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_133/reads.end1.paired.fastq.gz --pe1-2 /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_133/reads.end2.paired.fastq.gz -t 16 -o /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_133-dipSPAdes-3.5.0-trimmed dipSPAdes command line: -t 16 -o /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_133-dipSPAdes-3.5.0-trimmed/dipspades --hap /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_133-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_133-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_133-dipSPAdes-3.5.0-trimmed/dipspades Dir for temp files: /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_133-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_133-dipSPAdes-3.5.0-trimmed/dipspades/dipspades.log ===== Assembling started. 0:00:00.000 4M / 4M INFO General (memory_limit.hpp : 42) Memory limit set to 100 Gb 0:00:00.001 4M / 4M INFO General (main.cpp : 96) Assembling dataset (/N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_133-dipSPAdes-3.5.0-trimmed/dipspades/) with K=55 0:00:00.001 4M / 4M INFO General (dipspades.hpp : 188) dipSPAdes started 0:00:00.002 4M / 4M INFO StageManager (stage.cpp : 125) STAGE == dipSPAdes 0:00:00.002 4M / 4M INFO General (stage.cpp : 95) PROCEDURE == Construction of graph from contigs 0:00:00.005 4M / 4M INFO General (dipspades.hpp : 19) Addition of contigs from /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_133-dipSPAdes-3.5.0-trimmed/spades/contigs.fasta 0:00:00.011 4M / 4M INFO General (dipspades.hpp : 23) Construction of the de Bruijn graph with K=55 0:00:00.011 4M / 4M INFO General (graph_construction.hpp : 129) Constructing DeBruijn graph for k=55 0:00:00.013 4M / 4M INFO General (kmer_splitters.hpp : 172) Splitting kmer instances into 1 buckets. This might take a while. 0:00:00.014 4M / 4M INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:00:00.014 4M / 4M INFO General (kmer_splitters.hpp : 190) Memory available for splitting buffers: 33.332 Gb 0:00:00.014 4M / 4M INFO General (kmer_splitters.hpp : 199) Using cell size of 33554432 0:00:39.907 568M / 1G INFO General (kmer_splitters.hpp : 245) Used 23616 reads. Maximum read length 238705 0:00:39.908 568M / 1G INFO General (kmer_splitters.hpp : 246) Average read length 6359.06 0:00:39.912 4M / 1G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:01:05.161 4M / 1G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 73863043 kmers in total. 0:01:05.161 4M / 1G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:01:11.623 4M / 1G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:01:11.624 4M / 1G INFO General (kmer_splitters.hpp : 379) Splitting kmer instances into 16 buckets. This might take a while. 0:01:11.624 4M / 1G INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:01:11.624 4M / 1G INFO General (kmer_splitters.hpp : 397) Memory available for splitting buffers: 33.332 Gb 0:01:11.624 4M / 1G INFO General (kmer_splitters.hpp : 405) Using cell size of 2097152 0:03:17.186 640M / 1G INFO General (kmer_splitters.hpp : 428) Processed 16777216 kmers 0:05:44.562 640M / 1G INFO General (kmer_splitters.hpp : 428) Processed 33554432 kmers 0:06:27.974 640M / 1G INFO General (kmer_splitters.hpp : 428) Processed 50331648 kmers 0:06:51.322 640M / 1G INFO General (kmer_splitters.hpp : 428) Processed 67108864 kmers 0:07:00.740 640M / 1G INFO General (kmer_splitters.hpp : 428) Processed 73863043 kmers 0:07:00.741 640M / 1G INFO General (kmer_splitters.hpp : 437) Used 73863043 kmers. 0:07:00.749 64M / 1G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:07:36.991 64M / 1G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 73857028 kmers in total. 