elapsed: 0.1647' b' [utils.h : 126] Real: 329.9325\tuser: 4261.4648\tsys: 39.1334\tmaxrss: 14137992' --- [Fri Mar 29 02:17:17 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: 146.093050' b' [assembler.cpp : 152] Number of Edges: 2690349148; 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: 1749804; time elapsed: 8.1379' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 4; Accumulated tips removed: 5618076; time elapsed: 9.8074' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 8; Accumulated tips removed: 9878970; time elapsed: 13.7699' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 16; Accumulated tips removed: 15587624; time elapsed: 22.0802' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 32; Accumulated tips removed: 20770709; time elapsed: 32.4088' b' [assembly_algorithms.cpp : 170] Removing tips with length less than 42; Accumulated tips removed: 22347821; time elapsed: 35.4781' b' [assembler.cpp : 179] Tips removal done! Time elapsed(sec): 121.780214' b' [assembler.cpp : 188] unitig graph size: 58794966, time for building: 304.296526' b' [assembler.cpp : 211] Number of bubbles removed: 2445068, Time elapsed(sec): 21.179903' b' [assembler.cpp : 225] Number of complex bubbles removed: 314186, Time elapsed(sec): 16.422878' b' [assembler.cpp : 243] Number unitigs disconnected: 13613319, time: 22.943247' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 112210, time: 6.330687' b' [assembler.cpp : 200] Tips removed: 76525, time: 15.976247' b' [assembler.cpp : 211] Number of bubbles removed: 93413, Time elapsed(sec): 6.570725' b' [assembler.cpp : 225] Number of complex bubbles removed: 112425, Time elapsed(sec): 11.639739' b' [assembler.cpp : 243] Number unitigs disconnected: 1704091, time: 8.313666' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 89, time: 6.023870' b' [assembler.cpp : 200] Tips removed: 1475924, time: 16.282898' b' [assembler.cpp : 211] Number of bubbles removed: 97334, Time elapsed(sec): 6.287085' b' [assembler.cpp : 225] Number of complex bubbles removed: 11903, Time elapsed(sec): 11.169895' b' [assembler.cpp : 243] Number unitigs disconnected: 16537, time: 7.025091' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 6, time: 5.931226' b' [assembler.cpp : 200] Tips removed: 4791, time: 14.638029' b' [assembler.cpp : 211] Number of bubbles removed: 462, Time elapsed(sec): 5.801966' b' [assembler.cpp : 225] Number of complex bubbles removed: 288, Time elapsed(sec): 10.942873' b' [assembler.cpp : 243] Number unitigs disconnected: 368, time: 7.034025' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 0, time: 3.723200' b' [assembler.cpp : 200] Tips removed: 119, time: 14.738714' b' [assembler.cpp : 211] Number of bubbles removed: 0, Time elapsed(sec): 5.836818' b' [assembler.cpp : 225] Number of complex bubbles removed: 12, Time elapsed(sec): 10.192463' b' [assembler.cpp : 243] Number unitigs disconnected: 13, time: 7.023264' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 0, time: 3.734114' b' [assembler.cpp : 132] Total length: 2020840436, N50: 55, Mean: 46, number of contigs: 43231130' b' [assembler.cpp : 133] Maximum length: 12532' b' [assembler.cpp : 290] Time to output: 76.136527' b' [assembler.cpp : 317] Number of local low depth unitigs removed: 1741102, complex bubbles removed: 102561, time: 476.292864' b' [assembler.cpp : 132] Total length: 1567695901, N50: 45, Mean: 43, number of contigs: 35964327' b' [assembler.cpp : 133] Maximum length: 12532' b' [utils.h : 126] Real: 1410.7563\tuser: 33185.9058\tsys: 40.6008\tmaxrss: 9337084' --- [Fri Mar 29 02:40:49 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: 757370, Mapper size: 28435489' b' [read_lib_functions-inl.h : 256] Before reading, sizeof seq_package: 6222949328' b' [read_lib_functions-inl.h : 260] After reading, sizeof seq_package: 6222949328' b' [local_assembler.cpp : 330] Lib 0, insert size: 235.14 sd: 86.00' b' [local_assembler.cpp : 462] Lib 0: total 172333246 reads, aligned 40558811, added 19953201 reads for local assembly' b' [utils.h : 126] Real: 352.0395\tuser: 8999.3825\tsys: 14.9674\tmaxrss: 8095636' --- [Fri Mar 29 02:46:41 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: 7845016' b' [iterate_edges.cpp : 570] Number of crusial kmers: 79955774' b' [iterate_edges.cpp : 443] Processed: 67108864, aligned: 48249750. Iterative edges: 219779050' b' [iterate_edges.cpp : 443] Processed: 134217728, aligned: 96515525. Iterative edges: 285002150' b' [iterate_edges.cpp : 447] Total: 172333246, aligned: 124056714. Iterative edges: 306195357' b' [iterate_edges.cpp : 451] Writing iterative edges...' b' [utils.h : 126] Real: 352.1723\tuser: 8687.5857\tsys: 13.7283\tmaxrss: 10655960' --- [Fri Mar 29 02:52:33 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: 306195357' b' [cx1_seq2sdbg.cpp : 434] Bases to reserve: 13152861562, number contigs: 80201377, number multiplicity: 386396734' b' [cx1_seq2sdbg.cpp : 440] Before reading, sizeof seq_package: 3929826416, multiplicity vector: 386396734' b' [cx1_seq2sdbg.cpp : 529] After reading, sizeof seq_package: 3929826416, multiplicity vector: 386396734' b' [cx1.h : 457] Preparing data... Done. Time elapsed: 30.1511' b' [cx1.h : 464] Preparing partitions and initialing global data...' b' [cx1_seq2sdbg.cpp : 740] Memory for sequence: 4690538852' b' [cx1_seq2sdbg.cpp : 741] max # lv.1 items = 671882468' b' [cx1.h : 480] Preparing partitions and initialing global data... Done. Time elapsed: 9.0458' b' [cx1.h : 486] Start main loop...' b' [cx1.h : 515] Lv1 scanning from bucket 0 to 646' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 7.1199' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 8.1189' b' [cx1.h : 515] Lv1 scanning from bucket 646 to 2869' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 8.1688' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 10.6535' b' [cx1.h : 515] Lv1 scanning from bucket 2869 to 6768' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 9.4283' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 11.1661' b' [cx1.h : 515] Lv1 scanning from bucket 6768 to 12537' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 10.1964' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 12.1598' b' [cx1.h : 515] Lv1 scanning from bucket 12537 to 20572' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 10.4513' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 11.9421' b' [cx1.h : 515] Lv1 scanning from bucket 20572 to 31546' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 11.2342' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 12.4793' b' [cx1.h : 515] Lv1 scanning from bucket 31546 to 46950' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 11.8588' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 12.5809' b' [cx1.h : 515] Lv1 scanning from bucket 46950 to 65536' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 9.4710' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 9.7141' b' [cx1.h : 