Command line: /Users/Mike_Lee/happy_bin/SPAdes-3.11.1-Darwin/bin/spades.py -1 /Users/Mike_Lee/working_genomics_de_novo_temp/BCep_R1_QCd_err_cor.fastq.gz -2 /Users/Mike_Lee/working_genomics_de_novo_temp/BCep_R2_QCd_err_cor.fastq.gz -o /Users/Mike_Lee/working_genomics_de_novo_temp/spades_default_assembly -t 4 --only-assembler System information: SPAdes version: 3.11.1 Python version: 2.7.10 OS: Darwin-17.3.0-x86_64-i386-64bit Output dir: /Users/Mike_Lee/working_genomics_de_novo_temp/spades_default_assembly Mode: ONLY assembling (without read error correction) Debug mode is turned OFF Dataset parameters: Multi-cell mode (you should set '--sc' flag if input data was obtained with MDA (single-cell) technology or --meta flag if processing metagenomic dataset) Reads: Library number: 1, library type: paired-end orientation: fr left reads: ['/Users/Mike_Lee/working_genomics_de_novo_temp/BCep_R1_QCd_err_cor.fastq.gz'] right reads: ['/Users/Mike_Lee/working_genomics_de_novo_temp/BCep_R2_QCd_err_cor.fastq.gz'] interlaced reads: not specified single reads: not specified Assembly parameters: k: automatic selection based on read length Repeat resolution is enabled Mismatch careful mode is turned OFF MismatchCorrector will be SKIPPED Coverage cutoff is turned OFF Other parameters: Dir for temp files: /Users/Mike_Lee/working_genomics_de_novo_temp/spades_default_assembly/tmp Threads: 4 Memory limit (in Gb): 250 ======= SPAdes pipeline started. Log can be found here: /Users/Mike_Lee/working_genomics_de_novo_temp/spades_default_assembly/spades.log ===== Assembling started. == Running assembler: K21 0:00:00.000 4M / 4M INFO General (main.cpp : 76) Loading config from /Users/Mike_Lee/working_genomics_de_novo_temp/spades_default_assembly/K21/configs/config.info 0:00:00.001 4M / 4M INFO General (memory_limit.hpp : 51) Memory limit set to 250 Gb 0:00:00.001 4M / 4M INFO General (main.cpp : 89) Starting SPAdes, built from N/A, git revision N/A 0:00:00.001 4M / 4M INFO General (main.cpp : 90) Maximum k-mer length: 128 0:00:00.001 4M / 4M INFO General (main.cpp : 91) Assembling dataset (/Users/Mike_Lee/working_genomics_de_novo_temp/spades_default_assembly/dataset.info) with K=21 0:00:00.001 4M / 4M INFO General (launch.hpp : 51) SPAdes started 0:00:00.001 4M / 4M INFO General (launch.hpp : 58) Starting from stage: construction 0:00:00.001 4M / 4M INFO General (launch.hpp : 61) Two-step RR enabled: 0 0:00:00.002 4M / 4M INFO StageManager (stage.cpp : 126) STAGE == Construction 0:00:00.004 4M / 4M INFO General (read_converter.hpp : 84) Converting reads to binary format for library #0 (takes a while) 0:00:00.004 4M / 4M INFO General (read_converter.hpp : 85) Converting paired reads 0:00:00.353 80M / 84M INFO General (binary_converter.hpp : 139) 16384 reads processed 0:00:00.560 92M / 92M INFO General (binary_converter.hpp : 139) 32768 reads processed 0:00:00.948 116M / 116M INFO General (binary_converter.hpp : 139) 65536 reads processed 0:00:01.852 164M / 164M INFO General (binary_converter.hpp : 139) 131072 reads processed 0:00:03.397 264M / 264M INFO General (binary_converter.hpp : 139) 262144 reads processed 0:00:07.096 320M / 320M INFO General (binary_converter.hpp : 139) 524288 reads processed 0:00:14.154 344M / 344M INFO General (binary_converter.hpp : 139) 1048576 reads processed 0:00:20.280 288M / 352M INFO General (binary_converter.hpp : 159) 1484726 reads written 0:00:20.527 4M / 352M INFO General (read_converter.hpp : 94) Converting single reads 0:00:20.715 132M / 352M INFO General (binary_converter.hpp : 159) 0 reads written 0:00:20.768 4M / 352M INFO General (graph_construction.hpp : 120) Constructing DeBruijn graph for k=21 0:00:20.879 4M / 352M INFO General (kmer_index_builder.hpp : 106) Splitting kmer instances into 16 buckets using 4 threads. This might take a while. 0:00:20.881 4M / 352M INFO General (file_limit.hpp : 32) Open file limit set to 7168 0:00:20.882 4M / 352M INFO General (kmer_splitters.hpp : 74) Memory available for splitting buffers: 20.833 Gb 0:00:20.882 4M / 352M INFO General (kmer_splitters.hpp : 82) Using cell size of 4194304 0:00:46.854 2G / 2G INFO General (kmer_splitters.hpp : 291) Processed 4501245 reads 0:00:53.619 2G / 2G INFO General (kmer_splitters.hpp : 291) Processed 5938904 reads 0:00:53.619 2G / 2G INFO General (kmer_splitters.hpp : 297) Adding contigs from previous K 0:00:53.859 16M / 2G INFO General (kmer_splitters.hpp : 310) Used 5938904 reads. Maximum read length 140 0:00:53.859 16M / 2G INFO General (kmer_splitters.hpp : 311) Average read length 140 0:00:53.859 16M / 2G INFO General (kmer_index_builder.hpp : 109) Starting k-mer counting. 0:00:55.352 16M / 2G INFO General (kmer_index_builder.hpp : 115) K-mer counting done. There are 10173588 kmers in total. 0:00:55.352 16M / 2G INFO General (kmer_index_builder.hpp : 121) Merging temporary buckets. 0:00:55.467 16M / 2G INFO K-mer Index Building (kmer_index_builder.hpp : 289) Building kmer index 0:00:55.467 16M / 2G INFO General (kmer_index_builder.hpp : 106) Splitting kmer instances into 64 buckets using 4 threads. This might take a while. 0:00:55.467 16M / 2G INFO General (file_limit.hpp : 32) Open file limit set to 7168 0:00:55.467 16M / 2G INFO General (kmer_splitters.hpp : 74) Memory available for splitting buffers: 20.832 Gb 0:00:55.467 16M / 2G INFO General (kmer_splitters.hpp : 82) Using cell size of 1048576 0:00:57.672 3G / 3G INFO General (kmer_splitters.hpp : 381) Processed 10173588 kmers 0:00:57.672 3G / 3G INFO General (kmer_splitters.hpp : 386) Used 10173588 kmers. 0:00:57.702 16M / 3G INFO General (kmer_index_builder.hpp : 109) Starting k-mer counting. 0:00:58.715 16M / 3G INFO General (kmer_index_builder.hpp : 115) K-mer counting done. There are 10096148 kmers in total. 0:00:58.715 16M / 3G INFO General (kmer_index_builder.hpp : 121) Merging temporary buckets. 0:00:58.853 16M / 3G INFO K-mer Index Building (kmer_index_builder.hpp : 298) Building perfect hash indices 0:00:59.778 16M / 3G INFO General (kmer_index_builder.hpp : 137) Merging final buckets. 0:00:59.891 16M / 3G INFO K-mer Index Building (kmer_index_builder.hpp : 320) Index built. Total 4689888 bytes occupied (3.71618 bits per kmer). 0:00:59.902 28M / 3G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 87) Building k-mer extensions from k+1-mers 0:01:02.536 28M / 3G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 91) Building k-mer extensions from k+1-mers finished. 0:01:02.536 28M / 3G INFO Early tip clipping (early_simplification.hpp : 181) Early tip clipping 0:01:09.132 28M / 3G INFO Early tip clipping (early_simplification.hpp : 184) 550174 22-mers were removed by early tip clipper 0:01:09.132 28M / 3G INFO General (graph_construction.hpp : 136) Condensing graph 0:01:09.177 28M / 3G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 355) Extracting unbranching paths 0:01:12.055 40M / 3G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 374) Extracting unbranching paths finished. 221440 sequences extracted 0:01:13.427 40M / 3G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 310) Collecting perfect loops 0:01:14.078 40M / 3G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 343) Collecting perfect loops finished. 2 loops collected 0:01:14.301 92M / 3G INFO General (graph_construction.hpp : 141) Building index with from graph 0:01:14.302 92M / 3G INFO K-mer Index Building (kmer_index_builder.hpp : 289) Building kmer index 0:01:14.302 92M / 3G INFO General (kmer_index_builder.hpp : 106) Splitting kmer instances into 64 buckets using 4 threads. This might take a while. 0:01:14.302 92M / 3G INFO General (file_limit.hpp : 32) Open file limit set to 7168 0:01:14.302 92M / 3G INFO General (kmer_splitters.hpp : 74) Memory available for splitting buffers: 20.8258 Gb 0:01:14.302 92M / 3G INFO General (kmer_splitters.hpp : 82) Using cell size of 1048576 0:01:15.263 3G / 3G INFO General (edge_index_builders.hpp : 75) Processed 441975 edges 0:01:15.263 3G / 3G INFO General (edge_index_builders.hpp : 80) Used 441975 sequences. 0:01:15.272 92M / 3G INFO General (kmer_index_builder.hpp : 109) Starting k-mer counting. 0:01:16.043 92M / 3G INFO General (kmer_index_builder.hpp : 115) K-mer counting done. There are 9623414 kmers in total. 0:01:16.043 92M / 3G INFO General (kmer_index_builder.hpp : 121) Merging temporary buckets. 0:01:16.167 92M / 3G INFO K-mer Index Building (kmer_index_builder.hpp : 298) Building perfect hash indices 0:01:16.895 96M / 3G INFO General (kmer_index_builder.hpp : 137) Merging final buckets. 0:01:17.012 96M / 3G INFO K-mer Index Building (kmer_index_builder.hpp : 320) Index built. Total 4470584 bytes occupied (3.71642 bits per kmer). 0:01:17.163 320M / 3G INFO General (edge_index_builders.hpp : 105) Collecting k-mer coverage information from graph, this takes a while. 0:01:18.248 320M / 3G INFO General (edge_index.hpp : 91) Index refilled 0:01:18.262 308M / 3G INFO General (graph_construction.hpp : 173) Filling coverage index 0:01:18.262 308M / 3G INFO General (edge_index_builders.hpp : 183) Collecting k-mer coverage information from reads, this takes a while. 