0:07:36.991 64M / 1G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:07:43.544 64M / 1G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:08:56.820 88M / 1G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:09:03.374 88M / 1G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 25549948 bytes occupied (2.7675 bits per kmer). 0:09:03.478 160M / 1G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 382) Building k-mer extensions from k+1-mers 0:10:52.847 160M / 1G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 386) Building k-mer extensions from k+1-mers finished. 0:10:52.852 160M / 1G INFO General (graph_construction.hpp : 145) Condensing graph 0:10:52.852 160M / 1G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 337) Extracting unbranching paths 0:11:24.092 176M / 1G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 351) Extracting unbranching paths finished. 87389 sequences extracted 0:11:30.292 172M / 1G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 311) Collecting perfect loops 0:11:53.447 172M / 1G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 326) Collecting perfect loops finished. 334 loops collected 0:11:53.548 168M / 1G INFO General (graph_construction.hpp : 150) Building index with from graph 0:11:53.549 168M / 1G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:11:53.549 168M / 1G INFO General (kmer_splitters.hpp : 289) Splitting kmer instances into 16 buckets. This might take a while. 0:11:53.549 168M / 1G INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:11:53.549 168M / 1G INFO General (kmer_splitters.hpp : 307) Memory available for splitting buffers: 33.2786 Gb 0:11:53.549 168M / 1G INFO General (kmer_splitters.hpp : 312) Using cell size of 2097152 0:14:05.685 744M / 1G INFO General (kmer_splitters.hpp : 325) Processed 39788 edges 0:15:05.181 744M / 1G INFO General (kmer_splitters.hpp : 325) Processed 79646 edges 0:15:42.552 744M / 1G INFO General (kmer_splitters.hpp : 325) Processed 87723 edges 0:15:42.553 744M / 1G INFO General (kmer_splitters.hpp : 330) Used 87723 sequences. 0:15:42.557 168M / 1G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:16:04.409 168M / 1G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 73863043 kmers in total. 0:16:04.409 168M / 1G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:16:10.698 168M / 1G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:17:23.146 192M / 1G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:17:31.877 192M / 1G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 25552037 bytes occupied (2.7675 bits per kmer). 0:17:32.898 1G / 1G INFO General (edge_index_builders.hpp : 21) Collecting k-mer coverage information from graph, this takes a while. 0:19:19.805 1G / 1G INFO General (graph_construction.hpp : 182) Filling coverage index 0:19:19.805 1G / 1G INFO General (edge_index_builders.hpp : 99) Collecting k-mer coverage information from reads, this takes a while. 0:20:28.466 1G / 1G INFO General (graph_construction.hpp : 184) Filling coverage and flanking coverage from index 0:20:30.793 1G / 1G INFO General (stage.cpp : 95) PROCEDURE == Polymorphic bulge remover 0:20:30.793 1G / 1G INFO General (polymorphic_bulge_remover.: 94) Polymorphic bulge remover starts 0:20:30.793 1G / 1G INFO General (polymorphic_bulge_remover.: 36) Simple polymorphic bulge remover runs 0:30:25.450 2G / 3G INFO General (polymorphic_bulge_remover.: 42) 1 iteration: 5837 simple bulges were glued 0:42:24.413 3G / 3G INFO General (polymorphic_bulge_remover.: 42) 2 iteration: 233 simple bulges were glued 0:45:58.641 3G / 3G INFO General (polymorphic_bulge_remover.: 42) 3 iteration: 0 simple bulges were glued 0:45:58.641 3G / 3G INFO General (polymorphic_bulge_remover.: 