Command line: /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/conda/anaconda3/envs/de_novo_example/bin/spades.py -1 /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/genomics_de_novo_temp/working_dir/BCep_R1_QCd_err_cor.fastq.gz -2 /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/genomics_de_novo_temp/working_dir/BCep_R2_QCd_err_cor.fastq.gz -o /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/genomics_de_novo_temp/working_dir/spades_default_assembly -t 4 --only-assembler System information: SPAdes version: 3.11.1 Python version: 3.6.10 OS: Linux-3.10.0-1160.36.2.el7.x86_64-x86_64-with-redhat-7.9-Maipo Output dir: /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/genomics_de_novo_temp/working_dir/spades_default_assembly Mode: ONLY assembling (without read error correction) Debug mode is turned OFF Dataset parameters: Multi-cell mode (you should set '--sc' flag if input data was obtained with MDA (single-cell) technology or --meta flag if processing metagenomic dataset) Reads: Library number: 1, library type: paired-end orientation: fr left reads: ['/nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/genomics_de_novo_temp/working_dir/BCep_R1_QCd_err_cor.fastq.gz'] right reads: ['/nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/genomics_de_novo_temp/working_dir/BCep_R2_QCd_err_cor.fastq.gz'] interlaced reads: not specified single reads: not specified Assembly parameters: k: automatic selection based on read length Repeat resolution is enabled Mismatch careful mode is turned OFF MismatchCorrector will be SKIPPED Coverage cutoff is turned OFF Other parameters: Dir for temp files: /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/genomics_de_novo_temp/working_dir/spades_default_assembly/tmp Threads: 4 Memory limit (in Gb): 250 ======= SPAdes pipeline started. Log can be found here: /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/genomics_de_novo_temp/working_dir/spades_default_assembly/spades.log ===== Assembling started. == Running assembler: K21 0:00:00.000 4M / 4M INFO General (main.cpp : 76) Loading config from /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/genomics_de_novo_temp/working_dir/spades_default_assembly/K21/configs/config.info 0:00:00.001 4M / 4M INFO General (memory_limit.hpp : 51) Memory limit set to 250 Gb 0:00:00.001 4M / 4M INFO General (main.cpp : 89) Starting SPAdes, built from N/A, git revision N/A 0:00:00.001 4M / 4M INFO General (main.cpp : 90) Maximum k-mer length: 128 0:00:00.001 4M / 4M INFO General (main.cpp : 91) Assembling dataset (/nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/genomics_de_novo_temp/working_dir/spades_default_assembly/dataset.info) with K=21 0:00:00.001 4M / 4M INFO General (launch.hpp : 51) SPAdes started 0:00:00.001 4M / 4M INFO General (launch.hpp : 58) Starting from stage: construction 0:00:00.001 4M / 4M INFO General (launch.hpp : 61) Two-step RR enabled: 0 0:00:00.001 4M / 4M INFO StageManager (stage.cpp : 126) STAGE == Construction 0:00:00.003 4M / 4M INFO General (read_converter.hpp : 84) Converting reads to binary format for library #0 (takes a while) 0:00:00.003 4M / 4M INFO General (read_converter.hpp : 85) Converting paired reads 0:00:00.173 80M / 84M INFO General (binary_converter.hpp : 139) 16384 reads processed 0:00:00.279 92M / 92M INFO General (binary_converter.hpp : 139) 32768 reads processed 0:00:00.489 116M / 116M INFO General (binary_converter.hpp : 139) 65536 reads processed 0:00:00.903 164M / 164M INFO General (binary_converter.hpp : 139) 131072 reads processed 0:00:01.780 264M / 264M INFO General (binary_converter.hpp : 139) 262144 reads processed 0:00:03.871 320M / 320M INFO General (binary_converter.hpp : 139) 524288 reads processed 0:00:07.983 344M / 344M INFO General (binary_converter.hpp : 139) 1048576 reads processed 0:00:11.548 288M / 352M INFO General (binary_converter.hpp : 159) 1484726 reads written 0:00:11.684 4M / 352M INFO General (read_converter.hpp : 94) Converting single reads 0:00:11.849 132M / 352M INFO General (binary_converter.hpp : 159) 0 reads written 0:00:12.064 4M / 352M INFO General (graph_construction.hpp : 120) Constructing DeBruijn graph for k=21 0:00:12.065 4M / 352M INFO General (kmer_index_builder.hpp : 106) Splitting kmer instances into 16 buckets using 4 threads. This might take a while. 0:00:12.065 4M / 352M INFO General (file_limit.hpp : 32) Open file limit set to 1024 0:00:12.065 4M / 352M INFO General (kmer_splitters.hpp : 74) Memory available for splitting buffers: 20.833 Gb 0:00:12.065 4M / 352M INFO General (kmer_splitters.hpp : 82) Using cell size of 4194304 0:00:26.781 2G / 2G INFO General (kmer_splitters.hpp : 291) Processed 4501245 reads 0:00:31.645 2G / 2G INFO General (kmer_splitters.hpp : 291) Processed 5938904 reads 0:00:31.645 2G / 2G INFO General (kmer_splitters.hpp : 297) Adding contigs from previous K 0:00:31.932 16M / 2G INFO General (kmer_splitters.hpp : 310) Used 5938904 reads. Maximum read length 140 0:00:31.932 16M / 2G INFO General (kmer_splitters.hpp : 311) Average read length 140 0:00:31.932 16M / 2G INFO General (kmer_index_builder.hpp : 109) Starting k-mer counting. 0:00:32.374 16M / 2G INFO General (kmer_index_builder.hpp : 115) K-mer counting done. There are 10173588 kmers in total. 0:00:32.374 16M / 2G INFO General (kmer_index_builder.hpp : 121) Merging temporary buckets. 0:00:32.660 16M / 2G INFO K-mer Index Building (kmer_index_builder.hpp : 289) Building kmer index 0:00:32.660 16M / 2G INFO General (kmer_index_builder.hpp : 106) Splitting kmer instances into 64 buckets using 4 threads. This might take a while. 0:00:32.660 16M / 2G INFO General (file_limit.hpp : 32) Open file limit set to 1024 0:00:32.660 16M / 2G INFO General (kmer_splitters.hpp : 74) Memory available for splitting buffers: 20.832 Gb 0:00:32.660 16M / 2G INFO General (kmer_splitters.hpp : 82) Using cell size of 1048576 0:00:35.094 3G / 3G INFO General (kmer_splitters.hpp : 381) Processed 10173588 kmers 0:00:35.094 3G / 3G INFO General (kmer_splitters.hpp : 386) Used 10173588 kmers. 0:00:35.125 16M / 3G INFO General (kmer_index_builder.hpp : 109) Starting k-mer counting. 0:00:35.574 16M / 3G INFO General (kmer_index_builder.hpp : 115) K-mer counting done. There are 10096148 kmers in total. 0:00:35.574 16M / 3G INFO General (kmer_index_builder.hpp : 121) Merging temporary buckets. 