607] Main loop done. Time elapsed: 166.7447' 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] 18365463 715856014 446519671 446167400 716540813 4286397 3177204 2284923 4731935' b' [cx1_seq2sdbg.cpp :1151] Total number of edges: 2357929820' b' [cx1_seq2sdbg.cpp :1152] Total number of ONEs: 2325083898' b' [cx1_seq2sdbg.cpp :1153] Total number of $v edges: 18365463' b' [cx1.h : 621] Postprocess done. Time elapsed: 0.0388' b' [utils.h : 126] Real: 205.9912\tuser: 2791.9303\tsys: 21.7951\tmaxrss: 6552168' --- [Fri Mar 29 02:55:59 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: 138.026764' b' [assembler.cpp : 152] Number of Edges: 2357929820; 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: 604642; time elapsed: 7.3871' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 4; Accumulated tips removed: 2101892; time elapsed: 9.0996' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 8; Accumulated tips removed: 3667165; time elapsed: 13.1808' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 16; Accumulated tips removed: 6224568; time elapsed: 22.5343' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 32; Accumulated tips removed: 10777698; time elapsed: 38.2071' b' [assembly_algorithms.cpp : 170] Removing tips with length less than 58; Accumulated tips removed: 14556270; time elapsed: 50.8029' b' [assembler.cpp : 179] Tips removal done! Time elapsed(sec): 141.298735' b' [assembler.cpp : 188] unitig graph size: 19082287, time for building: 148.821713' b' [assembler.cpp : 211] Number of bubbles removed: 1860135, Time elapsed(sec): 21.433449' b' [assembler.cpp : 225] Number of complex bubbles removed: 332676, Time elapsed(sec): 8.618668' b' [assembler.cpp : 243] Number unitigs disconnected: 335290, time: 3.291291' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 22214, time: 2.643895' b' [assembler.cpp : 200] Tips removed: 19149, time: 4.922952' b' [assembler.cpp : 211] Number of bubbles removed: 27691, Time elapsed(sec): 2.783287' b' [assembler.cpp : 225] Number of complex bubbles removed: 12341, Time elapsed(sec): 3.746693' b' [assembler.cpp : 243] Number unitigs disconnected: 36656, time: 3.002724' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 127, time: 2.614132' b' [assembler.cpp : 200] Tips removed: 13819, time: 4.914916' b' [assembler.cpp : 211] Number of bubbles removed: 3696, Time elapsed(sec): 1.963342' b' [assembler.cpp : 225] Number of complex bubbles removed: 1334, Time elapsed(sec): 3.679144' b' [assembler.cpp : 243] Number unitigs disconnected: 2856, time: 2.942092' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 11, time: 2.574971' b' [assembler.cpp : 200] Tips removed: 270, time: 4.814671' b' [assembler.cpp : 211] Number of bubbles removed: 54, Time elapsed(sec): 1.856869' b' [assembler.cpp : 225] Number of complex bubbles removed: 48, Time elapsed(sec): 3.624775' b' [assembler.cpp : 243] Number unitigs disconnected: 333, time: 2.951067' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 0, time: 1.782608' b' [assembler.cpp : 200] Tips removed: 27, time: 4.841053' b' [assembler.cpp : 211] Number of bubbles removed: 6, Time elapsed(sec): 1.848466' b' [assembler.cpp : 225] Number of complex bubbles removed: 3, Time elapsed(sec): 3.625864' b' [assembler.cpp : 243] Number unitigs disconnected: 44, time: 2.953684' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 0, time: 1.794946' b' [assembler.cpp : 132] Total length: 1398196390, N50: 128, Mean: 93, number of contigs: 14927038' b' [assembler.cpp : 133] Maximum length: 117934' b' [assembler.cpp : 290] Time to output: 44.610883' b' [assembler.cpp : 317] Number of local low depth unitigs removed: 261586, complex bubbles removed: 31130, time: 162.134600' b' [assembler.cpp : 132] Total length: 759425717, N50: 83, Mean: 72, number of contigs: 10435796' b' [assembler.cpp : 133] Maximum length: 124635' b' [utils.h : 126] Real: 755.4839\tuser: 16097.4782\tsys: 29.0400\tmaxrss: 6779412' --- [Fri Mar 29 03:08:36 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: 1070286, Mapper size: 51947403' b' [read_lib_functions-inl.h : 256] Before reading, sizeof seq_package: 6222949328' b' [read_lib_functions-inl.h : 260] After reading, sizeof seq_package: 6222949328' b' [local_assembler.cpp : 330] Lib 0, insert size: 249.68 sd: 95.31' b' [local_assembler.cpp : 462] Lib 0: total 172333246 reads, aligned 69534442, added 23853398 reads for local assembly' b' [utils.h : 126] Real: 416.7281\tuser: 10955.0221\tsys: 17.1255\tmaxrss: 9272400' --- [Fri Mar 29 03:15:32 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: 6396620' b' [iterate_edges.cpp : 570] Number of crusial kmers: 27278073' b' [iterate_edges.cpp : 443] Processed: 67108864, aligned: 35491859. Iterative edges: 110636513' b' [iterate_edges.cpp : 443] Processed: 134217728, aligned: 70964947. Iterative edges: 139430696' b' [iterate_edges.cpp : 447] Total: 172333246, aligned: 91284486. Iterative edges: 148799989' b' [iterate_edges.cpp : 451] Writing iterative edges...' b' [utils.h : 126] Real: 311.0594\tuser: 7535.5813\tsys: 10.6447\tmaxrss: 5769536' --- [Fri Mar 29 03:20:43 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: 148799989' b' [cx1_seq2sdbg.cpp : 434] Bases to reserve: 8646135879, number contigs: 28239976, number multiplicity: 177039965' b' [cx1_seq2sdbg.cpp : 440] Before reading, sizeof seq_package: 2387453788, multiplicity vector: 177039965' b' [cx1_seq2sdbg.cpp : 529] After reading, sizeof seq_package: 2387453788, multiplicity vector: 177039965' b' [cx1.h : 457] Preparing data... Done. Time elapsed: 18.9081' b' [cx1.h : 464] Preparing partitions and initialing global data...' b' [cx1_seq2sdbg.cpp : 740] Memory for sequence: 2784598366' b' [cx1_seq2sdbg.cpp : 741] max # lv.1 items = 598241895' b' [cx1.h : 480] Preparing partitions and initialing global data... Done. Time elapsed: 8.4683' b' [cx1.h : 486] Start main loop...' b' [cx1.h : 515] Lv1 scanning from bucket 0 to 865' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 8.2021' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 7.8498' b' [cx1.h : 515] Lv1 scanning from bucket 865 to 3439' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 9.3056' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 9.7905' b' [cx1.h : 515] Lv1 scanning from bucket 3439 to 7675' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 9.6774' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 10.0829' b' [cx1.h : 515] Lv1 scanning from bucket 7675 to 13758' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 10.8139' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 10.5929' b' [cx1.h : 515] Lv1 scanning from bucket 13758 to 22060' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 11.8265' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 11.2218' b' [cx1.h : 515] Lv1 scanning from bucket 22060 to 33244' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 11.7072' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 