44) Simple polymorphic bulge remover ends 0:45:58.641 3G / 3G INFO General (polymorphic_bulge_remover.: 49) LightBulgeRemover starts 0:45:58.641 3G / 3G INFO General (polymorphic_bulge_remover.: 50) Maximal number of iterations: 15 0:45:58.642 3G / 3G INFO PolymorphicBulgeRemover (complex_bulge_remover.hpp : 108) Maximal length of glued bulge: 82612 1:47:10.159 4G / 5G INFO General (polymorphic_bulge_remover.: 60) 1 iteration: 2293 complex bulges were glued 1:47:10.159 4G / 5G INFO PolymorphicBulgeRemover (complex_bulge_remover.hpp : 108) Maximal length of glued bulge: 94271 2:33:57.972 4G / 5G INFO General (polymorphic_bulge_remover.: 60) 2 iteration: 109 complex bulges were glued 2:33:57.972 4G / 5G INFO PolymorphicBulgeRemover (complex_bulge_remover.hpp : 108) Maximal length of glued bulge: 104532 3:21:18.341 4G / 5G INFO General (polymorphic_bulge_remover.: 60) 3 iteration: 46 complex bulges were glued 3:21:18.341 4G / 5G INFO PolymorphicBulgeRemover (complex_bulge_remover.hpp : 108) Maximal length of glued bulge: 109634 4:08:59.989 4G / 5G INFO General (polymorphic_bulge_remover.: 60) 4 iteration: 33 complex bulges were glued 4:08:59.990 4G / 5G INFO PolymorphicBulgeRemover (complex_bulge_remover.hpp : 108) Maximal length of glued bulge: 109634 4:56:33.580 4G / 5G INFO General (polymorphic_bulge_remover.: 60) 5 iteration: 9 complex bulges were glued 4:56:33.580 4G / 5G INFO PolymorphicBulgeRemover (complex_bulge_remover.hpp : 108) Maximal length of glued bulge: 109634 5:43:46.820 4G / 5G INFO General (polymorphic_bulge_remover.: 60) 6 iteration: 4 complex bulges were glued 5:43:46.820 4G / 5G INFO PolymorphicBulgeRemover (complex_bulge_remover.hpp : 108) Maximal length of glued bulge: 109634 6:30:42.423 4G / 5G INFO General (polymorphic_bulge_remover.: 60) 7 iteration: 1 complex bulges were glued 6:30:42.424 4G / 5G INFO PolymorphicBulgeRemover (complex_bulge_remover.hpp : 108) Maximal length of glued bulge: 109634 7:17:39.490 4G / 5G INFO General (polymorphic_bulge_remover.: 60) 8 iteration: 0 complex bulges were glued 7:17:39.490 4G / 5G INFO General (polymorphic_bulge_remover.: 62) LightBulgeRemover ends 7:17:39.491 4G / 5G INFO General (polymorphic_bulge_remover.: 103) Index refilling 7:17:39.546 2G / 5G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 7:17:39.546 2G / 5G INFO General (kmer_splitters.hpp : 289) Splitting kmer instances into 16 buckets. This might take a while. 7:17:39.547 2G / 5G INFO General (file_limit.hpp : 29) Open file limit set to 32768 7:17:39.547 2G / 5G INFO General (kmer_splitters.hpp : 307) Memory available for splitting buffers: 32.431 Gb 7:17:39.547 2G / 5G INFO General (kmer_splitters.hpp : 312) Using cell size of 2097152 7:21:10.405 3G / 5G INFO General (kmer_splitters.hpp : 325) Processed 21430 edges 7:22:13.741 3G / 5G INFO General (kmer_splitters.hpp : 325) Processed 36775 edges 7:22:13.742 3G / 5G INFO General (kmer_splitters.hpp : 330) Used 36775 sequences. 7:22:13.750 2G / 5G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 7:22:31.201 2G / 5G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 58715209 kmers in total. 7:22:31.201 2G / 5G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 7:22:56.555 2G / 5G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 7:24:08.887 2G / 5G INFO General (kmer_index.hpp : 371) Merging final buckets. 7:24:13.987 2G / 5G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 20311837 bytes occupied (2.76751 bits per kmer). 7:24:14.785 4G / 5G INFO General (edge_index_builders.hpp : 21) Collecting k-mer coverage information from graph, this takes a while. 