MEGAHIT v1.1.3 --- [Mon Apr 15 13:12:21 2019] Start assembly. Number of CPU threads 28 --- --- [Mon Apr 15 13:12:21 2019] Available memory: 269759385600, used: 242783447040 --- [Mon Apr 15 13:12:21 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/scrubbed/samwhite/outputs/20190415_metagenomics_pgen_megahit/pH71.all.R1.fq.gz,/gscratch/scrubbed/samwhite/outputs/20190415_metagenomics_pgen_megahit/pH71.all.R2.fq.gz): pe, 483522908 reads, 131 max length' b' [utils.h : 126] Real: 474.0778\tuser: 431.2777\tsys: 40.1223\tmaxrss: 154664' --- [Mon Apr 15 13:20:15 2019] k list: 21,29,39,59,79,99,119,141 --- --- [Mon Apr 15 13:20:15 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: 17116574436' b' [read_lib_functions-inl.h : 260] After reading, sizeof seq_package: 17116574436' b' [cx1_kmer_count.cpp : 136] 483522908 reads, 131 max read length' b' [cx1.h : 457] Preparing data... Done. Time elapsed: 67.7414' 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: 24166399448, 224211365644' b' [cx1_kmer_count.cpp : 356] 5712134222, 54910940 24166399448 224211365644' b' [cx1_kmer_count.cpp : 363] Memory for reads: 17530586684' b' [cx1_kmer_count.cpp : 364] max # lv.1 items = 5712134222' b' [cx1.h : 480] Preparing partitions and initialing global data... Done. Time elapsed: 25.6326' b' [cx1.h : 486] Start main loop...' b' [cx1.h : 515] Lv1 scanning from bucket 0 to 245' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 24.1346' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 36.5934' b' [cx1.h : 515] Lv1 scanning from bucket 245 to 1363' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 26.0476' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 75.1264' b' [cx1.h : 515] Lv1 scanning from bucket 1363 to 3622' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 27.2674' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 87.2898' b' [cx1.h : 515] Lv1 scanning from bucket 3622 to 7286' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 28.6119' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 93.2792' b' [cx1.h : 515] Lv1 scanning from bucket 7286 to 12797' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 29.4924' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 93.2393' b' [cx1.h : 515] Lv1 scanning from bucket 12797 to 20912' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 30.4065' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 92.7396' b' [cx1.h : 515] Lv1 scanning from bucket 20912 to 33291' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 31.2799' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 89.7134' b' [cx1.h : 515] Lv1 scanning from bucket 33291 to 58116' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 32.1832' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 85.4678' b' [cx1.h : 515] Lv1 scanning from bucket 58116 to 65536' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 23.1374' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 7.5341' b' [cx1.h : 607] Main loop done. Time elapsed: 913.5456' b' [cx1.h : 613] Postprocessing...' b' [cx1_kmer_count.cpp : 860] Total number of candidate reads: 13581412(42268118)' b' [cx1_kmer_count.cpp : 871] Total number of solid edges: 2998825559' b' [cx1.h : 621] Postprocess done. Time elapsed: 9.1338' b' [utils.h : 126] Real: 1016.1031\tuser: 25724.1834\tsys: 64.7187\tmaxrss: 44575892' --- [Mon Apr 15 13:37:11 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: 2998825559' b' [cx1_seq2sdbg.cpp : 434] Bases to reserve: 82467702856, number contigs: 0, number multiplicity: 3748531948' b' [cx1_seq2sdbg.cpp : 440] Before reading, sizeof seq_package: 20616925724, multiplicity vector: 3748531948' b' [cx1_seq2sdbg.cpp : 455] Adding mercy edges...' b' [cx1_seq2sdbg.cpp : 373] Number of reads: 13581412, Number of mercy edges: 151171108' b' [cx1_seq2sdbg.cpp : 462] Done. Time elapsed: 149.5029' b' [cx1_seq2sdbg.cpp : 529] After reading, sizeof seq_package: 20616925724, multiplicity vector: 3748531948' b' [cx1.h : 457] Preparing data... Done. Time elapsed: 936.2757' b' [cx1.h : 464] Preparing partitions and initialing global data...' b' [cx1_seq2sdbg.cpp : 740] Memory for sequence: 27458324762' b' [cx1_seq2sdbg.cpp : 741] max # lv.1 items = 2519997333' b' [cx1.h : 480] Preparing partitions and initialing global data... Done. Time elapsed: 6.4941' b' [cx1.h : 486] Start main loop...' b' [cx1.h : 515] Lv1 scanning from bucket 0 to 1071' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 6.1434' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 23.5776' b' [cx1.h : 515] Lv1 scanning from bucket 1071 to 3890' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 6.3605' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 27.4048' b' [cx1.h : 515] Lv1 scanning from bucket 3890 to 8448' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 6.3904' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 27.2459' b' [cx1.h : 515] Lv1 scanning from bucket 8448 to 14934' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 6.5252' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 27.3531' b' [cx1.h : 515] Lv1 scanning from bucket 14934 to 23694' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 6.6921' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 26.6578' b' [cx1.h : 515] Lv1 scanning from bucket 23694 to 35273' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 7.1795' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 28.5823' b' [cx1.h : 515] Lv1 scanning from bucket 35273 to 51063' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 7.4915' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 27.9164' b' [cx1.h : 515] Lv1 scanning from bucket 51063 to 65536' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 6.3382' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 16.5221' b' [cx1.h : 607] Main loop done. Time elapsed: 258.3827' 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] 49544368 1880016027 1219967175 1216631389 1886427747 52663896 20347553 20036502 53426259' b' [cx1_seq2sdbg.cpp :1151] Total number of edges: 6399060916' b' [cx1_seq2sdbg.cpp :1152] Total number of ONEs: 6203042338' b' [cx1_seq2sdbg.cpp :1153] Total number of $v edges: 49544368' b' [cx1.h : 621] Postprocess done. Time elapsed: 0.0600' b' [utils.h : 126] Real: 1201.2787\tuser: 10863.0834\tsys: 109.7003\tmaxrss: 33434576' --- [Mon Apr 15 13:57:15 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: 500.354318' b' [assembler.cpp : 152] Number of Edges: 6399060916; 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: 5460396; time elapsed: 20.2895' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 4; Accumulated tips removed: 16692703; time elapsed: 23.9042' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 8; Accumulated tips removed: 27885692; time elapsed: 32.4961' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 16; Accumulated tips removed: 42076116; time elapsed: 52.0936' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 32; Accumulated tips removed: 54378324; time elapsed: 76.1787' b' [assembly_algorithms.cpp : 170] Removing tips with length less than 42; Accumulated tips removed: 58038461; time elapsed: 80.9142' b' [assembler.cpp : 179] Tips removal done! Time elapsed(sec): 286.106236' b' [assembler.cpp : 188] unitig graph size: 161496474, time for building: 847.725388' b' [assembler.cpp : 211] Number of bubbles removed: 5275069, Time elapsed(sec): 49.463236' b' [assembler.cpp : 225] Number of complex bubbles removed: 751690, Time elapsed(sec): 46.160588' b' [assembler.cpp : 243] Number unitigs disconnected: 49676813, time: 84.601416' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 395977, time: 20.924810' b' [assembler.cpp : 200] Tips removed: 347335, time: 45.014989' b' [assembler.cpp : 211] Number of bubbles removed: 201803, Time elapsed(sec): 18.198275' b' [assembler.cpp : 225] Number of complex bubbles removed: 494297, Time elapsed(sec): 34.124028' b' [assembler.cpp : 243] Number unitigs disconnected: 4945654, time: 27.269616' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 398, time: 19.769439' b' [assembler.cpp : 200] Tips removed: 4194427, time: 45.737163' b' [assembler.cpp : 211] Number of bubbles removed: 222259, Time elapsed(sec): 17.034620' b' [assembler.cpp : 225] Number of complex bubbles removed: 36480, Time elapsed(sec): 31.744530' b' [assembler.cpp : 243] Number unitigs disconnected: 