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_134/reads.end1.paired.fastq.gz --pe1-2 /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_134/reads.end2.paired.fastq.gz -t 16 -o /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_134-dipSPAdes-3.5.0-trimmed dipSPAdes command line: -t 16 -o /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_134-dipSPAdes-3.5.0-trimmed/dipspades --hap /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_134-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_134-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_134-dipSPAdes-3.5.0-trimmed/dipspades Dir for temp files: /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_134-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_134-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 0:00:00.005 4M / 4M INFO General (main.cpp : 96) Assembling dataset (/N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_134-dipSPAdes-3.5.0-trimmed/dipspades/) with K=55 0:00:00.005 4M / 4M INFO General (dipspades.hpp : 188) dipSPAdes started 0:00:00.009 4M / 4M INFO StageManager (stage.cpp : 125) STAGE == dipSPAdes 0:00:00.009 4M / 4M INFO General (stage.cpp : 95) PROCEDURE == Construction of graph from contigs 0:00:00.011 4M / 4M INFO General (dipspades.hpp : 19) Addition of contigs from /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_134-dipSPAdes-3.5.0-trimmed/spades/contigs.fasta 0:00:00.016 4M / 4M INFO General (dipspades.hpp : 23) Construction of the de Bruijn graph with K=55 0:00:00.016 4M / 4M INFO General (graph_construction.hpp : 129) Constructing DeBruijn graph for k=55 0:00:00.019 4M / 4M INFO General (kmer_splitters.hpp : 172) Splitting kmer instances into 1 buckets. This might take a while. 0:00:00.019 4M / 4M INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:00:00.019 4M / 4M INFO General (kmer_splitters.hpp : 190) Memory available for splitting buffers: 33.332 Gb 0:00:00.019 4M / 4M INFO General (kmer_splitters.hpp : 199) Using cell size of 33554432 0:00:56.726 568M / 1G INFO General (kmer_splitters.hpp : 245) Used 29900 reads. Maximum read length 184200 0:00:56.727 568M / 1G INFO General (kmer_splitters.hpp : 246) Average read length 4827.33 0:00:56.730 4M / 1G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:01:18.392 4M / 1G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 70638276 kmers in total. 0:01:18.393 4M / 1G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:01:23.681 4M / 1G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:01:23.682 4M / 1G INFO General (kmer_splitters.hpp : 379) Splitting kmer instances into 16 buckets. This might take a while. 0:01:23.682 4M / 1G INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:01:23.682 4M / 1G INFO General (kmer_splitters.hpp : 397) Memory available for splitting buffers: 33.332 Gb 0:01:23.682 4M / 1G INFO General (kmer_splitters.hpp : 405) Using cell size of 2097152 0:02:07.192 640M / 1G INFO General (kmer_splitters.hpp : 428) Processed 16777216 kmers 0:02:30.412 640M / 1G INFO General (kmer_splitters.hpp : 428) Processed 33554432 kmers 0:02:53.590 640M / 1G INFO General (kmer_splitters.hpp : 428) Processed 50331648 kmers 0:03:16.728 640M / 1G INFO General (kmer_splitters.hpp : 428) Processed 67108864 kmers 0:03:21.663 640M / 1G INFO General (kmer_splitters.hpp : 428) Processed 70638276 kmers 0:03:21.664 640M / 1G INFO General (kmer_splitters.hpp : 437) Used 70638276 kmers. 0:03:21.673 64M / 1G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:03:54.604 64M / 1G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 70631251 kmers in total. 0:03:54.604 64M / 1G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:04:20.462 64M / 1G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:05:28.913 88M / 1G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:05:34.202 88M / 1G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 24434030 bytes occupied (2.7675 bits per kmer). 0:05:34.301 156M / 1G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 382) Building k-mer extensions from k+1-mers 0:07:18.123 156M / 1G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 386) Building k-mer extensions from k+1-mers finished. 