MEGAHIT v1.1.3 --- [Thu Mar 28 07:43:41 2019] Start assembly. Number of CPU threads 28 --- --- [Thu Mar 28 07:43:41 2019] Available memory: 269759385600, used: 242783447040 --- [Thu Mar 28 07:43:41 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_1_S3_L002_R1_001_val_1_val_1_val_1.fq.gz,/gscratch/srlab/sam/data/metagenomics/P_generosa/Library_Geoduck_MG_1_S3_L002_R2_001_val_2_val_2_val_2.fq.gz): pe, 163236894 reads, 131 max length' b' [utils.h : 126] Real: 164.6185\tuser: 149.5836\tsys: 13.8791\tmaxrss: 154980' --- [Thu Mar 28 07:46:25 2019] k list: 21,29,39,59,79,99,119,141 --- --- [Thu Mar 28 07:46:25 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: 5956255852' b' [read_lib_functions-inl.h : 260] After reading, sizeof seq_package: 5956255852' b' [cx1_kmer_count.cpp : 136] 163236894 reads, 131 max read length' b' [cx1.h : 457] Preparing data... Done. Time elapsed: 22.7792' 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: 8559463848, 236280944704' b' [cx1_kmer_count.cpp : 356] 2023172994, 19448828 8559463848 236280944704' b' [cx1_kmer_count.cpp : 363] Memory for reads: 6101579652' b' [cx1_kmer_count.cpp : 364] max # lv.1 items = 2023172994' b' [cx1.h : 480] Preparing partitions and initialing global data... Done. Time elapsed: 8.8486' b' [cx1.h : 486] Start main loop...' b' [cx1.h : 515] Lv1 scanning from bucket 0 to 285' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 8.4760' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 13.1476' b' [cx1.h : 515] Lv1 scanning from bucket 285 to 1680' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 9.1950' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 27.2104' b' [cx1.h : 515] Lv1 scanning from bucket 1680 to 4489' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 9.4044' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 30.5929' b' [cx1.h : 515] Lv1 scanning from bucket 4489 to 8890' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 9.7042' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 30.7517' b' [cx1.h : 515] Lv1 scanning from bucket 8890 to 15139' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 9.9961' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 29.9956' b' [cx1.h : 515] Lv1 scanning from bucket 15139 to 23768' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 10.2220' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 29.5096' b' [cx1.h : 515] Lv1 scanning from bucket 23768 to 36228' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 10.5745' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 29.4675' b' [cx1.h : 515] Lv1 scanning from bucket 36228 to 63530' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 10.9461' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 29.8098' b' [cx1.h : 515] Lv1 scanning from bucket 63530 to 65536' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 7.7537' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 0.4231' b' [cx1.h : 607] Main loop done. Time elapsed: 307.1819' b' [cx1.h : 613] Postprocessing...' b' [cx1_kmer_count.cpp : 860] Total number of candidate reads: 6024232(20841104)' b' [cx1_kmer_count.cpp : 871] Total number of solid edges: 1468939921' b' [cx1.h : 621] Postprocess done. Time elapsed: 3.9815' b' [utils.h : 126] Real: 342.8099\tuser: 8693.2507\tsys: 30.9935\tmaxrss: 15670368' --- [Thu Mar 28 07:52:08 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: 1468939921' b' [cx1_seq2sdbg.cpp : 434] Bases to reserve: 40395847822, number contigs: 0, number multiplicity: 1836174901' b' [cx1_seq2sdbg.cpp : 440] Before reading, sizeof seq_package: 10098961964, multiplicity vector: 1836174901' b' [cx1_seq2sdbg.cpp : 455] Adding mercy edges...' b' [cx1_seq2sdbg.cpp : 373] Number of reads: 6024232, Number of mercy edges: 85939371' b' [cx1_seq2sdbg.cpp : 462] Done. Time elapsed: 58.3099' b' [cx1_seq2sdbg.cpp : 529] After reading, sizeof seq_package: 10098961964, multiplicity vector: 1836174901' b' [cx1.h : 457] Preparing data... Done. Time elapsed: 294.1308' b' [cx1.h : 464] Preparing partitions and initialing global data...' b' [cx1_seq2sdbg.cpp : 740] Memory for sequence: 13475965452' b' [cx1_seq2sdbg.cpp : 741] max # lv.1 items = 1243903433' b' [cx1.h : 480] Preparing partitions and initialing global data... Done. Time elapsed: 3.2714' b' [cx1.h : 486] Start main loop...' b' [cx1.h : 515] Lv1 scanning from bucket 0 to 1290' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 3.0240' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 11.3328' b' [cx1.h : 515] Lv1 scanning from bucket 1290 to 4785' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 3.1528' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 12.9702' b' [cx1.h : 515] Lv1 scanning from bucket 4785 to 10214' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 3.1225' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 13.0806' b' [cx1.h : 515] Lv1 scanning from bucket 10214 to 17526' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 3.2031' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 13.3864' b' [cx1.h : 515] Lv1 scanning from bucket 17526 to 26754' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 3.2909' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 13.3733' b' [cx1.h : 515] Lv1 scanning from bucket 26754 to 38281' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 3.4020' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 13.7714' b' [cx1.h : 515] Lv1 scanning from bucket 38281 to 53262' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 3.7753' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 14.1675' b' [cx1.h : 515] Lv1 scanning from bucket 53262 to 65536' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 2.9587' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 8.0778' b' [cx1.h : 607] Main loop done. Time elapsed: 126.0905' 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] 24081849 888521906 652234543 650559125 890586474 17917523 8005293 7837050 18166986' b' [cx1_seq2sdbg.cpp :1151] Total number of edges: 3157910749' b' [cx1_seq2sdbg.cpp :1152] Total number of ONEs: 3081902048' b' [cx1_seq2sdbg.cpp :1153] Total number of $v edges: 24081849' b' [cx1.h : 621] Postprocess done. Time elapsed: 0.0431' b' [utils.h : 126] Real: 423.5709\tuser: 4853.2799\tsys: 50.2257\tmaxrss: 16571188' --- [Thu Mar 28 07:59:13 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: 175.152259' b' [assembler.cpp : 152] Number of Edges: 3157910749; 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: 1880916; time elapsed: 9.4861' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 4; Accumulated tips removed: 5865151; time elapsed: 11.4742' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 8; Accumulated tips removed: 10096101; time elapsed: 16.0910' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 16; Accumulated tips removed: 15780435; time elapsed: 26.0954' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 32; Accumulated tips removed: 21307170; time elapsed: 39.4801' b' [assembly_algorithms.cpp : 170] Removing tips with length less than 42; Accumulated tips removed: 23166654; time elapsed: 43.9292' b' [assembler.cpp : 179] Tips removal done! Time elapsed(sec): 146.670796' b' [assembler.cpp : 188] unitig graph size: 60188534, time for building: 329.246295' b' [assembler.cpp : 211] Number of bubbles removed: 2734283, Time elapsed(sec): 23.902949' b' [assembler.cpp : 225] Number of complex bubbles removed: 329079, Time elapsed(sec): 16.163467' b' [assembler.cpp : 243] Number unitigs disconnected: 13791185, time: 28.523810' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 83656, time: 6.517589' b' [assembler.cpp : 200] Tips removed: 88691, time: 16.475922' b' [assembler.cpp : 211] Number