41357, time: 22.914383' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 36, time: 20.094412' b' [assembler.cpp : 200] Tips removed: 12117, time: 41.464863' b' [assembler.cpp : 211] Number of bubbles removed: 1036, Time elapsed(sec): 16.621362' b' [assembler.cpp : 225] Number of complex bubbles removed: 1034, Time elapsed(sec): 31.444504' b' [assembler.cpp : 243] Number unitigs disconnected: 986, time: 20.514825' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 3, time: 16.658922' b' [assembler.cpp : 200] Tips removed: 342, time: 41.273261' b' [assembler.cpp : 211] Number of bubbles removed: 8, Time elapsed(sec): 16.017373' b' [assembler.cpp : 225] Number of complex bubbles removed: 47, Time elapsed(sec): 31.431856' b' [assembler.cpp : 243] Number unitigs disconnected: 41, time: 19.995118' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 0, time: 10.700657' b' [assembler.cpp : 132] Total length: 5124557497, N50: 45, Mean: 43, number of contigs: 119050650' b' [assembler.cpp : 133] Maximum length: 9910' b' [assembler.cpp : 290] Time to output: 209.583193' b' [assembler.cpp : 317] Number of local low depth unitigs removed: 4398764, complex bubbles removed: 200780, time: 1593.407426' b' [assembler.cpp : 132] Total length: 4216148093, N50: 43, Mean: 41, number of contigs: 102511984' b' [assembler.cpp : 133] Maximum length: 9910' b' [utils.h : 126] Real: 4277.5357\tuser: 99228.3938\tsys: 121.0588\tmaxrss: 26894964' --- [Mon Apr 15 15:08:34 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: 1513097, Mapper size: 53628734' b' [read_lib_functions-inl.h : 256] Before reading, sizeof seq_package: 17116574436' b' [read_lib_functions-inl.h : 260] After reading, sizeof seq_package: 17116574436' b' [local_assembler.cpp : 330] Lib 0, insert size: 237.50 sd: 89.51' b' [local_assembler.cpp : 462] Lib 0: total 483522908 reads, aligned 98362585, added 52719315 reads for local assembly' b' [utils.h : 126] Real: 866.8901\tuser: 22025.6895\tsys: 42.0861\tmaxrss: 20696084' --- [Mon Apr 15 15:23:00 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: 18475392' b' [iterate_edges.cpp : 570] Number of crusial kmers: 217629137' b' [iterate_edges.cpp : 443] Processed: 67108864, aligned: 47934437. Iterative edges: 307625562' b' [iterate_edges.cpp : 443] Processed: 134217728, aligned: 95867166. Iterative edges: 404098465' b' [iterate_edges.cpp : 443] Processed: 201326592, aligned: 145330985. Iterative edges: 526961322' b' [iterate_edges.cpp : 443] Processed: 268435456, aligned: 196193817. Iterative edges: 624410706' b' [iterate_edges.cpp : 443] Processed: 335544320, aligned: 247024539. Iterative edges: 693210847' b' [iterate_edges.cpp : 443] Processed: 402653184, aligned: 297583129. Iterative edges: 750566625' b' [iterate_edges.cpp : 443] Processed: 469762048, aligned: 348261695. Iterative edges: 784482498' b' [iterate_edges.cpp : 447] Total: 483522908, aligned: 358701922. Iterative edges: 789827779' b' [iterate_edges.cpp : 451] Writing iterative edges...' b' [utils.h : 126] Real: 1046.2052\tuser: 26273.3415\tsys: 34.8422\tmaxrss: 25564428' --- [Mon Apr 15 15:40:27 2019] Building graph for k = 29 --- /gscratch/srlab/programs/megahit_v1.1.4_LINUX_CPUONLY_x86_64-bin/megahit_sdbg_build seq2sdbg --host_mem 242783447040 --mem_flag 1 --gpu_mem 0 --output_prefix ./megahit_out/tmp/k29/29 --num_cpu_threads 28 -k 29 --kmer_from 21 --num_edge_files 1 --input_prefix ./megahit_out/tmp/k29/29 --addi_contig ./megahit_out/intermediate_contigs/k21.addi.fa --local_contig ./megahit_out/intermediate_contigs/k21.local.fa --contig ./megahit_out/intermediate_contigs/k21.contigs.fa --bubble ./megahit_out/intermediate_contigs/k21.bubble_seq.fa b' [sdbg_builder.cpp : 339] Host memory to be used: 242783447040' b' [sdbg_builder.cpp : 340] Number CPU threads: 28' b' [cx1.h : 450] Preparing data...' b' [cx1_seq2sdbg.cpp : 394] Number edges: 789827779' b' [cx1_seq2sdbg.cpp : 434] Bases to reserve: 33932824962, number contigs: 223992556, number multiplicity: 1013820335' b' [cx1_seq2sdbg.cpp : 440] Before reading, sizeof seq_package: 10275146700, multiplicity vector: 1013820335' b' [cx1_seq2sdbg.cpp : 529] After reading, sizeof seq_package: 10275146700, multiplicity vector: 1013820335' b' [cx1.h : 457] Preparing data... Done. Time elapsed: 75.3246' b' [cx1.h : 464] Preparing partitions and initialing global data...' b' [cx1_seq2sdbg.cpp : 740] Memory for sequence: 12226372368' b' [cx1_seq2sdbg.cpp : 741] max # lv.1 items = 1585754437' b' [cx1.h : 480] Preparing partitions and initialing global data... Done. Time elapsed: 20.4418' b' [cx1.h : 486] Start main loop...' b' [cx1.h : 515] Lv1 scanning from bucket 0 to 737' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 15.4850' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 20.4379' b' [cx1.h : 515] Lv1 scanning from bucket 737 to 3100' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 20.0757' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 27.3343' b' [cx1.h : 515] Lv1 scanning from bucket 3100 to 7188' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 22.9548' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 27.4020' b' [cx1.h : 515] Lv1 scanning from bucket 7188 to 13182' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 25.4928' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 26.4917' b' [cx1.h : 515] Lv1 scanning from bucket 13182 to 21473' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 26.4854' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 26.5374' b' [cx1.h : 515] Lv1 scanning from bucket 21473 to 32701' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 28.0163' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 28.0088' b' [cx1.h : 515] Lv1 scanning from bucket 32701 to 48274' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 29.0649' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 28.0101' b' [cx1.h : 515] Lv1 scanning from bucket 48274 to 65536' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 22.9822' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 20.3888' b' [cx1.h : 607] Main loop done. Time elapsed: 395.1697' 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] 47257769 1660880851 1063363927 1062413762 1663287266 10032597 7012383 5550963 10714371' b' [cx1_seq2sdbg.cpp :1151] Total number of edges: 5530513889' b' [cx1_seq2sdbg.cpp :1152] Total number of ONEs: 5449945806' b' [cx1_seq2sdbg.cpp :1153] Total number of $v edges: 47257769' b' [cx1.h : 621] Postprocess done. Time elapsed: 0.0496' b' [utils.h : 126] Real: 491.0118\tuser: 6515.7396\tsys: 47.5530\tmaxrss: 15985560' --- [Mon Apr 15 15:48:38 2019] Assembling contigs from SdBG for k = 29 --- cmd: /gscratch/srlab/programs/megahit_v1.1.4_LINUX_CPUONLY_x86_64-bin/megahit_asm_core assemble -s ./megahit_out/tmp/k29/29 -o ./megahit_out/intermediate_contigs/k29 -t 28 --min_standalone 300.0 --prune_level 2 --merge_len 20 --merge_similar 0.95 --low_local_ratio 0.2 --min_depth 2 --bubble_level 2 --max_tip_len -1 --careful_bubble b' [assembler.cpp : 148] Loading succinct de Bruijn graph: ./megahit_out/tmp/k29/29 Done. Time elapsed: 363.430241' b' [assembler.cpp : 152] Number of Edges: 5530513889; 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: 2070596; time elapsed: 18.6625' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 4; Accumulated tips removed: 6463702; time elapsed: 23.2594' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 8; Accumulated tips removed: 11281562; time elapsed: 33.1591' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 16; Accumulated tips removed: 19605372; time elapsed: 54.7019' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 32; Accumulated tips removed: 31462010; time elapsed: 89.4701' b' [assembly_algorithms.cpp : 170] Removing tips with length less than 58; Accumulated tips removed: 40985672; time elapsed: 117.5101' b' [assembler.cpp : 179] Tips removal done! Time elapsed(sec): 336.969469' b' [assembler.cpp : 188] unitig graph size: 41904337, time for building: 403.408837' b' [assembler.cpp : 211] Number of bubbles removed: 4442883, Time elapsed(sec): 49.903372' b' [assembler.cpp : 225] Number of complex bubbles removed: 849345, Time elapsed(sec): 21.626758' b' [assembler.cpp : 243] Number unitigs disconnected: 1086978, time: 7.417927' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 55633, time: 5.767671' b' [assembler.cpp : 200] Tips