0:02:17.247 304M / 3G INFO General (graph_construction.hpp : 175) Filling coverage and flanking coverage from index 0:02:18.483 304M / 3G INFO General (construction.cpp : 30) Figured out: read length = 140 0:02:18.483 304M / 3G INFO StageManager (stage.cpp : 126) STAGE == EC Threshold Finding 0:02:18.830 304M / 3G INFO General (kmer_coverage_model.cpp : 181) Kmer coverage valley at: 7 0:02:18.830 304M / 3G INFO General (kmer_coverage_model.cpp : 201) K-mer histogram maximum: 40 0:02:18.830 304M / 3G INFO General (kmer_coverage_model.cpp : 237) Estimated median coverage: 41. Coverage mad: 13.3434 0:02:18.830 304M / 3G INFO General (kmer_coverage_model.cpp : 259) Fitting coverage model 0:02:18.877 304M / 3G INFO General (kmer_coverage_model.cpp : 295) ... iteration 2 0:02:18.982 304M / 3G INFO General (kmer_coverage_model.cpp : 295) ... iteration 4 0:02:19.364 304M / 3G INFO General (kmer_coverage_model.cpp : 295) ... iteration 8 0:02:20.152 304M / 3G INFO General (kmer_coverage_model.cpp : 295) ... iteration 16 0:02:21.069 304M / 3G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 41.213. Fitted coverage std. dev: 11.1916 0:02:21.071 304M / 3G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 0.776085 0:02:21.071 304M / 3G INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 18 0:02:21.071 304M / 3G INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 18 0:02:21.071 304M / 3G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 8270101 0:02:21.071 304M / 3G INFO General (genomic_info_filler.cpp : 127) Mean coverage was calculated as 41.213 0:02:21.071 304M / 3G INFO General (genomic_info_filler.cpp : 141) EC coverage threshold value was calculated as 18 0:02:21.071 304M / 3G INFO General (genomic_info_filler.cpp : 142) Trusted kmer low bound: 0 0:02:21.071 304M / 3G INFO StageManager (stage.cpp : 126) STAGE == Simplification 0:02:21.099 72M / 3G INFO General (simplification.cpp : 387) Graph simplification started 0:02:21.099 72M / 3G INFO General (simplification.cpp : 77) PROCEDURE == InitialCleaning 0:02:21.101 72M / 3G INFO General (graph_simplification.hpp : 645) Flanking coverage based disconnection disabled 0:02:21.101 72M / 3G INFO General (simplification.cpp : 356) Running Self conjugate edge remover 0:02:21.151 72M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:02:21.151 72M / 3G INFO General (simplification.cpp : 356) Running Initial isolated edge remover 0:02:21.204 72M / 3G INFO General (simplification.cpp : 358) Triggered 182 times 0:02:21.204 72M / 3G INFO General (simplification.cpp : 356) Running Initial tip clipper 0:02:21.272 68M / 3G INFO General (simplification.cpp : 358) Triggered 223 times 0:02:21.272 68M / 3G INFO General (simplification.cpp : 356) Running Initial ec remover 0:02:24.254 76M / 3G INFO General (simplification.cpp : 358) Triggered 58093 times 0:02:24.284 76M / 3G INFO General (graph_simplification.hpp : 617) Creating parallel br instance 0:02:24.284 76M / 3G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 1 0:02:24.284 76M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:02:24.317 76M / 3G INFO General (simplification.cpp : 358) Triggered 118 times 0:02:24.318 76M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:02:25.250 76M / 3G INFO General (simplification.cpp : 358) Triggered 8159 times 0:02:25.250 76M / 3G INFO General (simplification.cpp : 356) Running Low coverage edge remover 0:02:25.297 76M / 3G INFO General (simplification.cpp : 358) Triggered 678 times 0:02:25.297 76M / 3G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 2 0:02:25.297 76M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:02:25.304 76M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:02:25.304 76M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:02:25.308 76M / 3G INFO General (simplification.cpp : 358) Triggered 18 times 0:02:25.308 76M / 3G INFO General (simplification.cpp : 356) Running Low coverage edge remover 0:02:25.488 72M / 3G INFO General (simplification.cpp : 358) Triggered 2954 times 0:02:25.488 72M / 3G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 3 0:02:25.488 72M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:02:25.490 72M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:02:25.490 72M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:02:25.516 72M / 3G INFO General (simplification.cpp : 358) Triggered 90 times 0:02:25.516 72M / 3G INFO General (simplification.cpp : 356) Running Low coverage edge remover 0:02:25.599 72M / 3G INFO General (simplification.cpp : 358) Triggered 827 times 0:02:25.599 72M / 3G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 4 0:02:25.599 72M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:02:25.601 72M / 3G INFO General (simplification.cpp : 358) Triggered 1 times 0:02:25.601 72M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:02:25.607 72M / 3G INFO General (simplification.cpp : 358) Triggered 15 times 0:02:25.607 72M / 3G INFO General (simplification.cpp : 356) Running Low coverage edge remover 0:02:25.617 72M / 3G INFO General (simplification.cpp : 358) Triggered 138 times 0:02:25.617 72M / 3G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 5 0:02:25.617 72M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:02:25.617 72M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:02:25.617 72M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:02:25.619 72M / 3G INFO General (simplification.cpp : 358) Triggered 6 times 0:02:25.619 72M / 3G INFO General (simplification.cpp : 356) Running Low coverage edge remover 0:02:25.622 72M / 3G INFO General (simplification.cpp : 358) Triggered 48 times 0:02:25.622 72M / 3G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 6 0:02:25.622 72M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:02:25.622 72M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:02:25.622 72M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:02:25.624 72M / 3G INFO General (simplification.cpp : 358) Triggered 6 times 0:02:25.625 72M / 3G INFO General (simplification.cpp : 356) Running Low coverage edge remover 0:02:25.626 72M / 3G INFO General (simplification.cpp : 358) Triggered 30 times 0:02:25.626 72M / 3G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 7 0:02:25.626 72M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:02:25.626 72M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:02:25.626 72M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:02:25.627 72M / 3G INFO General (simplification.cpp : 358) Triggered 5 times 0:02:25.627 72M / 3G INFO General (simplification.cpp : 356) Running Low coverage edge remover 0:02:25.630 72M / 3G INFO General (simplification.cpp : 358) Triggered 40 times 0:02:25.630 72M / 3G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 8 0:02:25.630 72M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:02:25.630 72M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:02:25.630 72M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:02:25.631 72M / 3G INFO General (simplification.cpp : 358) Triggered 1 times 0:02:25.631 72M / 3G INFO General (simplification.cpp : 356) Running Low coverage edge remover 0:02:25.634 72M / 3G INFO General (simplification.cpp : 358) Triggered 34 times 0:02:25.634 72M / 3G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 9 0:02:25.634 72M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:02:25.634 72M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:02:25.634 72M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:02:25.635 72M / 3G INFO General (simplification.cpp : 358) Triggered 1 times 0:02:25.635 72M / 3G INFO General (simplification.cpp : 356) Running Low coverage edge remover 0:02:25.638 72M / 3G INFO General (simplification.cpp : 358) Triggered 32 times 0:02:25.638 72M / 3G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 10 0:02:25.638 72M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:02:25.644 72M / 3G INFO General (simplification.cpp : 358) Triggered 2 times 0:02:25.644 72M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:02:25.718 72M / 3G INFO General (simplification.cpp : 358) Triggered 7 times 0:02:25.718 72M / 3G INFO General (simplification.cpp : 356) Running Low coverage edge remover 0:02:25.728 72M / 3G INFO General (simplification.cpp : 358) Triggered 37 times 0:02:25.728 72M / 3G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 11 0:02:25.728 72M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:02:25.728 72M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:02:25.728 72M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:02:25.729 72M / 3G INFO General (simplification.cpp : 358) Triggered 1 times 0:02:25.729 72M / 3G INFO General (simplification.cpp : 356) Running Low coverage edge remover 0:02:25.729 72M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:02:25.729 72M / 3G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 12 0:02:25.729 72M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:02:25.729 72M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:02:25.729 72M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:02:25.729 72M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:02:25.729 72M / 3G INFO General (simplification.cpp : 356) Running Low coverage edge remover 0:02:25.729 72M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:02:25.729 