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_126/reads.end1.paired.fastq.gz --pe1-2 /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_126/reads.end2.paired.fastq.gz -t 16 -o /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_126-dipSPAdes-3.5.0-trimmed dipSPAdes command line: -t 16 -o /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_126-dipSPAdes-3.5.0-trimmed/dipspades --hap /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_126-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_126-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_126-dipSPAdes-3.5.0-trimmed/dipspades Dir for temp files: /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_126-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_126-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_126-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 0:00:00.003 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_126-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 0:00:00.014 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 0:00:37.145 568M / 1G INFO General (kmer_splitters.hpp : 228) Processed 36720 reads 0:00:37.145 568M / 1G INFO General (kmer_splitters.hpp : 245) Used 36720 reads. Maximum read length 222824 0:00:37.146 568M / 1G INFO General (kmer_splitters.hpp : 246) Average read length 3976.81 0:00:37.149 4M / 1G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:00:59.513 4M / 1G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 71177808 kmers in total. 0:00:59.513 4M / 1G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:01:05.511 4M / 1G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:01:05.511 4M / 1G INFO General (kmer_splitters.hpp : 379) Splitting kmer instances into 16 buckets. This might take a while. 0:01:05.511 4M / 1G INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:01:05.511 4M / 1G INFO General (kmer_splitters.hpp : 397) Memory available for splitting buffers: 33.332 Gb 0:01:05.511 4M / 1G INFO General (kmer_splitters.hpp : 405) Using cell size of 2097152 0:04:05.077 640M / 1G INFO General (kmer_splitters.hpp : 428) Processed 16777216 kmers 0:07:10.226 640M / 1G INFO General (kmer_splitters.hpp : 428) Processed 33554432 kmers 0:10:54.910 640M / 1G INFO General (kmer_splitters.hpp : 428) Processed 50331648 kmers 0:13:20.095 640M / 1G INFO General (kmer_splitters.hpp : 428) Processed 67108864 kmers 0:14:59.688 640M / 1G INFO General (kmer_splitters.hpp : 428) Processed 71177808 kmers 0:14:59.688 640M / 1G INFO General (kmer_splitters.hpp : 437) Used 71177808 kmers. 0:14:59.700 64M / 1G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:15:59.502 64M / 1G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 71169444 kmers in total. 0:15:59.502 64M / 1G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:16:05.981 64M / 1G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:17:16.883 88M / 1G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:17:23.211 88M / 1G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 24620222 bytes occupied (2.7675 bits per kmer). 0:17:23.311 156M / 1G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 382) Building k-mer extensions from k+1-mers 0:19:09.500 156M / 1G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 386) Building k-mer extensions from k+1-mers finished. 0:19:09.504 156M / 1G INFO General (graph_construction.hpp : 145) Condensing graph 0:19:09.504 156M / 1G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 337) Extracting unbranching paths 0:19:39.261 172M / 1G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 351) Extracting unbranching paths finished. 92701 sequences extracted 0:19:44.102 168M / 1G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 311) Collecting perfect loops 0:20:06.224 168M / 1G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 326) Collecting perfect loops finished. 152 loops collected 0:20:06.304 164M / 1G INFO General (graph_construction.hpp : 150) Building index with from graph 0:20:06.305 164M / 1G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:20:06.305 164M / 1G INFO General (kmer_splitters.hpp : 289) Splitting kmer instances into 16 buckets. This might take a while. 