MEGAHIT v1.1.3 --- [Thu Mar 28 19:55:06 2019] Start assembly. Number of CPU threads 28 --- --- [Thu Mar 28 19:55:06 2019] Available memory: 269759385600, used: 242783447040 --- [Thu Mar 28 19:55:06 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_5_S6_L002_R1_001_val_1_val_1_val_1.fq.gz,/gscratch/srlab/sam/data/metagenomics/P_generosa/Library_Geoduck_MG_5_S6_L002_R2_001_val_2_val_2_val_2.fq.gz): pe, 141110330 reads, 131 max length' b' [utils.h : 126] Real: 147.8093\tuser: 135.0187\tsys: 12.0106\tmaxrss: 153816' --- [Thu Mar 28 19:57:34 2019] k list: 21,29,39,59,79,99,119,141 --- --- [Thu Mar 28 19:57:34 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: 5157212184' b' [read_lib_functions-inl.h : 260] After reading, sizeof seq_package: 5157212184' b' [cx1_kmer_count.cpp : 136] 141110330 reads, 131 max read length' b' [cx1.h : 457] Preparing data... Done. Time elapsed: 19.9192' 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: 7418014456, 237143679972' b' [cx1_kmer_count.cpp : 356] 1753372318, 16855216 7418014456 237143679972' b' [cx1_kmer_count.cpp : 363] Memory for reads: 5283097512' b' [cx1_kmer_count.cpp : 364] max # lv.1 items = 1753372318' b' [cx1.h : 480] Preparing partitions and initialing global data... Done. Time elapsed: 7.5208' b' [cx1.h : 486] Start main loop...' b' [cx1.h : 515] Lv1 scanning from bucket 0 to 190' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 7.2050' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 9.7176' b' [cx1.h : 515] Lv1 scanning from bucket 190 to 1110' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 7.6810' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 21.2360' b' [cx1.h : 515] Lv1 scanning from bucket 1110 to 3033' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 7.9068' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 25.0423' b' [cx1.h : 515] Lv1 scanning from bucket 3033 to 6233' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 8.1703' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 26.1504' b' [cx1.h : 515] Lv1 scanning from bucket 6233 to 11129' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 8.4349' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 25.7912' b' [cx1.h : 515] Lv1 scanning from bucket 11129 to 18496' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 8.6783' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 25.3974' b' [cx1.h : 515] Lv1 scanning from bucket 18496 to 30074' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 8.9505' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 25.0522' b' [cx1.h : 515] Lv1 scanning from bucket 30074 to 52848' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 9.2745' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 25.8242' b' [cx1.h : 515] Lv1 scanning from bucket 52848 to 65536' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 7.1622' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 5.0490' b' [cx1.h : 607] Main loop done. Time elapsed: 262.7252' b' [cx1.h : 613] Postprocessing...' b' [cx1_kmer_count.cpp : 860] Total number of candidate reads: 4133612(13834014)' b' [cx1_kmer_count.cpp : 871] Total number of solid edges: 956808482' b' [cx1.h : 621] Postprocess done. Time elapsed: 3.0375' b' [utils.h : 126] Real: 293.2260\tuser: 7435.7341\tsys: 25.0210\tmaxrss: 13583808' --- [Thu Mar 28 20:02:27 2019] Building graph for k = 21 --- /gscratch/srlab/programs/megahit_v1.1.4_LINUX_CPUONLY_x86_64-bin/megahit_sdbg_build seq2sdbg --host_mem 242783447040 --mem_flag 1 --gpu_mem 0 --output_prefix ./megahit_out/tmp/k21/21 --num_cpu_threads 28 -k 21 --kmer_from 0 --num_edge_files 9 --input_prefix ./megahit_out/tmp/k21/21 --need_mercy b' [sdbg_builder.cpp : 339] Host memory to be used: 242783447040' b' [sdbg_builder.cpp : 340] Number CPU threads: 28' b' [cx1.h : 450] Preparing data...' b' [cx1_seq2sdbg.cpp : 394] Number edges: 956808482' b' [cx1_seq2sdbg.cpp : 434] Bases to reserve: 26312233244, number contigs: 0, number multiplicity: 1196010602' b' [cx1_seq2sdbg.cpp : 440] Before reading, sizeof seq_package: 6578058320, multiplicity vector: 1196010602' b' [cx1_seq2sdbg.cpp : 455] Adding mercy edges...' b' [cx1_seq2sdbg.cpp : 373] Number of reads: 4133612, Number of mercy edges: 54404468' b' [cx1_seq2sdbg.cpp : 462] Done. Time elapsed: 50.7943' b' [cx1_seq2sdbg.cpp : 529] After reading, sizeof seq_package: 6578058320, multiplicity vector: 1196010602' b' [cx1.h : 457] Preparing data... Done. Time elapsed: 200.5173' b' [cx1.h : 464] Preparing partitions and initialing global data...' b' [cx1_seq2sdbg.cpp : 740] Memory for sequence: 8774286476' b' [cx1_seq2sdbg.cpp : 741] max # lv.1 items = 808970360' b' [cx1.h : 480] Preparing partitions and initialing global data... Done. Time elapsed: 2.1882' b' [cx1.h : 486] Start main loop...' b' [cx1.h : 515] Lv1 scanning from bucket 0 to 721' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 1.8987' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 6.5782' b' [cx1.h : 515] Lv1 scanning from bucket 721 to 2850' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 1.9896' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 8.3702' b' [cx1.h : 515] Lv1 scanning from bucket 2850 to 6487' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 2.0377' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 8.4413' b' [cx1.h : 515] Lv1 scanning from bucket 6487 to 11852' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 2.0214' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 8.6146' b' [cx1.h : 515] Lv1 scanning from bucket 11852 to 19467' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 2.0638' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 9.0182' b' [cx1.h : 515] Lv1 scanning from bucket 19467 to 30284' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 2.1026' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 9.3545' b' [cx1.h : 515] Lv1 scanning from bucket 30284 to 46390' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 2.2126' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 9.5676' b' [cx1.h : 515] Lv1 scanning from bucket 46390 to 65536' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 2.0800' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 6.7378' b' [cx1.h : 607] Main loop done. Time elapsed: 83.0900' 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] 16569803 631961847 366958688 365864833 633696212 15183797 4991018 4897364 15433076' b' [cx1_seq2sdbg.cpp :1151] Total number of edges: 2055556638' b' [cx1_seq2sdbg.cpp :1152] Total number of ONEs: 1998481580' b' [cx1_seq2sdbg.cpp :1153] Total number of $v edges: 16569803' b' [cx1.h : 621] Postprocess done. Time elapsed: 0.0611' b' [utils.h : 126] Real: 285.8866\tuser: 3496.7949\tsys: 31.8741\tmaxrss: 11692908' --- [Thu Mar 28 20:07:13 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: 110.181332' b' [assembler.cpp : 152] Number of Edges: 2055556638; 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: 1453666; time elapsed: 6.3821' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 4; Accumulated tips removed: 4683844; time elapsed: 7.5521' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 8; Accumulated tips removed: 8217375; time elapsed: 10.7672' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 16; Accumulated tips removed: 12876699; time elapsed: 17.2873' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 32; Accumulated tips removed: 17025744; time elapsed: 25.4264' b' [assembly_algorithms.cpp : 170] Removing tips with length less than 42; Accumulated tips removed: 18268350; time elapsed: 27.4148' b' [assembler.cpp : 179] Tips removal done! Time elapsed(sec): 94.906133' b' [assembler.cpp : 188] unitig graph size: 46175426, time for building: 222.315302' b' [assembler.cpp : 211] Number of bubbles removed: 1850307, Time elapsed(sec): 15.692178' b' [assembler.cpp : 225] Number of complex bubbles removed: 