removed: 55894, time: 10.856616' b' [assembler.cpp : 211] Number of bubbles removed: 59889, Time elapsed(sec): 5.563598' b' [assembler.cpp : 225] Number of complex bubbles removed: 35273, Time elapsed(sec): 8.539564' b' [assembler.cpp : 243] Number unitigs disconnected: 152016, time: 6.563800' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 560, time: 5.684133' b' [assembler.cpp : 200] Tips removed: 49882, time: 10.677673' b' [assembler.cpp : 211] Number of bubbles removed: 9157, Time elapsed(sec): 4.259969' b' [assembler.cpp : 225] Number of complex bubbles removed: 5130, Time elapsed(sec): 8.126580' b' [assembler.cpp : 243] Number unitigs disconnected: 18376, time: 6.395011' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 67, time: 5.666757' b' [assembler.cpp : 200] Tips removed: 1715, time: 10.595621' b' [assembler.cpp : 211] Number of bubbles removed: 156, Time elapsed(sec): 4.026362' b' [assembler.cpp : 225] Number of complex bubbles removed: 226, Time elapsed(sec): 8.051207' b' [assembler.cpp : 243] Number unitigs disconnected: 3530, time: 6.401849' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 8, time: 5.635116' b' [assembler.cpp : 200] Tips removed: 218, time: 10.579430' b' [assembler.cpp : 211] Number of bubbles removed: 8, Time elapsed(sec): 4.011141' b' [assembler.cpp : 225] Number of complex bubbles removed: 36, Time elapsed(sec): 8.030572' b' [assembler.cpp : 243] Number unitigs disconnected: 911, time: 6.392438' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 1, time: 5.636772' b' [assembler.cpp : 132] Total length: 3128560904, N50: 130, Mean: 99, number of contigs: 31471473' b' [assembler.cpp : 133] Maximum length: 80834' b' [assembler.cpp : 290] Time to output: 99.231078' b' [assembler.cpp : 317] Number of local low depth unitigs removed: 853001, complex bubbles removed: 76417, time: 482.591259' b' [assembler.cpp : 132] Total length: 1718572069, N50: 105, Mean: 81, number of contigs: 21010515' b' [assembler.cpp : 133] Maximum length: 80834' b' [utils.h : 126] Real: 1961.1080\tuser: 42057.7079\tsys: 63.8148\tmaxrss: 16328680' --- [Mon Apr 15 16:21:21 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: 2510317, Mapper size: 126448006' b' [read_lib_functions-inl.h : 256] Before reading, sizeof seq_package: 17116574436' b' [read_lib_functions-inl.h : 260] After reading, sizeof seq_package: 17116574436' b' [local_assembler.cpp : 330] Lib 0, insert size: 251.70 sd: 98.09' b' [local_assembler.cpp : 462] Lib 0: total 483522908 reads, aligned 198235711, added 70514188 reads for local assembly' b' [utils.h : 126] Real: 1247.0925\tuser: 32761.0936\tsys: 49.6799\tmaxrss: 24251936' --- [Mon Apr 15 16:42:08 2019] Extracting iterative edges from k = 29 to 39 --- cmd: /gscratch/srlab/programs/megahit_v1.1.4_LINUX_CPUONLY_x86_64-bin/megahit_asm_core iterate -c ./megahit_out/intermediate_contigs/k29.contigs.fa -b ./megahit_out/intermediate_contigs/k29.bubble_seq.fa -t 28 -k 29 -s 10 -o ./megahit_out/tmp/k39/39 -r ./megahit_out/tmp/reads.lib.bin -f binary b' [iterate_edges.cpp : 570] Number of crusial kmers: 14919666' b' [iterate_edges.cpp : 570] Number of crusial kmers: 57870316' b' [iterate_edges.cpp : 443] Processed: 67108864, aligned: 29677100. Iterative edges: 123268713' b' [iterate_edges.cpp : 443] Processed: 134217728, aligned: 59314230. Iterative edges: 163889045' b' [iterate_edges.cpp : 443] Processed: 201326592, aligned: 92391799. Iterative edges: 216866045' b' [iterate_edges.cpp : 443] Processed: 268435456, aligned: 128656645. Iterative edges: 254299204' b' [iterate_edges.cpp : 443] Processed: 335544320, aligned: 164651180. Iterative edges: 278434924' b' [iterate_edges.cpp : 443] Processed: 402653184, aligned: 199847822. Iterative edges: 297384941' b' [iterate_edges.cpp : 443] Processed: 469762048, aligned: 235158880. Iterative edges: 308920701' b' [iterate_edges.cpp : 447] Total: 483522908, aligned: 242483777. Iterative edges: 310757827' b' [iterate_edges.cpp : 451] Writing iterative edges...' b' [utils.h : 126] Real: 855.3472\tuser: 21069.6268\tsys: 24.4813\tmaxrss: 11196936' --- [Mon Apr 15 16:56:23 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: 310757827' b' [cx1_seq2sdbg.cpp : 434] Bases to reserve: 18869034152, number contigs: 59713649, number multiplicity: 370471476' b' [cx1_seq2sdbg.cpp : 440] Before reading, sizeof seq_package: 5194967740, multiplicity vector: 370471476' b' [cx1_seq2sdbg.cpp : 529] After reading, sizeof seq_package: 5194967740, multiplicity vector: 370471476' b' [cx1.h : 457] Preparing data... Done. Time elapsed: 41.1848' b' [cx1.h : 464] Preparing partitions and initialing global data...' b' [cx1_seq2sdbg.cpp : 740] Memory for sequence: 6036689842' b' [cx1_seq2sdbg.cpp : 741] max # lv.1 items = 1433838021' b' [cx1.h : 480] Preparing partitions and initialing global data... Done. Time elapsed: 20.6125' b' [cx1.h : 486] Start main loop...' b' [cx1.h : 515] Lv1 scanning from bucket 0 to 966' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 18.0025' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 20.0154' b' [cx1.h : 515] Lv1 scanning from bucket 966 to 3615' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 23.6644' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 26.8091' b' [cx1.h : 515] Lv1 scanning from bucket 3615 to 7934' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 24.8772' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 26.5991' b' [cx1.h : 515] Lv1 scanning from bucket 7934 to 14097' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 28.8188' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 25.8903' b' [cx1.h : 515] Lv1 scanning from bucket 14097 to 22519' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 30.2855' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 26.9679' b' [cx1.h : 515] Lv1 scanning from bucket 22519 to 33893' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 30.7135' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 28.2255' b' [cx1.h : 515] Lv1 scanning from bucket 33893 to 49802' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 30.0317' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 28.4110' b' [cx1.h : 515] Lv1 scanning from bucket 49802 to 65536' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 20.3825' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 18.2015' b' [cx1.h : 607] Main loop done. Time elapsed: 407.8974' 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] 24697187 1436559609 930981223 929965608 1438249780 5286670 2775936 2751022 5299384' b' [cx1_seq2sdbg.cpp :1151] Total number of edges: 4776566419' b' [cx1_seq2sdbg.cpp :1152] Total number of ONEs: 4735756220' b' [cx1_seq2sdbg.cpp :1153] Total number of $v edges: 24697187' b' [cx1.h : 621] Postprocess done. Time elapsed: 0.0476' b' [utils.h : 126] Real: 469.7581\tuser: 6235.7769\tsys: 40.9506\tmaxrss: 11496476' --- [Mon Apr 15 17:04:13 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: 439.336647' b' [assembler.cpp : 152] Number of Edges: 4776566419; 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: 297030; time elapsed: 13.5255' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 4; Accumulated tips removed: 1324522; time elapsed: 15.9484' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 8; Accumulated tips removed: 2546602; time elapsed: 21.7969' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 16; Accumulated tips removed: 4042907; time elapsed: 35.7306' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 32; Accumulated tips removed: 6273535; time elapsed: 62.5683' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 64; Accumulated tips removed: 13288645; time elapsed: 102.2048' b' [assembly_algorithms.cpp : 170] Removing tips with length less than 78; Accumulated tips removed: 16756749; time elapsed: 100.4171' b' [assembler.cpp : 179] Tips removal done! Time elapsed(sec): 352.367117' b' [assembler.cpp : 188] unitig graph size: 24233409, time for building: 298.684990' b' [assembler.cpp : 211] Number of bubbles removed: 3134961, Time elapsed(sec): 51.556981' b' [assembler.cpp : 225] Number of complex bubbles removed: 612288, Time elapsed(sec): 19.091669' b' [assembler.cpp : 243] Number unitigs disconnected: 728671, time: 3.490268' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 160413, time: 2.875962' b' [assembler.cpp : 200] Tips removed: 39878, time: 7.080343' b' [assembler.cpp : 211] Number of bubbles removed: 66043, Time elapsed(sec): 4.335737' b' [assembler.cpp : 225] Number of complex bubbles removed: 39067, Time elapsed(sec): 5.471358' b' [assembler.cpp : 243] Number unitigs disconnected: 90792, time: 2.950637' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 2915, time: 2.543506' b' [assembler.cpp : 200] Tips removed: 30760, time: 6.761907' b' [assembler.cpp : 211] Number of bubbles removed: 5269, Time elapsed(sec): 2.302618' b' [assembler.cpp : 225] Number of complex bubbles removed: 4460, Time elapsed(sec): 4.455790' b' [assembler.cpp : 243] Number unitigs disconnected: 16357, time: 2.874776' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 662, time: 2.540749' b' [assembler.cpp : 200] Tips removed: 1654, time: 6.696370' b' [assembler.cpp : 211] Number of bubbles removed: 115, Time elapsed(sec): 2.057861' b' [assembler.cpp : 225] Number of complex bubbles removed: 279, Time elapsed(sec): 4.291682' b' [assembler.cpp : 243] Number unitigs disconnected: 4564, time: 2.854720' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 212, time: 2.542247' b' [assembler.cpp : 200] Tips removed: 295, time: 6.665956' b' [assembler.cpp : 211] Number of bubbles removed: 26, Time elapsed(sec): 2.065548' b' [assembler.cpp : 225] Number of complex bubbles removed: 48, Time elapsed(sec): 4.369087' b' [assembler.cpp : 243] Number unitigs disconnected: 1435, time: 2.849149' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 74, time: 2.532634' b' [assembler.cpp : 132] Total length: 2577031618, N50: 202, Mean: 156, number of contigs: 16510616' b' [assembler.cpp : 133] Maximum length: 258984' b' [assembler.cpp : 290] Time to output: 82.947331' b' [assembler.cpp : 317] Number of local low depth unitigs removed: 332547, complex bubbles removed: 29876, time: 227.245497' b' [assembler.cpp : 132] Total length: 1310986146, N50: 207, Mean: 131, number of contigs: 9969292' b' [assembler.cpp : 133] Maximum length: 258984' b' [utils.h : 126] Real: 1594.6813\tuser: 30185.9088\tsys: 57.3218\tmaxrss: 12433072' --- [Mon Apr 15 17:30:49 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: 2582267, Mapper size: 153360107' b' [read_lib_functions-inl.h : 256] Before reading, sizeof seq_package: 17116574436' b' [read_lib_functions-inl.h : 260] After reading, sizeof seq_package: 17116574436' b' [local_assembler.cpp : 330] Lib 0, insert size: 256.59 sd: 101.47' b' [local_assembler.cpp : 462] Lib 0: total 483522908 reads, aligned 248006641, added 80328254 reads for local assembly' b' [utils.h : 126] Real: 1669.3856\tuser: 44944.4875\tsys: 48.5117\tmaxrss: 25644616' --- [Mon Apr 15 17:58:39 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: 10167792' b' [iterate_edges.cpp : 570] Number of crusial kmers: 29970933' b' [iterate_edges.cpp : 443] Processed: 67108864, aligned: 17421934. Iterative edges: 108008804' b' [iterate_edges.cpp : 443] Processed: 134217728, aligned: 34731648. Iterative edges: 152790397' b' [iterate_edges.cpp : 443] Processed: 201326592, aligned: 55735682. Iterative edges: 204913125' b' [iterate_edges.cpp : 443] Processed: 268435456, aligned: 79982458. Iterative edges: 242491520' b' [iterate_edges.cpp : 443] Processed: 335544320, aligned: 103955646. Iterative edges: 267197988' b' [iterate_edges.cpp : 443] Processed: 402653184, aligned: 127037260. Iterative edges: 286816850' b' [iterate_edges.cpp : 443] Processed: 469762048, aligned: 150133090. Iterative edges: 299993016' b' [iterate_edges.cpp : 447] Total: 483522908, aligned: 155003117. Iterative edges: 302206276' b' [iterate_edges.cpp : 451] Writing iterative edges...' b' [utils.h : 126] Real: 768.4066\tuser: 18384.3393\tsys: 25.7295\tmaxrss: 11484020' --- [Mon Apr 15 18:11:27 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: 302206276' b' [cx1_seq2sdbg.cpp : 434] Bases to reserve: 24016371751, number contigs: 33262452, number multiplicity: 335468728' b' [cx1_seq2sdbg.cpp : 440] Before reading, sizeof seq_package: 6270192564, multiplicity vector: 335468728' b' [cx1_seq2sdbg.cpp : 529] After reading, sizeof seq_package: 6270192564, multiplicity vector: 335468728' b' [cx1.h : 457] Preparing data... Done. Time elapsed: 42.3648' b' [cx1.h : 464] Preparing partitions and initialing global data...' b' [cx1_seq2sdbg.cpp : 740] Memory for sequence: 7107599742' b' [cx1_seq2sdbg.cpp : 741] max # lv.1 items = 1376712764' b' [cx1.h : 480] Preparing partitions and initialing global data... Done. Time elapsed: 23.5630' b' [cx1.h : 486] Start main loop...' b' [cx1.h : 515] Lv1 scanning from bucket 0 to 855' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 20.5267' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 18.2286' b' [cx1.h : 515] Lv1 scanning from bucket 855 to 3352' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 26.7767' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 25.9202' b' [cx1.h : 515] Lv1 scanning from bucket 3352 to 7504' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 29.8152' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 26.1260' b' [cx1.h : 515] Lv1 scanning from bucket 7504 to 13477' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 32.1172' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 25.1330' b' [cx1.h : 515] Lv1 scanning from bucket 13477 to 21699' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 32.8389' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 24.4294' b' [cx1.h : 515] Lv1 scanning from bucket 21699 to 32903' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 33.2956' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 25.9368' b' [cx1.h : 515] Lv1 scanning from bucket 32903 to 48756' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 33.6254' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 26.1662' b' [cx1.h : 515] Lv1 scanning from bucket 48756 to 65536' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 25.0882' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 17.8028' b' [cx1.h : 607] Main loop done. Time elapsed: 423.8284' 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] 17852607 1275016314 813558091 812909295 1276389996 2611376 1884523 1517600 2786013' b' [cx1_seq2sdbg.cpp :1151] Total number of edges: 4204525815' b' [cx1_seq2sdbg.cpp :1152] Total number of ONEs: 4177873696' b' [cx1_seq2sdbg.cpp :1153] Total number of $v edges: 17852607' b' [cx1.h : 621] Postprocess done. Time elapsed: 0.0474' b' [utils.h : 126] Real: 489.8221\tuser: 5855.6711\tsys: 40.5463\tmaxrss: 12480308' --- [Mon Apr 15 18:19:37 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: 426.359457' b' [assembler.cpp : 152] Number of Edges: 4204525815; 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: 154712; time elapsed: 11.7695' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 4; Accumulated tips removed: 579807; time elapsed: 13.3177' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 8; Accumulated tips removed: 1281112; time elapsed: 18.0295' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 16; Accumulated tips removed: 2453462; time elapsed: 28.9304' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 32; Accumulated tips removed: 3838674; time elapsed: 48.6492' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 64; Accumulated tips removed: 8661833; time elapsed: 83.8896' b' [assembly_algorithms.cpp : 170] Removing tips with length less than 118; Accumulated tips removed: 16369702; time elapsed: 88.5964' b' [assembler.cpp : 179] Tips removal done! Time elapsed(sec): 293.337200' b' [assembler.cpp : 188] unitig graph size: 10732321, time for building: 209.043043' b' [assembler.cpp : 211] Number of bubbles removed: 1505705, Time elapsed(sec): 42.091880' b' [assembler.cpp : 225] Number of complex bubbles removed: 349752, Time elapsed(sec): 15.527272' b' [assembler.cpp : 243] Number unitigs disconnected: 712862, time: 1.745277' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 240009, time: 1.753576' b' [assembler.cpp : 200] Tips removed: 13071, time: 2.704284' b' [assembler.cpp : 211] Number of bubbles removed: 59079, Time elapsed(sec): 3.356334' b' [assembler.cpp : 225] Number of complex bubbles removed: 40410, Time elapsed(sec): 3.684914' b' [assembler.cpp : 243] Number unitigs disconnected: 57469, time: 1.282849' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 3631, time: 1.225939' b' [assembler.cpp : 200] Tips removed: 19961, time: 