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_127/reads.end1.paired.fastq.gz --pe1-2 /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_127/reads.end2.paired.fastq.gz -t 16 -o /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_127-dipSPAdes-3.5.0-trimmed dipSPAdes command line: -t 16 -o /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_127-dipSPAdes-3.5.0-trimmed/dipspades --hap /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_127-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_127-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_127-dipSPAdes-3.5.0-trimmed/dipspades Dir for temp files: /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_127-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_127-dipSPAdes-3.5.0-trimmed/dipspades/dipspades.log ===== Assembling started. 0:00:00.048 4M / 4M INFO General (memory_limit.hpp : 42) Memory limit set to 100 Gb 0:00:00.100 4M / 4M INFO General (main.cpp : 96) Assembling dataset (/N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_127-dipSPAdes-3.5.0-trimmed/dipspades/) with K=55 0:00:00.104 4M / 4M INFO General (dipspades.hpp : 188) dipSPAdes started 0:00:00.179 4M / 4M INFO StageManager (stage.cpp : 125) STAGE == dipSPAdes 0:00:00.187 4M / 4M INFO General (stage.cpp : 95) PROCEDURE == Construction of graph from contigs 0:00:00.197 4M / 4M INFO General (dipspades.hpp : 19) Addition of contigs from /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_127-dipSPAdes-3.5.0-trimmed/spades/contigs.fasta 0:00:00.217 4M / 4M INFO General (dipspades.hpp : 23) Construction of the de Bruijn graph with K=55 0:00:00.220 4M / 4M INFO General (graph_construction.hpp : 129) Constructing DeBruijn graph for k=55 0:00:00.234 4M / 4M INFO General (kmer_splitters.hpp : 172) Splitting kmer instances into 1 buckets. This might take a while. 0:00:00.235 4M / 4M INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:00:00.235 4M / 4M INFO General (kmer_splitters.hpp : 190) Memory available for splitting buffers: 33.332 Gb 0:00:00.235 4M / 4M INFO General (kmer_splitters.hpp : 199) Using cell size of 33554432 0:00:38.416 568M / 1G INFO General (kmer_splitters.hpp : 245) Used 28188 reads. Maximum read length 305157 0:00:38.416 568M / 1G INFO General (kmer_splitters.hpp : 246) Average read length 5269.08 0:00:38.419 4M / 1G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:01:00.882 4M / 1G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 72924334 kmers in total. 0:01:00.882 4M / 1G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:01:07.752 4M / 1G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:01:07.753 4M / 1G INFO General (kmer_splitters.hpp : 379) Splitting kmer instances into 16 buckets. This might take a while. 0:01:07.753 4M / 1G INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:01:07.753 4M / 1G INFO General (kmer_splitters.hpp : 397) Memory available for splitting buffers: 33.332 Gb 0:01:07.753 4M / 1G INFO General (kmer_splitters.hpp : 405) Using cell size of 2097152 0:01:37.539 640M / 1G INFO General (kmer_splitters.hpp : 428) Processed 16777216 kmers 0:02:00.576 640M / 1G INFO General (kmer_splitters.hpp : 428) Processed 33554432 kmers 0:02:43.882 640M / 1G INFO General (kmer_splitters.hpp : 428) Processed 50331648 kmers 0:03:07.504 640M / 1G INFO General (kmer_splitters.hpp : 428) Processed 67108864 kmers 0:03:15.566 640M / 1G INFO General (kmer_splitters.hpp : 428) Processed 72924334 kmers 0:03:15.566 640M / 1G INFO General (kmer_splitters.hpp : 437) Used 72924334 kmers. 0:03:15.572 64M / 1G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:03:50.259 64M / 1G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 72920778 kmers in total. 