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 -t 4 -o /Users/Mike_Lee/working_genomics_de_novo_temp/spades_kmers_set_careful_assembly -k 21,33,55,77 --careful --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_kmers_set_careful_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: [21, 33, 55, 77] Repeat resolution is enabled Mismatch careful mode is turned ON MismatchCorrector will be used Coverage cutoff is turned OFF Other parameters: Dir for temp files: /Users/Mike_Lee/working_genomics_de_novo_temp/spades_kmers_set_careful_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_kmers_set_careful_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_kmers_set_careful_assembly/K21/configs/config.info 0:00:00.000 4M / 4M INFO General (main.cpp : 76) Loading config from /Users/Mike_Lee/working_genomics_de_novo_temp/spades_kmers_set_careful_assembly/K21/configs/careful_mode.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_kmers_set_careful_assembly/dataset.info) with K=21 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 StageManager (stage.cpp : 126) STAGE == Construction 0:00:00.001 4M / 4M INFO General (read_converter.hpp : 84) Converting reads to binary format for library #0 (takes a while) 0:00:00.001 4M / 4M INFO General (read_converter.hpp : 85) Converting paired reads 0:00:00.318 80M / 84M INFO General (binary_converter.hpp : 139) 16384 reads processed 0:00:00.521 92M / 92M INFO General (binary_converter.hpp : 139) 32768 reads processed 0:00:00.905 116M / 116M INFO General (binary_converter.hpp : 139) 65536 reads processed 0:00:01.641 164M / 164M INFO General (binary_converter.hpp : 139) 131072 reads processed 0:00:03.384 264M / 264M INFO General (binary_converter.hpp : 139) 262144 reads processed 0:00:07.743 320M / 320M INFO General (binary_converter.hpp : 139) 524288 reads processed 0:00:15.358 344M / 344M INFO General (binary_converter.hpp : 139) 1048576 reads processed 0:00:21.765 288M / 352M INFO General (binary_converter.hpp : 159) 1484726 reads written 0:00:22.008 4M / 352M INFO General (read_converter.hpp : 94) Converting single reads 0:00:22.179 132M / 352M INFO General (binary_converter.hpp : 159) 0 reads written 0:00:22.213 4M / 352M INFO General (graph_construction.hpp : 120) Constructing DeBruijn graph for k=21 0:00:22.213 4M / 352M INFO General (kmer_index_builder.hpp : 106) Splitting kmer instances into 16 buckets using 4 threads. This might take a while. 0:00:22.213 4M / 352M INFO General (file_limit.hpp : 32) Open file limit set to 7168 0:00:22.213 4M / 352M INFO General (kmer_splitters.hpp : 74) Memory available for splitting buffers: 20.833 Gb 0:00:22.213 4M / 352M INFO General (kmer_splitters.hpp : 82) Using cell size of 4194304 0:00:47.742 2G / 2G INFO General (kmer_splitters.hpp : 291) Processed 4501245 reads 0:00:55.035 2G / 2G INFO General (kmer_splitters.hpp : 291) Processed 5938904 reads 0:00:55.035 2G / 2G INFO General (kmer_splitters.hpp : 297) Adding contigs from previous K 0:00:55.269 16M / 2G INFO General (kmer_splitters.hpp : 310) Used 5938904 reads. Maximum read length 140 0:00:55.269 16M / 2G INFO General (kmer_splitters.hpp : 311) Average read length 140 0:00:55.269 16M / 2G INFO General (kmer_index_builder.hpp : 109) Starting k-mer counting. 0:00:56.735 16M / 2G INFO General (kmer_index_builder.hpp : 115) K-mer counting done. There are 10173588 kmers in total. 0:00:56.735 16M / 2G INFO General (kmer_index_builder.hpp : 121) Merging temporary buckets. 0:00:56.875 16M / 2G INFO K-mer Index Building (kmer_index_builder.hpp : 289) Building kmer index 0:00:56.875 16M / 2G INFO General (kmer_index_builder.hpp : 106) Splitting kmer instances into 64 buckets using 4 threads. This might take a while. 0:00:56.876 16M / 2G INFO General (file_limit.hpp : 32) Open file limit set to 7168 0:00:56.876 16M / 2G INFO General (kmer_splitters.hpp : 74) Memory available for splitting buffers: 20.832 Gb 0:00:56.876 16M / 2G INFO General (kmer_splitters.hpp : 82) Using cell size of 1048576 0:00:59.058 3G / 3G INFO General (kmer_splitters.hpp : 381) Processed 10173588 kmers 0:00:59.058 3G / 3G INFO General (kmer_splitters.hpp : 386) Used 10173588 kmers. 0:00:59.081 16M / 3G INFO General (kmer_index_builder.hpp : 109) Starting k-mer counting. 0:01:00.116 16M / 3G INFO General (kmer_index_builder.hpp : 115) K-mer counting done. There are 10096148 kmers in total. 0:01:00.116 16M / 3G INFO General (kmer_index_builder.hpp : 121) Merging temporary buckets. 0:01:00.265 16M / 3G INFO K-mer Index Building (kmer_index_builder.hpp : 298) Building perfect hash indices 0:01:01.157 16M / 3G INFO General (kmer_index_builder.hpp : 137) Merging final buckets. 0:01:01.276 16M / 3G INFO K-mer Index Building (kmer_index_builder.hpp : 320) Index built. Total 4689888 bytes occupied (3.71618 bits per kmer). 0:01:01.287 28M / 3G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 87) Building k-mer extensions from k+1-mers 0:01:03.625 28M / 3G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 91) Building k-mer extensions from k+1-mers finished. 0:01:03.626 28M / 3G INFO Early tip clipping (early_simplification.hpp : 181) Early tip clipping 0:01:09.903 28M / 3G INFO Early tip clipping (early_simplification.hpp : 184) 550174 22-mers were removed by early tip clipper 0:01:09.903 28M / 3G INFO General (graph_construction.hpp : 136) Condensing graph 0:01:09.962 28M / 3G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 355) Extracting unbranching paths 0:01:13.003 40M / 3G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 374) Extracting unbranching paths finished. 221440 sequences extracted 0:01:14.564 40M / 3G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 310) Collecting perfect loops 0:01:15.335 40M / 3G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 343) Collecting perfect loops finished. 2 loops collected 0:01:15.532 92M / 3G INFO General (graph_construction.hpp : 141) Building index with from graph 0:01:15.576 92M / 3G INFO K-mer Index Building (kmer_index_builder.hpp : 289) Building kmer index 0:01:15.576 92M / 3G INFO General (kmer_index_builder.hpp : 106) Splitting kmer instances into 64 buckets using 4 threads. This might take a while. 0:01:15.576 92M / 3G INFO General (file_limit.hpp : 32) Open file limit set to 7168 0:01:15.576 92M / 3G INFO General (kmer_splitters.hpp : 74) Memory available for splitting buffers: 20.8258 Gb 0:01:15.576 92M / 3G INFO General (kmer_splitters.hpp : 82) Using cell size of 1048576 0:01:16.644 3G / 3G INFO General (edge_index_builders.hpp : 75) Processed 441975 edges 0:01:16.644 3G / 3G INFO General (edge_index_builders.hpp : 80) Used 441975 sequences. 0:01:16.652 92M / 3G INFO General (kmer_index_builder.hpp : 109) Starting k-mer counting. 0:01:17.498 92M / 3G INFO General (kmer_index_builder.hpp : 115) K-mer counting done. There are 9623414 kmers in total. 0:01:17.498 92M / 3G INFO General (kmer_index_builder.hpp : 121) Merging temporary buckets. 0:01:17.666 92M / 3G INFO K-mer Index Building (kmer_index_builder.hpp : 298) Building perfect hash indices 0:01:18.385 96M / 3G INFO General (kmer_index_builder.hpp : 137) Merging final buckets. 0:01:18.482 96M / 3G INFO K-mer Index Building (kmer_index_builder.hpp : 320) Index built. Total 4470584 bytes occupied (3.71642 bits per kmer). 0:01:18.623 320M / 3G INFO General (edge_index_builders.hpp : 105) Collecting k-mer coverage information from graph, this takes a while. 0:01:19.725 320M / 3G INFO General (edge_index.hpp : 91) Index refilled 0:01:19.738 304M / 3G INFO General (graph_construction.hpp : 173) Filling coverage index 0:01:19.738 304M / 3G INFO General (edge_index_builders.hpp : 183) Collecting k-mer coverage information from reads, this takes a while. 0:02:18.995 300M / 3G INFO General (graph_construction.hpp : 175) Filling coverage and flanking coverage from index 0:02:20.189 300M / 3G INFO General (construction.cpp : 30) Figured out: read length = 140 0:02:20.189 300M / 3G INFO StageManager (stage.cpp : 126) STAGE == EC Threshold Finding 0:02:20.539 304M / 3G INFO General (kmer_coverage_model.cpp : 181) Kmer coverage valley at: 7 0:02:20.539 304M / 3G INFO General (kmer_coverage_model.cpp : 201) K-mer histogram maximum: 40 0:02:20.539 304M / 3G INFO General (kmer_coverage_model.cpp : 237) Estimated median coverage: 41. Coverage mad: 13.3434 0:02:20.539 304M / 3G INFO General (kmer_coverage_model.cpp : 259) Fitting coverage model 0:02:20.579 304M / 3G INFO General (kmer_coverage_model.cpp : 295) ... iteration 2 0:02:20.684 304M / 3G INFO General (kmer_coverage_model.cpp : 295) ... iteration 4 0:02:21.046 304M / 3G INFO General (kmer_coverage_model.cpp : 295) ... iteration 8 0:02:21.752 304M / 3G INFO General (kmer_coverage_model.cpp : 295) ... iteration 16 0:02:22.661 304M / 3G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 41.213. Fitted coverage std. dev: 11.1916 0:02:22.662 304M / 3G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 0.776085 0:02:22.662 304M / 3G INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 18 0:02:22.662 304M / 3G INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 18 0:02:22.662 304M / 3G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 8270101 0:02:22.662 304M / 3G INFO General (genomic_info_filler.cpp : 127) Mean coverage was calculated as 41.213 0:02:22.662 304M / 3G INFO General (genomic_info_filler.cpp : 141) EC coverage threshold value was calculated as 18 0:02:22.662 304M / 3G INFO General (genomic_info_filler.cpp : 142) Trusted kmer low bound: 0 0:02:22.662 304M / 3G INFO StageManager (stage.cpp : 126) STAGE == Simplification 0:02:22.679 76M / 3G INFO General (simplification.cpp : 387) Graph simplification started 0:02:22.679 76M / 3G INFO General (simplification.cpp : 77) PROCEDURE == InitialCleaning 0:02:22.679 76M / 3G INFO General (graph_simplification.hpp : 645) Flanking coverage based disconnection disabled 0:02:22.679 76M / 3G INFO General (simplification.cpp : 356) Running Self conjugate edge remover 0:02:22.705 76M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:02:22.705 76M / 3G INFO General (graph_simplification.hpp : 617) Creating parallel br instance 0:02:22.705 76M / 3G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 1 0:02:22.705 76M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:02:22.753 68M / 3G INFO General (simplification.cpp : 358) Triggered 228 times 0:02:22.753 68M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:02:24.226 76M / 3G INFO General (simplification.cpp : 358) Triggered 17425 times 0:02:24.226 76M / 3G INFO General (simplification.cpp : 356) Running Low coverage edge remover 0:02:26.062 76M / 3G INFO General (simplification.cpp : 358) Triggered 41934 times 0:02:26.062 76M / 3G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 2 0:02:26.062 76M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:02:26.084 76M / 3G INFO General (simplification.cpp : 358) Triggered 106 times 0:02:26.085 76M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:02:26.192 76M / 3G INFO General (simplification.cpp : 358) Triggered 940 times 0:02:26.192 76M / 3G INFO General (simplification.cpp : 356) Running Low coverage edge remover 0:02:26.539 76M / 3G INFO General (simplification.cpp : 358) Triggered 8284 times 0:02:26.539 76M / 3G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 3 0:02:26.540 76M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:02:26.543 76M / 3G INFO General (simplification.cpp : 358) Triggered 2 times 0:02:26.543 76M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:02:26.564 76M / 3G INFO General (simplification.cpp : 358) Triggered 145 times 0:02:26.564 76M / 3G INFO General (simplification.cpp : 356) Running Low coverage edge remover 0:02:26.599 76M / 3G INFO General (simplification.cpp : 358) Triggered 848 times 0:02:26.599 76M / 3G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 4 0:02:26.599 76M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:02:26.600 76M / 3G INFO General (simplification.cpp : 358) Triggered 1 times 0:02:26.600 76M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:02:26.603 76M / 3G INFO General (simplification.cpp : 358) Triggered 9 times 0:02:26.603 76M / 3G INFO General (simplification.cpp : 356) Running Low coverage edge remover 0:02:26.609 76M / 3G INFO General (simplification.cpp : 358) Triggered 146 times 0:02:26.609 76M / 3G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 5 0:02:26.609 76M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:02:26.609 76M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:02:26.609 76M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:02:26.611 76M / 3G INFO General (simplification.cpp : 358) Triggered 6 times 0:02:26.611 76M / 3G INFO General (simplification.cpp : 356) Running Low coverage edge remover 0:02:26.613 76M / 3G INFO General (simplification.cpp : 358) Triggered 56 times 0:02:26.613 76M / 3G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 6 0:02:26.613 76M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:02:26.613 76M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:02:26.613 76M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:02:26.614 76M / 3G INFO General (simplification.cpp : 358) Triggered 3 times 0:02:26.614 76M / 3G INFO General (simplification.cpp : 356) Running Low coverage edge remover 0:02:26.616 76M / 3G INFO General (simplification.cpp : 358) Triggered 30 times 0:02:26.616 76M / 3G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 7 0:02:26.616 76M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:02:26.616 76M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:02:26.616 76M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:02:26.616 76M / 3G INFO General (simplification.cpp : 358) Triggered 2 times 0:02:26.616 76M / 3G INFO General (simplification.cpp : 356) Running Low coverage edge remover 0:02:26.618 76M / 3G INFO General (simplification.cpp : 358) Triggered 44 times 0:02:26.618 76M / 3G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 8 0:02:26.618 76M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:02:26.618 76M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:02:26.618 76M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:02:26.618 76M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:02:26.618 76M / 3G INFO General (simplification.cpp : 