0:00:36.135 16M / 3G INFO K-mer Index Building (kmer_index_builder.hpp : 298) Building perfect hash indices 0:00:36.757 16M / 3G INFO General (kmer_index_builder.hpp : 137) Merging final buckets. 0:00:36.976 16M / 3G INFO K-mer Index Building (kmer_index_builder.hpp : 320) Index built. Total 4689888 bytes occupied (3.71618 bits per kmer). 0:00:36.990 28M / 3G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 87) Building k-mer extensions from k+1-mers 0:00:38.601 28M / 3G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 91) Building k-mer extensions from k+1-mers finished. 0:00:38.602 28M / 3G INFO Early tip clipping (early_simplification.hpp : 181) Early tip clipping 0:00:40.819 28M / 3G INFO Early tip clipping (early_simplification.hpp : 184) 550174 22-mers were removed by early tip clipper 0:00:40.819 28M / 3G INFO General (graph_construction.hpp : 136) Condensing graph 0:00:40.829 28M / 3G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 355) Extracting unbranching paths 0:00:42.165 40M / 3G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 374) Extracting unbranching paths finished. 221440 sequences extracted 0:00:43.128 40M / 3G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 310) Collecting perfect loops 0:00:43.488 40M / 3G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 343) Collecting perfect loops finished. 2 loops collected 0:00:43.634 88M / 3G INFO General (graph_construction.hpp : 141) Building index with from graph 0:00:43.635 88M / 3G INFO K-mer Index Building (kmer_index_builder.hpp : 289) Building kmer index 0:00:43.635 88M / 3G INFO General (kmer_index_builder.hpp : 106) Splitting kmer instances into 64 buckets using 4 threads. This might take a while. 0:00:43.635 88M / 3G INFO General (file_limit.hpp : 32) Open file limit set to 1024 0:00:43.635 88M / 3G INFO General (kmer_splitters.hpp : 74) Memory available for splitting buffers: 20.8262 Gb 0:00:43.635 88M / 3G INFO General (kmer_splitters.hpp : 82) Using cell size of 1048576 0:00:44.346 3G / 3G INFO General (edge_index_builders.hpp : 75) Processed 441975 edges 0:00:44.346 3G / 3G INFO General (edge_index_builders.hpp : 80) Used 441975 sequences. 0:00:44.357 88M / 3G INFO General (kmer_index_builder.hpp : 109) Starting k-mer counting. 0:00:44.790 88M / 3G INFO General (kmer_index_builder.hpp : 115) K-mer counting done. There are 9623414 kmers in total. 0:00:44.790 88M / 3G INFO General (kmer_index_builder.hpp : 121) Merging temporary buckets. 0:00:45.322 88M / 3G INFO K-mer Index Building (kmer_index_builder.hpp : 298) Building perfect hash indices 0:00:45.858 96M / 3G INFO General (kmer_index_builder.hpp : 137) Merging final buckets. 0:00:46.050 96M / 3G INFO K-mer Index Building (kmer_index_builder.hpp : 320) Index built. Total 4470584 bytes occupied (3.71642 bits per kmer). 0:00:46.245 320M / 3G INFO General (edge_index_builders.hpp : 105) Collecting k-mer coverage information from graph, this takes a while. 0:00:47.038 320M / 3G INFO General (edge_index.hpp : 91) Index refilled 0:00:47.069 304M / 3G INFO General (graph_construction.hpp : 173) Filling coverage index 0:00:47.069 304M / 3G INFO General (edge_index_builders.hpp : 183) Collecting k-mer coverage information from reads, this takes a while. 0:01:26.851 300M / 3G INFO General (graph_construction.hpp : 175) Filling coverage and flanking coverage from index 0:01:27.616 300M / 3G INFO General (construction.cpp : 30) Figured out: read length = 140 0:01:27.618 300M / 3G INFO StageManager (stage.cpp : 126) STAGE == EC Threshold Finding 0:01:27.899 300M / 3G INFO General (kmer_coverage_model.cpp : 181) Kmer coverage valley at: 7 0:01:27.900 300M / 3G INFO General (kmer_coverage_model.cpp : 201) K-mer histogram maximum: 40 0:01:27.900 300M / 3G INFO General (kmer_coverage_model.cpp : 237) Estimated median coverage: 41. Coverage mad: 13.3434 0:01:27.900 300M / 3G INFO General (kmer_coverage_model.cpp : 259) Fitting coverage model 0:01:27.934 300M / 3G INFO General (kmer_coverage_model.cpp : 295) ... iteration 2 0:01:28.021 300M / 3G INFO General (kmer_coverage_model.cpp : 295) ... iteration 4 0:01:28.336 300M / 3G INFO General (kmer_coverage_model.cpp : 295) ... iteration 8 0:01:28.956 300M / 3G INFO General (kmer_coverage_model.cpp : 295) ... iteration 16 0:01:29.745 300M / 3G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 41.213. Fitted coverage std. dev: 11.1916 0:01:29.746 300M / 3G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 0.776085 0:01:29.746 300M / 3G INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 18 0:01:29.746 300M / 3G INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 18 0:01:29.746 300M / 3G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 8270101 0:01:29.746 300M / 3G INFO General (genomic_info_filler.cpp : 127) Mean coverage was calculated as 41.213 0:01:29.746 300M / 3G INFO General (genomic_info_filler.cpp : 141) EC coverage threshold value was calculated as 18 0:01:29.746 300M / 3G INFO General (genomic_info_filler.cpp : 142) Trusted kmer low bound: 0 0:01:29.746 300M / 3G INFO StageManager (stage.cpp : 126) STAGE == Simplification 0:01:29.788 72M / 3G INFO General (simplification.cpp : 387) Graph simplification started 0:01:29.788 72M / 3G INFO General (simplification.cpp : 77) PROCEDURE == InitialCleaning 0:01:29.788 72M / 3G INFO General (graph_simplification.hpp : 645) Flanking coverage based disconnection disabled 0:01:29.788 72M / 3G INFO General (simplification.cpp : 356) Running Self conjugate edge remover 0:01:29.832 72M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:01:29.832 72M / 3G INFO General (simplification.cpp : 356) Running Initial isolated edge remover 0:01:29.868 72M / 3G INFO General (simplification.cpp : 358) Triggered 182 times 0:01:29.868 72M / 3G INFO General (simplification.cpp : 356) Running Initial tip clipper 0:01:29.913 72M / 3G INFO General (simplification.cpp : 358) Triggered 223 times 0:01:29.913 72M / 3G INFO General (simplification.cpp : 356) Running Initial ec remover 0:01:31.360 80M / 3G INFO General (simplification.cpp : 358) Triggered 58093 times 0:01:31.366 76M / 3G INFO General (graph_simplification.hpp : 617) Creating parallel br instance 0:01:31.366 76M / 3G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 1 0:01:31.366 76M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:01:31.380 76M / 3G INFO General (simplification.cpp : 358) Triggered 118 times 0:01:31.380 