MEGAHIT v1.1.3 --- [Thu Mar 28 15:32:47 2019] Start assembly. Number of CPU threads 28 --- --- [Thu Mar 28 15:32:47 2019] Available memory: 269759385600, used: 242783447040 --- [Thu Mar 28 15:32:47 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_3_S1_L002_R1_001_val_1_val_1_val_1.fq.gz,/gscratch/srlab/sam/data/metagenomics/P_generosa/Library_Geoduck_MG_3_S1_L002_R2_001_val_2_val_2_val_2.fq.gz): pe, 167467174 reads, 131 max length' b' [utils.h : 126] Real: 157.9774\tuser: 143.8192\tsys: 13.2962\tmaxrss: 154932' --- [Thu Mar 28 15:35:25 2019] k list: 21,29,39,59,79,99,119,141 --- --- [Thu Mar 28 15:35:25 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: 5679132804' b' [read_lib_functions-inl.h : 260] After reading, sizeof seq_package: 5679132804' b' [cx1_kmer_count.cpp : 136] 167467174 reads, 131 max read length' b' [cx1.h : 457] Preparing data... Done. Time elapsed: 23.3805' 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: 7811269032, 236559324856' b' [cx1_kmer_count.cpp : 356] 1845533172, 17880681 7811269032 236559324856' b' [cx1_kmer_count.cpp : 363] Memory for reads: 5814738940' b' [cx1_kmer_count.cpp : 364] max # lv.1 items = 1845533172' b' [cx1.h : 480] Preparing partitions and initialing global data... Done. Time elapsed: 8.1387' b' [cx1.h : 486] Start main loop...' b' [cx1.h : 515] Lv1 scanning from bucket 0 to 231' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 7.6503' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 10.2462' b' [cx1.h : 515] Lv1 scanning from bucket 231 to 1391' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 8.2310' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 23.7902' b' [cx1.h : 515] Lv1 scanning from bucket 1391 to 3744' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 8.4915' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 26.7704' b' [cx1.h : 515] Lv1 scanning from bucket 3744 to 7519' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 8.7834' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 26.9660' b' [cx1.h : 515] Lv1 scanning from bucket 7519 to 13184' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 9.0512' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 26.5938' b' [cx1.h : 515] Lv1 scanning from bucket 13184 to 21449' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 9.2835' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 26.2754' b' [cx1.h : 515] Lv1 scanning from bucket 21449 to 33807' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 9.5545' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 26.1907' b' [cx1.h : 515] Lv1 scanning from bucket 33807 to 57614' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 9.9274' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 26.7411' b' [cx1.h : 515] Lv1 scanning from bucket 57614 to 65536' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 7.2796' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 2.7442' b' [cx1.h : 607] Main loop done. Time elapsed: 274.5719' b' [cx1.h : 613] Postprocessing...' b' [cx1_kmer_count.cpp : 860] Total number of candidate reads: 4591646(16718232)' b' [cx1_kmer_count.cpp : 871] Total number of solid edges: 1436894652' b' [cx1.h : 621] Postprocess done. Time elapsed: 3.1141' b' [utils.h : 126] Real: 309.2270\tuser: 7768.1790\tsys: 28.2899\tmaxrss: 14693696' --- [Thu Mar 28 15:40:34 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: 1436894652' b' [cx1_seq2sdbg.cpp : 434] Bases to reserve: 39514602930, number contigs: 0, number multiplicity: 1796118315' b' [cx1_seq2sdbg.cpp : 440] Before reading, sizeof seq_package: 9878650744, multiplicity vector: 1796118315' b' [cx1_seq2sdbg.cpp : 455] Adding mercy edges...' b' [cx1_seq2sdbg.cpp : 373] Number of reads: 4591646, Number of mercy edges: 64318776' b' [cx1_seq2sdbg.cpp : 462] Done. Time elapsed: 79.1015' b' [cx1_seq2sdbg.cpp : 529] After reading, sizeof seq_package: 9878650744, multiplicity vector: 1796118315' b' [cx1.h : 457] Preparing data... Done. Time elapsed: 502.9510' b' [cx1.h : 464] Preparing partitions and initialing global data...' b' [cx1_seq2sdbg.cpp : 740] Memory for sequence: 13139098688' b' [cx1_seq2sdbg.cpp : 741] max # lv.1 items = 1200970742' b' [cx1.h : 480] Preparing partitions and initialing global data... Done. Time elapsed: 3.2250' b' [cx1.h : 486] Start main loop...' b' [cx1.h : 515] Lv1 scanning from bucket 0 to 1204' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 2.9507' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 10.8127' b' [cx1.h : 515] Lv1 scanning from bucket 1204 to 4167' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 2.9991' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 12.3235' b' [cx1.h : 515] Lv1 scanning from bucket 4167 to 8877' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 3.0352' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 12.2657' b' [cx1.h : 515] Lv1 scanning from bucket 8877 to 15484' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 3.1017' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 12.6179' b' [cx1.h : 515] Lv1 scanning from bucket 15484 to 24349' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 3.2047' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 13.0449' b' [cx1.h : 515] Lv1 scanning from bucket 24349 to 35993' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 3.3205' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 13.4824' b' [cx1.h : 515] Lv1 scanning from bucket 35993 to 51780' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 3.4606' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 13.4943' b' [cx1.h : 515] Lv1 scanning from bucket 51780 to 65536' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 2.9606' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 8.0032' b' [cx1.h : 607] Main loop done. Time elapsed: 121.0788' 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] 19378084 897207736 589556286 588527409 899825763 15763000 7603064 7465703 15844280' b' [cx1_seq2sdbg.cpp :1151] Total number of edges: 3041171325' b' [cx1_seq2sdbg.cpp :1152] Total number of ONEs: 2975117194' b' [cx1_seq2sdbg.cpp :1153] Total number of $v edges: 19378084' b' [cx1.h : 621] Postprocess done. Time elapsed: 0.0458' b' [utils.h : 126] Real: 627.3318\tuser: 5245.4412\tsys: 52.9709\tmaxrss: 16004360' --- [Thu Mar 28 15:51:03 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: 163.744449' b' [assembler.cpp : 152] Number of Edges: 3041171325; 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: 1412990; time elapsed: 8.9979' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 4; Accumulated tips removed: 4345391; time elapsed: 10.6273' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 8; Accumulated tips removed: 7557643; time elapsed: 15.2127' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 16; Accumulated tips removed: 11939632; time elapsed: 25.3209' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 32; Accumulated tips removed: 16341152; time elapsed: 39.3807' b' [assembly_algorithms.cpp : 170] Removing tips with length less than 42; Accumulated tips removed: 17873158; time elapsed: 43.2822' b' [assembler.cpp : 179] Tips removal done! Time elapsed(sec): 142.932300' b' [assembler.cpp : 188] unitig graph size: 55058522, time for building: 315.653417' b' [assembler.cpp : 211] Number of bubbles removed: 3363631, Time elapsed(sec): 27.434182' b' [assembler.cpp : 225] Number of complex bubbles removed: 469725, Time elapsed(sec): 18.186008' b' [assembler.cpp : 243] Number unitigs disconnected: 13817505, time: 24.332727' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 55088, time: 6.014669' b' [assembler.cpp : 200] Tips removed: 126879, time: 15.200925' b' [assembler.cpp : 211] Number of bubbles