0:07:18.127 156M / 1G INFO General (graph_construction.hpp : 145) Condensing graph 0:07:18.127 156M / 1G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 337) Extracting unbranching paths 0:07:47.545 168M / 1G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 351) Extracting unbranching paths finished. 83423 sequences extracted 0:07:52.373 168M / 1G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 311) Collecting perfect loops 0:08:14.068 168M / 1G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 326) Collecting perfect loops finished. 84 loops collected 0:08:14.219 164M / 1G INFO General (graph_construction.hpp : 150) Building index with from graph 0:08:14.220 164M / 1G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:08:14.220 164M / 1G INFO General (kmer_splitters.hpp : 289) Splitting kmer instances into 16 buckets. This might take a while. 0:08:14.221 164M / 1G INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:08:14.221 164M / 1G INFO General (kmer_splitters.hpp : 307) Memory available for splitting buffers: 33.2799 Gb 0:08:14.221 164M / 1G INFO General (kmer_splitters.hpp : 312) Using cell size of 2097152 0:08:25.558 740M / 1G INFO General (kmer_splitters.hpp : 325) Processed 39978 edges 0:08:36.197 740M / 1G INFO General (kmer_splitters.hpp : 325) Processed 79512 edges 0:08:37.455 740M / 1G INFO General (kmer_splitters.hpp : 325) Processed 83507 edges 0:08:37.457 740M / 1G INFO General (kmer_splitters.hpp : 330) Used 83507 sequences. 0:08:37.460 164M / 1G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:08:57.512 164M / 1G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 70638276 kmers in total. 0:08:57.512 164M / 1G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:09:03.047 164M / 1G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:10:11.391 188M / 1G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:10:17.191 188M / 1G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 24436463 bytes occupied (2.7675 bits per kmer). 0:10:18.159 1G / 1G INFO General (edge_index_builders.hpp : 21) Collecting k-mer coverage information from graph, this takes a while. 0:12:00.866 1G / 1G INFO General (graph_construction.hpp : 182) Filling coverage index 0:12:00.867 1G / 1G INFO General (edge_index_builders.hpp : 99) Collecting k-mer coverage information from reads, this takes a while. 0:13:06.727 1G / 1G INFO General (graph_construction.hpp : 184) Filling coverage and flanking coverage from index 0:13:09.804 1G / 1G INFO General (stage.cpp : 95) PROCEDURE == Polymorphic bulge remover 0:13:09.804 1G / 1G INFO General (polymorphic_bulge_remover.: 94) Polymorphic bulge remover starts 0:13:09.804 1G / 1G INFO General (polymorphic_bulge_remover.: 36) Simple polymorphic bulge remover runs 0:18:00.929 2G / 3G INFO General (polymorphic_bulge_remover.: 42) 1 iteration: 6891 simple bulges were glued 0:26:27.914 2G / 3G INFO General (polymorphic_bulge_remover.: 42) 2 iteration: 357 simple bulges were glued 0:28:17.391 2G / 3G INFO General (polymorphic_bulge_remover.: 42) 3 iteration: 0 simple bulges were glued 0:28:17.391 2G / 3G INFO General (polymorphic_bulge_remover.: 44) Simple polymorphic bulge remover ends 0:28:17.391 2G / 3G INFO General (polymorphic_bulge_remover.: 49) LightBulgeRemover starts 0:28:17.391 2G / 3G INFO General (polymorphic_bulge_remover.: 50) Maximal number of iterations: 15 0:28:17.391 2G / 3G INFO PolymorphicBulgeRemover (complex_bulge_remover.hpp : 108) Maximal length of glued bulge: 50389 0:51:28.915 3G / 4G INFO General (polymorphic_bulge_remover.: 60) 1 iteration: 1689 complex bulges were glued 0:51:28.916 3G / 4G INFO PolymorphicBulgeRemover (complex_bulge_remover.hpp : 108) Maximal length of glued bulge: 52135 1:07:45.867 3G / 4G INFO General (polymorphic_bulge_remover.: 60) 2 iteration: 48 complex bulges were glued 1:07:45.868 3G / 4G INFO PolymorphicBulgeRemover (complex_bulge_remover.hpp : 108) Maximal length of glued bulge: 52135 1:22:50.914 3G / 4G INFO General (polymorphic_bulge_remover.: 60) 3 iteration: 4 complex bulges were glued 1:22:50.915 3G / 4G INFO PolymorphicBulgeRemover (complex_bulge_remover.hpp : 108) Maximal length of glued bulge: 52135 1:38:16.016 3G / 4G INFO General (polymorphic_bulge_remover.: 60) 4 iteration: 0 complex bulges were glued 1:38:16.017 3G / 4G INFO General (polymorphic_bulge_remover.: 62) LightBulgeRemover ends 1:38:16.017 3G / 4G INFO General (polymorphic_bulge_remover.: 103) Index refilling 1:38:16.030 1G / 4G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 1:38:16.030 1G / 4G INFO General (kmer_splitters.hpp : 289) Splitting kmer instances into 16 buckets. This might take a while. 