11.4243' b' [cx1.h : 515] Lv1 scanning from bucket 33244 to 48908' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 11.7643' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 12.0517' b' [cx1.h : 515] Lv1 scanning from bucket 48908 to 65536' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 8.5442' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 8.1769' b' [cx1.h : 607] Main loop done. Time elapsed: 163.0332' 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] 11405784 624825319 397098685 396525622 625452002 2530400 1172599 1164673 2537184' b' [cx1_seq2sdbg.cpp :1151] Total number of edges: 2062712268' b' [cx1_seq2sdbg.cpp :1152] Total number of ONEs: 2043901628' b' [cx1_seq2sdbg.cpp :1153] Total number of $v edges: 11405784' b' [cx1.h : 621] Postprocess done. Time elapsed: 0.0405' b' [utils.h : 126] Real: 190.4575\tuser: 2521.4181\tsys: 17.7323\tmaxrss: 5069932' --- [Fri Mar 29 03:23:54 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: 119.544846' b' [assembler.cpp : 152] Number of Edges: 2062712268; 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: 110924; time elapsed: 5.9791' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 4; Accumulated tips removed: 569281; time elapsed: 6.9800' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 8; Accumulated tips removed: 1118931; time elapsed: 9.7384' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 16; Accumulated tips removed: 1817171; time elapsed: 16.3321' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 32; Accumulated tips removed: 2782981; time elapsed: 27.9648' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 64; Accumulated tips removed: 5913039; time elapsed: 46.6185' b' [assembly_algorithms.cpp : 170] Removing tips with length less than 78; Accumulated tips removed: 7466118; time elapsed: 44.5584' b' [assembler.cpp : 179] Tips removal done! Time elapsed(sec): 158.247557' b' [assembler.cpp : 188] unitig graph size: 11318231, time for building: 117.752147' b' [assembler.cpp : 211] Number of bubbles removed: 1341863, Time elapsed(sec): 20.152742' b' [assembler.cpp : 225] Number of complex bubbles removed: 234785, Time elapsed(sec): 7.302911' b' [assembler.cpp : 243] Number unitigs disconnected: 167836, time: 1.840212' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 49742, time: 1.631649' b' [assembler.cpp : 200] Tips removed: 17421, time: 3.434051' b' [assembler.cpp : 211] Number of bubbles removed: 27984, Time elapsed(sec): 1.966809' b' [assembler.cpp : 225] Number of complex bubbles removed: 13735, Time elapsed(sec): 2.170229' b' [assembler.cpp : 243] Number unitigs disconnected: 11167, time: 1.721509' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 170, time: 1.540980' b' [assembler.cpp : 200] Tips removed: 6359, time: 3.324311' b' [assembler.cpp : 211] Number of bubbles removed: 1901, Time elapsed(sec): 1.104194' b' [assembler.cpp : 225] Number of complex bubbles removed: 1287, Time elapsed(sec): 1.799343' b' [assembler.cpp : 243] Number unitigs disconnected: 285, time: 1.711091' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 12, time: 1.538498' b' [assembler.cpp : 200] Tips removed: 67, time: 3.315915' b' [assembler.cpp : 211] Number of bubbles removed: 20, Time elapsed(sec): 1.028984' b' [assembler.cpp : 225] Number of complex bubbles removed: 23, Time elapsed(sec): 1.734087' b' [assembler.cpp : 243] Number unitigs disconnected: 20, time: 1.700586' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 1, time: 1.531147' b' [assembler.cpp : 200] Tips removed: 2, time: 3.300801' b' [assembler.cpp : 211] Number of bubbles removed: 0, Time elapsed(sec): 1.028621' b' [assembler.cpp : 225] Number of complex bubbles removed: 0, Time elapsed(sec): 1.724660' b' [assembler.cpp : 243] Number unitigs disconnected: 0, time: 1.693741' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 0, time: 1.050174' b' [assembler.cpp : 132] Total length: 1156374071, N50: 176, Mean: 139, number of contigs: 8290386' b' [assembler.cpp : 133] Maximum length: 281297' b' [assembler.cpp : 290] Time to output: 34.247931' b' [assembler.cpp : 317] Number of local low depth unitigs removed: 52263, complex bubbles removed: 8452, time: 105.288431' b' [assembler.cpp : 132] Total length: 573703468, N50: 127, Mean: 106, number of contigs: 5392334' b' [assembler.cpp : 133] Maximum length: 281297' b' [utils.h : 126] Real: 620.0145\tuser: 13168.8983\tsys: 22.1255\tmaxrss: 5372776' --- [Fri Mar 29 03:34:15 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: 1120793, Mapper size: 61589758' b' [read_lib_functions-inl.h : 256] Before reading, sizeof seq_package: 6222949328' b' [read_lib_functions-inl.h : 260] After reading, sizeof seq_package: 6222949328' b' [local_assembler.cpp : 330] Lib 0, insert size: 253.67 sd: 98.08' b' [local_assembler.cpp : 462] Lib 0: total 172333246 reads, aligned 85657331, added 27599795 reads for local assembly' b' [utils.h : 126] Real: 659.9369\tuser: 17686.4847\tsys: 18.5597\tmaxrss: 9620856' --- [Fri Mar 29 03:45:15 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: 4415368' b' [iterate_edges.cpp : 570] Number of crusial kmers: 14634931' b' [iterate_edges.cpp : 443] Processed: 67108864, aligned: 24714310. Iterative edges: 105769561' b' [iterate_edges.cpp : 443] Processed: 134217728, aligned: 49280278. Iterative edges: 138577276' b' [iterate_edges.cpp : 447] Total: 172333246, aligned: 63515518. Iterative edges: 150202315' b' [iterate_edges.cpp : 451] Writing iterative edges...' b' [utils.h : 126] Real: 277.4190\tuser: 6548.5721\tsys: 11.4057\tmaxrss: 5950156' --- [Fri Mar 29 03:49:52 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: 150202315' b' [cx1_seq2sdbg.cpp : 434] Bases to reserve: 11428410671, number contigs: 16397503, number multiplicity: 166599818' b' [cx1_seq2sdbg.cpp : 440] Before reading, sizeof seq_package: 2988282700, multiplicity vector: 166599818' b' [cx1_seq2sdbg.cpp : 529] After reading, sizeof seq_package: 2988282700, multiplicity vector: 166599818' b' [cx1.h : 457] Preparing data... Done. Time elapsed: 18.6207' b' [cx1.h : 464] Preparing partitions and initialing global data...' b' [cx1_seq2sdbg.cpp : 740] Memory for sequence: 3397924530' b' [cx1_seq2sdbg.cpp : 741] max # lv.1 items = 567054885' b' [cx1.h : 480] Preparing partitions and initialing global data... Done. Time elapsed: 9.6101' b' [cx1.h : 486] Start main loop...' b' [cx1.h : 515] Lv1 scanning from bucket 0 to 766' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 8.4759' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 7.2364' b' [cx1.h : 515] Lv1 scanning from bucket 766 to 3198' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 11.5509' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 9.1491' b' [cx1.h : 515] Lv1 scanning from bucket 3198 to 7283' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 11.0838' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 9.3925' b' [cx1.h : 515] Lv1 scanning from bucket 7283 