removed: 54272, Time elapsed(sec): 6.009034' b' [assembler.cpp : 225] Number of complex bubbles removed: 199079, Time elapsed(sec): 12.015185' b' [assembler.cpp : 243] Number unitigs disconnected: 915773, time: 7.741441' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 105, time: 5.866387' b' [assembler.cpp : 200] Tips removed: 720234, time: 15.442839' b' [assembler.cpp : 211] Number of bubbles removed: 38021, Time elapsed(sec): 5.729969' b' [assembler.cpp : 225] Number of complex bubbles removed: 11751, Time elapsed(sec): 11.602421' b' [assembler.cpp : 243] Number unitigs disconnected: 9966, time: 7.057171' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 7, time: 5.810919' b' [assembler.cpp : 200] Tips removed: 3397, time: 14.313489' b' [assembler.cpp : 211] Number of bubbles removed: 231, Time elapsed(sec): 5.544463' b' [assembler.cpp : 225] Number of complex bubbles removed: 495, Time elapsed(sec): 11.381524' b' [assembler.cpp : 243] Number unitigs disconnected: 251, time: 7.064456' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 1, time: 5.797413' b' [assembler.cpp : 200] Tips removed: 134, time: 14.318320' b' [assembler.cpp : 211] Number of bubbles removed: 0, Time elapsed(sec): 5.612951' b' [assembler.cpp : 225] Number of complex bubbles removed: 25, Time elapsed(sec): 11.569410' b' [assembler.cpp : 243] Number unitigs disconnected: 7, time: 7.036999' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 0, time: 3.594209' b' [assembler.cpp : 132] Total length: 2198361546, N50: 70, Mean: 52, number of contigs: 42146006' b' [assembler.cpp : 133] Maximum length: 14880' b' [assembler.cpp : 290] Time to output: 79.050770' b' [assembler.cpp : 317] Number of local low depth unitigs removed: 1437067, complex bubbles removed: 88582, time: 558.813900' b' [assembler.cpp : 132] Total length: 1706455110, N50: 58, Mean: 48, number of contigs: 35145520' b' [assembler.cpp : 133] Maximum length: 14880' b' [utils.h : 126] Real: 1561.4569\tuser: 36589.7554\tsys: 47.9270\tmaxrss: 9647152' --- [Thu Mar 28 16:17:05 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: 999001, Mapper size: 37294000' b' [read_lib_functions-inl.h : 256] Before reading, sizeof seq_package: 5679132804' b' [read_lib_functions-inl.h : 260] After reading, sizeof seq_package: 5679132804' b' [local_assembler.cpp : 330] Lib 0, insert size: 236.72 sd: 88.48' b' [local_assembler.cpp : 462] Lib 0: total 167467174 reads, aligned 35844671, added 18308337 reads for local assembly' b' [utils.h : 126] Real: 307.0341\tuser: 7846.2870\tsys: 12.1102\tmaxrss: 8217268' --- [Thu Mar 28 16:22:12 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: 11227176' b' [iterate_edges.cpp : 570] Number of crusial kmers: 79652247' b' [iterate_edges.cpp : 443] Processed: 67108864, aligned: 44943230. Iterative edges: 243785782' b' [iterate_edges.cpp : 443] Processed: 134217728, aligned: 89905352. Iterative edges: 305199163' b' [iterate_edges.cpp : 447] Total: 167467174, aligned: 112235400. Iterative edges: 320226521' b' [iterate_edges.cpp : 451] Writing iterative edges...' b' [utils.h : 126] Real: 314.6207\tuser: 7584.3687\tsys: 14.1163\tmaxrss: 10879984' --- [Thu Mar 28 16:27:27 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: 320226521' b' [cx1_seq2sdbg.cpp : 434] Bases to reserve: 14238911240, number contigs: 82251608, number multiplicity: 402478129' b' [cx1_seq2sdbg.cpp : 440] Before reading, sizeof seq_package: 4217740684, multiplicity vector: 402478129' b' [cx1_seq2sdbg.cpp : 529] After reading, sizeof seq_package: 4217740684, multiplicity vector: 402478129' b' [cx1.h : 457] Preparing data... Done. Time elapsed: 33.2224' b' [cx1.h : 464] Preparing partitions and initialing global data...' b' [cx1_seq2sdbg.cpp : 740] Memory for sequence: 5024220468' b' [cx1_seq2sdbg.cpp : 741] max # lv.1 items = 813382631' b' [cx1.h : 480] Preparing partitions and initialing global data... Done. Time elapsed: 10.5949' b' [cx1.h : 486] Start main loop...' b' [cx1.h : 515] Lv1 scanning from bucket 0 to 913' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 9.1527' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 10.4694' b' [cx1.h : 515] Lv1 scanning from bucket 913 to 3457' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 10.7631' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 12.6335' b' [cx1.h : 515] Lv1 scanning from bucket 3457 to 7682' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 12.2602' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 13.2514' b' [cx1.h : 515] Lv1 scanning from bucket 7682 to 13717' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 13.6465' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 13.9291' b' [cx1.h : 515] Lv1 scanning from bucket 13717 to 22027' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 14.6737' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 14.5916' b' [cx1.h : 515] Lv1 scanning from bucket 22027 to 33312' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 14.0248' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 15.1250' b' [cx1.h : 515] Lv1 scanning from bucket 33312 to 49182' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 15.0601' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 15.4166' b' [cx1.h : 515] Lv1 scanning from bucket 49182 to 65536' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 11.3526' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 10.2255' b' [cx1.h : 607] Main loop done. Time elapsed: 206.5771' 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] 19073104 837329674 542463227 541873931 839022214 4458460 2887458 2540575 4587161' b' [cx1_seq2sdbg.cpp :1151] Total number of edges: 2794235804' b' [cx1_seq2sdbg.cpp :1152] Total number of ONEs: 2760689046' b' [cx1_seq2sdbg.cpp :1153] Total number of $v edges: 19073104' b' [cx1.h : 621] Postprocess done. Time elapsed: 0.0421' b' [utils.h : 126] Real: 250.4485\tuser: 3322.5951\tsys: 24.0430\tmaxrss: 7461484' --- [Thu Mar 28 16:31:38 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: 180.641418' b' [assembler.cpp : 152] Number of Edges: 2794235804; 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: 775096; time elapsed: 8.6377' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 4; Accumulated tips removed: 2104737; time elapsed: 10.5529' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 8; Accumulated tips removed: 3640018; time elapsed: 14.1807' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 16; Accumulated tips removed: 6065557; time elapsed: 24.1083' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 32; Accumulated tips removed: 10632575; time elapsed: 42.0058' b' [assembly_algorithms.cpp : 170] Removing tips with length less than 58; Accumulated tips removed: 14690474; time elapsed: 58.9480' b' [assembler.cpp : 179] Tips removal done! Time elapsed(sec): 158.536807' b' [assembler.cpp : 188] unitig graph size: 19733897, time for building: 175.548936' b' [assembler.cpp : 211] Number of bubbles removed: 2643888, Time elapsed(sec): 30.621871' b' [assembler.cpp : 225] Number of complex bubbles removed: 537908, Time elapsed(sec): 13.512505' b' [assembler.cpp : 243] Number unitigs disconnected: 332431, time: 3.031281' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 35906, time: 3.180813' b' [assembler.cpp : 200] Tips removed: 26356, time: 4.479102' b' [assembler.cpp : 211] Number of bubbles removed: 23684, Time elapsed(sec): 2.471376' b' [assembler.cpp : 225] Number of complex bubbles removed: 11143, Time elapsed(sec): 4.482333' b' [assembler.cpp : 243] Number unitigs disconnected: 40033, time: 2.827531' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 638, time: 3.177990' b' [assembler.cpp : 200] Tips removed: 12455, time: 