of bubbles removed: 79636, Time elapsed(sec): 6.591934' b' [assembler.cpp : 225] Number of complex bubbles removed: 141449, Time elapsed(sec): 11.990681' b' [assembler.cpp : 243] Number unitigs disconnected: 1382986, time: 8.644009' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 103, time: 6.244270' b' [assembler.cpp : 200] Tips removed: 1168803, time: 16.731009' b' [assembler.cpp : 211] Number of bubbles removed: 73243, Time elapsed(sec): 6.317226' b' [assembler.cpp : 225] Number of complex bubbles removed: 10987, Time elapsed(sec): 11.439439' b' [assembler.cpp : 243] Number unitigs disconnected: 14866, time: 7.348305' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 6, time: 6.168826' b' [assembler.cpp : 200] Tips removed: 4393, time: 15.333531' b' [assembler.cpp : 211] Number of bubbles removed: 367, Time elapsed(sec): 6.003634' b' [assembler.cpp : 225] Number of complex bubbles removed: 242, Time elapsed(sec): 11.469922' b' [assembler.cpp : 243] Number unitigs disconnected: 419, time: 7.356021' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 1, time: 6.201807' b' [assembler.cpp : 200] Tips removed: 113, time: 15.418995' b' [assembler.cpp : 211] Number of bubbles removed: 4, Time elapsed(sec): 6.034895' b' [assembler.cpp : 225] Number of complex bubbles removed: 12, Time elapsed(sec): 11.363564' b' [assembler.cpp : 243] Number unitigs disconnected: 12, time: 7.318168' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 0, time: 3.851266' b' [assembler.cpp : 132] Total length: 2292496382, N50: 69, Mean: 50, number of contigs: 45448816' b' [assembler.cpp : 133] Maximum length: 12476' b' [assembler.cpp : 290] Time to output: 88.753771' b' [assembler.cpp : 317] Number of local low depth unitigs removed: 1676112, complex bubbles removed: 100471, time: 563.317678' b' [assembler.cpp : 132] Total length: 1696485575, N50: 52, Mean: 45, number of contigs: 37204009' b' [assembler.cpp : 133] Maximum length: 12523' b' [utils.h : 126] Real: 1611.7901\tuser: 37989.0963\tsys: 47.0408\tmaxrss: 9965888' --- [Thu Mar 28 08:26:06 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: 953381, Mapper size: 37540636' b' [read_lib_functions-inl.h : 256] Before reading, sizeof seq_package: 5956255852' b' [read_lib_functions-inl.h : 260] After reading, sizeof seq_package: 5956255852' b' [local_assembler.cpp : 330] Lib 0, insert size: 240.02 sd: 84.71' b' [local_assembler.cpp : 462] Lib 0: total 163236894 reads, aligned 40098911, added 20530400 reads for local assembly' b' [utils.h : 126] Real: 333.9642\tuser: 8533.1626\tsys: 15.9527\tmaxrss: 8449892' --- [Thu Mar 28 08:31:40 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: 8771444' b' [iterate_edges.cpp : 570] Number of crusial kmers: 82189300' b' [iterate_edges.cpp : 443] Processed: 67108864, aligned: 45275922. Iterative edges: 222607612' b' [iterate_edges.cpp : 443] Processed: 134217728, aligned: 90676940. Iterative edges: 290465644' b' [iterate_edges.cpp : 447] Total: 163236894, aligned: 110357373. Iterative edges: 308353205' b' [iterate_edges.cpp : 451] Writing iterative edges...' b' [utils.h : 126] Real: 335.5329\tuser: 8103.7336\tsys: 14.3966\tmaxrss: 10749740' --- [Thu Mar 28 08:37:15 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: 308353205' b' [cx1_seq2sdbg.cpp : 434] Bases to reserve: 13645702065, number contigs: 83785198, number multiplicity: 392138403' b' [cx1_seq2sdbg.cpp : 440] Before reading, sizeof seq_package: 4081707112, multiplicity vector: 392138403' b' [cx1_seq2sdbg.cpp : 529] After reading, sizeof seq_package: 4081707112, multiplicity vector: 392138403' b' [cx1.h : 457] Preparing data... Done. Time elapsed: 33.3748' b' [cx1.h : 464] Preparing partitions and initialing global data...' b' [cx1_seq2sdbg.cpp : 740] Memory for sequence: 4855633316' b' [cx1_seq2sdbg.cpp : 741] max # lv.1 items = 769456317' b' [cx1.h : 480] Preparing partitions and initialing global data... Done. Time elapsed: 10.8724' b' [cx1.h : 486] Start main loop...' b' [cx1.h : 515] Lv1 scanning from bucket 0 to 1001' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 7.9322' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 9.9642' b' [cx1.h : 515] Lv1 scanning from bucket 1001 to 4179' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 10.3021' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 12.6492' b' [cx1.h : 515] Lv1 scanning from bucket 4179 to 9338' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 11.5261' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 13.3270' b' [cx1.h : 515] Lv1 scanning from bucket 9338 to 16418' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 12.4718' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 13.8190' b' [cx1.h : 515] Lv1 scanning from bucket 16418 to 25463' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 13.4795' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 14.6985' b' [cx1.h : 515] Lv1 scanning from bucket 25463 to 36874' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 13.6641' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 14.7165' b' [cx1.h : 515] Lv1 scanning from bucket 36874 to 51782' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 13.1200' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 14.8731' b' [cx1.h : 515] Lv1 scanning from bucket 51782 to 65536' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 9.8732' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 9.5304' b' [cx1.h : 607] Main loop done. Time elapsed: 195.9481' 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] 22076748 797398687 585428163 584685973 798255717 4123943 3356625 2567082 4508512' b' [cx1_seq2sdbg.cpp :1151] Total number of edges: 2802401450' b' [cx1_seq2sdbg.cpp :1152] Total number of ONEs: 2765768540' b' [cx1_seq2sdbg.cpp :1153] Total number of $v edges: 22076748' b' [cx1.h : 621] Postprocess done. Time elapsed: 0.0416' b' [utils.h : 126] Real: 240.2478\tuser: 3242.2506\tsys: 24.6674\tmaxrss: 7103696' --- [Thu Mar 28 08:41:16 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: 159.147005' b' [assembler.cpp : 152] Number of Edges: 2802401450; 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: 723098; time elapsed: 8.7546' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 4; Accumulated tips removed: 2402909; time elapsed: 10.8086' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 8; Accumulated tips removed: 4137148; time elapsed: 15.5141' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 16; Accumulated tips removed: 6715820; time elapsed: 26.5027' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 32; Accumulated tips removed: 11440738; time elapsed: 45.9404' b' [assembly_algorithms.cpp : 170] Removing tips with length less than 58; Accumulated tips removed: 15752263; time elapsed: 63.6434' b' [assembler.cpp : 179] Tips removal done! Time elapsed(sec): 171.265606' b' [assembler.cpp : 188] unitig graph size: 20453156, time for building: 190.891091' b' [assembler.cpp : 211] Number of bubbles removed: 2003261, Time elapsed(sec): 23.388035' b' [assembler.cpp : 225] Number of complex bubbles removed: 339476, Time elapsed(sec): 8.803627' b' [assembler.cpp : 243] Number unitigs disconnected: 315728, time: 3.474498' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 23852, time: 2.800756' b' [assembler.cpp : 200] Tips removed: 25539, time: 5.258521' b' [assembler.cpp : 211] Number of bubbles removed: 23089, Time elapsed(sec): 2.713746' b' [assembler.cpp : 225] Number of complex bubbles removed: 10889, Time elapsed(sec): 3.736385' b' [assembler.cpp : 243] Number unitigs disconnected: 34035, time: 3.170514' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 253, time: 2.775058' b' [assembler.cpp : 200] Tips removed: 