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/Sample_Canal-1I/reads.end1.paired.fastq.gz --pe1-2 /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_Canal-1I/reads.end2.paired.fastq.gz -t 16 -o /N/dc2/projects/marinovg/2015-09-07-assemblies/Sample_Canal-1I-dipSPAdes-3.5.0-trimmed dipSPAdes command line: -t 16 -o /N/dc2/projects/marinovg/2015-09-07-assemblies/Sample_Canal-1I-dipSPAdes-3.5.0-trimmed/dipspades --hap /N/dc2/projects/marinovg/2015-09-07-assemblies/Sample_Canal-1I-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/Sample_Canal-1I-dipSPAdes-3.5.0-trimmed/spades/contigs.fasta'] Haplotype assembly stage: False Output directory: /N/dc2/projects/marinovg/2015-09-07-assemblies/Sample_Canal-1I-dipSPAdes-3.5.0-trimmed/dipspades Dir for temp files: /N/dc2/projects/marinovg/2015-09-07-assemblies/Sample_Canal-1I-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/Sample_Canal-1I-dipSPAdes-3.5.0-trimmed/dipspades/dipspades.log ===== Assembling started. 0:00:00.066 4M / 4M INFO General (memory_limit.hpp : 42) Memory limit set to 100 Gb 0:00:00.119 4M / 4M INFO General (main.cpp : 96) Assembling dataset (/N/dc2/projects/marinovg/2015-09-07-assemblies/Sample_Canal-1I-dipSPAdes-3.5.0-trimmed/dipspades/) with K=55 0:00:00.123 4M / 4M INFO General (dipspades.hpp : 188) dipSPAdes started 0:00:00.234 4M / 4M INFO StageManager (stage.cpp : 125) STAGE == dipSPAdes 0:00:00.241 4M / 4M INFO General (stage.cpp : 95) PROCEDURE == Construction of graph from contigs 0:00:00.251 4M / 4M INFO General (dipspades.hpp : 19) Addition of contigs from /N/dc2/projects/marinovg/2015-09-07-assemblies/Sample_Canal-1I-dipSPAdes-3.5.0-trimmed/spades/contigs.fasta 0:00:00.270 4M / 4M INFO General (dipspades.hpp : 23) Construction of the de Bruijn graph with K=55 0:00:00.273 4M / 4M INFO General (graph_construction.hpp : 129) Constructing DeBruijn graph for k=55 0:00:00.288 4M / 4M INFO General (kmer_splitters.hpp : 172) Splitting kmer instances into 1 buckets. This might take a while. 0:00:00.288 4M / 4M INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:00:00.288 4M / 4M INFO General (kmer_splitters.hpp : 190) Memory available for splitting buffers: 33.332 Gb 0:00:00.288 4M / 4M INFO General (kmer_splitters.hpp : 199) Using cell size of 33554432 0:00:36.362 568M / 1G INFO General (kmer_splitters.hpp : 228) Processed 115734 reads 0:00:40.088 568M / 1G INFO General (kmer_splitters.hpp : 228) Processed 208954 reads 0:00:40.089 568M / 1G INFO General (kmer_splitters.hpp : 245) Used 208954 reads. Maximum read length 53509 0:00:40.089 568M / 1G INFO General (kmer_splitters.hpp : 246) Average read length 755.817 0:00:40.092 4M / 1G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:01:21.236 4M / 1G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 64595965 kmers in total. 0:01:21.236 4M / 1G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:01:26.547 4M / 1G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:01:26.547 4M / 1G INFO General (kmer_splitters.hpp : 379) Splitting kmer instances into 16 buckets. This might take a while. 0:01:26.548 4M / 1G INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:01:26.548 4M / 1G INFO General (kmer_splitters.hpp : 397) Memory available for splitting buffers: 33.332 Gb 0:01:26.548 4M / 1G INFO General (kmer_splitters.hpp : 405) Using cell size of 2097152 0:04:10.665 640M / 1G INFO General (kmer_splitters.hpp : 428) Processed 16777216 kmers 0:07:03.683 640M / 1G INFO General (kmer_splitters.hpp : 428) Processed 33554432 kmers 0:08:37.031 640M / 1G INFO General (kmer_splitters.hpp : 428) Processed 50331648 kmers 0:12:00.418 640M / 1G INFO General (kmer_splitters.hpp : 428) Processed 64595965 kmers 0:12:00.419 640M / 1G INFO General (kmer_splitters.hpp : 437) Used 64595965 kmers. 