General command line: /N/dc2/projects/marinovg/programs/SPAdes-3.5.0-Linux/bin/dipspades.py --pe1-1 /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_132/reads.end1.paired.fastq.gz --pe1-2 /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_132/reads.end2.paired.fastq.gz -t 16 -o /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_132-dipSPAdes-3.5.0-trimmed dipSPAdes command line: -t 16 -o /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_132-dipSPAdes-3.5.0-trimmed/dipspades --hap /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_132-dipSPAdes-3.5.0-trimmed/spades/contigs.fasta dipSPAdes parameters: K value for dipSPAdes: 55 Expect gaps: False Expect rearrangements: False Files with haplocontigs : ['/N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_132-dipSPAdes-3.5.0-trimmed/spades/contigs.fasta'] Haplotype assembly stage: False Output directory: /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_132-dipSPAdes-3.5.0-trimmed/dipspades Dir for temp files: /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_132-dipSPAdes-3.5.0-trimmed/dipspades/tmp Threads: 16 Memory limit (in Gb): 250 ======= dipSPAdes started. Log can be found here: /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_132-dipSPAdes-3.5.0-trimmed/dipspades/dipspades.log ===== Assembling started. 0:00:00.000 4M / 4M INFO General (memory_limit.hpp : 42) Memory limit set to 100 Gb 0:00:00.001 4M / 4M INFO General (main.cpp : 96) Assembling dataset (/N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_132-dipSPAdes-3.5.0-trimmed/dipspades/) with K=55 0:00:00.001 4M / 4M INFO General (dipspades.hpp : 188) dipSPAdes started 0:00:00.002 4M / 4M INFO StageManager (stage.cpp : 125) STAGE == dipSPAdes 0:00:00.002 4M / 4M INFO General (stage.cpp : 95) PROCEDURE == Construction of graph from contigs 0:00:00.005 4M / 4M INFO General (dipspades.hpp : 19) Addition of contigs from /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_132-dipSPAdes-3.5.0-trimmed/spades/contigs.fasta 0:00:00.010 4M / 4M INFO General (dipspades.hpp : 23) Construction of the de Bruijn graph with K=55 0:00:00.010 4M / 4M INFO General (graph_construction.hpp : 129) Constructing DeBruijn graph for k=55 0:00:00.013 4M / 4M INFO General (kmer_splitters.hpp : 172) Splitting kmer instances into 1 buckets. This might take a while. 0:00:00.013 4M / 4M INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:00:00.013 4M / 4M INFO General (kmer_splitters.hpp : 190) Memory available for splitting buffers: 33.332 Gb 0:00:00.013 4M / 4M INFO General (kmer_splitters.hpp : 199) Using cell size of 33554432 0:00:59.989 568M / 1G INFO General (kmer_splitters.hpp : 228) Processed 39976 reads 0:00:59.990 568M / 1G INFO General (kmer_splitters.hpp : 245) Used 39976 reads. Maximum read length 217797 0:00:59.990 568M / 1G INFO General (kmer_splitters.hpp : 246) Average read length 3784.77 0:00:59.993 4M / 1G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:01:22.946 4M / 1G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 73961070 kmers in total. 0:01:22.946 4M / 1G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:01:31.140 4M / 1G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:01:31.140 4M / 1G INFO General (kmer_splitters.hpp : 379) Splitting kmer instances into 16 buckets. This might take a while. 0:01:31.140 4M / 1G INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:01:31.140 4M / 1G INFO General (kmer_splitters.hpp : 397) Memory available for splitting buffers: 33.332 Gb 0:01:31.140 4M / 1G INFO General (kmer_splitters.hpp : 405) Using cell size of 2097152 0:03:52.496 640M / 1G INFO General (kmer_splitters.hpp : 428) Processed 16777216 kmers 0:06:17.179 640M / 1G INFO General (kmer_splitters.hpp : 428) Processed 33554432 kmers 0:07:30.887 640M / 1G INFO General (kmer_splitters.hpp : 428) Processed 50331648 kmers 0:09:14.911 640M / 1G INFO General (kmer_splitters.hpp : 428) Processed 67108864 kmers 0:10:35.552 640M / 1G INFO General (kmer_splitters.hpp : 428) Processed 73961070 kmers 0:10:35.552 640M / 1G INFO General (kmer_splitters.hpp : 437) Used 73961070 kmers. 