76M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:01:31.661 76M / 3G INFO General (simplification.cpp : 358) Triggered 8159 times 0:01:31.661 76M / 3G INFO General (simplification.cpp : 356) Running Low coverage edge remover 0:01:31.684 76M / 3G INFO General (simplification.cpp : 358) Triggered 678 times 0:01:31.684 76M / 3G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 2 0:01:31.684 76M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:01:31.686 76M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:01:31.686 76M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:01:31.687 76M / 3G INFO General (simplification.cpp : 358) Triggered 18 times 0:01:31.687 76M / 3G INFO General (simplification.cpp : 356) Running Low coverage edge remover 0:01:31.751 76M / 3G INFO General (simplification.cpp : 358) Triggered 2954 times 0:01:31.751 76M / 3G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 3 0:01:31.751 76M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:01:31.753 76M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:01:31.753 76M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:01:31.759 76M / 3G INFO General (simplification.cpp : 358) Triggered 90 times 0:01:31.759 76M / 3G INFO General (simplification.cpp : 356) Running Low coverage edge remover 0:01:31.808 76M / 3G INFO General (simplification.cpp : 358) Triggered 827 times 0:01:31.808 76M / 3G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 4 0:01:31.808 76M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:01:31.809 76M / 3G INFO General (simplification.cpp : 358) Triggered 1 times 0:01:31.809 76M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:01:31.811 76M / 3G INFO General (simplification.cpp : 358) Triggered 15 times 0:01:31.811 76M / 3G INFO General (simplification.cpp : 356) Running Low coverage edge remover 0:01:31.815 76M / 3G INFO General (simplification.cpp : 358) Triggered 138 times 0:01:31.815 76M / 3G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 5 0:01:31.815 76M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:01:31.815 76M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:01:31.815 76M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:01:31.816 72M / 3G INFO General (simplification.cpp : 358) Triggered 6 times 0:01:31.816 72M / 3G INFO General (simplification.cpp : 356) Running Low coverage edge remover 0:01:31.817 72M / 3G INFO General (simplification.cpp : 358) Triggered 48 times 0:01:31.817 72M / 3G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 6 0:01:31.817 72M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:01:31.817 72M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:01:31.817 72M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:01:31.818 72M / 3G INFO General (simplification.cpp : 358) Triggered 6 times 0:01:31.818 72M / 3G INFO General (simplification.cpp : 356) Running Low coverage edge remover 0:01:31.818 72M / 3G INFO General (simplification.cpp : 358) Triggered 30 times 0:01:31.818 72M / 3G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 7 0:01:31.818 72M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:01:31.818 72M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:01:31.818 72M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:01:31.819 72M / 3G INFO General (simplification.cpp : 358) Triggered 5 times 0:01:31.819 72M / 3G INFO General (simplification.cpp : 356) Running Low coverage edge remover 0:01:31.820 72M / 3G INFO General (simplification.cpp : 358) Triggered 40 times 0:01:31.820 72M / 3G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 8 0:01:31.820 72M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:01:31.820 72M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:01:31.820 72M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:01:31.820 72M / 3G INFO General (simplification.cpp : 358) Triggered 1 times 0:01:31.820 72M / 3G INFO General (simplification.cpp : 356) Running Low coverage edge remover 0:01:31.821 72M / 3G INFO General (simplification.cpp : 358) Triggered 34 times 0:01:31.821 72M / 3G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 9 0:01:31.821 72M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:01:31.821 72M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:01:31.821 72M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:01:31.821 72M / 3G INFO General (simplification.cpp : 358) Triggered 1 times 0:01:31.821 72M / 3G INFO General (simplification.cpp : 356) Running Low coverage edge remover 0:01:31.821 72M / 3G INFO General (simplification.cpp : 358) Triggered 32 times 0:01:31.821 72M / 3G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 10 0:01:31.821 72M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:01:31.827 72M / 3G INFO General (simplification.cpp : 358) Triggered 2 times 0:01:31.827 72M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:01:31.845 72M / 3G INFO General (simplification.cpp : 358) Triggered 7 times 0:01:31.845 72M / 3G INFO General (simplification.cpp : 356) Running Low coverage edge remover 0:01:31.849 72M / 3G INFO General (simplification.cpp : 358) Triggered 37 times 0:01:31.849 72M / 3G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 11 0:01:31.849 72M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:01:31.849 72M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:01:31.849 72M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:01:31.849 72M / 3G INFO General (simplification.cpp : 358) Triggered 1 times 0:01:31.849 72M / 3G INFO General (simplification.cpp : 356) Running Low coverage edge remover 0:01:31.849 72M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:01:31.849 72M / 3G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 12 0:01:31.849 72M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:01:31.849 72M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:01:31.849 72M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:01:31.849 72M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:01:31.849 72M / 3G INFO General (simplification.cpp : 356) Running Low coverage edge remover 0:01:31.849 72M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:01:31.849 72M / 3G INFO General (simplification.cpp : 167) PROCEDURE == Post simplification 0:01:31.849 72M / 3G INFO General (graph_simplification.hpp : 447) Disconnection of relatively low covered edges disabled 0:01:31.849 72M / 3G INFO General (graph_simplification.hpp : 477) Complex tip clipping disabled 0:01:31.849 72M / 3G INFO General (graph_simplification.hpp : 617) Creating parallel br instance 0:01:31.849 72M / 3G INFO General (simplification.cpp : 301) Iteration 1 0:01:31.849 72M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:01:31.851 72M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:01:31.851 72M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:01:31.866 72M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:01:31.866 72M / 3G INFO General (simplification.cpp : 301) Iteration 2 0:01:31.866 72M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:01:31.868 72M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:01:31.868 72M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:01:31.883 72M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:01:31.883 72M / 3G INFO General (simplification.cpp : 333) Disrupting self-conjugate edges 0:01:31.892 72M / 3G INFO StageManager (stage.cpp : 126) STAGE == Simplification Cleanup 0:01:31.892 72M / 3G INFO General (simplification.cpp : 547) Removing isolated edges 0:01:31.893 72M / 3G INFO General (simplification.cpp : 570) Counting average coverage 0:01:31.897 72M / 3G INFO General (simplification.cpp : 575) Average coverage = 41.9907 0:01:31.897 72M / 3G INFO StageManager (stage.cpp : 126) STAGE == Contig Output 0:01:31.897 72M / 3G INFO General (contig_output_stage.cpp : 40) Writing GFA to /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/genomics_de_novo_temp/working_dir/spades_default_assembly//K21/assembly_graph_with_scaffolds.gfa 0:01:31.959 72M / 3G INFO General (contig_output.hpp : 22) Outputting contigs to /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/genomics_de_novo_temp/working_dir/spades_default_assembly//K21/before_rr.fasta 0:01:32.079 72M / 3G INFO General (contig_output_stage.cpp : 50) Outputting FastG graph to /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/genomics_de_novo_temp/working_dir/spades_default_assembly//K21/assembly_graph.fastg 0:01:32.331 72M / 3G INFO General (contig_output.hpp : 22) Outputting contigs to /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/genomics_de_novo_temp/working_dir/spades_default_assembly//K21/simplified_contigs.fasta 0:01:32.435 72M / 3G INFO General (contig_output.hpp : 22) Outputting contigs to /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/genomics_de_novo_temp/working_dir/spades_default_assembly//K21/final_contigs.fasta 0:01:32.556 72M / 3G INFO StageManager (stage.cpp : 126) STAGE == Contig Output 0:01:32.556 72M / 3G INFO General (contig_output_stage.cpp : 40) Writing GFA to /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/genomics_de_novo_temp/working_dir/spades_default_assembly//K21/assembly_graph_with_scaffolds.gfa 0:01:32.624 72M / 3G INFO General (contig_output.hpp : 22) Outputting contigs to /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/genomics_de_novo_temp/working_dir/spades_default_assembly//K21/before_rr.fasta 0:01:32.731 72M / 3G INFO General (contig_output_stage.cpp : 50) Outputting FastG graph to /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/genomics_de_novo_temp/working_dir/spades_default_assembly//K21/assembly_graph.fastg 0:01:32.989 72M / 3G INFO General (contig_output.hpp : 22) Outputting contigs to /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/genomics_de_novo_temp/working_dir/spades_default_assembly//K21/simplified_contigs.fasta 0:01:33.130 72M / 3G INFO General (contig_output.hpp : 22) Outputting contigs to /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/genomics_de_novo_temp/working_dir/spades_default_assembly//K21/final_contigs.fasta 0:01:33.255 72M / 3G INFO General (launch.hpp : 137) SPAdes finished 0:01:33.335 16M / 3G INFO General (main.cpp : 110) Assembling time: 0 hours 1 minutes 33 seconds == Running assembler: K33 0:00:00.000 4M / 4M INFO General (main.cpp : 76) Loading config from /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/genomics_de_novo_temp/working_dir/spades_default_assembly/K33/configs/config.info 0:00:00.001 4M / 4M INFO General (memory_limit.hpp : 51) Memory limit set to 250 Gb 0:00:00.001 4M / 4M INFO General (main.cpp : 89) Starting SPAdes, built from N/A, git revision N/A 0:00:00.001 4M / 4M INFO General (main.cpp : 90) Maximum k-mer length: 128 0:00:00.001 4M / 4M INFO General (main.cpp : 91) Assembling dataset (/nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/genomics_de_novo_temp/working_dir/spades_default_assembly/dataset.info) with K=33 0:00:00.001 4M / 4M INFO General (launch.hpp : 51) SPAdes started 0:00:00.001 4M / 4M INFO General (launch.hpp : 58) Starting from stage: construction 0:00:00.001 4M / 4M INFO General (launch.hpp : 61) Two-step RR enabled: 0 0:00:00.001 4M / 4M INFO StageManager (stage.cpp : 126) STAGE == Construction 0:00:00.006 4M / 4M INFO General (read_converter.hpp : 67) Binary reads detected 0:00:00.007 4M / 4M INFO General (graph_construction.hpp : 120) Constructing DeBruijn graph for k=33 0:00:00.009 4M / 4M INFO General (kmer_index_builder.hpp : 106) Splitting kmer instances into 16 buckets using 4 threads. This might take a while. 0:00:00.009 4M / 4M INFO General (file_limit.hpp : 32) Open file limit set to 1024 0:00:00.009 4M / 4M INFO General (kmer_splitters.hpp : 74) Memory available for splitting buffers: 20.833 Gb 0:00:00.009 4M / 4M INFO General (kmer_splitters.hpp : 82) Using cell size of 2097152 0:00:08.610 2G / 2G INFO General (kmer_splitters.hpp : 291) Processed 2500256 reads 0:00:17.140 2G / 2G INFO General (kmer_splitters.hpp : 291) Processed 5002200 reads 0:00:20.427 2G / 2G INFO General (kmer_splitters.hpp : 291) Processed 5938904 reads 0:00:20.427 2G / 2G INFO General (kmer_splitters.hpp : 297) Adding contigs from previous K 0:00:21.843 16M / 2G INFO General (kmer_splitters.hpp : 310) Used 5938904 reads. Maximum read length 140 0:00:21.843 16M / 2G INFO General (kmer_splitters.hpp : 311) Average read length 140 0:00:21.843 16M / 2G INFO General (kmer_index_builder.hpp : 109) Starting k-mer counting. 0:00:22.948 16M / 2G INFO General (kmer_index_builder.hpp : 115) K-mer counting done. There are 10745487 kmers in total. 0:00:22.948 16M / 2G INFO General (kmer_index_builder.hpp : 121) Merging temporary buckets. 0:00:23.462 16M / 2G INFO K-mer Index Building (kmer_index_builder.hpp : 289) Building kmer index 0:00:23.462 16M / 2G INFO General (kmer_index_builder.hpp : 106) Splitting kmer instances into 64 buckets using 4 threads. This might take a while. 