237434, Time elapsed(sec): 12.315148' b' [assembler.cpp : 243] Number unitigs disconnected: 11278985, time: 20.980786' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 105537, time: 5.079192' b' [assembler.cpp : 200] Tips removed: 62013, time: 12.132205' b' [assembler.cpp : 211] Number of bubbles removed: 85539, Time elapsed(sec): 5.154948' b' [assembler.cpp : 225] Number of complex bubbles removed: 91570, Time elapsed(sec): 8.823428' b' [assembler.cpp : 243] Number unitigs disconnected: 1488406, time: 6.993907' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 80, time: 4.772817' b' [assembler.cpp : 200] Tips removed: 1286559, time: 12.567363' b' [assembler.cpp : 211] Number of bubbles removed: 85309, Time elapsed(sec): 4.913854' b' [assembler.cpp : 225] Number of complex bubbles removed: 11085, Time elapsed(sec): 8.412096' b' [assembler.cpp : 243] Number unitigs disconnected: 14322, time: 5.602579' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 4, time: 4.741921' b' [assembler.cpp : 200] Tips removed: 4259, time: 11.182449' b' [assembler.cpp : 211] Number of bubbles removed: 373, Time elapsed(sec): 4.389785' b' [assembler.cpp : 225] Number of complex bubbles removed: 167, Time elapsed(sec): 8.429677' b' [assembler.cpp : 243] Number unitigs disconnected: 366, time: 5.593821' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 2, time: 4.739818' b' [assembler.cpp : 200] Tips removed: 101, time: 11.109046' b' [assembler.cpp : 211] Number of bubbles removed: 0, Time elapsed(sec): 4.356328' b' [assembler.cpp : 225] Number of complex bubbles removed: 10, Time elapsed(sec): 8.406421' b' [assembler.cpp : 243] Number unitigs disconnected: 9, time: 5.583426' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 0, time: 3.045184' b' [assembler.cpp : 132] Total length: 1543601590, N50: 54, Mean: 46, number of contigs: 33499716' b' [assembler.cpp : 133] Maximum length: 12476' b' [assembler.cpp : 290] Time to output: 62.428482' b' [assembler.cpp : 317] Number of local low depth unitigs removed: 1385703, complex bubbles removed: 81839, time: 430.412559' b' [assembler.cpp : 132] Total length: 1188106393, N50: 44, Mean: 42, number of contigs: 27709750' b' [assembler.cpp : 133] Maximum length: 12523' b' [utils.h : 126] Real: 1146.0727\tuser: 27428.3289\tsys: 34.2743\tmaxrss: 7712284' --- [Thu Mar 28 20:26:20 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: 517444, Mapper size: 19515951' b' [read_lib_functions-inl.h : 256] Before reading, sizeof seq_package: 5157212184' b' [read_lib_functions-inl.h : 260] After reading, sizeof seq_package: 5157212184' b' [local_assembler.cpp : 330] Lib 0, insert size: 248.09 sd: 92.42' b' [local_assembler.cpp : 462] Lib 0: total 141110330 reads, aligned 39854979, added 18817530 reads for local assembly' b' [utils.h : 126] Real: 258.4005\tuser: 6623.3527\tsys: 11.5812\tmaxrss: 6520680' --- [Thu Mar 28 20:30:39 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: 5877605' b' [iterate_edges.cpp : 570] Number of crusial kmers: 61678292' b' [iterate_edges.cpp : 443] Processed: 67108864, aligned: 46649349. Iterative edges: 184560940' b' [iterate_edges.cpp : 443] Processed: 134217728, aligned: 93355941. Iterative edges: 231981647' b' [iterate_edges.cpp : 447] Total: 141110330, aligned: 98197407. Iterative edges: 235114022' b' [iterate_edges.cpp : 451] Writing iterative edges...' b' [utils.h : 126] Real: 308.8028\tuser: 7701.6310\tsys: 10.9119\tmaxrss: 7590948' --- [Thu Mar 28 20:35:47 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: 235114022' b' [cx1_seq2sdbg.cpp : 434] Bases to reserve: 10043583834, number contigs: 61567724, number multiplicity: 296681746' b' [cx1_seq2sdbg.cpp : 440] Before reading, sizeof seq_package: 3003437760, multiplicity vector: 296681746' b' [cx1_seq2sdbg.cpp : 529] After reading, sizeof seq_package: 3003437760, multiplicity vector: 296681746' b' [cx1.h : 457] Preparing data... Done. Time elapsed: 23.6107' b' [cx1.h : 464] Preparing partitions and initialing global data...' b' [cx1_seq2sdbg.cpp : 740] Memory for sequence: 3587119824' b' [cx1_seq2sdbg.cpp : 741] max # lv.1 items = 507664120' b' [cx1.h : 480] Preparing partitions and initialing global data... Done. Time elapsed: 6.9335' b' [cx1.h : 486] Start main loop...' b' [cx1.h : 515] Lv1 scanning from bucket 0 to 524' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 5.1250' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 5.8843' b' [cx1.h : 515] Lv1 scanning from bucket 524 to 2397' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 6.6304' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 7.8413' b' [cx1.h : 515] Lv1 scanning from bucket 2397 to 5776' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 6.7452' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 8.1945' b' [cx1.h : 515] Lv1 scanning from bucket 5776 to 10836' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 7.6074' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 8.8348' b' [cx1.h : 515] Lv1 scanning from bucket 10836 to 18064' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 7.8785' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 8.9823' b' [cx1.h : 515] Lv1 scanning from bucket 18064 to 28355' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 9.3787' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 9.4109' b' [cx1.h : 515] Lv1 scanning from bucket 28355 to 43664' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 8.9877' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 9.8593' b' [cx1.h : 515] Lv1 scanning from bucket 43664 to 65536' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 7.9405' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 8.4123' b' [cx1.h : 607] Main loop done. Time elapsed: 127.7146' 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] 14532719 555808739 319843216 319630244 556298893 3369254 2418614 1720554 3711668' b' [cx1_seq2sdbg.cpp :1151] Total number of edges: 1777333901' b' [cx1_seq2sdbg.cpp :1152] Total number of ONEs: 1751581092' b' [cx1_seq2sdbg.cpp :1153] Total number of $v edges: 14532719' b' [cx1.h : 621] Postprocess done. Time elapsed: 0.0393' b' [utils.h : 126] Real: 158.3069\tuser: 2116.3529\tsys: 17.9779\tmaxrss: 5002428' --- [Thu Mar 28 20:38:26 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: 94.591006' b' [assembler.cpp : 152] Number of Edges: 1777333901; 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: 488028; time elapsed: 5.8222' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 4; Accumulated tips removed: 1709691; time elapsed: 6.9781' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 8; Accumulated tips removed: 2979860; time elapsed: 10.1241' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 16; Accumulated tips removed: 5005616; time elapsed: 17.4133' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 32; Accumulated tips removed: 8606192; time elapsed: 29.3719' b' [assembly_algorithms.cpp : 170] Removing tips with length less than 58; Accumulated tips removed: 11605831; time elapsed: 39.8218' b' [assembler.cpp : 179] Tips removal done! Time elapsed(sec): 109.597775' b' [assembler.cpp : 188] unitig graph size: 14757535, time for building: 119.095074' b' [assembler.cpp : 211] Number of bubbles removed: 1378766, Time elapsed(sec): 15.062165' b' [assembler.cpp : 225] Number of complex bubbles removed: 241259, Time elapsed(sec): 6.195277' b' [assembler.cpp : 243] Number unitigs disconnected: 232169, time: 2.375225' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 18669, time: 2.272093' b' [assembler.cpp : 200] Tips removed: 16194, time: 3.845202' b' [assembler.cpp : 211] Number of bubbles removed: 20869, Time elapsed(sec): 2.113707' b' [assembler.cpp : 225] Number of complex bubbles removed: 8250, Time elapsed(sec): 2.873656' b' [assembler.cpp : 243] Number unitigs disconnected: 23339, time: 