356) Running Low coverage edge remover 0:02:26.620 76M / 3G INFO General (simplification.cpp : 358) Triggered 38 times 0:02:26.620 76M / 3G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 9 0:02:26.620 76M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:02:26.620 76M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:02:26.620 76M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:02:26.620 76M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:02:26.620 76M / 3G INFO General (simplification.cpp : 356) Running Low coverage edge remover 0:02:26.622 76M / 3G INFO General (simplification.cpp : 358) Triggered 42 times 0:02:26.622 76M / 3G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 10 0:02:26.622 76M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:02:26.627 76M / 3G INFO General (simplification.cpp : 358) Triggered 10 times 0:02:26.628 76M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:02:26.669 76M / 3G INFO General (simplification.cpp : 358) Triggered 10 times 0:02:26.669 76M / 3G INFO General (simplification.cpp : 356) Running Low coverage edge remover 0:02:26.680 72M / 3G INFO General (simplification.cpp : 358) Triggered 57 times 0:02:26.680 72M / 3G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 11 0:02:26.680 72M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:02:26.680 72M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:02:26.680 72M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:02:26.681 72M / 3G INFO General (simplification.cpp : 358) Triggered 1 times 0:02:26.681 72M / 3G INFO General (simplification.cpp : 356) Running Low coverage edge remover 0:02:26.681 72M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:02:26.681 72M / 3G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 12 0:02:26.681 72M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:02:26.681 72M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:02:26.681 72M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:02:26.681 72M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:02:26.681 72M / 3G INFO General (simplification.cpp : 356) Running Low coverage edge remover 0:02:26.681 72M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:02:26.681 72M / 3G INFO General (simplification.cpp : 167) PROCEDURE == Post simplification 0:02:26.681 72M / 3G INFO General (graph_simplification.hpp : 447) Disconnection of relatively low covered edges disabled 0:02:26.681 72M / 3G INFO General (graph_simplification.hpp : 477) Complex tip clipping disabled 0:02:26.681 72M / 3G INFO General (graph_simplification.hpp : 617) Creating parallel br instance 0:02:26.681 72M / 3G INFO General (simplification.cpp : 301) Iteration 1 0:02:26.681 72M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:02:26.686 72M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:02:26.686 72M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:02:26.725 72M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:02:26.725 72M / 3G INFO General (simplification.cpp : 301) Iteration 2 0:02:26.725 72M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:02:26.730 72M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:02:26.730 72M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:02:26.767 72M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:02:26.767 72M / 3G INFO General (simplification.cpp : 333) Disrupting self-conjugate edges 0:02:26.790 72M / 3G INFO StageManager (stage.cpp : 126) STAGE == Simplification Cleanup 0:02:26.790 72M / 3G INFO General (simplification.cpp : 547) Removing isolated edges 0:02:26.795 72M / 3G INFO General (simplification.cpp : 570) Counting average coverage 0:02:26.805 72M / 3G INFO General (simplification.cpp : 575) Average coverage = 41.7495 0:02:26.805 72M / 3G INFO StageManager (stage.cpp : 126) STAGE == Contig Output 0:02:26.805 72M / 3G INFO General (contig_output_stage.cpp : 40) Writing GFA to /Users/Mike_Lee/working_genomics_de_novo_temp/spades_kmers_set_careful_assembly//K21/assembly_graph_with_scaffolds.gfa 0:02:26.990 72M / 3G INFO General (contig_output.hpp : 22) Outputting contigs to /Users/Mike_Lee/working_genomics_de_novo_temp/spades_kmers_set_careful_assembly//K21/before_rr.fasta 0:02:27.344 72M / 3G INFO General (contig_output_stage.cpp : 50) Outputting FastG graph to /Users/Mike_Lee/working_genomics_de_novo_temp/spades_kmers_set_careful_assembly//K21/assembly_graph.fastg 0:02:28.066 72M / 3G INFO General (contig_output.hpp : 22) Outputting contigs to /Users/Mike_Lee/working_genomics_de_novo_temp/spades_kmers_set_careful_assembly//K21/simplified_contigs.fasta 0:02:28.465 72M / 3G INFO General (contig_output.hpp : 22) Outputting contigs to /Users/Mike_Lee/working_genomics_de_novo_temp/spades_kmers_set_careful_assembly//K21/final_contigs.fasta 0:02:28.862 72M / 3G INFO StageManager (stage.cpp : 126) STAGE == Contig Output 0:02:28.862 72M / 3G INFO General (contig_output_stage.cpp : 40) Writing GFA to /Users/Mike_Lee/working_genomics_de_novo_temp/spades_kmers_set_careful_assembly//K21/assembly_graph_with_scaffolds.gfa 0:02:29.051 72M / 3G INFO General (contig_output.hpp : 22) Outputting contigs to /Users/Mike_Lee/working_genomics_de_novo_temp/spades_kmers_set_careful_assembly//K21/before_rr.fasta 0:02:29.371 72M / 3G INFO General (contig_output_stage.cpp : 50) Outputting FastG graph to /Users/Mike_Lee/working_genomics_de_novo_temp/spades_kmers_set_careful_assembly//K21/assembly_graph.fastg 0:02:30.043 72M / 3G INFO General (contig_output.hpp : 22) Outputting contigs to /Users/Mike_Lee/working_genomics_de_novo_temp/spades_kmers_set_careful_assembly//K21/simplified_contigs.fasta 0:02:30.418 72M / 3G INFO General (contig_output.hpp : 22) Outputting contigs to /Users/Mike_Lee/working_genomics_de_novo_temp/spades_kmers_set_careful_assembly//K21/final_contigs.fasta 0:02:30.825 72M / 3G INFO General (launch.hpp : 137) SPAdes finished 0:02:30.954 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_kmers_set_careful_assembly/K33/configs/config.info 0:00:00.000 4M / 4M INFO General (main.cpp : 76) Loading config from /Users/Mike_Lee/working_genomics_de_novo_temp/spades_kmers_set_careful_assembly/K33/configs/careful_mode.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_kmers_set_careful_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 0:00:00.012 4M / 4M INFO StageManager (stage.cpp : 126) STAGE == Construction 0:00:00.013 4M / 4M INFO General (read_converter.hpp : 67) Binary reads detected 0:00:00.013 4M / 4M INFO General (graph_construction.hpp : 120) Constructing DeBruijn graph for k=33 0:00:00.013 4M / 4M INFO General (kmer_index_builder.hpp : 106) Splitting kmer instances into 16 buckets using 4 threads. This might take a while. 0:00:00.013 4M / 4M INFO General (file_limit.hpp : 32) Open file limit set to 7168 0:00:00.013 4M / 4M INFO General (kmer_splitters.hpp : 74) Memory available for splitting buffers: 20.833 Gb 0:00:00.013 4M / 4M INFO General (kmer_splitters.hpp : 82) Using cell size of 2097152 0:00:12.218 2G / 2G INFO General (kmer_splitters.hpp : 291) Processed 2500256 reads 0:00:23.723 2G / 2G INFO General (kmer_splitters.hpp : 291) Processed 5002200 reads 0:00:29.146 2G / 2G INFO General (kmer_splitters.hpp : 291) Processed 5938904 reads 0:00:29.146 2G / 2G INFO General (kmer_splitters.hpp : 297) Adding contigs from previous K 0:00:31.212 16M / 2G INFO General (kmer_splitters.hpp : 310) Used 5938904 reads. Maximum read length 140 0:00:31.212 16M / 2G INFO General (kmer_splitters.hpp : 311) Average read length 140 0:00:31.212 16M / 2G INFO General (kmer_index_builder.hpp : 109) Starting k-mer counting. 0:00:34.796 16M / 2G INFO General (kmer_index_builder.hpp : 115) K-mer counting done. There are 10745075 kmers in total. 0:00:34.796 16M / 2G INFO General (kmer_index_builder.hpp : 121) Merging temporary buckets. 0:00:35.033 16M / 2G INFO K-mer Index Building (kmer_index_builder.hpp : 289) Building kmer index 0:00:35.033 16M / 2G INFO General (kmer_index_builder.hpp : 106) Splitting kmer instances into 64 buckets using 4 threads. This might take a while. 0:00:35.033 16M / 2G INFO General (file_limit.hpp : 32) Open file limit set to 7168 0:00:35.033 16M / 2G INFO General (kmer_splitters.hpp : 74) Memory available for splitting buffers: 20.832 Gb 0:00:35.033 16M / 2G INFO General (kmer_splitters.hpp : 82) Using cell size of 524288 0:00:37.871 3G / 3G INFO General (kmer_splitters.hpp : 381) Processed 10745075 kmers 0:00:37.872 3G / 3G INFO General (kmer_splitters.hpp : 386) Used 10745075 kmers. 0:00:37.917 16M / 3G INFO General (kmer_index_builder.hpp : 109) Starting k-mer counting. 0:00:38.895 16M / 3G INFO General (kmer_index_builder.hpp : 115) K-mer counting done. There are 10709395 kmers in total. 0:00:38.895 16M / 3G INFO General (kmer_index_builder.hpp : 121) Merging temporary buckets. 0:00:39.171 16M / 3G INFO K-mer Index Building (kmer_index_builder.hpp : 298) Building perfect hash indices 0:00:39.970 16M / 3G INFO General (kmer_index_builder.hpp : 137) Merging final buckets. 0:00:40.239 16M / 3G INFO K-mer Index Building (kmer_index_builder.hpp : 320) Index built. Total 4973872 bytes occupied (3.71552 bits per kmer). 0:00:40.254 28M / 3G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 87) Building k-mer extensions from k+1-mers 0:00:42.619 28M / 3G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 91) Building k-mer extensions from k+1-mers finished. 0:00:42.620 28M / 3G INFO Early tip clipping (early_simplification.hpp : 181) Early tip clipping 0:00:48.357 28M / 3G INFO Early tip clipping (early_simplification.hpp : 184) 1082335 34-mers were removed by early tip clipper 0:00:48.357 28M / 3G INFO General (graph_construction.hpp : 136) Condensing graph 0:00:48.554 28M / 3G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 355) Extracting unbranching paths 0:00:51.529 32M / 3G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 374) Extracting unbranching paths finished. 108471 sequences extracted 0:00:52.978 32M / 3G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 310) Collecting perfect loops 0:00:53.878 32M / 3G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 343) Collecting perfect loops finished. 0 loops collected 0:00:53.994 64M / 3G INFO General (graph_construction.hpp : 141) Building index with from graph 0:00:53.994 64M / 3G INFO K-mer Index Building (kmer_index_builder.hpp : 289) Building kmer index 0:00:53.994 64M / 3G INFO General (kmer_index_builder.hpp : 106) Splitting kmer instances into 64 buckets using 4 threads. This might take a while. 0:00:53.994 64M / 3G INFO General (file_limit.hpp : 32) Open file limit set to 7168 0:00:53.994 64M / 3G INFO General (kmer_splitters.hpp : 74) Memory available for splitting buffers: 20.8281 Gb 0:00:53.994 64M / 3G INFO General (kmer_splitters.hpp : 82) Using cell size of 524288 0:00:55.035 3G / 3G INFO General (edge_index_builders.hpp : 75) Processed 216629 edges 0:00:55.035 3G / 3G INFO General (edge_index_builders.hpp : 80) Used 216629 sequences. 0:00:55.058 64M / 3G INFO General (kmer_index_builder.hpp : 109) Starting k-mer counting. 0:00:56.010 64M / 3G INFO General (kmer_index_builder.hpp : 115) K-mer counting done. There are 9662740 kmers in total. 0:00:56.010 64M / 3G INFO General (kmer_index_builder.hpp : 121) Merging temporary buckets. 0:00:56.256 64M / 3G INFO K-mer Index Building (kmer_index_builder.hpp : 298) Building perfect hash indices 0:00:57.014 64M / 3G INFO General (kmer_index_builder.hpp : 137) Merging final buckets. 0:00:57.241 64M / 3G INFO K-mer Index Building (kmer_index_builder.hpp : 320) Index built. Total 4488744 bytes occupied (3.71633 bits per kmer). 0:00:57.400 288M / 3G INFO General (edge_index_builders.hpp : 105) Collecting k-mer coverage information from graph, this takes a while. 0:00:58.562 288M / 3G INFO General (edge_index.hpp : 91) Index refilled 0:00:58.586 276M / 3G INFO General (graph_construction.hpp : 173) Filling coverage index 0:00:58.586 276M / 3G INFO General (edge_index_builders.hpp : 183) Collecting k-mer coverage information from reads, this takes a while. 0:02:13.344 276M / 3G INFO General (graph_construction.hpp : 175) Filling coverage and flanking coverage from index 0:02:14.264 276M / 3G INFO General (construction.cpp : 30) Figured out: read length = 140 0:02:14.264 276M / 3G INFO StageManager (stage.cpp : 126) STAGE == EC Threshold Finding 0:02:14.621 276M / 3G INFO General (kmer_coverage_model.cpp : 181) Kmer coverage valley at: 5 0:02:14.621 276M / 3G INFO General (kmer_coverage_model.cpp : 201) K-mer histogram maximum: 35 0:02:14.621 276M / 3G INFO General (kmer_coverage_model.cpp : 237) Estimated median coverage: 37. Coverage mad: 11.8608 0:02:14.621 276M / 3G INFO General (kmer_coverage_model.cpp : 259) Fitting coverage model 0:02:14.656 276M / 3G INFO General (kmer_coverage_model.cpp : 295) ... iteration 2 0:02:14.748 276M / 3G INFO General (kmer_coverage_model.cpp : 295) ... iteration 4 0:02:15.054 276M / 3G INFO General (kmer_coverage_model.cpp : 295) ... iteration 8 0:02:15.688 276M / 3G INFO General (kmer_coverage_model.cpp : 295) ... iteration 16 0:02:16.275 276M / 3G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 37.0004. Fitted coverage std. dev: 10.2607 0:02:16.277 276M / 3G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 0.906114 0:02:16.277 276M / 3G INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 17 0:02:16.277 276M / 3G INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 17 0:02:16.277 276M / 3G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 8243812 0:02:16.277 276M / 3G INFO General (genomic_info_filler.cpp : 127) Mean coverage was calculated as 37.0004 0:02:16.277 276M / 3G INFO General (genomic_info_filler.cpp : 141) EC coverage threshold value was calculated as 17 0:02:16.277 276M / 3G INFO General (genomic_info_filler.cpp : 142) Trusted kmer low bound: 0 0:02:16.277 276M / 3G INFO StageManager (stage.cpp : 126) STAGE == Simplification 0:02:16.296 48M / 3G INFO General (simplification.cpp : 387) Graph simplification started 0:02:16.296 48M / 3G INFO General (simplification.cpp : 77) PROCEDURE == InitialCleaning 0:02:16.296 48M / 3G INFO General (graph_simplification.hpp : 645) Flanking coverage based disconnection disabled 0:02:16.296 48M / 3G INFO General (simplification.cpp : 356) Running Self conjugate edge remover 0:02:16.310 