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_265/reads.end1.paired.fastq.gz --pe1-2 /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_265/reads.end2.paired.fastq.gz -t 16 -o /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_265-dipSPAdes-3.5.0-trimmed dipSPAdes command line: -t 16 -o /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_265-dipSPAdes-3.5.0-trimmed/dipspades --hap /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_265-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_265-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_265-dipSPAdes-3.5.0-trimmed/dipspades Dir for temp files: /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_265-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_265-dipSPAdes-3.5.0-trimmed/dipspades/dipspades.log ===== Assembling started. 0:00:00.120 4M / 4M INFO General (memory_limit.hpp : 42) Memory limit set to 100 Gb 0:00:00.250 4M / 4M INFO General (main.cpp : 96) Assembling dataset (/N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_265-dipSPAdes-3.5.0-trimmed/dipspades/) with K=55 0:00:00.272 4M / 4M INFO General (dipspades.hpp : 188) dipSPAdes started 0:00:00.440 4M / 4M INFO StageManager (stage.cpp : 125) STAGE == dipSPAdes 0:00:00.460 4M / 4M INFO General (stage.cpp : 95) PROCEDURE == Construction of graph from contigs 0:00:00.481 4M / 4M INFO General (dipspades.hpp : 19) Addition of contigs from /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_265-dipSPAdes-3.5.0-trimmed/spades/contigs.fasta 0:00:00.521 4M / 4M INFO General (dipspades.hpp : 23) Construction of the de Bruijn graph with K=55 0:00:00.529 4M / 4M INFO General (graph_construction.hpp : 129) Constructing DeBruijn graph for k=55 0:00:00.546 4M / 4M INFO General (kmer_splitters.hpp : 172) Splitting kmer instances into 1 buckets. This might take a while. 0:00:00.546 4M / 4M INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:00:00.546 4M / 4M INFO General (kmer_splitters.hpp : 190) Memory available for splitting buffers: 33.332 Gb 0:00:00.546 4M / 4M INFO General (kmer_splitters.hpp : 199) Using cell size of 33554432 0:00:39.822 568M / 1G INFO General (kmer_splitters.hpp : 228) Processed 36306 reads 0:00:39.822 568M / 1G INFO General (kmer_splitters.hpp : 245) Used 36306 reads. Maximum read length 159001 0:00:39.822 568M / 1G INFO General (kmer_splitters.hpp : 246) Average read length 4058.15 0:00:39.825 4M / 1G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:03:56.468 4M / 1G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 72097356 kmers in total. 0:03:56.468 4M / 1G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:04:15.655 4M / 1G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:04:15.655 4M / 1G INFO General (kmer_splitters.hpp : 379) Splitting kmer instances into 16 buckets. This might take a while. 0:04:15.655 4M / 1G INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:04:15.655 4M / 1G INFO General (kmer_splitters.hpp : 397) Memory available for splitting buffers: 33.332 Gb 0:04:15.655 4M / 1G INFO General (kmer_splitters.hpp : 405) Using cell size of 2097152 0:08:11.457 640M / 1G INFO General (kmer_splitters.hpp : 428) Processed 16777216 kmers 0:11:59.164 640M / 1G INFO General (kmer_splitters.hpp : 428) Processed 33554432 kmers 0:16:33.155 640M / 1G INFO General (kmer_splitters.hpp : 428) Processed 50331648 kmers 0:22:11.848 640M / 1G INFO General (kmer_splitters.hpp : 428) Processed 67108864 kmers 0:25:30.567 640M / 1G INFO General (kmer_splitters.hpp : 428) Processed 72097356 kmers 0:25:30.567 640M / 1G INFO General (kmer_splitters.hpp : 437) Used 72097356 kmers. 0:25:30.573 64M / 1G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:28:07.789 64M / 1G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 72096201 kmers in total. 0:28:07.789 64M / 1G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:28:15.755 64M / 1G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:29:50.217 88M / 1G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:30:18.573 88M / 1G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 24940812 bytes occupied (2.7675 bits per kmer). 0:30:18.683 160M / 1G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 382) Building k-mer extensions from k+1-mers 0:32:21.039 160M / 1G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 386) Building k-mer extensions from k+1-mers finished. 