11820, time: 5.087869' b' [assembler.cpp : 211] Number of bubbles removed: 2986, Time elapsed(sec): 2.063390' b' [assembler.cpp : 225] Number of complex bubbles removed: 1078, Time elapsed(sec): 3.558139' b' [assembler.cpp : 243] Number unitigs disconnected: 3091, time: 3.134904' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 35, time: 2.772917' b' [assembler.cpp : 200] Tips removed: 271, time: 5.055468' b' [assembler.cpp : 211] Number of bubbles removed: 37, Time elapsed(sec): 1.960461' b' [assembler.cpp : 225] Number of complex bubbles removed: 40, Time elapsed(sec): 3.567104' b' [assembler.cpp : 243] Number unitigs disconnected: 418, time: 3.107686' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 7, time: 2.750683' b' [assembler.cpp : 200] Tips removed: 19, time: 5.109951' b' [assembler.cpp : 211] Number of bubbles removed: 0, Time elapsed(sec): 1.968285' b' [assembler.cpp : 225] Number of complex bubbles removed: 4, Time elapsed(sec): 3.563101' b' [assembler.cpp : 243] Number unitigs disconnected: 70, time: 3.135056' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 3, time: 2.774807' b' [assembler.cpp : 132] Total length: 1634444679, N50: 129, Mean: 101, number of contigs: 16101529' b' [assembler.cpp : 133] Maximum length: 76927' b' [assembler.cpp : 290] Time to output: 51.391072' b' [assembler.cpp : 317] Number of local low depth unitigs removed: 237007, complex bubbles removed: 27088, time: 189.960423' b' [assembler.cpp : 132] Total length: 783881345, N50: 91, Mean: 76, number of contigs: 10299692' b' [assembler.cpp : 133] Maximum length: 76927' b' [utils.h : 126] Real: 890.0549\tuser: 19274.5376\tsys: 31.6778\tmaxrss: 7644016' --- [Thu Mar 28 08:56:07 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: 1223456, Mapper size: 63215542' b' [read_lib_functions-inl.h : 256] Before reading, sizeof seq_package: 5956255852' b' [read_lib_functions-inl.h : 260] After reading, sizeof seq_package: 5956255852' b' [local_assembler.cpp : 330] Lib 0, insert size: 257.35 sd: 95.53' b' [local_assembler.cpp : 462] Lib 0: total 163236894 reads, aligned 67454196, added 21654600 reads for local assembly' b' [utils.h : 126] Real: 457.9019\tuser: 11998.5180\tsys: 16.4810\tmaxrss: 9501980' --- [Thu Mar 28 09:03:45 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: 6804065' b' [iterate_edges.cpp : 570] Number of crusial kmers: 27150890' b' [iterate_edges.cpp : 443] Processed: 67108864, aligned: 30949892. Iterative edges: 108872676' b' [iterate_edges.cpp : 443] Processed: 134217728, aligned: 62025430. Iterative edges: 138342190' b' [iterate_edges.cpp : 447] Total: 163236894, aligned: 75525109. Iterative edges: 146028056' b' [iterate_edges.cpp : 451] Writing iterative edges...' b' [utils.h : 126] Real: 301.9728\tuser: 7318.7440\tsys: 9.9366\tmaxrss: 5768048' --- [Thu Mar 28 09:08:47 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: 146028056' b' [cx1_seq2sdbg.cpp : 434] Bases to reserve: 8677297813, number contigs: 28418038, number multiplicity: 174446094' b' [cx1_seq2sdbg.cpp : 440] Before reading, sizeof seq_package: 2396668768, multiplicity vector: 174446094' b' [cx1_seq2sdbg.cpp : 529] After reading, sizeof seq_package: 2396668768, multiplicity vector: 174446094' b' [cx1.h : 457] Preparing data... Done. Time elapsed: 20.0240' b' [cx1.h : 464] Preparing partitions and initialing global data...' b' [cx1_seq2sdbg.cpp : 740] Memory for sequence: 2793170734' b' [cx1_seq2sdbg.cpp : 741] max # lv.1 items = 667511274' b' [cx1.h : 480] Preparing partitions and initialing global data... Done. Time elapsed: 9.1730' b' [cx1.h : 486] Start main loop...' b' [cx1.h : 515] Lv1 scanning from bucket 0 to 1227' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 7.6840' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 9.3225' b' [cx1.h : 515] Lv1 scanning from bucket 1227 to 4664' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 9.5160' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 11.4059' b' [cx1.h : 515] Lv1 scanning from bucket 4664 to 9997' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 10.6449' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 11.8636' b' [cx1.h : 515] Lv1 scanning from bucket 9997 to 17192' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 11.1266' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 12.5013' b' [cx1.h : 515] Lv1 scanning from bucket 17192 to 26337' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 12.4965' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 13.2751' b' [cx1.h : 515] Lv1 scanning from bucket 26337 to 37857' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 11.8242' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 13.8794' b' [cx1.h : 515] Lv1 scanning from bucket 37857 to 52998' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 11.6472' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 13.5647' b' [cx1.h : 515] Lv1 scanning from bucket 52998 to 65536' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 8.3537' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 7.8950' b' [cx1.h : 607] Main loop done. Time elapsed: 177.0021' 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] 14232908 696559869 517149799 516354809 697331975 2378782 1298377 1285378 2384293' b' [cx1_seq2sdbg.cpp :1151] Total number of edges: 2448976190' b' [cx1_seq2sdbg.cpp :1152] Total number of ONEs: 2427396452' b' [cx1_seq2sdbg.cpp :1153] Total number of $v edges: 14232908' b' [cx1.h : 621] Postprocess done. Time elapsed: 0.0418' b' [utils.h : 126] Real: 206.2486\tuser: 2891.4618\tsys: 18.2616\tmaxrss: 5420136' --- [Thu Mar 28 09:12:13 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: 172.057826' b' [assembler.cpp : 152] Number of Edges: 2448976190; 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: 129292; time elapsed: 7.0460' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 4; Accumulated tips removed: 600005; time elapsed: 8.3357' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 8; Accumulated tips removed: 1157892; time elapsed: 11.7012' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 16; Accumulated tips removed: 1841673; time elapsed: 19.7868' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 32; Accumulated tips removed: 2826495; time elapsed: 35.6178' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 64; Accumulated tips removed: 6497573; time elapsed: 58.3924' b' [assembly_algorithms.cpp : 170] Removing tips with length less than 78; Accumulated tips removed: 8503495; time elapsed: 57.4780' b' [assembler.cpp : 179] Tips removal done! Time elapsed(sec): 198.448591' b' [assembler.cpp : 188] unitig graph size: 12187592, time for building: 155.211031' b' [assembler.cpp : 211] Number of bubbles removed: 1377251, Time elapsed(sec): 22.934429' b' [assembler.cpp : 225] Number of complex bubbles removed: 226712, Time elapsed(sec): 7.043686' b' [assembler.cpp : 243] Number unitigs disconnected: 185605, time: 1.634749' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 49818, time: 1.422181' b' [assembler.cpp : 200] Tips removed: 26103, time: 3.781121' b' [assembler.cpp : 211] Number of bubbles removed: 25231, Time elapsed(sec): 1.977816' b' [assembler.cpp : 225] Number of complex bubbles removed: 12308, Time elapsed(sec): 2.180771' b' [assembler.cpp : 243] Number unitigs disconnected: 13613, time: 1.477437' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 324, time: 1.329998' b' [assembler.cpp : 200] Tips removed: 6758, time: 3.639695' b' [assembler.cpp : 211] Number of bubbles removed: 1794, Time elapsed(sec): 1.223556' b' [assembler.cpp : 225] Number of complex bubbles removed: 1198, Time elapsed(sec): 1.894096' b' [assembler.cpp : 243] Number unitigs disconnected: 