72M / 3G INFO General (simplification.cpp : 167) PROCEDURE == Post simplification 0:02:25.729 72M / 3G INFO General (graph_simplification.hpp : 447) Disconnection of relatively low covered edges disabled 0:02:25.729 72M / 3G INFO General (graph_simplification.hpp : 477) Complex tip clipping disabled 0:02:25.729 72M / 3G INFO General (graph_simplification.hpp : 617) Creating parallel br instance 0:02:25.730 72M / 3G INFO General (simplification.cpp : 301) Iteration 1 0:02:25.730 72M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:02:25.741 72M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:02:25.741 72M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:02:25.809 72M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:02:25.809 72M / 3G INFO General (simplification.cpp : 301) Iteration 2 0:02:25.809 72M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:02:25.820 72M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:02:25.820 72M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:02:25.902 72M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:02:25.902 72M / 3G INFO General (simplification.cpp : 333) Disrupting self-conjugate edges 0:02:25.930 72M / 3G INFO StageManager (stage.cpp : 126) STAGE == Simplification Cleanup 0:02:25.930 72M / 3G INFO General (simplification.cpp : 547) Removing isolated edges 0:02:25.939 72M / 3G INFO General (simplification.cpp : 570) Counting average coverage 0:02:25.952 72M / 3G INFO General (simplification.cpp : 575) Average coverage = 41.9907 0:02:25.952 72M / 3G INFO StageManager (stage.cpp : 126) STAGE == Contig Output 0:02:25.954 72M / 3G INFO General (contig_output_stage.cpp : 40) Writing GFA to /Users/Mike_Lee/working_genomics_de_novo_temp/spades_default_assembly//K21/assembly_graph_with_scaffolds.gfa 0:02:26.322 72M / 3G INFO General (contig_output.hpp : 22) Outputting contigs to /Users/Mike_Lee/working_genomics_de_novo_temp/spades_default_assembly//K21/before_rr.fasta 0:02:26.700 72M / 3G INFO General (contig_output_stage.cpp : 50) Outputting FastG graph to /Users/Mike_Lee/working_genomics_de_novo_temp/spades_default_assembly//K21/assembly_graph.fastg 0:02:27.356 72M / 3G INFO General (contig_output.hpp : 22) Outputting contigs to /Users/Mike_Lee/working_genomics_de_novo_temp/spades_default_assembly//K21/simplified_contigs.fasta 0:02:27.745 72M / 3G INFO General (contig_output.hpp : 22) Outputting contigs to /Users/Mike_Lee/working_genomics_de_novo_temp/spades_default_assembly//K21/final_contigs.fasta 0:02:28.066 72M / 3G INFO StageManager (stage.cpp : 126) STAGE == Contig Output 0:02:28.066 72M / 3G INFO General (contig_output_stage.cpp : 40) Writing GFA to /Users/Mike_Lee/working_genomics_de_novo_temp/spades_default_assembly//K21/assembly_graph_with_scaffolds.gfa 0:02:28.220 72M / 3G INFO General (contig_output.hpp : 22) Outputting contigs to /Users/Mike_Lee/working_genomics_de_novo_temp/spades_default_assembly//K21/before_rr.fasta 0:02:28.637 72M / 3G INFO General (contig_output_stage.cpp : 50) Outputting FastG graph to /Users/Mike_Lee/working_genomics_de_novo_temp/spades_default_assembly//K21/assembly_graph.fastg 0:02:29.214 72M / 3G INFO General (contig_output.hpp : 22) Outputting contigs to /Users/Mike_Lee/working_genomics_de_novo_temp/spades_default_assembly//K21/simplified_contigs.fasta 0:02:29.506 72M / 3G INFO General (contig_output.hpp : 22) Outputting contigs to /Users/Mike_Lee/working_genomics_de_novo_temp/spades_default_assembly//K21/final_contigs.fasta 0:02:29.917 72M / 3G INFO General (launch.hpp : 137) SPAdes finished 0:02:30.034 16M / 3G INFO General (main.cpp : 110) Assembling time: 0 hours 2 minutes 30 seconds == Running assembler: K33 0:00:00.000 4M / 4M INFO General (main.cpp : 76) Loading config from /Users/Mike_Lee/working_genomics_de_novo_temp/spades_default_assembly/K33/configs/config.info 0:00:00.000 4M / 4M INFO General (memory_limit.hpp : 51) Memory limit set to 250 Gb 0:00:00.000 4M / 4M INFO General (main.cpp : 89) Starting SPAdes, built from N/A, git revision N/A 0:00:00.000 4M / 4M INFO General (main.cpp : 90) Maximum k-mer length: 128 0:00:00.000 4M / 4M INFO General (main.cpp : 91) Assembling dataset (/Users/Mike_Lee/working_genomics_de_novo_temp/spades_default_assembly/dataset.info) with K=33 0:00:00.000 4M / 4M INFO General (launch.hpp : 51) SPAdes started 0:00:00.000 4M / 4M INFO General (launch.hpp : 58) Starting from stage: construction 0:00:00.000 4M / 4M INFO General (launch.hpp : 61) Two-step RR enabled: 0 0:00:00.001 4M / 4M INFO StageManager (stage.cpp : 126) STAGE == Construction 0:00:00.001 4M / 4M INFO General (read_converter.hpp : 67) Binary reads detected 0:00:00.002 4M / 4M INFO General (graph_construction.hpp : 120) Constructing DeBruijn graph for k=33 0:00:00.002 4M / 4M INFO General (kmer_index_builder.hpp : 106) Splitting kmer instances into 16 buckets using 4 threads. This might take a while. 0:00:00.002 4M / 4M INFO General (file_limit.hpp : 32) Open file limit set to 7168 0:00:00.002 4M / 4M INFO General (kmer_splitters.hpp : 74) Memory available for splitting buffers: 20.833 Gb 0:00:00.002 4M / 4M INFO General (kmer_splitters.hpp : 82) Using cell size of 2097152 0:00:16.325 2G / 2G INFO General (kmer_splitters.hpp : 291) Processed 2500256 reads 0:00:31.117 2G / 2G INFO General (kmer_splitters.hpp : 291) Processed 5002200 reads 0:00:36.822 2G / 2G INFO General (kmer_splitters.hpp : 291) Processed 5938904 reads 0:00:36.822 2G / 2G INFO General (kmer_splitters.hpp : 297) Adding contigs from previous K 0:00:38.631 16M / 2G INFO General (kmer_splitters.hpp : 310) Used 5938904 reads. Maximum read length 140 0:00:38.631 16M / 2G INFO General (kmer_splitters.hpp : 311) Average read length 140 0:00:38.631 16M / 2G INFO General (kmer_index_builder.hpp : 109) Starting k-mer counting. 0:00:42.514 16M / 2G INFO General (kmer_index_builder.hpp : 115) K-mer counting done. There are 10745487 kmers in total. 0:00:42.514 16M / 2G INFO General (kmer_index_builder.hpp : 121) Merging temporary buckets. 0:00:42.766 16M / 2G INFO K-mer Index Building (kmer_index_builder.hpp : 289) Building kmer index 0:00:42.766 16M / 2G INFO General (kmer_index_builder.hpp : 106) Splitting kmer instances into 64 buckets using 4 threads. This might take a while. 0:00:42.766 16M / 2G INFO General (file_limit.hpp : 32) Open file limit set to 7168 0:00:42.766 16M / 2G INFO General (kmer_splitters.hpp : 74) Memory available for splitting buffers: 20.832 Gb 0:00:42.766 16M / 2G INFO General (kmer_splitters.hpp : 82) Using cell size of 524288 0:00:45.524 3G / 3G INFO General (kmer_splitters.hpp : 381) Processed 10745487 kmers 0:00:45.524 3G / 3G INFO General (kmer_splitters.hpp : 386) Used 10745487 kmers. 0:00:45.569 16M / 3G INFO General (kmer_index_builder.hpp : 109) Starting k-mer counting. 0:00:46.561 16M / 3G INFO General (kmer_index_builder.hpp : 115) K-mer counting done. There are 10709744 kmers in total. 0:00:46.561 16M / 3G INFO General (kmer_index_builder.hpp : 121) Merging temporary buckets. 0:00:46.801 16M / 3G INFO K-mer Index Building (kmer_index_builder.hpp : 298) Building perfect hash indices 0:00:47.623 16M / 3G INFO General (kmer_index_builder.hpp : 137) Merging final buckets. 0:00:47.857 16M / 3G INFO K-mer Index Building (kmer_index_builder.hpp : 320) Index built. Total 4973992 bytes occupied (3.71549 bits per kmer). 0:00:47.867 28M / 3G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 87) Building k-mer extensions from k+1-mers 0:00:50.158 28M / 3G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 91) Building k-mer extensions from k+1-mers finished. 0:00:50.159 28M / 3G INFO Early tip clipping (early_simplification.hpp : 181) Early tip clipping 0:00:56.340 28M / 3G INFO Early tip clipping (early_simplification.hpp : 184) 1082368 34-mers were removed by early tip clipper 0:00:56.340 28M / 3G INFO General (graph_construction.hpp : 136) Condensing graph 0:00:56.544 28M / 3G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 355) Extracting unbranching paths 0:01:00.670 32M / 3G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 374) Extracting unbranching paths finished. 108656 sequences extracted 0:01:02.479 32M / 3G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 310) Collecting perfect loops 0:01:03.557 32M / 3G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 343) Collecting perfect loops finished. 0 loops collected 0:01:03.669 64M / 3G INFO General (graph_construction.hpp : 141) Building index with from graph 0:01:03.669 64M / 3G INFO K-mer Index Building (kmer_index_builder.hpp : 289) Building kmer index 0:01:03.669 64M / 3G INFO General (kmer_index_builder.hpp : 106) Splitting kmer instances into 64 buckets using 4 threads. This might take a while. 0:01:03.669 64M / 3G INFO General (file_limit.hpp : 32) Open file limit set to 7168 0:01:03.669 64M / 3G INFO General (kmer_splitters.hpp : 74) Memory available for splitting buffers: 20.8281 Gb 0:01:03.669 64M / 3G INFO General (kmer_splitters.hpp : 82) Using cell size of 524288 0:01:04.791 3G / 3G INFO General (edge_index_builders.hpp : 75) Processed 216999 edges 0:01:04.791 3G / 3G INFO General (edge_index_builders.hpp : 80) Used 216999 sequences. 