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_130/reads.end1.paired.fastq.gz --pe1-2 /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_130/reads.end2.paired.fastq.gz -t 16 -o /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_130-dipSPAdes-3.5.0-trimmed dipSPAdes command line: -t 16 -o /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_130-dipSPAdes-3.5.0-trimmed/dipspades --hap /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_130-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_130-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_130-dipSPAdes-3.5.0-trimmed/dipspades Dir for temp files: /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_130-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_130-dipSPAdes-3.5.0-trimmed/dipspades/dipspades.log ===== Assembling started. 0:00:00.005 4M / 4M INFO General (memory_limit.hpp : 42) Memory limit set to 100 Gb 0:00:00.139 4M / 4M INFO General (main.cpp : 96) Assembling dataset (/N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_130-dipSPAdes-3.5.0-trimmed/dipspades/) with K=55 0:00:00.139 4M / 4M INFO General (dipspades.hpp : 188) dipSPAdes started 0:00:00.224 4M / 4M INFO StageManager (stage.cpp : 125) STAGE == dipSPAdes 0:00:00.224 4M / 4M INFO General (stage.cpp : 95) PROCEDURE == Construction of graph from contigs 0:00:00.227 4M / 4M INFO General (dipspades.hpp : 19) Addition of contigs from /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_130-dipSPAdes-3.5.0-trimmed/spades/contigs.fasta 0:00:00.233 4M / 4M INFO General (dipspades.hpp : 23) Construction of the de Bruijn graph with K=55 0:00:00.233 4M / 4M INFO General (graph_construction.hpp : 129) Constructing DeBruijn graph for k=55 0:00:00.263 4M / 4M INFO General (kmer_splitters.hpp : 172) Splitting kmer instances into 1 buckets. This might take a while. 0:00:00.311 4M / 4M INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:00:00.311 4M / 4M INFO General (kmer_splitters.hpp : 190) Memory available for splitting buffers: 33.332 Gb 0:00:00.311 4M / 4M INFO General (kmer_splitters.hpp : 199) Using cell size of 33554432 0:00:42.361 568M / 1G INFO General (kmer_splitters.hpp : 245) Used 25472 reads. Maximum read length 187748 0:00:42.362 568M / 1G INFO General (kmer_splitters.hpp : 246) Average read length 5673.67 0:00:42.365 4M / 1G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:01:05.488 4M / 1G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 70913016 kmers in total. 0:01:05.489 4M / 1G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:01:14.694 4M / 1G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:01:14.694 4M / 1G INFO General (kmer_splitters.hpp : 379) Splitting kmer instances into 16 buckets. This might take a while. 0:01:14.695 4M / 1G INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:01:14.695 4M / 1G INFO General (kmer_splitters.hpp : 397) Memory available for splitting buffers: 33.332 Gb 0:01:14.695 4M / 1G INFO General (kmer_splitters.hpp : 405) Using cell size of 2097152 0:04:38.202 640M / 1G INFO General (kmer_splitters.hpp : 428) Processed 16777216 kmers 0:07:44.486 640M / 1G INFO General (kmer_splitters.hpp : 428) Processed 33554432 kmers 0:11:46.076 640M / 1G INFO General (kmer_splitters.hpp : 428) Processed 50331648 kmers 0:15:26.087 640M / 1G INFO General (kmer_splitters.hpp : 428) Processed 67108864 kmers 0:16:27.509 640M / 1G INFO General (kmer_splitters.hpp : 428) Processed 70913016 kmers 0:16:27.510 640M / 1G INFO General (kmer_splitters.hpp : 437) Used 70913016 kmers. 0:16:27.522 64M / 1G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:17:26.927 64M / 1G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 70906136 kmers in total. 0:17:26.927 64M / 1G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:17:33.158 64M / 1G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:18:42.116 88M / 1G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:18:48.084 88M / 1G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 24529132 bytes occupied (2.7675 bits per kmer). 0:18:48.183 156M / 1G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 382) Building k-mer extensions from k+1-mers 0:20:32.178 156M / 1G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 386) Building k-mer extensions from k+1-mers finished. 