0:00:23.462 16M / 2G INFO General (file_limit.hpp : 32) Open file limit set to 1024 0:00:23.462 16M / 2G INFO General (kmer_splitters.hpp : 74) Memory available for splitting buffers: 20.832 Gb 0:00:23.462 16M / 2G INFO General (kmer_splitters.hpp : 82) Using cell size of 524288 0:00:25.439 3G / 3G INFO General (kmer_splitters.hpp : 381) Processed 10745487 kmers 0:00:25.439 3G / 3G INFO General (kmer_splitters.hpp : 386) Used 10745487 kmers. 0:00:25.489 16M / 3G INFO General (kmer_index_builder.hpp : 109) Starting k-mer counting. 0:00:26.106 16M / 3G INFO General (kmer_index_builder.hpp : 115) K-mer counting done. There are 10709744 kmers in total. 0:00:26.106 16M / 3G INFO General (kmer_index_builder.hpp : 121) Merging temporary buckets. 0:00:27.006 16M / 3G INFO K-mer Index Building (kmer_index_builder.hpp : 298) Building perfect hash indices 0:00:27.648 16M / 3G INFO General (kmer_index_builder.hpp : 137) Merging final buckets. 0:00:28.050 16M / 3G INFO K-mer Index Building (kmer_index_builder.hpp : 320) Index built. Total 4973992 bytes occupied (3.71549 bits per kmer). 0:00:28.065 28M / 3G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 87) Building k-mer extensions from k+1-mers 0:00:29.075 28M / 3G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 91) Building k-mer extensions from k+1-mers finished. 0:00:29.078 28M / 3G INFO Early tip clipping (early_simplification.hpp : 181) Early tip clipping 0:00:31.385 28M / 3G INFO Early tip clipping (early_simplification.hpp : 184) 1082368 34-mers were removed by early tip clipper 0:00:31.386 28M / 3G INFO General (graph_construction.hpp : 136) Condensing graph 0:00:31.395 28M / 3G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 355) Extracting unbranching paths 0:00:32.659 32M / 3G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 374) Extracting unbranching paths finished. 108656 sequences extracted 0:00:33.492 32M / 3G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 310) Collecting perfect loops 0:00:33.878 32M / 3G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 343) Collecting perfect loops finished. 0 loops collected 0:00:33.963 64M / 3G INFO General (graph_construction.hpp : 141) Building index with from graph 0:00:33.964 64M / 3G INFO K-mer Index Building (kmer_index_builder.hpp : 289) Building kmer index 0:00:33.964 64M / 3G INFO General (kmer_index_builder.hpp : 106) Splitting kmer instances into 64 buckets using 4 threads. This might take a while. 0:00:33.964 64M / 3G INFO General (file_limit.hpp : 32) Open file limit set to 1024 0:00:33.964 64M / 3G INFO General (kmer_splitters.hpp : 74) Memory available for splitting buffers: 20.8281 Gb 0:00:33.964 64M / 3G INFO General (kmer_splitters.hpp : 82) Using cell size of 524288 0:00:34.830 3G / 3G INFO General (edge_index_builders.hpp : 75) Processed 216999 edges 0:00:34.830 3G / 3G INFO General (edge_index_builders.hpp : 80) Used 216999 sequences. 0:00:34.849 64M / 3G INFO General (kmer_index_builder.hpp : 109) Starting k-mer counting. 0:00:35.434 64M / 3G INFO General (kmer_index_builder.hpp : 115) K-mer counting done. There are 9663119 kmers in total. 0:00:35.434 64M / 3G INFO General (kmer_index_builder.hpp : 121) Merging temporary buckets. 0:00:36.250 64M / 3G INFO K-mer Index Building (kmer_index_builder.hpp : 298) Building perfect hash indices 0:00:36.781 64M / 3G INFO General (kmer_index_builder.hpp : 137) Merging final buckets. 0:00:37.158 64M / 3G INFO K-mer Index Building (kmer_index_builder.hpp : 320) Index built. Total 4488872 bytes occupied (3.71629 bits per kmer). 0:00:37.353 288M / 3G INFO General (edge_index_builders.hpp : 105) Collecting k-mer coverage information from graph, this takes a while. 0:00:38.043 288M / 3G INFO General (edge_index.hpp : 91) Index refilled 0:00:38.115 276M / 3G INFO General (graph_construction.hpp : 173) Filling coverage index 0:00:38.115 276M / 3G INFO General (edge_index_builders.hpp : 183) Collecting k-mer coverage information from reads, this takes a while. 0:01:16.526 276M / 3G INFO General (graph_construction.hpp : 175) Filling coverage and flanking coverage from index 0:01:16.912 276M / 3G INFO General (construction.cpp : 30) Figured out: read length = 140 0:01:16.913 276M / 3G INFO StageManager (stage.cpp : 126) STAGE == EC Threshold Finding 0:01:17.216 276M / 3G INFO General (kmer_coverage_model.cpp : 181) Kmer coverage valley at: 5 0:01:17.216 276M / 3G INFO General (kmer_coverage_model.cpp : 201) K-mer histogram maximum: 35 0:01:17.216 276M / 3G INFO General (kmer_coverage_model.cpp : 237) Estimated median coverage: 37. Coverage mad: 11.8608 0:01:17.216 276M / 3G INFO General (kmer_coverage_model.cpp : 259) Fitting coverage model 0:01:17.245 276M / 3G INFO General (kmer_coverage_model.cpp : 295) ... iteration 2 0:01:17.320 276M / 3G INFO General (kmer_coverage_model.cpp : 295) ... iteration 4 0:01:17.578 276M / 3G INFO General (kmer_coverage_model.cpp : 295) ... iteration 8 0:01:18.140 276M / 3G INFO General (kmer_coverage_model.cpp : 295) ... iteration 16 0:01:18.793 276M / 3G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 37.0011. Fitted coverage std. dev: 10.2612 0:01:18.795 276M / 3G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 0.90626 0:01:18.795 276M / 3G INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 17 0:01:18.795 276M / 3G INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 17 0:01:18.795 276M / 3G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 8243812 0:01:18.795 276M / 3G INFO General (genomic_info_filler.cpp : 127) Mean coverage was calculated as 37.0011 0:01:18.795 276M / 3G INFO General (genomic_info_filler.cpp : 141) EC coverage threshold value was calculated as 17 0:01:18.795 276M / 3G INFO General (genomic_info_filler.cpp : 142) Trusted kmer low bound: 0 0:01:18.795 276M / 3G INFO StageManager (stage.cpp : 126) STAGE == Simplification 0:01:18.815 44M / 3G INFO General (simplification.cpp : 387) Graph simplification started 0:01:18.815 44M / 3G INFO General (simplification.cpp : 77) PROCEDURE == InitialCleaning 0:01:18.815 44M / 3G INFO General (graph_simplification.hpp : 645) Flanking coverage based disconnection disabled 0:01:18.815 44M / 3G INFO General (simplification.cpp : 356) Running Self conjugate edge remover 0:01:18.832 