4.523223' b' [assembler.cpp : 211] Number of bubbles removed: 3378, Time elapsed(sec): 1.827315' b' [assembler.cpp : 225] Number of complex bubbles removed: 1582, Time elapsed(sec): 4.252215' b' [assembler.cpp : 243] Number unitigs disconnected: 5060, time: 2.789799' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 104, time: 3.158006' b' [assembler.cpp : 200] Tips removed: 344, time: 4.438607' b' [assembler.cpp : 211] Number of bubbles removed: 38, Time elapsed(sec): 1.649497' b' [assembler.cpp : 225] Number of complex bubbles removed: 59, Time elapsed(sec): 4.101162' b' [assembler.cpp : 243] Number unitigs disconnected: 1092, time: 2.761367' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 9, time: 3.156433' b' [assembler.cpp : 200] Tips removed: 46, time: 4.371876' b' [assembler.cpp : 211] Number of bubbles removed: 0, Time elapsed(sec): 1.640121' b' [assembler.cpp : 225] Number of complex bubbles removed: 7, Time elapsed(sec): 4.238602' b' [assembler.cpp : 243] Number unitigs disconnected: 333, time: 2.761062' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 6, time: 3.150409' b' [assembler.cpp : 132] Total length: 1557464742, N50: 139, Mean: 112, number of contigs: 13801238' b' [assembler.cpp : 133] Maximum length: 56102' b' [assembler.cpp : 290] Time to output: 50.434788' b' [assembler.cpp : 317] Number of local low depth unitigs removed: 171417, complex bubbles removed: 21896, time: 286.221579' b' [assembler.cpp : 132] Total length: 889721370, N50: 137, Mean: 95, number of contigs: 9296380' b' [assembler.cpp : 133] Maximum length: 56102' b' [utils.h : 126] Real: 993.7877\tuser: 21434.9864\tsys: 36.4954\tmaxrss: 7603632' --- [Thu Mar 28 16:48:12 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: 1347102, Mapper size: 70376064' b' [read_lib_functions-inl.h : 256] Before reading, sizeof seq_package: 5679132804' b' [read_lib_functions-inl.h : 260] After reading, sizeof seq_package: 5679132804' b' [local_assembler.cpp : 330] Lib 0, insert size: 251.87 sd: 97.77' b' [local_assembler.cpp : 462] Lib 0: total 167467174 reads, aligned 66229861, added 21307052 reads for local assembly' b' [utils.h : 126] Real: 416.1249\tuser: 10929.2964\tsys: 19.0966\tmaxrss: 9814132' --- [Thu Mar 28 16:55:08 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: 9159764' b' [iterate_edges.cpp : 570] Number of crusial kmers: 26605837' b' [iterate_edges.cpp : 443] Processed: 67108864, aligned: 29196211. Iterative edges: 110027048' b' [iterate_edges.cpp : 443] Processed: 134217728, aligned: 58370014. Iterative edges: 139957175' b' [iterate_edges.cpp : 447] Total: 167467174, aligned: 72896024. Iterative edges: 147546198' b' [iterate_edges.cpp : 451] Writing iterative edges...' b' [utils.h : 126] Real: 278.8886\tuser: 6620.0556\tsys: 10.5172\tmaxrss: 5745076' --- [Thu Mar 28 16:59:47 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: 147546198' b' [cx1_seq2sdbg.cpp : 434] Bases to reserve: 9456044623, number contigs: 29295667, number multiplicity: 176841865' b' [cx1_seq2sdbg.cpp : 440] Before reading, sizeof seq_package: 2598376500, multiplicity vector: 176841865' b' [cx1_seq2sdbg.cpp : 529] After reading, sizeof seq_package: 2598376500, multiplicity vector: 176841865' b' [cx1.h : 457] Preparing data... Done. Time elapsed: 22.3711' b' [cx1.h : 464] Preparing partitions and initialing global data...' b' [cx1_seq2sdbg.cpp : 740] Memory for sequence: 3005269914' b' [cx1_seq2sdbg.cpp : 741] max # lv.1 items = 776728465' b' [cx1.h : 480] Preparing partitions and initialing global data... Done. Time elapsed: 10.5998' b' [cx1.h : 486] Start main loop...' b' [cx1.h : 515] Lv1 scanning from bucket 0 to 981' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 9.4142' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 10.6055' b' [cx1.h : 515] Lv1 scanning from bucket 981 to 3518' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 11.9334' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 12.8877' b' [cx1.h : 515] Lv1 scanning from bucket 3518 to 7667' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 11.9752' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 12.6999' b' [cx1.h : 515] Lv1 scanning from bucket 7667 to 13564' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 14.2125' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 13.8867' b' [cx1.h : 515] Lv1 scanning from bucket 13564 to 21741' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 13.6410' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 14.4967' b' [cx1.h : 515] Lv1 scanning from bucket 21741 to 32983' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 14.4632' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 14.7094' b' [cx1.h : 515] Lv1 scanning from bucket 32983 to 49209' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 13.6827' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 15.4805' b' [cx1.h : 515] Lv1 scanning from bucket 49209 to 65536' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 10.8669' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 9.7592' b' [cx1.h : 607] Main loop done. Time elapsed: 204.7162' 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] 11697649 755708871 485666350 485129491 756978492 2499858 1409732 1395539 2502736' b' [cx1_seq2sdbg.cpp :1151] Total number of edges: 2502988718' b' [cx1_seq2sdbg.cpp :1152] Total number of ONEs: 2483483204' b' [cx1_seq2sdbg.cpp :1153] Total number of $v edges: 11697649' b' [cx1.h : 621] Postprocess done. Time elapsed: 0.0431' b' [utils.h : 126] Real: 237.7384\tuser: 3229.4933\tsys: 21.1541\tmaxrss: 6025996' --- [Thu Mar 28 17:03:45 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: 143.523324' b' [assembler.cpp : 152] Number of Edges: 2502988718; 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: 136530; time elapsed: 7.3814' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 4; Accumulated tips removed: 474719; time elapsed: 8.2294' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 8; Accumulated tips removed: 888782; time elapsed: 11.4076' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 16; Accumulated tips removed: 1355154; time elapsed: 18.8799' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 32; Accumulated tips removed: 2239104; time elapsed: 32.9748' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 64; Accumulated tips removed: 5533188; time elapsed: 55.7427' b' [assembly_algorithms.cpp : 170] Removing tips with length less than 78; Accumulated tips removed: 7208068; time elapsed: 55.1004' b' [assembler.cpp : 179] Tips removal done! Time elapsed(sec): 189.808554' b' [assembler.cpp : 188] unitig graph size: 12275976, time for building: 148.002039' b' [assembler.cpp : 211] Number of bubbles removed: 1836706, Time elapsed(sec): 30.243462' b' [assembler.cpp : 225] Number of complex bubbles removed: 393780, Time elapsed(sec): 12.065803' b' [assembler.cpp : 243] Number unitigs disconnected: 415910, time: 2.083330' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 78026, time: 1.854357' b' [assembler.cpp : 200] Tips removed: 22790, time: 3.236370' b' [assembler.cpp : 211] Number of bubbles removed: 27653, Time elapsed(sec): 1.720079' b' [assembler.cpp : 225] Number of complex bubbles removed: 18224, Time elapsed(sec): 2.912551' b' [assembler.cpp : 243] Number unitigs disconnected: 56819, time: 1.818912' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 1992, time: 1.742026' b' [assembler.cpp : 200] Tips removed: 19022, time: 3.190164' b' [assembler.cpp : 211] Number of bubbles removed: 2760, Time elapsed(sec): 1.133902' b' [assembler.cpp : 225] Number of complex bubbles removed: 2515, Time elapsed(sec): 2.441142' b' [assembler.cpp : 243] Number unitigs disconnected: 9641, time: 