0:01:04.814 64M / 3G INFO General (kmer_index_builder.hpp : 109) Starting k-mer counting. 0:01:05.719 64M / 3G INFO General (kmer_index_builder.hpp : 115) K-mer counting done. There are 9663119 kmers in total. 0:01:05.719 64M / 3G INFO General (kmer_index_builder.hpp : 121) Merging temporary buckets. 0:01:05.972 64M / 3G INFO K-mer Index Building (kmer_index_builder.hpp : 298) Building perfect hash indices 0:01:06.833 64M / 3G INFO General (kmer_index_builder.hpp : 137) Merging final buckets. 0:01:07.064 64M / 3G INFO K-mer Index Building (kmer_index_builder.hpp : 320) Index built. Total 4488872 bytes occupied (3.71629 bits per kmer). 0:01:07.221 288M / 3G INFO General (edge_index_builders.hpp : 105) Collecting k-mer coverage information from graph, this takes a while. 0:01:08.855 288M / 3G INFO General (edge_index.hpp : 91) Index refilled 0:01:08.890 276M / 3G INFO General (graph_construction.hpp : 173) Filling coverage index 0:01:08.890 276M / 3G INFO General (edge_index_builders.hpp : 183) Collecting k-mer coverage information from reads, this takes a while. 0:02:25.728 272M / 3G INFO General (graph_construction.hpp : 175) Filling coverage and flanking coverage from index 0:02:26.696 272M / 3G INFO General (construction.cpp : 30) Figured out: read length = 140 0:02:26.697 272M / 3G INFO StageManager (stage.cpp : 126) STAGE == EC Threshold Finding 0:02:27.046 276M / 3G INFO General (kmer_coverage_model.cpp : 181) Kmer coverage valley at: 5 0:02:27.046 276M / 3G INFO General (kmer_coverage_model.cpp : 201) K-mer histogram maximum: 35 0:02:27.046 276M / 3G INFO General (kmer_coverage_model.cpp : 237) Estimated median coverage: 37. Coverage mad: 11.8608 0:02:27.046 276M / 3G INFO General (kmer_coverage_model.cpp : 259) Fitting coverage model 0:02:27.079 276M / 3G INFO General (kmer_coverage_model.cpp : 295) ... iteration 2 0:02:27.169 276M / 3G INFO General (kmer_coverage_model.cpp : 295) ... iteration 4 0:02:27.486 276M / 3G INFO General (kmer_coverage_model.cpp : 295) ... iteration 8 0:02:28.175 276M / 3G INFO General (kmer_coverage_model.cpp : 295) ... iteration 16 0:02:29.007 276M / 3G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 37.0011. Fitted coverage std. dev: 10.2612 0:02:29.008 276M / 3G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 0.90626 0:02:29.008 276M / 3G INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 17 0:02:29.008 276M / 3G INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 17 0:02:29.008 276M / 3G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 8243812 0:02:29.008 276M / 3G INFO General (genomic_info_filler.cpp : 127) Mean coverage was calculated as 37.0011 0:02:29.008 276M / 3G INFO General (genomic_info_filler.cpp : 141) EC coverage threshold value was calculated as 17 0:02:29.008 276M / 3G INFO General (genomic_info_filler.cpp : 142) Trusted kmer low bound: 0 0:02:29.008 276M / 3G INFO StageManager (stage.cpp : 126) STAGE == Simplification 0:02:29.031 44M / 3G INFO General (simplification.cpp : 387) Graph simplification started 0:02:29.031 44M / 3G INFO General (simplification.cpp : 77) PROCEDURE == InitialCleaning 0:02:29.031 44M / 3G INFO General (graph_simplification.hpp : 645) Flanking coverage based disconnection disabled 0:02:29.031 44M / 3G INFO General (simplification.cpp : 356) Running Self conjugate edge remover 0:02:29.049 44M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:02:29.049 44M / 3G INFO General (simplification.cpp : 356) Running Initial isolated edge remover 0:02:29.070 44M / 3G INFO General (simplification.cpp : 358) Triggered 215 times 0:02:29.070 44M / 3G INFO General (simplification.cpp : 356) Running Initial tip clipper 0:02:29.108 44M / 3G INFO General (simplification.cpp : 358) Triggered 605 times 0:02:29.108 44M / 3G INFO General (simplification.cpp : 356) Running Initial ec remover 0:02:30.510 48M / 3G INFO General (simplification.cpp : 358) Triggered 25922 times 0:02:30.522 48M / 3G INFO General (graph_simplification.hpp : 617) Creating parallel br instance 0:02:30.522 48M / 3G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 1 0:02:30.522 48M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:02:30.538 48M / 3G INFO General (simplification.cpp : 358) Triggered 150 times 0:02:30.538 48M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:02:31.166 40M / 3G INFO General (simplification.cpp : 358) Triggered 7948 times 0:02:31.166 40M / 3G INFO General (simplification.cpp : 356) Running Low coverage edge remover 0:02:31.305 40M / 3G INFO General (simplification.cpp : 358) Triggered 1073 times 0:02:31.305 40M / 3G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 2 0:02:31.305 40M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:02:31.306 40M / 3G INFO General (simplification.cpp : 358) Triggered 2 times 0:02:31.307 40M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:02:31.309 40M / 3G INFO General (simplification.cpp : 358) Triggered 16 times 0:02:31.309 40M / 3G INFO General (simplification.cpp : 356) Running Low coverage edge remover 0:02:31.372 40M / 3G INFO General (simplification.cpp : 358) Triggered 357 times 0:02:31.372 40M / 3G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 3 0:02:31.372 40M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:02:31.372 40M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:02:31.372 40M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:02:31.374 40M / 3G INFO General (simplification.cpp : 358) Triggered 16 times 0:02:31.374 40M / 3G INFO General (simplification.cpp : 356) Running Low coverage edge remover 0:02:31.378 40M / 3G INFO General (simplification.cpp : 358) Triggered 57 times 0:02:31.378 40M / 3G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 4 0:02:31.378 40M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:02:31.378 40M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:02:31.378 40M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:02:31.379 40M / 3G INFO General (simplification.cpp : 358) Triggered 5 times 0:02:31.379 40M / 3G INFO General (simplification.cpp : 356) Running Low coverage edge remover 0:02:31.380 40M / 3G INFO General (simplification.cpp : 358) Triggered 13 times 0:02:31.380 40M / 3G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 5 0:02:31.380 40M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:02:31.380 40M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:02:31.380 40M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:02:31.380 40M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:02:31.380 40M / 3G INFO General (simplification.cpp : 356) Running Low coverage edge remover 0:02:31.383 40M / 3G INFO General (simplification.cpp : 358) Triggered 12 times 0:02:31.383 40M / 3G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 6 0:02:31.383 40M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:02:31.383 40M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:02:31.383 40M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:02:31.383 40M / 3G INFO General (simplification.cpp : 358) Triggered 1 times 0:02:31.383 40M / 3G INFO General (simplification.cpp : 356) Running Low coverage edge remover 0:02:31.383 40M / 3G INFO General (simplification.cpp : 358) Triggered 2 times 0:02:31.383 40M / 3G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 7 0:02:31.383 40M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:02:31.383 40M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:02:31.383 40M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:02:31.383 40M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:02:31.383 40M / 3G INFO General (simplification.cpp : 356) Running Low coverage edge remover 0:02:31.385 40M / 3G INFO General (simplification.cpp : 358) Triggered 9 times 0:02:31.385 40M / 3G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 8 0:02:31.385 40M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:02:31.385 40M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:02:31.385 40M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:02:31.385 40M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:02:31.385 40M / 3G INFO General (simplification.cpp : 356) Running Low coverage edge remover 0:02:31.386 40M / 3G INFO General (simplification.cpp : 358) Triggered 7 times 0:02:31.386 40M / 3G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 9 0:02:31.386 40M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:02:31.386 40M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:02:31.386 40M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:02:31.386 40M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:02:31.386 40M / 3G INFO General (simplification.cpp : 356) Running Low coverage edge remover 0:02:31.387 40M / 3G INFO General (simplification.cpp : 358) Triggered 5 times 0:02:31.387 40M / 3G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 10 0:02:31.387 40M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:02:31.388 40M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:02:31.388 40M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:02:31.389 40M / 3G INFO General (simplification.cpp : 358) Triggered 2 times 0:02:31.389 40M / 3G INFO General (simplification.cpp : 356) Running Low coverage edge remover 0:02:31.392 40M / 3G INFO General (simplification.cpp : 358) Triggered 7 times 0:02:31.392 40M / 3G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 11 0:02:31.392 40M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:02:31.392 40M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:02:31.392 40M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:02:31.392 40M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:02:31.392 40M / 3G INFO General (simplification.cpp : 356) Running Low coverage edge remover 0:02:31.392 40M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:02:31.392 40M / 3G INFO General (simplification.cpp : 167) PROCEDURE == Post simplification 0:02:31.392 40M / 3G INFO General (graph_simplification.hpp : 447) Disconnection of relatively low covered edges disabled 0:02:31.392 40M / 3G INFO General (graph_simplification.hpp : 477) Complex tip clipping disabled 0:02:31.392 40M / 3G INFO General (graph_simplification.hpp : 617) Creating parallel br instance 0:02:31.392 40M / 3G INFO General (simplification.cpp : 301) Iteration 1 0:02:31.393 40M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:02:31.394 40M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:02:31.394 40M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:02:31.397 40M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:02:31.397 40M / 3G INFO General (simplification.cpp : 301) Iteration 2 0:02:31.397 40M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:02:31.397 40M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:02:31.397 40M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:02:31.400 40M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:02:31.400 40M / 3G INFO General (simplification.cpp : 333) Disrupting self-conjugate edges 0:02:31.406 40M / 3G INFO StageManager (stage.cpp : 126) STAGE == Simplification Cleanup 0:02:31.407 40M / 3G INFO General (simplification.cpp : 547) Removing isolated edges 0:02:31.409 40M / 3G INFO General (simplification.cpp : 570) Counting average coverage 0:02:31.410 40M / 3G INFO General (simplification.cpp : 575) Average coverage = 37.375 0:02:31.410 40M / 3G INFO StageManager (stage.cpp : 126) STAGE == Contig Output 0:02:31.410 40M / 3G INFO General (contig_output_stage.cpp : 40) Writing GFA to /Users/Mike_Lee/working_genomics_de_novo_temp/spades_default_assembly//K33/assembly_graph_with_scaffolds.gfa 0:02:31.468 40M / 3G INFO General (contig_output.hpp : 22) Outputting contigs to /Users/Mike_Lee/working_genomics_de_novo_temp/spades_default_assembly//K33/before_rr.fasta 0:02:31.692 40M / 3G INFO General (contig_output_stage.cpp : 50) Outputting FastG graph to /Users/Mike_Lee/working_genomics_de_novo_temp/spades_default_assembly//K33/assembly_graph.fastg 0:02:32.090 40M / 3G INFO General (contig_output.hpp : 22) Outputting contigs to /Users/Mike_Lee/working_genomics_de_novo_temp/spades_default_assembly//K33/simplified_contigs.fasta 0:02:32.265 40M / 3G INFO General (contig_output.hpp : 22) Outputting contigs to /Users/Mike_Lee/working_genomics_de_novo_temp/spades_default_assembly//K33/final_contigs.fasta 0:02:32.439 40M / 3G INFO StageManager (stage.cpp : 126) STAGE == Contig Output 0:02:32.439 40M / 3G INFO General (contig_output_stage.cpp : 40) Writing GFA to /Users/Mike_Lee/working_genomics_de_novo_temp/spades_default_assembly//K33/assembly_graph_with_scaffolds.gfa 0:02:32.479 40M / 3G INFO General (contig_output.hpp : 22) Outputting contigs to /Users/Mike_Lee/working_genomics_de_novo_temp/spades_default_assembly//K33/before_rr.fasta 0:02:32.622 40M / 3G INFO General (contig_output_stage.cpp : 50) Outputting FastG graph to /Users/Mike_Lee/working_genomics_de_novo_temp/spades_default_assembly//K33/assembly_graph.fastg 0:02:32.920 40M / 3G INFO General (contig_output.hpp : 22) Outputting contigs to /Users/Mike_Lee/working_genomics_de_novo_temp/spades_default_assembly//K33/simplified_contigs.fasta 0:02:33.112 40M / 3G INFO General (contig_output.hpp : 22) Outputting contigs to /Users/Mike_Lee/working_genomics_de_novo_temp/spades_default_assembly//K33/final_contigs.fasta 0:02:33.297 40M / 3G INFO General (launch.hpp : 137) SPAdes finished 0:02:33.326 20M / 3G INFO General (main.cpp : 110) Assembling time: 0 hours 2 minutes 33 seconds == Running assembler: K55 0:00:00.000 4M / 4M INFO General (main.cpp : 76) Loading config from /Users/Mike_Lee/working_genomics_de_novo_temp/spades_default_assembly/K55/configs/config.info 0:00:00.000 4M / 4M INFO General (memory_limit.hpp : 51) Memory limit set to 250 Gb 0:00:00.000 4M / 4M INFO General (main.cpp : 89) Starting SPAdes, built from N/A, git revision N/A 0:00:00.000 4M / 4M INFO General (main.cpp : 90) Maximum k-mer length: 128 0:00:00.000 4M / 4M INFO General (main.cpp : 91) Assembling dataset (/Users/Mike_Lee/working_genomics_de_novo_temp/spades_default_assembly/dataset.info) with K=55 0:00:00.000 4M / 4M INFO General (launch.hpp : 51) SPAdes started 0:00:00.000 4M / 4M INFO General (launch.hpp : 58) Starting from stage: construction 0:00:00.000 4M / 4M INFO General (launch.hpp : 61) Two-step RR enabled: 0 0:00:00.000 4M / 4M INFO General (launch.hpp : 79) Will need read mapping, kmer mapper will be attached 0:00:00.000 4M / 4M INFO StageManager (stage.cpp : 126) STAGE == Construction 0:00:00.000 4M / 4M INFO General (read_converter.hpp : 67) Binary reads detected 0:00:00.001 4M / 4M INFO General (graph_construction.hpp : 120) Constructing DeBruijn graph for k=55 0:00:00.001 4M / 4M INFO General (kmer_index_builder.hpp : 106) Splitting kmer instances into 16 buckets using 4 threads. This might take a while. 0:00:00.001 4M / 4M INFO General (file_limit.hpp : 32) Open file limit set to 7168 0:00:00.001 4M / 4M INFO General (kmer_splitters.hpp : 74) Memory available for splitting buffers: 20.833 Gb 0:00:00.001 4M / 4M INFO General (kmer_splitters.hpp : 82) Using cell size of 2097152 0:00:14.284 2G / 2G INFO General (kmer_splitters.hpp : 291) Processed 3142047 reads 0:00:26.614 2G / 2G INFO General (kmer_splitters.hpp : 291) Processed 5938904 reads 0:00:26.614 2G / 2G INFO General (kmer_splitters.hpp : 297) Adding contigs from previous K 0:00:28.213 16M / 2G INFO General (kmer_splitters.hpp : 310) Used 5938904 reads. Maximum read length 140 0:00:28.213 16M / 2G INFO General (kmer_splitters.hpp : 311) Average read length 140 0:00:28.213 16M / 2G INFO General (kmer_index_builder.hpp : 109) Starting k-mer counting. 0:00:30.833 16M / 2G INFO General (kmer_index_builder.hpp : 115) K-mer counting done. There are 11239689 kmers in total. 0:00:30.833 16M / 2G INFO General (kmer_index_builder.hpp : 121) Merging temporary buckets. 0:00:31.076 16M / 2G INFO K-mer Index Building (kmer_index_builder.hpp : 289) Building kmer index 0:00:31.076 16M / 2G INFO General (kmer_index_builder.hpp : 106) Splitting kmer instances into 64 buckets using 4 threads. This might take a while. 0:00:31.077 16M / 2G INFO General (file_limit.hpp : 32) Open file limit set to 7168 0:00:31.077 16M / 2G INFO General (kmer_splitters.hpp : 74) Memory available for splitting buffers: 20.832 Gb 0:00:31.077 16M / 2G INFO General (kmer_splitters.hpp : 82) Using cell size of 524288 0:00:33.816 3G / 3G INFO General (kmer_splitters.hpp : 381) Processed 11239689 kmers 0:00:33.816 3G / 3G INFO General (kmer_splitters.hpp : 386) Used 11239689 kmers. 0:00:33.862 16M / 3G INFO General (kmer_index_builder.hpp : 109) Starting k-mer counting. 0:00:34.878 16M / 3G INFO General (kmer_index_builder.hpp : 115) K-mer counting done. There are 11226322 kmers in total. 0:00:34.878 16M / 3G INFO General (kmer_index_builder.hpp : 121) Merging temporary buckets. 0:00:35.128 16M / 3G INFO K-mer Index Building (kmer_index_builder.hpp : 298) Building perfect hash indices 0:00:35.988 16M / 3G INFO General (kmer_index_builder.hpp : 137) Merging final buckets. 0:00:36.242 16M / 3G INFO K-mer Index Building (kmer_index_builder.hpp : 320) Index built. Total 5213632 bytes occupied (3.71529 bits per kmer). 0:00:36.255 28M / 3G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 87) Building k-mer extensions from k+1-mers 0:00:38.721 28M / 3G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 91) Building k-mer extensions from k+1-mers finished. 0:00:38.721 28M / 3G INFO General (graph_construction.hpp : 136) Condensing graph 0:00:38.883 28M / 3G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 355) Extracting unbranching paths 0:00:42.188 52M / 3G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 374) Extracting unbranching paths finished. 260813 sequences extracted 0:00:43.890 52M / 3G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 310) Collecting perfect loops 0:00:44.807 52M / 3G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 343) Collecting perfect loops finished. 0 loops collected 0:00:45.088 112M / 3G INFO General (graph_construction.hpp : 141) Building index with from graph 0:00:45.088 112M / 3G INFO K-mer Index Building (kmer_index_builder.hpp : 289) Building kmer index 0:00:45.088 112M / 3G INFO General (kmer_index_builder.hpp : 106) Splitting kmer instances into 64 buckets using 4 threads. This might take a while. 