44M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:01:18.832 44M / 3G INFO General (simplification.cpp : 356) Running Initial isolated edge remover 0:01:18.844 44M / 3G INFO General (simplification.cpp : 358) Triggered 215 times 0:01:18.844 44M / 3G INFO General (simplification.cpp : 356) Running Initial tip clipper 0:01:18.862 40M / 3G INFO General (simplification.cpp : 358) Triggered 605 times 0:01:18.862 40M / 3G INFO General (simplification.cpp : 356) Running Initial ec remover 0:01:19.421 44M / 3G INFO General (simplification.cpp : 358) Triggered 25922 times 0:01:19.423 40M / 3G INFO General (graph_simplification.hpp : 617) Creating parallel br instance 0:01:19.423 40M / 3G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 1 0:01:19.423 40M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:01:19.430 40M / 3G INFO General (simplification.cpp : 358) Triggered 150 times 0:01:19.430 40M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:01:19.712 40M / 3G INFO General (simplification.cpp : 358) Triggered 7948 times 0:01:19.712 40M / 3G INFO General (simplification.cpp : 356) Running Low coverage edge remover 0:01:19.794 40M / 3G INFO General (simplification.cpp : 358) Triggered 1073 times 0:01:19.794 40M / 3G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 2 0:01:19.794 40M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:01:19.795 40M / 3G INFO General (simplification.cpp : 358) Triggered 2 times 0:01:19.795 40M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:01:19.796 40M / 3G INFO General (simplification.cpp : 358) Triggered 16 times 0:01:19.796 40M / 3G INFO General (simplification.cpp : 356) Running Low coverage edge remover 0:01:19.834 40M / 3G INFO General (simplification.cpp : 358) Triggered 357 times 0:01:19.834 40M / 3G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 3 0:01:19.834 40M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:01:19.834 40M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:01:19.834 40M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:01:19.835 40M / 3G INFO General (simplification.cpp : 358) Triggered 16 times 0:01:19.835 40M / 3G INFO General (simplification.cpp : 356) Running Low coverage edge remover 0:01:19.838 40M / 3G INFO General (simplification.cpp : 358) Triggered 57 times 0:01:19.838 40M / 3G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 4 0:01:19.838 40M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:01:19.838 40M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:01:19.838 40M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:01:19.838 40M / 3G INFO General (simplification.cpp : 358) Triggered 5 times 0:01:19.838 40M / 3G INFO General (simplification.cpp : 356) Running Low coverage edge remover 0:01:19.839 40M / 3G INFO General (simplification.cpp : 358) Triggered 13 times 0:01:19.839 40M / 3G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 5 0:01:19.839 40M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:01:19.839 40M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:01:19.839 40M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:01:19.839 40M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:01:19.839 40M / 3G INFO General (simplification.cpp : 356) Running Low coverage edge remover 0:01:19.840 40M / 3G INFO General (simplification.cpp : 358) Triggered 12 times 0:01:19.840 40M / 3G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 6 0:01:19.840 40M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:01:19.840 40M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:01:19.840 40M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:01:19.840 40M / 3G INFO General (simplification.cpp : 358) Triggered 1 times 0:01:19.840 40M / 3G INFO General (simplification.cpp : 356) Running Low coverage edge remover 0:01:19.840 40M / 3G INFO General (simplification.cpp : 358) Triggered 2 times 0:01:19.840 40M / 3G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 7 0:01:19.840 40M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:01:19.840 40M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:01:19.840 40M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:01:19.840 40M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:01:19.840 40M / 3G INFO General (simplification.cpp : 356) Running Low coverage edge remover 0:01:19.841 40M / 3G INFO General (simplification.cpp : 358) Triggered 9 times 0:01:19.841 40M / 3G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 8 0:01:19.841 40M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:01:19.841 40M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:01:19.841 40M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:01:19.841 40M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:01:19.841 40M / 3G INFO General (simplification.cpp : 356) Running Low coverage edge remover 0:01:19.841 40M / 3G INFO General (simplification.cpp : 358) Triggered 7 times 0:01:19.841 40M / 3G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 9 0:01:19.841 40M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:01:19.841 40M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:01:19.841 40M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:01:19.841 40M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:01:19.841 40M / 3G INFO General (simplification.cpp : 356) Running Low coverage edge remover 0:01:19.842 40M / 3G INFO General (simplification.cpp : 358) Triggered 5 times 0:01:19.842 40M / 3G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 10 0:01:19.842 40M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:01:19.843 40M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:01:19.843 40M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:01:19.844 40M / 3G INFO General (simplification.cpp : 358) Triggered 2 times 0:01:19.844 40M / 3G INFO General (simplification.cpp : 356) Running Low coverage edge remover 0:01:19.845 40M / 3G INFO General (simplification.cpp : 358) Triggered 7 times 0:01:19.845 40M / 3G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 11 0:01:19.845 40M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:01:19.845 40M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:01:19.845 40M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:01:19.845 40M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:01:19.845 40M / 3G INFO General (simplification.cpp : 356) Running Low coverage edge remover 