0:10:35.558 64M / 1G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:11:11.170 64M / 1G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 73964170 kmers in total. 0:11:11.170 64M / 1G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:11:17.404 64M / 1G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:12:30.101 88M / 1G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:12:36.131 88M / 1G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 25587014 bytes occupied (2.7675 bits per kmer). 0:12:36.235 160M / 1G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 382) Building k-mer extensions from k+1-mers 0:14:25.613 160M / 1G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 386) Building k-mer extensions from k+1-mers finished. 0:14:25.618 160M / 1G INFO General (graph_construction.hpp : 145) Condensing graph 0:14:25.618 160M / 1G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 337) Extracting unbranching paths 0:14:57.095 176M / 1G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 351) Extracting unbranching paths finished. 97247 sequences extracted 0:15:02.916 172M / 1G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 311) Collecting perfect loops 0:15:25.760 172M / 1G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 326) Collecting perfect loops finished. 254 loops collected 0:15:25.871 172M / 1G INFO General (graph_construction.hpp : 150) Building index with from graph 0:15:25.872 172M / 1G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:15:25.872 172M / 1G INFO General (kmer_splitters.hpp : 289) Splitting kmer instances into 16 buckets. This might take a while. 0:15:25.872 172M / 1G INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:15:25.873 172M / 1G INFO General (kmer_splitters.hpp : 307) Memory available for splitting buffers: 33.2773 Gb 0:15:25.873 172M / 1G INFO General (kmer_splitters.hpp : 312) Using cell size of 2097152 0:17:43.932 748M / 1G INFO General (kmer_splitters.hpp : 325) Processed 44137 edges 0:19:21.006 748M / 1G INFO General (kmer_splitters.hpp : 325) Processed 88582 edges 0:19:38.954 748M / 1G INFO General (kmer_splitters.hpp : 325) Processed 97501 edges 0:19:38.954 748M / 1G INFO General (kmer_splitters.hpp : 330) Used 97501 sequences. 0:19:38.958 172M / 1G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:20:00.028 172M / 1G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 73961070 kmers in total. 0:20:00.028 172M / 1G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:20:06.967 172M / 1G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:21:20.006 196M / 1G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:21:26.767 196M / 1G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 25585950 bytes occupied (2.7675 bits per kmer). 0:21:27.780 1G / 1G INFO General (edge_index_builders.hpp : 21) Collecting k-mer coverage information from graph, this takes a while. 0:23:14.148 1G / 1G INFO General (graph_construction.hpp : 182) Filling coverage index 0:23:14.148 1G / 1G INFO General (edge_index_builders.hpp : 99) Collecting k-mer coverage information from reads, this takes a while. 