0:12:00.427 64M / 1G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:12:31.127 64M / 1G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 64532438 kmers in total. 0:12:31.127 64M / 1G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:12:36.248 64M / 1G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:13:36.989 84M / 1G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:14:09.956 84M / 1G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 22324229 bytes occupied (2.7675 bits per kmer). 0:14:10.047 148M / 1G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 382) Building k-mer extensions from k+1-mers 0:15:43.013 148M / 1G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 386) Building k-mer extensions from k+1-mers finished. 0:15:43.017 148M / 1G INFO General (graph_construction.hpp : 145) Condensing graph 0:15:43.017 148M / 1G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 337) Extracting unbranching paths 0:16:10.617 204M / 1G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 351) Extracting unbranching paths finished. 565137 sequences extracted 0:16:14.813 200M / 1G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 311) Collecting perfect loops 0:16:35.011 200M / 1G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 326) Collecting perfect loops finished. 374 loops collected 0:16:35.542 252M / 1G INFO General (graph_construction.hpp : 150) Building index with from graph 0:16:35.543 252M / 1G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:16:35.544 252M / 1G INFO General (kmer_splitters.hpp : 289) Splitting kmer instances into 16 buckets. This might take a while. 0:16:35.544 252M / 1G INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:16:35.544 252M / 1G INFO General (kmer_splitters.hpp : 307) Memory available for splitting buffers: 33.2513 Gb 0:16:35.544 252M / 1G INFO General (kmer_splitters.hpp : 312) Using cell size of 2097152 0:20:14.427 828M / 1G INFO General (kmer_splitters.hpp : 325) Processed 294184 edges 0:22:04.518 828M / 1G INFO General (kmer_splitters.hpp : 325) Processed 565511 edges 0:22:04.518 828M / 1G INFO General (kmer_splitters.hpp : 330) Used 565511 sequences. 0:22:04.521 252M / 1G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:22:42.537 252M / 1G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 64595965 kmers in total. 0:22:42.537 252M / 1G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:23:03.258 252M / 1G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:24:04.521 276M / 1G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:24:10.531 276M / 1G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 22346207 bytes occupied (2.7675 bits per kmer). 0:24:11.414 1G / 1G INFO General (edge_index_builders.hpp : 21) Collecting k-mer coverage information from graph, this takes a while. 0:25:42.756 1G / 1G INFO General (graph_construction.hpp : 182) Filling coverage index 0:25:42.767 1G / 1G INFO General (edge_index_builders.hpp : 99) Collecting k-mer coverage information from reads, this takes a while. 0:26:49.556 1G / 1G INFO General (graph_construction.hpp : 184) Filling coverage and flanking coverage from index 0:26:54.375 1G / 1G INFO General (stage.cpp : 95) PROCEDURE == Polymorphic bulge remover 0:26:54.375 1G / 1G INFO General (polymorphic_bulge_remover.: 94) Polymorphic bulge remover starts 0:26:54.397 1G / 1G INFO General (polymorphic_bulge_remover.: 36) Simple polymorphic bulge remover runs 0:29:29.890 2G / 3G INFO General (polymorphic_bulge_remover.: 42) 1 iteration: 71451 simple bulges were glued 0:29:31.848 2G / 3G INFO General (polymorphic_bulge_remover.: 42) 2 iteration: 104 simple bulges were glued 0:29:32.295 2G / 3G INFO General (polymorphic_bulge_remover.: 42) 3 iteration: 0 simple bulges were glued 