2.174848' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 76, time: 2.258297' b' [assembler.cpp : 200] Tips removed: 8402, time: 3.785171' b' [assembler.cpp : 211] Number of bubbles removed: 2355, Time elapsed(sec): 1.649906' b' [assembler.cpp : 225] Number of complex bubbles removed: 894, Time elapsed(sec): 2.771295' b' [assembler.cpp : 243] Number unitigs disconnected: 1744, time: 2.149680' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 13, time: 2.253587' b' [assembler.cpp : 200] Tips removed: 152, time: 3.914947' b' [assembler.cpp : 211] Number of bubbles removed: 26, Time elapsed(sec): 1.460354' b' [assembler.cpp : 225] Number of complex bubbles removed: 24, Time elapsed(sec): 2.736238' b' [assembler.cpp : 243] Number unitigs disconnected: 191, time: 2.143043' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 1, time: 2.252769' b' [assembler.cpp : 200] Tips removed: 10, time: 3.744625' b' [assembler.cpp : 211] Number of bubbles removed: 2, Time elapsed(sec): 1.458221' b' [assembler.cpp : 225] Number of complex bubbles removed: 0, Time elapsed(sec): 2.739510' b' [assembler.cpp : 243] Number unitigs disconnected: 23, time: 2.143786' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 0, time: 1.608642' b' [assembler.cpp : 132] Total length: 1061758083, N50: 125, Mean: 90, number of contigs: 11711968' b' [assembler.cpp : 133] Maximum length: 56317' b' [assembler.cpp : 290] Time to output: 31.328980' b' [assembler.cpp : 317] Number of local low depth unitigs removed: 177404, complex bubbles removed: 21751, time: 208.680258' b' [assembler.cpp : 132] Total length: 586304036, N50: 77, Mean: 70, number of contigs: 8267864' b' [assembler.cpp : 133] Maximum length: 56317' b' [utils.h : 126] Real: 655.1398\tuser: 14802.5982\tsys: 23.3320\tmaxrss: 4762076' --- [Thu Mar 28 20:49:22 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: 757411, Mapper size: 36301386' b' [read_lib_functions-inl.h : 256] Before reading, sizeof seq_package: 5157212184' b' [read_lib_functions-inl.h : 260] After reading, sizeof seq_package: 5157212184' b' [local_assembler.cpp : 330] Lib 0, insert size: 261.10 sd: 100.20' b' [local_assembler.cpp : 462] Lib 0: total 141110330 reads, aligned 62734944, added 20876340 reads for local assembly' b' [utils.h : 126] Real: 349.0905\tuser: 9147.7071\tsys: 13.1827\tmaxrss: 7401448' --- [Thu Mar 28 20:55:11 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: 4740363' b' [iterate_edges.cpp : 570] Number of crusial kmers: 21138686' b' [iterate_edges.cpp : 443] Processed: 67108864, aligned: 34340787. Iterative edges: 94010045' b' [iterate_edges.cpp : 443] Processed: 134217728, aligned: 68750786. Iterative edges: 114582019' b' [iterate_edges.cpp : 447] Total: 141110330, aligned: 72349494. Iterative edges: 115923130' b' [iterate_edges.cpp : 451] Writing iterative edges...' b' [utils.h : 126] Real: 231.7703\tuser: 5849.5515\tsys: 7.8600\tmaxrss: 4130936' --- [Thu Mar 28 20:59:03 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: 115923130' b' [cx1_seq2sdbg.cpp : 434] Bases to reserve: 6699145496, number contigs: 22032656, number multiplicity: 137955786' b' [cx1_seq2sdbg.cpp : 440] Before reading, sizeof seq_package: 1851047632, multiplicity vector: 137955786' b' [cx1_seq2sdbg.cpp : 529] After reading, sizeof seq_package: 1851047632, multiplicity vector: 137955786' b' [cx1.h : 457] Preparing data... Done. Time elapsed: 14.3568' b' [cx1.h : 464] Preparing partitions and initialing global data...' b' [cx1_seq2sdbg.cpp : 740] Memory for sequence: 2159488490' b' [cx1_seq2sdbg.cpp : 741] max # lv.1 items = 452711713' b' [cx1.h : 480] Preparing partitions and initialing global data... Done. Time elapsed: 6.9415' b' [cx1.h : 486] Start main loop...' b' [cx1.h : 515] Lv1 scanning from bucket 0 to 705' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 6.8045' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 5.6030' b' [cx1.h : 515] Lv1 scanning from bucket 705 to 2875' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 7.6473' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 7.2412' b' [cx1.h : 515] Lv1 scanning from bucket 2875 to 6529' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 8.2037' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 7.4829' b' [cx1.h : 515] Lv1 scanning from bucket 6529 to 11857' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 8.3413' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 8.0499' b' [cx1.h : 515] Lv1 scanning from bucket 11857 to 19345' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 8.8759' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 8.6675' b' [cx1.h : 515] Lv1 scanning from bucket 19345 to 29891' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 9.1991' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 8.8826' b' [cx1.h : 515] Lv1 scanning from bucket 29891 to 45561' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 10.0375' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 9.1903' b' [cx1.h : 515] Lv1 scanning from bucket 45561 to 65536' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 7.4389' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 6.8461' b' [cx1.h : 607] Main loop done. Time elapsed: 128.5129' 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] 8825843 482322290 281577658 281136796 482814178 2024621 864340 860063 2028830' b' [cx1_seq2sdbg.cpp :1151] Total number of edges: 1542454619' b' [cx1_seq2sdbg.cpp :1152] Total number of ONEs: 1527850922' b' [cx1_seq2sdbg.cpp :1153] Total number of $v edges: 8825843' b' [cx1.h : 621] Postprocess done. Time elapsed: 0.0389' b' [utils.h : 126] Real: 149.8565\tuser: 1923.6392\tsys: 14.5195\tmaxrss: 3893292' --- [Thu Mar 28 21:01:33 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: 79.956677' b' [assembler.cpp : 152] Number of Edges: 1542454619; 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: 87246; time elapsed: 4.6270' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 4; Accumulated tips removed: 452472; time elapsed: 5.3589' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 8; Accumulated tips removed: 885195; time elapsed: 7.3618' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 16; Accumulated tips removed: 1432521; time elapsed: 12.3511' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 32; Accumulated tips removed: 2160619; time elapsed: 21.9767' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 64; Accumulated tips removed: 4586279; time elapsed: 36.7083' b' [assembly_algorithms.cpp : 170] Removing tips with length less than 78; Accumulated tips removed: 5822741; time elapsed: 35.2765' b' [assembler.cpp : 179] Tips removal done! Time elapsed(sec): 123.718247' b' [assembler.cpp : 188] unitig graph size: 8853978, time for building: 89.462613' b' [assembler.cpp : 211] Number of bubbles removed: 1009229, Time elapsed(sec): 15.368528' b' [assembler.cpp : 225] Number of complex bubbles removed: 171151, Time elapsed(sec): 5.384677' b' [assembler.cpp : 243] Number unitigs disconnected: 123996, time: 1.708920' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 40085, time: 1.765060' b' [assembler.cpp : 200] Tips removed: 14312, time: 2.591858' b' [assembler.cpp : 211] Number of bubbles removed: 21758, Time elapsed(sec): 1.642002' b' [assembler.cpp : 225] Number of complex bubbles removed: 10213, Time elapsed(sec): 1.716145' b' [assembler.cpp : 243] Number unitigs disconnected: 7202, time: 1.638254' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 133, time: 1.699937' b' [assembler.cpp : 200] Tips removed: 3561, time: 2.529333' b' [assembler.cpp : 211] Number of bubbles removed: 1280, Time elapsed(sec): 0.873772' b' [assembler.cpp : 225] Number of complex bubbles removed: 641, Time elapsed(sec): 1.419910' b' [assembler.cpp : 243] Number unitigs disconnected: 148, time: 1.630518' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 7, time: 