739, time: 1.461586' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 39, time: 1.326315' b' [assembler.cpp : 200] Tips removed: 104, time: 3.629709' b' [assembler.cpp : 211] Number of bubbles removed: 14, Time elapsed(sec): 1.111533' b' [assembler.cpp : 225] Number of complex bubbles removed: 22, Time elapsed(sec): 1.817334' b' [assembler.cpp : 243] Number unitigs disconnected: 116, time: 1.460132' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 9, time: 1.321154' b' [assembler.cpp : 200] Tips removed: 11, time: 3.605135' b' [assembler.cpp : 211] Number of bubbles removed: 0, Time elapsed(sec): 1.093688' b' [assembler.cpp : 225] Number of complex bubbles removed: 1, Time elapsed(sec): 1.867697' b' [assembler.cpp : 243] Number unitigs disconnected: 35, time: 1.461946' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 2, time: 1.325856' b' [assembler.cpp : 132] Total length: 1350607562, N50: 178, Mean: 148, number of contigs: 9122872' b' [assembler.cpp : 133] Maximum length: 123010' b' [assembler.cpp : 290] Time to output: 41.591673' b' [assembler.cpp : 317] Number of local low depth unitigs removed: 55519, complex bubbles removed: 7964, time: 119.331294' b' [assembler.cpp : 132] Total length: 585926756, N50: 138, Mean: 111, number of contigs: 5272800' b' [assembler.cpp : 133] Maximum length: 122240' b' [utils.h : 126] Real: 775.5675\tuser: 15732.2743\tsys: 28.2904\tmaxrss: 6121036' --- [Thu Mar 28 09:25:09 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: 1265018, Mapper size: 72633790' b' [read_lib_functions-inl.h : 256] Before reading, sizeof seq_package: 5956255852' b' [read_lib_functions-inl.h : 260] After reading, sizeof seq_package: 5956255852' b' [local_assembler.cpp : 330] Lib 0, insert size: 261.22 sd: 97.83' b' [local_assembler.cpp : 462] Lib 0: total 163236894 reads, aligned 79922651, added 24440893 reads for local assembly' b' [utils.h : 126] Real: 589.9428\tuser: 15757.4948\tsys: 17.5669\tmaxrss: 10099212' --- [Thu Mar 28 09:34:59 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: 4530667' b' [iterate_edges.cpp : 570] Number of crusial kmers: 14446213' b' [iterate_edges.cpp : 443] Processed: 67108864, aligned: 21252564. Iterative edges: 103559766' b' [iterate_edges.cpp : 443] Processed: 134217728, aligned: 42543298. Iterative edges: 137568809' b' [iterate_edges.cpp : 447] Total: 163236894, aligned: 51873198. Iterative edges: 146983277' b' [iterate_edges.cpp : 451] Writing iterative edges...' b' [utils.h : 126] Real: 275.0311\tuser: 6464.1424\tsys: 11.7797\tmaxrss: 5946392' --- [Thu Mar 28 09:39:34 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: 146983277' b' [cx1_seq2sdbg.cpp : 434] Bases to reserve: 11334147170, number contigs: 16306612, number multiplicity: 163289889' b' [cx1_seq2sdbg.cpp : 440] Before reading, sizeof seq_package: 2963989700, multiplicity vector: 163289889' b' [cx1_seq2sdbg.cpp : 529] After reading, sizeof seq_package: 5797526496, multiplicity vector: 163289889' b' [cx1.h : 457] Preparing data... Done. Time elapsed: 20.8179' b' [cx1.h : 464] Preparing partitions and initialing global data...' b' [cx1_seq2sdbg.cpp : 740] Memory for sequence: 6203340620' b' [cx1_seq2sdbg.cpp : 741] max # lv.1 items = 621386794' b' [cx1.h : 480] Preparing partitions and initialing global data... Done. Time elapsed: 10.5954' b' [cx1.h : 486] Start main loop...' b' [cx1.h : 515] Lv1 scanning from bucket 0 to 1105' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 9.2953' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 8.2891' b' [cx1.h : 515] Lv1 scanning from bucket 1105 to 4376' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 11.6615' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 10.6964' b' [cx1.h : 515] Lv1 scanning from bucket 4376 to 9561' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 13.6629' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 10.7472' b' [cx1.h : 515] Lv1 scanning from bucket 9561 to 16633' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 13.3539' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 11.5747' b' [cx1.h : 515] Lv1 scanning from bucket 16633 to 25703' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 13.7217' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 11.8886' b' [cx1.h : 515] Lv1 scanning from bucket 25703 to 37211' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 14.7034' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 12.2289' b' [cx1.h : 515] Lv1 scanning from bucket 37211 to 52434' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 14.1351' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 12.3159' b' [cx1.h : 515] Lv1 scanning from bucket 52434 to 65536' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 10.8281' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 7.2977' b' [cx1.h : 607] Main loop done. Time elapsed: 186.4015' 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] 10463808 590412104 436987361 436500397 591020418 1106903 914794 697103 1214687' b' [cx1_seq2sdbg.cpp :1151] Total number of edges: 2069317575' b' [cx1_seq2sdbg.cpp :1152] Total number of ONEs: 2054920280' b' [cx1_seq2sdbg.cpp :1153] Total number of $v edges: 10463808' b' [cx1.h : 621] Postprocess done. Time elapsed: 0.0404' b' [utils.h : 126] Real: 217.8647\tuser: 2620.0241\tsys: 21.0089\tmaxrss: 5939036' --- [Thu Mar 28 09:43:13 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: 124.612985' b' [assembler.cpp : 152] Number of Edges: 2069317575; 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: 69774; time elapsed: 5.8593' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 4; Accumulated tips removed: 273781; time elapsed: 6.7455' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 8; Accumulated tips removed: 601519; time elapsed: 9.3110' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 16; Accumulated tips removed: 1148956; time elapsed: 15.1582' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 32; Accumulated tips removed: 1781020; time elapsed: 26.0020' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 64; Accumulated tips removed: 4381017; time elapsed: 45.0992' b' [assembly_algorithms.cpp : 170] Removing tips with length less than 118; Accumulated tips removed: 9418224; time elapsed: 47.1745' b' [assembler.cpp : 179] Tips removal done! Time elapsed(sec): 155.424416' b' [assembler.cpp : 188] unitig graph size: 5004740, time for building: 106.343801' b' [assembler.cpp : 211] Number of bubbles removed: 611391, Time elapsed(sec): 16.399180' b' [assembler.cpp : 225] Number of complex bubbles removed: 126734, Time elapsed(sec): 5.728647' b' [assembler.cpp : 243] Number unitigs disconnected: 211302, time: 0.760506' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 79087, time: 0.749839' b' [assembler.cpp : 200] Tips removed: 4879, time: 1.363339' b' [assembler.cpp : 211] Number of bubbles removed: 24859, Time elapsed(sec): 1.528392' b' [assembler.cpp : 225] Number of complex bubbles removed: 15138, Time elapsed(sec): 1.437901' b' [assembler.cpp : 243] Number unitigs disconnected: 11029, time: 0.607729' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 606, time: 0.540452' b' [assembler.cpp : 200] Tips removed: 5724, time: 1.328643' b' [assembler.cpp : 211] Number of bubbles removed: 1031, Time elapsed(sec): 0.608291' b' [assembler.cpp : 225] Number of complex bubbles removed: 1064, Time elapsed(sec): 0.838156' b' [assembler.cpp : 243] Number unitigs disconnected: 342, time: 0.598240' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 61, time: 0.541812' b' [assembler.cpp : 200] Tips removed: 79, time: 1.306095' b' [assembler.cpp : 211] Number of bubbles removed: 12, Time elapsed(sec): 0.407419' b' [assembler.cpp : 