1:38:16.030 1G / 4G INFO General (file_limit.hpp : 29) Open file limit set to 32768 1:38:16.030 1G / 4G INFO General (kmer_splitters.hpp : 307) Memory available for splitting buffers: 32.8294 Gb 1:38:16.030 1G / 4G INFO General (kmer_splitters.hpp : 312) Using cell size of 2097152 1:38:42.627 2G / 4G INFO General (kmer_splitters.hpp : 325) Processed 15508 edges 1:38:47.797 2G / 4G INFO General (kmer_splitters.hpp : 325) Processed 29967 edges 1:38:47.798 2G / 4G INFO General (kmer_splitters.hpp : 330) Used 29967 sequences. 1:38:47.811 1G / 4G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 1:39:06.004 1G / 4G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 62292927 kmers in total. 1:39:06.004 1G / 4G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 1:39:10.983 1G / 4G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 1:40:22.631 1G / 4G INFO General (kmer_index.hpp : 371) Merging final buckets. 1:40:27.631 1G / 4G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 21549498 bytes occupied (2.7675 bits per kmer). 1:40:28.484 2G / 4G INFO General (edge_index_builders.hpp : 21) Collecting k-mer coverage information from graph, this takes a while. 1:41:58.157 2G / 4G INFO General (polymorphic_bulge_remover.: 106) Glueing equal kmers 1:44:44.356 2G / 4G INFO General (equal_sequence_gluer.hpp : 105) 4 kmers glued 1:44:44.357 2G / 4G INFO General (polymorphic_bulge_remover.: 108) Polymorphic ends remover ends 1:44:44.357 2G / 4G INFO General (dipspades.hpp : 96) Consensus graph was constructed 1:44:44.357 2G / 4G INFO General (stage.cpp : 95) PROCEDURE == Consensus contigs construction 1:44:44.357 2G / 4G INFO ConsensusContigsConstruc (consensus_contigs_construc: 274) Consensus contigs constructor starts 1:44:45.707 2G / 4G INFO ConsensusContigsConstruc (consensus_contigs_construc: 51) 14950 contigs from /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_134-dipSPAdes-3.5.0-trimmed/spades/contigs.fasta were read 1:44:45.713 2G / 4G INFO ConsensusContigsConstruc (consensus_contigs_construc: 276) Total: 14950 contigs were read 1:45:08.612 2G / 4G INFO ConsensusContigsConstruc (consensus_contigs_construc: 79) 7 contigs with total length 635 have mapped path with zero length 1:45:08.635 2G / 4G INFO ConsensusContigsConstruc (consensus_contigs_construc: 105) Removing repetitive edges in contigs mapping starts 1:45:08.659 2G / 4G INFO ConsensusContigsConstruc (consensus_contigs_construc: 109) Removing repetitive edges in contigs mapping ends 1:45:08.659 2G / 4G INFO ConsensusContigsConstruc (consensus_contigs_construc: 111) Close gaps in contigs mappings starts 1:45:08.664 2G / 4G INFO General (close_gaps_corrector.hpp : 83) 354 contigs from 14943 have gaps before correction 1:45:08.667 2G / 4G INFO General (close_gaps_corrector.hpp : 68) 10% contigs were processed 1:45:08.669 2G / 4G INFO General (close_gaps_corrector.hpp : 68) 20% contigs were processed 1:45:08.671 2G / 4G INFO General (close_gaps_corrector.hpp : 68) 30% contigs were processed 1:45:08.674 2G / 4G INFO General (close_gaps_corrector.hpp : 68) 40% contigs were processed 1:45:08.676 2G / 4G INFO General (close_gaps_corrector.hpp : 68) 50% contigs were processed 1:45:08.677 2G / 4G INFO General (close_gaps_corrector.hpp : 68) 60% contigs were processed 1:45:08.678 2G / 4G INFO General (close_gaps_corrector.hpp : 68) 70% contigs were processed 1:45:08.678 2G / 4G INFO General (close_gaps_corrector.hpp : 68) 80% contigs were processed 1:45:08.678 2G / 4G INFO General (close_gaps_corrector.hpp : 68) 90% contigs were processed 1:45:08.680 2G / 4G INFO General (close_gaps_corrector.hpp : 72) 100% contigs were processed 1:45:08.680 2G / 4G INFO General (close_gaps_corrector.hpp : 87) 14943 contigs from 14943 were corrected 1:45:08.680 2G / 4G INFO General (close_gaps_corrector.hpp : 88) 0 contigs from 14943 have gaps after correction 1:45:08.680 2G / 4G INFO ConsensusContigsConstruc (consensus_contigs_construc: 115) Close gaps in contigs mappings ends 1:45:08.680 2G / 4G INFO ConsensusContigsConstruc (consensus_contigs_construc: 117) Removing incorrect contigs 1:45:08.684 2G / 4G INFO General (incorrect_contig_remover.h: 25) 0 contigs from 14943 were deleted 1:45:08.739 2G / 4G INFO ConsensusContigsConstruc (consensus_contigs_construc: 144) Addition of RC contigs. 