0:20:32.182 156M / 1G INFO General (graph_construction.hpp : 145) Condensing graph 0:20:32.199 156M / 1G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 337) Extracting unbranching paths 0:21:03.118 172M / 1G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 351) Extracting unbranching paths finished. 80162 sequences extracted 0:21:09.169 168M / 1G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 311) Collecting perfect loops 0:21:31.084 168M / 1G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 326) Collecting perfect loops finished. 76 loops collected 0:21:31.193 164M / 1G INFO General (graph_construction.hpp : 150) Building index with from graph 0:21:31.194 164M / 1G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:21:31.194 164M / 1G INFO General (kmer_splitters.hpp : 289) Splitting kmer instances into 16 buckets. This might take a while. 0:21:31.194 164M / 1G INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:21:31.194 164M / 1G INFO General (kmer_splitters.hpp : 307) Memory available for splitting buffers: 33.2799 Gb 0:21:31.194 164M / 1G INFO General (kmer_splitters.hpp : 312) Using cell size of 2097152 0:25:18.621 740M / 1G INFO General (kmer_splitters.hpp : 325) Processed 37921 edges 0:29:05.055 740M / 1G INFO General (kmer_splitters.hpp : 325) Processed 75977 edges 0:30:21.559 740M / 1G INFO General (kmer_splitters.hpp : 325) Processed 80238 edges 0:30:21.559 740M / 1G INFO General (kmer_splitters.hpp : 330) Used 80238 sequences. 0:30:21.563 164M / 1G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:30:53.905 164M / 1G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 70913016 kmers in total. 0:30:53.905 164M / 1G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:31:01.017 164M / 1G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:32:09.699 188M / 1G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:32:15.340 188M / 1G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 24531515 bytes occupied (2.7675 bits per kmer). 0:32:16.453 1G / 1G INFO General (edge_index_builders.hpp : 21) Collecting k-mer coverage information from graph, this takes a while. 0:34:08.342 1G / 1G INFO General (graph_construction.hpp : 182) Filling coverage index 0:34:08.343 1G / 1G INFO General (edge_index_builders.hpp : 99) Collecting k-mer coverage information from reads, this takes a while. 0:35:17.962 1G / 1G INFO General (graph_construction.hpp : 184) Filling coverage and flanking coverage from index 0:35:20.335 1G / 1G INFO General (stage.cpp : 95) PROCEDURE == Polymorphic bulge remover 0:35:20.335 1G / 1G INFO General (polymorphic_bulge_remover.: 94) Polymorphic bulge remover starts 0:35:20.335 1G / 1G INFO General (polymorphic_bulge_remover.: 36) Simple polymorphic bulge remover runs 0:40:56.080 2G / 3G INFO General (polymorphic_bulge_remover.: 42) 1 iteration: 6389 simple bulges were glued 0:50:43.233 2G / 3G INFO General (polymorphic_bulge_remover.: 42) 2 iteration: 327 simple bulges were glued 0:52:17.925 2G / 3G INFO General (polymorphic_bulge_remover.: 42) 3 iteration: 1 simple bulges were glued 0:53:52.471 2G / 3G INFO General (polymorphic_bulge_remover.: 42) 4 iteration: 0 simple bulges were glued 0:53:52.471 2G / 3G INFO General (polymorphic_bulge_remover.: 44) Simple polymorphic bulge remover ends 0:53:52.471 2G / 3G INFO General (polymorphic_bulge_remover.: 49) LightBulgeRemover starts 0:53:52.471 2G / 3G INFO General (polymorphic_bulge_remover.: 50) Maximal number of iterations: 15 0:53:52.472 2G / 3G INFO PolymorphicBulgeRemover (complex_bulge_remover.hpp : 108) Maximal length of glued bulge: 53954 1:24:46.981 3G / 4G INFO General (polymorphic_bulge_remover.: 60) 1 iteration: 1921 complex bulges were glued 1:24:46.982 3G / 4G INFO PolymorphicBulgeRemover (complex_bulge_remover.hpp : 108) Maximal length of glued bulge: 61740 1:50:35.319 3G / 4G INFO General (polymorphic_bulge_remover.: 60) 2 iteration: 57 complex bulges were glued 1:50:35.319 3G / 4G INFO PolymorphicBulgeRemover (complex_bulge_remover.hpp : 108) Maximal length of glued bulge: 73848 2:18:19.597 3G / 4G INFO General (polymorphic_bulge_remover.: 60) 3 iteration: 10 complex bulges were glued 2:18:19.598 3G / 4G INFO PolymorphicBulgeRemover (complex_bulge_remover.hpp : 108) Maximal length of glued bulge: 73876 2:45:52.717 3G / 4G INFO General (polymorphic_bulge_remover.: 60) 4 iteration: 3 complex bulges were glued 2:45:52.718 3G / 4G INFO PolymorphicBulgeRemover (complex_bulge_remover.hpp : 108) Maximal length of glued bulge: 73876 3:13:20.111 3G / 4G INFO General (polymorphic_bulge_remover.: 60) 5 iteration: 0 complex bulges were glued 3:13:20.111 3G / 4G INFO General (polymorphic_bulge_remover.: 62) LightBulgeRemover ends 3:13:20.111 3G / 4G INFO General (polymorphic_bulge_remover.: 103) Index refilling 3:13:20.126 1G / 4G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 3:13:20.126 1G / 4G INFO General (kmer_splitters.hpp : 289) Splitting kmer instances into 16 buckets. This might take a while. 