0:03:50.259 64M / 1G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:03:55.813 64M / 1G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:05:07.135 88M / 1G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:05:13.401 88M / 1G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 25226074 bytes occupied (2.7675 bits per kmer). 0:05:13.504 160M / 1G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 382) Building k-mer extensions from k+1-mers 0:07:01.258 160M / 1G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 386) Building k-mer extensions from k+1-mers finished. 0:07:01.263 160M / 1G INFO General (graph_construction.hpp : 145) Condensing graph 0:07:01.285 160M / 1G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 337) Extracting unbranching paths 0:07:32.455 176M / 1G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 351) Extracting unbranching paths finished. 89211 sequences extracted 0:07:37.437 172M / 1G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 311) Collecting perfect loops 0:07:59.921 172M / 1G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 326) Collecting perfect loops finished. 608 loops collected 0:08:00.091 168M / 1G INFO General (graph_construction.hpp : 150) Building index with from graph 0:08:00.092 168M / 1G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:08:00.092 168M / 1G INFO General (kmer_splitters.hpp : 289) Splitting kmer instances into 16 buckets. This might take a while. 0:08:00.092 168M / 1G INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:08:00.092 168M / 1G INFO General (kmer_splitters.hpp : 307) Memory available for splitting buffers: 33.2786 Gb 0:08:00.092 168M / 1G INFO General (kmer_splitters.hpp : 312) Using cell size of 2097152 0:08:06.350 744M / 1G INFO General (kmer_splitters.hpp : 325) Processed 41292 edges 0:08:12.461 744M / 1G INFO General (kmer_splitters.hpp : 325) Processed 82709 edges 0:08:13.585 744M / 1G INFO General (kmer_splitters.hpp : 325) Processed 89819 edges 0:08:13.587 744M / 1G INFO General (kmer_splitters.hpp : 330) Used 89819 sequences. 0:08:13.590 168M / 1G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:08:35.124 168M / 1G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 72924334 kmers in total. 0:08:35.125 168M / 1G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:08:41.005 168M / 1G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:09:52.247 192M / 1G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:09:57.539 192M / 1G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 25227294 bytes occupied (2.7675 bits per kmer). 0:09:58.543 1G / 1G INFO General (edge_index_builders.hpp : 21) Collecting k-mer coverage information from graph, this takes a while. 0:11:43.824 1G / 1G INFO General (graph_construction.hpp : 182) Filling coverage index 0:11:43.842 1G / 1G INFO General (edge_index_builders.hpp : 99) Collecting k-mer coverage information from reads, this takes a while. 0:12:52.112 1G / 1G INFO General (graph_construction.hpp : 184) Filling coverage and flanking coverage from index 0:12:55.298 1G / 1G INFO General (stage.cpp : 95) PROCEDURE == Polymorphic bulge remover 0:12:55.299 1G / 1G INFO General (polymorphic_bulge_remover.: 94) Polymorphic bulge remover starts 0:12:55.312 1G / 1G INFO General (polymorphic_bulge_remover.: 36) Simple polymorphic bulge remover runs 0:24:08.197 2G / 3G INFO General (polymorphic_bulge_remover.: 42) 1 iteration: 5393 simple bulges were glued 0:33:21.777 3G / 3G INFO General (polymorphic_bulge_remover.: 42) 2 iteration: 200 simple bulges were glued 0:35:56.483 3G / 4G INFO General (polymorphic_bulge_remover.: 42) 3 iteration: 0 simple bulges were glued 0:35:56.483 3G / 4G INFO General (polymorphic_bulge_remover.: 44) Simple polymorphic bulge remover ends 0:35:56.496 3G / 4G INFO General (polymorphic_bulge_remover.: 