1.697911' b' [assembler.cpp : 200] Tips removed: 27, time: 2.500600' b' [assembler.cpp : 211] Number of bubbles removed: 5, Time elapsed(sec): 0.795515' b' [assembler.cpp : 225] Number of complex bubbles removed: 8, Time elapsed(sec): 1.397334' b' [assembler.cpp : 243] Number unitigs disconnected: 14, time: 1.633706' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 0, time: 1.354073' b' [assembler.cpp : 200] Tips removed: 0, time: 2.454994' b' [assembler.cpp : 211] Number of bubbles removed: 0, Time elapsed(sec): 0.819526' b' [assembler.cpp : 225] Number of complex bubbles removed: 0, Time elapsed(sec): 1.382930' b' [assembler.cpp : 243] Number unitigs disconnected: 1, time: 1.631398' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 0, time: 1.340625' b' [assembler.cpp : 132] Total length: 875057190, N50: 161, Mean: 132, number of contigs: 6595847' b' [assembler.cpp : 133] Maximum length: 71710' b' [assembler.cpp : 290] Time to output: 25.685208' b' [assembler.cpp : 317] Number of local low depth unitigs removed: 27288, complex bubbles removed: 4400, time: 149.479947' b' [assembler.cpp : 132] Total length: 456682865, N50: 119, Mean: 103, number of contigs: 4417946' b' [assembler.cpp : 133] Maximum length: 71710' b' [utils.h : 126] Real: 537.6283\tuser: 12064.5981\tsys: 19.6640\tmaxrss: 4266272' --- [Thu Mar 28 21:10:31 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: 797980, Mapper size: 43433728' b' [read_lib_functions-inl.h : 256] Before reading, sizeof seq_package: 5157212184' b' [read_lib_functions-inl.h : 260] After reading, sizeof seq_package: 5157212184' b' [local_assembler.cpp : 330] Lib 0, insert size: 264.60 sd: 102.34' b' [local_assembler.cpp : 462] Lib 0: total 141110330 reads, aligned 74435817, added 23092196 reads for local assembly' b' [utils.h : 126] Real: 522.0882\tuser: 14000.4950\tsys: 13.2978\tmaxrss: 7662328' --- [Thu Mar 28 21:19:13 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: 3320347' b' [iterate_edges.cpp : 570] Number of crusial kmers: 11596592' b' [iterate_edges.cpp : 443] Processed: 67108864, aligned: 24318982. Iterative edges: 93932117' b' [iterate_edges.cpp : 443] Processed: 134217728, aligned: 48642190. Iterative edges: 118866920' b' [iterate_edges.cpp : 447] Total: 141110330, aligned: 51238402. Iterative edges: 120626811' b' [iterate_edges.cpp : 451] Writing iterative edges...' b' [utils.h : 126] Real: 208.0656\tuser: 5095.1219\tsys: 8.3190\tmaxrss: 4478836' --- [Thu Mar 28 21:22:41 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: 120626811' b' [cx1_seq2sdbg.cpp : 434] Bases to reserve: 9090350071, number contigs: 12995685, number multiplicity: 133622496' b' [cx1_seq2sdbg.cpp : 440] Before reading, sizeof seq_package: 2376553008, multiplicity vector: 133622496' b' [cx1_seq2sdbg.cpp : 529] After reading, sizeof seq_package: 2376553008, multiplicity vector: 133622496' b' [cx1.h : 457] Preparing data... Done. Time elapsed: 14.2215' b' [cx1.h : 464] Preparing partitions and initialing global data...' b' [cx1_seq2sdbg.cpp : 740] Memory for sequence: 2703536560' b' [cx1_seq2sdbg.cpp : 741] max # lv.1 items = 425430975' b' [cx1.h : 480] Preparing partitions and initialing global data... Done. Time elapsed: 8.1143' b' [cx1.h : 486] Start main loop...' b' [cx1.h : 515] Lv1 scanning from bucket 0 to 626' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 6.6806' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 4.8260' b' [cx1.h : 515] Lv1 scanning from bucket 626 to 2683' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 8.6762' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 6.5686' b' [cx1.h : 515] Lv1 scanning from bucket 2683 to 6219' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 8.7582' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 6.8966' b' [cx1.h : 515] Lv1 scanning from bucket 6219 to 11403' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 10.1289' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 7.2507' b' [cx1.h : 515] Lv1 scanning from bucket 11403 to 18713' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 10.9871' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 7.6698' b' [cx1.h : 515] Lv1 scanning from bucket 18713 to 29027' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 10.3799' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 7.7275' b' [cx1.h : 515] Lv1 scanning from bucket 29027 to 44379' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 10.8073' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 8.2331' b' [cx1.h : 515] Lv1 scanning from bucket 44379 to 65536' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 9.0168' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 6.3871' b' [cx1.h : 607] Main loop done. Time elapsed: 130.9956' 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] 6511467 415658186 241984264 241758767 416064009 953750 713396 517894 1048556' b' [cx1_seq2sdbg.cpp :1151] Total number of edges: 1325210289' b' [cx1_seq2sdbg.cpp :1152] Total number of ONEs: 1315465226' b' [cx1_seq2sdbg.cpp :1153] Total number of $v edges: 6511467' b' [cx1.h : 621] Postprocess done. Time elapsed: 0.1041' b' [utils.h : 126] Real: 153.4462\tuser: 1715.8249\tsys: 15.9167\tmaxrss: 4359020' --- [Thu Mar 28 21:25:15 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: 55.518561' b' [assembler.cpp : 152] Number of Edges: 1325210289; 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: 50344; time elapsed: 4.0229' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 4; Accumulated tips removed: 209116; time elapsed: 4.3593' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 8; Accumulated tips removed: 466942; time elapsed: 5.9926' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 16; Accumulated tips removed: 901180; time elapsed: 9.7521' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 32; Accumulated tips removed: 1395639; time elapsed: 16.6976' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 64; Accumulated tips removed: 3147983; time elapsed: 28.1969' b' [assembly_algorithms.cpp : 170] Removing tips with length less than 118; Accumulated tips removed: 6113559; time elapsed: 29.2972' b' [assembler.cpp : 179] Tips removal done! Time elapsed(sec): 98.369721' b' [assembler.cpp : 188] unitig graph size: 3939229, time for building: 63.929622' b' [assembler.cpp : 211] Number of bubbles removed: 505619, Time elapsed(sec): 11.846643' b' [assembler.cpp : 225] Number of complex bubbles removed: 104999, Time elapsed(sec): 4.524661' b' [assembler.cpp : 243] Number unitigs disconnected: 170851, time: 0.576288' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 67418, time: 0.575352' b' [assembler.cpp : 200] Tips removed: 3424, time: 1.089036' b' [assembler.cpp : 211] Number of bubbles removed: 23322, Time elapsed(sec): 1.365144' b' [assembler.cpp : 225] Number of complex bubbles removed: 13053, Time elapsed(sec): 1.298259' b' [assembler.cpp : 243] Number unitigs disconnected: 7396, time: 0.456681' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 354, time: 0.474387' b' [assembler.cpp : 200] Tips removed: 3705, time: 1.274651' b' [assembler.cpp : 211] Number of bubbles removed: 787, Time elapsed(sec): 0.404457' b' [assembler.cpp : 225] Number of complex bubbles removed: 750, Time elapsed(sec): 0.671457' b' [assembler.cpp : 243] Number unitigs disconnected: 138, time: 0.450508' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 27, time: 0.405870' b' [assembler.cpp : 200] Tips removed: 28, time: 1.042907' b' [assembler.cpp : 211] Number of bubbles removed: 0, Time elapsed(sec): 0.323171' b' [assembler.cpp : 225] Number of complex bubbles removed: 13, Time elapsed(sec): 0.628968' b' [assembler.cpp : 243] Number unitigs disconnected: 2, time: 0.449437' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 1, time: 0.405291' b' [assembler.cpp : 200] Tips removed: 1, time: 1.039048' b' [assembler.cpp : 211] Number of bubbles removed: 0, Time elapsed(sec): 0.323761' b' [assembler.cpp : 225] Number of complex bubbles removed: 0, Time elapsed(sec): 0.625789' b' [assembler.cpp : 243] Number unitigs disconnected: 0, time: 0.448592' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 0, time: 0.251772' b' [assembler.cpp : 132] Total length: 610060759, N50: 345, Mean: 238, number of contigs: 2554604' b' [assembler.cpp : 133] Maximum length: 210872' b' [assembler.cpp : 290] Time to output: 18.092665' b' [assembler.cpp : 317] Number of local low depth unitigs removed: 8580, complex bubbles removed: 1289, time: 35.556087' b' [assembler.cpp : 132] Total length: 327035325, N50: 278, Mean: 187, number of contigs: 1744663' b' [assembler.cpp : 133] Maximum length: 210872' b' [utils.h : 126] Real: 311.6392\tuser: 6624.2923\tsys: 13.3012\tmaxrss: 3225200' --- [Thu Mar 28 21:30:27 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: 853897, Mapper size: 50501700' b' [read_lib_functions-inl.h : 256] Before reading, sizeof seq_package: 5157212184' b' [read_lib_functions-inl.h : 260] After reading, sizeof seq_package: 5157212184' b' [local_assembler.cpp : 330] Lib 0, insert size: 268.12 sd: 104.93' b' [local_assembler.cpp : 462] Lib 0: total 141110330 reads, aligned 83965700, added 24196535 reads for local assembly' b' [utils.h : 126] Real: 626.0153\tuser: 16852.0196\tsys: 14.0977\tmaxrss: 7931708' --- [Thu Mar 28 21:40:53 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: 1682965' b' [iterate_edges.cpp : 570] Number of crusial kmers: 4931967' b' [iterate_edges.cpp : 443] Processed: 67108864, aligned: 13354351. Iterative edges: 37935436' b' [iterate_edges.cpp : 443] Processed: 134217728, aligned: 26590808. Iterative edges: 47195491' b' [iterate_edges.cpp : 447] Total: 141110330, aligned: 28050141. Iterative edges: 47868694' b' [iterate_edges.cpp : 451] Writing iterative edges...' b' [utils.h : 126] Real: 142.9451\tuser: 3459.8067\tsys: 5.9230\tmaxrss: 2302000' --- [Thu Mar 28 21:43:16 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: 47868694' b' [cx1_seq2sdbg.cpp : 434] Bases to reserve: 5356789310, number contigs: 5971635, number multiplicity: 53840329' b' [cx1_seq2sdbg.cpp : 440] Before reading, sizeof seq_package: 1386970416, multiplicity vector: 53840329' b' [cx1_seq2sdbg.cpp : 529] After reading, sizeof seq_package: 1386970416, multiplicity vector: 53840329' b' [cx1.h : 457] Preparing data... Done. Time elapsed: 8.7403' b' [cx1.h : 464] Preparing partitions and initialing global data...' b' [cx1_seq2sdbg.cpp : 740] Memory for sequence: 1532427390' b' [cx1_seq2sdbg.cpp : 741] max # lv.1 items = 333317956' b' [cx1.h : 480] Preparing partitions and initialing global data... Done. Time elapsed: 6.0907' b' [cx1.h : 486] Start main loop...' b' [cx1.h : 515] Lv1 scanning from bucket 0 to 543' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 4.8259' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 3.4165' b' [cx1.h : 515] Lv1 scanning from bucket 543 to 2461' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 5.7958' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 4.8609' b' [cx1.h : 515] Lv1 scanning from bucket 2461 to 5848' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 6.9993' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 5.1297' b' [cx1.h : 515] Lv1 scanning from bucket 5848 to 10850' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 6.5147' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 5.5323' b' [cx1.h : 515] Lv1 scanning from bucket 10850 to 17933' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 7.7599' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 5.5681' b' [cx1.h : 515] Lv1 scanning from bucket 17933 to 27956' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 8.0572' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 6.0248' b' [cx1.h : 515] Lv1 scanning from bucket 27956 to 42904' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 7.9141' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 6.2006' b' [cx1.h : 515] Lv1 scanning from bucket 42904 to 65536' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 6.7993' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 5.1512' b' [cx1.h : 607] Main loop done. Time elapsed: 96.5517' 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] 2864810 329626381 189574778 189415520 329876297 607332 299824 410466 554044' b' [cx1_seq2sdbg.cpp :1151] Total number of edges: 1043229452' b' [cx1_seq2sdbg.cpp :1152] Total number of ONEs: 1038492976' b' [cx1_seq2sdbg.cpp :1153] Total number of $v edges: 2864810' b' [cx1.h : 621] Postprocess done. Time elapsed: 0.0372' b' [utils.h : 126] Real: 111.4248\tuser: 1289.2684\tsys: 11.0370\tmaxrss: 2913764' --- [Thu Mar 28 21:45:07 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: 39.133655' b' [assembler.cpp : 152] Number of Edges: 1043229452; 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: 27260; time elapsed: 2.9916' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 4; Accumulated tips removed: 106616; time elapsed: 3.1456' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 8; Accumulated tips removed: 237110; time elapsed: 3.8353' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 16; Accumulated tips removed: 469057; time elapsed: 5.4803' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 32; Accumulated tips removed: 732684; time elapsed: 8.2523' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 64; Accumulated tips removed: 1294780; time elapsed: 13.3597' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 128; Accumulated tips removed: 2258291; time elapsed: 19.2966' b' [assembly_algorithms.cpp : 170] Removing tips with length less than 158; Accumulated tips removed: 2599237; time elapsed: 17.2890' b' [assembler.cpp : 179] Tips removal done! Time elapsed(sec): 73.692272' b' [assembler.cpp : 188] unitig graph size: 2227953, time for building: 50.838253' b' [assembler.cpp : 211] Number of bubbles removed: 267725, Time elapsed(sec): 9.549500' b' [assembler.cpp : 225] Number of complex bubbles removed: 61518, Time elapsed(sec): 3.935462' b' [assembler.cpp : 243] Number unitigs disconnected: 199481, time: 0.422785' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 77732, time: 0.518604' b' [assembler.cpp : 200] Tips removed: 2454, time: 0.682733' b' [assembler.cpp : 211] Number of bubbles removed: 18826, Time elapsed(sec): 1.108565' b' [assembler.cpp : 225] Number of complex bubbles removed: 12221, Time elapsed(sec): 1.117295' b' [assembler.cpp : 243] Number unitigs disconnected: 7845, time: 0.304995' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 990, time: 0.284019' b' [assembler.cpp : 200] Tips removed: 4938, time: 0.637070' b' [assembler.cpp : 211] Number of bubbles removed: 552, Time elapsed(sec): 0.309229' b' [assembler.cpp : 225] Number of complex bubbles removed: 740, Time elapsed(sec): 0.450183' b' [assembler.cpp : 243] Number unitigs disconnected: 214, time: 0.299036' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 102, time: 0.281462' b' [assembler.cpp : 200] Tips removed: 121, time: 0.616176' b' [assembler.cpp : 211] Number of bubbles removed: 4, Time elapsed(sec): 0.155486' b' [assembler.cpp : 225] Number of complex bubbles removed: 16, Time elapsed(sec): 0.374253' b' [assembler.cpp : 243] Number unitigs disconnected: 11, time: 0.297783' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 18, time: 0.279285' b' [assembler.cpp : 200] Tips removed: 5, time: 0.614307' b' [assembler.cpp : 211] Number of bubbles removed: 0, Time elapsed(sec): 0.155186' b' [assembler.cpp : 225] Number of complex bubbles removed: 0, Time elapsed(sec): 0.361333' b' [assembler.cpp : 243] Number unitigs disconnected: 0, time: 0.297400' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 4, time: 0.280275' b' [assembler.cpp : 132] Total length: 