0:24:22.660 1G / 1G INFO General (graph_construction.hpp : 184) Filling coverage and flanking coverage from index 0:24:25.922 1G / 1G INFO General (stage.cpp : 95) PROCEDURE == Polymorphic bulge remover 0:24:25.922 1G / 1G INFO General (polymorphic_bulge_remover.: 94) Polymorphic bulge remover starts 0:24:25.922 1G / 1G INFO General (polymorphic_bulge_remover.: 36) Simple polymorphic bulge remover runs 0:32:55.250 2G / 3G INFO General (polymorphic_bulge_remover.: 42) 1 iteration: 5585 simple bulges were glued 0:45:33.068 2G / 3G INFO General (polymorphic_bulge_remover.: 42) 2 iteration: 263 simple bulges were glued 0:50:04.309 2G / 3G INFO General (polymorphic_bulge_remover.: 42) 3 iteration: 0 simple bulges were glued 0:50:04.309 2G / 3G INFO General (polymorphic_bulge_remover.: 44) Simple polymorphic bulge remover ends 0:50:04.309 2G / 3G INFO General (polymorphic_bulge_remover.: 49) LightBulgeRemover starts 0:50:04.309 2G / 3G INFO General (polymorphic_bulge_remover.: 50) Maximal number of iterations: 15 0:50:04.309 2G / 3G INFO PolymorphicBulgeRemover (complex_bulge_remover.hpp : 108) Maximal length of glued bulge: 82596 1:40:07.662 4G / 5G INFO General (polymorphic_bulge_remover.: 60) 1 iteration: 1936 complex bulges were glued 1:40:07.663 4G / 5G INFO PolymorphicBulgeRemover (complex_bulge_remover.hpp : 108) Maximal length of glued bulge: 94425 2:16:29.840 4G / 5G INFO General (polymorphic_bulge_remover.: 60) 2 iteration: 96 complex bulges were glued 2:16:29.841 4G / 5G INFO PolymorphicBulgeRemover (complex_bulge_remover.hpp : 108) Maximal length of glued bulge: 97018 2:52:24.985 4G / 5G INFO General (polymorphic_bulge_remover.: 60) 3 iteration: 11 complex bulges were glued 2:52:24.986 4G / 5G INFO PolymorphicBulgeRemover (complex_bulge_remover.hpp : 108) Maximal length of glued bulge: 97018 3:28:27.985 4G / 5G INFO General (polymorphic_bulge_remover.: 60) 4 iteration: 5 complex bulges were glued 3:28:27.986 4G / 5G INFO PolymorphicBulgeRemover (complex_bulge_remover.hpp : 108) Maximal length of glued bulge: 97018 4:04:05.581 4G / 5G INFO General (polymorphic_bulge_remover.: 60) 5 iteration: 3 complex bulges were glued 4:04:05.581 4G / 5G INFO PolymorphicBulgeRemover (complex_bulge_remover.hpp : 108) Maximal length of glued bulge: 97018 4:39:43.408 4G / 5G INFO General (polymorphic_bulge_remover.: 60) 6 iteration: 1 complex bulges were glued 4:39:43.409 4G / 5G INFO PolymorphicBulgeRemover (complex_bulge_remover.hpp : 108) Maximal length of glued bulge: 97018 5:15:19.928 4G / 5G INFO General (polymorphic_bulge_remover.: 60) 7 iteration: 3 complex bulges were glued 5:15:19.928 4G / 5G INFO PolymorphicBulgeRemover (complex_bulge_remover.hpp : 108) Maximal length of glued bulge: 97018 5:50:59.958 4G / 5G INFO General (polymorphic_bulge_remover.: 60) 8 iteration: 0 complex bulges were glued 5:50:59.958 4G / 5G INFO General (polymorphic_bulge_remover.: 62) LightBulgeRemover ends 5:50:59.958 4G / 5G INFO General (polymorphic_bulge_remover.: 103) Index refilling 5:50:59.971 2G / 5G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 5:50:59.971 2G / 5G INFO General (kmer_splitters.hpp : 289) Splitting kmer instances into 16 buckets. This might take a while. 5:50:59.971 2G / 5G INFO General (file_limit.hpp : 29) Open file limit set to 32768 5:50:59.971 2G / 5G INFO General (kmer_splitters.hpp : 307) Memory available for splitting buffers: 32.5143 Gb 5:50:59.971 2G / 5G INFO General (kmer_splitters.hpp : 312) Using cell size of 2097152 5:52:54.242 3G / 5G INFO General (kmer_splitters.hpp : 325) Processed 28788 edges 5:55:11.903 3G / 5G INFO General (kmer_splitters.hpp : 325) Processed 50477 edges 5:55:11.903 3G / 5G INFO General (kmer_splitters.hpp : 330) Used 50477 sequences. 5:55:11.907 2G / 5G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 5:55:29.388 2G / 5G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 60468612 kmers in total. 5:55:29.388 2G / 5G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 5:55:34.450 2G / 5G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 5:56:42.974 2G / 5G INFO General (kmer_index.hpp : 371) Merging final buckets. 5:56:47.924 2G / 5G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 20918397 bytes occupied (2.7675 bits per kmer). 5:56:48.754 3G / 5G INFO General (edge_index_builders.hpp : 21) Collecting k-mer coverage information from graph, this takes a while. 