to 13202' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 12.3249' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 10.1226' b' [cx1.h : 515] Lv1 scanning from bucket 13202 to 21335' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 13.4427' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 10.3149' b' [cx1.h : 515] Lv1 scanning from bucket 21335 to 32370' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 13.5435' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 10.4669' b' [cx1.h : 515] Lv1 scanning from bucket 32370 to 47919' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 13.2684' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 11.0266' b' [cx1.h : 515] Lv1 scanning from bucket 47919 to 65536' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 11.0740' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 7.6978' b' [cx1.h : 607] Main loop done. Time elapsed: 170.1725' 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] 8561619 542093720 343635382 343329671 542620807 1176567 907099 668081 1295016' b' [cx1_seq2sdbg.cpp :1151] Total number of edges: 1784287962' b' [cx1_seq2sdbg.cpp :1152] Total number of ONEs: 1771679580' b' [cx1_seq2sdbg.cpp :1153] Total number of $v edges: 8561619' b' [cx1.h : 621] Postprocess done. Time elapsed: 0.0364' b' [utils.h : 126] Real: 198.4491\tuser: 2324.0469\tsys: 18.8212\tmaxrss: 5615620' --- [Fri Mar 29 03:53:11 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: 105.259634' b' [assembler.cpp : 152] Number of Edges: 1784287962; 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: 64286; time elapsed: 5.1808' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 4; Accumulated tips removed: 266732; time elapsed: 5.9708' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 8; Accumulated tips removed: 597784; time elapsed: 7.9584' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 16; Accumulated tips removed: 1159682; time elapsed: 12.6852' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 32; Accumulated tips removed: 1804239; time elapsed: 21.9730' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 64; Accumulated tips removed: 4108472; time elapsed: 37.2439' b' [assembly_algorithms.cpp : 170] Removing tips with length less than 118; Accumulated tips removed: 7863117; time elapsed: 39.6827' b' [assembler.cpp : 179] Tips removal done! Time elapsed(sec): 130.762112' b' [assembler.cpp : 188] unitig graph size: 4941720, time for building: 79.023061' b' [assembler.cpp : 211] Number of bubbles removed: 635902, Time elapsed(sec): 15.983331' b' [assembler.cpp : 225] Number of complex bubbles removed: 136248, Time elapsed(sec): 6.023192' b' [assembler.cpp : 243] Number unitigs disconnected: 208418, time: 0.696962' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 81357, time: 0.736079' b' [assembler.cpp : 200] Tips removed: 4577, time: 1.358525' b' [assembler.cpp : 211] Number of bubbles removed: 26899, Time elapsed(sec): 1.691029' b' [assembler.cpp : 225] Number of complex bubbles removed: 16146, Time elapsed(sec): 1.583917' b' [assembler.cpp : 243] Number unitigs disconnected: 9618, time: 0.570311' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 481, time: 0.515805' b' [assembler.cpp : 200] Tips removed: 5161, time: 1.322895' b' [assembler.cpp : 211] Number of bubbles removed: 1044, Time elapsed(sec): 0.533089' b' [assembler.cpp : 225] Number of complex bubbles removed: 1050, Time elapsed(sec): 0.865451' b' [assembler.cpp : 243] Number unitigs disconnected: 150, time: 0.559320' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 31, time: 0.513243' b' [assembler.cpp : 200] Tips removed: 51, time: 1.309083' b' [assembler.cpp : 211] Number of bubbles removed: 4, Time elapsed(sec): 0.399978' b' [assembler.cpp : 225] Number of complex bubbles removed: 18, Time elapsed(sec): 0.768857' b' [assembler.cpp : 243] Number unitigs disconnected: 3, time: 0.558660' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 0, time: 0.319498' b' [assembler.cpp : 200] Tips removed: 2, time: 1.283196' b' [assembler.cpp : 211] Number of bubbles removed: 0, Time elapsed(sec): 0.397880' b' [assembler.cpp : 225] Number of complex bubbles removed: 0, Time elapsed(sec): 0.758892' b' [assembler.cpp : 243] Number unitigs disconnected: 1, time: 0.556840' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 0, time: 0.319913' b' [assembler.cpp : 132] Total length: 819511178, N50: 375, Mean: 256, number of contigs: 3199339' b' [assembler.cpp : 133] Maximum length: 485821' b' [assembler.cpp : 290] Time to output: 25.821450' b' [assembler.cpp : 317] Number of local low depth unitigs removed: 12923, complex bubbles removed: 1964, time: 37.016685' b' [assembler.cpp : 132] Total length: 395666682, N50: 304, Mean: 193, number of contigs: 2043518' b' [assembler.cpp : 133] Maximum length: 485821' b' [utils.h : 126] Real: 429.1324\tuser: 8337.8521\tsys: 18.2698\tmaxrss: 4402236' --- [Fri Mar 29 04:00:21 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: 1188342, Mapper size: 70936944' b' [read_lib_functions-inl.h : 256] Before reading, sizeof seq_package: 6222949328' b' [read_lib_functions-inl.h : 260] After reading, sizeof seq_package: 6222949328' b' [local_assembler.cpp : 330] Lib 0, insert size: 256.74 sd: 100.52' b' [local_assembler.cpp : 462] Lib 0: total 172333246 reads, aligned 98757280, added 29308922 reads for local assembly' b' [utils.h : 126] Real: 730.4394\tuser: 19728.6118\tsys: 17.5030\tmaxrss: 10227212' --- [Fri Mar 29 04:12:31 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: 2121788' b' [iterate_edges.cpp : 570] Number of crusial kmers: 5957745' b' [iterate_edges.cpp : 443] Processed: 67108864, aligned: 13144340. Iterative edges: 40958269' b' [iterate_edges.cpp : 443] Processed: 134217728, aligned: 26029527. Iterative edges: 52276093' b' [iterate_edges.cpp : 447] Total: 172333246, aligned: 33647152. Iterative edges: 56279870' b' [iterate_edges.cpp : 451] Writing iterative edges...' b' [utils.h : 126] Real: 178.8248\tuser: 4409.2922\tsys: 6.9105\tmaxrss: 2577552' --- [Fri Mar 29 04:15:30 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: 56279870' b' [cx1_seq2sdbg.cpp : 434] Bases to reserve: 6434655949, number contigs: 7322158, number multiplicity: 63602028' b' [cx1_seq2sdbg.cpp : 440] Before reading, sizeof seq_package: 1667241260, multiplicity vector: 63602028' b' [cx1_seq2sdbg.cpp : 529] After reading, sizeof seq_package: 1667241260, multiplicity vector: 63602028' b' [cx1.h : 457] Preparing data... Done. Time elapsed: 11.0113' b' [cx1.h : 464] Preparing partitions and initialing global data...' b' [cx1_seq2sdbg.cpp : 740] Memory for sequence: 1840990258' b' [cx1_seq2sdbg.cpp : 741] max # lv.1 items = 439475569' b' [cx1.h : 480] Preparing partitions and initialing global data... Done. Time elapsed: 7.9596' b' [cx1.h : 486] Start main loop...' b' [cx1.h : 515] Lv1 scanning from bucket 0 to 663' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 