0:00:45.088 112M / 3G INFO General (file_limit.hpp : 32) Open file limit set to 7168 0:00:45.088 112M / 3G INFO General (kmer_splitters.hpp : 74) Memory available for splitting buffers: 20.8242 Gb 0:00:45.088 112M / 3G INFO General (kmer_splitters.hpp : 82) Using cell size of 524288 0:00:46.352 3G / 3G INFO General (edge_index_builders.hpp : 75) Processed 521584 edges 0:00:46.352 3G / 3G INFO General (edge_index_builders.hpp : 80) Used 521584 sequences. 0:00:46.371 112M / 3G INFO General (kmer_index_builder.hpp : 109) Starting k-mer counting. 0:00:47.377 112M / 3G INFO General (kmer_index_builder.hpp : 115) K-mer counting done. There are 11239689 kmers in total. 0:00:47.377 112M / 3G INFO General (kmer_index_builder.hpp : 121) Merging temporary buckets. 0:00:47.689 112M / 3G INFO K-mer Index Building (kmer_index_builder.hpp : 298) Building perfect hash indices 0:00:48.530 116M / 3G INFO General (kmer_index_builder.hpp : 137) Merging final buckets. 0:00:48.875 116M / 3G INFO K-mer Index Building (kmer_index_builder.hpp : 320) Index built. Total 5219944 bytes occupied (3.71537 bits per kmer). 0:00:49.046 376M / 3G INFO General (edge_index_builders.hpp : 105) Collecting k-mer coverage information from graph, this takes a while. 0:00:50.362 376M / 3G INFO General (edge_index.hpp : 91) Index refilled 0:00:50.390 364M / 3G INFO General (graph_construction.hpp : 173) Filling coverage index 0:00:50.390 364M / 3G INFO General (edge_index_builders.hpp : 183) Collecting k-mer coverage information from reads, this takes a while. 0:01:53.941 360M / 3G INFO General (graph_construction.hpp : 175) Filling coverage and flanking coverage from index 0:01:55.755 360M / 3G INFO General (construction.cpp : 30) Figured out: read length = 140 0:01:55.755 360M / 3G INFO StageManager (stage.cpp : 126) STAGE == EC Threshold Finding 0:01:56.215 360M / 3G INFO General (kmer_coverage_model.cpp : 181) Kmer coverage valley at: 4 0:01:56.215 360M / 3G INFO General (kmer_coverage_model.cpp : 201) K-mer histogram maximum: 27 0:01:56.215 360M / 3G INFO General (kmer_coverage_model.cpp : 237) Estimated median coverage: 29. Coverage mad: 10.3782 0:01:56.215 360M / 3G INFO General (kmer_coverage_model.cpp : 259) Fitting coverage model 0:01:56.248 360M / 3G INFO General (kmer_coverage_model.cpp : 295) ... iteration 2 0:01:56.329 360M / 3G INFO General (kmer_coverage_model.cpp : 295) ... iteration 4 0:01:56.582 360M / 3G INFO General (kmer_coverage_model.cpp : 295) ... iteration 8 0:01:57.093 360M / 3G INFO General (kmer_coverage_model.cpp : 295) ... iteration 16 0:01:57.655 360M / 3G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 29.2949. Fitted coverage std. dev: 8.56469 0:01:57.656 360M / 3G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 0.892381 0:01:57.656 360M / 3G INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 14 0:01:57.656 360M / 3G INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 14 0:01:57.656 360M / 3G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 8179565 0:01:57.656 360M / 3G INFO General (genomic_info_filler.cpp : 127) Mean coverage was calculated as 29.2949 0:01:57.656 360M / 3G INFO General (genomic_info_filler.cpp : 141) EC coverage threshold value was calculated as 14 0:01:57.656 360M / 3G INFO General (genomic_info_filler.cpp : 142) Trusted kmer low bound: 0 0:01:57.656 360M / 3G INFO StageManager (stage.cpp : 126) STAGE == Gap Closer 0:01:57.657 360M / 3G INFO General (gap_closer.cpp : 159) Preparing shift maps 0:01:57.904 376M / 3G INFO General (gap_closer.cpp : 119) Processing paired reads (takes a while) 0:02:04.209 380M / 3G INFO General (gap_closer.cpp : 138) Used 1484726 paired reads 0:02:04.209 380M / 3G INFO General (gap_closer.cpp : 140) Merging paired indices 0:02:04.289 364M / 3G INFO GapCloser (gap_closer.cpp : 346) Closing short gaps 0:02:04.895 364M / 3G INFO GapCloser (gap_closer.cpp : 380) Closing short gaps complete: filled 11 gaps after checking 176 candidates 0:02:04.916 360M / 3G INFO StageManager (stage.cpp : 126) STAGE == Simplification 0:02:04.941 96M / 3G INFO General (simplification.cpp : 387) Graph simplification started 0:02:04.941 96M / 3G INFO General (simplification.cpp : 77) PROCEDURE == InitialCleaning 0:02:04.941 96M / 3G INFO General (graph_simplification.hpp : 645) Flanking coverage based disconnection disabled 0:02:04.941 96M / 3G INFO General (simplification.cpp : 356) Running Self conjugate edge remover 0:02:04.985 96M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:02:04.985 96M / 3G INFO General (simplification.cpp : 356) Running Initial isolated edge remover 0:02:05.052 96M / 3G INFO General (simplification.cpp : 358) Triggered 593 times 0:02:05.052 96M / 3G INFO General (simplification.cpp : 356) Running Initial tip clipper 0:02:07.685 100M / 3G INFO General (simplification.cpp : 358) Triggered 109413 times 0:02:07.685 100M / 3G INFO General (simplification.cpp : 356) Running Initial ec remover 0:02:08.255 92M / 3G INFO General (simplification.cpp : 358) Triggered 9266 times 0:02:08.267 92M / 3G INFO General (graph_simplification.hpp : 617) Creating parallel br instance 0:02:08.267 92M / 3G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 1 0:02:08.267 92M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:02:08.281 92M / 3G INFO General (simplification.cpp : 358) Triggered 163 times 0:02:08.281 92M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:02:09.648 80M / 3G INFO General (simplification.cpp : 358) Triggered 4190 times 0:02:09.648 80M / 3G INFO General (simplification.cpp : 356) Running Low coverage edge remover 0:02:09.721 80M / 3G INFO General (simplification.cpp : 358) Triggered 277 times 0:02:09.721 80M / 3G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 2 0:02:09.721 80M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:02:09.724 80M / 3G INFO General (simplification.cpp : 358) Triggered 16 times 0:02:09.724 80M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:02:09.726 80M / 3G INFO General (simplification.cpp : 358) Triggered 4 times 0:02:09.726 80M / 3G INFO General (simplification.cpp : 356) Running Low coverage edge remover 0:02:09.754 80M / 3G INFO General (simplification.cpp : 358) Triggered 82 times 0:02:09.754 80M / 3G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 3 0:02:09.754 80M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:02:09.754 80M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:02:09.754 80M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:02:09.754 80M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:02:09.754 80M / 3G INFO General (simplification.cpp : 356) Running Low coverage edge remover 0:02:09.756 80M / 3G INFO General (simplification.cpp : 358) Triggered 16 times 0:02:09.756 80M / 3G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 4 0:02:09.756 80M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:02:09.756 80M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:02:09.756 80M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:02:09.758 80M / 3G INFO General (simplification.cpp : 358) Triggered 3 times 0:02:09.758 80M / 3G INFO General (simplification.cpp : 356) Running Low coverage edge remover 0:02:09.758 80M / 3G INFO General (simplification.cpp : 358) Triggered 3 times 0:02:09.758 80M / 3G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 5 0:02:09.758 80M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:02:09.758 80M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:02:09.758 80M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:02:09.758 80M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:02:09.758 80M / 3G INFO General (simplification.cpp : 356) Running Low coverage edge remover 0:02:09.758 80M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:02:09.758 80M / 3G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 6 0:02:09.758 80M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:02:09.758 80M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:02:09.758 80M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:02:09.759 80M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:02:09.759 80M / 3G INFO General (simplification.cpp : 356) Running Low coverage edge remover 0:02:09.760 80M / 3G INFO General (simplification.cpp : 358) Triggered 4 times 0:02:09.760 80M / 3G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 7 0:02:09.760 80M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:02:09.760 80M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:02:09.760 80M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:02:09.760 80M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:02:09.760 80M / 3G INFO General (simplification.cpp : 356) Running Low coverage edge remover 0:02:09.763 80M / 3G INFO General (simplification.cpp : 358) Triggered 5 times 0:02:09.763 80M / 3G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 8 0:02:09.763 80M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:02:09.763 80M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:02:09.763 80M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:02:09.763 80M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:02:09.763 80M / 3G INFO General (simplification.cpp : 356) Running Low coverage edge remover 0:02:09.764 80M / 3G INFO General (simplification.cpp : 358) Triggered 3 times 0:02:09.765 80M / 