0:29:32.295 2G / 3G INFO General (polymorphic_bulge_remover.: 44) Simple polymorphic bulge remover ends 0:29:32.307 2G / 3G INFO General (polymorphic_bulge_remover.: 49) LightBulgeRemover starts 0:29:32.307 2G / 3G INFO General (polymorphic_bulge_remover.: 50) Maximal number of iterations: 15 0:29:32.335 2G / 3G INFO PolymorphicBulgeRemover (complex_bulge_remover.hpp : 108) Maximal length of glued bulge: 6163 0:45:59.282 3G / 4G INFO General (polymorphic_bulge_remover.: 60) 1 iteration: 6298 complex bulges were glued 0:45:59.283 3G / 4G INFO PolymorphicBulgeRemover (complex_bulge_remover.hpp : 108) Maximal length of glued bulge: 25147 1:00:59.085 3G / 4G INFO General (polymorphic_bulge_remover.: 60) 2 iteration: 131 complex bulges were glued 1:00:59.086 3G / 4G INFO PolymorphicBulgeRemover (complex_bulge_remover.hpp : 108) Maximal length of glued bulge: 25147 1:15:28.587 3G / 4G INFO General (polymorphic_bulge_remover.: 60) 3 iteration: 18 complex bulges were glued 1:15:28.588 3G / 4G INFO PolymorphicBulgeRemover (complex_bulge_remover.hpp : 108) Maximal length of glued bulge: 25147 1:29:38.757 3G / 4G INFO General (polymorphic_bulge_remover.: 60) 4 iteration: 9 complex bulges were glued 1:29:38.758 3G / 4G INFO PolymorphicBulgeRemover (complex_bulge_remover.hpp : 108) Maximal length of glued bulge: 25147 1:43:43.998 3G / 4G INFO General (polymorphic_bulge_remover.: 60) 5 iteration: 1 complex bulges were glued 1:43:43.999 3G / 4G INFO PolymorphicBulgeRemover (complex_bulge_remover.hpp : 108) Maximal length of glued bulge: 25147 1:57:50.985 3G / 4G INFO General (polymorphic_bulge_remover.: 60) 6 iteration: 0 complex bulges were glued 1:57:50.985 3G / 4G INFO General (polymorphic_bulge_remover.: 62) LightBulgeRemover ends 1:57:50.985 3G / 4G INFO General (polymorphic_bulge_remover.: 103) Index refilling 1:57:50.998 1G / 4G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 1:57:50.998 1G / 4G INFO General (kmer_splitters.hpp : 289) Splitting kmer instances into 16 buckets. This might take a while. 1:57:50.998 1G / 4G INFO General (file_limit.hpp : 29) Open file limit set to 32768 1:57:50.998 1G / 4G INFO General (kmer_splitters.hpp : 307) Memory available for splitting buffers: 32.7083 Gb 1:57:50.998 1G / 4G INFO General (kmer_splitters.hpp : 312) Using cell size of 2097152 2:01:01.431 2G / 4G INFO General (kmer_splitters.hpp : 325) Processed 62671 edges 2:04:19.410 2G / 4G INFO General (kmer_splitters.hpp : 325) Processed 99665 edges 2:04:19.410 2G / 4G INFO General (kmer_splitters.hpp : 330) Used 99665 sequences. 2:04:19.413 1G / 4G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 2:05:12.478 1G / 4G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 54440358 kmers in total. 2:05:12.479 1G / 4G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 2:05:33.883 1G / 4G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 2:06:22.024 1G / 4G INFO General (kmer_index.hpp : 371) Merging final buckets. 2:06:27.402 1G / 4G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 18833005 bytes occupied (2.76751 bits per kmer). 2:06:28.158 3G / 4G INFO General (edge_index_builders.hpp : 21) Collecting k-mer coverage information from graph, this takes a while. 