225] Number of complex bubbles removed: 22, Time elapsed(sec): 0.740418' b' [assembler.cpp : 243] Number unitigs disconnected: 40, time: 0.597217' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 9, time: 0.542974' b' [assembler.cpp : 200] Tips removed: 6, time: 1.302215' b' [assembler.cpp : 211] Number of bubbles removed: 0, Time elapsed(sec): 0.404550' b' [assembler.cpp : 225] Number of complex bubbles removed: 1, Time elapsed(sec): 0.742298' b' [assembler.cpp : 243] Number unitigs disconnected: 7, time: 0.596206' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 0, time: 0.347611' b' [assembler.cpp : 132] Total length: 915935218, N50: 400, Mean: 274, number of contigs: 3333204' b' [assembler.cpp : 133] Maximum length: 175414' b' [assembler.cpp : 290] Time to output: 28.686693' b' [assembler.cpp : 317] Number of local low depth unitigs removed: 15129, complex bubbles removed: 2152, time: 46.122223' b' [assembler.cpp : 132] Total length: 398175969, N50: 341, Mean: 202, number of contigs: 1970923' b' [assembler.cpp : 133] Maximum length: 175414' b' [utils.h : 126] Real: 512.7794\tuser: 10120.3187\tsys: 19.2431\tmaxrss: 4939024' --- [Thu Mar 28 09:51:46 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: 1329352, Mapper size: 81773454' b' [read_lib_functions-inl.h : 256] Before reading, sizeof seq_package: 5956255852' b' [read_lib_functions-inl.h : 260] After reading, sizeof seq_package: 5956255852' b' [local_assembler.cpp : 330] Lib 0, insert size: 263.22 sd: 99.50' b' [local_assembler.cpp : 462] Lib 0: total 163236894 reads, aligned 90809721, added 26225585 reads for local assembly' b' [utils.h : 126] Real: 696.1981\tuser: 18761.5486\tsys: 18.3276\tmaxrss: 10421896' --- [Thu Mar 28 10:03:22 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: 2032018' b' [iterate_edges.cpp : 570] Number of crusial kmers: 5667605' b' [iterate_edges.cpp : 443] Processed: 67108864, aligned: 10969258. Iterative edges: 38222444' b' [iterate_edges.cpp : 443] Processed: 134217728, aligned: 21833817. Iterative edges: 49438467' b' [iterate_edges.cpp : 447] Total: 163236894, aligned: 26680875. Iterative edges: 52505891' b' [iterate_edges.cpp : 451] Writing iterative edges...' b' [utils.h : 126] Real: 172.7727\tuser: 4236.3557\tsys: 6.9077\tmaxrss: 2467644' --- [Thu Mar 28 10:06:15 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: 52505891' b' [cx1_seq2sdbg.cpp : 434] Bases to reserve: 6100891465, number contigs: 6969644, number multiplicity: 59475535' b' [cx1_seq2sdbg.cpp : 440] Before reading, sizeof seq_package: 1580980028, multiplicity vector: 59475535' b' [cx1_seq2sdbg.cpp : 529] After reading, sizeof seq_package: 3106202896, multiplicity vector: 59475535' b' [cx1.h : 457] Preparing data... Done. Time elapsed: 12.1187' b' [cx1.h : 464] Preparing partitions and initialing global data...' b' [cx1_seq2sdbg.cpp : 740] Memory for sequence: 3270469316' b' [cx1_seq2sdbg.cpp : 741] max # lv.1 items = 454084009' b' [cx1.h : 480] Preparing partitions and initialing global data... Done. Time elapsed: 7.1586' b' [cx1.h : 486] Start main loop...' b' [cx1.h : 515] Lv1 scanning from bucket 0 to 950' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 6.8053' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 5.4857' b' [cx1.h : 515] Lv1 scanning from bucket 950 to 3974' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 8.0311' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 7.2638' b' [cx1.h : 515] Lv1 scanning from bucket 3974 to 8915' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 8.1859' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 7.6997' b' [cx1.h : 515] Lv1 scanning from bucket 8915 to 15772' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 8.5207' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 8.2991' b' [cx1.h : 515] Lv1 scanning from bucket 15772 to 24696' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 9.5391' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 8.6065' b' [cx1.h : 515] Lv1 scanning from bucket 24696 to 36153' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 8.7716' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 9.0351' b' [cx1.h : 515] Lv1 scanning from bucket 36153 to 51443' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 8.9094' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 8.9148' b' [cx1.h : 515] Lv1 scanning from bucket 51443 to 65536' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 6.4077' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 5.5815' b' [cx1.h : 607] Main loop done. Time elapsed: 126.0581' 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] 4259934 451165620 330374491 330093459 451497874 652442 366265 479614 595593' b' [cx1_seq2sdbg.cpp :1151] Total number of edges: 1569485292' b' [cx1_seq2sdbg.cpp :1152] Total number of ONEs: 1563131444' b' [cx1_seq2sdbg.cpp :1153] Total number of $v edges: 4259934' b' [cx1.h : 621] Postprocess done. Time elapsed: 0.0380' b' [utils.h : 126] Real: 145.3789\tuser: 1869.9691\tsys: 14.1498\tmaxrss: 3665528' --- [Thu Mar 28 10:08:41 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: 91.265754' b' [assembler.cpp : 152] Number of Edges: 1569485292; 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: 34176; time elapsed: 4.3726' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 4; Accumulated tips removed: 130191; time elapsed: 4.6036' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 8; Accumulated tips removed: 287501; time elapsed: 5.6620' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 16; Accumulated tips removed: 564237; time elapsed: 8.1718' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 32; Accumulated tips removed: 878355; time elapsed: 12.5028' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 64; Accumulated tips removed: 1586363; time elapsed: 20.4692' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 128; Accumulated tips removed: 2948886; time elapsed: 30.3726' b' [assembly_algorithms.cpp : 170] Removing tips with length less than 158; Accumulated tips removed: 3503153; time elapsed: 27.8754' b' [assembler.cpp : 179] Tips removal done! Time elapsed(sec): 114.089295' b' [assembler.cpp : 188] unitig graph size: 2698713, time for building: 83.697607' b' [assembler.cpp : 211] Number of bubbles removed: 284745, Time elapsed(sec): 11.403540' b' [assembler.cpp : 225] Number of complex bubbles removed: 67025, Time elapsed(sec): 4.527230' b' [assembler.cpp : 243] Number unitigs disconnected: 221281, time: 0.491719' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 84898, time: 0.584423' b' [assembler.cpp : 200] Tips removed: 3118, time: 0.865737' b' [assembler.cpp : 211] Number of bubbles removed: 18641, Time elapsed(sec): 1.086586' b' [assembler.cpp : 225] Number of complex bubbles removed: 13261, Time elapsed(sec): 1.200197' b' [assembler.cpp : 243] Number unitigs disconnected: 9464, time: 0.325431' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 1215, time: 0.327099' b' [assembler.cpp : 200] Tips removed: 6075, time: 0.826690' b' [assembler.cpp : 211] Number of bubbles removed: 582, Time elapsed(sec): 0.256400' b' [assembler.cpp : 225] Number of complex bubbles removed: 837, Time elapsed(sec): 0.510799' b' [assembler.cpp : 243] Number unitigs disconnected: 315, time: 0.316478' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 170, time: 0.321623' b' [assembler.cpp : 200] Tips removed: 151, time: 0.804926' b' [assembler.cpp : 211] Number of bubbles removed: 12, Time elapsed(sec): 0.200732' b' [assembler.cpp : 225] Number of complex bubbles removed: 25, Time elapsed(sec): 0.434654' b' [assembler.cpp : 243] Number unitigs disconnected: 25, time: 0.314067' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 