48M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:02:16.310 48M / 3G INFO General (graph_simplification.hpp : 617) Creating parallel br instance 0:02:16.310 48M / 3G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 1 0:02:16.310 48M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:02:16.341 40M / 3G INFO General (simplification.cpp : 358) Triggered 606 times 0:02:16.341 40M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:02:17.530 44M / 3G INFO General (simplification.cpp : 358) Triggered 19740 times 0:02:17.530 44M / 3G INFO General (simplification.cpp : 356) Running Low coverage edge remover 0:02:18.156 44M / 3G INFO General (simplification.cpp : 358) Triggered 13192 times 0:02:18.156 44M / 3G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 2 0:02:18.156 44M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:02:18.164 44M / 3G INFO General (simplification.cpp : 358) Triggered 141 times 0:02:18.164 44M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:02:18.218 44M / 3G INFO General (simplification.cpp : 358) Triggered 537 times 0:02:18.218 44M / 3G INFO General (simplification.cpp : 356) Running Low coverage edge remover 0:02:18.332 44M / 3G INFO General (simplification.cpp : 358) Triggered 1259 times 0:02:18.332 44M / 3G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 3 0:02:18.332 44M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:02:18.332 44M / 3G INFO General (simplification.cpp : 358) Triggered 3 times 0:02:18.332 44M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:02:18.341 44M / 3G INFO General (simplification.cpp : 358) Triggered 54 times 0:02:18.341 44M / 3G INFO General (simplification.cpp : 356) Running Low coverage edge remover 0:02:18.347 44M / 3G INFO General (simplification.cpp : 358) Triggered 64 times 0:02:18.347 44M / 3G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 4 0:02:18.347 44M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:02:18.347 44M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:02:18.347 44M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:02:18.347 44M / 3G INFO General (simplification.cpp : 358) Triggered 2 times 0:02:18.347 44M / 3G INFO General (simplification.cpp : 356) Running Low coverage edge remover 0:02:18.349 44M / 3G INFO General (simplification.cpp : 358) Triggered 18 times 0:02:18.349 44M / 3G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 5 0:02:18.349 44M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:02:18.349 44M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:02:18.349 44M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:02:18.349 44M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:02:18.349 44M / 3G INFO General (simplification.cpp : 356) Running Low coverage edge remover 0:02:18.351 40M / 3G INFO General (simplification.cpp : 358) Triggered 16 times 0:02:18.351 40M / 3G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 6 0:02:18.351 40M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:02:18.351 40M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:02:18.351 40M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:02:18.351 40M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:02:18.351 40M / 3G INFO General (simplification.cpp : 356) Running Low coverage edge remover 0:02:18.352 40M / 3G INFO General (simplification.cpp : 358) Triggered 2 times 0:02:18.352 40M / 3G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 7 0:02:18.352 40M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:02:18.352 40M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:02:18.352 40M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:02:18.352 40M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:02:18.352 40M / 3G INFO General (simplification.cpp : 356) Running Low coverage edge remover 0:02:18.353 40M / 3G INFO General (simplification.cpp : 358) Triggered 10 times 0:02:18.353 40M / 3G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 8 0:02:18.353 40M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:02:18.353 40M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:02:18.353 40M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:02:18.353 40M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:02:18.353 40M / 3G INFO General (simplification.cpp : 356) Running Low coverage edge remover 0:02:18.354 40M / 3G INFO General (simplification.cpp : 358) Triggered 9 times 0:02:18.354 40M / 3G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 9 0:02:18.354 40M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:02:18.354 40M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:02:18.354 40M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:02:18.354 40M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:02:18.354 40M / 3G INFO General (simplification.cpp : 356) Running Low coverage edge remover 0:02:18.355 40M / 3G INFO General (simplification.cpp : 358) Triggered 11 times 0:02:18.355 40M / 3G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 10 0:02:18.355 40M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:02:18.357 40M / 3G INFO General (simplification.cpp : 358) Triggered 6 times 0:02:18.357 40M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:02:18.367 40M / 3G INFO General (simplification.cpp : 358) Triggered 3 times 0:02:18.367 40M / 3G INFO General (simplification.cpp : 356) Running Low coverage edge remover 0:02:18.370 40M / 3G INFO General (simplification.cpp : 358) Triggered 17 times 0:02:18.370 40M / 3G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 11 0:02:18.370 40M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:02:18.370 40M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:02:18.370 40M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:02:18.370 40M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:02:18.370 40M / 3G INFO General (simplification.cpp : 356) Running Low coverage edge remover 0:02:18.370 40M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:02:18.370 40M / 3G INFO General (simplification.cpp : 167) PROCEDURE == Post simplification 0:02:18.370 40M / 3G INFO General (graph_simplification.hpp : 447) Disconnection of relatively low covered edges disabled 0:02:18.370 40M / 3G INFO General (graph_simplification.hpp : 477) Complex tip clipping disabled 0:02:18.370 40M / 3G INFO General (graph_simplification.hpp : 617) Creating parallel br instance 0:02:18.370 40M / 3G INFO General (simplification.cpp : 301) Iteration 1 0:02:18.370 40M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:02:18.371 40M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:02:18.371 40M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:02:18.378 40M / 3G INFO General (simplification.cpp : 358) Triggered 1 times 0:02:18.378 40M / 3G INFO General (simplification.cpp : 301) Iteration 2 0:02:18.378 40M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:02:18.380 40M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:02:18.380 40M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:02:18.387 40M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:02:18.387 40M / 3G INFO General (simplification.cpp : 333) Disrupting self-conjugate edges 0:02:18.390 40M / 3G INFO StageManager (stage.cpp : 126) STAGE == Simplification Cleanup 0:02:18.390 40M / 3G INFO General (simplification.cpp : 547) Removing isolated edges 0:02:18.393 40M / 3G INFO General (simplification.cpp : 570) Counting average coverage 0:02:18.394 40M / 3G INFO General (simplification.cpp : 575) Average coverage = 37.3251 0:02:18.394 40M / 3G INFO StageManager (stage.cpp : 126) STAGE == Contig Output 0:02:18.394 40M / 3G INFO General (contig_output_stage.cpp : 40) Writing GFA to /Users/Mike_Lee/working_genomics_de_novo_temp/spades_kmers_set_careful_assembly//K33/assembly_graph_with_scaffolds.gfa 0:02:18.442 40M / 3G INFO General (contig_output.hpp : 22) Outputting contigs to /Users/Mike_Lee/working_genomics_de_novo_temp/spades_kmers_set_careful_assembly//K33/before_rr.fasta 0:02:18.644 40M / 3G INFO General (contig_output_stage.cpp : 50) Outputting FastG graph to /Users/Mike_Lee/working_genomics_de_novo_temp/spades_kmers_set_careful_assembly//K33/assembly_graph.fastg 0:02:19.027 40M / 3G INFO General (contig_output.hpp : 22) Outputting contigs to /Users/Mike_Lee/working_genomics_de_novo_temp/spades_kmers_set_careful_assembly//K33/simplified_contigs.fasta 0:02:19.211 40M / 3G INFO General (contig_output.hpp : 22) Outputting contigs to /Users/Mike_Lee/working_genomics_de_novo_temp/spades_kmers_set_careful_assembly//K33/final_contigs.fasta 0:02:19.393 40M / 3G INFO StageManager (stage.cpp : 126) STAGE == Contig Output 0:02:19.393 40M / 3G INFO General (contig_output_stage.cpp : 40) Writing GFA to /Users/Mike_Lee/working_genomics_de_novo_temp/spades_kmers_set_careful_assembly//K33/assembly_graph_with_scaffolds.gfa 0:02:19.451 40M / 3G INFO General (contig_output.hpp : 22) Outputting contigs to /Users/Mike_Lee/working_genomics_de_novo_temp/spades_kmers_set_careful_assembly//K33/before_rr.fasta 0:02:19.596 40M / 3G INFO General (contig_output_stage.cpp : 50) Outputting FastG graph to /Users/Mike_Lee/working_genomics_de_novo_temp/spades_kmers_set_careful_assembly//K33/assembly_graph.fastg 0:02:19.909 40M / 3G INFO General (contig_output.hpp : 22) Outputting contigs to /Users/Mike_Lee/working_genomics_de_novo_temp/spades_kmers_set_careful_assembly//K33/simplified_contigs.fasta 0:02:20.080 40M / 3G INFO General (contig_output.hpp : 22) Outputting contigs to /Users/Mike_Lee/working_genomics_de_novo_temp/spades_kmers_set_careful_assembly//K33/final_contigs.fasta 0:02:20.265 40M / 3G INFO General (launch.hpp : 137) SPAdes finished 0:02:20.295 20M / 3G INFO General (main.cpp : 110) Assembling time: 0 hours 2 minutes 20 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_kmers_set_careful_assembly/K55/configs/config.info 0:00:00.000 4M / 4M INFO General (main.cpp : 76) Loading config from /Users/Mike_Lee/working_genomics_de_novo_temp/spades_kmers_set_careful_assembly/K55/configs/careful_mode.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_kmers_set_careful_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 0:00:00.001 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. 0:00:00.002 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 0:00:12.486 2G / 2G INFO General (kmer_splitters.hpp : 291) Processed 3142047 reads 0:00:22.523 2G / 2G INFO General (kmer_splitters.hpp : 291) Processed 5938904 reads 0:00:22.523 2G / 2G INFO General (kmer_splitters.hpp : 297) Adding contigs from previous K 0:00:24.270 16M / 2G INFO General (kmer_splitters.hpp : 310) Used 5938904 reads. Maximum read length 140 0:00:24.270 16M / 2G INFO General (kmer_splitters.hpp : 311) Average read length 140 0:00:24.270 16M / 2G INFO General (kmer_index_builder.hpp : 109) Starting k-mer counting. 0:00:26.807 16M / 2G INFO General (kmer_index_builder.hpp : 115) K-mer counting done. There are 11239275 kmers in total. 0:00:26.807 16M / 2G INFO General (kmer_index_builder.hpp : 121) Merging temporary buckets. 0:00:27.047 16M / 2G INFO K-mer Index Building (kmer_index_builder.hpp : 289) Building kmer index 0:00:27.047 16M / 2G INFO General (kmer_index_builder.hpp : 106) Splitting kmer instances into 64 buckets using 4 threads. This might take a while. 0:00:27.047 16M / 2G INFO General (file_limit.hpp : 32) Open file limit set to 7168 0:00:27.048 16M / 2G INFO General (kmer_splitters.hpp : 74) Memory available for splitting buffers: 20.832 Gb 0:00:27.048 16M / 2G INFO General (kmer_splitters.hpp : 82) Using cell size of 524288 0:00:29.759 3G / 3G INFO General (kmer_splitters.hpp : 381) Processed 11239275 kmers 0:00:29.759 3G / 3G INFO General (kmer_splitters.hpp : 386) Used 11239275 kmers. 0:00:29.807 16M / 3G INFO General (kmer_index_builder.hpp : 109) Starting k-mer counting. 0:00:30.844 16M / 3G INFO General (kmer_index_builder.hpp : 115) K-mer counting done. There are 11225939 kmers in total. 0:00:30.844 16M / 3G INFO General (kmer_index_builder.hpp : 121) Merging temporary buckets. 0:00:31.104 16M / 3G INFO K-mer Index Building (kmer_index_builder.hpp : 298) Building perfect hash indices 0:00:31.957 16M / 3G INFO General (kmer_index_builder.hpp : 137) Merging final buckets. 0:00:32.245 16M / 3G INFO K-mer Index Building (kmer_index_builder.hpp : 320) Index built. Total 5213488 bytes occupied (3.71532 bits per kmer). 0:00:32.257 28M / 3G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 87) Building k-mer extensions from k+1-mers 0:00:34.727 28M / 3G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 91) Building k-mer extensions from k+1-mers finished. 0:00:34.727 28M / 3G INFO General (graph_construction.hpp : 136) Condensing graph 0:00:34.910 28M / 3G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 355) Extracting unbranching paths 0:00:39.688 52M / 3G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 374) Extracting unbranching paths finished. 260722 sequences extracted 0:00:42.185 52M / 3G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 310) Collecting perfect loops 0:00:43.442 52M / 3G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 343) Collecting perfect loops finished. 0 loops collected 0:00:43.734 112M / 3G INFO General (graph_construction.hpp : 141) Building index with from graph 0:00:43.734 112M / 3G INFO K-mer Index Building (kmer_index_builder.hpp : 289) Building kmer index 0:00:43.734 112M / 3G INFO General (kmer_index_builder.hpp : 106) Splitting kmer instances into 64 buckets using 4 threads. This might take a while. 0:00:43.734 112M / 3G INFO General (file_limit.hpp : 32) Open file limit set to 7168 0:00:43.734 112M / 3G INFO General (kmer_splitters.hpp : 74) Memory available for splitting buffers: 20.8242 Gb 0:00:43.734 112M / 3G INFO General (kmer_splitters.hpp : 82) Using cell size of 524288 0:00:45.261 3G / 3G INFO General (edge_index_builders.hpp : 75) Processed 521402 edges 0:00:45.261 3G / 3G INFO General (edge_index_builders.hpp : 80) Used 521402 sequences. 0:00:45.285 112M / 3G INFO General (kmer_index_builder.hpp : 109) Starting k-mer counting. 0:00:46.314 112M / 3G INFO General (kmer_index_builder.hpp : 115) K-mer counting done. There are 11239275 kmers in total. 0:00:46.314 112M / 3G INFO General (kmer_index_builder.hpp : 121) Merging temporary buckets. 