5:58:15.092 3G / 5G INFO General (polymorphic_bulge_remover.: 106) Glueing equal kmers 6:00:54.391 3G / 5G INFO General (equal_sequence_gluer.hpp : 105) 0 kmers glued 6:00:54.392 3G / 5G INFO General (polymorphic_bulge_remover.: 108) Polymorphic ends remover ends 6:00:54.392 3G / 5G INFO General (dipspades.hpp : 96) Consensus graph was constructed 6:00:54.392 3G / 5G INFO General (stage.cpp : 95) PROCEDURE == Consensus contigs construction 6:00:54.392 3G / 5G INFO ConsensusContigsConstruc (consensus_contigs_construc: 274) Consensus contigs constructor starts 6:00:55.832 3G / 5G INFO ConsensusContigsConstruc (consensus_contigs_construc: 51) 19988 contigs from /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_132-dipSPAdes-3.5.0-trimmed/spades/contigs.fasta were read 6:00:55.841 3G / 5G INFO ConsensusContigsConstruc (consensus_contigs_construc: 276) Total: 19988 contigs were read 6:01:29.284 3G / 5G INFO ConsensusContigsConstruc (consensus_contigs_construc: 79) 14 contigs with total length 1274 have mapped path with zero length 6:01:29.315 3G / 5G INFO ConsensusContigsConstruc (consensus_contigs_construc: 105) Removing repetitive edges in contigs mapping starts 6:01:29.345 3G / 5G INFO ConsensusContigsConstruc (consensus_contigs_construc: 109) Removing repetitive edges in contigs mapping ends 6:01:29.345 3G / 5G INFO ConsensusContigsConstruc (consensus_contigs_construc: 111) Close gaps in contigs mappings starts 6:01:29.351 3G / 5G INFO General (close_gaps_corrector.hpp : 83) 417 contigs from 19974 have gaps before correction 6:01:29.357 3G / 5G INFO General (close_gaps_corrector.hpp : 68) 10% contigs were processed 6:01:29.362 3G / 5G INFO General (close_gaps_corrector.hpp : 68) 20% contigs were processed 6:01:29.365 3G / 5G INFO General (close_gaps_corrector.hpp : 68) 30% contigs were processed 6:01:29.367 3G / 5G INFO General (close_gaps_corrector.hpp : 68) 40% contigs were processed 6:01:29.367 3G / 5G INFO General (close_gaps_corrector.hpp : 68) 50% contigs were processed 6:01:29.369 3G / 5G INFO General (close_gaps_corrector.hpp : 68) 60% contigs were processed 6:01:29.369 3G / 5G INFO General (close_gaps_corrector.hpp : 68) 70% contigs were processed 6:01:29.370 3G / 5G INFO General (close_gaps_corrector.hpp : 68) 80% contigs were processed 6:01:29.371 3G / 5G INFO General (close_gaps_corrector.hpp : 68) 90% contigs were processed 6:01:29.372 3G / 5G INFO General (close_gaps_corrector.hpp : 72) 100% contigs were processed 6:01:29.372 3G / 5G INFO General (close_gaps_corrector.hpp : 87) 19974 contigs from 19974 were corrected 6:01:29.372 3G / 5G INFO General (close_gaps_corrector.hpp : 88) 0 contigs from 19974 have gaps after correction 6:01:29.372 3G / 5G INFO ConsensusContigsConstruc (consensus_contigs_construc: 115) Close gaps in contigs mappings ends 6:01:29.372 3G / 5G INFO ConsensusContigsConstruc (consensus_contigs_construc: 117) Removing incorrect contigs 6:01:29.378 3G / 5G INFO General (incorrect_contig_remover.h: 25) 0 contigs from 19974 were deleted 6:01:29.456 3G / 5G INFO ConsensusContigsConstruc (consensus_contigs_construc: 144) Addition of RC contigs. 39948 contigs will be used 6:01:29.459 3G / 5G INFO ConsensusContigsConstruc (consensus_contigs_construc: 149) Redundant contigs remover starts 6:01:29.460 3G / 5G INFO General (iterative_redundant_contig: 30) Equal path remover starts 6:01:29.460 3G / 5G INFO General (path_index.hpp : 27) Initialization of vertex-paths index starts 6:01:29.579 3G / 5G INFO General (path_index.hpp : 40) Initialization of vertex-paths index ends 6:01:29.580 3G / 5G INFO General (equal_path_deletion_correc: 27) Computing redundant equal contigs starts 6:01:33.469 3G / 5G INFO General (equal_path_deletion_correc: 58) 2452 contigs from 39948 are redundant 6:01:33.475 3G / 5G INFO General (equal_path_deletion_correc: 61) Computing redundant equal