29886 contigs will be used 1:45:08.742 2G / 4G INFO ConsensusContigsConstruc (consensus_contigs_construc: 149) Redundant contigs remover starts 1:45:08.742 2G / 4G INFO General (iterative_redundant_contig: 30) Equal path remover starts 1:45:08.742 2G / 4G INFO General (path_index.hpp : 27) Initialization of vertex-paths index starts 1:45:08.823 2G / 4G INFO General (path_index.hpp : 40) Initialization of vertex-paths index ends 1:45:08.824 2G / 4G INFO General (equal_path_deletion_correc: 27) Computing redundant equal contigs starts 1:45:12.219 2G / 4G INFO General (equal_path_deletion_correc: 58) 8542 contigs from 29886 are redundant 1:45:12.225 2G / 4G INFO General (equal_path_deletion_correc: 61) Computing redundant equal contigs ends 1:45:12.277 2G / 4G INFO General (iterative_redundant_contig: 36) 21344 contigs will be used further 1:45:12.282 2G / 4G INFO General (iterative_redundant_contig: 39) Iterative loop corrector starts 1:45:12.282 2G / 4G INFO General (iterative_redundant_contig: 41) Only exact match iteration with parameters: 1:45:12.283 2G / 4G INFO General (iterative_redundant_contig: 42) Maximal loop length - 500 1:45:12.283 2G / 4G INFO General (iterative_redundant_contig: 43) Minimal lcs length - 1500 1:45:12.283 2G / 4G INFO General (iterative_redundant_contig: 44) Maximal tail length - 0 1:45:12.283 2G / 4G INFO General (path_index.hpp : 27) Initialization of vertex-paths index starts 1:45:12.352 2G / 4G INFO General (path_index.hpp : 40) Initialization of vertex-paths index ends 1:45:12.352 2G / 4G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 708) Computing redundant contigs starts 1:45:24.618 2G / 4G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 852) 10% contigs were processed 1:45:31.765 2G / 4G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 852) 20% contigs were processed 1:45:36.133 2G / 4G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 852) 30% contigs were processed 1:45:40.207 2G / 4G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 852) 40% contigs were processed 1:45:43.170 2G / 4G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 852) 50% contigs were processed 1:45:43.232 2G / 4G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 852) 60% contigs were processed 1:45:43.241 2G / 4G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 852) 70% contigs were processed 1:45:43.252 2G / 4G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 852) 80% contigs were processed 1:45:43.256 2G / 4G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 852) 90% contigs were processed 1:45:43.500 2G / 4G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 856) 100% contigs were processed 1:45:43.581 2G / 4G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 861) 6336 contigs from 21344 are redundant 1:45:43.586 2G / 4G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 865) Computing redundant contigs ends 1:45:43.900 2G / 4G INFO General (iterative_redundant_contig: 55) 15008 contigs will be used further 1:45:43.918 2G / 4G INFO General (iterative_redundant_contig: 59) Tails allowing match iteration with parameters: 1:45:43.918 2G / 4G INFO General (iterative_redundant_contig: 60) Maximal loop length - 500 1:45:43.918 2G / 4G INFO General (iterative_redundant_contig: 61) Minimal lcs length - 1500 1:45:43.918 2G / 4G INFO General (iterative_redundant_contig: 62) Maximal tail length - 41460 1:45:43.918 2G / 4G INFO General (path_index.hpp : 27) Initialization of vertex-paths index starts 1:45:43.970 2G / 4G INFO General (path_index.hpp : 40) Initialization of vertex-paths index ends 1:45:43.970 2G / 4G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 708) Computing redundant contigs starts 1:45:52.191 2G / 4G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 852) 10% contigs were processed 1:45:56.296 2G / 4G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 852) 20% contigs were processed 1:46:02.467 2G / 