0:00:46.602 112M / 3G INFO K-mer Index Building (kmer_index_builder.hpp : 298) Building perfect hash indices 0:00:47.481 116M / 3G INFO General (kmer_index_builder.hpp : 137) Merging final buckets. 0:00:47.774 116M / 3G INFO K-mer Index Building (kmer_index_builder.hpp : 320) Index built. Total 5219760 bytes occupied (3.71537 bits per kmer). 0:00:47.944 376M / 3G INFO General (edge_index_builders.hpp : 105) Collecting k-mer coverage information from graph, this takes a while. 0:00:49.334 376M / 3G INFO General (edge_index.hpp : 91) Index refilled 0:00:49.358 360M / 3G INFO General (graph_construction.hpp : 173) Filling coverage index 0:00:49.358 360M / 3G INFO General (edge_index_builders.hpp : 183) Collecting k-mer coverage information from reads, this takes a while. 0:01:50.352 360M / 3G INFO General (graph_construction.hpp : 175) Filling coverage and flanking coverage from index 0:01:51.954 360M / 3G INFO General (construction.cpp : 30) Figured out: read length = 140 0:01:51.955 360M / 3G INFO StageManager (stage.cpp : 126) STAGE == EC Threshold Finding 0:01:52.320 360M / 3G INFO General (kmer_coverage_model.cpp : 181) Kmer coverage valley at: 4 0:01:52.320 360M / 3G INFO General (kmer_coverage_model.cpp : 201) K-mer histogram maximum: 27 0:01:52.320 360M / 3G INFO General (kmer_coverage_model.cpp : 237) Estimated median coverage: 29. Coverage mad: 10.3782 0:01:52.320 360M / 3G INFO General (kmer_coverage_model.cpp : 259) Fitting coverage model 0:01:52.350 360M / 3G INFO General (kmer_coverage_model.cpp : 295) ... iteration 2 0:01:52.424 360M / 3G INFO General (kmer_coverage_model.cpp : 295) ... iteration 4 0:01:52.688 360M / 3G INFO General (kmer_coverage_model.cpp : 295) ... iteration 8 0:01:53.215 360M / 3G INFO General (kmer_coverage_model.cpp : 295) ... iteration 16 0:01:53.801 360M / 3G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 29.2949. Fitted coverage std. dev: 8.56469 0:01:53.802 360M / 3G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 0.892381 0:01:53.802 360M / 3G INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 14 0:01:53.802 360M / 3G INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 14 0:01:53.802 360M / 3G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 8179565 0:01:53.802 360M / 3G INFO General (genomic_info_filler.cpp : 127) Mean coverage was calculated as 29.2949 0:01:53.802 360M / 3G INFO General (genomic_info_filler.cpp : 141) EC coverage threshold value was calculated as 14 0:01:53.802 360M / 3G INFO General (genomic_info_filler.cpp : 142) Trusted kmer low bound: 0 0:01:53.802 360M / 3G INFO StageManager (stage.cpp : 126) STAGE == Gap Closer 0:01:53.803 360M / 3G INFO General (gap_closer.cpp : 159) Preparing shift maps 0:01:54.066 376M / 3G INFO General (gap_closer.cpp : 119) Processing paired reads (takes a while) 0:02:00.596 380M / 3G INFO General (gap_closer.cpp : 138) Used 1484726 paired reads 0:02:00.596 380M / 3G INFO General (gap_closer.cpp : 140) Merging paired indices 0:02:00.665 360M / 3G INFO GapCloser (gap_closer.cpp : 346) Closing short gaps 0:02:01.297 360M / 3G INFO GapCloser (gap_closer.cpp : 380) Closing short gaps complete: filled 11 gaps after checking 180 candidates 0:02:01.320 360M / 3G INFO StageManager (stage.cpp : 126) STAGE == Simplification 0:02:01.340 92M / 3G INFO General (simplification.cpp : 387) Graph simplification started 0:02:01.340 92M / 3G INFO General (simplification.cpp : 77) PROCEDURE == InitialCleaning 0:02:01.340 92M / 3G INFO General (graph_simplification.hpp : 645) Flanking coverage based disconnection disabled 0:02:01.340 92M / 3G INFO General (simplification.cpp : 356) Running Self conjugate edge remover 0:02:01.380 92M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:02:01.380 92M / 3G INFO General (graph_simplification.hpp : 617) Creating parallel br instance 0:02:01.380 92M / 3G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 1 0:02:01.380 92M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:02:03.708 96M / 3G INFO General (simplification.cpp : 358) Triggered 109413 times 0:02:03.708 96M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:02:06.466 140M / 3G INFO General (simplification.cpp : 358) Triggered 10497 times 0:02:06.466 140M / 3G INFO General (simplification.cpp : 356) Running Low coverage edge remover 0:02:06.702 128M / 3G INFO General (simplification.cpp : 358) Triggered 2480 times 0:02:06.702 128M / 3G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 2 0:02:06.702 128M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:02:06.716 128M / 3G INFO General (simplification.cpp : 358) Triggered 152 times 0:02:06.716 128M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:02:06.831 128M / 3G INFO General (simplification.cpp : 358) Triggered 218 times 0:02:06.831 128M / 3G INFO General (simplification.cpp : 356) Running Low coverage edge remover 0:02:06.918 128M / 3G INFO General (simplification.cpp : 358) Triggered 391 times 0:02:06.918 128M / 3G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 3 0:02:06.918 128M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:02:06.926 128M / 3G INFO General (simplification.cpp : 358) Triggered 28 times 0:02:06.926 128M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:02:06.941 128M / 3G INFO General (simplification.cpp : 358) Triggered 19 times 0:02:06.942 128M / 3G INFO General (simplification.cpp : 356) Running Low coverage edge remover 0:02:06.944 128M / 3G INFO General (simplification.cpp : 358) Triggered 25 times 0:02:06.944 128M / 3G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 4 0:02:06.944 128M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:02:06.944 128M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:02:06.945 128M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:02:06.945 128M / 3G INFO General (simplification.cpp : 358) Triggered 1 times 0:02:06.945 128M / 3G INFO General (simplification.cpp : 356) Running Low coverage edge remover 0:02:06.945 128M / 3G INFO General (simplification.cpp : 358) Triggered 4 times 0:02:06.945 128M / 3G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 5 0:02:06.945 128M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:02:06.945 128M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:02:06.945 128M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:02:06.945 128M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:02:06.945 128M / 3G INFO General (simplification.cpp : 356) Running Low coverage edge remover 0:02:06.946 128M / 3G INFO General (simplification.cpp : 358) Triggered 2 times 0:02:06.946 128M / 3G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 6 0:02:06.946 128M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:02:06.946 128M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:02:06.946 128M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:02:06.946 128M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:02:06.946 128M / 3G INFO General (simplification.cpp : 356) Running Low coverage edge remover 0:02:06.948 128M / 3G INFO General (simplification.cpp : 358) Triggered 8 times 0:02:06.948 128M / 3G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 7 0:02:06.948 128M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:02:06.948 128M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:02:06.948 128M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:02:06.948 128M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:02:06.948 128M / 3G INFO General (simplification.cpp : 356) Running Low coverage edge remover 0:02:06.952 128M / 3G INFO General (simplification.cpp : 358) Triggered 5 times 0:02:06.952 128M / 3G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 8 0:02:06.952 128M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:02:06.952 128M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:02:06.952 128M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:02:06.952 128M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:02:06.953 128M / 3G INFO General (simplification.cpp : 356) Running Low coverage edge remover 0:02:06.953 128M / 3G INFO General (simplification.cpp : 358) Triggered 2 times 0:02:06.953 128M / 3G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 9 0:02:06.953 128M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:02:06.953 128M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:02:06.953 128M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:02:06.953 128M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:02:06.953 128M / 3G INFO General (simplification.cpp : 356) Running Low coverage edge remover 0:02:06.953 128M / 3G INFO General (simplification.cpp : 358) Triggered 7 times 0:02:06.953 128M / 3G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 10 0:02:06.953 128M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:02:06.954 128M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:02:06.954 128M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:02:06.958 128M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:02:06.958 128M / 3G INFO General (simplification.cpp : 356) Running Low coverage edge remover 0:02:06.960 128M / 3G INFO General (simplification.cpp : 358) Triggered 9 times 0:02:06.960 128M / 3G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 11 0:02:06.960 128M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:02:06.960 128M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:02:06.960 128M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:02:06.960 128M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:02:06.960 128M / 3G INFO General (simplification.cpp : 356) Running Low coverage edge remover 0:02:06.960 128M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:02:06.960 128M / 3G INFO General (simplification.cpp : 167) PROCEDURE == Post simplification 0:02:06.960 128M / 3G INFO General (graph_simplification.hpp : 447) Disconnection of relatively low covered edges disabled 0:02:06.960 128M / 3G INFO General (graph_simplification.hpp : 477) Complex tip clipping disabled 0:02:06.960 128M / 3G INFO General (graph_simplification.hpp : 617) Creating parallel br instance 0:02:06.960 128M / 3G INFO General (simplification.cpp : 301) Iteration 1 0:02:06.960 128M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:02:06.961 128M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:02:06.961 128M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:02:06.964 128M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:02:06.964 128M / 3G INFO General (simplification.cpp : 301) Iteration 2 0:02:06.964 128M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:02:06.965 128M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:02:06.965 128M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:02:06.969 128M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:02:06.969 128M / 3G INFO General (simplification.cpp : 333) Disrupting self-conjugate edges 0:02:06.971 128M / 3G INFO StageManager (stage.cpp : 126) STAGE == Gap Closer 0:02:06.971 128M / 3G INFO General (graph_pack.hpp : 99) Index refill 0:02:06.971 128M / 3G INFO K-mer Index Building (kmer_index_builder.hpp : 289) Building kmer index 0:02:06.971 128M / 3G INFO General (kmer_index_builder.hpp : 106) Splitting kmer instances into 64 buckets using 4 threads. This might take a while. 0:02:06.971 128M / 3G INFO General (file_limit.hpp : 32) Open file limit set to 7168 0:02:06.971 128M / 3G INFO General (kmer_splitters.hpp : 74) Memory available for splitting buffers: 20.8229 Gb 0:02:06.971 128M / 3G INFO General (kmer_splitters.hpp : 82) Using cell size of 524288 0:02:07.866 3G / 3G INFO General (edge_index_builders.hpp : 75) Processed 3668 edges 0:02:07.866 3G / 3G INFO General (edge_index_builders.hpp : 80) Used 3668 sequences. 0:02:07.886 128M / 3G INFO General (kmer_index_builder.hpp : 109) Starting k-mer counting. 0:02:08.688 128M / 3G INFO General (kmer_index_builder.hpp : 115) K-mer counting done. There are 8534796 kmers in total. 0:02:08.688 128M / 3G INFO General (kmer_index_builder.hpp : 121) Merging temporary buckets. 0:02:08.888 128M / 3G INFO K-mer Index Building (kmer_index_builder.hpp : 298) Building perfect hash indices 0:02:09.549 128M / 3G INFO General (kmer_index_builder.hpp : 137) Merging final buckets. 0:02:09.766 128M / 3G INFO K-mer Index Building (kmer_index_builder.hpp : 320) Index built. Total 3965776 bytes occupied (3.71728 bits per kmer). 0:02:09.912 324M / 3G INFO General (edge_index_builders.hpp : 105) Collecting k-mer coverage information from graph, this takes a while. 0:02:10.985 324M / 3G INFO General (edge_index.hpp : 91) Index refilled 0:02:10.985 324M / 3G INFO General (gap_closer.cpp : 159) Preparing shift maps 0:02:10.987 324M / 3G INFO General (gap_closer.cpp : 119) Processing paired reads (takes a while) 0:02:17.232 324M / 3G INFO General (gap_closer.cpp : 138) Used 1484726 paired reads 0:02:17.232 324M / 3G INFO General (gap_closer.cpp : 140) Merging paired indices 0:02:17.235 324M / 3G INFO GapCloser (gap_closer.cpp : 346) Closing short gaps 0:02:17.239 324M / 3G INFO GapCloser (gap_closer.cpp : 380) Closing short gaps complete: filled 6 gaps after checking 111 candidates 0:02:17.758 324M / 3G INFO StageManager (stage.cpp : 126) STAGE == Simplification Cleanup 0:02:17.759 324M / 3G INFO General (simplification.cpp : 547) Removing isolated edges 0:02:17.804 324M / 3G INFO General (simplification.cpp : 570) Counting average coverage 0:02:17.805 324M / 3G INFO General (simplification.cpp : 575) Average coverage = 29.4677 0:02:17.805 324M / 3G INFO StageManager (stage.cpp : 126) STAGE == Contig Output 0:02:17.805 324M / 3G INFO General (contig_output_stage.cpp : 40) Writing GFA to /Users/Mike_Lee/working_genomics_de_novo_temp/spades_kmers_set_careful_assembly//K55/assembly_graph_with_scaffolds.gfa 0:02:17.840 324M / 3G INFO General (contig_output.hpp : 22) Outputting contigs to /Users/Mike_Lee/working_genomics_de_novo_temp/spades_kmers_set_careful_assembly//K55/before_rr.fasta 0:02:18.025 324M / 3G INFO General (contig_output_stage.cpp : 50) Outputting FastG graph to /Users/Mike_Lee/working_genomics_de_novo_temp/spades_kmers_set_careful_assembly//K55/assembly_graph.fastg 0:02:18.438 324M / 3G INFO General (contig_output.hpp : 22) Outputting contigs to /Users/Mike_Lee/working_genomics_de_novo_temp/spades_kmers_set_careful_assembly//K55/simplified_contigs.fasta 0:02:18.640 324M / 3G INFO General (contig_output.hpp : 22) Outputting contigs to /Users/Mike_Lee/working_genomics_de_novo_temp/spades_kmers_set_careful_assembly//K55/final_contigs.fasta 0:02:18.847 324M / 3G INFO StageManager (stage.cpp : 126) STAGE == Contig Output 0:02:18.847 324M / 3G INFO General (contig_output_stage.cpp : 40) Writing GFA to /Users/Mike_Lee/working_genomics_de_novo_temp/spades_kmers_set_careful_assembly//K55/assembly_graph_with_scaffolds.gfa 0:02:18.894 324M / 3G INFO General (contig_output.hpp : 22) Outputting contigs to /Users/Mike_Lee/working_genomics_de_novo_temp/spades_kmers_set_careful_assembly//K55/before_rr.fasta 0:02:19.032 324M / 3G INFO General (contig_output_stage.cpp : 50) Outputting FastG graph to /Users/Mike_Lee/working_genomics_de_novo_temp/spades_kmers_set_careful_assembly//K55/assembly_graph.fastg 0:02:19.309 324M / 3G INFO General (contig_output.hpp : 22) Outputting contigs to /Users/Mike_Lee/working_genomics_de_novo_temp/spades_kmers_set_careful_assembly//K55/simplified_contigs.fasta 0:02:19.481 324M / 3G INFO General (contig_output.hpp : 22) Outputting contigs to /Users/Mike_Lee/working_genomics_de_novo_temp/spades_kmers_set_careful_assembly//K55/final_contigs.fasta 0:02:19.656 324M / 3G INFO General (launch.hpp : 137) SPAdes finished 0:02:20.303 24M / 3G INFO General (main.cpp : 110) Assembling time: 0 hours 2 minutes 20 seconds == Running assembler: K77 0:00:00.000 4M / 4M INFO General (main.cpp : 76) Loading config from /Users/Mike_Lee/working_genomics_de_novo_temp/spades_kmers_set_careful_assembly/K77/configs/config.info 0:00:00.000 4M / 4M INFO General (main.cpp : 76) Loading config from /Users/Mike_Lee/working_genomics_de_novo_temp/spades_kmers_set_careful_assembly/K77/configs/careful_mode.