0:32:21.048 160M / 1G INFO General (graph_construction.hpp : 145) Condensing graph 0:32:21.048 160M / 1G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 337) Extracting unbranching paths 0:32:52.102 176M / 1G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 351) Extracting unbranching paths finished. 93210 sequences extracted 0:32:57.329 172M / 1G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 311) Collecting perfect loops 0:33:19.888 172M / 1G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 326) Collecting perfect loops finished. 126 loops collected 0:33:20.097 168M / 1G INFO General (graph_construction.hpp : 150) Building index with from graph 0:33:20.102 168M / 1G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:33:20.102 168M / 1G INFO General (kmer_splitters.hpp : 289) Splitting kmer instances into 16 buckets. This might take a while. 0:33:20.102 168M / 1G INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:33:20.102 168M / 1G INFO General (kmer_splitters.hpp : 307) Memory available for splitting buffers: 33.2786 Gb 0:33:20.103 168M / 1G INFO General (kmer_splitters.hpp : 312) Using cell size of 2097152 0:37:45.698 744M / 1G INFO General (kmer_splitters.hpp : 325) Processed 43320 edges 0:42:10.680 744M / 1G INFO General (kmer_splitters.hpp : 325) Processed 87206 edges 0:43:44.370 744M / 1G INFO General (kmer_splitters.hpp : 325) Processed 93336 edges 0:43:44.371 744M / 1G INFO General (kmer_splitters.hpp : 330) Used 93336 sequences. 0:43:44.375 168M / 1G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:46:36.347 168M / 1G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 72097356 kmers in total. 0:46:36.347 168M / 1G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:46:43.845 168M / 1G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:47:54.604 192M / 1G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:48:01.233 192M / 1G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 24941220 bytes occupied (2.7675 bits per kmer). 0:48:02.250 1G / 1G INFO General (edge_index_builders.hpp : 21) Collecting k-mer coverage information from graph, this takes a while. 0:49:46.640 1G / 1G INFO General (graph_construction.hpp : 182) Filling coverage index 0:49:46.658 1G / 1G INFO General (edge_index_builders.hpp : 99) Collecting k-mer coverage information from reads, this takes a while. 0:51:03.699 1G / 1G INFO General (graph_construction.hpp : 184) Filling coverage and flanking coverage from index 0:51:06.958 1G / 1G INFO General (stage.cpp : 95) PROCEDURE == Polymorphic bulge remover 0:51:06.958 1G / 1G INFO General (polymorphic_bulge_remover.: 94) Polymorphic bulge remover starts 0:51:06.976 1G / 1G INFO General (polymorphic_bulge_remover.: 36) Simple polymorphic bulge remover runs 0:55:37.429 2G / 3G INFO General (polymorphic_bulge_remover.: 42) 1 iteration: 5723 simple bulges were glued 0:58:47.232 2G / 3G INFO General (polymorphic_bulge_remover.: 42) 2 iteration: 209 simple bulges were glued 0:58:47.515 2G / 3G INFO General (polymorphic_bulge_remover.: 42) 3 iteration: 0 simple bulges were glued 0:58:47.516 2G / 3G INFO General (polymorphic_bulge_remover.: 44) Simple polymorphic bulge remover ends 0:58:47.580 2G / 3G INFO General (polymorphic_bulge_remover.: 49) LightBulgeRemover starts 0:58:47.580 2G / 3G INFO General (polymorphic_bulge_remover.: 50) Maximal number of iterations: 15 0:58:47.629 2G / 3G INFO PolymorphicBulgeRemover (complex_bulge_remover.hpp : 108) Maximal length of glued bulge: 52360 1:18:44.150 2G / 3G INFO General (polymorphic_bulge_remover.: 60) 1 iteration: 2074 complex bulges were glued 1:18:44.151 2G / 3G INFO PolymorphicBulgeRemover (complex_bulge_remover.hpp : 108) Maximal length of glued bulge: 52578 1:32:23.274 2G / 3G INFO General (polymorphic_bulge_remover.: 60) 2 iteration: 79 complex bulges were glued 1:32:23.275 2G / 3G INFO PolymorphicBulgeRemover (complex_bulge_remover.hpp : 108) Maximal length of glued bulge: 53254 1:44:39.044 2G / 3G INFO General (polymorphic_bulge_remover.: 60) 3 iteration: 15 complex bulges were glued 1:44:39.044 2G / 3G INFO PolymorphicBulgeRemover (complex_bulge_remover.hpp : 108) Maximal length of glued bulge: 53254 1:56:55.262 2G / 3G INFO General (polymorphic_bulge_remover.: 60) 4 iteration: 6 complex bulges were glued 1:56:55.263 2G / 3G INFO PolymorphicBulgeRemover (complex_bulge_remover.hpp : 108) Maximal length of glued bulge: 53254 2:09:04.988 2G / 3G INFO General (polymorphic_bulge_remover.: 60) 5 iteration: 