1.751432' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 449, time: 1.728389' b' [assembler.cpp : 200] Tips removed: 1055, time: 3.083773' b' [assembler.cpp : 211] Number of bubbles removed: 46, Time elapsed(sec): 0.923199' b' [assembler.cpp : 225] Number of complex bubbles removed: 127, Time elapsed(sec): 2.357106' b' [assembler.cpp : 243] Number unitigs disconnected: 2458, time: 1.727783' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 126, time: 1.711249' b' [assembler.cpp : 200] Tips removed: 203, time: 3.075768' b' [assembler.cpp : 211] Number of bubbles removed: 4, Time elapsed(sec): 0.913569' b' [assembler.cpp : 225] Number of complex bubbles removed: 40, Time elapsed(sec): 2.338363' b' [assembler.cpp : 243] Number unitigs disconnected: 661, time: 1.752844' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 32, time: 1.751006' b' [assembler.cpp : 132] Total length: 1327717766, N50: 222, Mean: 171, number of contigs: 7741737' b' [assembler.cpp : 133] Maximum length: 248040' b' [assembler.cpp : 290] Time to output: 41.479920' b' [assembler.cpp : 317] Number of local low depth unitigs removed: 129070, complex bubbles removed: 10879, time: 163.375807' b' [assembler.cpp : 132] Total length: 694277860, N50: 288, Mean: 154, number of contigs: 4497740' b' [assembler.cpp : 133] Maximum length: 248040' b' [utils.h : 126] Real: 794.4945\tuser: 16724.1015\tsys: 27.1998\tmaxrss: 6285564' --- [Thu Mar 28 17:17:00 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: 1411634, Mapper size: 83734915' b' [read_lib_functions-inl.h : 256] Before reading, sizeof seq_package: 5679132804' b' [read_lib_functions-inl.h : 260] After reading, sizeof seq_package: 5679132804' b' [local_assembler.cpp : 330] Lib 0, insert size: 255.49 sd: 100.37' b' [local_assembler.cpp : 462] Lib 0: total 167467174 reads, aligned 81213473, added 25006870 reads for local assembly' b' [utils.h : 126] Real: 648.0224\tuser: 17367.4240\tsys: 18.7337\tmaxrss: 10292852' --- [Thu Mar 28 17:27:48 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: 6286796' b' [iterate_edges.cpp : 570] Number of crusial kmers: 14845290' b' [iterate_edges.cpp : 443] Processed: 67108864, aligned: 17608731. Iterative edges: 102339331' b' [iterate_edges.cpp : 443] Processed: 134217728, aligned: 35121542. Iterative edges: 141305551' b' [iterate_edges.cpp : 447] Total: 167467174, aligned: 43916741. Iterative edges: 152811691' b' [iterate_edges.cpp : 451] Writing iterative edges...' b' [utils.h : 126] Real: 251.8367\tuser: 5807.9661\tsys: 11.8982\tmaxrss: 5937772' --- [Thu Mar 28 17:32:00 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: 152811691' b' [cx1_seq2sdbg.cpp : 434] Bases to reserve: 12440295456, number contigs: 16989532, number multiplicity: 169801223' b' [cx1_seq2sdbg.cpp : 440] Before reading, sizeof seq_package: 3245990132, multiplicity vector: 169801223' b' [cx1_seq2sdbg.cpp : 529] After reading, sizeof seq_package: 3245990132, multiplicity vector: 169801223' b' [cx1.h : 457] Preparing data... Done. Time elapsed: 23.8661' b' [cx1.h : 464] Preparing partitions and initialing global data...' b' [cx1_seq2sdbg.cpp : 740] Memory for sequence: 3673782644' b' [cx1_seq2sdbg.cpp : 741] max # lv.1 items = 753506544' b' [cx1.h : 480] Preparing partitions and initialing global data... Done. Time elapsed: 12.3968' b' [cx1.h : 486] Start main loop...' b' [cx1.h : 515] Lv1 scanning from bucket 0 to 832' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 10.7157' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 9.1639' b' [cx1.h : 515] Lv1 scanning from bucket 832 to 3160' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 14.6893' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 12.5200' b' [cx1.h : 515] Lv1 scanning from bucket 3160 to 7057' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 15.2152' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 12.1085' b' [cx1.h : 515] Lv1 scanning from bucket 7057 to 12654' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 16.4193' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 12.6500' b' [cx1.h : 515] Lv1 scanning from bucket 12654 to 20485' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 15.4608' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 13.1829' b' [cx1.h : 515] Lv1 scanning from bucket 20485 to 31374' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 16.1062' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 13.9788' b' [cx1.h : 515] Lv1 scanning from bucket 31374 to 47405' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 16.6486' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 14.4057' b' [cx1.h : 515] Lv1 scanning from bucket 47405 to 65536' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 13.7087' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 9.8251' b' [cx1.h : 607] Main loop done. Time elapsed: 216.8001' 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] 9205565 681419651 426933543 426583664 682459488 1355305 879807 772925 1400778' b' [cx1_seq2sdbg.cpp :1151] Total number of edges: 2231010726' b' [cx1_seq2sdbg.cpp :1152] Total number of ONEs: 2217396346' b' [cx1_seq2sdbg.cpp :1153] Total number of $v edges: 9205565' b' [cx1.h : 621] Postprocess done. Time elapsed: 0.0707' b' [utils.h : 126] Real: 253.1461\tuser: 3031.6659\tsys: 22.0039\tmaxrss: 6668048' --- [Thu Mar 28 17:36:14 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: 132.424667' b' [assembler.cpp : 152] Number of Edges: 2231010726; 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: 93584; time elapsed: 6.3740' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 4; Accumulated tips removed: 308961; time elapsed: 7.0983' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 8; Accumulated tips removed: 647520; time elapsed: 9.7629' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 16; Accumulated tips removed: 1167075; time elapsed: 15.8016' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 32; Accumulated tips removed: 1760707; time elapsed: 26.5370' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 64; Accumulated tips removed: 4301958; time elapsed: 46.3745' b' [assembly_algorithms.cpp : 170] Removing tips with length less than 118; Accumulated tips removed: 8447552; time elapsed: 49.3088' b' [assembler.cpp : 179] Tips removal done! Time elapsed(sec): 161.340482' b' [assembler.cpp : 188] unitig graph size: 5340408, time for building: 110.893561' b' [assembler.cpp : 211] Number of bubbles removed: 829072, Time elapsed(sec): 21.588412' b' [assembler.cpp : 225] Number of complex bubbles removed: 208322, Time elapsed(sec): 9.183193' b' [assembler.cpp : 243] Number unitigs disconnected: 357144, time: 1.317716' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 104394, time: 1.319604' b' [assembler.cpp : 200] Tips removed: 5990, time: 1.221375' b' [assembler.cpp : 211] Number of bubbles removed: 24102, Time elapsed(sec): 1.349287' b' [assembler.cpp : 225] Number of complex bubbles removed: 18010, Time elapsed(sec): 1.768781' b' [assembler.cpp : 243] Number unitigs disconnected: 38716, time: 1.042957' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 1858, time: 1.139412' b' [assembler.cpp : 200] Tips removed: 13585, time: 1.209728' b' [assembler.cpp : 211] Number of bubbles removed: 1452, Time elapsed(sec): 0.451938' b' [assembler.cpp : 225] Number of complex bubbles removed: 1993, Time elapsed(sec): 1.069492' b' [assembler.cpp : 243] Number unitigs disconnected: 5237, time: 1.000161' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 366, time: 1.139930' b' [assembler.cpp : 200] Tips removed: 528, time: 1.165897' b' [assembler.cpp : 211] Number of bubbles removed: 54, Time elapsed(sec): 0.343468' b' [assembler.cpp : 225] Number of complex bubbles removed: 117, Time elapsed(sec): 0.957584' b' [assembler.cpp : 243] Number unitigs disconnected: 1112, time: 0.991303' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 99, time: 1.140854' b' [assembler.cpp : 200] Tips removed: 68, time: 1.171135' b' [assembler.cpp : 211] Number of bubbles removed: 2, Time elapsed(sec): 0.345943' b' [assembler.cpp : 225] Number of complex bubbles removed: 29, Time elapsed(sec): 0.954348' b' [assembler.cpp : 243] Number unitigs disconnected: 243, time: 0.996199' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 40, time: 1.139994' b' [assembler.cpp : 132] Total length: 991101317, N50: 550, Mean: 342, number of contigs: 2891718' b' [assembler.cpp : 133] Maximum length: 501086' b' [assembler.cpp : 290] Time to output: 31.439432' b' [assembler.cpp : 317] Number of local low depth unitigs removed: 69225, complex bubbles removed: 5048, time: 105.793639' b' [assembler.cpp : 132] Total length: 471447391, N50: 683, Mean: 310, number of contigs: 1519643' b' [assembler.cpp : 133] Maximum length: 501086' b' [utils.h : 126] Real: 610.8106\tuser: 12229.2153\tsys: 25.7413\tmaxrss: 5841856' --- [Thu Mar 28 17:46:25 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: 1453614, Mapper size: 96974140' b' [read_lib_functions-inl.h : 256] Before reading, sizeof seq_package: 5679132804' b' [read_lib_functions-inl.h : 260] After reading, sizeof seq_package: 5679132804' b' [local_assembler.cpp : 330] Lib 0, insert size: 260.93 sd: 103.69' b' [local_assembler.cpp : 462] Lib 0: total 167467174 reads, aligned 88224953, added 21188468 reads for local assembly' b' [utils.h : 126] Real: 660.9358\tuser: 17701.1273\tsys: 16.5693\tmaxrss: 10667088' --- [Thu Mar 28 17:57:26 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: 2820497' b' [iterate_edges.cpp : 570] Number of crusial kmers: 5762489' b' [iterate_edges.cpp : 443] Processed: 67108864, aligned: 7378679. Iterative edges: 30835024' b' [iterate_edges.cpp : 443] Processed: 134217728, aligned: 14623485. Iterative edges: 43210946' b' [iterate_edges.cpp : 447] Total: 167467174, aligned: 18324500. Iterative edges: 47119914' b' [iterate_edges.cpp : 451] Writing iterative edges...' b' [utils.h : 126] Real: 154.5630\tuser: 3730.4894\tsys: 6.4823\tmaxrss: 2287788' --- [Thu Mar 28 18:00:01 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: 47119914' b' [cx1_seq2sdbg.cpp : 434] Bases to reserve: 6245835264, number contigs: 7176721, number multiplicity: 54296635' b' [cx1_seq2sdbg.cpp : 440] Before reading, sizeof seq_package: 1618872596, multiplicity vector: 54296635' b' [cx1_seq2sdbg.cpp : 529] After reading, sizeof seq_package: 3180331416, multiplicity vector: 54296635' b' [cx1.h : 457] Preparing data... Done. Time elapsed: 13.0133' b' [cx1.h : 464] Preparing partitions and initialing global data...' b' [cx1_seq2sdbg.cpp : 740] Memory for sequence: 3336550176' b' [cx1_seq2sdbg.cpp : 741] max # lv.1 items = 575910502' b' [cx1.h : 480] Preparing partitions and initialing global data... Done. Time elapsed: 7.2148' b' [cx1.h : 486] Start main loop...' b' [cx1.h : 515] Lv1 scanning from bucket 0 to 696' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 6.1480' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 6.6060' b' [cx1.h : 515] Lv1 scanning from bucket 696 to 2830' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 8.0035' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 9.7682' b' [cx1.h : 515] Lv1 scanning from bucket 2830 to 6491' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 8.2663' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 9.4689' b' [cx1.h : 515] Lv1 scanning from bucket 6491 to 11819' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 8.3930' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 9.7997' b' [cx1.h : 515] Lv1 scanning from bucket 11819 to 19315' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 8.8172' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 10.5065' b' [cx1.h : 515] Lv1 scanning from bucket 19315 to 29815' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 9.2576' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 10.7280' b' [cx1.h : 515] Lv1 scanning from bucket 29815 to 45462' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 9.3792' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 11.0488' b' [cx1.h : 515] Lv1 scanning from bucket 45462 to 65536' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 7.2457' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 8.6173' b' [cx1.h : 607] Main loop done. Time elapsed: 142.0552' 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] 4285507 559712233 338161590 337986065 560279834 660183 361312 415982 639799' b' [cx1_seq2sdbg.cpp :1151] Total number of edges: 1802502505' b' [cx1_seq2sdbg.cpp :1152] Total number of ONEs: 1796139722' b' [cx1_seq2sdbg.cpp :1153] Total number of $v edges: 4285507' b' [cx1.h : 621] Postprocess done. Time elapsed: 0.0381' b' [utils.h : 126] Real: 162.3273\tuser: 2341.4219\tsys: 15.4313\tmaxrss: 4210688' --- [Thu Mar 28 18:02:43 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: 105.169242' b' [assembler.cpp : 152] Number of Edges: 1802502505; 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: 43670; time elapsed: 5.0509' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 4; Accumulated tips removed: 144831; time elapsed: 5.2956' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 8; Accumulated tips removed: 315491; time elapsed: 6.4557' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 16; Accumulated tips removed: 604414; time elapsed: 9.1281' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 32; Accumulated tips removed: 915394; time elapsed: 13.7590' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 64; Accumulated tips removed: 1651966; time elapsed: 22.6436' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 128; Accumulated tips removed: 2996470; time elapsed: 34.3857' b' [assembly_algorithms.cpp : 170] Removing tips with length less than 158; Accumulated tips removed: 3485437; time elapsed: 31.9812' b' [assembler.cpp : 179] Tips removal done! Time elapsed(sec): 128.767840' b' [assembler.cpp : 188] unitig graph size: 2601908, time for building: 90.146895' b' [assembler.cpp : 211] Number of bubbles removed: 346361, Time elapsed(sec): 14.580253' b' [assembler.cpp : 225] Number of complex bubbles removed: 88845, Time elapsed(sec): 5.959774' b' [assembler.cpp : 243] Number unitigs disconnected: 198462, time: 0.528387' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 66952, time: 0.471723' b' [assembler.cpp : 200] Tips removed: 3308, time: 0.715550' b' [assembler.cpp : 211] Number of bubbles removed: 12284, Time elapsed(sec): 0.948583' b' [assembler.cpp : 225] Number of complex bubbles removed: 9856, Time elapsed(sec): 1.178477' b' [assembler.cpp : 243] Number unitigs disconnected: 13730, time: 0.288240' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 1158, time: 0.256202' b' [assembler.cpp : 200] Tips removed: 6841, time: 0.687171' b' [assembler.cpp : 211] Number of bubbles removed: 527, Time elapsed(sec): 0.213267' b' [assembler.cpp : 225] Number of complex bubbles removed: 849, Time elapsed(sec): 0.577507' b' [assembler.cpp : 243] Number unitigs disconnected: 1218, time: 0.273575' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 150, time: 0.255717' b' [assembler.cpp : 200] Tips removed: 185, time: 0.666422' b' [assembler.cpp : 211] Number of bubbles removed: 12, Time elapsed(sec): 0.167616' b' [assembler.cpp : 225] Number of complex bubbles removed: 23, Time elapsed(sec): 0.502362' b' [assembler.cpp : 243] Number unitigs disconnected: 226, time: 0.270039' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 