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_kmers_set_careful_assembly/dataset.info) with K=77 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=77 0:00:00.036 4M / 4M INFO General (kmer_index_builder.hpp : 106) Splitting kmer instances into 16 buckets using 4 threads. This might take a while. 0:00:00.036 4M / 4M INFO General (file_limit.hpp : 32) Open file limit set to 7168 0:00:00.036 4M / 4M INFO General (kmer_splitters.hpp : 74) Memory available for splitting buffers: 20.833 Gb 0:00:00.036 4M / 4M INFO General (kmer_splitters.hpp : 82) Using cell size of 1398101 0:00:10.241 2G / 2G INFO General (kmer_splitters.hpp : 291) Processed 2830375 reads 0:00:19.755 2G / 2G INFO General (kmer_splitters.hpp : 291) Processed 5662465 reads 0:00:20.844 2G / 2G INFO General (kmer_splitters.hpp : 291) Processed 5938904 reads 0:00:20.844 2G / 2G INFO General (kmer_splitters.hpp : 297) Adding contigs from previous K 0:00:22.837 16M / 2G INFO General (kmer_splitters.hpp : 310) Used 5938904 reads. Maximum read length 140 0:00:22.837 16M / 2G INFO General (kmer_splitters.hpp : 311) Average read length 140 0:00:22.837 16M / 2G INFO General (kmer_index_builder.hpp : 109) Starting k-mer counting. 0:00:26.667 16M / 2G INFO General (kmer_index_builder.hpp : 115) K-mer counting done. There are 11356793 kmers in total. 0:00:26.667 16M / 2G INFO General (kmer_index_builder.hpp : 121) Merging temporary buckets. 0:00:27.055 16M / 2G INFO K-mer Index Building (kmer_index_builder.hpp : 289) Building kmer index 0:00:27.055 16M / 2G INFO General (kmer_index_builder.hpp : 106) Splitting kmer instances into 64 buckets using 4 threads. This might take a while. 0:00:27.055 16M / 2G INFO General (file_limit.hpp : 32) Open file limit set to 7168 0:00:27.055 16M / 2G INFO General (kmer_splitters.hpp : 74) Memory available for splitting buffers: 20.832 Gb 0:00:27.055 16M / 2G INFO General (kmer_splitters.hpp : 82) Using cell size of 349525 0:00:30.616 3G / 3G INFO General (kmer_splitters.hpp : 381) Processed 11356793 kmers 0:00:30.616 3G / 3G INFO General (kmer_splitters.hpp : 386) Used 11356793 kmers. 0:00:30.691 16M / 3G INFO General (kmer_index_builder.hpp : 109) Starting k-mer counting. 0:00:32.180 16M / 3G INFO General (kmer_index_builder.hpp : 115) K-mer counting done. There are 11358688 kmers in total. 0:00:32.180 16M / 3G INFO General (kmer_index_builder.hpp : 121) Merging temporary buckets. 0:00:32.602 16M / 3G INFO K-mer Index Building (kmer_index_builder.hpp : 298) Building perfect hash indices 0:00:33.688 16M / 3G INFO General (kmer_index_builder.hpp : 137) Merging final buckets. 0:00:34.102 16M / 3G INFO K-mer Index Building (kmer_index_builder.hpp : 320) Index built. Total 5275224 bytes occupied (3.71538 bits per kmer). 0:00:34.119 28M / 3G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 87) Building k-mer extensions from k+1-mers 0:00:37.089 28M / 3G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 91) Building k-mer extensions from k+1-mers finished. 0:00:37.089 28M / 3G INFO General (graph_construction.hpp : 136) Condensing graph 0:00:37.415 28M / 3G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 355) Extracting unbranching paths 0:00:41.213 52M / 3G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 374) Extracting unbranching paths finished. 246417 sequences extracted 0:00:43.480 52M / 3G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 310) Collecting perfect loops 0:00:45.281 52M / 3G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 343) Collecting perfect loops finished. 0 loops collected 0:00:45.713 112M / 3G INFO General (graph_construction.hpp : 141) Building index with from graph 0:00:45.714 112M / 3G INFO K-mer Index Building (kmer_index_builder.hpp : 289) Building kmer index 0:00:45.714 112M / 3G INFO General (kmer_index_builder.hpp : 106) Splitting kmer instances into 64 buckets using 4 threads. This might take a while. 0:00:45.715 112M / 3G INFO General (file_limit.hpp : 32) Open file limit set to 7168 0:00:45.715 112M / 3G INFO General (kmer_splitters.hpp : 74) Memory available for splitting buffers: 20.8242 Gb 0:00:45.715 112M / 3G INFO General (kmer_splitters.hpp : 82) Using cell size of 349525 0:00:47.849 3G / 3G INFO General (edge_index_builders.hpp : 75) Processed 492830 edges 0:00:47.849 3G / 3G INFO General (edge_index_builders.hpp : 80) Used 492830 sequences. 0:00:47.894 112M / 3G INFO General (kmer_index_builder.hpp : 109) Starting k-mer counting. 0:00:49.475 112M / 3G INFO General (kmer_index_builder.hpp : 115) K-mer counting done. There are 11356793 kmers in total. 0:00:49.475 112M / 3G INFO General (kmer_index_builder.hpp : 121) Merging temporary buckets. 0:00:50.001 112M / 3G INFO K-mer Index Building (kmer_index_builder.hpp : 298) Building perfect hash indices 0:00:51.369 112M / 3G INFO General (kmer_index_builder.hpp : 137) Merging final buckets. 0:00:51.782 112M / 3G INFO K-mer Index Building (kmer_index_builder.hpp : 320) Index built. Total 5274312 bytes occupied (3.71535 bits per kmer). 0:00:51.973 372M / 3G INFO General (edge_index_builders.hpp : 105) Collecting k-mer coverage information from graph, this takes a while. 0:00:53.360 372M / 3G INFO General (edge_index.hpp : 91) Index refilled 0:00:53.403 360M / 3G INFO General (graph_construction.hpp : 173) Filling coverage index 0:00:53.403 360M / 3G INFO General (edge_index_builders.hpp : 183) Collecting k-mer coverage information from reads, this takes a while. 0:01:48.419 360M / 3G INFO General (graph_construction.hpp : 175) Filling coverage and flanking coverage from index 0:01:50.176 360M / 3G INFO General (construction.cpp : 30) Figured out: read length = 140 0:01:50.177 356M / 3G INFO StageManager (stage.cpp : 126) STAGE == EC Threshold Finding 0:01:50.499 356M / 3G INFO General (kmer_coverage_model.cpp : 181) Kmer coverage valley at: 4 0:01:50.499 356M / 3G INFO General (kmer_coverage_model.cpp : 201) K-mer histogram maximum: 20 0:01:50.499 356M / 3G INFO General (kmer_coverage_model.cpp : 237) Estimated median coverage: 21. Coverage mad: 8.8956 0:01:50.499 356M / 3G INFO General (kmer_coverage_model.cpp : 259) Fitting coverage model 0:01:50.526 356M / 3G INFO General (kmer_coverage_model.cpp : 295) ... iteration 2 0:01:50.584 356M / 3G INFO General (kmer_coverage_model.cpp : 295) ... iteration 4 0:01:50.781 356M / 3G INFO General (kmer_coverage_model.cpp : 295) ... iteration 8 0:01:51.193 356M / 3G INFO General (kmer_coverage_model.cpp : 295) ... iteration 16 0:01:51.572 356M / 3G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 21.6619. Fitted coverage std. dev: 6.82922 0:01:51.573 356M / 3G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 0.685717 0:01:51.573 356M / 3G INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 11 0:01:51.573 356M / 3G INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 11 0:01:51.573 356M / 3G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 8033755 0:01:51.573 356M / 3G INFO General (genomic_info_filler.cpp : 127) Mean coverage was calculated as 21.6619 0:01:51.573 356M / 3G INFO General (genomic_info_filler.cpp : 141) EC coverage threshold value was calculated as 11 0:01:51.573 356M / 3G INFO General (genomic_info_filler.cpp : 142) Trusted kmer low bound: 0 0:01:51.573 356M / 3G INFO StageManager (stage.cpp : 126) STAGE == Gap Closer 0:01:51.573 356M / 3G INFO General (gap_closer.cpp : 159) Preparing shift maps 0:01:51.842 376M / 3G INFO General (gap_closer.cpp : 119) Processing paired reads (takes a while) 0:01:57.154 380M / 3G INFO General (gap_closer.cpp : 138) Used 1484726 paired reads 0:01:57.154 380M / 3G INFO General (gap_closer.cpp : 140) Merging paired indices 0:01:57.236 360M / 3G INFO GapCloser (gap_closer.cpp : 346) Closing short gaps 0:01:57.810 360M / 3G INFO GapCloser (gap_closer.cpp : 380) Closing short gaps complete: filled 13 gaps after checking 253 candidates 0:01:57.837 360M / 3G INFO StageManager (stage.cpp : 126) STAGE == Simplification 0:01:57.859 92M / 3G INFO General (simplification.cpp : 387) Graph simplification started 0:01:57.859 92M / 3G INFO General (simplification.cpp : 77) PROCEDURE == InitialCleaning 0:01:57.859 92M / 3G INFO General (simplification.cpp : 50) Most init cleaning disabled on main iteration 0:01:57.859 92M / 3G INFO General (simplification.cpp : 356) Running Self conjugate edge remover 0:01:57.897 92M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:01:57.897 92M / 3G INFO General (graph_simplification.hpp : 617) Creating parallel br instance 0:01:57.897 92M / 3G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 1 0:01:57.897 92M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:02:00.293 88M / 3G INFO General (simplification.cpp : 358) Triggered 116285 times 0:02:00.293 88M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:02:01.300 96M / 3G INFO General (simplification.cpp : 358) Triggered 2718 times 0:02:01.300 96M / 3G INFO General (simplification.cpp : 356) Running Low coverage edge remover 0:02:01.317 100M / 3G INFO General (simplification.cpp : 358) Triggered 96 times 0:02:01.317 100M / 3G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 2 0:02:01.317 100M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:02:01.331 100M / 3G INFO General (simplification.cpp : 358) Triggered 81 times 0:02:01.331 100M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:02:01.345 96M / 3G INFO General (simplification.cpp : 358) Triggered 24 times 0:02:01.345 96M / 3G INFO General (simplification.cpp : 356) Running Low coverage edge remover 0:02:01.387 100M / 3G INFO General (simplification.cpp : 358) Triggered 102 times 0:02:01.388 100M / 3G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 3 0:02:01.388 100M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:02:01.389 100M / 3G INFO General (simplification.cpp : 358) Triggered 12 times 0:02:01.389 100M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:02:01.393 100M / 3G INFO General (simplification.cpp : 358) Triggered 5 times 0:02:01.393 100M / 3G INFO General (simplification.cpp : 356) Running Low coverage edge remover 0:02:01.394 100M / 3G INFO General (simplification.cpp : 358) Triggered 9 times 0:02:01.394 100M / 3G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 4 0:02:01.394 100M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:02:01.394 100M / 3G INFO General (simplification.cpp : 358) Triggered 1 times 0:02:01.394 100M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:02:01.395 100M / 3G INFO General (simplification.cpp : 358) Triggered 2 times 0:02:01.395 100M / 3G INFO General (simplification.cpp : 356) Running Low coverage edge remover 0:02:01.395 100M / 3G INFO General (simplification.cpp : 358) Triggered 3 times 0:02:01.396 100M / 3G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 5 0:02:01.396 100M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:02:01.396 100M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:02:01.396 100M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:02:01.396 100M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:02:01.396 100M / 3G INFO General (simplification.cpp : 356) Running Low coverage edge remover 0:02:01.396 100M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:02:01.396 100M / 3G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 6 0:02:01.396 100M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:02:01.396 100M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:02:01.396 100M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:02:01.396 100M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:02:01.396 100M / 3G INFO General (simplification.cpp : 356) Running Low coverage edge remover 0:02:01.396 100M / 3G INFO General (simplification.cpp : 358) Triggered 2 times 0:02:01.396 100M / 3G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 7 0:02:01.396 100M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:02:01.396 100M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:02:01.396 100M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:02:01.396 100M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:02:01.396 100M / 3G INFO General (simplification.cpp : 356) Running Low coverage edge remover 0:02:01.397 100M / 3G INFO General (simplification.cpp : 358) Triggered 1 times 0:02:01.397 100M / 3G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 8 0:02:01.397 100M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:02:01.397 100M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:02:01.397 100M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:02:01.397 