2.679841' b' [assembler.cpp : 211] Number of bubbles removed: 2854, Time elapsed(sec): 0.975903' b' [assembler.cpp : 225] Number of complex bubbles removed: 3114, Time elapsed(sec): 1.984696' b' [assembler.cpp : 243] Number unitigs disconnected: 7053, time: 1.204549' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 685, time: 1.176525' b' [assembler.cpp : 200] Tips removed: 730, time: 2.585599' b' [assembler.cpp : 211] Number of bubbles removed: 76, Time elapsed(sec): 0.785495' b' [assembler.cpp : 225] Number of complex bubbles removed: 151, Time elapsed(sec): 1.800367' b' [assembler.cpp : 243] Number unitigs disconnected: 1682, time: 1.199095' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 206, time: 1.178106' b' [assembler.cpp : 200] Tips removed: 121, time: 2.686768' b' [assembler.cpp : 211] Number of bubbles removed: 8, Time elapsed(sec): 0.785825' b' [assembler.cpp : 225] Number of complex bubbles removed: 24, Time elapsed(sec): 1.794330' b' [assembler.cpp : 243] Number unitigs disconnected: 496, time: 1.199981' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 83, time: 1.173832' b' [assembler.cpp : 132] Total length: 1909724254, N50: 490, Mean: 307, number of contigs: 6213744' b' [assembler.cpp : 133] Maximum length: 485820' b' [assembler.cpp : 290] Time to output: 62.646530' b' [assembler.cpp : 317] Number of local low depth unitigs removed: 130031, complex bubbles removed: 11483, time: 111.021800' b' [assembler.cpp : 132] Total length: 910393069, N50: 555, Mean: 259, number of contigs: 3509501' b' [assembler.cpp : 133] Maximum length: 485820' b' [utils.h : 126] Real: 1227.5700\tuser: 20636.2840\tsys: 46.2620\tmaxrss: 11134632' --- [Mon Apr 15 18:40:06 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: 2719341, Mapper size: 178837048' b' [read_lib_functions-inl.h : 256] Before reading, sizeof seq_package: 17116574436' b' [read_lib_functions-inl.h : 260] After reading, sizeof seq_package: 17116574436' b' [local_assembler.cpp : 330] Lib 0, insert size: 261.45 sd: 104.28' b' [local_assembler.cpp : 462] Lib 0: total 483522908 reads, aligned 276590941, added 78828127 reads for local assembly' b' [utils.h : 126] Real: 2026.5028\tuser: 54776.0933\tsys: 52.8303\tmaxrss: 26465304' --- [Mon Apr 15 19:13:53 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: 4880936' b' [iterate_edges.cpp : 570] Number of crusial kmers: 11850733' b' [iterate_edges.cpp : 443] Processed: 67108864, aligned: 7583325. Iterative edges: 36162571' b' [iterate_edges.cpp : 443] Processed: 134217728, aligned: 15028922. Iterative edges: 52290522' b' [iterate_edges.cpp : 443] Processed: 201326592, aligned: 25127596. Iterative edges: 71956983' b' [iterate_edges.cpp : 443] Processed: 268435456, aligned: 37420850. Iterative edges: 85656502' b' [iterate_edges.cpp : 443] Processed: 335544320, aligned: 49548371. Iterative edges: 94343112' b' [iterate_edges.cpp : 443] Processed: 402653184, aligned: 61078343. Iterative edges: 100790181' b' [iterate_edges.cpp : 443] Processed: 469762048, aligned: 72482388. Iterative edges: 104933647' b' [iterate_edges.cpp : 447] Total: 483522908, aligned: 74953950. Iterative edges: 105672434' b' [iterate_edges.cpp : 451] Writing iterative edges...' b' [utils.h : 126] Real: 511.7922\tuser: 12495.1285\tsys: 18.0359\tmaxrss: 4539452' --- [Mon Apr 15 19:22:24 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: 105672434' b' [cx1_seq2sdbg.cpp : 434] Bases to reserve: 13157866845, number contigs: 14662720, number multiplicity: 120335154' b' [cx1_seq2sdbg.cpp : 440] Before reading, sizeof seq_package: 3406768480, multiplicity vector: 120335154' b' [cx1_seq2sdbg.cpp : 529] After reading, sizeof seq_package: 6696235192, multiplicity vector: 120335154' b' [cx1.h : 457] Preparing data... Done. Time elapsed: 25.2662' b' [cx1.h : 464] Preparing partitions and initialing global data...' b' [cx1_seq2sdbg.cpp : 740] Memory for sequence: 7035727720' b' [cx1_seq2sdbg.cpp : 741] max # lv.1 items = 1093826337' b' [cx1.h : 480] Preparing partitions and initialing global data... Done. Time elapsed: 14.9231' b' [cx1.h : 486] Start main loop...' b' [cx1.h : 515] Lv1 scanning from bucket 0 to 719' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 14.0763' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 13.7847' b' [cx1.h : 515] Lv1 scanning from bucket 719 to 3011' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 16.3499' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 20.9610' b' [cx1.h : 515] Lv1 scanning from bucket 3011 to 6932' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 19.6339' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 21.6978' b' [cx1.h : 515] Lv1 scanning from bucket 6932 to 12643' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 19.8637' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 20.9954' b' [cx1.h : 515] Lv1 scanning from bucket 12643 to 20581' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 20.6326' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 20.5280' b' [cx1.h : 515] Lv1 scanning from bucket 20581 to 31509' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 20.9997' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 21.0993' b' [cx1.h : 515] Lv1 scanning from bucket 31509 to 47179' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 23.6439' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 21.9986' b' [cx1.h : 515] Lv1 scanning from bucket 47179 to 65536' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 17.6260' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 16.2147' b' [cx1.h : 607] Main loop done. Time elapsed: 310.1068' 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] 8348895 1066526414 661311465 660878838 1067436469 1550332 841744 1047636 1453231' b' [cx1_seq2sdbg.cpp :1151] Total number of edges: 3469395024' b' [cx1_seq2sdbg.cpp :1152] Total number of ONEs: 3456153186' b' [cx1_seq2sdbg.cpp :1153] Total number of $v edges: 8348895' b' [cx1.h : 621] Postprocess done. Time elapsed: 0.0424' b' [utils.h : 126] Real: 350.3492\tuser: 4816.9401\tsys: 28.8187\tmaxrss: 8271752' --- [Mon Apr 15 19:28:15 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: 356.114750' b' [assembler.cpp : 152] Number of Edges: 3469395024; 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: 76404; time elapsed: 9.3007' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 4; Accumulated tips removed: 277618; time elapsed: 10.1235' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 8; Accumulated tips removed: 618507; time elapsed: 12.3884' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 16; Accumulated tips removed: 1224143; time elapsed: 17.3139' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 32; Accumulated tips removed: 1942653; time elapsed: 26.5475' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 64; Accumulated tips removed: 3464148; time elapsed: 42.6739' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 128; Accumulated tips removed: 6149499; time elapsed: 63.4259' b' [assembly_algorithms.cpp : 170] Removing tips with length less than 158; Accumulated tips removed: 7061371; time elapsed: 57.9664' b' [assembler.cpp : 179] Tips removal done! Time elapsed(sec): 239.870260' b' [assembler.cpp : 188] unitig graph size: 6002764, time for building: 204.097082' b' [assembler.cpp : 211] Number of bubbles removed: 720702, Time elapsed(sec): 30.672247' b' [assembler.cpp : 225] Number of complex bubbles removed: 174405, Time elapsed(sec): 11.551311' b' [assembler.cpp : 243] Number unitigs disconnected: 625134, time: 1.500042' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 218572, time: 1.343900' b' [assembler.cpp : 200] Tips removed: 10622, time: 1.823762' b' [assembler.cpp : 211] Number of bubbles removed: 40556, Time elapsed(sec): 2.389838' b' [assembler.cpp : 225] Number of complex bubbles removed: 31076, Time elapsed(sec): 2.863992' b' [assembler.cpp : 243] Number unitigs disconnected: 36504, time: 0.676663' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 5229, time: 0.608423' b' [assembler.cpp : 200] Tips removed: 18506, time: 1.724585' b' [assembler.cpp : 211] Number of bubbles removed: 1392, Time elapsed(sec): 0.532561' b' [assembler.cpp : 225] Number of complex bubbles removed: 1946, Time elapsed(sec): 1.265884' b' [assembler.cpp : 243] Number unitigs disconnected: 3241, time: 0.642273' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 