contigs ends 6:01:33.551 3G / 5G INFO General (iterative_redundant_contig: 36) 37496 contigs will be used further 6:01:33.558 3G / 5G INFO General (iterative_redundant_contig: 39) Iterative loop corrector starts 6:01:33.558 3G / 5G INFO General (iterative_redundant_contig: 41) Only exact match iteration with parameters: 6:01:33.558 3G / 5G INFO General (iterative_redundant_contig: 42) Maximal loop length - 500 6:01:33.559 3G / 5G INFO General (iterative_redundant_contig: 43) Minimal lcs length - 1500 6:01:33.559 3G / 5G INFO General (iterative_redundant_contig: 44) Maximal tail length - 0 6:01:33.559 3G / 5G INFO General (path_index.hpp : 27) Initialization of vertex-paths index starts 6:01:33.672 3G / 5G INFO General (path_index.hpp : 40) Initialization of vertex-paths index ends 6:01:33.672 3G / 5G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 708) Computing redundant contigs starts 6:02:43.339 3G / 5G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 852) 10% contigs were processed 6:03:21.027 3G / 5G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 852) 20% contigs were processed 6:03:25.143 3G / 5G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 852) 30% contigs were processed 6:03:25.895 3G / 5G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 852) 40% contigs were processed 6:03:26.023 3G / 5G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 852) 50% contigs were processed 6:03:26.209 3G / 5G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 852) 60% contigs were processed 6:03:26.252 3G / 5G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 852) 70% contigs were processed 6:03:26.309 3G / 5G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 852) 80% contigs were processed 6:03:26.339 3G / 5G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 852) 90% contigs were processed 6:03:27.025 3G / 5G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 856) 100% contigs were processed 6:03:27.157 3G / 5G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 861) 3940 contigs from 37496 are redundant 6:03:27.164 3G / 5G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 865) Computing redundant contigs ends 6:03:27.601 3G / 5G INFO General (iterative_redundant_contig: 55) 33556 contigs will be used further 6:03:27.630 3G / 5G INFO General (iterative_redundant_contig: 59) Tails allowing match iteration with parameters: 6:03:27.630 3G / 5G INFO General (iterative_redundant_contig: 60) Maximal loop length - 500 6:03:27.630 3G / 5G INFO General (iterative_redundant_contig: 61) Minimal lcs length - 1500 6:03:27.630 3G / 5G INFO General (iterative_redundant_contig: 62) Maximal tail length - 67165 6:03:27.630 3G / 5G INFO General (path_index.hpp : 27) Initialization of vertex-paths index starts 6:03:27.728 3G / 5G INFO General (path_index.hpp : 40) Initialization of vertex-paths index ends 6:03:27.728 3G / 5G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 708) Computing redundant contigs starts 6:04:31.890 3G / 5G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 852) 10% contigs were processed 6:04:44.712 3G / 5G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 852) 20% contigs were processed 6:04:45.185 3G / 5G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 852) 30% contigs were processed 6:04:45.597 3G / 5G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 852) 40% contigs were processed 6:04:45.702 3G / 5G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 852) 50% contigs were processed 6:04:45.783 3G / 5G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 852) 60% contigs were processed 6:04:45.838 3G / 5G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 852) 70% contigs were processed 6:04:45.879 3G / 5G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 852) 80% contigs were processed 6:04:45.916 3G / 5G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 