0:20:06.305 164M / 1G INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:20:06.305 164M / 1G INFO General (kmer_splitters.hpp : 307) Memory available for splitting buffers: 33.2799 Gb 0:20:06.305 164M / 1G INFO General (kmer_splitters.hpp : 312) Using cell size of 2097152 0:23:14.479 740M / 1G INFO General (kmer_splitters.hpp : 325) Processed 44044 edges 0:27:02.684 740M / 1G INFO General (kmer_splitters.hpp : 325) Processed 87656 edges 0:28:07.128 740M / 1G INFO General (kmer_splitters.hpp : 325) Processed 92853 edges 0:28:07.129 740M / 1G INFO General (kmer_splitters.hpp : 330) Used 92853 sequences. 0:28:07.132 164M / 1G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:28:48.260 164M / 1G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 71177808 kmers in total. 0:28:48.260 164M / 1G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:29:34.529 164M / 1G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:30:44.396 188M / 1G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:30:51.848 188M / 1G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 24623110 bytes occupied (2.7675 bits per kmer). 0:30:52.825 1G / 1G INFO General (edge_index_builders.hpp : 21) Collecting k-mer coverage information from graph, this takes a while. 0:32:36.805 1G / 1G INFO General (graph_construction.hpp : 182) Filling coverage index 0:32:36.805 1G / 1G INFO General (edge_index_builders.hpp : 99) Collecting k-mer coverage information from reads, this takes a while. 0:33:43.290 1G / 1G INFO General (graph_construction.hpp : 184) Filling coverage and flanking coverage from index 0:33:46.461 1G / 1G INFO General (stage.cpp : 95) PROCEDURE == Polymorphic bulge remover 0:33:46.461 1G / 1G INFO General (polymorphic_bulge_remover.: 94) Polymorphic bulge remover starts 0:33:46.461 1G / 1G INFO General (polymorphic_bulge_remover.: 36) Simple polymorphic bulge remover runs 0:38:31.800 2G / 2G INFO General (polymorphic_bulge_remover.: 42) 1 iteration: 7988 simple bulges were glued 0:54:10.616 3G / 3G INFO General (polymorphic_bulge_remover.: 42) 2 iteration: 515 simple bulges were glued 0:56:02.809 3G / 4G INFO General (polymorphic_bulge_remover.: 42) 3 iteration: 0 simple bulges were glued 0:56:02.810 3G / 4G INFO General (polymorphic_bulge_remover.: 44) Simple polymorphic bulge remover ends 0:56:02.810 3G / 4G INFO General (polymorphic_bulge_remover.: 49) LightBulgeRemover starts 0:56:02.810 3G / 4G INFO General (polymorphic_bulge_remover.: 50) Maximal number of iterations: 15 0:56:02.810 3G / 4G INFO PolymorphicBulgeRemover (complex_bulge_remover.hpp : 108) Maximal length of glued bulge: 70476 1:44:21.817 4G / 4G INFO General (polymorphic_bulge_remover.: 60) 1 iteration: 1932 complex bulges were glued 1:44:21.817 4G / 4G INFO PolymorphicBulgeRemover (complex_bulge_remover.hpp : 108) Maximal length of glued bulge: 78451 2:24:28.319 4G / 4G INFO General (polymorphic_bulge_remover.: 60) 2 iteration: 71 complex bulges were glued 2:24:28.320 4G / 4G INFO PolymorphicBulgeRemover (complex_bulge_remover.hpp : 108) Maximal length of glued bulge: 78451 3:03:28.645 4G / 5G INFO General (polymorphic_bulge_remover.: 60) 3 iteration: 20 complex bulges were glued 3:03:28.646 4G / 5G INFO PolymorphicBulgeRemover (complex_bulge_remover.hpp : 108) Maximal length of glued bulge: 78451 3:42:22.398 4G / 5G INFO General (polymorphic_bulge_remover.: 60) 4 iteration: 9 complex bulges were glued 3:42:22.399 4G / 5G INFO PolymorphicBulgeRemover (complex_bulge_remover.hpp : 108) Maximal length of glued bulge: 78451 4:21:03.915 4G / 5G INFO General (polymorphic_bulge_remover.: 60) 5 iteration: 2 complex bulges were glued 4:21:03.916 4G / 5G INFO PolymorphicBulgeRemover (complex_bulge_remover.hpp : 108) Maximal length of glued bulge: 78451 4:59:45.564 4G / 5G INFO General (polymorphic_bulge_remover.: 60) 6 iteration: 10 complex bulges were glued 4:59:45.565 4G / 5G INFO PolymorphicBulgeRemover (complex_bulge_remover.hpp : 108) Maximal length of glued bulge: 78451 5:38:27.471 4G / 5G INFO General (polymorphic_bulge_remover.: 60) 7 iteration: 2 complex bulges were glued 5:38:27.472 4G / 5G INFO PolymorphicBulgeRemover (complex_bulge_remover.hpp : 108) Maximal length of glued bulge: 78451 6:17:02.567 4G / 5G INFO General (polymorphic_bulge_remover.: 60) 8 iteration: 0 complex bulges were glued 6:17:02.567 4G / 5G INFO General (polymorphic_bulge_remover.: 62) LightBulgeRemover ends 6:17:02.567 4G / 5G INFO General (polymorphic_bulge_remover.: 103) Index refilling 6:17:02.576 2G / 5G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 6:17:02.577 2G / 5G INFO General (kmer_splitters.hpp : 289) Splitting kmer instances into 16 buckets. This might take a while. 