2:07:45.117 3G / 4G INFO General (polymorphic_bulge_remover.: 106) Glueing equal kmers 2:10:05.951 3G / 4G INFO General (equal_sequence_gluer.hpp : 105) 0 kmers glued 2:10:05.951 3G / 4G INFO General (polymorphic_bulge_remover.: 108) Polymorphic ends remover ends 2:10:05.951 3G / 4G INFO General (dipspades.hpp : 96) Consensus graph was constructed 2:10:05.951 3G / 4G INFO General (stage.cpp : 95) PROCEDURE == Consensus contigs construction 2:10:05.951 3G / 4G INFO ConsensusContigsConstruc (consensus_contigs_construc: 274) Consensus contigs constructor starts 2:10:07.927 3G / 4G INFO ConsensusContigsConstruc (consensus_contigs_construc: 51) 104477 contigs from /N/dc2/projects/marinovg/2015-09-07-assemblies/Sample_Canal-1I-dipSPAdes-3.5.0-trimmed/spades/contigs.fasta were read 2:10:07.972 3G / 4G INFO ConsensusContigsConstruc (consensus_contigs_construc: 276) Total: 104477 contigs were read 2:10:38.094 3G / 4G INFO ConsensusContigsConstruc (consensus_contigs_construc: 79) 43 contigs with total length 3991 have mapped path with zero length 2:10:38.238 3G / 4G INFO ConsensusContigsConstruc (consensus_contigs_construc: 105) Removing repetitive edges in contigs mapping starts 2:10:38.371 3G / 4G INFO ConsensusContigsConstruc (consensus_contigs_construc: 109) Removing repetitive edges in contigs mapping ends 2:10:38.371 3G / 4G INFO ConsensusContigsConstruc (consensus_contigs_construc: 111) Close gaps in contigs mappings starts 2:10:38.396 3G / 4G INFO General (close_gaps_corrector.hpp : 83) 580 contigs from 104434 have gaps before correction 2:10:38.416 3G / 4G INFO General (close_gaps_corrector.hpp : 68) 10% contigs were processed 2:10:38.419 3G / 4G INFO General (close_gaps_corrector.hpp : 68) 20% contigs were processed 2:10:38.423 3G / 4G INFO General (close_gaps_corrector.hpp : 68) 30% contigs were processed 2:10:38.427 3G / 4G INFO General (close_gaps_corrector.hpp : 68) 40% contigs were processed 2:10:38.431 3G / 4G INFO General (close_gaps_corrector.hpp : 68) 50% contigs were processed 2:10:38.436 3G / 4G INFO General (close_gaps_corrector.hpp : 68) 60% contigs were processed 2:10:38.439 3G / 4G INFO General (close_gaps_corrector.hpp : 68) 70% contigs were processed 2:10:38.444 3G / 4G INFO General (close_gaps_corrector.hpp : 68) 80% contigs were processed 2:10:38.445 3G / 4G INFO General (close_gaps_corrector.hpp : 68) 90% contigs were processed 2:10:38.450 3G / 4G INFO General (close_gaps_corrector.hpp : 72) 100% contigs were processed 2:10:38.450 3G / 4G INFO General (close_gaps_corrector.hpp : 87) 104434 contigs from 104434 were corrected 2:10:38.450 3G / 4G INFO General (close_gaps_corrector.hpp : 88) 0 contigs from 104434 have gaps after correction 2:10:38.451 3G / 4G INFO ConsensusContigsConstruc (consensus_contigs_construc: 115) Close gaps in contigs mappings ends 2:10:38.451 3G / 4G INFO ConsensusContigsConstruc (consensus_contigs_construc: 117) Removing incorrect contigs 2:10:38.479 3G / 4G INFO General (incorrect_contig_remover.h: 25) 0 contigs from 104434 were deleted 2:10:38.837 3G / 4G INFO ConsensusContigsConstruc (consensus_contigs_construc: 144) Addition of RC contigs. 208868 contigs will be used 2:10:38.853 3G / 4G INFO ConsensusContigsConstruc (consensus_contigs_construc: 149) Redundant contigs remover starts 2:10:38.856 3G / 4G INFO General (iterative_redundant_contig: 30) Equal path remover starts 2:10:38.858 3G / 4G INFO General (path_index.hpp : 27) Initialization of vertex-paths index starts 2:10:39.362 3G / 4G INFO General (path_index.hpp : 40) Initialization of vertex-paths index ends 2:10:39.364 3G / 4G INFO General (equal_path_deletion_correc: 27) Computing redundant equal contigs starts 2:10:53.376 3G / 4G INFO General (equal_path_deletion_correc: 58) 140366 contigs from 208868 are redundant 2:10:53.449 3G / 4G INFO General (equal_path_deletion_correc: 61) Computing redundant equal contigs ends 2:10:53.811 3G / 4G INFO General (iterative_redundant_contig: 36) 68502 contigs will be used further 2:10:53.860 3G / 4G INFO General (iterative_redundant_contig: 39) Iterative loop corrector starts 2:10:53.860 3G / 4G INFO General (iterative_redundant_contig: 41) Only exact match iteration with parameters: 2:10:53.860 3G / 4G INFO General (iterative_redundant_contig: 42) Maximal loop length - 500 2:10:53.860 3G / 4G INFO General (iterative_redundant_contig: 43) Minimal lcs length - 1500 2:10:53.860 3G / 4G INFO General (iterative_redundant_contig: 44) Maximal tail length - 0 2:10:53.860 3G / 4G INFO General (path_index.hpp : 27) Initialization of vertex-paths index starts 2:10:54.095 3G / 4G INFO General (path_index.hpp : 40) Initialization of vertex-paths index ends 2:10:54.095 3G / 4G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 708) Computing redundant contigs starts 2:13:01.161 3G / 4G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 852) 10% contigs were processed 2:13:14.860 3G / 4G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 852) 20% contigs were processed 2:13:16.236 3G / 4G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 852) 30% contigs were processed 2:13:27.302 3G / 4G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 852) 40% contigs were processed 2:13:29.015 3G / 4G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 852) 50% contigs were processed 2:13:29.345 3G / 4G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 852) 60% contigs were processed 2:13:29.749 3G / 4G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 852) 70% contigs were processed 2:13:29.972 3G / 4G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 852) 80% contigs were processed 2:13:30.076 3G / 4G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 852) 90% contigs were processed 2:13:30.242 3G / 4G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 856) 100% contigs were processed 2:13:30.540 3G / 4G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 861) 9946 contigs from 68502 are redundant 2:13:30.559 3G / 4G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 865) Computing redundant contigs ends 2:13:33.344 3G / 4G INFO General (iterative_redundant_contig: 55) 58556 contigs will be used further 2:13:33.425 3G / 4G INFO General (iterative_redundant_contig: 59) Tails allowing match iteration with parameters: 2:13:33.425 3G / 4G INFO General (iterative_redundant_contig: 60) Maximal loop length - 500 2:13:33.425 3G / 4G INFO General (iterative_redundant_contig: 61) Minimal lcs length - 1500 2:13:33.425 3G / 4G INFO General (iterative_redundant_contig: 62) Maximal tail length - 6653 2:13:33.425 3G / 4G INFO General (path_index.hpp : 27) Initialization of vertex-paths index starts 2:13:33.616 3G / 4G INFO General (path_index.hpp : 40) Initialization of vertex-paths index ends 2:13:33.616 3G / 4G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 708) Computing redundant contigs starts 2:15:17.519 3G / 4G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 852) 10% contigs were processed 2:15:23.775 3G / 4G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 852) 20% contigs were processed 2:15:24.586 3G / 4G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 852) 30% contigs were processed 2:15:25.862 3G / 4G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 852) 40% contigs were processed 2:15:26.264 3G / 4G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 852) 50% contigs were processed 2:15:26.415 3G / 4G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 852) 60% contigs were processed 2:15:26.615 3G / 4G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 852) 70% contigs were processed 2:15:26.681 3G / 4G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 852) 80% contigs were processed 2:15:26.724 3G / 4G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 852) 90% contigs were processed 2:15:26.791 3G / 4G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 856) 100% contigs were processed 2:15:27.230 3G / 4G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 861) 14602 contigs from 58556 are redundant 2:15:27.248 3G / 4G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 