506607871, N50: 574, Mean: 393, number of contigs: 1288184' b' [assembler.cpp : 133] Maximum length: 222219' b' [assembler.cpp : 290] Time to output: 15.028328' b' [assembler.cpp : 317] Number of local low depth unitigs removed: 6645, complex bubbles removed: 682, time: 21.374743' b' [assembler.cpp : 132] Total length: 251867695, N50: 669, Mean: 321, number of contigs: 784496' b' [assembler.cpp : 133] Maximum length: 222219' b' [utils.h : 126] Real: 230.7777\tuser: 5005.9997\tsys: 11.4664\tmaxrss: 2596256' --- [Thu Mar 28 21:48:58 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: 716068, Mapper size: 51386580' b' [read_lib_functions-inl.h : 256] Before reading, sizeof seq_package: 5157212184' b' [read_lib_functions-inl.h : 260] After reading, sizeof seq_package: 5157212184' b' [local_assembler.cpp : 330] Lib 0, insert size: 272.99 sd: 107.00' b' [local_assembler.cpp : 462] Lib 0: total 141110330 reads, aligned 82194853, added 17907613 reads for local assembly' b' [utils.h : 126] Real: 539.7092\tuser: 14444.0503\tsys: 11.8002\tmaxrss: 7736396' --- [Thu Mar 28 21:57:58 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: 894460' b' [iterate_edges.cpp : 570] Number of crusial kmers: 2330346' b' [iterate_edges.cpp : 443] Processed: 67108864, aligned: 6173439. Iterative edges: 16098766' b' [iterate_edges.cpp : 443] Processed: 134217728, aligned: 12259587. Iterative edges: 20536864' b' [iterate_edges.cpp : 447] Total: 141110330, aligned: 12950886. Iterative edges: 20878224' b' [iterate_edges.cpp : 451] Writing iterative edges...' b' [utils.h : 126] Real: 89.9225\tuser: 2145.0675\tsys: 4.3999\tmaxrss: 1426332' --- [Thu Mar 28 21:59:28 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: 20878224' b' [cx1_seq2sdbg.cpp : 434] Bases to reserve: 3318030973, number contigs: 3066182, number multiplicity: 23944406' b' [cx1_seq2sdbg.cpp : 440] Before reading, sizeof seq_package: 854037208, multiplicity vector: 23944406' b' [cx1_seq2sdbg.cpp : 529] After reading, sizeof seq_package: 854037208, multiplicity vector: 23944406' b' [cx1.h : 457] Preparing data... Done. Time elapsed: 6.0550' b' [cx1.h : 464] Preparing partitions and initialing global data...' b' [cx1_seq2sdbg.cpp : 740] Memory for sequence: 926694954' b' [cx1_seq2sdbg.cpp : 741] max # lv.1 items = 275053942' b' [cx1.h : 480] Preparing partitions and initialing global data... Done. Time elapsed: 4.2290' b' [cx1.h : 486] Start main loop...' b' [cx1.h : 515] Lv1 scanning from bucket 0 to 469' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 3.1437' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 2.6060' b' [cx1.h : 515] Lv1 scanning from bucket 469 to 2263' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 4.6463' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 3.9419' b' [cx1.h : 515] Lv1 scanning from bucket 2263 to 5527' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 4.7531' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 4.3243' b' [cx1.h : 515] Lv1 scanning from bucket 5527 to 10386' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 4.5890' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 4.5836' b' [cx1.h : 515] Lv1 scanning from bucket 10386 to 17303' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 5.2762' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 4.6440' b' [cx1.h : 515] Lv1 scanning from bucket 17303 to 27109' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 4.6244' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 4.8992' b' [cx1.h : 515] Lv1 scanning from bucket 27109 to 41720' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 4.8538' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 5.0546' b' [cx1.h : 515] Lv1 scanning from bucket 41720 to 65536' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 4.1484' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 4.4399' b' [cx1.h : 607] Main loop done. Time elapsed: 70.5295' 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] 1835674 284418584 163111562 163006621 284598369 345740 157185 155932 345822' b' [cx1_seq2sdbg.cpp :1151] Total number of edges: 897975489' b' [cx1_seq2sdbg.cpp :1152] Total number of ONEs: 895135136' b' [cx1_seq2sdbg.cpp :1153] Total number of $v edges: 1835674' b' [cx1.h : 621] Postprocess done. Time elapsed: 0.0343' b' [utils.h : 126] Real: 80.8512\tuser: 1058.1172\tsys: 7.7361\tmaxrss: 2128540' --- [Thu Mar 28 22:00:49 2019] Assembling contigs from SdBG for k = 99 --- cmd: /gscratch/srlab/programs/megahit_v1.1.4_LINUX_CPUONLY_x86_64-bin/megahit_asm_core assemble -s ./megahit_out/tmp/k99/99 -o ./megahit_out/intermediate_contigs/k99 -t 28 --min_standalone 300.0 --prune_level 2 --merge_len 20 --merge_similar 0.95 --low_local_ratio 0.2 --min_depth 2 --bubble_level 2 --max_tip_len -1 --careful_bubble b' [assembler.cpp : 148] Loading succinct de Bruijn graph: ./megahit_out/tmp/k99/99 Done. Time elapsed: 15.729809' b' [assembler.cpp : 152] Number of Edges: 897975489; 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: 18058; time elapsed: 2.6398' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 4; Accumulated tips removed: 67680; time elapsed: 2.6417' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 8; Accumulated tips removed: 155108; time elapsed: 3.0687' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 16; Accumulated tips removed: 308728; time elapsed: 4.0191' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 32; Accumulated tips removed: 476138; time elapsed: 5.8323' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 64; Accumulated tips removed: 702290; time elapsed: 9.1174' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 128; Accumulated tips removed: 1141871; time elapsed: 14.5138' b' [assembly_algorithms.cpp : 170] Removing tips with length less than 198; Accumulated tips removed: 1522437; time elapsed: 16.6827' b' [assembler.cpp : 179] Tips removal done! Time elapsed(sec): 58.551390' b' [assembler.cpp : 188] unitig graph size: 1216619, time for building: 45.343366' b' [assembler.cpp : 211] Number of bubbles removed: 129513, Time elapsed(sec): 7.205384' b' [assembler.cpp : 225] Number of complex bubbles removed: 31499, Time elapsed(sec): 2.980266' b' [assembler.cpp : 243] Number unitigs disconnected: 123482, time: 0.263861' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 47548, time: 0.307336' b' [assembler.cpp : 200] Tips removed: 1539, time: 0.351761' b' [assembler.cpp : 211] Number of bubbles removed: 8929, Time elapsed(sec): 0.676326' b' [assembler.cpp : 225] Number of complex bubbles removed: 7585, Time elapsed(sec): 0.946989' b' [assembler.cpp : 243] Number unitigs disconnected: 4271, time: 0.136082' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 624, time: 0.140892' b' [assembler.cpp : 200] Tips removed: 2499, time: 0.343457' b' [assembler.cpp : 211] Number of bubbles removed: 232, Time elapsed(sec): 0.097615' b' [assembler.cpp : 225] Number of complex bubbles removed: 476, Time elapsed(sec): 0.296431' b' [assembler.cpp : 243] Number unitigs disconnected: 143, time: 0.132065' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 76, time: 0.138050' b' [assembler.cpp : 200] Tips removed: 72, time: 0.333859' b' [assembler.cpp : 211] Number of bubbles removed: 2, Time elapsed(sec): 0.083090' b' [assembler.cpp : 225] Number of complex bubbles removed: 17, Time elapsed(sec): 0.248564' b' [assembler.cpp : 243] Number unitigs disconnected: 4, time: 0.133729' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 8, time: 0.137778' b' [assembler.cpp : 200] Tips removed: 0, time: 0.332741' b' [assembler.cpp : 211] Number of bubbles removed: 0, Time elapsed(sec): 0.082994' b' [assembler.cpp : 225] Number of complex bubbles removed: 0, Time elapsed(sec): 0.243510' b' [assembler.cpp : 243] Number unitigs disconnected: 1, time: 0.133677' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 