6.3782' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 5.0379' b' [cx1.h : 515] Lv1 scanning from bucket 663 to 2926' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 7.7833' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 6.9172' b' [cx1.h : 515] Lv1 scanning from bucket 2926 to 6820' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 7.7579' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 7.3196' b' [cx1.h : 515] Lv1 scanning from bucket 6820 to 12521' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 8.4145' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 7.7354' b' [cx1.h : 515] Lv1 scanning from bucket 12521 to 20426' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 9.5510' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 8.2842' b' [cx1.h : 515] Lv1 scanning from bucket 20426 to 31251' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 9.9180' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 8.4983' b' [cx1.h : 515] Lv1 scanning from bucket 31251 to 46640' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 10.2626' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 8.6758' b' [cx1.h : 515] Lv1 scanning from bucket 46640 to 65536' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 7.5575' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 6.5705' b' [cx1.h : 607] Main loop done. Time elapsed: 126.6629' 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] 3889298 433103907 270620298 270389774 433432693 724917 367752 499497 659796' b' [cx1_seq2sdbg.cpp :1151] Total number of edges: 1413687932' b' [cx1_seq2sdbg.cpp :1152] Total number of ONEs: 1407546672' b' [cx1_seq2sdbg.cpp :1153] Total number of $v edges: 3889298' b' [cx1.h : 621] Postprocess done. Time elapsed: 0.0384' b' [utils.h : 126] Real: 145.6781\tuser: 1809.4719\tsys: 13.8943\tmaxrss: 3672352' --- [Fri Mar 29 04:17:56 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: 67.155759' b' [assembler.cpp : 152] Number of Edges: 1413687932; 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: 33694; time elapsed: 4.0780' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 4; Accumulated tips removed: 131815; time elapsed: 4.2301' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 8; Accumulated tips removed: 294064; time elapsed: 5.2562' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 16; Accumulated tips removed: 584487; time elapsed: 7.3923' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 32; Accumulated tips removed: 917558; time elapsed: 11.6124' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 64; Accumulated tips removed: 1634601; time elapsed: 18.2998' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 128; Accumulated tips removed: 2888085; time elapsed: 26.9612' b' [assembly_algorithms.cpp : 170] Removing tips with length less than 158; Accumulated tips removed: 3337929; time elapsed: 24.7132' b' [assembler.cpp : 179] Tips removal done! Time elapsed(sec): 102.596320' b' [assembler.cpp : 188] unitig graph size: 2751294, time for building: 65.774669' b' [assembler.cpp : 211] Number of bubbles removed: 313780, Time elapsed(sec): 11.718789' b' [assembler.cpp : 225] Number of complex bubbles removed: 72315, Time elapsed(sec): 4.820234' b' [assembler.cpp : 243] Number unitigs disconnected: 235377, time: 0.529345' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 90924, time: 0.638749' b' [assembler.cpp : 200] Tips removed: 3318, time: 0.885348' b' [assembler.cpp : 211] Number of bubbles removed: 20703, Time elapsed(sec): 1.232817' b' [assembler.cpp : 225] Number of complex bubbles removed: 14070, Time elapsed(sec): 1.294815' b' [assembler.cpp : 243] Number unitigs disconnected: 9713, time: 0.355475' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 1254, time: 0.357647' b' [assembler.cpp : 200] Tips removed: 6206, time: 0.834648' b' [assembler.cpp : 211] Number of bubbles removed: 631, Time elapsed(sec): 0.260395' b' [assembler.cpp : 225] Number of complex bubbles removed: 842, Time elapsed(sec): 0.511209' b' [assembler.cpp : 243] Number unitigs disconnected: 286, time: 0.345291' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 140, time: 0.354986' b' [assembler.cpp : 200] Tips removed: 131, time: 0.812008' b' [assembler.cpp : 211] Number of bubbles removed: 10, Time elapsed(sec): 0.204671' b' [assembler.cpp : 225] Number of complex bubbles removed: 16, Time elapsed(sec): 0.430654' b' [assembler.cpp : 243] Number unitigs disconnected: 21, time: 0.344147' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 12, time: 0.355105' b' [assembler.cpp : 200] Tips removed: 7, time: 0.816330' b' [assembler.cpp : 211] Number of bubbles removed: 0, Time elapsed(sec): 0.204649' b' [assembler.cpp : 225] Number of complex bubbles removed: 1, Time elapsed(sec): 0.429255' b' [assembler.cpp : 243] Number unitigs disconnected: 3, time: 0.347630' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 1, time: 0.362452' b' [assembler.cpp : 132] Total length: 688122787, N50: 598, Mean: 417, number of contigs: 1649418' b' [assembler.cpp : 133] Maximum length: 558487' b' [assembler.cpp : 290] Time to output: 21.683862' b' [assembler.cpp : 317] Number of local low depth unitigs removed: 8592, complex bubbles removed: 902, time: 21.663517' b' [assembler.cpp : 132] Total length: 297160917, N50: 674, Mean: 326, number of contigs: 909395' b' [assembler.cpp : 133] Maximum length: 558487' b' [utils.h : 126] Real: 316.4529\tuser: 6495.2991\tsys: 14.1908\tmaxrss: 3382524' --- [Fri Mar 29 04:23:13 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: 996459, Mapper size: 71733431' b' [read_lib_functions-inl.h : 256] Before reading, sizeof seq_package: 6222949328' b' [read_lib_functions-inl.h : 260] After reading, sizeof seq_package: 6222949328' b' [local_assembler.cpp : 330] Lib 0, insert size: 261.59 sd: 102.92' b' [local_assembler.cpp : 462] Lib 0: total 172333246 reads, aligned 96707714, added 22118725 reads for local assembly' b' [utils.h : 126] Real: 633.8845\tuser: 17124.0060\tsys: 13.0419\tmaxrss: 9948016' --- [Fri Mar 29 04:33:47 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: 1041635' b' [iterate_edges.cpp : 570] Number of crusial kmers: 2732238' b' [iterate_edges.cpp : 443] Processed: 67108864, aligned: 5947944. Iterative edges: 17024610' b' [iterate_edges.cpp : 443] Processed: 134217728, aligned: 11737322. Iterative edges: 22137195' b' [iterate_edges.cpp : 447] Total: 172333246, aligned: 15200288. Iterative edges: 24001775' b' [iterate_edges.cpp : 451] Writing iterative edges...' b' [utils.h : 126] Real: 114.2383\tuser: 2742.4048\tsys: 5.2394\tmaxrss: 1554272' --- [Fri Mar 29 04:35:41 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: 24001775' b' [cx1_seq2sdbg.cpp : 434] Bases to reserve: 3914798709, number contigs: 3724890, number multiplicity: 27726665' b' [cx1_seq2sdbg.cpp : 440] Before reading, sizeof seq_package: 1008498808, multiplicity vector: 27726665' b' [cx1_seq2sdbg.cpp : 529] After reading, sizeof