6:17:02.577 2G / 5G INFO General (file_limit.hpp : 29) Open file limit set to 32768 6:17:02.577 2G / 5G INFO General (kmer_splitters.hpp : 307) Memory available for splitting buffers: 32.5195 Gb 6:17:02.577 2G / 5G INFO General (kmer_splitters.hpp : 312) Using cell size of 2097152 6:22:32.589 3G / 5G INFO General (kmer_splitters.hpp : 325) Processed 17052 edges 6:24:38.126 3G / 5G INFO General (kmer_splitters.hpp : 325) Processed 30021 edges 6:24:38.126 3G / 5G INFO General (kmer_splitters.hpp : 330) Used 30021 sequences. 6:24:38.129 2G / 5G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 6:26:09.126 2G / 5G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 57783776 kmers in total. 6:26:09.127 2G / 5G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 6:26:14.181 2G / 5G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 6:27:14.638 2G / 5G INFO General (kmer_index.hpp : 371) Merging final buckets. 6:27:39.741 2G / 5G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 19989614 bytes occupied (2.76751 bits per kmer). 6:27:40.530 3G / 5G INFO General (edge_index_builders.hpp : 21) Collecting k-mer coverage information from graph, this takes a while. 6:29:01.892 3G / 5G INFO General (polymorphic_bulge_remover.: 106) Glueing equal kmers 6:31:34.673 3G / 5G INFO General (equal_sequence_gluer.hpp : 105) 13 kmers glued 6:31:34.673 3G / 5G INFO General (polymorphic_bulge_remover.: 108) Polymorphic ends remover ends 6:31:34.673 3G / 5G INFO General (dipspades.hpp : 96) Consensus graph was constructed 6:31:34.673 3G / 5G INFO General (stage.cpp : 95) PROCEDURE == Consensus contigs construction 6:31:34.673 3G / 5G INFO ConsensusContigsConstruc (consensus_contigs_construc: 274) Consensus contigs constructor starts 6:31:36.064 3G / 5G INFO ConsensusContigsConstruc (consensus_contigs_construc: 51) 18360 contigs from /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_126-dipSPAdes-3.5.0-trimmed/spades/contigs.fasta were read 6:31:36.072 3G / 5G INFO ConsensusContigsConstruc (consensus_contigs_construc: 276) Total: 18360 contigs were read 6:32:09.359 3G / 5G INFO ConsensusContigsConstruc (consensus_contigs_construc: 79) 23 contigs with total length 2095 have mapped path with zero length 6:32:09.388 3G / 5G INFO ConsensusContigsConstruc (consensus_contigs_construc: 105) Removing repetitive edges in contigs mapping starts 6:32:09.416 3G / 5G INFO ConsensusContigsConstruc (consensus_contigs_construc: 109) Removing repetitive edges in contigs mapping ends 6:32:09.416 3G / 5G INFO ConsensusContigsConstruc (consensus_contigs_construc: 111) Close gaps in contigs mappings starts 6:32:09.421 3G / 5G INFO General (close_gaps_corrector.hpp : 83) 455 contigs from 18337 have gaps before correction 6:32:09.432 3G / 5G INFO General (close_gaps_corrector.hpp : 68) 10% contigs were processed 6:32:09.439 3G / 5G INFO General (close_gaps_corrector.hpp : 68) 20% contigs were processed 6:32:09.444 3G / 5G INFO General (close_gaps_corrector.hpp : 68) 30% contigs were processed 6:32:09.451 3G / 5G INFO General (close_gaps_corrector.hpp : 68) 40% contigs were processed 6:32:09.460 3G / 5G INFO General (close_gaps_corrector.hpp : 68) 50% contigs were processed 6:32:09.462 3G / 5G INFO General (close_gaps_corrector.hpp : 68) 60% contigs were processed 6:32:09.463 3G / 5G INFO General (close_gaps_corrector.hpp : 68) 70% contigs were processed 6:32:09.463 3G / 5G INFO General (close_gaps_corrector.hpp : 68) 80% contigs were processed 6:32:09.463 3G / 5G INFO General (close_gaps_corrector.hpp : 68) 90% contigs were processed 6:32:09.468 3G / 5G INFO General (close_gaps_corrector.hpp : 72) 100% contigs were processed 6:32:09.468 3G / 5G INFO General (close_gaps_corrector.hpp : 87) 18337 contigs from 18337 were corrected 6:32:09.468 3G / 5G INFO General (close_gaps_corrector.hpp : 88) 0 contigs from 18337 have gaps after correction 6:32:09.468 3G / 5G INFO ConsensusContigsConstruc (consensus_contigs_construc: 115) Close gaps in contigs mappings ends 6:32:09.468 3G / 5G INFO ConsensusContigsConstruc (consensus_contigs_construc: 117) Removing incorrect contigs 6:32:09.473 3G / 5G INFO General (incorrect_contig_remover.h: 25) 0 contigs from 18337 were deleted 6:32:09.543 3G / 5G INFO ConsensusContigsConstruc (consensus_contigs_construc: 144) Addition of RC contigs. 