767, time: 0.596117' b' [assembler.cpp : 200] Tips removed: 809, time: 1.639023' b' [assembler.cpp : 211] Number of bubbles removed: 44, Time elapsed(sec): 0.420070' b' [assembler.cpp : 225] Number of complex bubbles removed: 101, Time elapsed(sec): 1.099352' b' [assembler.cpp : 243] Number unitigs disconnected: 526, time: 0.634596' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 130, time: 0.587885' b' [assembler.cpp : 200] Tips removed: 85, time: 1.615238' b' [assembler.cpp : 211] Number of bubbles removed: 2, Time elapsed(sec): 0.411972' b' [assembler.cpp : 225] Number of complex bubbles removed: 4, Time elapsed(sec): 1.096369' b' [assembler.cpp : 243] Number unitigs disconnected: 107, time: 0.632879' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 16, time: 0.590586' b' [assembler.cpp : 132] Total length: 1677598588, N50: 772, Mean: 502, number of contigs: 3338443' b' [assembler.cpp : 133] Maximum length: 590059' b' [assembler.cpp : 290] Time to output: 54.979222' b' [assembler.cpp : 317] Number of local low depth unitigs removed: 58945, complex bubbles removed: 5623, time: 47.813276' b' [assembler.cpp : 132] Total length: 678106131, N50: 1013, Mean: 431, number of contigs: 1570580' b' [assembler.cpp : 133] Maximum length: 590059' b' [utils.h : 126] Real: 991.7581\tuser: 16370.3641\tsys: 37.9691\tmaxrss: 9109172' --- [Mon Apr 15 19:44:48 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: 2286057, Mapper size: 182805345' b' [read_lib_functions-inl.h : 256] Before reading, sizeof seq_package: 17116574436' b' [read_lib_functions-inl.h : 260] After reading, sizeof seq_package: 17116574436' b' [local_assembler.cpp : 330] Lib 0, insert size: 266.10 sd: 106.52' b' [local_assembler.cpp : 462] Lib 0: total 483522908 reads, aligned 261754265, added 53029605 reads for local assembly' b' [utils.h : 126] Real: 1497.7004\tuser: 40096.0944\tsys: 41.4481\tmaxrss: 25825788' --- [Mon Apr 15 20:09:45 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: 2302701' b' [iterate_edges.cpp : 570] Number of crusial kmers: 5367252' b' [iterate_edges.cpp : 443] Processed: 67108864, aligned: 2888312. Iterative edges: 12571427' b' [iterate_edges.cpp : 443] Processed: 134217728, aligned: 5719632. Iterative edges: 19122094' b' [iterate_edges.cpp : 443] Processed: 201326592, aligned: 10047842. Iterative edges: 27795995' b' [iterate_edges.cpp : 443] Processed: 268435456, aligned: 15636605. Iterative edges: 34031957' b' [iterate_edges.cpp : 443] Processed: 335544320, aligned: 21128105. Iterative edges: 38047081' b' [iterate_edges.cpp : 443] Processed: 402653184, aligned: 26325039. Iterative edges: 41005065' b' [iterate_edges.cpp : 443] Processed: 469762048, aligned: 31436684. Iterative edges: 42939637' b' [iterate_edges.cpp : 447] Total: 483522908, aligned: 32572035. Iterative edges: 43300934' b' [iterate_edges.cpp : 451] Writing iterative edges...' b' [utils.h : 126] Real: 324.7350\tuser: 8025.7434\tsys: 13.1882\tmaxrss: 2536984' --- [Mon Apr 15 20:15:10 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: 43300934' b' [cx1_seq2sdbg.cpp : 434] Bases to reserve: 7785519785, number contigs: 7201193, number multiplicity: 50502127' b' [cx1_seq2sdbg.cpp : 440] Before reading, sizeof seq_package: 2003989500, multiplicity vector: 50502127' b' [cx1_seq2sdbg.cpp : 529] After reading, sizeof seq_package: 3950369448, multiplicity vector: 50502127' b' [cx1.h : 457] Preparing data... Done. Time elapsed: 17.1636' b' [cx1.h : 464] Preparing partitions and initialing global data...' b' [cx1_seq2sdbg.cpp : 740] Memory for sequence: 4114346690' b' [cx1_seq2sdbg.cpp : 741] max # lv.1 items = 860726577' b' [cx1.h : 480] Preparing partitions and initialing global data... Done. Time elapsed: 8.2999' b' [cx1.h : 486] Start main loop...' b' [cx1.h : 515] Lv1 scanning from bucket 0 to 624' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 6.9030' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 10.0300' b' [cx1.h : 515] Lv1 scanning from bucket 624 to 2781' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 8.5207' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 16.1691' b' [cx1.h : 515] Lv1 scanning from bucket 2781 to 6563' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 9.8499' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 16.6968' b' [cx1.h : 515] Lv1 scanning from bucket 6563 to 12125' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 10.6453' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 16.2959' b' [cx1.h : 515] Lv1 scanning from bucket 12125 to 19897' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 11.4208' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 16.2973' b' [cx1.h : 515] Lv1 scanning from bucket 19897 to 30635' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 11.6797' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 17.4075' b' [cx1.h : 515] Lv1 scanning from bucket 30635 to 46085' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 11.7773' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 18.0561' b' [cx1.h : 515] Lv1 scanning from bucket 46085 to 65536' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 9.3133' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 13.6686' b' [cx1.h : 607] Main loop done. Time elapsed: 204.7329' 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] 5450295 943916332 577625142 577293399 944590369 795588 412627 412805 798909' b' [cx1_seq2sdbg.cpp :1151] Total number of edges: 3051295466' b' [cx1_seq2sdbg.cpp :1152] Total number of ONEs: 3043425242' b' [cx1_seq2sdbg.cpp :1153] Total number of $v edges: 5450295' b' [cx1.h : 621] Postprocess done. Time elapsed: 0.0409' b' [utils.h : 126] Real: 230.2442\tuser: 3781.8631\tsys: 21.3135\tmaxrss: 5895544' --- [Mon Apr 15 20:19:01 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: 181.395181' b' [assembler.cpp : 152] Number of Edges: 3051295466; 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: 44226; time elapsed: 8.0500' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 4; Accumulated tips removed: 158516; time elapsed: 8.5444' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 8; Accumulated tips removed: 362120; time elapsed: 10.0443' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 16; Accumulated tips removed: 722646; time elapsed: 13.3387' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 32; Accumulated tips removed: 1126972; time elapsed: 19.1743' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 64; Accumulated tips removed: 1704981; time elapsed: 30.2362' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 128; Accumulated tips removed: 2793889; time elapsed: 48.8266' b' [assembly_algorithms.cpp : 170] Removing tips with length less than 198; Accumulated tips removed: 3848753; time elapsed: 59.5312' b' [assembler.cpp : 179] Tips removal done! Time elapsed(sec): 197.858716' b' [assembler.cpp : 188] unitig graph size: 3334158, time for building: 156.547856' b' [assembler.cpp : 211] Number of bubbles removed: 313337, Time elapsed(sec): 18.977666' b' [assembler.cpp : 225] Number of complex bubbles removed: 74380, Time elapsed(sec): 7.144710' b' [assembler.cpp : 243] Number unitigs disconnected: 329825, time: 0.910055' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 112954, time: 0.996064' b' [assembler.cpp : 200] Tips removed: 4746, time: 1.024282' b' [assembler.cpp : 211] Number of bubbles removed: 17987, Time elapsed(sec): 1.619637' b' [assembler.cpp : 225] Number of complex bubbles removed: 17030, Time elapsed(sec): 2.239616' b' [assembler.cpp : 243] Number unitigs disconnected: 16096, time: 0.627667' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 2294, time: 0.539951' b' [assembler.cpp : 200] Tips removed: 7782, time: 0.967969' b' [assembler.cpp : 211] Number of bubbles removed: 592, Time elapsed(sec): 0.368086' b' [assembler.cpp : 225] Number of complex bubbles removed: 1142, Time elapsed(sec): 0.809445' b' [assembler.cpp : 243] Number unitigs disconnected: 1212, time: 0.595938' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 356, time: 0.530655' b' [assembler.cpp : 200] Tips removed: 340, time: 0.931409' b' [assembler.cpp : 211] Number of bubbles removed: 20, Time elapsed(sec): 0.231504' b' [assembler.cpp : 225] Number of complex bubbles removed: 36, Time elapsed(sec): 0.638947' b' [assembler.cpp : 243] Number unitigs disconnected: 