seq_package: 1987198488, multiplicity vector: 27726665' b' [cx1.h : 457] Preparing data... Done. Time elapsed: 8.4264' b' [cx1.h : 464] Preparing partitions and initialing global data...' b' [cx1_seq2sdbg.cpp : 740] Memory for sequence: 2072922358' b' [cx1_seq2sdbg.cpp : 741] max # lv.1 items = 357947394' b' [cx1.h : 480] Preparing partitions and initialing global data... Done. Time elapsed: 3.9581' b' [cx1.h : 486] Start main loop...' b' [cx1.h : 515] Lv1 scanning from bucket 0 to 568' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 3.3879' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 3.7452' b' [cx1.h : 515] Lv1 scanning from bucket 568 to 2665' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 4.5738' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 5.5615' b' [cx1.h : 515] Lv1 scanning from bucket 2665 to 6382' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 4.8723' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 5.8591' b' [cx1.h : 515] Lv1 scanning from bucket 6382 to 11882' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 4.8461' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 6.4167' b' [cx1.h : 515] Lv1 scanning from bucket 11882 to 19583' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 5.4595' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 6.7409' b' [cx1.h : 515] Lv1 scanning from bucket 19583 to 30205' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 5.6023' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 6.9810' b' [cx1.h : 515] Lv1 scanning from bucket 30205 to 45383' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 5.8940' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 6.8598' b' [cx1.h : 515] Lv1 scanning from bucket 45383 to 65536' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 5.1916' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 5.5329' b' [cx1.h : 607] Main loop done. Time elapsed: 87.5259' 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] 2486961 374827025 232687608 232527161 375111120 409385 186691 186995 410920' b' [cx1_seq2sdbg.cpp :1151] Total number of edges: 1218833866' b' [cx1_seq2sdbg.cpp :1152] Total number of ONEs: 1215152914' b' [cx1_seq2sdbg.cpp :1153] Total number of $v edges: 2486961' b' [cx1.h : 621] Postprocess done. Time elapsed: 0.0351' b' [utils.h : 126] Real: 99.9495\tuser: 1459.7221\tsys: 9.8963\tmaxrss: 2661856' --- [Fri Mar 29 04:37:21 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: 41.616351' b' [assembler.cpp : 152] Number of Edges: 1218833866; 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: 21550; time elapsed: 3.4671' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 4; Accumulated tips removed: 80896; time elapsed: 3.4869' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 8; Accumulated tips removed: 185540; time elapsed: 4.1576' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 16; Accumulated tips removed: 370492; time elapsed: 5.5917' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 32; Accumulated tips removed: 577404; time elapsed: 8.1538' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 64; Accumulated tips removed: 860080; time elapsed: 12.7732' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 128; Accumulated tips removed: 1387131; time elapsed: 20.7835' b' [assembly_algorithms.cpp : 170] Removing tips with length less than 198; Accumulated tips removed: 1903227; time elapsed: 25.1695' b' [assembler.cpp : 179] Tips removal done! Time elapsed(sec): 83.630116' b' [assembler.cpp : 188] unitig graph size: 1531980, time for building: 56.876442' b' [assembler.cpp : 211] Number of bubbles removed: 145599, Time elapsed(sec): 7.874994' b' [assembler.cpp : 225] Number of complex bubbles removed: 34109, Time elapsed(sec): 3.351486' b' [assembler.cpp : 243] Number unitigs disconnected: 149352, time: 0.328694' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 56798, time: 0.482355' b' [assembler.cpp : 200] Tips removed: 1936, time: 0.472980' b' [assembler.cpp : 211] Number of bubbles removed: 10666, Time elapsed(sec): 0.841873' b' [assembler.cpp : 225] Number of complex bubbles removed: 8769, Time elapsed(sec): 1.098071' b' [assembler.cpp : 243] Number unitigs disconnected: 5371, time: 0.236361' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 869, time: 0.280059' b' [assembler.cpp : 200] Tips removed: 3294, time: 0.457254' b' [assembler.cpp : 211] Number of bubbles removed: 251, Time elapsed(sec): 0.127371' b' [assembler.cpp : 225] Number of complex bubbles removed: 557, Time elapsed(sec): 0.447654' b' [assembler.cpp : 243] Number unitigs disconnected: 202, time: 0.240002' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 97, time: 0.275537' b' [assembler.cpp : 200] Tips removed: 97, time: 0.443811' b' [assembler.cpp : 211] Number of bubbles removed: 4, Time elapsed(sec): 0.109029' b' [assembler.cpp : 225] Number of complex bubbles removed: 13, Time elapsed(sec): 0.276459' b' [assembler.cpp : 243] Number unitigs disconnected: 19, time: 0.241645' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 17, time: 0.276484' b' [assembler.cpp : 200] Tips removed: 7, time: 0.451168' b' [assembler.cpp : 211] Number of bubbles removed: 0, Time elapsed(sec): 0.109968' b' [assembler.cpp : 225] Number of complex bubbles removed: 0, Time elapsed(sec): 0.278687' b' [assembler.cpp : 243] Number unitigs disconnected: 1, time: 0.232133' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 5, time: 0.273492' b' [assembler.cpp : 132] Total length: 606785029, N50: 851, Mean: 636, number of contigs: 953186' b' [assembler.cpp : 133] Maximum length: 888384' b' [assembler.cpp : 290] Time to output: 19.234598' b' [assembler.cpp : 317] Number of local low depth unitigs removed: 4339, complex bubbles removed: 497, time: 15.402558' b' [assembler.cpp : 132] Total length: 212046041, N50: 1543, Mean: 571, number of contigs: 370728' b' [assembler.cpp : 133] Maximum length: 888384' b' [utils.h : 126] Real: 243.0862\tuser: 5186.4256\tsys: 11.2171\tmaxrss: 2873320' --- [Fri Mar 29 04:41:24 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: 757621, Mapper size: 68743956' b' [read_lib_functions-inl.h : 256] Before reading, sizeof seq_package: 6222949328' b' [read_lib_functions-inl.h : 260] After reading, sizeof seq_package: 6222949328' b' [local_assembler.cpp : 330] Lib 0, insert size: 266.11 sd: 105.10' b' [local_assembler.cpp : 462] Lib 0: total 172333246 reads, aligned 90505981, added 13334904 reads for local assembly' b' [utils.h : 126] Real: 439.4150\tuser: 11640.0311\tsys: 13.1703\tmaxrss: 9499364' --- [Fri Mar 29 04:48:44 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: 458849' b' [iterate_edges.cpp : 570] Number of crusial kmers: 1129494' b' [iterate_edges.cpp : 443] Processed: 67108864, aligned: 1812701. Iterative edges: 4359565' b' [iterate_edges.cpp : 443] Processed: 134217728, aligned: 3568532. Iterative edges: 6217596' b' [iterate_edges.cpp : 447] Total: 