2 complex bulges were glued 2:09:04.989 2G / 3G INFO PolymorphicBulgeRemover (complex_bulge_remover.hpp : 108) Maximal length of glued bulge: 53254 2:21:18.558 2G / 3G INFO General (polymorphic_bulge_remover.: 60) 6 iteration: 1 complex bulges were glued 2:21:18.559 2G / 3G INFO PolymorphicBulgeRemover (complex_bulge_remover.hpp : 108) Maximal length of glued bulge: 53254 2:33:29.777 2G / 3G INFO General (polymorphic_bulge_remover.: 60) 7 iteration: 0 complex bulges were glued 2:33:29.777 2G / 3G INFO General (polymorphic_bulge_remover.: 62) LightBulgeRemover ends 2:33:29.777 2G / 3G INFO General (polymorphic_bulge_remover.: 103) Index refilling 2:33:29.795 1G / 3G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 2:33:29.795 1G / 3G INFO General (kmer_splitters.hpp : 289) Splitting kmer instances into 16 buckets. This might take a while. 2:33:29.795 1G / 3G INFO General (file_limit.hpp : 29) Open file limit set to 32768 2:33:29.795 1G / 3G INFO General (kmer_splitters.hpp : 307) Memory available for splitting buffers: 32.8971 Gb 2:33:29.796 1G / 3G INFO General (kmer_splitters.hpp : 312) Using cell size of 2097152 2:38:23.185 1G / 3G INFO General (kmer_splitters.hpp : 325) Processed 22846 edges 2:42:14.768 1G / 3G INFO General (kmer_splitters.hpp : 325) Processed 44978 edges 2:42:14.768 1G / 3G INFO General (kmer_splitters.hpp : 330) Used 44978 sequences. 2:42:14.771 1G / 3G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 2:43:33.605 1G / 3G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 65063795 kmers in total. 2:43:33.605 1G / 3G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 2:43:40.925 1G / 3G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 2:44:56.461 1G / 3G INFO General (kmer_index.hpp : 371) Merging final buckets. 2:45:02.268 1G / 3G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 22508044 bytes occupied (2.7675 bits per kmer). 2:45:03.190 2G / 3G INFO General (edge_index_builders.hpp : 21) Collecting k-mer coverage information from graph, this takes a while. 2:46:42.435 2G / 3G INFO General (polymorphic_bulge_remover.: 106) Glueing equal kmers 2:49:37.863 2G / 3G INFO General (equal_sequence_gluer.hpp : 105) 0 kmers glued 2:49:37.863 2G / 3G INFO General (polymorphic_bulge_remover.: 108) Polymorphic ends remover ends 2:49:37.863 2G / 3G INFO General (dipspades.hpp : 96) Consensus graph was constructed 2:49:37.863 2G / 3G INFO General (stage.cpp : 95) PROCEDURE == Consensus contigs construction 2:49:37.863 2G / 3G INFO ConsensusContigsConstruc (consensus_contigs_construc: 274) Consensus contigs constructor starts 2:49:39.342 2G / 3G INFO ConsensusContigsConstruc (consensus_contigs_construc: 51) 18153 contigs from /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_265-dipSPAdes-3.5.0-trimmed/spades/contigs.fasta were read 2:49:39.349 2G / 3G INFO ConsensusContigsConstruc (consensus_contigs_construc: 276) Total: 18153 contigs were read 2:50:01.738 2G / 3G INFO ConsensusContigsConstruc (consensus_contigs_construc: 79) 15 contigs with total length 1387 have mapped path with zero length 2:50:01.819 2G / 3G INFO ConsensusContigsConstruc (consensus_contigs_construc: 105) Removing repetitive edges in contigs mapping starts 2:50:01.883 2G / 3G INFO ConsensusContigsConstruc (consensus_contigs_construc: 109) Removing repetitive edges in contigs mapping ends 2:50:01.883 2G / 3G INFO ConsensusContigsConstruc (consensus_contigs_construc: 111) Close gaps in contigs mappings starts 2:50:01.890 2G / 3G INFO General (close_gaps_corrector.hpp : 83) 423 contigs from 18138 have gaps before correction 2:50:02.125 2G / 3G INFO General (close_gaps_corrector.hpp : 68) 10% contigs were processed 2:50:02.129 2G / 3G INFO General (close_gaps_corrector.hpp : 68) 20% contigs were processed 2:50:02.134 2G / 3G INFO General (close_gaps_corrector.hpp : 68) 30% contigs were processed 2:50:02.137 2G / 3G INFO General (close_gaps_corrector.hpp : 68) 40% contigs were processed 2:50:02.138 2G / 3G INFO General (close_gaps_corrector.hpp : 68) 50% contigs were processed 2:50:02.140 2G / 3G INFO General (close_gaps_corrector.hpp : 68) 60% contigs were processed 2:50:02.141 2G / 3G INFO General (close_gaps_corrector.hpp : 68) 70% contigs were processed 2:50:02.141 2G / 3G INFO General (close_gaps_corrector.hpp : 68) 80% contigs were processed 2:50:02.143 2G / 3G INFO General (close_gaps_corrector.hpp : 68) 90% contigs were processed 2:50:02.145 2G / 