153, time: 0.618180' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 62, time: 0.532439' b' [assembler.cpp : 200] Tips removed: 39, time: 0.935617' b' [assembler.cpp : 211] Number of bubbles removed: 8, Time elapsed(sec): 0.231478' b' [assembler.cpp : 225] Number of complex bubbles removed: 3, Time elapsed(sec): 0.640863' b' [assembler.cpp : 243] Number unitigs disconnected: 33, time: 0.595603' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 11, time: 0.531347' b' [assembler.cpp : 132] Total length: 1532672278, N50: 1053, Mean: 732, number of contigs: 2091905' b' [assembler.cpp : 133] Maximum length: 893392' b' [assembler.cpp : 290] Time to output: 49.391822' b' [assembler.cpp : 317] Number of local low depth unitigs removed: 22012, complex bubbles removed: 2371, time: 39.122354' b' [assembler.cpp : 132] Total length: 464891795, N50: 1914, Mean: 694, number of contigs: 669151' b' [assembler.cpp : 133] Maximum length: 893392' b' [utils.h : 126] Real: 683.3524\tuser: 12998.1425\tsys: 28.5462\tmaxrss: 8028520' --- [Mon Apr 15 20:30:25 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: 1751153, Mapper size: 176767020' b' [read_lib_functions-inl.h : 256] Before reading, sizeof seq_package: 17116574436' b' [read_lib_functions-inl.h : 260] After reading, sizeof seq_package: 17116574436' b' [local_assembler.cpp : 330] Lib 0, insert size: 269.21 sd: 107.89' b' [local_assembler.cpp : 462] Lib 0: total 483522908 reads, aligned 246833209, added 32508919 reads for local assembly' b' [utils.h : 126] Real: 1125.6653\tuser: 29720.1081\tsys: 35.9664\tmaxrss: 24844412' --- [Mon Apr 15 20:49:10 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: 918120' b' [iterate_edges.cpp : 570] Number of crusial kmers: 2151911' b' [iterate_edges.cpp : 443] Processed: 67108864, aligned: 749009. Iterative edges: 2389264' b' [iterate_edges.cpp : 443] Processed: 134217728, aligned: 1484468. Iterative edges: 3979615' b' [iterate_edges.cpp : 443] Processed: 201326592, aligned: 2770722. Iterative edges: 6561523' b' [iterate_edges.cpp : 443] Processed: 268435456, aligned: 4531430. Iterative edges: 8793565' b' [iterate_edges.cpp : 443] Processed: 335544320, aligned: 6253814. Iterative edges: 10323471' b' [iterate_edges.cpp : 443] Processed: 402653184, aligned: 7880297. Iterative edges: 11518336' b' [iterate_edges.cpp : 443] Processed: 469762048, aligned: 9463602. Iterative edges: 12347362' b' [iterate_edges.cpp : 447] Total: 483522908, aligned: 9827240. Iterative edges: 12512065' b' [iterate_edges.cpp : 451] Writing iterative edges...' b' [utils.h : 126] Real: 157.3216\tuser: 3828.3511\tsys: 9.8762\tmaxrss: 1101576' --- [Mon Apr 15 20:51:48 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: 12512065' b' [cx1_seq2sdbg.cpp : 434] Bases to reserve: 3867572227, number contigs: 3566972, number multiplicity: 16079037' b' [cx1_seq2sdbg.cpp : 440] Before reading, sizeof seq_package: 995428844, multiplicity vector: 16079037' b' [cx1_seq2sdbg.cpp : 529] After reading, sizeof seq_package: 1990857688, multiplicity vector: 32158074' b' [cx1.h : 457] Preparing data... Done. Time elapsed: 12.1769' b' [cx1.h : 464] Preparing partitions and initialing global data...' b' [cx1_seq2sdbg.cpp : 740] Memory for sequence: 2059343316' b' [cx1_seq2sdbg.cpp : 741] max # lv.1 items = 673506174' b' [cx1.h : 480] Preparing partitions and initialing global data... Done. Time elapsed: 4.8146' b' [cx1.h : 486] Start main loop...' b' [cx1.h : 515] Lv1 scanning from bucket 0 to 473' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 3.8975' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 7.5126' b' [cx1.h : 515] Lv1 scanning from bucket 473 to 2390' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 5.1256' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 13.9043' b' [cx1.h : 515] Lv1 scanning from bucket 2390 to 5950' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 5.1996' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 14.3695' b' [cx1.h : 515] Lv1 scanning from bucket 5950 to 11303' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 5.8029' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 13.6498' b' [cx1.h : 515] Lv1 scanning from bucket 11303 to 18850' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 5.8122' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 13.4874' b' [cx1.h : 515] Lv1 scanning from bucket 18850 to 29322' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 6.5827' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 14.6651' b' [cx1.h : 515] Lv1 scanning from bucket 29322 to 44322' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 6.4263' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 14.7653' b' [cx1.h : 515] Lv1 scanning from bucket 44322 to 65536' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 5.3915' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 12.5122' b' [cx1.h : 607] Main loop done. Time elapsed: 149.1054' 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] 4228965 855236781 520154448 519927733 855763674 303559 221648 173885 326780' b' [cx1_seq2sdbg.cpp :1151] Total number of edges: 2756337473' b' [cx1_seq2sdbg.cpp :1152] Total number of ONEs: 2751082636' b' [cx1_seq2sdbg.cpp :1153] Total number of $v edges: 4228965' b' [cx1.h : 621] Postprocess done. Time elapsed: 0.0396' b' [utils.h : 126] Real: 166.1404\tuser: 3173.0108\tsys: 16.4025\tmaxrss: 4173836' --- [Mon Apr 15 20:54:34 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: 167.442474' b' [assembler.cpp : 152] Number of Edges: 2756337473; 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: 37028; time elapsed: 7.1938' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 4; Accumulated tips removed: 131884; time elapsed: 7.6283' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 8; Accumulated tips removed: 309800; time elapsed: 8.7538' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 16; Accumulated tips removed: 673324; time elapsed: 11.1078' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 32; Accumulated tips removed: 887216; time elapsed: 15.4862' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 64; Accumulated tips removed: 1160597; time elapsed: 24.4740' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 128; Accumulated tips removed: 1758082; time elapsed: 39.8932' b' [assembly_algorithms.cpp : 170] Removing tips with length less than 182; Accumulated tips removed: 1931234; time elapsed: 49.4326' b' [assembler.cpp : 179] Tips removal done! Time elapsed(sec): 164.071826' b' [assembler.cpp : 188] unitig graph size: 2154841, time for building: 150.041324' b' [assembler.cpp : 211] Number of bubbles removed: 110471, Time elapsed(sec): 4.127345' b' [assembler.cpp : 225] Number of complex bubbles removed: 22309, Time elapsed(sec): 2.469516' b' [assembler.cpp : 243] Number unitigs disconnected: 129769, time: 0.409766' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 38376, time: 0.398712' b' [assembler.cpp : 200] Tips removed: 1660, time: 0.731023' b' [assembler.cpp : 211] Number of bubbles removed: 3813, Time elapsed(sec): 0.631944' b' [assembler.cpp : 225] Number of complex bubbles removed: 5560, Time elapsed(sec): 1.362696' b' [assembler.cpp : 243] Number unitigs disconnected: 7237, time: 0.258148' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 665, time: 0.228446' b' [assembler.cpp : 200] Tips removed: 2298, time: 0.715939' b' [assembler.cpp : 211] Number of bubbles removed: 208, Time elapsed(sec): 0.222049' b' [assembler.cpp : 225] Number of complex bubbles removed: 510, Time elapsed(sec): 0.600326' b' [assembler.cpp : 243] Number unitigs disconnected: 331, time: 0.250855' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 85, time: 0.227422' b' [assembler.cpp : 200] Tips removed: 54, time: 0.708305' b' [assembler.cpp : 211] Number of bubbles removed: 2, Time elapsed(sec): 0.171256' b' [assembler.cpp : 225] Number of complex bubbles removed: 12, Time elapsed(sec): 0.480974' b' [assembler.cpp : 243] Number unitigs disconnected: 37, time: 0.249782' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 13, time: 0.226186' b' [assembler.cpp : 200] Tips removed: 9, time: 0.718211' b' [assembler.cpp : 211] Number of bubbles removed: 0, Time elapsed(sec): 0.181742' b' [assembler.cpp : 225] Number of complex bubbles removed: 2, Time elapsed(sec): 0.481728' b' [assembler.cpp : 243] Number unitigs