172333246, aligned: 4626844. Iterative edges: 6956878' b' [iterate_edges.cpp : 451] Writing iterative edges...' b' [utils.h : 126] Real: 54.0036\tuser: 1270.1475\tsys: 4.0312\tmaxrss: 772468' --- [Fri Mar 29 04:49:38 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: 6956878' b' [cx1_seq2sdbg.cpp : 434] Bases to reserve: 1876122468, number contigs: 1723934, number multiplicity: 8680812' b' [cx1_seq2sdbg.cpp : 440] Before reading, sizeof seq_package: 482822100, multiplicity vector: 8680812' b' [cx1_seq2sdbg.cpp : 529] After reading, sizeof seq_package: 965644200, multiplicity vector: 17361624' b' [cx1.h : 457] Preparing data... Done. Time elapsed: 4.9621' b' [cx1.h : 464] Preparing partitions and initialing global data...' b' [cx1_seq2sdbg.cpp : 740] Memory for sequence: 999331804' b' [cx1_seq2sdbg.cpp : 741] max # lv.1 items = 272765299' b' [cx1.h : 480] Preparing partitions and initialing global data... Done. Time elapsed: 2.3258' b' [cx1.h : 486] Start main loop...' b' [cx1.h : 515] Lv1 scanning from bucket 0 to 412' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 1.7966' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 2.5940' b' [cx1.h : 515] Lv1 scanning from bucket 412 to 2215' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 2.2712' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 4.4953' b' [cx1.h : 515] Lv1 scanning from bucket 2215 to 5639' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 2.3527' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 4.7409' b' [cx1.h : 515] Lv1 scanning from bucket 5639 to 10812' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 2.5288' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 5.1037' b' [cx1.h : 515] Lv1 scanning from bucket 10812 to 18165' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 2.7090' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 5.5577' b' [cx1.h : 515] Lv1 scanning from bucket 18165 to 28409' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 2.9632' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 5.4879' b' [cx1.h : 515] Lv1 scanning from bucket 28409 to 43100' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 3.0109' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 5.7289' b' [cx1.h : 515] Lv1 scanning from bucket 43100 to 65536' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 2.7374' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 5.1275' b' [cx1.h : 607] Main loop done. Time elapsed: 59.2069' 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] 1939527 330570465 205427425 205329683 330793315 143279 104735 78378 158206' b' [cx1_seq2sdbg.cpp :1151] Total number of edges: 1074545013' b' [cx1_seq2sdbg.cpp :1152] Total number of ONEs: 1072120888' b' [cx1_seq2sdbg.cpp :1153] Total number of $v edges: 1939527' b' [cx1.h : 621] Postprocess done. Time elapsed: 0.0333' b' [utils.h : 126] Real: 66.5305\tuser: 1174.6220\tsys: 7.8500\tmaxrss: 1799444' --- [Fri Mar 29 04:50:44 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: 25.835096' b' [assembler.cpp : 152] Number of Edges: 1074545013; 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: 19796; time elapsed: 2.9913' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 4; Accumulated tips removed: 71122; time elapsed: 3.0475' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 8; Accumulated tips removed: 168052; time elapsed: 3.5203' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 16; Accumulated tips removed: 370402; time elapsed: 4.4957' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 32; Accumulated tips removed: 479252; time elapsed: 6.3444' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 64; Accumulated tips removed: 613178; time elapsed: 9.9254' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 128; Accumulated tips removed: 919001; time elapsed: 15.9808' b' [assembly_algorithms.cpp : 170] Removing tips with length less than 182; Accumulated tips removed: 1007633; time elapsed: 19.8617' b' [assembler.cpp : 179] Tips removal done! Time elapsed(sec): 66.209630' b' [assembler.cpp : 188] unitig graph size: 916901, time for building: 52.879995' b' [assembler.cpp : 211] Number of bubbles removed: 47665, Time elapsed(sec): 2.077943' b' [assembler.cpp : 225] Number of complex bubbles removed: 10342, Time elapsed(sec): 1.112095' b' [assembler.cpp : 243] Number unitigs disconnected: 52123, time: 0.177613' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 17629, time: 0.248495' b' [assembler.cpp : 200] Tips removed: 660, time: 0.319464' b' [assembler.cpp : 211] Number of bubbles removed: 1985, Time elapsed(sec): 0.311373' b' [assembler.cpp : 225] Number of complex bubbles removed: 2888, Time elapsed(sec): 0.634831' b' [assembler.cpp : 243] Number unitigs disconnected: 2352, time: 0.140310' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 216, time: 0.170798' b' [assembler.cpp : 200] Tips removed: 969, time: 0.312385' b' [assembler.cpp : 211] Number of bubbles removed: 100, Time elapsed(sec): 0.094119' b' [assembler.cpp : 225] Number of complex bubbles removed: 243, Time elapsed(sec): 0.242737' b' [assembler.cpp : 243] Number unitigs disconnected: 53, time: 0.140762' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 19, time: 0.169798' b' [assembler.cpp : 200] Tips removed: 21, time: 0.308764' b' [assembler.cpp : 211] Number of bubbles removed: 0, Time elapsed(sec): 0.072688' b' [assembler.cpp : 225] Number of complex bubbles removed: 4, Time elapsed(sec): 0.203404' b' [assembler.cpp : 243] Number unitigs disconnected: 2, time: 0.141365' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 3, time: 0.169610' b' [assembler.cpp : 200] Tips removed: 1, time: 0.308002' b' [assembler.cpp : 211] Number of bubbles removed: 0, Time elapsed(sec): 0.072265' b' [assembler.cpp : 225] Number of complex bubbles removed: 0, Time elapsed(sec): 0.200416' b' [assembler.cpp : 243] Number unitigs disconnected: 1, time: 0.140700' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 0, time: 0.130007' b' [assembler.cpp : 132] Total length: 588155386, N50: 1011, Mean: 804, number of contigs: 730760' b' [assembler.cpp : 133] Maximum length: 888526' b' [assembler.cpp : 290] Time to output: 18.430954' b' [assembler.cpp : 317] Number of local low depth unitigs removed: 1210, complex bubbles removed: 148, time: 7.515342' b' [assembler.cpp : 132] Total length: 137314162, N50: 3686, Mean: 1166, number of contigs: 117751' b' [assembler.cpp : 133] Maximum length: 888526' b' [utils.h : 126] Real: 183.9111\tuser: 4069.4380\tsys: 8.8542\tmaxrss: 2520312' --- [Fri Mar 29 04:53:49 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: 700231, Mapper size: 69446169' b' [read_lib_functions-inl.h : 256] Before reading, sizeof seq_package: 6222949328' b' [read_lib_functions-inl.h : 260] After reading, sizeof seq_package: 6222949328' b' [local_assembler.cpp : 330] Lib 0, insert size: 267.94 sd: 106.14' b' [local_assembler.cpp : 462] Lib 0: total 172333246 reads, aligned 