49) LightBulgeRemover starts 0:35:56.496 3G / 4G INFO General (polymorphic_bulge_remover.: 50) Maximal number of iterations: 15 0:35:56.526 3G / 4G INFO PolymorphicBulgeRemover (complex_bulge_remover.hpp : 108) Maximal length of glued bulge: 55896 1:20:46.074 4G / 5G INFO General (polymorphic_bulge_remover.: 60) 1 iteration: 2556 complex bulges were glued 1:20:46.075 4G / 5G INFO PolymorphicBulgeRemover (complex_bulge_remover.hpp : 108) Maximal length of glued bulge: 83594 2:09:43.491 4G / 5G INFO General (polymorphic_bulge_remover.: 60) 2 iteration: 186 complex bulges were glued 2:09:43.492 4G / 5G INFO PolymorphicBulgeRemover (complex_bulge_remover.hpp : 108) Maximal length of glued bulge: 93380 2:57:15.642 4G / 5G INFO General (polymorphic_bulge_remover.: 60) 3 iteration: 28 complex bulges were glued 2:57:15.643 4G / 5G INFO PolymorphicBulgeRemover (complex_bulge_remover.hpp : 108) Maximal length of glued bulge: 95547 3:45:28.193 4G / 5G INFO General (polymorphic_bulge_remover.: 60) 4 iteration: 14 complex bulges were glued 3:45:28.194 4G / 5G INFO PolymorphicBulgeRemover (complex_bulge_remover.hpp : 108) Maximal length of glued bulge: 95547 4:33:10.391 4G / 5G INFO General (polymorphic_bulge_remover.: 60) 5 iteration: 8 complex bulges were glued 4:33:10.392 4G / 5G INFO PolymorphicBulgeRemover (complex_bulge_remover.hpp : 108) Maximal length of glued bulge: 95547 5:20:50.200 4G / 5G INFO General (polymorphic_bulge_remover.: 60) 6 iteration: 3 complex bulges were glued 5:20:50.201 4G / 5G INFO PolymorphicBulgeRemover (complex_bulge_remover.hpp : 108) Maximal length of glued bulge: 95547 6:08:12.375 4G / 5G INFO General (polymorphic_bulge_remover.: 60) 7 iteration: 4 complex bulges were glued 6:08:12.376 4G / 5G INFO PolymorphicBulgeRemover (complex_bulge_remover.hpp : 108) Maximal length of glued bulge: 95547 6:55:23.407 4G / 5G INFO General (polymorphic_bulge_remover.: 60) 8 iteration: 1 complex bulges were glued 6:55:23.408 4G / 5G INFO PolymorphicBulgeRemover (complex_bulge_remover.hpp : 108) Maximal length of glued bulge: 95547 7:42:32.591 4G / 5G INFO General (polymorphic_bulge_remover.: 60) 9 iteration: 0 complex bulges were glued 7:42:32.591 4G / 5G INFO General (polymorphic_bulge_remover.: 62) LightBulgeRemover ends 7:42:32.591 4G / 5G INFO General (polymorphic_bulge_remover.: 103) Index refilling 7:42:32.604 2G / 5G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 7:42:32.604 2G / 5G INFO General (kmer_splitters.hpp : 289) Splitting kmer instances into 16 buckets. This might take a while. 7:42:32.604 2G / 5G INFO General (file_limit.hpp : 29) Open file limit set to 32768 7:42:32.604 2G / 5G INFO General (kmer_splitters.hpp : 307) Memory available for splitting buffers: 32.4401 Gb 7:42:32.604 2G / 5G INFO General (kmer_splitters.hpp : 312) Using cell size of 2097152 7:45:27.997 3G / 5G INFO General (kmer_splitters.hpp : 325) Processed 23095 edges 7:46:07.594 3G / 5G INFO General (kmer_splitters.hpp : 325) Processed 40127 edges 7:46:07.594 3G / 5G INFO General (kmer_splitters.hpp : 330) Used 40127 sequences. 7:46:07.613 2G / 5G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 7:46:24.469 2G / 5G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 57948514 kmers in total. 7:46:24.469 2G / 5G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 7:46:29.102 2G / 5G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 7:47:41.959 2G / 5G INFO General (kmer_index.hpp : 371) Merging final buckets. 7:48:06.865 2G / 5G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 20046604 bytes occupied (2.76751 bits per kmer). 7:48:07.660 3G / 5G INFO General (edge_index_builders.hpp : 21) Collecting k-mer coverage information from graph, this takes a while. 