0:01:19.845 40M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:01:19.845 40M / 3G INFO General (simplification.cpp : 167) PROCEDURE == Post simplification 0:01:19.845 40M / 3G INFO General (graph_simplification.hpp : 447) Disconnection of relatively low covered edges disabled 0:01:19.845 40M / 3G INFO General (graph_simplification.hpp : 477) Complex tip clipping disabled 0:01:19.845 40M / 3G INFO General (graph_simplification.hpp : 617) Creating parallel br instance 0:01:19.845 40M / 3G INFO General (simplification.cpp : 301) Iteration 1 0:01:19.845 40M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:01:19.845 40M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:01:19.845 40M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:01:19.846 40M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:01:19.846 40M / 3G INFO General (simplification.cpp : 301) Iteration 2 0:01:19.846 40M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:01:19.846 40M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:01:19.846 40M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:01:19.847 40M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:01:19.847 40M / 3G INFO General (simplification.cpp : 333) Disrupting self-conjugate edges 0:01:19.848 40M / 3G INFO StageManager (stage.cpp : 126) STAGE == Simplification Cleanup 0:01:19.848 40M / 3G INFO General (simplification.cpp : 547) Removing isolated edges 0:01:19.848 40M / 3G INFO General (simplification.cpp : 570) Counting average coverage 0:01:19.849 40M / 3G INFO General (simplification.cpp : 575) Average coverage = 37.375 0:01:19.849 40M / 3G INFO StageManager (stage.cpp : 126) STAGE == Contig Output 0:01:19.849 40M / 3G INFO General (contig_output_stage.cpp : 40) Writing GFA to /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/genomics_de_novo_temp/working_dir/spades_default_assembly//K33/assembly_graph_with_scaffolds.gfa 0:01:19.874 40M / 3G INFO General (contig_output.hpp : 22) Outputting contigs to /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/genomics_de_novo_temp/working_dir/spades_default_assembly//K33/before_rr.fasta 0:01:19.932 40M / 3G INFO General (contig_output_stage.cpp : 50) Outputting FastG graph to /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/genomics_de_novo_temp/working_dir/spades_default_assembly//K33/assembly_graph.fastg 0:01:20.053 40M / 3G INFO General (contig_output.hpp : 22) Outputting contigs to /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/genomics_de_novo_temp/working_dir/spades_default_assembly//K33/simplified_contigs.fasta 0:01:20.112 40M / 3G INFO General (contig_output.hpp : 22) Outputting contigs to /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/genomics_de_novo_temp/working_dir/spades_default_assembly//K33/final_contigs.fasta 0:01:20.184 40M / 3G INFO StageManager (stage.cpp : 126) STAGE == Contig Output 0:01:20.184 40M / 3G INFO General (contig_output_stage.cpp : 40) Writing GFA to /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/genomics_de_novo_temp/working_dir/spades_default_assembly//K33/assembly_graph_with_scaffolds.gfa 0:01:20.211 40M / 3G INFO General (contig_output.hpp : 22) Outputting contigs to /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/genomics_de_novo_temp/working_dir/spades_default_assembly//K33/before_rr.fasta 0:01:20.268 40M / 3G INFO General (contig_output_stage.cpp : 50) Outputting FastG graph to /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/genomics_de_novo_temp/working_dir/spades_default_assembly//K33/assembly_graph.fastg 0:01:20.391 40M / 3G INFO General (contig_output.hpp : 22) Outputting contigs to /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/genomics_de_novo_temp/working_dir/spades_default_assembly//K33/simplified_contigs.fasta 0:01:20.447 40M / 3G INFO General (contig_output.hpp : 22) Outputting contigs to /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/genomics_de_novo_temp/working_dir/spades_default_assembly//K33/final_contigs.fasta 0:01:20.516 40M / 3G INFO General (launch.hpp : 137) SPAdes finished 0:01:20.556 20M / 3G INFO General (main.cpp : 110) Assembling time: 0 hours 1 minutes 20 seconds == Running assembler: K55 0:00:00.000 4M / 4M INFO General (main.cpp : 76) Loading config from /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/genomics_de_novo_temp/working_dir/spades_default_assembly/K55/configs/config.info 0:00:00.001 4M / 4M INFO General (memory_limit.hpp : 51) Memory limit set to 250 Gb 0:00:00.001 4M / 4M INFO General (main.cpp : 89) Starting SPAdes, built from N/A, git revision N/A 0:00:00.001 4M / 4M INFO General (main.cpp : 90) Maximum k-mer length: 128 0:00:00.001 4M / 4M INFO General (main.cpp : 91) Assembling dataset (/nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/genomics_de_novo_temp/working_dir/spades_default_assembly/dataset.info) with K=55 0:00:00.001 4M / 4M INFO General (launch.hpp : 51) SPAdes started 0:00:00.001 4M / 4M INFO General (launch.hpp : 58) Starting from stage: construction 0:00:00.001 4M / 4M INFO General (launch.hpp : 61) Two-step RR enabled: 0 0:00:00.001 4M / 4M INFO General (launch.hpp : 79) Will need read mapping, kmer mapper will be attached 0:00:00.001 4M / 4M INFO StageManager (stage.cpp : 126) STAGE == Construction 0:00:00.005 4M / 4M INFO General (read_converter.hpp : 67) Binary reads detected 0:00:00.005 4M / 4M INFO General (graph_construction.hpp : 120) Constructing DeBruijn graph for k=55 0:00:00.007 4M / 4M INFO General (kmer_index_builder.hpp : 106) Splitting kmer instances into 16 buckets using 4 threads. This might take a while. 0:00:00.007 4M / 4M INFO General (file_limit.hpp : 32) Open file limit set to 1024 0:00:00.007 4M / 4M INFO General (kmer_splitters.hpp : 74) Memory available for splitting buffers: 20.833 Gb 0:00:00.007 4M / 4M INFO General (kmer_splitters.hpp : 82) Using cell size of 2097152 0:00:09.408 2G / 2G INFO General (kmer_splitters.hpp : 291) Processed 3142047 reads 0:00:16.972 2G / 2G INFO General (kmer_splitters.hpp : 291) Processed 5938904 reads 0:00:16.972 2G / 2G INFO General (kmer_splitters.hpp : 297) Adding contigs from previous K 0:00:18.315 16M / 2G INFO General (kmer_splitters.hpp : 310) Used 5938904 reads. Maximum read length 140 0:00:18.315 16M / 2G INFO General (kmer_splitters.hpp : 311) Average read length 140 0:00:18.315 16M / 2G INFO General (kmer_index_builder.hpp : 109) Starting k-mer counting. 