51, time: 0.252025' b' [assembler.cpp : 200] Tips removed: 28, time: 0.657456' b' [assembler.cpp : 211] Number of bubbles removed: 2, Time elapsed(sec): 0.160986' b' [assembler.cpp : 225] Number of complex bubbles removed: 4, Time elapsed(sec): 0.501274' b' [assembler.cpp : 243] Number unitigs disconnected: 48, time: 0.269451' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 14, time: 0.249696' b' [assembler.cpp : 132] Total length: 861066221, N50: 894, Mean: 580, number of contigs: 1482620' b' [assembler.cpp : 133] Maximum length: 891947' b' [assembler.cpp : 290] Time to output: 27.518962' b' [assembler.cpp : 317] Number of local low depth unitigs removed: 24155, complex bubbles removed: 2060, time: 18.472643' b' [assembler.cpp : 132] Total length: 310786932, N50: 1211, Mean: 530, number of contigs: 585548' b' [assembler.cpp : 133] Maximum length: 891947' b' [utils.h : 126] Real: 410.6558\tuser: 7757.1248\tsys: 17.4639\tmaxrss: 4698692' --- [Thu Mar 28 18:09:34 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: 1153041, Mapper size: 97046199' b' [read_lib_functions-inl.h : 256] Before reading, sizeof seq_package: 5679132804' b' [read_lib_functions-inl.h : 260] After reading, sizeof seq_package: 5679132804' b' [local_assembler.cpp : 330] Lib 0, insert size: 266.46 sd: 106.38' b' [local_assembler.cpp : 462] Lib 0: total 167467174 reads, aligned 85399834, added 14090912 reads for local assembly' b' [utils.h : 126] Real: 455.9337\tuser: 12113.0188\tsys: 14.9711\tmaxrss: 10219656' --- [Thu Mar 28 18:17:11 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: 1127624' b' [iterate_edges.cpp : 570] Number of crusial kmers: 2225333' b' [iterate_edges.cpp : 443] Processed: 67108864, aligned: 2502211. Iterative edges: 9412072' b' [iterate_edges.cpp : 443] Processed: 134217728, aligned: 4952151. Iterative edges: 13847348' b' [iterate_edges.cpp : 447] Total: 167467174, aligned: 6216668. Iterative edges: 15412048' b' [iterate_edges.cpp : 451] Writing iterative edges...' b' [utils.h : 126] Real: 85.3374\tuser: 2050.0099\tsys: 4.5771\tmaxrss: 1131372' --- [Thu Mar 28 18:18:36 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: 15412048' b' [cx1_seq2sdbg.cpp : 434] Bases to reserve: 3162892334, number contigs: 3063788, number multiplicity: 18475836' b' [cx1_seq2sdbg.cpp : 440] Before reading, sizeof seq_package: 815233396, multiplicity vector: 18475836' b' [cx1_seq2sdbg.cpp : 529] After reading, sizeof seq_package: 1630466792, multiplicity vector: 36951672' b' [cx1.h : 457] Preparing data... Done. Time elapsed: 9.4504' b' [cx1.h : 464] Preparing partitions and initialing global data...' b' [cx1_seq2sdbg.cpp : 740] Memory for sequence: 1694460744' b' [cx1_seq2sdbg.cpp : 741] max # lv.1 items = 427169581' b' [cx1.h : 480] Preparing partitions and initialing global data... Done. Time elapsed: 3.8281' b' [cx1.h : 486] Start main loop...' b' [cx1.h : 515] Lv1 scanning from bucket 0 to 611' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 3.2155' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 4.4900' b' [cx1.h : 515] Lv1 scanning from bucket 611 to 2631' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 4.0256' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 7.1245' b' [cx1.h : 515] Lv1 scanning from bucket 2631 to 6167' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 4.3384' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 7.2151' b' [cx1.h : 515] Lv1 scanning from bucket 6167 to 11370' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 4.6704' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 7.7581' b' [cx1.h : 515] Lv1 scanning from bucket 11370 to 18703' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 5.4555' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 8.2358' b' [cx1.h : 515] Lv1 scanning from bucket 18703 to 29002' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 4.8779' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 8.7144' b' [cx1.h : 515] Lv1 scanning from bucket 29002 to 44337' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 4.9642' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 8.7247' b' [cx1.h : 515] Lv1 scanning from bucket 44337 to 65536' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 4.4719' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 6.9601' b' [cx1.h : 607] Main loop done. Time elapsed: 95.2431' 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] 2686294 488042302 290805161 290677784 488429979 263392 144960 144899 261722' b' [cx1_seq2sdbg.cpp :1151] Total number of edges: 1561456493' b' [cx1_seq2sdbg.cpp :1152] Total number of ONEs: 1557955226' b' [cx1_seq2sdbg.cpp :1153] Total number of $v edges: 2686294' b' [cx1.h : 621] Postprocess done. Time elapsed: 0.0365' b' [utils.h : 126] Real: 108.5614\tuser: 1811.6174\tsys: 10.4527\tmaxrss: 2801744' --- [Thu Mar 28 18:20:25 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: 87.747295' b' [assembler.cpp : 152] Number of Edges: 1561456493; 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: 20654; time elapsed: 4.3519' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 4; Accumulated tips removed: 69788; time elapsed: 4.4055' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 8; Accumulated tips removed: 157828; time elapsed: 5.1740' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 16; Accumulated tips removed: 310408; time elapsed: 6.7669' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 32; Accumulated tips removed: 466684; time elapsed: 9.9313' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 64; Accumulated tips removed: 671681; time elapsed: 15.4290' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 128; Accumulated tips removed: 1147328; time elapsed: 25.5088' b' [assembly_algorithms.cpp : 170] Removing tips with length less than 198; Accumulated tips removed: 1662623; time elapsed: 31.9054' b' [assembler.cpp : 179] Tips removal done! Time elapsed(sec): 103.532315' b' [assembler.cpp : 188] unitig graph size: 1322527, time for building: 79.790077' b' [assembler.cpp : 211] Number of bubbles removed: 117403, Time elapsed(sec): 8.010582' b' [assembler.cpp : 225] Number of complex bubbles removed: 26420, Time elapsed(sec): 2.688257' b' [assembler.cpp : 243] Number unitigs disconnected: 71368, time: 0.308835' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 23713, time: 0.341407' b' [assembler.cpp : 200] Tips removed: 1060, time: 0.409337' b' [assembler.cpp : 211] Number of bubbles removed: 3332, Time elapsed(sec): 0.534131' b' [assembler.cpp : 225] Number of complex bubbles removed: 3670, Time elapsed(sec): 0.799423' b' [assembler.cpp : 243] Number unitigs disconnected: 4046, time: 0.206887' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 320, time: 0.246092' b' [assembler.cpp : 200] Tips removed: 1828, time: 0.402994' b' [assembler.cpp : 211] Number of bubbles removed: 118, Time elapsed(sec): 0.157864' b' [assembler.cpp : 225] Number of complex bubbles removed: 280, Time elapsed(sec): 0.317829' b' [assembler.cpp : 243] Number unitigs disconnected: 310, time: 0.201752' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 41, time: 0.271407' b' [assembler.cpp : 200] Tips removed: 41, time: 0.394391' b' [assembler.cpp : 211] Number of bubbles removed: 4, Time elapsed(sec): 0.095504' b' [assembler.cpp : 225] Number of complex bubbles removed: 10, Time elapsed(sec): 0.280438' b' [assembler.cpp : 243] Number unitigs disconnected: 49, time: 0.230707' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 6, time: 0.280566' b' [assembler.cpp : 200] Tips removed: 3, time: 0.392800' b' [assembler.cpp : 211] Number of bubbles removed: 0, Time elapsed(sec): 0.096129' b' [assembler.cpp : 225] Number of complex bubbles removed: 2, Time elapsed(sec): 0.276280' b' [assembler.cpp : 243] Number unitigs disconnected: 5, time: 0.229464' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 2, time: 0.285153' b' [assembler.cpp : 132] Total length: 789281015, N50: 1189, Mean: 830, number of contigs: 950351' b' [assembler.cpp : 133] Maximum length: 893392' b' [assembler.cpp : 290] Time to output: 25.221736' b' [assembler.cpp : 317] Number of local low depth unitigs removed: 6637, complex bubbles removed: 642, time: 23.671769' b' [assembler.cpp : 132] Total length: 177203014, N50: 2299, Mean: 858, number of contigs: 206437' b' [assembler.cpp : 133] Maximum length: 893392' b' [utils.h : 126] Real: 343.7849\tuser: 6540.0710\tsys: 14.2967\tmaxrss: 4091312' --- [Thu Mar 28 18:26:09 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: 859474, Mapper size: 92831062' b' [read_lib_functions-inl.h : 256] Before reading, sizeof seq_package: 5679132804' b' [read_lib_functions-inl.h : 260] After reading, sizeof seq_package: 5679132804' b' [local_assembler.cpp : 330] Lib 0, insert size: 269.95 sd: 108.14' b' [local_assembler.cpp : 462] Lib 0: total 167467174 reads, aligned 83232627, added 9674125 reads for local assembly' b' [utils.h : 126] Real: 386.8686\tuser: 10204.1412\tsys: 12.5625\tmaxrss: 9709996' --- [Thu Mar 28 18:32:36 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: 322248' b' [iterate_edges.cpp : 570] Number of crusial kmers: 664849' b' [iterate_edges.cpp : 443] Processed: 67108864, aligned: 538662. Iterative edges: 1473198' b' [iterate_edges.cpp : 443] Processed: 134217728, aligned: 1064883. Iterative edges: 2352572' b' [iterate_edges.cpp : 447] Total: 167467174, aligned: 1338280. Iterative edges: 2704438' b' [iterate_edges.cpp : 451] Writing iterative edges...' b' [utils.h : 126] Real: 39.3245\tuser: 911.9733\tsys: 3.3792\tmaxrss: 544172' --- [Thu Mar 28 18:33:15 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: 2704438' b' [cx1_seq2sdbg.cpp : 434] Bases to reserve: 1282716818, number contigs: 1330316, number multiplicity: 4034754' b' [cx1_seq2sdbg.cpp : 440] Before reading, sizeof seq_package: 331321744, multiplicity vector: 4034754' b' [cx1_seq2sdbg.cpp : 529] After reading, sizeof seq_package: 662643488, multiplicity vector: 8069508' b' [cx1.h : 457] Preparing data... Done. Time elapsed: 5.5732' b' [cx1.h : 464] Preparing partitions and initialing global data...' b' [cx1_seq2sdbg.cpp : 740] Memory for sequence: 685246232' b' [cx1_seq2sdbg.cpp : 741] max # lv.1 items = 318689326' b' [cx1.h : 480] Preparing partitions and initialing global data... Done. Time elapsed: 1.6522' b' [cx1.h : 486] Start main loop...' b' [cx1.h : 515] Lv1 scanning from bucket 0 to 464' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 1.3594' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 3.1330' b' [cx1.h : 515] Lv1 scanning from bucket 464 to 2279' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 1.4458' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 5.6374' b' [cx1.h : 515] Lv1 scanning from bucket 2279 to 5609' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 1.7456' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 5.9237' b' [cx1.h : 515] Lv1 scanning from bucket 5609 to 10639' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 1.7177' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 6.2499' b' [cx1.h : 515] Lv1 scanning from bucket 10639 to 17776' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 1.8641' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 6.5321' b' [cx1.h : 515] Lv1 scanning from bucket 17776 to 27844' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 1.9795' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 6.8919' b' [cx1.h : 515] Lv1 scanning from bucket 27844 to 42683' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 2.1689' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 7.1270' b' [cx1.h : 515] Lv1 scanning from bucket 42683 to 65536' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 2.0611' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 6.0946' b' [cx1.h : 607] Main loop done. Time elapsed: 61.9326' 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] 1953864 442599712 262183486 262090549 442895303 82972 56060 48826 85996' b' [cx1_seq2sdbg.cpp :1151] Total number of edges: 1411996768' b' [cx1_seq2sdbg.cpp :1152] Total number of ONEs: 1409769050' b' [cx1_seq2sdbg.cpp :1153] Total number of $v edges: 1953864' b' [cx1.h : 621] Postprocess done. Time elapsed: 0.0340' b' [utils.h : 126] Real: 69.1941\tuser: 1441.3852\tsys: 7.9194\tmaxrss: 1912200' --- [Thu Mar 28 18:34:24 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: 71.706974' b' [assembler.cpp : 152] Number of Edges: 1411996768; 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: 11704; time elapsed: 3.8587' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 4; Accumulated tips removed: 40886; time elapsed: 3.9166' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 8; Accumulated tips removed: 95582; time elapsed: 4.4591' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 16; Accumulated tips removed: 210990; time elapsed: 5.5860' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 32; Accumulated tips removed: 274644; time elapsed: 7.7699' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 64; Accumulated tips removed: 357261; time elapsed: 12.1775' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 128; Accumulated tips removed: 544442; time elapsed: 19.9344' b' [assembly_algorithms.cpp : 170] Removing tips with length less than 182; Accumulated tips removed: 603482; time elapsed: 25.2836' b' [assembler.cpp : 179] Tips removal done! Time elapsed(sec): 83.040027' b' [assembler.cpp : 188] unitig graph size: 954746, time for building: 78.836343' b' [assembler.cpp : 211] Number of bubbles removed: 34140, Time elapsed(sec): 1.730522' b' [assembler.cpp : 225] Number of complex bubbles removed: 5002, Time elapsed(sec): 0.701171' b' [assembler.cpp : 243] Number unitigs disconnected: 24677, time: 0.187728' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 6675, time: 0.161785' b' [assembler.cpp : 200] Tips removed: 310, time: 0.336856' b' [assembler.cpp : 211] Number of bubbles removed: 358, Time elapsed(sec): 0.193640' b' [assembler.cpp : 225] Number of complex bubbles removed: 804, Time elapsed(sec): 0.539539' b' [assembler.cpp : 243] Number unitigs disconnected: 1395, time: 0.125554' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 89, time: 0.126292' b' [assembler.cpp : 200] Tips removed: 473, time: 0.336392' b' [assembler.cpp : 211] Number of bubbles removed: 40, Time elapsed(sec): 0.115436' b' [assembler.cpp : 225] Number of complex bubbles removed: 63, Time elapsed(sec): 0.204452' b' [assembler.cpp : 243] Number unitigs disconnected: 89, time: 0.118673' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 13, time: 0.125106' b' [assembler.cpp : 200] Tips removed: 4, time: 0.337842' b' [assembler.cpp : 211] Number of bubbles removed: 0, Time elapsed(sec): 0.084017' b' [assembler.cpp : 225] Number of complex bubbles removed: 3, Time elapsed(sec): 0.179351' b' [assembler.cpp : 243] Number unitigs disconnected: 9, time: 0.113985' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 5, time: 0.124743' b' [assembler.cpp : 200] Tips removed: 1, time: 0.329878' b' [assembler.cpp : 211] Number of bubbles removed: 0, Time elapsed(sec): 0.080981' b' [assembler.cpp : 225] Number of complex bubbles removed: 0, Time elapsed(sec): 0.176525' b' [assembler.cpp : 243] Number unitigs disconnected: 0, time: 0.114317' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 2, time: 0.125057' b' [assembler.cpp : 132] Total