7:49:31.317 3G / 5G INFO General (polymorphic_bulge_remover.: 106) Glueing equal kmers 7:52:07.404 3G / 5G INFO General (equal_sequence_gluer.hpp : 105) 1 kmers glued 7:52:07.404 3G / 5G INFO General (polymorphic_bulge_remover.: 108) Polymorphic ends remover ends 7:52:07.404 3G / 5G INFO General (dipspades.hpp : 96) Consensus graph was constructed 7:52:07.404 3G / 5G INFO General (stage.cpp : 95) PROCEDURE == Consensus contigs construction 7:52:07.404 3G / 5G INFO ConsensusContigsConstruc (consensus_contigs_construc: 274) Consensus contigs constructor starts 7:52:08.805 4G / 5G INFO ConsensusContigsConstruc (consensus_contigs_construc: 51) 14094 contigs from /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_127-dipSPAdes-3.5.0-trimmed/spades/contigs.fasta were read 7:52:08.810 4G / 5G INFO ConsensusContigsConstruc (consensus_contigs_construc: 276) Total: 14094 contigs were read 7:52:51.651 4G / 5G INFO ConsensusContigsConstruc (consensus_contigs_construc: 79) 11 contigs with total length 1015 have mapped path with zero length 7:52:51.876 4G / 5G INFO ConsensusContigsConstruc (consensus_contigs_construc: 105) Removing repetitive edges in contigs mapping starts 7:52:51.922 4G / 5G INFO ConsensusContigsConstruc (consensus_contigs_construc: 109) Removing repetitive edges in contigs mapping ends 7:52:51.922 4G / 5G INFO ConsensusContigsConstruc (consensus_contigs_construc: 111) Close gaps in contigs mappings starts 7:52:51.928 4G / 5G INFO General (close_gaps_corrector.hpp : 83) 710 contigs from 14083 have gaps before correction 7:52:52.010 4G / 5G INFO General (close_gaps_corrector.hpp : 68) 10% contigs were processed 7:52:52.026 4G / 5G INFO General (close_gaps_corrector.hpp : 68) 20% contigs were processed 7:52:52.032 4G / 5G INFO General (close_gaps_corrector.hpp : 68) 30% contigs were processed 7:52:52.036 4G / 5G INFO General (close_gaps_corrector.hpp : 68) 40% contigs were processed 7:52:52.038 4G / 5G INFO General (close_gaps_corrector.hpp : 68) 50% contigs were processed 7:52:52.039 4G / 5G INFO General (close_gaps_corrector.hpp : 68) 60% contigs were processed 7:52:52.039 4G / 5G INFO General (close_gaps_corrector.hpp : 68) 70% contigs were processed 7:52:52.040 4G / 5G INFO General (close_gaps_corrector.hpp : 68) 80% contigs were processed 7:52:52.043 4G / 5G INFO General (close_gaps_corrector.hpp : 68) 90% contigs were processed 7:52:52.046 4G / 5G INFO General (close_gaps_corrector.hpp : 72) 100% contigs were processed 7:52:52.046 4G / 5G INFO General (close_gaps_corrector.hpp : 87) 14082 contigs from 14083 were corrected 7:52:52.046 4G / 5G INFO General (close_gaps_corrector.hpp : 88) 1 contigs from 14083 have gaps after correction 7:52:52.046 4G / 5G INFO ConsensusContigsConstruc (consensus_contigs_construc: 115) Close gaps in contigs mappings ends 7:52:52.046 4G / 5G INFO ConsensusContigsConstruc (consensus_contigs_construc: 117) Removing incorrect contigs 7:52:52.056 4G / 5G INFO General (incorrect_contig_remover.h: 25) 1 contigs from 14083 were deleted 7:52:52.144 4G / 5G INFO ConsensusContigsConstruc (consensus_contigs_construc: 144) Addition of RC contigs. 28164 contigs will be used 7:52:52.146 4G / 5G INFO ConsensusContigsConstruc (consensus_contigs_construc: 149) Redundant contigs remover starts 7:52:52.149 4G / 5G INFO General (iterative_redundant_contig: 30) Equal path remover starts 7:52:52.153 4G / 5G INFO General (path_index.hpp : 27) Initialization of vertex-paths index starts 7:52:52.276 4G / 5G INFO General (path_index.hpp : 40) Initialization of vertex-paths index ends 7:52:52.299 4G / 5G INFO General (equal_path_deletion_correc: 27) Computing redundant equal contigs starts 7:53:05.117 4G / 5G INFO General (equal_path_deletion_correc: 58) 2272 contigs from 28164 are redundant 7:53:05.122 4G / 5G INFO General (equal_path_deletion_correc: 