0, time: 0.092612' b' [assembler.cpp : 132] Total length: 442467619, N50: 856, Mean: 620, number of contigs: 713432' b' [assembler.cpp : 133] Maximum length: 280538' b' [assembler.cpp : 290] Time to output: 13.741227' b' [assembler.cpp : 317] Number of local low depth unitigs removed: 3448, complex bubbles removed: 400, time: 10.858545' b' [assembler.cpp : 132] Total length: 183152492, N50: 1678, Mean: 575, number of contigs: 318196' b' [assembler.cpp : 133] Maximum length: 280538' b' [utils.h : 126] Real: 166.0633\tuser: 3889.9683\tsys: 8.5602\tmaxrss: 2191560' --- [Thu Mar 28 22:03:35 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: 540895, Mapper size: 49543260' b' [read_lib_functions-inl.h : 256] Before reading, sizeof seq_package: 5157212184' b' [read_lib_functions-inl.h : 260] After reading, sizeof seq_package: 5157212184' b' [local_assembler.cpp : 330] Lib 0, insert size: 277.23 sd: 108.64' b' [local_assembler.cpp : 462] Lib 0: total 141110330 reads, aligned 77691532, added 10579665 reads for local assembly' b' [utils.h : 126] Real: 388.9574\tuser: 10355.3804\tsys: 9.8042\tmaxrss: 7411428' --- [Thu Mar 28 22:10:04 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: 416194' b' [iterate_edges.cpp : 570] Number of crusial kmers: 971950' b' [iterate_edges.cpp : 443] Processed: 67108864, aligned: 1888723. Iterative edges: 4213415' b' [iterate_edges.cpp : 443] Processed: 134217728, aligned: 3734252. Iterative edges: 5860790' b' [iterate_edges.cpp : 447] Total: 141110330, aligned: 3953444. Iterative edges: 6003687' b' [iterate_edges.cpp : 451] Writing iterative edges...' b' [utils.h : 126] Real: 50.3613\tuser: 1172.5903\tsys: 3.3254\tmaxrss: 746440' --- [Thu Mar 28 22:10:55 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: 6003687' b' [cx1_seq2sdbg.cpp : 434] Bases to reserve: 1623756875, number contigs: 1472115, number multiplicity: 7475802' b' [cx1_seq2sdbg.cpp : 440] Before reading, sizeof seq_package: 417716148, multiplicity vector: 7475802' b' [cx1_seq2sdbg.cpp : 529] After reading, sizeof seq_package: 835432296, multiplicity vector: 14951604' b' [cx1.h : 457] Preparing data... Done. Time elapsed: 4.7755' b' [cx1.h : 464] Preparing partitions and initialing global data...' b' [cx1_seq2sdbg.cpp : 740] Memory for sequence: 863665816' b' [cx1_seq2sdbg.cpp : 741] max # lv.1 items = 218787451' b' [cx1.h : 480] Preparing partitions and initialing global data... Done. Time elapsed: 1.8592' b' [cx1.h : 486] Start main loop...' b' [cx1.h : 515] Lv1 scanning from bucket 0 to 329' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 1.4474' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 1.8678' b' [cx1.h : 515] Lv1 scanning from bucket 329 to 1839' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 1.6500' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 3.2270' b' [cx1.h : 515] Lv1 scanning from bucket 1839 to 4827' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 1.8146' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 3.6846' b' [cx1.h : 515] Lv1 scanning from bucket 4827 to 9392' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 1.9374' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 3.9639' b' [cx1.h : 515] Lv1 scanning from bucket 9392 to 15965' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 2.0815' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 4.1039' b' [cx1.h : 515] Lv1 scanning from bucket 15965 to 25327' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 2.2383' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 4.1181' b' [cx1.h : 515] Lv1 scanning from bucket 25327 to 39192' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 2.5345' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 4.3018' b' [cx1.h : 515] Lv1 scanning from bucket 39192 to 65536' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 2.3290' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 4.4394' b' [cx1.h : 607] Main loop done. Time elapsed: 45.7405' 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] 1447650 250126036 143744767 143677877 250254396 121177 89484 66287 133106' b' [cx1_seq2sdbg.cpp :1151] Total number of edges: 789660780' b' [cx1_seq2sdbg.cpp :1152] Total number of ONEs: 787803076' b' [cx1_seq2sdbg.cpp :1153] Total number of $v edges: 1447650' b' [cx1.h : 621] Postprocess done. Time elapsed: 0.0323' b' [utils.h : 126] Real: 52.4095\tuser: 907.7907\tsys: 5.9280\tmaxrss: 1471420' --- [Thu Mar 28 22:11:47 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: 13.891561' b' [assembler.cpp : 152] Number of Edges: 789660780; 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: 16894; time elapsed: 2.1988' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 4; Accumulated tips removed: 61562; time elapsed: 2.2749' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 8; Accumulated tips removed: 145566; time elapsed: 2.6086' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 16; Accumulated tips removed: 322192; time elapsed: 3.3217' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 32; Accumulated tips removed: 412944; time elapsed: 4.6499' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 64; Accumulated tips removed: 521603; time elapsed: 7.2794' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 128; Accumulated tips removed: 785564; time elapsed: 11.2916' b' [assembly_algorithms.cpp : 170] Removing tips with length less than 182; Accumulated tips removed: 857962; time elapsed: 13.9890' b' [assembler.cpp : 179] Tips removal done! Time elapsed(sec): 47.645584' b' [assembler.cpp : 188] unitig graph size: 684431, time for building: 41.299564' b' [assembler.cpp : 211] Number of bubbles removed: 40562, Time elapsed(sec): 2.266040' b' [assembler.cpp : 225] Number of complex bubbles removed: 9633, Time elapsed(sec): 1.458008' b' [assembler.cpp : 243] Number unitigs disconnected: 42201, time: 0.116235' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 14351, time: 0.148178' b' [assembler.cpp : 200] Tips removed: 495, time: 0.221104' b' [assembler.cpp : 211] Number of bubbles removed: 1554, Time elapsed(sec): 0.217210' b' [assembler.cpp : 225] Number of complex bubbles removed: 2417, Time elapsed(sec): 0.586200' b' [assembler.cpp : 243] Number unitigs disconnected: 1864, time: 0.081773' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 124, time: 0.086854' b' [assembler.cpp : 200] Tips removed: 711, time: 0.215699' b' [assembler.cpp : 211] Number of bubbles removed: 72, Time elapsed(sec): 0.088421' b' [assembler.cpp : 225] Number of complex bubbles removed: 211, Time elapsed(sec): 0.220903' b' [assembler.cpp : 243] Number unitigs disconnected: 25, time: 0.080362' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 10, time: 0.086258' b' [assembler.cpp : 200] Tips removed: 5, time: 0.210170' b' [assembler.cpp : 211] Number of bubbles removed: 0, Time elapsed(sec): 0.050888' b' [assembler.cpp : 225] Number of complex bubbles removed: 3, Time elapsed(sec): 0.171968' b' [assembler.cpp : 243] Number unitigs disconnected: 0, time: 0.079873' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 0, time: 0.056479' b' [assembler.cpp : 200] Tips removed: 0, time: 0.209474' b' [assembler.cpp : 211] Number of bubbles removed: 0, Time elapsed(sec): 0.050750' b' [assembler.cpp : 225] Number of complex bubbles removed: 0, Time elapsed(sec): 0.169739' b' [assembler.cpp : 243] Number unitigs disconnected: 0, time: 0.080988' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 0, time: 0.056432' b' [assembler.cpp : 132] Total length: 427180169, N50: 1060, Mean: 810, number of contigs: 527022' b' [assembler.cpp : 133] Maximum length: 588002' b' [assembler.cpp : 290] Time to output: 12.941551' b' [assembler.cpp : 317] Number of local low depth unitigs removed: 969, complex bubbles removed: 111, time: 5.780485' b' [assembler.cpp : 132] Total length: 126516424, N50: 4070, Mean: 