3:13:20.127 1G / 4G INFO General (file_limit.hpp : 29) Open file limit set to 32768 3:13:20.127 1G / 4G INFO General (kmer_splitters.hpp : 307) Memory available for splitting buffers: 32.7318 Gb 3:13:20.127 1G / 4G INFO General (kmer_splitters.hpp : 312) Using cell size of 2097152 3:15:15.263 2G / 4G INFO General (kmer_splitters.hpp : 325) Processed 15203 edges 3:18:32.718 2G / 4G INFO General (kmer_splitters.hpp : 325) Processed 28508 edges 3:18:32.718 2G / 4G INFO General (kmer_splitters.hpp : 330) Used 28508 sequences. 3:18:32.732 1G / 4G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 3:19:06.560 1G / 4G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 60625472 kmers in total. 3:19:06.560 1G / 4G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 3:19:11.662 1G / 4G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 3:20:28.084 1G / 4G INFO General (kmer_index.hpp : 371) Merging final buckets. 3:20:48.410 1G / 4G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 20972663 bytes occupied (2.76751 bits per kmer). 3:20:49.249 3G / 4G INFO General (edge_index_builders.hpp : 21) Collecting k-mer coverage information from graph, this takes a while. 3:22:28.771 3G / 4G INFO General (polymorphic_bulge_remover.: 106) Glueing equal kmers 3:25:37.283 3G / 4G INFO General (equal_sequence_gluer.hpp : 105) 1 kmers glued 3:25:37.283 3G / 4G INFO General (polymorphic_bulge_remover.: 108) Polymorphic ends remover ends 3:25:37.283 3G / 4G INFO General (dipspades.hpp : 96) Consensus graph was constructed 3:25:37.283 3G / 4G INFO General (stage.cpp : 95) PROCEDURE == Consensus contigs construction 3:25:37.283 3G / 4G INFO ConsensusContigsConstruc (consensus_contigs_construc: 274) Consensus contigs constructor starts 3:25:38.638 3G / 4G INFO ConsensusContigsConstruc (consensus_contigs_construc: 51) 12736 contigs from /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_130-dipSPAdes-3.5.0-trimmed/spades/contigs.fasta were read 3:25:38.644 3G / 4G INFO ConsensusContigsConstruc (consensus_contigs_construc: 276) Total: 12736 contigs were read 3:26:07.068 3G / 4G INFO ConsensusContigsConstruc (consensus_contigs_construc: 79) 14 contigs with total length 1319 have mapped path with zero length 3:26:07.088 3G / 4G INFO ConsensusContigsConstruc (consensus_contigs_construc: 105) Removing repetitive edges in contigs mapping starts 3:26:07.106 3G / 4G INFO ConsensusContigsConstruc (consensus_contigs_construc: 109) Removing repetitive edges in contigs mapping ends 3:26:07.106 3G / 4G INFO ConsensusContigsConstruc (consensus_contigs_construc: 111) Close gaps in contigs mappings starts 3:26:07.111 3G / 4G INFO General (close_gaps_corrector.hpp : 83) 318 contigs from 12722 have gaps before correction 3:26:07.114 3G / 4G INFO General (close_gaps_corrector.hpp : 68) 10% contigs were processed 3:26:07.115 3G / 4G INFO General (close_gaps_corrector.hpp : 68) 20% contigs were processed 3:26:07.118 3G / 4G INFO General (close_gaps_corrector.hpp : 68) 30% contigs were processed 3:26:07.120 3G / 4G INFO General (close_gaps_corrector.hpp : 68) 40% contigs were processed 3:26:07.121 3G / 4G INFO General (close_gaps_corrector.hpp : 68) 50% contigs were processed 3:26:07.122 3G / 4G INFO General (close_gaps_corrector.hpp : 68) 60% contigs were processed 3:26:07.122 3G / 4G INFO General (close_gaps_corrector.hpp : 68) 70% contigs were processed 3:26:07.123 3G / 4G INFO General (close_gaps_corrector.hpp : 68) 80% contigs were processed 3:26:07.123 3G / 4G INFO General (close_gaps_corrector.hpp : 68) 90% contigs were processed 3:26:07.125 3G / 4G INFO General (close_gaps_corrector.hpp : 72) 100% contigs were processed 3:26:07.125 3G / 4G INFO General (close_gaps_corrector.hpp : 87) 12721 contigs from 12722 were corrected 3:26:07.125 3G / 4G INFO General (close_gaps_corrector.hpp : 88) 1 contigs from 12722 have gaps after correction 3:26:07.125 3G / 4G INFO ConsensusContigsConstruc (consensus_contigs_construc: 115) Close gaps in contigs mappings ends 3:26:07.125 3G / 4G INFO ConsensusContigsConstruc (consensus_contigs_construc: 117) Removing incorrect contigs 3:26:07.129 3G / 4G INFO General (incorrect_contig_remover.h: 25) 1 contigs from 12722 were deleted 3:26:07.182 3G / 4G INFO ConsensusContigsConstruc (consensus_contigs_construc: 144) Addition of RC contigs. 