7:25:39.289 4G / 5G INFO General (polymorphic_bulge_remover.: 106) Glueing equal kmers 7:28:15.602 4G / 5G INFO General (equal_sequence_gluer.hpp : 105) 3 kmers glued 7:28:15.602 4G / 5G INFO General (polymorphic_bulge_remover.: 108) Polymorphic ends remover ends 7:28:15.602 4G / 5G INFO General (dipspades.hpp : 96) Consensus graph was constructed 7:28:15.602 4G / 5G INFO General (stage.cpp : 95) PROCEDURE == Consensus contigs construction 7:28:15.602 4G / 5G INFO ConsensusContigsConstruc (consensus_contigs_construc: 274) Consensus contigs constructor starts 7:28:17.002 4G / 5G INFO ConsensusContigsConstruc (consensus_contigs_construc: 51) 11808 contigs from /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_133-dipSPAdes-3.5.0-trimmed/spades/contigs.fasta were read 7:28:17.007 4G / 5G INFO ConsensusContigsConstruc (consensus_contigs_construc: 276) Total: 11808 contigs were read 7:29:00.109 4G / 5G INFO ConsensusContigsConstruc (consensus_contigs_construc: 79) 1 contigs with total length 81 have mapped path with zero length 7:29:00.131 4G / 5G INFO ConsensusContigsConstruc (consensus_contigs_construc: 105) Removing repetitive edges in contigs mapping starts 7:29:00.152 4G / 5G INFO ConsensusContigsConstruc (consensus_contigs_construc: 109) Removing repetitive edges in contigs mapping ends 7:29:00.152 4G / 5G INFO ConsensusContigsConstruc (consensus_contigs_construc: 111) Close gaps in contigs mappings starts 7:29:00.158 4G / 5G INFO General (close_gaps_corrector.hpp : 83) 412 contigs from 11807 have gaps before correction 7:29:00.170 4G / 5G INFO General (close_gaps_corrector.hpp : 68) 10% contigs were processed 7:29:00.180 4G / 5G INFO General (close_gaps_corrector.hpp : 68) 20% contigs were processed 7:29:00.194 4G / 5G INFO General (close_gaps_corrector.hpp : 68) 30% contigs were processed 7:29:00.198 4G / 5G INFO General (close_gaps_corrector.hpp : 68) 40% contigs were processed 7:29:00.200 4G / 5G INFO General (close_gaps_corrector.hpp : 68) 50% contigs were processed 7:29:00.204 4G / 5G INFO General (close_gaps_corrector.hpp : 68) 60% contigs were processed 7:29:00.204 4G / 5G INFO General (close_gaps_corrector.hpp : 68) 70% contigs were processed 7:29:00.205 4G / 5G INFO General (close_gaps_corrector.hpp : 68) 80% contigs were processed 7:29:00.206 4G / 5G INFO General (close_gaps_corrector.hpp : 68) 90% contigs were processed 7:29:00.208 4G / 5G INFO General (close_gaps_corrector.hpp : 72) 100% contigs were processed 7:29:00.208 4G / 5G INFO General (close_gaps_corrector.hpp : 87) 11807 contigs from 11807 were corrected 7:29:00.208 4G / 5G INFO General (close_gaps_corrector.hpp : 88) 0 contigs from 11807 have gaps after correction 7:29:00.208 4G / 5G INFO ConsensusContigsConstruc (consensus_contigs_construc: 115) Close gaps in contigs mappings ends 7:29:00.208 4G / 5G INFO ConsensusContigsConstruc (consensus_contigs_construc: 117) Removing incorrect contigs 7:29:00.213 4G / 5G INFO General (incorrect_contig_remover.h: 25) 0 contigs from 11807 were deleted 7:29:00.280 4G / 5G INFO ConsensusContigsConstruc (consensus_contigs_construc: 144) Addition of RC contigs. 23614 contigs will be used 7:29:00.282 4G / 5G INFO ConsensusContigsConstruc (consensus_contigs_construc: 149) Redundant contigs remover starts 7:29:00.282 4G / 5G INFO General (iterative_redundant_contig: 30) Equal path remover starts 7:29:00.282 4G / 5G INFO General (path_index.hpp : 27) Initialization of vertex-paths index starts 7:29:00.370 4G / 5G INFO General (path_index.hpp : 40) Initialization of vertex-paths index ends 7:29:00.370 4G / 5G INFO General (equal_path_deletion_correc: 27) Computing redundant equal contigs starts 7:29:05.559 4G / 5G INFO General (equal_path_deletion_correc: 58) 2252 contigs from 23614 are redundant 7:29:05.563 4G / 5G INFO General (equal_path_deletion_correc: 