3G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 9 0:02:09.765 80M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:02:09.765 80M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:02:09.765 80M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:02:09.765 80M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:02:09.765 80M / 3G INFO General (simplification.cpp : 356) Running Low coverage edge remover 0:02:09.765 80M / 3G INFO General (simplification.cpp : 358) Triggered 4 times 0:02:09.765 80M / 3G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 10 0:02:09.765 80M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:02:09.766 80M / 3G INFO General (simplification.cpp : 358) Triggered 1 times 0:02:09.766 80M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:02:09.769 76M / 3G INFO General (simplification.cpp : 358) Triggered 3 times 0:02:09.769 76M / 3G INFO General (simplification.cpp : 356) Running Low coverage edge remover 0:02:09.771 72M / 3G INFO General (simplification.cpp : 358) Triggered 2 times 0:02:09.771 72M / 3G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 11 0:02:09.771 72M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:02:09.771 72M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:02:09.771 72M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:02:09.771 72M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:02:09.771 72M / 3G INFO General (simplification.cpp : 356) Running Low coverage edge remover 0:02:09.771 72M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:02:09.771 72M / 3G INFO General (simplification.cpp : 167) PROCEDURE == Post simplification 0:02:09.771 72M / 3G INFO General (graph_simplification.hpp : 447) Disconnection of relatively low covered edges disabled 0:02:09.771 72M / 3G INFO General (graph_simplification.hpp : 477) Complex tip clipping disabled 0:02:09.771 72M / 3G INFO General (graph_simplification.hpp : 617) Creating parallel br instance 0:02:09.771 72M / 3G INFO General (simplification.cpp : 301) Iteration 1 0:02:09.771 72M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:02:09.772 72M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:02:09.772 72M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:02:09.773 72M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:02:09.773 72M / 3G INFO General (simplification.cpp : 301) Iteration 2 0:02:09.773 72M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:02:09.774 72M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:02:09.774 72M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:02:09.775 72M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:02:09.775 72M / 3G INFO General (simplification.cpp : 333) Disrupting self-conjugate edges 0:02:09.777 72M / 3G INFO StageManager (stage.cpp : 126) STAGE == Gap Closer 0:02:09.777 72M / 3G INFO General (graph_pack.hpp : 99) Index refill 0:02:09.777 72M / 3G INFO K-mer Index Building (kmer_index_builder.hpp : 289) Building kmer index 0:02:09.777 72M / 3G INFO General (kmer_index_builder.hpp : 106) Splitting kmer instances into 64 buckets using 4 threads. This might take a while. 0:02:09.777 72M / 3G INFO General (file_limit.hpp : 32) Open file limit set to 7168 0:02:09.777 72M / 3G INFO General (kmer_splitters.hpp : 74) Memory available for splitting buffers: 20.8275 Gb 0:02:09.777 72M / 3G INFO General (kmer_splitters.hpp : 82) Using cell size of 524288 0:02:10.961 3G / 3G INFO General (edge_index_builders.hpp : 75) Processed 1514 edges 0:02:10.961 3G / 3G INFO General (edge_index_builders.hpp : 80) Used 1514 sequences. 0:02:10.978 68M / 3G INFO General (kmer_index_builder.hpp : 109) Starting k-mer counting. 0:02:11.815 68M / 3G INFO General (kmer_index_builder.hpp : 115) K-mer counting done. There are 8470296 kmers in total. 0:02:11.815 68M / 3G INFO General (kmer_index_builder.hpp : 121) Merging temporary buckets. 0:02:12.013 68M / 3G INFO K-mer Index Building (kmer_index_builder.hpp : 298) Building perfect hash indices 0:02:12.770 80M / 3G INFO General (kmer_index_builder.hpp : 137) Merging final buckets. 0:02:12.984 80M / 3G INFO K-mer Index Building (kmer_index_builder.hpp : 320) Index built. Total 3935920 bytes occupied (3.71739 bits per kmer). 0:02:13.118 276M / 3G INFO General (edge_index_builders.hpp : 105) Collecting k-mer coverage information from graph, this takes a while. 0:02:13.976 276M / 3G INFO General (edge_index.hpp : 91) Index refilled 0:02:13.976 276M / 3G INFO General (gap_closer.cpp : 159) Preparing shift maps 0:02:13.977 276M / 3G INFO General (gap_closer.cpp : 119) Processing paired reads (takes a while) 0:02:19.927 276M / 3G INFO General (gap_closer.cpp : 138) Used 1484726 paired reads 0:02:19.927 276M / 3G INFO General (gap_closer.cpp : 140) Merging paired indices 0:02:19.927 276M / 3G INFO GapCloser (gap_closer.cpp : 346) Closing short gaps 0:02:19.929 276M / 3G INFO GapCloser (gap_closer.cpp : 380) Closing short gaps complete: filled 6 gaps after checking 105 candidates 0:02:20.442 276M / 3G INFO StageManager (stage.cpp : 126) STAGE == Simplification Cleanup 0:02:20.442 276M / 3G INFO General (simplification.cpp : 547) Removing isolated edges 0:02:20.445 276M / 3G INFO General (simplification.cpp : 570) Counting average coverage 0:02:20.445 276M / 3G INFO General (simplification.cpp : 575) Average coverage = 29.4548 0:02:20.445 276M / 3G INFO StageManager (stage.cpp : 126) STAGE == Mismatch Correction 0:02:20.446 276M / 3G INFO General (graph_pack.hpp : 108) Normalizing k-mer map. Total 499374 kmers to process 0:02:20.814 276M / 3G INFO General (graph_pack.hpp : 110) Normalizing done 0:02:38.237 276M / 3G INFO General (mismatch_shall_not_pass.hp: 187) Finished collecting potential mismatches positions 0:02:38.358 276M / 3G INFO General (mismatch_shall_not_pass.hp: 284) All edges processed 0:02:38.361 276M / 3G INFO General (mismatch_correction.cpp : 26) Corrected 0 nucleotides 0:02:38.361 276M / 3G INFO StageManager (stage.cpp : 126) STAGE == Contig Output 0:02:38.362 276M / 3G INFO General (contig_output_stage.cpp : 40) Writing GFA to /Users/Mike_Lee/working_genomics_de_novo_temp/spades_default_assembly//K55/assembly_graph_with_scaffolds.gfa 0:02:38.398 276M / 3G INFO General (contig_output.hpp : 22) Outputting contigs to /Users/Mike_Lee/working_genomics_de_novo_temp/spades_default_assembly//K55/before_rr.fasta 0:02:38.568 276M / 3G INFO General (contig_output_stage.cpp : 50) Outputting FastG graph to /Users/Mike_Lee/working_genomics_de_novo_temp/spades_default_assembly//K55/assembly_graph.fastg 0:02:38.907 276M / 3G INFO General (contig_output.hpp : 22) Outputting contigs to /Users/Mike_Lee/working_genomics_de_novo_temp/spades_default_assembly//K55/simplified_contigs.fasta 0:02:39.070 276M / 3G INFO General (contig_output.hpp : 22) Outputting contigs to /Users/Mike_Lee/working_genomics_de_novo_temp/spades_default_assembly//K55/intermediate_contigs.fasta 0:02:39.229 276M / 3G INFO StageManager (stage.cpp : 126) STAGE == Paired Information Counting 0:02:39.246 276M / 3G INFO General (graph_pack.hpp : 108) Normalizing k-mer map. Total 499374 kmers to process 0:02:39.246 276M / 3G INFO General (graph_pack.hpp : 110) Normalizing done 0:02:39.247 276M / 3G INFO General (pair_info_count.cpp : 317) Min edge length for estimation: 63359 0:02:39.247 276M / 3G INFO General (pair_info_count.cpp : 328) Estimating insert size for library #0 0:02:39.247 276M / 3G INFO General (pair_info_count.cpp : 176) Estimating insert size (takes a while) 0:02:39.303 356M / 3G INFO General (short_read_mapper.hpp : 88) Selecting usual mapper 0:02:42.815 356M / 3G INFO General (sequence_mapper_notifier.h: 81) Processed 200000 reads 0:02:42.859 356M / 3G INFO General (sequence_mapper_notifier.h: 81) Processed 400000 reads 0:02:42.895 356M / 3G INFO General (sequence_mapper_notifier.h: 81) Processed 600000 reads 0:02:42.948 356M / 3G INFO General (sequence_mapper_notifier.h: 81) Processed 800000 reads 0:02:46.044 356M / 3G INFO General (sequence_mapper_notifier.h: 99) Total 1484726 reads processed 0:02:46.122 356M / 3G INFO General (pair_info_count.cpp : 194) Edge pairs: 67108864 (rough upper limit) 0:02:46.122 356M / 3G INFO General (pair_info_count.cpp : 198) 733713 paired reads (49.4174% of all) aligned to long edges 0:02:46.128 276M / 3G INFO General (pair_info_count.cpp : 351) Insert size = 375.197, deviation = 112.039, left quantile = 234, right quantile = 521, read length = 140 0:02:46.263 468M / 3G INFO General (pair_info_count.cpp : 368) Filtering data for library #0 0:02:46.263 468M / 3G INFO General (short_read_mapper.hpp : 88) Selecting usual mapper 0:02:49.670 468M / 3G INFO General (sequence_mapper_notifier.h: 81) Processed 200000 reads 0:02:49.675 468M / 3G INFO General (sequence_mapper_notifier.h: 81) Processed 400000 reads 0:02:49.705 468M / 3G INFO General (sequence_mapper_notifier.h: 81) Processed 600000 reads 0:02:49.710 468M / 3G INFO General (sequence_mapper_notifier.h: 81) Processed 800000 reads 0:02:52.719 468M / 3G INFO General (sequence_mapper_notifier.h: 99) Total 1484726 reads processed 0:02:52.719 468M / 3G INFO General (pair_info_count.cpp : 380) Mapping library #0 0:02:52.719 468M / 3G INFO General (pair_info_count.cpp : 382) Mapping paired reads (takes a while) 0:02:52.719 468M / 3G INFO General (pair_info_count.cpp : 275) Left insert size quantile 234, right insert size quantile 521, filtering threshold 2, rounding threshold 0 0:02:52.729 480M / 3G INFO General (short_read_mapper.hpp : 88) Selecting usual mapper 0:02:56.572 480M / 3G INFO General (sequence_mapper_notifier.h: 81) Processed 200000 reads 0:02:56.593 480M / 3G INFO General (sequence_mapper_notifier.h: 81) Processed 400000 reads 0:02:56.609 480M / 3G INFO General (sequence_mapper_notifier.h: 81) Processed 600000 reads 0:02:56.684 480M / 3G INFO General (sequence_mapper_notifier.h: 81) Processed 800000 reads 0:03:00.113 480M / 3G INFO General (sequence_mapper_notifier.h: 99) Total 1484726 reads processed 0:03:00.133 276M / 3G INFO StageManager (stage.cpp : 126) STAGE == Distance Estimation 0:03:00.133 276M / 3G INFO General (distance_estimation.cpp : 224) Processing library #0 0:03:00.133 276M / 3G INFO General (distance_estimation.cpp : 130) Weight Filter Done 0:03:00.134 276M / 3G INFO DistanceEstimator (distance_estimation.hpp : 116) Using SIMPLE distance estimator 0:03:00.148 276M / 3G INFO General (distance_estimation.cpp : 35) Filtering info 0:03:00.148 276M / 3G INFO General (pair_info_filters.hpp : 242) Start filtering; index size: 5506 0:03:00.151 276M / 3G INFO General (pair_info_filters.hpp : 263) Done filtering 0:03:00.151 276M / 3G INFO General (distance_estimation.cpp : 172) Refining clustered pair information 0:03:00.155 276M / 3G INFO General (distance_estimation.cpp : 174) The refining of clustered pair information has been finished 0:03:00.155 276M / 3G INFO General (distance_estimation.cpp : 176) Improving paired information 0:03:00.168 276M / 3G INFO PairInfoImprover (pair_info_improver.hpp : 103) Paired info stats: missing = 117; contradictional = 112 0:03:00.184 276M / 3G INFO PairInfoImprover (pair_info_improver.hpp : 103) Paired info stats: missing = 2; contradictional = 4 0:03:00.184 276M / 3G INFO General (distance_estimation.cpp : 183) Filling scaffolding index 0:03:00.184 276M / 3G INFO DistanceEstimator (distance_estimation.hpp : 116) Using SMOOTHING distance estimator 0:03:00.321 276M / 3G INFO General (distance_estimation.cpp : 35) Filtering info 0:03:00.321 276M / 3G INFO General (pair_info_filters.hpp : 242) Start filtering; index size: 1627 0:03:00.322 276M / 3G INFO General (pair_info_filters.hpp : 263) Done filtering 0:03:00.322 276M / 3G INFO General (distance_estimation.cpp : 228) Clearing raw paired index 0:03:00.324 276M / 3G INFO StageManager (stage.cpp : 126) STAGE == Repeat Resolving 0:03:00.324 276M / 3G INFO General (repeat_resolving.cpp : 69) Using Path-Extend repeat resolving 0:03:00.325 276M / 3G INFO General (launcher.cpp : 478) ExSPAnder repeat resolving tool started 0:03:00.329 276M / 3G INFO General (launcher.cpp : 393) Creating main extenders, unique edge length = 2000 0:03:00.329 276M / 3G INFO General (extenders_logic.cpp : 275) Estimated coverage of library #0 is 29.4548 0:03:00.330 276M / 3G INFO General (extenders_logic.cpp : 275) Estimated coverage of library #0 is 29.4548 0:03:00.332 276M / 3G INFO General (extenders_logic.cpp : 472) Using 1 paired-end library 0:03:00.332 276M / 3G INFO General (extenders_logic.cpp : 473) Using 1 paired-end scaffolding library 0:03:00.332 276M / 3G INFO General (extenders_logic.cpp : 474) Using 0 single read libraries 0:03:00.332 276M / 3G INFO General (launcher.cpp : 421) Total number of extenders is 3 0:03:00.332 276M / 3G INFO General (path_extender.hpp : 867) Processed 0 paths from 696 (0%) 0:03:00.453 280M / 3G INFO General (path_extender.hpp : 867) Processed 70 paths from 696 (10%) 0:03:00.519 280M / 3G INFO General (path_extender.hpp : 865) Processed 128 paths from 696 (18%) 0:03:00.522 280M / 3G INFO General (path_extender.hpp : 867) Processed 140 paths from 696 (20%) 0:03:00.558 280M / 3G INFO General (path_extender.hpp : 867) Processed 210 paths from 696 (30%) 0:03:00.567 280M / 3G INFO General (path_extender.hpp : 865) Processed 256 paths from 696 (36%) 0:03:00.570 280M / 3G INFO General (path_extender.hpp : 867) Processed 280 paths from 696 (40%) 0:03:00.574 280M / 3G INFO General (path_extender.hpp : 867) Processed 350 paths from 696 (50%) 0:03:00.577 280M / 3G INFO General (path_extender.hpp : 867) Processed 420 paths from 696 (60%) 0:03:00.580 280M / 3G INFO General (path_extender.hpp : 867) Processed 490 paths from 696 (70%) 0:03:00.585 280M / 3G INFO General (path_extender.hpp : 865) Processed 512 paths from 696 (73%) 0:03:00.595 280M / 3G INFO General (path_extender.hpp : 867) Processed 560 paths from 696 (80%) 0:03:00.602 280M / 3G INFO General (path_extender.hpp : 867) Processed 630 paths from 696 (90%) 0:03:00.602 280M / 3G INFO General (launcher.cpp : 234) Finalizing paths 0:03:00.602 280M / 3G INFO General (launcher.cpp : 236) Deduplicating paths 0:03:00.605 280M / 3G INFO General (launcher.cpp : 240) Paths deduplicated 0:03:00.605 280M / 3G INFO PEResolver (pe_resolver.hpp : 299) Removing overlaps 0:03:00.605 280M / 3G INFO PEResolver (pe_resolver.hpp : 302) Sorting paths 0:03:00.605 280M / 3G INFO PEResolver (pe_resolver.hpp : 309) Marking overlaps 0:03:00.605 280M / 3G INFO OverlapRemover (pe_resolver.hpp : 132) Marking start/end overlaps 0:03:00.607 280M / 3G INFO OverlapRemover (pe_resolver.hpp : 135) Marking remaining overlaps 0:03:00.609 280M / 3G INFO PEResolver (pe_resolver.hpp : 312) Splitting paths 0:03:00.610 280M / 3G INFO PEResolver (pe_resolver.hpp : 317) Deduplicating paths 0:03:00.612 280M / 3G INFO PEResolver (pe_resolver.hpp : 319) Overlaps removed 0:03:00.612 280M / 3G INFO General (launcher.cpp : 257) Paths finalized 0:03:00.612 280M / 3G INFO General (launcher.cpp : 287) Traversing tandem repeats 0:03:00.617 280M / 3G INFO General (launcher.cpp : 297) Traversed 4 loops 0:03:00.617 280M / 3G INFO General (launcher.cpp : 428) Closing gaps in paths 0:03:00.620 280M / 3G INFO General (launcher.cpp : 456) Gap closing completed 0:03:00.622 280M / 3G INFO General (launcher.cpp : 234) Finalizing paths 0:03:00.622 280M / 3G INFO General (launcher.cpp : 236) Deduplicating paths 0:03:00.622 280M / 3G INFO General (launcher.cpp : 240) Paths deduplicated 0:03:00.622 280M / 3G INFO PEResolver (pe_resolver.hpp : 299) Removing overlaps 0:03:00.622 280M / 3G INFO PEResolver (pe_resolver.hpp : 302) Sorting paths 0:03:00.622 280M / 3G INFO PEResolver (pe_resolver.hpp : 309) Marking overlaps 0:03:00.622 280M / 3G INFO OverlapRemover (pe_resolver.hpp : 132) Marking start/end overlaps 0:03:00.623 280M / 3G INFO OverlapRemover (pe_resolver.hpp : 135) Marking remaining overlaps 0:03:00.624 280M / 3G INFO PEResolver (pe_resolver.hpp : 312) Splitting paths 0:03:00.624 280M / 3G INFO PEResolver (pe_resolver.hpp : 317) Deduplicating paths 0:03:00.625 280M / 3G INFO PEResolver (pe_resolver.hpp : 319) Overlaps removed 0:03:00.626 280M / 3G INFO General (launcher.cpp : 257) Paths finalized 0:03:00.627 280M / 3G INFO General (launcher.cpp : 531) ExSPAnder repeat resolving tool finished 0:03:00.636 280M / 3G INFO StageManager (stage.cpp : 126) STAGE == Contig Output 0:03:00.636 280M / 3G INFO General (contig_output_stage.cpp : 40) Writing GFA to /Users/Mike_Lee/working_genomics_de_novo_temp/spades_default_assembly//K55/assembly_graph_with_scaffolds.gfa 0:03:00.674 280M / 3G INFO General (contig_output.hpp : 22) Outputting contigs to /Users/Mike_Lee/working_genomics_de_novo_temp/spades_default_assembly//K55/before_rr.fasta 0:03:00.810 276M / 3G INFO General (contig_output_stage.cpp : 50) Outputting FastG graph to /Users/Mike_Lee/working_genomics_de_novo_temp/spades_default_assembly//K55/assembly_graph.fastg 0:03:01.109 276M / 3G INFO General (contig_output_stage.cpp : 20) Outputting FastG paths to /Users/Mike_Lee/working_genomics_de_novo_temp/spades_default_assembly//K55/final_contigs.paths 0:03:01.331 280M / 3G INFO General (contig_output_stage.cpp : 20) Outputting FastG paths to /Users/Mike_Lee/working_genomics_de_novo_temp/spades_default_assembly//K55/scaffolds.paths 0:03:01.526 280M / 3G INFO General (launch.hpp : 137) SPAdes finished 0:03:01.875 24M / 3G INFO General (main.cpp : 110) Assembling time: 0 hours 3 minutes 1 seconds ===== Assembling finished. Used k-mer sizes: 21, 33, 55 * Assembled contigs are in /Users/Mike_Lee/working_genomics_de_novo_temp/spades_default_assembly/contigs.fasta * Assembled scaffolds are in /Users/Mike_Lee/working_genomics_de_novo_temp/spades_default_assembly/scaffolds.fasta * Assembly graph is in /Users/Mike_Lee/working_genomics_de_novo_temp/spades_default_assembly/assembly_graph.fastg * Assembly graph in GFA format is in /Users/Mike_Lee/working_genomics_de_novo_temp/spades_default_assembly/assembly_graph_with_scaffolds.gfa * Paths in the assembly graph corresponding to the contigs are in /Users/Mike_Lee/working_genomics_de_novo_temp/spades_default_assembly/contigs.paths * Paths in the assembly graph corresponding to the scaffolds are in /Users/Mike_Lee/working_genomics_de_novo_temp/spades_default_assembly/scaffolds.paths ======= SPAdes pipeline finished. SPAdes log can be found here: /Users/Mike_Lee/working_genomics_de_novo_temp/spades_default_assembly/spades.log Thank you for using SPAdes!