3G INFO General (close_gaps_corrector.hpp : 72) 100% contigs were processed 2:50:02.145 2G / 3G INFO General (close_gaps_corrector.hpp : 87) 18138 contigs from 18138 were corrected 2:50:02.145 2G / 3G INFO General (close_gaps_corrector.hpp : 88) 0 contigs from 18138 have gaps after correction 2:50:02.145 2G / 3G INFO ConsensusContigsConstruc (consensus_contigs_construc: 115) Close gaps in contigs mappings ends 2:50:02.145 2G / 3G INFO ConsensusContigsConstruc (consensus_contigs_construc: 117) Removing incorrect contigs 2:50:02.155 2G / 3G INFO General (incorrect_contig_remover.h: 25) 0 contigs from 18138 were deleted 2:50:02.234 2G / 3G INFO ConsensusContigsConstruc (consensus_contigs_construc: 144) Addition of RC contigs. 36276 contigs will be used 2:50:02.236 2G / 3G INFO ConsensusContigsConstruc (consensus_contigs_construc: 149) Redundant contigs remover starts 2:50:02.249 2G / 3G INFO General (iterative_redundant_contig: 30) Equal path remover starts 2:50:02.281 2G / 3G INFO General (path_index.hpp : 27) Initialization of vertex-paths index starts 2:50:02.406 2G / 3G INFO General (path_index.hpp : 40) Initialization of vertex-paths index ends 2:50:02.414 2G / 3G INFO General (equal_path_deletion_correc: 27) Computing redundant equal contigs starts 2:50:13.697 2G / 3G INFO General (equal_path_deletion_correc: 58) 4286 contigs from 36276 are redundant 2:50:13.704 2G / 3G INFO General (equal_path_deletion_correc: 61) Computing redundant equal contigs ends 2:50:13.796 2G / 3G INFO General (iterative_redundant_contig: 36) 31990 contigs will be used further 2:50:13.803 2G / 3G INFO General (iterative_redundant_contig: 39) Iterative loop corrector starts 2:50:13.803 2G / 3G INFO General (iterative_redundant_contig: 41) Only exact match iteration with parameters: 2:50:13.803 2G / 3G INFO General (iterative_redundant_contig: 42) Maximal loop length - 500 2:50:13.803 2G / 3G INFO General (iterative_redundant_contig: 43) Minimal lcs length - 1500 2:50:13.803 2G / 3G INFO General (iterative_redundant_contig: 44) Maximal tail length - 0 2:50:13.803 2G / 3G INFO General (path_index.hpp : 27) Initialization of vertex-paths index starts 2:50:13.916 2G / 3G INFO General (path_index.hpp : 40) Initialization of vertex-paths index ends 2:50:13.916 2G / 3G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 708) Computing redundant contigs starts 2:50:43.184 2G / 3G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 852) 10% contigs were processed 2:51:02.488 2G / 3G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 852) 20% contigs were processed 2:51:29.948 2G / 3G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 852) 30% contigs were processed 2:51:34.062 2G / 3G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 852) 40% contigs were processed 2:51:34.233 2G / 3G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 852) 50% contigs were processed 2:51:34.350 2G / 3G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 852) 60% contigs were processed 2:51:34.390 2G / 3G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 852) 70% contigs were processed 2:51:34.453 2G / 3G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 852) 80% contigs were processed 2:51:34.501 2G / 3G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 852) 90% contigs were processed 2:51:36.344 2G / 3G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 856) 100% contigs were processed 2:51:36.469 2G / 3G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 861) 5046 contigs from 31990 are redundant 2:51:36.476 2G / 3G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 865) Computing redundant contigs ends 2:51:36.900 2G / 3G INFO General (iterative_redundant_contig: 55) 26944 contigs will be used further 2:51:36.925 2G / 3G INFO General (iterative_redundant_contig: 59) Tails allowing match iteration with parameters: 2:51:36.925 2G / 3G INFO General (iterative_redundant_contig: 60) Maximal loop length - 500 2:51:36.925 2G / 3G INFO General (iterative_redundant_contig: 61) Minimal lcs length - 1500 2:51:36.926 2G / 3G INFO General (iterative_redundant_contig: 62) Maximal tail length - 46896 2:51:36.926 2G / 3G INFO General (path_index.hpp : 27) Initialization of vertex-paths index starts 2:51:37.019 2G / 3G INFO General (path_index.hpp : 40) Initialization of vertex-paths index ends 2:51:37.020 2G / 3G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 708) Computing redundant