25442 contigs will be used 3:26:07.184 3G / 4G INFO ConsensusContigsConstruc (consensus_contigs_construc: 149) Redundant contigs remover starts 3:26:07.184 3G / 4G INFO General (iterative_redundant_contig: 30) Equal path remover starts 3:26:07.184 3G / 4G INFO General (path_index.hpp : 27) Initialization of vertex-paths index starts 3:26:07.262 3G / 4G INFO General (path_index.hpp : 40) Initialization of vertex-paths index ends 3:26:07.262 3G / 4G INFO General (equal_path_deletion_correc: 27) Computing redundant equal contigs starts 3:26:10.487 3G / 4G INFO General (equal_path_deletion_correc: 58) 6116 contigs from 25442 are redundant 3:26:10.493 3G / 4G INFO General (equal_path_deletion_correc: 61) Computing redundant equal contigs ends 3:26:10.543 3G / 4G INFO General (iterative_redundant_contig: 36) 19326 contigs will be used further 3:26:10.548 3G / 4G INFO General (iterative_redundant_contig: 39) Iterative loop corrector starts 3:26:10.548 3G / 4G INFO General (iterative_redundant_contig: 41) Only exact match iteration with parameters: 3:26:10.548 3G / 4G INFO General (iterative_redundant_contig: 42) Maximal loop length - 500 3:26:10.548 3G / 4G INFO General (iterative_redundant_contig: 43) Minimal lcs length - 1500 3:26:10.548 3G / 4G INFO General (iterative_redundant_contig: 44) Maximal tail length - 0 3:26:10.548 3G / 4G INFO General (path_index.hpp : 27) Initialization of vertex-paths index starts 3:26:10.616 3G / 4G INFO General (path_index.hpp : 40) Initialization of vertex-paths index ends 3:26:10.616 3G / 4G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 708) Computing redundant contigs starts 3:26:51.102 3G / 4G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 852) 10% contigs were processed 3:26:58.820 3G / 4G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 852) 20% contigs were processed 3:27:10.775 3G / 4G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 852) 30% contigs were processed 3:27:21.831 3G / 4G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 852) 40% contigs were processed 3:27:21.959 3G / 4G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 852) 50% contigs were processed 3:27:22.040 3G / 4G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 852) 60% contigs were processed 3:27:22.046 3G / 4G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 852) 70% contigs were processed 3:27:22.051 3G / 4G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 852) 80% contigs were processed 3:27:22.060 3G / 4G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 852) 90% contigs were processed 3:27:22.229 3G / 4G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 856) 100% contigs were processed 3:27:22.300 3G / 4G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 861) 5474 contigs from 19326 are redundant 3:27:22.305 3G / 4G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 865) Computing redundant contigs ends 3:27:22.583 3G / 4G INFO General (iterative_redundant_contig: 55) 13852 contigs will be used further 3:27:22.599 3G / 4G INFO General (iterative_redundant_contig: 59) Tails allowing match iteration with parameters: 3:27:22.599 3G / 4G INFO General (iterative_redundant_contig: 60) Maximal loop length - 500 3:27:22.599 3G / 4G INFO General (iterative_redundant_contig: 61) Minimal lcs length - 1500 3:27:22.600 3G / 4G INFO General (iterative_redundant_contig: 62) Maximal tail length - 53485 3:27:22.600 3G / 4G INFO General (path_index.hpp : 27) Initialization of vertex-paths index starts 3:27:22.648 3G / 4G INFO General (path_index.hpp : 40) Initialization of vertex-paths index ends 3:27:22.648 3G / 4G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 708) Computing redundant contigs starts 3:27:46.911 3G / 4G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 852) 10% contigs were processed 3:27:54.088 3G / 4G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 