36674 contigs will be used 6:32:09.546 3G / 5G INFO ConsensusContigsConstruc (consensus_contigs_construc: 149) Redundant contigs remover starts 6:32:09.547 3G / 5G INFO General (iterative_redundant_contig: 30) Equal path remover starts 6:32:09.547 3G / 5G INFO General (path_index.hpp : 27) Initialization of vertex-paths index starts 6:32:09.641 3G / 5G INFO General (path_index.hpp : 40) Initialization of vertex-paths index ends 6:32:09.641 3G / 5G INFO General (equal_path_deletion_correc: 27) Computing redundant equal contigs starts 6:32:14.526 3G / 5G INFO General (equal_path_deletion_correc: 58) 14394 contigs from 36674 are redundant 6:32:14.534 3G / 5G INFO General (equal_path_deletion_correc: 61) Computing redundant equal contigs ends 6:32:14.594 3G / 5G INFO General (iterative_redundant_contig: 36) 22280 contigs will be used further 6:32:14.601 3G / 5G INFO General (iterative_redundant_contig: 39) Iterative loop corrector starts 6:32:14.601 3G / 5G INFO General (iterative_redundant_contig: 41) Only exact match iteration with parameters: 6:32:14.601 3G / 5G INFO General (iterative_redundant_contig: 42) Maximal loop length - 500 6:32:14.601 3G / 5G INFO General (iterative_redundant_contig: 43) Minimal lcs length - 1500 6:32:14.601 3G / 5G INFO General (iterative_redundant_contig: 44) Maximal tail length - 0 6:32:14.601 3G / 5G INFO General (path_index.hpp : 27) Initialization of vertex-paths index starts 6:32:14.674 3G / 5G INFO General (path_index.hpp : 40) Initialization of vertex-paths index ends 6:32:14.675 3G / 5G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 708) Computing redundant contigs starts 6:33:44.925 3G / 5G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 852) 10% contigs were processed 6:33:55.976 3G / 5G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 852) 20% contigs were processed 6:34:18.340 3G / 5G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 852) 30% contigs were processed 6:34:27.557 3G / 5G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 852) 40% contigs were processed 6:34:31.759 3G / 5G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 852) 50% contigs were processed 6:34:32.038 3G / 5G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 852) 60% contigs were processed 6:34:32.238 3G / 5G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 852) 70% contigs were processed 6:34:32.315 3G / 5G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 852) 80% contigs were processed 6:34:32.334 3G / 5G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 852) 90% contigs were processed 6:34:32.400 3G / 5G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 856) 100% contigs were processed 6:34:32.486 3G / 5G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 861) 7006 contigs from 22280 are redundant 6:34:32.492 3G / 5G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 865) Computing redundant contigs ends 6:34:32.873 3G / 5G INFO General (iterative_redundant_contig: 55) 15274 contigs will be used further 6:34:32.892 3G / 5G INFO General (iterative_redundant_contig: 59) Tails allowing match iteration with parameters: 6:34:32.892 3G / 5G INFO General (iterative_redundant_contig: 60) Maximal loop length - 500 6:34:32.892 3G / 5G INFO General (iterative_redundant_contig: 61) Minimal lcs length - 1500 6:34:32.892 3G / 5G INFO General (iterative_redundant_contig: 62) Maximal tail length - 60130 6:34:32.892 3G / 5G INFO General (path_index.hpp : 27) Initialization of vertex-paths index starts 6:34:32.943 3G / 5G INFO General (path_index.hpp : 40) Initialization of vertex-paths index ends 6:34:32.943 3G / 5G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 708) Computing redundant contigs starts 6:35:24.113 3G / 5G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 852) 10% contigs were processed 6:35:50.874 3G / 