61) Computing redundant equal contigs ends 7:53:05.191 4G / 5G INFO General (iterative_redundant_contig: 36) 25892 contigs will be used further 7:53:05.197 4G / 5G INFO General (iterative_redundant_contig: 39) Iterative loop corrector starts 7:53:05.197 4G / 5G INFO General (iterative_redundant_contig: 41) Only exact match iteration with parameters: 7:53:05.197 4G / 5G INFO General (iterative_redundant_contig: 42) Maximal loop length - 500 7:53:05.197 4G / 5G INFO General (iterative_redundant_contig: 43) Minimal lcs length - 1500 7:53:05.197 4G / 5G INFO General (iterative_redundant_contig: 44) Maximal tail length - 0 7:53:05.198 4G / 5G INFO General (path_index.hpp : 27) Initialization of vertex-paths index starts 7:53:05.313 4G / 5G INFO General (path_index.hpp : 40) Initialization of vertex-paths index ends 7:53:05.313 4G / 5G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 708) Computing redundant contigs starts 7:58:36.420 4G / 5G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 852) 10% contigs were processed 8:02:27.241 4G / 5G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 852) 20% contigs were processed 8:02:29.152 4G / 5G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 852) 30% contigs were processed 8:02:29.245 4G / 5G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 852) 40% contigs were processed 8:02:29.319 4G / 5G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 852) 50% contigs were processed 8:02:29.354 4G / 5G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 852) 60% contigs were processed 8:02:29.392 4G / 5G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 852) 70% contigs were processed 8:02:29.417 4G / 5G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 852) 80% contigs were processed 8:02:29.439 4G / 5G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 852) 90% contigs were processed 8:02:29.899 4G / 5G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 856) 100% contigs were processed 8:02:29.994 4G / 5G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 861) 4036 contigs from 25892 are redundant 8:02:29.999 4G / 5G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 865) Computing redundant contigs ends 8:02:30.313 4G / 5G INFO General (iterative_redundant_contig: 55) 21856 contigs will be used further 8:02:30.332 4G / 5G INFO General (iterative_redundant_contig: 59) Tails allowing match iteration with parameters: 8:02:30.332 4G / 5G INFO General (iterative_redundant_contig: 60) Maximal loop length - 500 8:02:30.332 4G / 5G INFO General (iterative_redundant_contig: 61) Minimal lcs length - 1500 8:02:30.332 4G / 5G INFO General (iterative_redundant_contig: 62) Maximal tail length - 72278 8:02:30.332 4G / 5G INFO General (path_index.hpp : 27) Initialization of vertex-paths index starts 8:02:30.411 4G / 5G INFO General (path_index.hpp : 40) Initialization of vertex-paths index ends 8:02:30.411 4G / 5G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 708) Computing redundant contigs starts 8:05:52.965 4G / 5G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 852) 10% contigs were processed 8:07:05.958 4G / 5G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 852) 20% contigs were processed 8:07:06.186 4G / 5G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 852) 30% contigs were processed 8:07:06.271 4G / 5G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 852) 40% contigs were processed 8:07:06.311 4G / 5G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 852) 50% contigs were processed 8:07:06.335 4G / 5G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 852) 60% contigs were processed 8:07:06.364 4G / 5G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 852) 70% contigs were processed 8:07:06.382 4G / 