865) Computing redundant contigs ends 2:15:30.921 3G / 4G INFO General (iterative_redundant_contig: 72) 43954 contigs will be used further 2:15:30.998 3G / 4G INFO General (iterative_redundant_contig: 74) Iterative loop corrector ends 2:15:30.998 3G / 4G INFO ConsensusContigsConstruc (consensus_contigs_construc: 161) Redundant contigs remover ends 2:15:31.069 3G / 4G INFO ConsensusContigsConstruc (consensus_contigs_construc: 166) Overlapping search starts 2:15:31.069 3G / 4G INFO General (path_index.hpp : 27) Initialization of vertex-paths index starts 2:15:31.195 3G / 4G INFO General (path_index.hpp : 40) Initialization of vertex-paths index ends 2:15:31.196 3G / 4G INFO OverlapCorrector (overlap_searcher.hpp : 350) Computing overlaps starts 2:15:49.868 3G / 4G INFO OverlapCorrector (overlap_searcher.hpp : 478) Overlap graph with 43954 vertices and 992 edges constructed 2:15:49.893 3G / 4G INFO General (overlap_graph.hpp :1100) 40 tips and 48 transitive edges were deleted in overlap graph 2:15:49.895 3G / 4G INFO General (overlap_graph.hpp :1100) 2 tips and 0 transitive edges were deleted in overlap graph 2:15:49.898 3G / 4G INFO General (overlap_graph.hpp :1100) 0 tips and 0 transitive edges were deleted in overlap graph 2:15:49.898 3G / 4G INFO General (overlap_graph.hpp :1103) Bulge remover starts 2:22:54.604 3G / 4G INFO General (overlap_graph.hpp :1108) 13 bulges were deleted in overlap graph 2:29:59.453 3G / 4G INFO General (overlap_graph.hpp :1108) 0 bulges were deleted in overlap graph 2:29:59.460 3G / 4G INFO OverlapCorrector (overlap_searcher.hpp : 486) Simplified overlap graph contains 43892 vertices and 867 edges 2:32:55.024 3G / 4G INFO OverlapCorrector (overlap_searcher.hpp : 525) Computing overlaps ends 2:32:55.130 3G / 4G INFO ConsensusContigsConstruc (consensus_contigs_construc: 174) Overlapping search ends 2:33:08.844 3G / 4G INFO ConsensusContigsConstruc (consensus_contigs_construc: 190) 21520 with total length 39486350 were written in /N/dc2/projects/marinovg/2015-09-07-assemblies/Sample_Canal-1I-dipSPAdes-3.5.0-trimmed/dipspades/consensus_contigs.fasta 2:33:09.175 3G / 4G INFO ConsensusContigsConstruc (consensus_contigs_construc: 190) 2931 with total length 29615872 were written in /N/dc2/projects/marinovg/2015-09-07-assemblies/Sample_Canal-1I-dipSPAdes-3.5.0-trimmed/dipspades/paired_consensus_contigs.fasta 2:33:09.703 3G / 4G INFO ConsensusContigsConstruc (consensus_contigs_construc: 190) 18589 with total length 9870478 were written in /N/dc2/projects/marinovg/2015-09-07-assemblies/Sample_Canal-1I-dipSPAdes-3.5.0-trimmed/dipspades/unpaired_consensus_contigs.fasta 2:33:09.704 3G / 4G INFO ConsensusContigsConstruc (consensus_contigs_construc: 216) Writing haplocontigs alignment to /N/dc2/projects/marinovg/2015-09-07-assemblies/Sample_Canal-1I-dipSPAdes-3.5.0-trimmed/dipspades/haplocontigs_alignment 2:38:58.917 3G / 4G INFO ConsensusContigsConstruc (consensus_contigs_construc: 311) Consensus contigs constructor ends 2:38:59.035 3G / 4G INFO General (dipspades.hpp : 211) dipSPAdes finished 2:39:11.157 232M / 4G INFO General (main.cpp : 115) Assembling time: 2 hours 39 minutes 11 seconds ===== Assembling finished. * Assembled consensus contigs are in: /N/dc2/projects/marinovg/2015-09-07-assemblies/Sample_Canal-1I-dipSPAdes-3.5.0-trimmed/dipspades/consensus_contigs.fasta * Assembled paired consensus contigs are in: /N/dc2/projects/marinovg/2015-09-07-assemblies/Sample_Canal-1I-dipSPAdes-3.5.0-trimmed/dipspades/paired_consensus_contigs.fasta * Assembled unpaired consensus contigs are in: /N/dc2/projects/marinovg/2015-09-07-assemblies/Sample_Canal-1I-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/Sample_Canal-1I-dipSPAdes-3.5.0-trimmed/dipspades/dipspades.log Thank you for using dipSPAdes!