852) 20% contigs were processed 3:28:03.974 3G / 4G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 852) 30% contigs were processed 3:28:09.572 3G / 4G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 852) 40% contigs were processed 3:28:09.685 3G / 4G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 852) 50% contigs were processed 3:28:09.712 3G / 4G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 852) 60% contigs were processed 3:28:09.721 3G / 4G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 852) 70% contigs were processed 3:28:09.724 3G / 4G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 852) 80% contigs were processed 3:28:09.730 3G / 4G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 852) 90% contigs were processed 3:28:09.848 3G / 4G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 856) 100% contigs were processed 3:28:10.039 3G / 4G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 861) 3830 contigs from 13852 are redundant 3:28:10.044 3G / 4G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 865) Computing redundant contigs ends 3:28:10.652 3G / 4G INFO General (iterative_redundant_contig: 72) 10022 contigs will be used further 3:28:10.677 3G / 4G INFO General (iterative_redundant_contig: 74) Iterative loop corrector ends 3:28:10.677 3G / 4G INFO ConsensusContigsConstruc (consensus_contigs_construc: 161) Redundant contigs remover ends 3:28:10.691 3G / 4G INFO ConsensusContigsConstruc (consensus_contigs_construc: 166) Overlapping search starts 3:28:10.691 3G / 4G INFO General (path_index.hpp : 27) Initialization of vertex-paths index starts 3:28:10.723 3G / 4G INFO General (path_index.hpp : 40) Initialization of vertex-paths index ends 3:28:10.724 3G / 4G INFO OverlapCorrector (overlap_searcher.hpp : 350) Computing overlaps starts 3:28:19.954 3G / 4G INFO OverlapCorrector (overlap_searcher.hpp : 478) Overlap graph with 10022 vertices and 34 edges constructed 3:28:19.955 3G / 4G INFO General (overlap_graph.hpp :1100) 2 tips and 0 transitive edges were deleted in overlap graph 3:28:19.955 3G / 4G INFO General (overlap_graph.hpp :1100) 0 tips and 0 transitive edges were deleted in overlap graph 3:28:19.955 3G / 4G INFO General (overlap_graph.hpp :1103) Bulge remover starts 3:28:37.616 3G / 4G INFO General (overlap_graph.hpp :1108) 0 bulges were deleted in overlap graph 3:28:37.618 3G / 4G INFO OverlapCorrector (overlap_searcher.hpp : 486) Simplified overlap graph contains 10020 vertices and 32 edges 3:28:45.872 3G / 4G INFO OverlapCorrector (overlap_searcher.hpp : 525) Computing overlaps ends 3:28:45.895 3G / 4G INFO ConsensusContigsConstruc (consensus_contigs_construc: 174) Overlapping search ends 3:28:46.258 3G / 4G INFO ConsensusContigsConstruc (consensus_contigs_construc: 190) 4994 with total length 30338662 were written in /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_130-dipSPAdes-3.5.0-trimmed/dipspades/consensus_contigs.fasta 3:28:46.478 3G / 4G INFO ConsensusContigsConstruc (consensus_contigs_construc: 190) 712 with total length 26711334 were written in /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_130-dipSPAdes-3.5.0-trimmed/dipspades/paired_consensus_contigs.fasta 3:28:46.614 3G / 4G INFO ConsensusContigsConstruc (consensus_contigs_construc: 190) 4282 with total length 3627328 were written in /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_130-dipSPAdes-3.5.0-trimmed/dipspades/unpaired_consensus_contigs.fasta 3:28:46.616 3G / 4G INFO ConsensusContigsConstruc (consensus_contigs_construc: 216) Writing haplocontigs alignment to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_130-dipSPAdes-3.5.0-trimmed/dipspades/haplocontigs_alignment 3:28:52.164 3G / 4G INFO ConsensusContigsConstruc (consensus_contigs_construc: 311) Consensus contigs constructor ends 3:28:52.182 3G / 4G INFO General (dipspades.hpp : 211) dipSPAdes finished 3:29:05.335 112M / 4G INFO General (main.cpp : 115) Assembling time: 3 hours 29 minutes 5 seconds ===== Assembling finished. * Assembled consensus contigs are in: /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_130-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_130-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_130-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_130-dipSPAdes-3.5.0-trimmed/dipspades/dipspades.log Thank you for using dipSPAdes!