61) Computing redundant equal contigs ends 7:29:05.615 4G / 5G INFO General (iterative_redundant_contig: 36) 21362 contigs will be used further 7:29:05.619 4G / 5G INFO General (iterative_redundant_contig: 39) Iterative loop corrector starts 7:29:05.619 4G / 5G INFO General (iterative_redundant_contig: 41) Only exact match iteration with parameters: 7:29:05.619 4G / 5G INFO General (iterative_redundant_contig: 42) Maximal loop length - 500 7:29:05.619 4G / 5G INFO General (iterative_redundant_contig: 43) Minimal lcs length - 1500 7:29:05.619 4G / 5G INFO General (iterative_redundant_contig: 44) Maximal tail length - 0 7:29:05.619 4G / 5G INFO General (path_index.hpp : 27) Initialization of vertex-paths index starts 7:29:05.703 4G / 5G INFO General (path_index.hpp : 40) Initialization of vertex-paths index ends 7:29:05.703 4G / 5G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 708) Computing redundant contigs starts 7:33:00.637 4G / 5G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 852) 10% contigs were processed 7:35:19.068 4G / 5G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 852) 20% contigs were processed 7:36:02.797 4G / 5G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 852) 30% contigs were processed 7:36:06.301 4G / 5G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 852) 40% contigs were processed 7:36:06.518 4G / 5G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 852) 50% contigs were processed 7:36:06.579 4G / 5G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 852) 60% contigs were processed 7:36:06.594 4G / 5G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 852) 70% contigs were processed 7:36:06.613 4G / 5G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 852) 80% contigs were processed 7:36:06.641 4G / 5G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 852) 90% contigs were processed 7:36:06.889 4G / 5G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 856) 100% contigs were processed 7:36:06.966 4G / 5G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 861) 3682 contigs from 21362 are redundant 7:36:06.970 4G / 5G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 865) Computing redundant contigs ends 7:36:07.219 4G / 5G INFO General (iterative_redundant_contig: 55) 17680 contigs will be used further 7:36:07.236 4G / 5G INFO General (iterative_redundant_contig: 59) Tails allowing match iteration with parameters: 7:36:07.236 4G / 5G INFO General (iterative_redundant_contig: 60) Maximal loop length - 500 7:36:07.236 4G / 5G INFO General (iterative_redundant_contig: 61) Minimal lcs length - 1500 7:36:07.236 4G / 5G INFO General (iterative_redundant_contig: 62) Maximal tail length - 78821 7:36:07.236 4G / 5G INFO General (path_index.hpp : 27) Initialization of vertex-paths index starts 7:36:07.305 4G / 5G INFO General (path_index.hpp : 40) Initialization of vertex-paths index ends 7:36:07.305 4G / 5G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 708) Computing redundant contigs starts 7:39:12.426 4G / 5G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 852) 10% contigs were processed 7:40:31.634 4G / 5G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 852) 20% contigs were processed 7:40:58.246 4G / 5G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 852) 30% contigs were processed 7:40:58.834 4G / 5G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 852) 40% contigs were processed 7:40:58.961 4G / 5G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 852) 50% contigs were processed 7:40:59.021 4G / 5G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 852) 60% contigs were processed 7:40:59.029 4G / 5G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 