29, time: 0.320324' b' [assembler.cpp : 200] Tips removed: 11, time: 0.787407' b' [assembler.cpp : 211] Number of bubbles removed: 0, Time elapsed(sec): 0.199399' b' [assembler.cpp : 225] Number of complex bubbles removed: 1, Time elapsed(sec): 0.437181' b' [assembler.cpp : 243] Number unitigs disconnected: 3, time: 0.314291' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 1, time: 0.321282' b' [assembler.cpp : 132] Total length: 757353971, N50: 663, Mean: 450, number of contigs: 1681817' b' [assembler.cpp : 133] Maximum length: 324378' b' [assembler.cpp : 290] Time to output: 24.724339' b' [assembler.cpp : 317] Number of local low depth unitigs removed: 8705, complex bubbles removed: 866, time: 27.038149' b' [assembler.cpp : 132] Total length: 291571366, N50: 722, Mean: 337, number of contigs: 863706' b' [assembler.cpp : 133] Maximum length: 324378' b' [utils.h : 126] Real: 376.6401\tuser: 7384.1375\tsys: 15.9970\tmaxrss: 3628252' --- [Thu Mar 28 10:14:58 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: 1066237, Mapper size: 80643634' b' [read_lib_functions-inl.h : 256] Before reading, sizeof seq_package: 5956255852' b' [read_lib_functions-inl.h : 260] After reading, sizeof seq_package: 5956255852' b' [local_assembler.cpp : 330] Lib 0, insert size: 267.83 sd: 101.76' b' [local_assembler.cpp : 462] Lib 0: total 163236894 reads, aligned 88594208, added 19492281 reads for local assembly' b' [utils.h : 126] Real: 596.0838\tuser: 16011.2016\tsys: 15.1723\tmaxrss: 9999424' --- [Thu Mar 28 10:24:54 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: 955826' b' [iterate_edges.cpp : 570] Number of crusial kmers: 2492875' b' [iterate_edges.cpp : 443] Processed: 67108864, aligned: 4756426. Iterative edges: 14947041' b' [iterate_edges.cpp : 443] Processed: 134217728, aligned: 9453840. Iterative edges: 19855413' b' [iterate_edges.cpp : 447] Total: 163236894, aligned: 11569810. Iterative edges: 21242872' b' [iterate_edges.cpp : 451] Writing iterative edges...' b' [utils.h : 126] Real: 105.0008\tuser: 2542.0387\tsys: 4.8619\tmaxrss: 1440432' --- [Thu Mar 28 10:26:39 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: 21242872' b' [cx1_seq2sdbg.cpp : 434] Bases to reserve: 3559817186, number contigs: 3432574, number multiplicity: 24675446' b' [cx1_seq2sdbg.cpp : 440] Before reading, sizeof seq_package: 917414900, multiplicity vector: 24675446' b' [cx1_seq2sdbg.cpp : 529] After reading, sizeof seq_package: 1807369200, multiplicity vector: 24675446' b' [cx1.h : 457] Preparing data... Done. Time elapsed: 8.1025' b' [cx1.h : 464] Preparing partitions and initialing global data...' b' [cx1_seq2sdbg.cpp : 740] Memory for sequence: 1885177266' b' [cx1_seq2sdbg.cpp : 741] max # lv.1 items = 360602460' b' [cx1.h : 480] Preparing partitions and initialing global data... Done. Time elapsed: 3.7925' b' [cx1.h : 486] Start main loop...' b' [cx1.h : 515] Lv1 scanning from bucket 0 to 824' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 3.1212' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 4.1645' b' [cx1.h : 515] Lv1 scanning from bucket 824 to 3652' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 4.2457' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 5.8087' b' [cx1.h : 515] Lv1 scanning from bucket 3652 to 8408' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 4.5881' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 6.3905' b' [cx1.h : 515] Lv1 scanning from bucket 8408 to 15108' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 4.5170' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 6.8943' b' [cx1.h : 515] Lv1 scanning from bucket 15108 to 23922' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 4.6931' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 6.9800' b' [cx1.h : 515] Lv1 scanning from bucket 23922 to 35321' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 4.9268' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 7.0023' b' [cx1.h : 515] Lv1 scanning from bucket 35321 to 50601' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 5.0208' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 7.5164' b' [cx1.h : 515] Lv1 scanning from bucket 50601 to 65536' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 3.9715' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 4.9363' b' [cx1.h : 607] Main loop done. Time elapsed: 84.7782' 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] 2586579 384856189 281712297 281518977 385081829 350897 180741 180891 351858' b' [cx1_seq2sdbg.cpp :1151] Total number of edges: 1336820258' b' [cx1_seq2sdbg.cpp :1152] Total number of ONEs: 1333169292' b' [cx1_seq2sdbg.cpp :1153] Total number of $v edges: 2586579' b' [cx1.h : 621] Postprocess done. Time elapsed: 0.1158' b' [utils.h : 126] Real: 96.7945\tuser: 1506.0243\tsys: 9.8620\tmaxrss: 2601160' --- [Thu Mar 28 10:28:16 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: 63.893116' b' [assembler.cpp : 152] Number of Edges: 1336820258; 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: 20514; time elapsed: 3.6626' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 4; Accumulated tips removed: 76264; time elapsed: 3.7737' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 8; Accumulated tips removed: 173774; time elapsed: 4.4076' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 16; Accumulated tips removed: 345538; time elapsed: 5.8656' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 32; Accumulated tips removed: 533298; time elapsed: 8.6079' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 64; Accumulated tips removed: 791303; time elapsed: 13.7750' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 128; Accumulated tips removed: 1282645; time elapsed: 22.0106' b' [assembly_algorithms.cpp : 170] Removing tips with length less than 198; Accumulated tips removed: 1848490; time elapsed: 27.1752' b' [assembler.cpp : 179] Tips removal done! Time elapsed(sec): 89.329435' b' [assembler.cpp : 188] unitig graph size: 1494675, time for building: 75.510465' b' [assembler.cpp : 211] Number of bubbles removed: 126156, Time elapsed(sec): 7.464600' b' [assembler.cpp : 225] Number of complex bubbles removed: 30811, Time elapsed(sec): 3.032006' b' [assembler.cpp : 243] Number unitigs disconnected: 129448, time: 0.278438' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 48695, time: 0.345085' b' [assembler.cpp : 200] Tips removed: 1581, time: 0.466906' b' [assembler.cpp : 211] Number of bubbles removed: 8240, Time elapsed(sec): 0.660168' b' [assembler.cpp : 225] Number of complex bubbles removed: 7758, Time elapsed(sec): 1.029322' b' [assembler.cpp : 243] Number unitigs disconnected: 4949, time: 0.168614' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 721, time: 0.155223' b' [assembler.cpp : 200] Tips removed: 2983, time: 0.464177' b' [assembler.cpp : 211] Number of bubbles removed: 222, Time elapsed(sec): 0.148643' b' [assembler.cpp : 225] Number of complex bubbles removed: 514, Time elapsed(sec): 0.372658' b' [assembler.cpp : 243] Number unitigs disconnected: 187, time: 0.162238' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 100, time: 0.150459' b' [assembler.cpp : 200] Tips removed: 84, time: 0.438159' b' [assembler.cpp : 211] Number of bubbles removed: 2, Time elapsed(sec): 0.107423' b' [assembler.cpp : 225] Number of complex bubbles removed: 11, Time elapsed(sec): 0.291233' b' [assembler.cpp : 243] Number unitigs disconnected: 9, time: 0.163404' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 6, time: 0.149328' b' [assembler.cpp : 200] Tips removed: 2, time: 0.437869' b' [assembler.cpp : 211] Number of bubbles removed: 0, Time elapsed(sec): 0.108075' b' [assembler.cpp : 225] Number of