96M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:02:01.397 96M / 3G INFO General (simplification.cpp : 356) Running Low coverage edge remover 0:02:01.397 96M / 3G INFO General (simplification.cpp : 358) Triggered 1 times 0:02:01.397 96M / 3G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 9 0:02:01.397 96M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:02:01.397 96M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:02:01.397 96M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:02:01.397 96M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:02:01.397 96M / 3G INFO General (simplification.cpp : 356) Running Low coverage edge remover 0:02:01.397 96M / 3G INFO General (simplification.cpp : 358) Triggered 4 times 0:02:01.397 96M / 3G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 10 0:02:01.397 96M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:02:01.401 96M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:02:01.401 96M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:02:01.406 96M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:02:01.406 96M / 3G INFO General (simplification.cpp : 356) Running Low coverage edge remover 0:02:01.409 96M / 3G INFO General (simplification.cpp : 358) Triggered 7 times 0:02:01.409 96M / 3G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 11 0:02:01.409 96M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:02:01.409 96M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:02:01.409 96M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:02:01.409 96M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:02:01.409 96M / 3G INFO General (simplification.cpp : 356) Running Low coverage edge remover 0:02:01.409 96M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:02:01.409 96M / 3G INFO General (simplification.cpp : 167) PROCEDURE == Post simplification 0:02:01.410 96M / 3G INFO General (graph_simplification.hpp : 447) Disconnection of relatively low covered edges disabled 0:02:01.410 96M / 3G INFO General (graph_simplification.hpp : 477) Complex tip clipping disabled 0:02:01.410 96M / 3G INFO General (graph_simplification.hpp : 617) Creating parallel br instance 0:02:01.410 96M / 3G INFO General (simplification.cpp : 301) Iteration 1 0:02:01.410 96M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:02:01.412 96M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:02:01.412 96M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:02:01.417 96M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:02:01.417 96M / 3G INFO General (simplification.cpp : 301) Iteration 2 0:02:01.417 96M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:02:01.419 96M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:02:01.419 96M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:02:01.423 96M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:02:01.423 96M / 3G INFO General (simplification.cpp : 333) Disrupting self-conjugate edges 0:02:01.429 96M / 3G INFO StageManager (stage.cpp : 126) STAGE == Gap Closer 0:02:01.429 96M / 3G INFO General (graph_pack.hpp : 99) Index refill 0:02:01.429 96M / 3G INFO K-mer Index Building (kmer_index_builder.hpp : 289) Building kmer index 0:02:01.429 96M / 3G INFO General (kmer_index_builder.hpp : 106) Splitting kmer instances into 64 buckets using 4 threads. This might take a while. 0:02:01.429 96M / 3G INFO General (file_limit.hpp : 32) Open file limit set to 7168 0:02:01.429 96M / 3G INFO General (kmer_splitters.hpp : 74) Memory available for splitting buffers: 20.8255 Gb 0:02:01.429 96M / 3G INFO General (kmer_splitters.hpp : 82) Using cell size of 349525 0:02:02.503 3G / 3G INFO General (edge_index_builders.hpp : 75) Processed 11512 edges 0:02:02.503 3G / 3G INFO General (edge_index_builders.hpp : 80) Used 11512 sequences. 0:02:02.529 96M / 3G INFO General (kmer_index_builder.hpp : 109) Starting k-mer counting. 0:02:03.520 96M / 3G INFO General (kmer_index_builder.hpp : 115) K-mer counting done. There are 8807354 kmers in total. 0:02:03.521 96M / 3G INFO General (kmer_index_builder.hpp : 121) Merging temporary buckets. 0:02:03.847 96M / 3G INFO K-mer Index Building (kmer_index_builder.hpp : 298) Building perfect hash indices 0:02:04.580 104M / 3G INFO General (kmer_index_builder.hpp : 137) Merging final buckets. 0:02:04.877 104M / 3G INFO K-mer Index Building (kmer_index_builder.hpp : 320) Index built. Total 4092232 bytes occupied (3.7171 bits per kmer). 0:02:05.007 308M / 3G INFO General (edge_index_builders.hpp : 105) Collecting k-mer coverage information from graph, this takes a while. 0:02:05.971 308M / 3G INFO General (edge_index.hpp : 91) Index refilled 0:02:05.972 308M / 3G INFO General (gap_closer.cpp : 159) Preparing shift maps 0:02:05.982 308M / 3G INFO General (gap_closer.cpp : 119) Processing paired reads (takes a while) 0:02:11.564 308M / 3G INFO General (gap_closer.cpp : 138) Used 1484726 paired reads 0:02:11.564 308M / 3G INFO General (gap_closer.cpp : 140) Merging paired indices 0:02:11.572 308M / 3G INFO GapCloser (gap_closer.cpp : 346) Closing short gaps 0:02:11.585 308M / 3G INFO GapCloser (gap_closer.cpp : 380) Closing short gaps complete: filled 3 gaps after checking 164 candidates 0:02:11.893 308M / 3G INFO StageManager (stage.cpp : 126) STAGE == Simplification Cleanup 0:02:11.893 308M / 3G INFO General (simplification.cpp : 547) Removing isolated edges 0:02:12.187 288M / 3G INFO General (simplification.cpp : 570) Counting average coverage 0:02:12.188 288M / 3G INFO General (simplification.cpp : 575) Average coverage = 21.6667 0:02:12.188 288M / 3G INFO StageManager (stage.cpp : 126) STAGE == Mismatch Correction 0:02:12.188 288M / 3G INFO General (graph_pack.hpp : 108) Normalizing k-mer map. Total 432464 kmers to process 0:02:12.515 288M / 3G INFO General (graph_pack.hpp : 110) Normalizing done 0:02:29.800 288M / 3G INFO General (mismatch_shall_not_pass.hp: 187) Finished collecting potential mismatches positions 0:02:29.900 288M / 3G INFO General (mismatch_shall_not_pass.hp: 284) All edges processed 0:02:29.901 288M / 3G INFO General (mismatch_correction.cpp : 26) Corrected 0 nucleotides 0:02:29.901 288M / 3G INFO StageManager (stage.cpp : 126) STAGE == Contig Output 0:02:29.901 288M / 3G INFO General (contig_output_stage.cpp : 40) Writing GFA to /Users/Mike_Lee/working_genomics_de_novo_temp/spades_kmers_set_careful_assembly//K77/assembly_graph_with_scaffolds.gfa 0:02:29.933 288M / 3G INFO General (contig_output.hpp : 22) Outputting contigs to /Users/Mike_Lee/working_genomics_de_novo_temp/spades_kmers_set_careful_assembly//K77/before_rr.fasta 0:02:30.090 288M / 3G INFO General (contig_output_stage.cpp : 50) Outputting FastG graph to /Users/Mike_Lee/working_genomics_de_novo_temp/spades_kmers_set_careful_assembly//K77/assembly_graph.fastg 0:02:30.422 288M / 3G INFO General (contig_output.hpp : 22) Outputting contigs to /Users/Mike_Lee/working_genomics_de_novo_temp/spades_kmers_set_careful_assembly//K77/simplified_contigs.fasta 0:02:30.572 288M / 3G INFO General (contig_output.hpp : 22) Outputting contigs to /Users/Mike_Lee/working_genomics_de_novo_temp/spades_kmers_set_careful_assembly//K77/intermediate_contigs.fasta 0:02:30.732 288M / 3G INFO StageManager (stage.cpp : 126) STAGE == Paired Information Counting 0:02:30.735 288M / 3G INFO General (graph_pack.hpp : 108) Normalizing k-mer map. Total 432464 kmers to process 0:02:30.735 288M / 3G INFO General (graph_pack.hpp : 110) Normalizing done 0:02:30.735 288M / 3G INFO General (pair_info_count.cpp : 317) Min edge length for estimation: 114373 0:02:30.735 288M / 3G INFO General (pair_info_count.cpp : 328) Estimating insert size for library #0 0:02:30.735 288M / 3G INFO General (pair_info_count.cpp : 176) Estimating insert size (takes a while) 0:02:30.788 368M / 3G INFO General (short_read_mapper.hpp : 88) Selecting usual mapper 0:02:34.396 368M / 3G INFO General (sequence_mapper_notifier.h: 81) Processed 200000 reads 0:02:34.450 368M / 3G INFO General (sequence_mapper_notifier.h: 81) Processed 400000 reads 0:02:34.511 368M / 3G INFO General (sequence_mapper_notifier.h: 81) Processed 600000 reads 0:02:34.560 368M / 3G INFO General (sequence_mapper_notifier.h: 81) Processed 800000 reads 0:02:37.904 368M / 3G INFO General (sequence_mapper_notifier.h: 99) Total 1484726 reads processed 0:02:37.973 368M / 3G INFO General (pair_info_count.cpp : 194) Edge pairs: 67108864 (rough upper limit) 0:02:37.973 368M / 3G INFO General (pair_info_count.cpp : 198) 751521 paired reads (50.6168% of all) aligned to long edges 0:02:37.980 288M / 3G INFO General (pair_info_count.cpp : 351) Insert size = 375.349, deviation = 112.162, left quantile = 233, right quantile = 522, read length = 140 0:02:38.102 480M / 3G INFO General (pair_info_count.cpp : 368) Filtering data for library #0 0:02:38.102 480M / 3G INFO General (short_read_mapper.hpp : 88) Selecting usual mapper 0:02:41.448 480M / 3G INFO General (sequence_mapper_notifier.h: 81) Processed 200000 reads 0:02:41.452 480M / 3G INFO General (sequence_mapper_notifier.h: 81) Processed 400000 reads 0:02:41.458 480M / 3G INFO General (sequence_mapper_notifier.h: 81) Processed 600000 reads 0:02:41.459 480M / 3G INFO General (sequence_mapper_notifier.h: 81) Processed 800000 reads 0:02:44.368 480M / 3G INFO General (sequence_mapper_notifier.h: 99) Total 1484726 reads processed 0:02:44.368 480M / 3G INFO General (pair_info_count.cpp : 380) Mapping library #0 0:02:44.368 480M / 3G INFO General (pair_info_count.cpp : 382) Mapping paired reads (takes a while) 0:02:44.368 480M / 3G INFO General (pair_info_count.cpp : 275) Left insert size quantile 233, right insert size quantile 522, filtering threshold 2, rounding threshold 0 0:02:44.379 492M / 3G INFO General (short_read_mapper.hpp : 88) Selecting usual mapper 0:02:48.016 492M / 3G INFO General (sequence_mapper_notifier.h: 81) Processed 200000 reads 0:02:48.047 492M / 3G INFO General (sequence_mapper_notifier.h: 81) Processed 400000 reads 0:02:48.050 492M / 3G INFO General (sequence_mapper_notifier.h: 81) Processed 600000 reads 0:02:48.081 492M / 3G INFO General (sequence_mapper_notifier.h: 81) Processed 800000 reads 0:02:51.288 492M / 3G INFO General (sequence_mapper_notifier.h: 99) Total 1484726 reads processed 0:02:51.310 288M / 3G INFO StageManager (stage.cpp : 126) STAGE == Distance Estimation 0:02:51.310 288M / 3G INFO General (distance_estimation.cpp : 224) Processing library #0 0:02:51.310 288M / 3G INFO General (distance_estimation.cpp : 130) Weight Filter Done 0:02:51.310 288M / 3G INFO DistanceEstimator (distance_estimation.hpp : 116) Using SIMPLE distance estimator 0:02:51.324 288M / 3G INFO General (distance_estimation.cpp : 35) Filtering info 0:02:51.324 288M / 3G INFO General (pair_info_filters.hpp : 242) Start filtering; index size: 6424 0:02:51.327 288M / 3G INFO General (pair_info_filters.hpp : 263) Done filtering 0:02:51.327 288M / 3G INFO General (distance_estimation.cpp : 172) Refining clustered pair information 0:02:51.329 288M / 3G INFO General (distance_estimation.cpp : 174) The refining of clustered pair information has been finished 0:02:51.329 288M / 3G INFO General (distance_estimation.cpp : 176) Improving paired information 0:02:51.343 288M / 3G INFO PairInfoImprover (pair_info_improver.hpp : 103) Paired info stats: missing = 240; contradictional = 90 0:02:51.360 288M / 3G INFO PairInfoImprover (pair_info_improver.hpp : 103) Paired info stats: missing = 9; contradictional = 12 0:02:51.360 288M / 3G INFO General (distance_estimation.cpp : 183) Filling scaffolding index 0:02:51.360 288M / 3G INFO DistanceEstimator (distance_estimation.hpp : 116) Using SMOOTHING distance estimator 0:02:51.446 288M / 3G INFO General (distance_estimation.cpp : 35) Filtering info 0:02:51.446 288M / 3G INFO General (pair_info_filters.hpp : 242) Start filtering; index size: 1603 0:02:51.447 288M / 3G INFO General (pair_info_filters.hpp : 263) Done filtering 0:02:51.447 288M / 3G INFO General (distance_estimation.cpp : 228) Clearing raw paired index 0:02:51.448 288M / 3G INFO StageManager (stage.cpp : 126) STAGE == Repeat Resolving 0:02:51.448 288M / 3G INFO General (repeat_resolving.cpp : 69) Using Path-Extend repeat resolving 0:02:51.448 288M / 3G INFO General (launcher.cpp : 478) ExSPAnder repeat resolving tool started 0:02:51.450 292M / 3G INFO General (launcher.cpp : 393) Creating main extenders, unique edge length = 2000 0:02:51.450 292M / 3G INFO General (extenders_logic.cpp : 275) Estimated coverage of library #0 is 21.6667 0:02:51.451 292M / 3G INFO General (extenders_logic.cpp : 275) Estimated coverage of library #0 is 21.6667 0:02:51.451 292M / 3G INFO General (extenders_logic.cpp : 472) Using 1 paired-end library 0:02:51.451 292M / 3G INFO General (extenders_logic.cpp : 473) Using 1 paired-end scaffolding library 0:02:51.451 292M / 3G INFO General (extenders_logic.cpp : 474) Using 0 single read libraries 0:02:51.451 292M / 3G INFO General (launcher.cpp : 421) Total number of extenders is 3 0:02:51.451 292M / 3G INFO General (path_extender.hpp : 867) Processed 0 paths from 720 (0%) 0:02:51.643 292M / 3G INFO General (path_extender.hpp : 867) Processed 73 paths from 720 (10%) 0:02:51.696 292M / 3G INFO General (path_extender.hpp : 865) Processed 128 paths from 720 (17%) 0:02:51.709 292M / 3G INFO General (path_extender.hpp : 867) Processed 146 paths from 720 (20%) 0:02:51.715 292M / 3G INFO General (path_extender.hpp : 867) Processed 219 paths from 720 (30%) 0:02:51.722 292M / 3G INFO General (path_extender.hpp : 865) Processed 256 paths from 720 (35%) 0:02:51.725 292M / 3G INFO General (path_extender.hpp : 867) Processed 292 paths from 720 (40%) 0:02:51.727 292M / 3G INFO General (path_extender.hpp : 867) Processed 365 paths from 720 (50%) 0:02:51.728 292M / 3G INFO General (path_extender.hpp : 867) Processed 438 paths from 720 (60%) 0:02:51.729 292M / 3G INFO General (path_extender.hpp : 867) Processed 511 paths from 720 (70%) 0:02:51.729 292M / 3G INFO General (path_extender.hpp : 865) Processed 512 paths from 720 (71%) 0:02:51.737 292M / 3G INFO General (path_extender.hpp : 867) Processed 584 paths from 720 (81%) 0:02:51.737 292M / 3G INFO General (path_extender.hpp : 867) Processed 657 paths from 720 (91%) 0:02:51.737 292M / 3G INFO General (launcher.cpp : 234) Finalizing paths 0:02:51.737 292M / 3G INFO