5G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 852) 80% contigs were processed 8:07:06.397 4G / 5G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 852) 90% contigs were processed 8:07:06.741 4G / 5G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 856) 100% contigs were processed 8:07:06.921 4G / 5G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 861) 4046 contigs from 21856 are redundant 8:07:06.926 4G / 5G INFO LoopBulgeDeletionCorrect (redundant_contig_remover.h: 865) Computing redundant contigs ends 8:07:07.478 4G / 5G INFO General (iterative_redundant_contig: 72) 17810 contigs will be used further 8:07:07.509 4G / 5G INFO General (iterative_redundant_contig: 74) Iterative loop corrector ends 8:07:07.509 4G / 5G INFO ConsensusContigsConstruc (consensus_contigs_construc: 161) Redundant contigs remover ends 8:07:07.523 4G / 5G INFO ConsensusContigsConstruc (consensus_contigs_construc: 166) Overlapping search starts 8:07:07.524 4G / 5G INFO General (path_index.hpp : 27) Initialization of vertex-paths index starts 8:07:07.571 4G / 5G INFO General (path_index.hpp : 40) Initialization of vertex-paths index ends 8:07:07.571 4G / 5G INFO OverlapCorrector (overlap_searcher.hpp : 350) Computing overlaps starts 8:07:29.312 4G / 5G INFO OverlapCorrector (overlap_searcher.hpp : 478) Overlap graph with 17810 vertices and 58 edges constructed 8:07:29.342 4G / 5G INFO General (overlap_graph.hpp :1100) 4 tips and 0 transitive edges were deleted in overlap graph 8:07:29.342 4G / 5G INFO General (overlap_graph.hpp :1100) 0 tips and 0 transitive edges were deleted in overlap graph 8:07:29.342 4G / 5G INFO General (overlap_graph.hpp :1103) Bulge remover starts 8:08:27.454 4G / 5G INFO General (overlap_graph.hpp :1108) 0 bulges were deleted in overlap graph 8:08:27.457 4G / 5G INFO OverlapCorrector (overlap_searcher.hpp : 486) Simplified overlap graph contains 17806 vertices and 54 edges 8:08:55.918 4G / 5G INFO OverlapCorrector (overlap_searcher.hpp : 525) Computing overlaps ends 8:08:55.953 4G / 5G INFO ConsensusContigsConstruc (consensus_contigs_construc: 174) Overlapping search ends 8:08:56.376 4G / 5G INFO ConsensusContigsConstruc (consensus_contigs_construc: 190) 8876 with total length 29251637 were written in /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_127-dipSPAdes-3.5.0-trimmed/dipspades/consensus_contigs.fasta 8:08:56.588 4G / 5G INFO ConsensusContigsConstruc (consensus_contigs_construc: 190) 623 with total length 25790092 were written in /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_127-dipSPAdes-3.5.0-trimmed/dipspades/paired_consensus_contigs.fasta 8:08:56.805 4G / 5G INFO ConsensusContigsConstruc (consensus_contigs_construc: 190) 8253 with total length 3461545 were written in /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_127-dipSPAdes-3.5.0-trimmed/dipspades/unpaired_consensus_contigs.fasta 8:08:56.806 4G / 5G INFO ConsensusContigsConstruc (consensus_contigs_construc: 216) Writing haplocontigs alignment to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_127-dipSPAdes-3.5.0-trimmed/dipspades/haplocontigs_alignment 8:09:02.029 4G / 5G INFO ConsensusContigsConstruc (consensus_contigs_construc: 311) Consensus contigs constructor ends 8:09:02.049 4G / 5G INFO General (dipspades.hpp : 211) dipSPAdes finished 8:09:19.921 128M / 5G INFO General (main.cpp : 115) Assembling time: 8 hours 9 minutes 20 seconds ===== Assembling finished. * Assembled consensus contigs are in: /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_127-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_127-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_127-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_127-dipSPAdes-3.5.0-trimmed/dipspades/dipspades.log Thank you for using dipSPAdes!