5G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 852) 20% contigs were processed 6:36:03.604 3G / 5G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 852) 30% contigs were processed 6:36:06.393 3G / 5G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 852) 40% contigs were processed 6:36:07.739 3G / 5G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 852) 50% contigs were processed 6:36:07.912 3G / 5G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 852) 60% contigs were processed 6:36:08.062 3G / 5G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 852) 70% contigs were processed 6:36:08.096 3G / 5G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 852) 80% contigs were processed 6:36:08.145 3G / 5G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 852) 90% contigs were processed 6:36:08.208 3G / 5G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 856) 100% contigs were processed 6:36:08.337 3G / 5G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 861) 4644 contigs from 15274 are redundant 6:36:08.341 3G / 5G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 865) Computing redundant contigs ends 6:36:08.929 3G / 5G INFO General (iterative_redundant_contig: 72) 10630 contigs will be used further 6:36:08.949 3G / 5G INFO General (iterative_redundant_contig: 74) Iterative loop corrector ends 6:36:08.950 3G / 5G INFO ConsensusContigsConstruc (consensus_contigs_construc: 161) Redundant contigs remover ends 6:36:08.962 3G / 5G INFO ConsensusContigsConstruc (consensus_contigs_construc: 166) Overlapping search starts 6:36:08.962 3G / 5G INFO General (path_index.hpp : 27) Initialization of vertex-paths index starts 6:36:08.990 3G / 5G INFO General (path_index.hpp : 40) Initialization of vertex-paths index ends 6:36:08.990 3G / 5G INFO OverlapCorrector (overlap_searcher.hpp : 350) Computing overlaps starts 6:36:18.366 3G / 5G INFO OverlapCorrector (overlap_searcher.hpp : 478) Overlap graph with 10630 vertices and 12 edges constructed 6:36:18.367 3G / 5G INFO General (overlap_graph.hpp :1100) 0 tips and 0 transitive edges were deleted in overlap graph 6:36:18.367 3G / 5G INFO General (overlap_graph.hpp :1103) Bulge remover starts 6:36:38.742 3G / 5G INFO General (overlap_graph.hpp :1108) 0 bulges were deleted in overlap graph 6:36:38.744 3G / 5G INFO OverlapCorrector (overlap_searcher.hpp : 486) Simplified overlap graph contains 10630 vertices and 12 edges 6:36:47.814 3G / 5G INFO OverlapCorrector (overlap_searcher.hpp : 525) Computing overlaps ends 6:36:47.834 3G / 5G INFO ConsensusContigsConstruc (consensus_contigs_construc: 174) Overlapping search ends 6:36:48.141 3G / 5G INFO ConsensusContigsConstruc (consensus_contigs_construc: 190) 5309 with total length 23028133 were written in /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_126-dipSPAdes-3.5.0-trimmed/dipspades/consensus_contigs.fasta 6:36:48.316 3G / 5G INFO ConsensusContigsConstruc (consensus_contigs_construc: 190) 705 with total length 19923792 were written in /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_126-dipSPAdes-3.5.0-trimmed/dipspades/paired_consensus_contigs.fasta 6:36:48.453 3G / 5G INFO ConsensusContigsConstruc (consensus_contigs_construc: 190) 4604 with total length 3104341 were written in /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_126-dipSPAdes-3.5.0-trimmed/dipspades/unpaired_consensus_contigs.fasta 6:36:48.455 3G / 5G INFO ConsensusContigsConstruc (consensus_contigs_construc: 216) Writing haplocontigs alignment to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_126-dipSPAdes-3.5.0-trimmed/dipspades/haplocontigs_alignment 6:36:54.270 3G / 5G INFO ConsensusContigsConstruc (consensus_contigs_construc: 311) Consensus contigs constructor ends 6:36:54.288 3G / 5G INFO General (dipspades.hpp : 211) dipSPAdes finished 6:37:07.297 120M / 5G INFO General (main.cpp : 115) Assembling time: 6 hours 37 minutes 7 seconds ===== Assembling finished. * Assembled consensus contigs are in: /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_126-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_126-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_126-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_126-dipSPAdes-3.5.0-trimmed/dipspades/dipspades.log Thank you for using dipSPAdes!