General (launcher.cpp : 236) Deduplicating paths 0:02:51.739 292M / 3G INFO General (launcher.cpp : 240) Paths deduplicated 0:02:51.739 292M / 3G INFO PEResolver (pe_resolver.hpp : 299) Removing overlaps 0:02:51.739 292M / 3G INFO PEResolver (pe_resolver.hpp : 302) Sorting paths 0:02:51.739 292M / 3G INFO PEResolver (pe_resolver.hpp : 309) Marking overlaps 0:02:51.739 292M / 3G INFO OverlapRemover (pe_resolver.hpp : 132) Marking start/end overlaps 0:02:51.741 292M / 3G INFO OverlapRemover (pe_resolver.hpp : 135) Marking remaining overlaps 0:02:51.742 292M / 3G INFO PEResolver (pe_resolver.hpp : 312) Splitting paths 0:02:51.743 292M / 3G INFO PEResolver (pe_resolver.hpp : 317) Deduplicating paths 0:02:51.744 292M / 3G INFO PEResolver (pe_resolver.hpp : 319) Overlaps removed 0:02:51.745 292M / 3G INFO General (launcher.cpp : 257) Paths finalized 0:02:51.745 292M / 3G INFO General (launcher.cpp : 287) Traversing tandem repeats 0:02:51.748 292M / 3G INFO General (launcher.cpp : 297) Traversed 3 loops 0:02:51.748 292M / 3G INFO General (launcher.cpp : 428) Closing gaps in paths 0:02:51.751 292M / 3G INFO General (launcher.cpp : 456) Gap closing completed 0:02:51.751 292M / 3G INFO General (launcher.cpp : 234) Finalizing paths 0:02:51.751 292M / 3G INFO General (launcher.cpp : 236) Deduplicating paths 0:02:51.751 292M / 3G INFO General (launcher.cpp : 240) Paths deduplicated 0:02:51.751 292M / 3G INFO PEResolver (pe_resolver.hpp : 299) Removing overlaps 0:02:51.751 292M / 3G INFO PEResolver (pe_resolver.hpp : 302) Sorting paths 0:02:51.752 292M / 3G INFO PEResolver (pe_resolver.hpp : 309) Marking overlaps 0:02:51.752 292M / 3G INFO OverlapRemover (pe_resolver.hpp : 132) Marking start/end overlaps 0:02:51.752 292M / 3G INFO OverlapRemover (pe_resolver.hpp : 135) Marking remaining overlaps 0:02:51.753 292M / 3G INFO PEResolver (pe_resolver.hpp : 312) Splitting paths 0:02:51.753 292M / 3G INFO PEResolver (pe_resolver.hpp : 317) Deduplicating paths 0:02:51.753 292M / 3G INFO PEResolver (pe_resolver.hpp : 319) Overlaps removed 0:02:51.754 292M / 3G INFO General (launcher.cpp : 257) Paths finalized 0:02:51.755 292M / 3G INFO General (launcher.cpp : 531) ExSPAnder repeat resolving tool finished 0:02:51.765 292M / 3G INFO StageManager (stage.cpp : 126) STAGE == Contig Output 0:02:51.765 292M / 3G INFO General (contig_output_stage.cpp : 40) Writing GFA to /Users/Mike_Lee/working_genomics_de_novo_temp/spades_kmers_set_careful_assembly//K77/assembly_graph_with_scaffolds.gfa 0:02:51.795 292M / 3G INFO General (contig_output.hpp : 22) Outputting contigs to /Users/Mike_Lee/working_genomics_de_novo_temp/spades_kmers_set_careful_assembly//K77/before_rr.fasta 0:02:51.929 288M / 3G INFO General (contig_output_stage.cpp : 50) Outputting FastG graph to /Users/Mike_Lee/working_genomics_de_novo_temp/spades_kmers_set_careful_assembly//K77/assembly_graph.fastg 0:02:52.198 288M / 3G INFO General (contig_output_stage.cpp : 20) Outputting FastG paths to /Users/Mike_Lee/working_genomics_de_novo_temp/spades_kmers_set_careful_assembly//K77/final_contigs.paths 0:02:52.390 288M / 3G INFO General (contig_output_stage.cpp : 20) Outputting FastG paths to /Users/Mike_Lee/working_genomics_de_novo_temp/spades_kmers_set_careful_assembly//K77/scaffolds.paths 0:02:52.556 288M / 3G INFO General (launch.hpp : 137) SPAdes finished 0:02:52.795 24M / 3G INFO General (main.cpp : 110) Assembling time: 0 hours 2 minutes 52 seconds ===== Assembling finished. Used k-mer sizes: 21, 33, 55, 77 ===== Mismatch correction started. == Processing of contigs == Running contig polishing tool: /Users/Mike_Lee/happy_bin/SPAdes-3.11.1-Darwin/bin/corrector /Users/Mike_Lee/working_genomics_de_novo_temp/spades_kmers_set_careful_assembly/mismatch_corrector/contigs/configs/corrector.info /Users/Mike_Lee/working_genomics_de_novo_temp/spades_kmers_set_careful_assembly/misc/assembled_contigs.fasta == Dataset description file was created: /Users/Mike_Lee/working_genomics_de_novo_temp/spades_kmers_set_careful_assembly/mismatch_corrector/contigs/configs/corrector.info /Users/Mike_Lee/working_genomics_de_novo_temp/spades_kmers_set_careful_assembly/mismatch_corrector/contigs/configs/log.properties 0:00:00.000 4M / 4M INFO General (main.cpp : 58) Starting MismatchCorrector, built from N/A, git revision N/A 0:00:00.001 4M / 4M INFO DatasetProcessor (dataset_processor.cpp : 195) Splitting assembly... 0:00:00.001 4M / 4M INFO DatasetProcessor (dataset_processor.cpp : 196) Assembly file: /Users/Mike_Lee/working_genomics_de_novo_temp/spades_kmers_set_careful_assembly/misc/assembled_contigs.fasta 0:00:00.287 4M / 8M INFO DatasetProcessor (dataset_processor.cpp : 203) Processing paired sublib of number 0 0:00:00.287 4M / 8M INFO DatasetProcessor (dataset_processor.cpp : 206) /Users/Mike_Lee/working_genomics_de_novo_temp/BCep_R1_QCd_err_cor.fastq.gz /Users/Mike_Lee/working_genomics_de_novo_temp/BCep_R2_QCd_err_cor.fastq.gz 0:00:00.287 4M / 8M INFO DatasetProcessor (dataset_processor.cpp : 140) Running bwa index ...: /Users/Mike_Lee/happy_bin/SPAdes-3.11.1-Darwin/bin/bwa-spades index -a is /Users/Mike_Lee/working_genomics_de_novo_temp/spades_kmers_set_careful_assembly/misc/assembled_contigs.fasta [bwa_index] Pack FASTA... 0.08 sec [bwa_index] Construct BWT for the packed sequence... [bwa_index] 4.61 seconds elapse. [bwa_index] Update BWT... 0.05 sec [bwa_index] Pack forward-only FASTA... 0.05 sec [bwa_index] Construct SA from BWT and Occ... 1.91 sec [main] Version: 0.7.12-r1039 [main] CMD: /Users/Mike_Lee/happy_bin/SPAdes-3.11.1-Darwin/bin/bwa-spades index -a is /Users/Mike_Lee/working_genomics_de_novo_temp/spades_kmers_set_careful_assembly/misc/assembled_contigs.fasta [main] Real time: 6.783 sec; CPU: 6.705 sec 0:00:07.084 4M / 8M INFO DatasetProcessor (dataset_processor.cpp : 149) Running bwa mem ...:/Users/Mike_Lee/happy_bin/SPAdes-3.11.1-Darwin/bin/bwa-spades mem -v 1 -t 4 /Users/Mike_Lee/working_genomics_de_novo_temp/spades_kmers_set_careful_assembly/misc/assembled_contigs.fasta /Users/Mike_Lee/working_genomics_de_novo_temp/BCep_R1_QCd_err_cor.fastq.gz /Users/Mike_Lee/working_genomics_de_novo_temp/BCep_R2_QCd_err_cor.fastq.gz > /Users/Mike_Lee/working_genomics_de_novo_temp/spades_kmers_set_careful_assembly/tmp/corrector_912OI_/lib0_CYgv2Y/tmp.sam [main] Version: 0.7.12-r1039 [main] CMD: /Users/Mike_Lee/happy_bin/SPAdes-3.11.1-Darwin/bin/bwa-spades mem -v 1 -t 4 /Users/Mike_Lee/working_genomics_de_novo_temp/spades_kmers_set_careful_assembly/misc/assembled_contigs.fasta /Users/Mike_Lee/working_genomics_de_novo_temp/BCep_R1_QCd_err_cor.fastq.gz /Users/Mike_Lee/working_genomics_de_novo_temp/BCep_R2_QCd_err_cor.fastq.gz [main] Real time: 77.736 sec; CPU: 284.216 sec 0:01:24.834 4M / 8M INFO DatasetProcessor (dataset_processor.cpp : 209) Adding samfile /Users/Mike_Lee/working_genomics_de_novo_temp/spades_kmers_set_careful_assembly/tmp/corrector_912OI_/lib0_CYgv2Y/tmp.sam 0:01:33.787 52M / 52M INFO DatasetProcessor (dataset_processor.cpp : 105) processed 1000000reads, flushing 0:01:42.016 52M / 52M INFO DatasetProcessor (dataset_processor.cpp : 105) processed 2000000reads, flushing 0:01:49.965 52M / 52M INFO DatasetProcessor (dataset_processor.cpp : 105) processed 3000000reads, flushing 0:01:59.377 52M / 52M INFO DatasetProcessor (dataset_processor.cpp : 105) processed 4000000reads, flushing 0:02:03.998 8M / 52M INFO DatasetProcessor (dataset_processor.cpp : 235) Processing contigs 0:02:23.682 280M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_4_length_364479_cov_21.546089 processed with 3 changes in thread 2 0:02:27.626 276M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_2_length_472579_cov_19.238748 processed with 4 changes in thread 1 0:02:28.238 260M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_3_length_440862_cov_21.072605 processed with 4 changes in thread 3 0:02:43.120 244M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_6_length_306432_cov_19.636862 processed with 3 changes in thread 1 0:02:46.153 244M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_5_length_344685_cov_25.459394 processed with 5 changes in thread 2 0:02:47.153 232M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_7_length_299227_cov_24.655313 processed with 2 changes in thread 3 0:02:50.022 224M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_1_length_961949_cov_19.621119 processed with 6 changes in thread 0 0:02:59.764 136M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_9_length_234109_cov_21.678835 processed with 0 changes in thread 2 0:03:00.650 136M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_8_length_268954_cov_23.278852 processed with 1 changes in thread 1 0:03:01.002 132M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_10_length_233751_cov_21.940400 processed with 4 changes in thread 3 0:03:02.925 136M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_11_length_230050_cov_22.620221 processed with 0 changes in thread 0 0:03:11.998 128M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_14_length_197116_cov_20.332609 processed with 4 changes in thread 3 0:03:12.320 124M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_12_length_217699_cov_21.270837 processed with 2 changes in thread 2 0:03:12.691 116M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_13_length_198969_cov_21.176749 processed with 2 changes in thread 1 0:03:14.569 112M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_15_length_187413_cov_22.794412 processed with 1 changes in thread 0 0:03:21.188 104M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_18_length_158486_cov_20.793945 processed with 0 changes in thread 1 0:03:22.650 96M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_19_length_143955_cov_24.086900 processed with 1 changes in thread 0 0:03:22.651 96M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_16_length_185852_cov_22.792948 processed with 0 changes in thread 3 0:03:22.820 80M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_17_length_169218_cov_25.408121 processed with 6 changes in thread 2 0:03:29.008 80M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_23_length_110572_cov_22.487307 processed with 0 changes in thread 2 0:03:29.406 80M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_22_length_110696_cov_23.729631 processed with 0 changes in thread 3 0:03:29.500 76M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_20_length_137841_cov_23.290054 processed with 0 changes in thread 1 0:03:30.072 72M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_21_length_132351_cov_23.399875 processed with 1 changes in thread 0 0:03:35.231 72M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_24_length_110289_cov_22.734357 processed with 0 changes in thread 2 0:03:35.242 72M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_25_length_108332_cov_21.130054 processed with 0 changes in thread 3 0:03:35.319 72M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_26_length_107910_cov_20.836618 processed with 0 changes in thread 1 0:03:35.621 68M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_27_length_98944_cov_23.022151 processed with 4 changes in thread 0 0:03:39.940 64M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_28_length_97291_cov_20.455418 processed with 1 changes in thread 2 0:03:39.946 52M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_31_length_92827_cov_19.998857 processed with 0 changes in thread 0 0:03:40.263 60M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_29_length_96001_cov_21.316803 processed with 0 changes in thread 3 0:03:40.606 56M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_30_length_95246_cov_22.232229 processed with 0 changes in thread 1 0:03:43.912 56M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_33_length_79870_cov_21.181206 processed with 0 changes in thread 0 0:03:44.465 56M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_32_length_90163_cov_21.067780 processed with 0 changes in thread 2 0:03:44.905 56M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_34_length_79606_cov_22.817488 processed with 1 changes in thread 3 0:03:45.154 56M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_35_length_78062_cov_23.423812 processed with 0 changes in thread 1 0:03:48.310 56M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_36_length_75123_cov_24.300229 processed with 0 changes in thread 0 0:03:48.386 56M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_39_length_55189_cov_22.543312 processed with 0 changes in thread 1 0:03:48.456 56M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_37_length_73714_cov_22.161889 processed with 1 changes in thread 2 0:03:48.733 56M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_38_length_68531_cov_22.212829 processed with 0 changes in thread 3 0:03:50.243 56M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_43_length_50921_cov_12.211785 processed with 0 changes in thread 3 0:03:50.951 56M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_40_length_55064_cov_20.018459 processed with 0 changes in thread 0 0:03:51.026 48M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_42_length_51172_cov_20.956963 processed with 0 changes in thread 2 0:03:51.369 44M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_41_length_51580_cov_23.217832 processed with 0 changes in thread 1 0:03:52.822 40M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_44_length_49790_cov_20.959065 processed with 0 changes in thread 3 0:03:53.044 36M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_46_length_42523_cov_19.967300 processed with 0 changes in thread 2 0:03:53.077 36M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_45_length_44894_cov_19.954839 processed with 0 changes in thread 0 0:03:53.673 36M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_47_length_41288_cov_22.147655 processed with 0 changes in thread 1 0:03:54.183 32M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_48_length_38254_cov_13.331849 processed with 2 changes in thread 3 0:03:54.863 32M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_50_length_34581_cov_21.672850 processed with 0 changes in thread 0 0:03:54.943 36M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_49_length_36434_cov_21.153946 processed with 0 changes in thread 2 0:03:55.562 32M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_51_length_32176_cov_22.353500 