length: 785145167, N50: 1294, Mean: 920, number of contigs: 853153' b' [assembler.cpp : 133] Maximum length: 968757' b' [assembler.cpp : 290] Time to output: 25.064489' b' [assembler.cpp : 317] Number of local low depth unitigs removed: 1223, complex bubbles removed: 84, time: 7.404922' b' [assembler.cpp : 132] Total length: 108500425, N50: 4816, Mean: 1203, number of contigs: 90164' b' [assembler.cpp : 133] Maximum length: 968757' b' [utils.h : 126] Real: 277.5230\tuser: 5176.9176\tsys: 12.9718\tmaxrss: 3719628' --- [Thu Mar 28 18:39:02 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: 811288, Mapper size: 93176540' b' [read_lib_functions-inl.h : 256] Before reading, sizeof seq_package: 5679132804' b' [read_lib_functions-inl.h : 260] After reading, sizeof seq_package: 5679132804' b' [local_assembler.cpp : 330] Lib 0, insert size: 270.49 sd: 108.62' b' [local_assembler.cpp : 462] Lib 0: total 167467174 reads, aligned 81944264, added 7989803 reads for local assembly' b' [utils.h : 126] Real: 328.1000\tuser: 8585.4338\tsys: 12.5040\tmaxrss: 9649304' --- [Thu Mar 28 18:44:30 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: 35816' b' [iterate_edges.cpp : 570] Number of crusial kmers: 144920' 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: 167467174, aligned: 0. Iterative edges: 0' b' [utils.h : 126] Real: 16.5204\tuser: 21.5366\tsys: 2.9536\tmaxrss: 408648' --- [Thu Mar 28 18:44:47 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: 537961332, number contigs: 751701, number multiplicity: 751701' b' [cx1_seq2sdbg.cpp : 440] Before reading, sizeof seq_package: 140503952, multiplicity vector: 751701' b' [cx1_seq2sdbg.cpp : 529] After reading, sizeof seq_package: 549988576, multiplicity vector: 1503402' b' [cx1.h : 457] Preparing data... Done. Time elapsed: 3.9975' b' [cx1.h : 464] Preparing partitions and initialing global data...' b' [cx1_seq2sdbg.cpp : 740] Memory for sequence: 561502608' b' [cx1_seq2sdbg.cpp : 741] max # lv.1 items = 243435067' b' [cx1.h : 480] Preparing partitions and initialing global data... Done. Time elapsed: 0.6400' b' [cx1.h : 486] Start main loop...' b' [cx1.h : 515] Lv1 scanning from bucket 0 to 333' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 0.4579' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 2.2100' b' [cx1.h : 515] Lv1 scanning from bucket 333 to 1924' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 0.5370' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 4.6596' b' [cx1.h : 515] Lv1 scanning from bucket 1924 to 4964' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 0.5482' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 5.0547' b' [cx1.h : 515] Lv1 scanning from bucket 4964 to 9713' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 0.6153' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 5.6532' b' [cx1.h : 515] Lv1 scanning from bucket 9713 to 16522' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 0.6197' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 5.7189' b' [cx1.h : 515] Lv1 scanning from bucket 16522 to 26234' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 0.6319' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 5.9848' b' [cx1.h : 515] Lv1 scanning from bucket 26234 to 40500' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 0.6305' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 6.2354' b' [cx1.h : 515] Lv1 scanning from bucket 40500 to 65536' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 0.6217' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 6.1487' b' [cx1.h : 607] Main loop done. Time elapsed: 46.3282' 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] 1643543 426257597 252227256 252167327 426549108 38067 21452 21315 37947' b' [cx1_seq2sdbg.cpp :1151] Total number of edges: 1358963612' b' [cx1_seq2sdbg.cpp :1152] Total number of ONEs: 1357201288' b' [cx1_seq2sdbg.cpp :1153] Total number of $v edges: 1643543' b' [cx1.h : 621] Postprocess done. Time elapsed: 0.0341' b' [utils.h : 126] Real: 51.0015\tuser: 1255.1640\tsys: 6.2238\tmaxrss: 1431308' --- [Thu Mar 28 18:45:38 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: 70.030123' b' [assembler.cpp : 152] Number of Edges: 1358963612; 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: 2058; time elapsed: 3.6878' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 4; Accumulated tips removed: 6484; time elapsed: 3.7862' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 8; Accumulated tips removed: 15150; time elapsed: 4.2145' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 16; Accumulated tips removed: 31038; time elapsed: 5.3849' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 32; Accumulated tips removed: 59050; time elapsed: 7.3175' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 64; Accumulated tips removed: 101342; time elapsed: 11.3990' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 128; Accumulated tips removed: 149097; time elapsed: 18.5958' b' [assembly_algorithms.cpp : 170] Removing tips with length less than 160; Accumulated tips removed: 160949; time elapsed: 22.7701' b' [assembler.cpp : 179] Tips removal done! Time elapsed(sec): 77.208694' b' [assembler.cpp : 188] unitig graph size: 893106, time for building: 77.576794' b' [assembler.cpp : 211] Number of bubbles removed: 22521, Time elapsed(sec): 0.178348' b' [assembler.cpp : 225] Number of complex bubbles removed: 2327, Time elapsed(sec): 0.221640' b' [assembler.cpp : 243] Number unitigs disconnected: 12717, time: 0.205713' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 2732, time: 0.136171' b' [assembler.cpp : 200] Tips removed: 250, time: 0.328645' b' [assembler.cpp : 211] Number of bubbles removed: 58, Time elapsed(sec): 0.079252' b' [assembler.cpp : 225] Number of complex bubbles removed: 252, Time elapsed(sec): 0.158364' b' [assembler.cpp : 243] Number unitigs disconnected: 763, time: 0.156372' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 27, time: 0.120269' b' [assembler.cpp : 200] Tips removed: 159, time: 0.333713' b' [assembler.cpp : 211] Number of bubbles removed: 8, Time elapsed(sec): 0.079796' b' [assembler.cpp : 225] Number of complex bubbles removed: 25, Time elapsed(sec): 0.148726' b' [assembler.cpp : 243] Number unitigs disconnected: 31, time: 0.152258' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 7, time: 0.120843' b' [assembler.cpp : 200] Tips removed: 3, time: 0.326545' b' [assembler.cpp : 211] Number of bubbles removed: 0, Time elapsed(sec): 0.080083' b' [assembler.cpp : 225] Number of complex bubbles removed: 0, Time elapsed(sec): 0.143358' b' [assembler.cpp : 243] Number unitigs disconnected: 1, time: 0.151371' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 3, time: 0.119658' b' [assembler.cpp : 200] Tips removed: 0, time: 0.328316' b' [assembler.cpp : 211] Number of bubbles removed: 0, Time elapsed(sec): 0.082153' b' [assembler.cpp : 225] Number of complex bubbles removed: 0, Time elapsed(sec): 0.147762' b' [assembler.cpp : 243] Number unitigs disconnected: 0, time: 0.152235' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 0, time: 0.074320' b' [assembler.cpp : 317] Number of local low depth unitigs removed: 367, complex bubbles removed: 5, time: 5.936644' b' [assembler.cpp : 132] Total length: 788649359, N50: 1321, Mean: 944, number of contigs: 834948' b' [assembler.cpp : 133] Maximum length: 2036122' b' [utils.h : 126] Real: 259.4253\tuser: 4787.1536\tsys: 13.7856\tmaxrss: 3607620' --- [Thu Mar 28 18:49:57 2019] Merging to output final contigs --- --- [STAT] 812928 contigs, total 784622124 bp, min 200 bp, max 2036122 bp, avg 965 bp, N50 1330 bp --- [Thu Mar 28 18:50:01 2019] ALL DONE. Time elapsed: 11833.579602 seconds ---