852) 70% contigs were processed 7:40:59.041 4G / 5G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 852) 80% contigs were processed 7:40:59.063 4G / 5G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 852) 90% contigs were processed 7:40:59.290 4G / 5G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 856) 100% contigs were processed 7:40:59.507 4G / 5G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 861) 4836 contigs from 17680 are redundant 7:40:59.512 4G / 5G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 865) Computing redundant contigs ends 7:41:00.026 4G / 5G INFO General (iterative_redundant_contig: 72) 12844 contigs will be used further 7:41:00.056 4G / 5G INFO General (iterative_redundant_contig: 74) Iterative loop corrector ends 7:41:00.056 4G / 5G INFO ConsensusContigsConstruc (consensus_contigs_construc: 161) Redundant contigs remover ends 7:41:00.069 4G / 5G INFO ConsensusContigsConstruc (consensus_contigs_construc: 166) Overlapping search starts 7:41:00.069 4G / 5G INFO General (path_index.hpp : 27) Initialization of vertex-paths index starts 7:41:00.105 4G / 5G INFO General (path_index.hpp : 40) Initialization of vertex-paths index ends 7:41:00.105 4G / 5G INFO OverlapCorrector (overlap_searcher.hpp : 350) Computing overlaps starts 7:41:06.983 4G / 5G INFO OverlapCorrector (overlap_searcher.hpp : 478) Overlap graph with 12844 vertices and 24 edges constructed 7:41:06.984 4G / 5G INFO General (overlap_graph.hpp :1100) 0 tips and 0 transitive edges were deleted in overlap graph 7:41:06.984 4G / 5G INFO General (overlap_graph.hpp :1103) Bulge remover starts 7:41:37.544 4G / 5G INFO General (overlap_graph.hpp :1108) 0 bulges were deleted in overlap graph 7:41:37.546 4G / 5G INFO OverlapCorrector (overlap_searcher.hpp : 486) Simplified overlap graph contains 12844 vertices and 24 edges 7:41:51.976 4G / 5G INFO OverlapCorrector (overlap_searcher.hpp : 525) Computing overlaps ends 7:41:52.003 4G / 5G INFO ConsensusContigsConstruc (consensus_contigs_construc: 174) Overlapping search ends 7:42:10.967 4G / 5G INFO ConsensusContigsConstruc (consensus_contigs_construc: 190) 6410 with total length 26144445 were written in /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_133-dipSPAdes-3.5.0-trimmed/dipspades/consensus_contigs.fasta 7:42:11.169 4G / 5G INFO ConsensusContigsConstruc (consensus_contigs_construc: 190) 662 with total length 22562982 were written in /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_133-dipSPAdes-3.5.0-trimmed/dipspades/paired_consensus_contigs.fasta 7:42:11.336 4G / 5G INFO ConsensusContigsConstruc (consensus_contigs_construc: 190) 5748 with total length 3581463 were written in /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_133-dipSPAdes-3.5.0-trimmed/dipspades/unpaired_consensus_contigs.fasta 7:42:11.337 4G / 5G INFO ConsensusContigsConstruc (consensus_contigs_construc: 216) Writing haplocontigs alignment to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_133-dipSPAdes-3.5.0-trimmed/dipspades/haplocontigs_alignment 7:42:16.065 4G / 5G INFO ConsensusContigsConstruc (consensus_contigs_construc: 311) Consensus contigs constructor ends 7:42:16.085 4G / 5G INFO General (dipspades.hpp : 211) dipSPAdes finished 7:42:34.167 120M / 5G INFO General (main.cpp : 115) Assembling time: 7 hours 42 minutes 34 seconds ===== Assembling finished. * Assembled consensus contigs are in: /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_133-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_133-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_133-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_133-dipSPAdes-3.5.0-trimmed/dipspades/dipspades.log Thank you for using dipSPAdes!