1168, number of contigs: 108249' b' [assembler.cpp : 133] Maximum length: 588002' b' [utils.h : 126] Real: 132.8497\tuser: 3061.7350\tsys: 6.5938\tmaxrss: 1913552' --- [Thu Mar 28 22:14:00 2019] Local assembling k = 119 --- cmd: /gscratch/srlab/programs/megahit_v1.1.4_LINUX_CPUONLY_x86_64-bin/megahit_asm_core local -c ./megahit_out/intermediate_contigs/k119.contigs.fa -l ./megahit_out/tmp/reads.lib -t 28 -o ./megahit_out/intermediate_contigs/k119.local.fa --kmax 141 b' [local_assembler.cpp : 89] Number of contigs: 492774, Mapper size: 50140921' b' [read_lib_functions-inl.h : 256] Before reading, sizeof seq_package: 5157212184' b' [read_lib_functions-inl.h : 260] After reading, sizeof seq_package: 5157212184' b' [local_assembler.cpp : 330] Lib 0, insert size: 278.74 sd: 109.45' b' [local_assembler.cpp : 462] Lib 0: total 141110330 reads, aligned 75117722, added 6941571 reads for local assembly' b' [utils.h : 126] Real: 289.0719\tuser: 7548.5456\tsys: 9.3931\tmaxrss: 7343672' --- [Thu Mar 28 22:18:49 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: 87927' b' [iterate_edges.cpp : 570] Number of crusial kmers: 253483' 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: 141110330, aligned: 0. Iterative edges: 0' b' [utils.h : 126] Real: 15.8174\tuser: 21.6585\tsys: 2.8503\tmaxrss: 430776' --- [Thu Mar 28 22:19:05 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: 526495274, number contigs: 634492, number multiplicity: 634492' b' [cx1_seq2sdbg.cpp : 440] Before reading, sizeof seq_package: 136699764, multiplicity vector: 634492' b' [cx1_seq2sdbg.cpp : 529] After reading, sizeof seq_package: 273399528, multiplicity vector: 1268984' b' [cx1.h : 457] Preparing data... Done. Time elapsed: 2.5088' b' [cx1.h : 464] Preparing partitions and initialing global data...' b' [cx1_seq2sdbg.cpp : 740] Memory for sequence: 280754032' b' [cx1_seq2sdbg.cpp : 741] max # lv.1 items = 152512811' b' [cx1.h : 480] Preparing partitions and initialing global data... Done. Time elapsed: 0.5487' b' [cx1.h : 486] Start main loop...' b' [cx1.h : 515] Lv1 scanning from bucket 0 to 205' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 0.3733' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 1.1425' b' [cx1.h : 515] Lv1 scanning from bucket 205 to 1364' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 0.3957' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 2.2033' b' [cx1.h : 515] Lv1 scanning from bucket 1364 to 3919' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 0.4246' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 2.7488' b' [cx1.h : 515] Lv1 scanning from bucket 3919 to 8015' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 0.4401' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 2.9576' b' [cx1.h : 515] Lv1 scanning from bucket 8015 to 14014' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 0.4764' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 3.0842' b' [cx1.h : 515] Lv1 scanning from bucket 14014 to 22668' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 0.5174' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 3.1158' b' [cx1.h : 515] Lv1 scanning from bucket 22668 to 35511' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 0.5400' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 3.2725' b' [cx1.h : 515] Lv1 scanning from bucket 35511 to 58157' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 0.5285' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 3.7294' b' [cx1.h : 515] Lv1 scanning from bucket 58157 to 65536' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 0.3429' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 0.7161' b' [cx1.h : 607] Main loop done. Time elapsed: 27.0100' 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] 1008292 234824274 135088728 135025287 234914939 51004 23805 23901 50713' b' [cx1_seq2sdbg.cpp :1151] Total number of edges: 741010943' b' [cx1_seq2sdbg.cpp :1152] Total number of ONEs: 739853228' b' [cx1_seq2sdbg.cpp :1153] Total number of $v edges: 1008292' b' [cx1.h : 621] Postprocess done. Time elapsed: 0.1079' b' [utils.h : 126] Real: 30.1779\tuser: 704.5325\tsys: 4.0454\tmaxrss: 921684' --- [Thu Mar 28 22:19:35 2019] Assembling contigs from SdBG for k = 141 --- cmd: /gscratch/srlab/programs/megahit_v1.1.4_LINUX_CPUONLY_x86_64-bin/megahit_asm_core assemble -s ./megahit_out/tmp/k141/141 -o ./megahit_out/intermediate_contigs/k141 -t 28 --min_standalone 300.0 --prune_level 2 --merge_len 20 --merge_similar 0.95 --low_local_ratio 0.2 --min_depth 2 --bubble_level 2 --max_tip_len 160.0 --is_final_round b' [assembler.cpp : 148] Loading succinct de Bruijn graph: ./megahit_out/tmp/k141/141 Done. Time elapsed: 13.334931' b' [assembler.cpp : 152] Number of Edges: 741010943; 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: 2044; time elapsed: 2.0527' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 4; Accumulated tips removed: 7040; time elapsed: 2.0646' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 8; Accumulated tips removed: 16102; time elapsed: 2.4798' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 16; Accumulated tips removed: 33262; time elapsed: 2.8753' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 32; Accumulated tips removed: 63026; time elapsed: 3.9844' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 64; Accumulated tips removed: 110256; time elapsed: 6.0755' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 128; Accumulated tips removed: 185502; time elapsed: 9.9248' b' [assembly_algorithms.cpp : 170] Removing tips with length less than 160; Accumulated tips removed: 203254; time elapsed: 11.8197' b' [assembler.cpp : 179] Tips removal done! Time elapsed(sec): 41.306247' b' [assembler.cpp : 188] unitig graph size: 572248, time for building: 39.799285' b' [assembler.cpp : 211] Number of bubbles removed: 21417, Time elapsed(sec): 0.141007' b' [assembler.cpp : 225] Number of complex bubbles removed: 3462, Time elapsed(sec): 0.247698' b' [assembler.cpp : 243] Number unitigs disconnected: 21647, time: 0.105870' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 6248, time: 0.130567' b' [assembler.cpp : 200] Tips removed: 298, time: 0.203574' b' [assembler.cpp : 211] Number of bubbles removed: 201, Time elapsed(sec): 0.050620' b' [assembler.cpp : 225] Number of complex bubbles removed: 832, Time elapsed(sec): 0.179018' b' [assembler.cpp : 243] Number unitigs disconnected: 1158, time: 0.088531' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 59, time: 0.105236' b' [assembler.cpp : 200] Tips removed: 241, time: 0.200624' b' [assembler.cpp : 211] Number of bubbles removed: 22, Time elapsed(sec): 0.049312' b' [assembler.cpp : 225] Number of complex bubbles removed: 79, Time elapsed(sec): 0.146169' b' [assembler.cpp : 243] Number unitigs disconnected: 20, time: 0.087109' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 5, time: 0.105090' b' [assembler.cpp : 200] Tips removed: 7, time: 0.199837' b' [assembler.cpp : 211] Number of bubbles removed: 0, Time elapsed(sec): 0.049055' b' [assembler.cpp : 225] Number of complex bubbles removed: 0, Time elapsed(sec): 0.140399' b' [assembler.cpp : 243] Number unitigs disconnected: 0, time: 0.089027' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 0, time: 0.076388' b' [assembler.cpp : 317] Number of local low depth unitigs removed: 328, complex bubbles removed: 19, time: 5.718054' b' [assembler.cpp : 132] Total length: 429991088, N50: 1132, Mean: 864, number of contigs: 497601' b' [assembler.cpp : 133] Maximum length: 588024' b' [utils.h : 126] Real: 115.4086\tuser: 2633.5181\tsys: 6.3507\tmaxrss: 1802568' --- [Thu Mar 28 22:21:31 2019] Merging to output final contigs --- --- [STAT] 483496 contigs, total 427499988 bp, min 200 bp, max 588024 bp, avg 884 bp, N50 1144 bp --- [Thu Mar 28 22:21:33 2019] ALL DONE. Time elapsed: 8786.971793 seconds ---