complex bubbles removed: 0, Time elapsed(sec): 0.291446' b' [assembler.cpp : 243] Number unitigs disconnected: 0, time: 0.163467' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 2, time: 0.148489' b' [assembler.cpp : 132] Total length: 670150936, N50: 955, Mean: 676, number of contigs: 990865' b' [assembler.cpp : 133] Maximum length: 368845' b' [assembler.cpp : 290] Time to output: 21.790413' b' [assembler.cpp : 317] Number of local low depth unitigs removed: 4231, complex bubbles removed: 478, time: 8.254161' b' [assembler.cpp : 132] Total length: 203342089, N50: 1535, Mean: 568, number of contigs: 357491' b' [assembler.cpp : 133] Maximum length: 368845' b' [utils.h : 126] Real: 282.5954\tuser: 5595.6047\tsys: 12.6242\tmaxrss: 3036204' --- [Thu Mar 28 10:32:59 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: 793861, Mapper size: 76520497' b' [read_lib_functions-inl.h : 256] Before reading, sizeof seq_package: 5956255852' b' [read_lib_functions-inl.h : 260] After reading, sizeof seq_package: 5956255852' b' [local_assembler.cpp : 330] Lib 0, insert size: 272.13 sd: 103.07' b' [local_assembler.cpp : 462] Lib 0: total 163236894 reads, aligned 83462352, added 11804006 reads for local assembly' b' [utils.h : 126] Real: 436.7207\tuser: 11571.7184\tsys: 13.3392\tmaxrss: 9501464' --- [Thu Mar 28 10:40:16 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: 397225' b' [iterate_edges.cpp : 570] Number of crusial kmers: 977477' b' [iterate_edges.cpp : 443] Processed: 67108864, aligned: 1357327. Iterative edges: 3413261' b' [iterate_edges.cpp : 443] Processed: 134217728, aligned: 2695138. Iterative edges: 5002165' b' [iterate_edges.cpp : 447] Total: 163236894, aligned: 3303257. Iterative edges: 5506235' b' [iterate_edges.cpp : 451] Writing iterative edges...' b' [utils.h : 126] Real: 57.2090\tuser: 1350.0695\tsys: 3.9323\tmaxrss: 726356' --- [Thu Mar 28 10:41:13 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: 5506235' b' [cx1_seq2sdbg.cpp : 434] Bases to reserve: 1661596316, number contigs: 1652797, number multiplicity: 7159032' b' [cx1_seq2sdbg.cpp : 440] Before reading, sizeof seq_package: 428621464, multiplicity vector: 7159032' b' [cx1_seq2sdbg.cpp : 529] After reading, sizeof seq_package: 857242928, multiplicity vector: 14318064' b' [cx1.h : 457] Preparing data... Done. Time elapsed: 5.6217' b' [cx1.h : 464] Preparing partitions and initialing global data...' b' [cx1_seq2sdbg.cpp : 740] Memory for sequence: 887012182' b' [cx1_seq2sdbg.cpp : 741] max # lv.1 items = 282698112' b' [cx1.h : 480] Preparing partitions and initialing global data... Done. Time elapsed: 2.0815' b' [cx1.h : 486] Start main loop...' b' [cx1.h : 515] Lv1 scanning from bucket 0 to 657' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 1.6882' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 3.1114' b' [cx1.h : 515] Lv1 scanning from bucket 657 to 3256' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 2.1484' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 4.7331' b' [cx1.h : 515] Lv1 scanning from bucket 3256 to 7840' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 2.2024' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 5.2255' b' [cx1.h : 515] Lv1 scanning from bucket 7840 to 14415' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 2.2846' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 5.4246' b' [cx1.h : 515] Lv1 scanning from bucket 14415 to 23135' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 2.8163' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 5.9966' b' [cx1.h : 515] Lv1 scanning from bucket 23135 to 34446' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 2.4176' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 5.8986' b' [cx1.h : 515] Lv1 scanning from bucket 34446 to 49583' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 2.4817' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 6.1407' b' [cx1.h : 515] Lv1 scanning from bucket 49583 to 65536' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 1.9495' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 4.3330' b' [cx1.h : 607] Main loop done. Time elapsed: 58.8535' 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] 1956107 340279293 251065039 250925496 340456614 120867 94115 71922 132402' b' [cx1_seq2sdbg.cpp :1151] Total number of edges: 1185101855' b' [cx1_seq2sdbg.cpp :1152] Total number of ONEs: 1182726442' b' [cx1_seq2sdbg.cpp :1153] Total number of $v edges: 1956107' b' [cx1.h : 621] Postprocess done. Time elapsed: 0.0346' b' [utils.h : 126] Real: 66.5936\tuser: 1246.6619\tsys: 6.9839\tmaxrss: 1811976' --- [Thu Mar 28 10:42:19 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: 40.227690' b' [assembler.cpp : 152] Number of Edges: 1185101855; 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: 17032; time elapsed: 3.3129' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 4; Accumulated tips removed: 62584; time elapsed: 3.3098' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 8; Accumulated tips removed: 146976; time elapsed: 3.7829' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 16; Accumulated tips removed: 324240; time elapsed: 4.8738' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 32; Accumulated tips removed: 421688; time elapsed: 6.8375' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 64; Accumulated tips removed: 541767; time elapsed: 10.8377' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 128; Accumulated tips removed: 809153; time elapsed: 17.2639' b' [assembly_algorithms.cpp : 170] Removing tips with length less than 182; Accumulated tips removed: 892803; time elapsed: 21.6347' b' [assembler.cpp : 179] Tips removal done! Time elapsed(sec): 71.898734' b' [assembler.cpp : 188] unitig graph size: 955850, time for building: 72.926909' b' [assembler.cpp : 211] Number of bubbles removed: 40783, Time elapsed(sec): 1.544442' b' [assembler.cpp : 225] Number of complex bubbles removed: 8697, Time elapsed(sec): 0.945433' b' [assembler.cpp : 243] Number unitigs disconnected: 43213, time: 0.154421' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 14260, time: 0.160251' b' [assembler.cpp : 200] Tips removed: 595, time: 0.331559' b' [assembler.cpp : 211] Number of bubbles removed: 1351, Time elapsed(sec): 0.226490' b' [assembler.cpp : 225] Number of complex bubbles removed: 2179, Time elapsed(sec): 0.576588' b' [assembler.cpp : 243] Number unitigs disconnected: 1973, time: 0.114217' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 181, time: 0.100264' b' [assembler.cpp : 200] Tips removed: 849, time: 0.331967' b' [assembler.cpp : 211] Number of bubbles removed: 62, Time elapsed(sec): 0.095189' b' [assembler.cpp : 225] Number of complex bubbles removed: 166, Time elapsed(sec): 0.229800' b' [assembler.cpp : 243] Number unitigs disconnected: 37, time: 0.112378' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 18, time: 0.098002' b' [assembler.cpp : 200] Tips removed: 17, time: 0.328167' b' [assembler.cpp : 211] Number of bubbles removed: 0, Time elapsed(sec): 0.079607' b' [assembler.cpp : 225] Number of complex bubbles removed: 2, Time elapsed(sec): 0.181721' b' [assembler.cpp : 243] Number unitigs disconnected: 2, time: 0.109254' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 1, time: 0.098198' b' [assembler.cpp : 200] Tips removed: 0, time: 0.317847' b' [assembler.cpp : 211] Number of bubbles removed: 0, Time elapsed(sec): 0.075619' b' [assembler.cpp : 225] Number of complex bubbles removed: 0, Time elapsed(sec): 0.184668' b' [assembler.cpp : 243] Number unitigs disconnected: 0, time: 0.110502' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 1, time: 0.097800' b' [assembler.cpp : 132] Total length: 