87243966, added 8699771 reads for local assembly' b' [utils.h : 126] Real: 321.0075\tuser: 8329.1633\tsys: 11.4595\tmaxrss: 9416112' --- [Fri Mar 29 04:59:10 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: 96883' b' [iterate_edges.cpp : 570] Number of crusial kmers: 294427' 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: 172333246, aligned: 0. Iterative edges: 0' b' [utils.h : 126] Real: 15.0681\tuser: 22.5622\tsys: 2.7075\tmaxrss: 433016' --- [Fri Mar 29 04:59:25 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: 587933474, number contigs: 757547, number multiplicity: 757547' b' [cx1_seq2sdbg.cpp : 440] Before reading, sizeof seq_package: 153043756, multiplicity vector: 757547' b' [cx1_seq2sdbg.cpp : 529] After reading, sizeof seq_package: 306087512, multiplicity vector: 1515094' b' [cx1.h : 457] Preparing data... Done. Time elapsed: 3.2457' b' [cx1.h : 464] Preparing partitions and initialing global data...' b' [cx1_seq2sdbg.cpp : 740] Memory for sequence: 315620944' b' [cx1_seq2sdbg.cpp : 741] max # lv.1 items = 194546680' b' [cx1.h : 480] Preparing partitions and initialing global data... Done. Time elapsed: 0.6168' b' [cx1.h : 486] Start main loop...' b' [cx1.h : 515] Lv1 scanning from bucket 0 to 271' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 0.4416' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 1.6110' b' [cx1.h : 515] Lv1 scanning from bucket 271 to 1702' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 0.4689' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 3.1326' b' [cx1.h : 515] Lv1 scanning from bucket 1702 to 4711' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 0.4949' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 3.7148' b' [cx1.h : 515] Lv1 scanning from bucket 4711 to 9430' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 0.5680' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 4.1081' b' [cx1.h : 515] Lv1 scanning from bucket 9430 to 16282' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 0.5724' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 4.2400' b' [cx1.h : 515] Lv1 scanning from bucket 16282 to 25967' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 0.6100' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 4.6150' b' [cx1.h : 515] Lv1 scanning from bucket 25967 to 39889' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 0.6215' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 4.4787' b' [cx1.h : 515] Lv1 scanning from bucket 39889 to 64126' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 0.5906' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 4.7757' b' [cx1.h : 515] Lv1 scanning from bucket 64126 to 65536' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 0.2823' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 0.1717' b' [cx1.h : 607] Main loop done. Time elapsed: 35.4985' 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] 1433534 311594143 194169250 194092417 311775972 63560 29111 29623 63620' b' [cx1_seq2sdbg.cpp :1151] Total number of edges: 1013251230' b' [cx1_seq2sdbg.cpp :1152] Total number of ONEs: 1011631782' b' [cx1_seq2sdbg.cpp :1153] Total number of $v edges: 1433534' b' [cx1.h : 621] Postprocess done. Time elapsed: 0.0350' b' [utils.h : 126] Real: 39.3977\tuser: 940.3945\tsys: 4.8518\tmaxrss: 1161364' --- [Fri Mar 29 05:00:04 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: 19.590051' b' [assembler.cpp : 152] Number of Edges: 1013251230; 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: 2664; time elapsed: 2.8845' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 4; Accumulated tips removed: 9000; time elapsed: 2.7956' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 8; Accumulated tips removed: 20500; time elapsed: 3.2150' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 16; Accumulated tips removed: 42618; time elapsed: 4.0388' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 32; Accumulated tips removed: 80540; time elapsed: 5.7166' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 64; Accumulated tips removed: 140280; time elapsed: 8.8982' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 128; Accumulated tips removed: 231400; time elapsed: 14.5816' b' [assembly_algorithms.cpp : 170] Removing tips with length less than 160; Accumulated tips removed: 253324; time elapsed: 17.3477' b' [assembler.cpp : 179] Tips removal done! Time elapsed(sec): 59.517554' b' [assembler.cpp : 188] unitig graph size: 789784, time for building: 50.631631' b' [assembler.cpp : 211] Number of bubbles removed: 26794, Time elapsed(sec): 0.176735' b' [assembler.cpp : 225] Number of complex bubbles removed: 4025, Time elapsed(sec): 0.254562' b' [assembler.cpp : 243] Number unitigs disconnected: 27522, time: 0.117048' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 7701, time: 0.117027' b' [assembler.cpp : 200] Tips removed: 425, time: 0.282533' b' [assembler.cpp : 211] Number of bubbles removed: 256, Time elapsed(sec): 0.071395' b' [assembler.cpp : 225] Number of complex bubbles removed: 948, Time elapsed(sec): 0.184569' b' [assembler.cpp : 243] Number unitigs disconnected: 1607, time: 0.095673' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 91, time: 0.084010' b' [assembler.cpp : 200] Tips removed: 375, time: 0.279992' b' [assembler.cpp : 211] Number of bubbles removed: 16, Time elapsed(sec): 0.069849' b' [assembler.cpp : 225] Number of complex bubbles removed: 104, Time elapsed(sec): 0.162447' b' [assembler.cpp : 243] Number unitigs disconnected: 29, time: 0.097539' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 4, time: 0.085136' b' [assembler.cpp : 200] Tips removed: 3, time: 0.287333' b' [assembler.cpp : 211] Number of bubbles removed: 0, Time elapsed(sec): 0.068364' b' [assembler.cpp : 225] Number of complex bubbles removed: 4, Time elapsed(sec): 0.149161' b' [assembler.cpp : 243] Number unitigs disconnected: 1, time: 0.096648' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 2, time: 0.085504' b' [assembler.cpp : 200] Tips removed: 1, time: 0.278221' b' [assembler.cpp : 211] Number of bubbles removed: 0, Time elapsed(sec): 0.065760' b' [assembler.cpp : 225] Number of complex bubbles removed: 0, Time elapsed(sec): 0.143034' b' [assembler.cpp : 243] Number unitigs disconnected: 0, time: 0.095219' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 0, time: 0.043960' b' [assembler.cpp : 317] Number of local low depth unitigs removed: 420, complex bubbles removed: 27, time: 3.712234' b' [assembler.cpp : 132] Total length: 591582861, N50: 1066, Mean: 848, number of contigs: 696981' b' [assembler.cpp : 133] Maximum length: 935935' b' [utils.h : 126] Real: 154.7892\tuser: 3482.1018\tsys: 8.2950\tmaxrss: 2381020' --- [Fri Mar 29 05:02:39 2019] Merging to output final contigs --- --- [STAT] 686407 contigs, total 589725900 bp, min 200 bp, max 935935 bp, avg 859 bp, N50 1072 bp --- [Fri Mar 29 05:02:42 2019] ALL DONE. Time elapsed: 10781.317743 seconds ---