processed with 0 changes in thread 1 0:03:55.772 28M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_52_length_31930_cov_20.079302 processed with 0 changes in thread 3 0:03:56.285 24M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_53_length_31095_cov_20.054646 processed with 0 changes in thread 0 0:03:56.609 28M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_54_length_30188_cov_23.285211 processed with 0 changes in thread 2 0:03:57.198 28M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_55_length_28221_cov_23.648238 processed with 0 changes in thread 1 0:03:57.305 24M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_56_length_27922_cov_22.091183 processed with 0 changes in thread 3 0:03:57.406 24M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_58_length_25618_cov_12.825026 processed with 0 changes in thread 2 0:03:57.821 24M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_57_length_27126_cov_23.426596 processed with 0 changes in thread 0 0:03:58.415 24M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_59_length_22905_cov_20.985719 processed with 0 changes in thread 1 0:03:58.678 24M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_60_length_22537_cov_23.265227 processed with 0 changes in thread 3 0:04:01.175 20M / 284M INFO DatasetProcessor (dataset_processor.cpp : 255) Gluing processed contigs 0:04:01.414 16M / 284M INFO General (main.cpp : 71) Correcting time: 0 hours 4 minutes 1 seconds == Processing of scaffolds == Running contig polishing tool: /Users/Mike_Lee/happy_bin/SPAdes-3.11.1-Darwin/bin/corrector /Users/Mike_Lee/working_genomics_de_novo_temp/spades_kmers_set_careful_assembly/mismatch_corrector/scaffolds/configs/corrector.info /Users/Mike_Lee/working_genomics_de_novo_temp/spades_kmers_set_careful_assembly/misc/assembled_scaffolds.fasta == Dataset description file was created: /Users/Mike_Lee/working_genomics_de_novo_temp/spades_kmers_set_careful_assembly/mismatch_corrector/scaffolds/configs/corrector.info /Users/Mike_Lee/working_genomics_de_novo_temp/spades_kmers_set_careful_assembly/mismatch_corrector/scaffolds/configs/log.properties 0:00:00.000 4M / 4M INFO General (main.cpp : 58) Starting MismatchCorrector, built from N/A, git revision N/A 0:00:00.000 4M / 4M INFO DatasetProcessor (dataset_processor.cpp : 195) Splitting assembly... 0:00:00.000 4M / 4M INFO DatasetProcessor (dataset_processor.cpp : 196) Assembly file: /Users/Mike_Lee/working_genomics_de_novo_temp/spades_kmers_set_careful_assembly/misc/assembled_scaffolds.fasta 0:00:00.257 4M / 8M INFO DatasetProcessor (dataset_processor.cpp : 203) Processing paired sublib of number 0 0:00:00.257 4M / 8M INFO DatasetProcessor (dataset_processor.cpp : 206) /Users/Mike_Lee/working_genomics_de_novo_temp/BCep_R1_QCd_err_cor.fastq.gz /Users/Mike_Lee/working_genomics_de_novo_temp/BCep_R2_QCd_err_cor.fastq.gz 0:00:00.257 4M / 8M INFO DatasetProcessor (dataset_processor.cpp : 140) Running bwa index ...: /Users/Mike_Lee/happy_bin/SPAdes-3.11.1-Darwin/bin/bwa-spades index -a is /Users/Mike_Lee/working_genomics_de_novo_temp/spades_kmers_set_careful_assembly/misc/assembled_scaffolds.fasta [bwa_index] Pack FASTA... 0.07 sec [bwa_index] Construct BWT for the packed sequence... [bwa_index] 4.58 seconds elapse. [bwa_index] Update BWT... 0.05 sec [bwa_index] Pack forward-only FASTA... 0.05 sec [bwa_index] Construct SA from BWT and Occ... 1.91 sec [main] Version: 0.7.12-r1039 [main] CMD: /Users/Mike_Lee/happy_bin/SPAdes-3.11.1-Darwin/bin/bwa-spades index -a is /Users/Mike_Lee/working_genomics_de_novo_temp/spades_kmers_set_careful_assembly/misc/assembled_scaffolds.fasta [main] Real time: 6.849 sec; CPU: 6.666 sec 0:00:07.124 4M / 8M INFO DatasetProcessor (dataset_processor.cpp : 149) Running bwa mem ...:/Users/Mike_Lee/happy_bin/SPAdes-3.11.1-Darwin/bin/bwa-spades mem -v 1 -t 4 /Users/Mike_Lee/working_genomics_de_novo_temp/spades_kmers_set_careful_assembly/misc/assembled_scaffolds.fasta /Users/Mike_Lee/working_genomics_de_novo_temp/BCep_R1_QCd_err_cor.fastq.gz /Users/Mike_Lee/working_genomics_de_novo_temp/BCep_R2_QCd_err_cor.fastq.gz > /Users/Mike_Lee/working_genomics_de_novo_temp/spades_kmers_set_careful_assembly/tmp/corrector_O7o6Bs/lib0_FXejN5/tmp.sam [main] Version: 0.7.12-r1039 [main] CMD: /Users/Mike_Lee/happy_bin/SPAdes-3.11.1-Darwin/bin/bwa-spades mem -v 1 -t 4 /Users/Mike_Lee/working_genomics_de_novo_temp/spades_kmers_set_careful_assembly/misc/assembled_scaffolds.fasta /Users/Mike_Lee/working_genomics_de_novo_temp/BCep_R1_QCd_err_cor.fastq.gz /Users/Mike_Lee/working_genomics_de_novo_temp/BCep_R2_QCd_err_cor.fastq.gz [main] Real time: 80.319 sec; CPU: 285.803 sec 0:01:27.460 4M / 8M INFO DatasetProcessor (dataset_processor.cpp : 209) Adding samfile /Users/Mike_Lee/working_genomics_de_novo_temp/spades_kmers_set_careful_assembly/tmp/corrector_O7o6Bs/lib0_FXejN5/tmp.sam 0:01:35.330 52M / 52M INFO DatasetProcessor (dataset_processor.cpp : 105) processed 1000000reads, flushing 0:01:43.074 52M / 52M INFO DatasetProcessor (dataset_processor.cpp : 105) processed 2000000reads, flushing 0:01:51.523 52M / 52M INFO DatasetProcessor (dataset_processor.cpp : 105) processed 3000000reads, flushing 0:01:59.708 52M / 52M INFO DatasetProcessor (dataset_processor.cpp : 105) processed 4000000reads, flushing 0:02:03.711 8M / 52M INFO DatasetProcessor (dataset_processor.cpp : 235) Processing contigs 0:02:22.405 280M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_4_length_364479_cov_21.546089 processed with 3 changes in thread 2 0:02:25.834 276M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_2_length_472579_cov_19.238748 processed with 4 changes in thread 1 0:02:26.336 260M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_3_length_440862_cov_21.072605 processed with 4 changes in thread 3 0:02:40.773 244M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_6_length_306432_cov_19.636862 processed with 3 changes in thread 1 0:02:44.492 244M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_5_length_344685_cov_25.459394 processed with 5 changes in thread 2 0:02:45.712 240M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_7_length_299227_cov_24.655313 processed with 2 changes in thread 3 0:02:47.542 232M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_1_length_961949_cov_19.621119 processed with 6 changes in thread 0 0:02:57.389 144M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_8_length_288984_cov_22.507994 processed with 10 changes in thread 1 0:02:58.114 136M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_10_length_234109_cov_21.678835 processed with 0 changes in thread 3 0:02:59.204 140M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_11_length_233751_cov_21.940400 processed with 4 changes in thread 0 0:02:59.880 136M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_9_length_268954_cov_23.278852 processed with 1 changes in thread 2 0:03:09.425 136M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_14_length_209358_cov_20.199010 processed with 3 changes in thread 0 0:03:10.072 128M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_13_length_217699_cov_21.270837 processed with 2 changes in thread 3 0:03:10.329 120M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_15_length_198969_cov_21.176749 processed with 2 changes in thread 2 0:03:10.951 112M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_12_length_230050_cov_22.620221 processed with 0 changes in thread 1 0:03:18.366 104M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_18_length_158486_cov_20.793945 processed with 0 changes in thread 2 0:03:19.665 96M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_16_length_187413_cov_22.794412 processed with 1 changes in thread 0 0:03:19.908 88M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_19_length_143955_cov_24.086900 processed with 1 changes in thread 1 0:03:21.063 80M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_17_length_169218_cov_25.408121 processed with 0 changes in thread 3 0:03:26.557 80M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_20_length_137841_cov_23.290054 processed with 0 changes in thread 2 0:03:26.981 76M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_22_length_127106_cov_20.994009 processed with 0 changes in thread 1 0:03:27.513 72M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_21_length_132351_cov_23.399875 processed with 1 changes in thread 0 0:03:28.548 76M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_23_length_120680_cov_22.522450 processed with 1 changes in thread 3 0:03:33.143 72M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_26_length_108332_cov_21.130054 processed with 0 changes in thread 0 0:03:33.410 76M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_24_length_110696_cov_23.729631 processed with 0 changes in thread 2 0:03:33.690 76M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_25_length_110572_cov_22.487307 processed with 0 changes in thread 1 0:03:34.453 68M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_27_length_107910_cov_20.836618 processed with 0 changes in thread 3 0:03:38.382 64M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_29_length_97291_cov_20.455418 processed with 1 changes in thread 2 0:03:38.613 60M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_28_length_98944_cov_23.022151 processed with 4 changes in thread 0 0:03:39.166 56M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_30_length_95246_cov_22.232229 processed with 0 changes in thread 1 0:03:39.231 56M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_31_length_92827_cov_19.998857 processed with 0 changes in thread 3 0:03:42.596 56M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_33_length_79870_cov_21.181206 processed with 0 changes in thread 0 0:03:43.188 56M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_32_length_90163_cov_21.067780 processed with 0 changes in thread 2 0:03:43.775 56M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_34_length_79606_cov_22.817488 processed with 1 changes in thread 1 0:03:43.922 56M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_35_length_78062_cov_23.423812 processed with 0 changes in thread 3 0:03:46.788 56M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_39_length_55064_cov_20.018459 processed with 0 changes in thread 3 0:03:46.889 56M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_37_length_73714_cov_22.161889 processed with 1 changes in thread 2 0:03:46.948 56M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_38_length_55189_cov_22.543312 processed with 0 changes in thread 1 0:03:47.015 56M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_36_length_75123_cov_24.300229 processed with 0 changes in thread 0 0:03:48.533 52M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_42_length_50921_cov_12.211785 processed with 0 changes in thread 1 0:03:49.357 56M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_41_length_51172_cov_20.956963 processed with 4 changes in thread 2 0:03:49.541 52M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_43_length_50891_cov_20.787421 processed with 19 changes in thread 0 0:03:49.826 44M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_40_length_51580_cov_23.217832 processed with 0 changes in thread 3 0:03:51.142 40M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_44_length_49790_cov_20.959065 processed with 0 changes in thread 1 0:03:51.429 36M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_45_length_44894_cov_19.954839 processed with 0 changes in thread 2 0:03:51.579 32M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_46_length_42523_cov_19.967300 processed with 0 changes in thread 0 0:03:52.164 32M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_47_length_41288_cov_22.147655 processed with 0 changes in thread 3 0:03:52.432 32M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_48_length_38254_cov_13.331849 processed with 5 changes in thread 1 0:03:53.070 28M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_49_length_32176_cov_22.353500 processed with 0 changes in thread 2 0:03:53.128 24M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_50_length_31930_cov_20.079302 processed with 0 changes in thread 0 0:03:53.894 28M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_51_length_30188_cov_23.285211 processed with 0 changes in thread 3 0:03:54.045 24M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_52_length_28221_cov_23.648238 processed with 0 changes in thread 1 0:03:54.439 24M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_53_length_27922_cov_22.091183 processed with 0 changes in thread 2 0:03:54.571 24M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_54_length_27126_cov_23.426596 processed with 0 changes in thread 0 0:03:54.711 24M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_55_length_25618_cov_12.825026 processed with 0 changes in thread 3 0:03:55.255 24M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_56_length_22905_cov_20.985719 processed with 0 changes in thread 1 0:03:55.724 20M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_57_length_22537_cov_23.265227 processed with 0 changes in thread 2 0:03:57.594 20M / 284M INFO DatasetProcessor (dataset_processor.cpp : 255) Gluing processed contigs 0:03:57.820 16M / 284M INFO General (main.cpp : 71) Correcting time: 0 hours 3 minutes 57 seconds ===== Mismatch correction finished. * Assembled contigs are in /Users/Mike_Lee/working_genomics_de_novo_temp/spades_kmers_set_careful_assembly/contigs.fasta * Assembled scaffolds are in /Users/Mike_Lee/working_genomics_de_novo_temp/spades_kmers_set_careful_assembly/scaffolds.fasta * Assembly graph is in /Users/Mike_Lee/working_genomics_de_novo_temp/spades_kmers_set_careful_assembly/assembly_graph.fastg * Assembly graph in GFA format is in /Users/Mike_Lee/working_genomics_de_novo_temp/spades_kmers_set_careful_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_kmers_set_careful_assembly/contigs.paths * Paths in the assembly graph corresponding to the scaffolds are in /Users/Mike_Lee/working_genomics_de_novo_temp/spades_kmers_set_careful_assembly/scaffolds.paths ======= SPAdes pipeline finished. SPAdes log can be found here: /Users/Mike_Lee/working_genomics_de_novo_temp/spades_kmers_set_careful_assembly/spades.log Thank you for using SPAdes!