655703561, N50: 1113, Mean: 818, number of contigs: 800772' b' [assembler.cpp : 133] Maximum length: 474029' b' [assembler.cpp : 290] Time to output: 20.930197' b' [assembler.cpp : 317] Number of local low depth unitigs removed: 1097, complex bubbles removed: 119, time: 3.744860' b' [assembler.cpp : 132] Total length: 136456050, N50: 3166, Mean: 960, number of contigs: 142098' b' [assembler.cpp : 133] Maximum length: 474029' b' [utils.h : 126] Real: 221.1627\tuser: 4598.8652\tsys: 9.8269\tmaxrss: 2621432' --- [Thu Mar 28 10:46:01 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: 738375, Mapper size: 77095324' b' [read_lib_functions-inl.h : 256] Before reading, sizeof seq_package: 5956255852' b' [read_lib_functions-inl.h : 260] After reading, sizeof seq_package: 5956255852' b' [local_assembler.cpp : 330] Lib 0, insert size: 273.27 sd: 103.51' b' [local_assembler.cpp : 462] Lib 0: total 163236894 reads, aligned 80985434, added 8360941 reads for local assembly' b' [utils.h : 126] Real: 346.1073\tuser: 9074.2323\tsys: 11.9663\tmaxrss: 9423008' --- [Thu Mar 28 10:51:47 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: 72254' b' [iterate_edges.cpp : 570] Number of crusial kmers: 250822' 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: 163236894, aligned: 0. Iterative edges: 0' b' [utils.h : 126] Real: 14.9266\tuser: 20.0277\tsys: 2.8445\tmaxrss: 429408' --- [Thu Mar 28 10:52:02 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: 578317862, number contigs: 813820, number multiplicity: 813820' b' [cx1_seq2sdbg.cpp : 440] Before reading, sizeof seq_package: 151090036, multiplicity vector: 813820' b' [cx1_seq2sdbg.cpp : 529] After reading, sizeof seq_package: 302180072, multiplicity vector: 1627640' b' [cx1.h : 457] Preparing data... Done. Time elapsed: 3.9249' b' [cx1.h : 464] Preparing partitions and initialing global data...' b' [cx1_seq2sdbg.cpp : 740] Memory for sequence: 312337954' b' [cx1_seq2sdbg.cpp : 741] max # lv.1 items = 207821239' b' [cx1.h : 480] Preparing partitions and initialing global data... Done. Time elapsed: 0.6394' b' [cx1.h : 486] Start main loop...' b' [cx1.h : 515] Lv1 scanning from bucket 0 to 541' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 0.5514' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 2.1199' b' [cx1.h : 515] Lv1 scanning from bucket 541 to 2990' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 0.5344' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 3.6855' b' [cx1.h : 515] Lv1 scanning from bucket 2990 to 7500' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 0.5970' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 4.2695' b' [cx1.h : 515] Lv1 scanning from bucket 7500 to 14044' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 0.6107' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 4.8254' b' [cx1.h : 515] Lv1 scanning from bucket 14044 to 22734' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 0.6266' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 4.8393' b' [cx1.h : 515] Lv1 scanning from bucket 22734 to 33968' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 0.6454' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 5.0210' b' [cx1.h : 515] Lv1 scanning from bucket 33968 to 48875' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 0.6362' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 4.9582' b' [cx1.h : 515] Lv1 scanning from bucket 48875 to 65536' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 0.5382' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 3.7280' b' [cx1.h : 607] Main loop done. Time elapsed: 38.1879' 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] 1501543 322654502 239331921 239204446 322797681 54027 28487 28370 53994' b' [cx1_seq2sdbg.cpp :1151] Total number of edges: 1125654971' b' [cx1_seq2sdbg.cpp :1152] Total number of ONEs: 1123988550' b' [cx1_seq2sdbg.cpp :1153] Total number of $v edges: 1501543' b' [cx1.h : 621] Postprocess done. Time elapsed: 0.0342' b' [utils.h : 126] Real: 42.7881\tuser: 1018.2378\tsys: 5.3291\tmaxrss: 1237464' --- [Thu Mar 28 10:52:45 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: 32.948255' b' [assembler.cpp : 152] Number of Edges: 1125654971; 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: 2478; time elapsed: 3.0035' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 4; Accumulated tips removed: 8158; time elapsed: 3.0798' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 8; Accumulated tips removed: 18508; time elapsed: 3.4575' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 16; Accumulated tips removed: 38276; time elapsed: 4.3273' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 32; Accumulated tips removed: 72740; time elapsed: 6.0251' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 64; Accumulated tips removed: 127536; time elapsed: 9.3205' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 128; Accumulated tips removed: 203774; time elapsed: 15.8925' b' [assembly_algorithms.cpp : 170] Removing tips with length less than 160; Accumulated tips removed: 222806; time elapsed: 19.0057' b' [assembler.cpp : 179] Tips removal done! Time elapsed(sec): 64.155602' b' [assembler.cpp : 188] unitig graph size: 848530, time for building: 70.534585' b' [assembler.cpp : 211] Number of bubbles removed: 24858, Time elapsed(sec): 0.185144' b' [assembler.cpp : 225] Number of complex bubbles removed: 3514, Time elapsed(sec): 0.256062' b' [assembler.cpp : 243] Number unitigs disconnected: 21795, time: 0.127148' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 5914, time: 0.114202' b' [assembler.cpp : 200] Tips removed: 310, time: 0.297398' b' [assembler.cpp : 211] Number of bubbles removed: 142, Time elapsed(sec): 0.072282' b' [assembler.cpp : 225] Number of complex bubbles removed: 682, Time elapsed(sec): 0.180492' b' [assembler.cpp : 243] Number unitigs disconnected: 1307, time: 0.101858' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 102, time: 0.087505' b' [assembler.cpp : 200] Tips removed: 325, time: 0.296381' b' [assembler.cpp : 211] Number of bubbles removed: 10, Time elapsed(sec): 0.071177' b' [assembler.cpp : 225] Number of complex bubbles removed: 71, Time elapsed(sec): 0.156849' b' [assembler.cpp : 243] Number unitigs disconnected: 14, time: 0.101306' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 7, time: 0.098175' b' [assembler.cpp : 200] Tips removed: 3, time: 0.315214' b' [assembler.cpp : 211] Number of bubbles removed: 0, Time elapsed(sec): 0.071745' b' [assembler.cpp : 225] Number of complex bubbles removed: 1, Time elapsed(sec): 0.151091' b' [assembler.cpp : 243] Number unitigs disconnected: 0, time: 0.101978' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 0, time: 0.045313' b' [assembler.cpp : 200] Tips removed: 0, time: 0.296764' b' [assembler.cpp : 211] Number of bubbles removed: 0, Time elapsed(sec): 0.071861' b' [assembler.cpp : 225] Number of complex bubbles removed: 0, Time elapsed(sec): 0.150331' b' [assembler.cpp : 243] Number unitigs disconnected: 0, time: 0.101910' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 0, time: 0.045298' b' [assembler.cpp : 317] Number of local low depth unitigs removed: 424, complex bubbles removed: 18, time: 3.887389' b' [assembler.cpp : 132] Total length: 659503749, N50: 1165, Mean: 857, number of contigs: 769023' b' [assembler.cpp : 133] Maximum length: 504904' b' [utils.h : 126] Real: 195.7946\tuser: 4148.7047\tsys: 8.9423\tmaxrss: 2490272' --- [Thu Mar 28 10:56:01 2019] Merging to output final contigs --- --- [STAT] 737440 contigs, total 653900791 bp, min 200 bp, max 504904 bp, avg 887 bp, N50 1184 bp --- [Thu Mar 28 10:56:04 2019] ALL DONE. Time elapsed: 11542.803933 seconds ---