4G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 852) 30% contigs were processed 1:46:05.473 2G / 4G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 852) 40% contigs were processed 1:46:06.188 2G / 4G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 852) 50% contigs were processed 1:46:06.209 2G / 4G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 852) 60% contigs were processed 1:46:06.232 2G / 4G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 852) 70% contigs were processed 1:46:06.239 2G / 4G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 852) 80% contigs were processed 1:46:06.244 2G / 4G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 852) 90% contigs were processed 1:46:06.386 2G / 4G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 856) 100% contigs were processed 1:46:06.638 2G / 4G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 861) 4338 contigs from 15008 are redundant 1:46:06.642 2G / 4G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 865) Computing redundant contigs ends 1:46:07.344 2G / 4G INFO General (iterative_redundant_contig: 72) 10670 contigs will be used further 1:46:07.369 2G / 4G INFO General (iterative_redundant_contig: 74) Iterative loop corrector ends 1:46:07.369 2G / 4G INFO ConsensusContigsConstruc (consensus_contigs_construc: 161) Redundant contigs remover ends 1:46:07.383 2G / 4G INFO ConsensusContigsConstruc (consensus_contigs_construc: 166) Overlapping search starts 1:46:07.383 2G / 4G INFO General (path_index.hpp : 27) Initialization of vertex-paths index starts 1:46:07.415 2G / 4G INFO General (path_index.hpp : 40) Initialization of vertex-paths index ends 1:46:07.415 2G / 4G INFO OverlapCorrector (overlap_searcher.hpp : 350) Computing overlaps starts 1:46:12.351 2G / 4G INFO OverlapCorrector (overlap_searcher.hpp : 478) Overlap graph with 10670 vertices and 60 edges constructed 1:46:12.352 2G / 4G INFO General (overlap_graph.hpp :1100) 4 tips and 0 transitive edges were deleted in overlap graph 1:46:12.353 2G / 4G INFO General (overlap_graph.hpp :1100) 0 tips and 0 transitive edges were deleted in overlap graph 1:46:12.353 2G / 4G INFO General (overlap_graph.hpp :1103) Bulge remover starts 1:46:33.295 2G / 4G INFO General (overlap_graph.hpp :1108) 0 bulges were deleted in overlap graph 1:46:33.297 2G / 4G INFO OverlapCorrector (overlap_searcher.hpp : 486) Simplified overlap graph contains 10666 vertices and 56 edges 1:46:42.608 2G / 4G INFO OverlapCorrector (overlap_searcher.hpp : 525) Computing overlaps ends 1:46:42.629 2G / 4G INFO ConsensusContigsConstruc (consensus_contigs_construc: 174) Overlapping search ends 1:46:43.014 2G / 4G INFO ConsensusContigsConstruc (consensus_contigs_construc: 190) 5305 with total length 32510765 were written in /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_134-dipSPAdes-3.5.0-trimmed/dipspades/consensus_contigs.fasta 1:46:43.253 2G / 4G INFO ConsensusContigsConstruc (consensus_contigs_construc: 190) 981 with total length 28172680 were written in /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_134-dipSPAdes-3.5.0-trimmed/dipspades/paired_consensus_contigs.fasta 1:46:43.390 2G / 4G INFO ConsensusContigsConstruc (consensus_contigs_construc: 190) 4324 with total length 4338085 were written in /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_134-dipSPAdes-3.5.0-trimmed/dipspades/unpaired_consensus_contigs.fasta 1:46:43.391 2G / 4G INFO ConsensusContigsConstruc (consensus_contigs_construc: 216) Writing haplocontigs alignment to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_134-dipSPAdes-3.5.0-trimmed/dipspades/haplocontigs_alignment 1:46:50.908 2G / 4G INFO ConsensusContigsConstruc (consensus_contigs_construc: 311) Consensus contigs constructor ends 1:46:50.927 2G / 4G INFO General (dipspades.hpp : 211) dipSPAdes finished 1:46:58.957 116M / 4G INFO General (main.cpp : 115) Assembling time: 1 hours 46 minutes 59 seconds ===== Assembling finished. * Assembled consensus contigs are in: /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_134-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_134-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_134-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_134-dipSPAdes-3.5.0-trimmed/dipspades/dipspades.log Thank you for using dipSPAdes!