disconnected: 7, time: 0.249570' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 2, time: 0.226185' b' [assembler.cpp : 132] Total length: 1510873711, N50: 1199, Mean: 875, number of contigs: 1724776' b' [assembler.cpp : 133] Maximum length: 893432' b' [assembler.cpp : 290] Time to output: 49.791908' b' [assembler.cpp : 317] Number of local low depth unitigs removed: 4648, complex bubbles removed: 495, time: 13.316818' b' [assembler.cpp : 132] Total length: 317644433, N50: 3936, Mean: 1184, number of contigs: 268196' b' [assembler.cpp : 133] Maximum length: 893432' b' [utils.h : 126] Real: 573.8158\tuser: 10355.1112\tsys: 22.9842\tmaxrss: 7404436' --- [Mon Apr 15 21:04:08 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: 1636725, Mapper size: 178453689' b' [read_lib_functions-inl.h : 256] Before reading, sizeof seq_package: 17116574436' b' [read_lib_functions-inl.h : 260] After reading, sizeof seq_package: 17116574436' b' [local_assembler.cpp : 330] Lib 0, insert size: 269.94 sd: 108.50' b' [local_assembler.cpp : 462] Lib 0: total 483522908 reads, aligned 238240310, added 22502710 reads for local assembly' b' [utils.h : 126] Real: 915.6951\tuser: 23996.3954\tsys: 29.1029\tmaxrss: 24679108' --- [Mon Apr 15 21:19:24 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: 192766' b' [iterate_edges.cpp : 570] Number of crusial kmers: 618774' 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 : 443] Processed: 201326592, aligned: 0. Iterative edges: 0' b' [iterate_edges.cpp : 443] Processed: 268435456, aligned: 0. Iterative edges: 0' b' [iterate_edges.cpp : 443] Processed: 335544320, aligned: 0. Iterative edges: 0' b' [iterate_edges.cpp : 443] Processed: 402653184, aligned: 0. Iterative edges: 0' b' [iterate_edges.cpp : 443] Processed: 469762048, aligned: 0. Iterative edges: 0' b' [iterate_edges.cpp : 447] Total: 483522908, aligned: 0. Iterative edges: 0' b' [utils.h : 126] Real: 43.1832\tuser: 61.1004\tsys: 7.4424\tmaxrss: 435748' --- [Mon Apr 15 21:20:07 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: 1418661285, number contigs: 1849261, number multiplicity: 1849261' b' [cx1_seq2sdbg.cpp : 440] Before reading, sizeof seq_package: 369459420, multiplicity vector: 1849261' b' [cx1_seq2sdbg.cpp : 529] After reading, sizeof seq_package: 738918840, multiplicity vector: 3698522' b' [cx1.h : 457] Preparing data... Done. Time elapsed: 8.1342' b' [cx1.h : 464] Preparing partitions and initialing global data...' b' [cx1_seq2sdbg.cpp : 740] Memory for sequence: 762938516' b' [cx1_seq2sdbg.cpp : 741] max # lv.1 items = 502080610' b' [cx1.h : 480] Preparing partitions and initialing global data... Done. Time elapsed: 1.3381' b' [cx1.h : 486] Start main loop...' b' [cx1.h : 515] Lv1 scanning from bucket 0 to 345' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 1.0375' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 4.8017' b' [cx1.h : 515] Lv1 scanning from bucket 345 to 1968' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 1.1752' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 9.7462' b' [cx1.h : 515] Lv1 scanning from bucket 1968 to 5172' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 1.2641' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 10.4764' b' [cx1.h : 515] Lv1 scanning from bucket 5172 to 10146' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 1.3990' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 10.4492' b' [cx1.h : 515] Lv1 scanning from bucket 10146 to 17291' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 1.4683' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 11.0951' b' [cx1.h : 515] Lv1 scanning from bucket 17291 to 27345' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 1.6112' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 11.9266' b' [cx1.h : 515] Lv1 scanning from bucket 27345 to 41849' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 1.6362' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 12.5802' b' [cx1.h : 515] Lv1 scanning from bucket 41849 to 65536' b' [cx1.h : 528] Lv1 scanning done. Large diff: 0. Time elapsed: 1.5081' b' [cx1.h : 594] Lv1 fetching & sorting done. Time elapsed: 12.1783' b' [cx1.h : 607] Main loop done. Time elapsed: 94.3545' 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] 3344477 817847732 496956203 496765501 818327002 141946 73013 72913 142172' b' [cx1_seq2sdbg.cpp :1151] Total number of edges: 2633670959' b' [cx1_seq2sdbg.cpp :1152] Total number of ONEs: 2629896438' b' [cx1_seq2sdbg.cpp :1153] Total number of $v edges: 3344477' b' [cx1.h : 621] Postprocess done. Time elapsed: 0.0369' b' [utils.h : 126] Real: 103.8693\tuser: 2513.2443\tsys: 12.4972\tmaxrss: 2875728' --- [Mon Apr 15 21:21:51 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: 162.629687' b' [assembler.cpp : 152] Number of Edges: 2633670959; 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: 6096; time elapsed: 6.8380' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 4; Accumulated tips removed: 20342; time elapsed: 7.2237' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 8; Accumulated tips removed: 47268; time elapsed: 8.1167' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 16; Accumulated tips removed: 98138; time elapsed: 10.2484' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 32; Accumulated tips removed: 186608; time elapsed: 14.1916' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 64; Accumulated tips removed: 325002; time elapsed: 21.8595' b' [assembly_algorithms.cpp : 162] Removing tips with length less than 128; Accumulated tips removed: 523453; time elapsed: 36.7178' b' [assembly_algorithms.cpp : 170] Removing tips with length less than 160; Accumulated tips removed: 571179; time elapsed: 43.5531' b' [assembler.cpp : 179] Tips removal done! Time elapsed(sec): 148.845862' b' [assembler.cpp : 188] unitig graph size: 1870495, time for building: 144.248526' b' [assembler.cpp : 211] Number of bubbles removed: 63047, Time elapsed(sec): 0.449993' b' [assembler.cpp : 225] Number of complex bubbles removed: 9208, Time elapsed(sec): 0.648464' b' [assembler.cpp : 243] Number unitigs disconnected: 68736, time: 0.328138' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 16897, time: 0.278481' b' [assembler.cpp : 200] Tips removed: 920, time: 0.681745' b' [assembler.cpp : 211] Number of bubbles removed: 520, Time elapsed(sec): 0.167282' b' [assembler.cpp : 225] Number of complex bubbles removed: 1824, Time elapsed(sec): 0.466267' b' [assembler.cpp : 243] Number unitigs disconnected: 4251, time: 0.225363' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 276, time: 0.200937' b' [assembler.cpp : 200] Tips removed: 767, time: 0.678957' b' [assembler.cpp : 211] Number of bubbles removed: 46, Time elapsed(sec): 0.160219' b' [assembler.cpp : 225] Number of complex bubbles removed: 213, Time elapsed(sec): 0.387686' b' [assembler.cpp : 243] Number unitigs disconnected: 168, time: 0.219121' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 33, time: 0.197778' b' [assembler.cpp : 200] Tips removed: 19, time: 0.671701' b' [assembler.cpp : 211] Number of bubbles removed: 0, Time elapsed(sec): 0.160717' b' [assembler.cpp : 225] Number of complex bubbles removed: 6, Time elapsed(sec): 0.384231' b' [assembler.cpp : 243] Number unitigs disconnected: 16, time: 0.219751' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 3, time: 0.207911' b' [assembler.cpp : 200] Tips removed: 4, time: 0.668568' b' [assembler.cpp : 211] Number of bubbles removed: 0, Time elapsed(sec): 0.159668' b' [assembler.cpp : 225] Number of complex bubbles removed: 0, Time elapsed(sec): 0.381683' b' [assembler.cpp : 243] Number unitigs disconnected: 0, time: 0.259405' b' [assembler.cpp : 265] Unitigs removed in excessive pruning: 2, time: 0.231046' b' [assembler.cpp : 317] Number of local low depth unitigs removed: 1349, complex bubbles removed: 62, time: 12.829889' b' [assembler.cpp : 132] Total length: 1520143784, N50: 1253, Mean: 921, number of contigs: 1650296' b' [assembler.cpp : 133] Maximum length: 1436649' b' [utils.h : 126] Real: 524.7299\tuser: 9352.5560\tsys: 22.8991\tmaxrss: 7039932' --- [Mon Apr 15 21:30:36 2019] Merging to output final contigs --- --- [STAT] 1613870 contigs, total 1513177150 bp, min 200 bp, max 1436649 bp, avg 938 bp, N50 1261 bp --- [Mon Apr 15 21:30:42 2019] ALL DONE. Time elapsed: 29900.748773 seconds ---