contigs starts 2:51:59.251 2G / 3G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 852) 10% contigs were processed 2:52:14.080 2G / 3G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 852) 20% contigs were processed 2:52:35.580 2G / 3G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 852) 30% contigs were processed 2:52:37.311 2G / 3G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 852) 40% contigs were processed 2:52:37.422 2G / 3G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 852) 50% contigs were processed 2:52:37.524 2G / 3G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 852) 60% contigs were processed 2:52:37.562 2G / 3G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 852) 70% contigs were processed 2:52:37.600 2G / 3G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 852) 80% contigs were processed 2:52:37.638 2G / 3G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 852) 90% contigs were processed 2:52:38.771 2G / 3G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 856) 100% contigs were processed 2:52:40.585 2G / 3G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 861) 5540 contigs from 26944 are redundant 2:52:40.592 2G / 3G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 865) Computing redundant contigs ends 2:52:43.943 2G / 3G INFO General (iterative_redundant_contig: 72) 21404 contigs will be used further 2:52:44.025 2G / 3G INFO General (iterative_redundant_contig: 74) Iterative loop corrector ends 2:52:44.025 2G / 3G INFO ConsensusContigsConstruc (consensus_contigs_construc: 161) Redundant contigs remover ends 2:52:44.071 2G / 3G INFO ConsensusContigsConstruc (consensus_contigs_construc: 166) Overlapping search starts 2:52:44.071 2G / 3G INFO General (path_index.hpp : 27) Initialization of vertex-paths index starts 2:52:44.128 2G / 3G INFO General (path_index.hpp : 40) Initialization of vertex-paths index ends 2:52:44.128 2G / 3G INFO OverlapCorrector (overlap_searcher.hpp : 350) Computing overlaps starts 2:52:57.253 2G / 3G INFO OverlapCorrector (overlap_searcher.hpp : 478) Overlap graph with 21404 vertices and 12 edges constructed 2:52:57.290 2G / 3G INFO General (overlap_graph.hpp :1100) 0 tips and 0 transitive edges were deleted in overlap graph 2:52:57.290 2G / 3G INFO General (overlap_graph.hpp :1103) Bulge remover starts 2:54:24.323 2G / 3G INFO General (overlap_graph.hpp :1108) 0 bulges were deleted in overlap graph 2:54:24.327 2G / 3G INFO OverlapCorrector (overlap_searcher.hpp : 486) Simplified overlap graph contains 21404 vertices and 12 edges 2:55:04.968 2G / 3G INFO OverlapCorrector (overlap_searcher.hpp : 525) Computing overlaps ends 2:55:05.019 2G / 3G INFO ConsensusContigsConstruc (consensus_contigs_construc: 174) Overlapping search ends 2:55:18.554 2G / 3G INFO ConsensusContigsConstruc (consensus_contigs_construc: 190) 10696 with total length 36286248 were written in /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_265-dipSPAdes-3.5.0-trimmed/dipspades/consensus_contigs.fasta 2:55:18.816 2G / 3G INFO ConsensusContigsConstruc (consensus_contigs_construc: 190) 1391 with total length 27544647 were written in /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_265-dipSPAdes-3.5.0-trimmed/dipspades/paired_consensus_contigs.fasta 2:55:19.111 2G / 3G INFO ConsensusContigsConstruc (consensus_contigs_construc: 190) 9305 with total length 8741601 were written in /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_265-dipSPAdes-3.5.0-trimmed/dipspades/unpaired_consensus_contigs.fasta 2:55:19.114 2G / 3G INFO ConsensusContigsConstruc (consensus_contigs_construc: 216) Writing haplocontigs alignment to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_265-dipSPAdes-3.5.0-trimmed/dipspades/haplocontigs_alignment 2:55:53.956 2G / 3G INFO ConsensusContigsConstruc (consensus_contigs_construc: 311) Consensus contigs constructor ends 2:55:54.009 2G / 3G INFO General (dipspades.hpp : 211) dipSPAdes finished 2:56:02.765 132M / 3G INFO General (main.cpp : 115) Assembling time: 2 hours 56 minutes 3 seconds ===== Assembling finished. * Assembled consensus contigs are in: /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_265-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_265-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_265-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_265-dipSPAdes-3.5.0-trimmed/dipspades/dipspades.log Thank you for using dipSPAdes!