852) 90% contigs were processed 6:04:46.470 3G / 5G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 856) 100% contigs were processed 6:04:46.849 3G / 5G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 861) 4840 contigs from 33556 are redundant 6:04:46.856 3G / 5G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 865) Computing redundant contigs ends 6:04:47.834 3G / 5G INFO General (iterative_redundant_contig: 72) 28716 contigs will be used further 6:04:47.881 3G / 5G INFO General (iterative_redundant_contig: 74) Iterative loop corrector ends 6:04:47.881 3G / 5G INFO ConsensusContigsConstruc (consensus_contigs_construc: 161) Redundant contigs remover ends 6:04:47.902 3G / 5G INFO ConsensusContigsConstruc (consensus_contigs_construc: 166) Overlapping search starts 6:04:47.902 3G / 5G INFO General (path_index.hpp : 27) Initialization of vertex-paths index starts 6:04:47.970 3G / 5G INFO General (path_index.hpp : 40) Initialization of vertex-paths index ends 6:04:47.970 3G / 5G INFO OverlapCorrector (overlap_searcher.hpp : 350) Computing overlaps starts 6:04:58.062 3G / 5G INFO OverlapCorrector (overlap_searcher.hpp : 478) Overlap graph with 28716 vertices and 38 edges constructed 6:04:58.065 3G / 5G INFO General (overlap_graph.hpp :1100) 0 tips and 0 transitive edges were deleted in overlap graph 6:04:58.065 3G / 5G INFO General (overlap_graph.hpp :1103) Bulge remover starts 6:07:30.948 3G / 5G INFO General (overlap_graph.hpp :1108) 0 bulges were deleted in overlap graph 6:07:30.953 3G / 5G INFO OverlapCorrector (overlap_searcher.hpp : 486) Simplified overlap graph contains 28716 vertices and 38 edges 6:08:42.417 3G / 5G INFO OverlapCorrector (overlap_searcher.hpp : 525) Computing overlaps ends 6:08:42.467 3G / 5G INFO ConsensusContigsConstruc (consensus_contigs_construc: 174) Overlapping search ends 6:08:43.021 3G / 5G INFO ConsensusContigsConstruc (consensus_contigs_construc: 190) 14339 with total length 29165858 were written in /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_132-dipSPAdes-3.5.0-trimmed/dipspades/consensus_contigs.fasta 6:08:43.217 3G / 5G INFO ConsensusContigsConstruc (consensus_contigs_construc: 190) 701 with total length 22562367 were written in /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_132-dipSPAdes-3.5.0-trimmed/dipspades/paired_consensus_contigs.fasta 6:08:43.582 3G / 5G INFO ConsensusContigsConstruc (consensus_contigs_construc: 190) 13638 with total length 6603491 were written in /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_132-dipSPAdes-3.5.0-trimmed/dipspades/unpaired_consensus_contigs.fasta 6:08:43.584 3G / 5G INFO ConsensusContigsConstruc (consensus_contigs_construc: 216) Writing haplocontigs alignment to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_132-dipSPAdes-3.5.0-trimmed/dipspades/haplocontigs_alignment 6:08:53.599 3G / 5G INFO ConsensusContigsConstruc (consensus_contigs_construc: 311) Consensus contigs constructor ends 6:08:53.628 3G / 5G INFO General (dipspades.hpp : 211) dipSPAdes finished 6:09:06.807 128M / 5G INFO General (main.cpp : 115) Assembling time: 6 hours 9 minutes 6 seconds ===== Assembling finished. * Assembled consensus contigs are in: /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_132-dipSPAdes-3.5.0-trimmed/dipspades/consensus_contigs.fasta * Assembled paired consensus contigs are in: /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_132-dipSPAdes-3.5.0-trimmed/dipspades/paired_consensus_contigs.fasta * Assembled unpaired consensus contigs are in: /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_132-dipSPAdes-3.5.0-trimmed/dipspades/unpaired_consensus_contigs.fasta ======= dipSPAdes finished. dipSPAdes log can be found here: /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_132-dipSPAdes-3.5.0-trimmed/dipspades/dipspades.log Thank you for using dipSPAdes!