0:00:19.266 16M / 2G INFO General (kmer_index_builder.hpp : 115) K-mer counting done. There are 11239689 kmers in total. 0:00:19.266 16M / 2G INFO General (kmer_index_builder.hpp : 121) Merging temporary buckets. 0:00:19.837 16M / 2G INFO K-mer Index Building (kmer_index_builder.hpp : 289) Building kmer index 0:00:19.837 16M / 2G INFO General (kmer_index_builder.hpp : 106) Splitting kmer instances into 64 buckets using 4 threads. This might take a while. 0:00:19.837 16M / 2G INFO General (file_limit.hpp : 32) Open file limit set to 1024 0:00:19.837 16M / 2G INFO General (kmer_splitters.hpp : 74) Memory available for splitting buffers: 20.832 Gb 0:00:19.837 16M / 2G INFO General (kmer_splitters.hpp : 82) Using cell size of 524288 0:00:22.712 3G / 3G INFO General (kmer_splitters.hpp : 381) Processed 11239689 kmers 0:00:22.712 3G / 3G INFO General (kmer_splitters.hpp : 386) Used 11239689 kmers. 0:00:22.759 16M / 3G INFO General (kmer_index_builder.hpp : 109) Starting k-mer counting. 0:00:23.393 16M / 3G INFO General (kmer_index_builder.hpp : 115) K-mer counting done. There are 11226322 kmers in total. 0:00:23.393 16M / 3G INFO General (kmer_index_builder.hpp : 121) Merging temporary buckets. 0:00:24.194 16M / 3G INFO K-mer Index Building (kmer_index_builder.hpp : 298) Building perfect hash indices 0:00:24.862 16M / 3G INFO General (kmer_index_builder.hpp : 137) Merging final buckets. 0:00:25.294 16M / 3G INFO K-mer Index Building (kmer_index_builder.hpp : 320) Index built. Total 5213632 bytes occupied (3.71529 bits per kmer). 0:00:25.310 28M / 3G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 87) Building k-mer extensions from k+1-mers 0:00:27.628 28M / 3G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 91) Building k-mer extensions from k+1-mers finished. 0:00:27.631 28M / 3G INFO General (graph_construction.hpp : 136) Condensing graph 0:00:27.662 28M / 3G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 355) Extracting unbranching paths 0:00:29.232 52M / 3G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 374) Extracting unbranching paths finished. 260813 sequences extracted 0:00:30.350 52M / 3G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 310) Collecting perfect loops 0:00:30.776 52M / 3G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 343) Collecting perfect loops finished. 0 loops collected 0:00:30.984 108M / 3G INFO General (graph_construction.hpp : 141) Building index with from graph 0:00:30.986 108M / 3G INFO K-mer Index Building (kmer_index_builder.hpp : 289) Building kmer index 0:00:30.986 108M / 3G INFO General (kmer_index_builder.hpp : 106) Splitting kmer instances into 64 buckets using 4 threads. This might take a while. 0:00:30.986 112M / 3G INFO General (file_limit.hpp : 32) Open file limit set to 1024 0:00:30.986 112M / 3G INFO General (kmer_splitters.hpp : 74) Memory available for splitting buffers: 20.8242 Gb 0:00:30.986 112M / 3G INFO General (kmer_splitters.hpp : 82) Using cell size of 524288 0:00:31.955 3G / 3G INFO General (edge_index_builders.hpp : 75) Processed 521584 edges 0:00:31.955 3G / 3G INFO General (edge_index_builders.hpp : 80) Used 521584 sequences. 0:00:31.974 112M / 3G INFO General (kmer_index_builder.hpp : 109) Starting k-mer counting. 0:00:32.633 112M / 3G INFO General (kmer_index_builder.hpp : 115) K-mer counting done. There are 11239689 kmers in total. 0:00:32.633 112M / 3G INFO General (kmer_index_builder.hpp : 121) Merging temporary buckets. 0:00:33.433 112M / 3G INFO K-mer Index Building (kmer_index_builder.hpp : 298) Building perfect hash indices 0:00:34.152 120M / 3G INFO General (kmer_index_builder.hpp : 137) Merging final buckets. 0:00:34.594 120M / 3G INFO K-mer Index Building (kmer_index_builder.hpp : 320) Index built. Total 5219944 bytes occupied (3.71537 bits per kmer). 0:00:34.823 380M / 3G INFO General (edge_index_builders.hpp : 105) Collecting k-mer coverage information from graph, this takes a while. 0:00:35.816 380M / 3G INFO General (edge_index.hpp : 91) Index refilled 0:00:35.865 360M / 3G INFO General (graph_construction.hpp : 173) Filling coverage index 0:00:35.865 360M / 3G INFO General (edge_index_builders.hpp : 183) Collecting k-mer coverage information from reads, this takes a while. 0:01:12.036 356M / 3G INFO General (graph_construction.hpp : 175) Filling coverage and flanking coverage from index 0:01:13.073 356M / 3G INFO General (construction.cpp : 30) Figured out: read length = 140 0:01:13.073 356M / 3G INFO StageManager (stage.cpp : 126) STAGE == EC Threshold Finding 0:01:13.390 360M / 3G INFO General (kmer_coverage_model.cpp : 181) Kmer coverage valley at: 4 0:01:13.390 356M / 3G INFO General (kmer_coverage_model.cpp : 201) K-mer histogram maximum: 27 0:01:13.390 356M / 3G INFO General (kmer_coverage_model.cpp : 237) Estimated median coverage: 29. Coverage mad: 10.3782 0:01:13.390 356M / 3G INFO General (kmer_coverage_model.cpp : 259) Fitting coverage model 0:01:13.415 360M / 3G INFO General (kmer_coverage_model.cpp : 295) ... iteration 2 0:01:13.479 360M / 3G INFO General (kmer_coverage_model.cpp : 295) ... iteration 4 0:01:13.696 360M / 3G INFO General (kmer_coverage_model.cpp : 295) ... iteration 8 0:01:14.138 360M / 3G INFO General (kmer_coverage_model.cpp : 295) ... iteration 16 0:01:14.623 360M / 3G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 29.2949. Fitted coverage std. dev: 8.56469 0:01:14.624 360M / 3G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 0.892381 0:01:14.624 360M / 3G INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 14 0:01:14.624 360M / 3G INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 14 0:01:14.624 360M / 3G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 8179565 0:01:14.624 360M / 3G INFO General (genomic_info_filler.cpp : 127) Mean coverage was calculated as 29.2949 0:01:14.624 360M / 3G INFO General (genomic_info_filler.cpp : 141) EC coverage threshold value was calculated as 14 0:01:14.624 360M / 3G INFO General (genomic_info_filler.cpp : 142) Trusted kmer low bound: 0 0:01:14.624 360M / 3G INFO StageManager (stage.cpp : 126) STAGE == Gap Closer 0:01:14.626 360M / 3G INFO General (gap_closer.cpp : 159) Preparing shift maps 0:01:14.858 376M / 3G INFO General (gap_closer.cpp : 119) Processing paired reads (takes a while) 0:01:17.360 376M / 3G INFO General (gap_closer.cpp : 138) Used 1484726 paired reads 0:01:17.360 376M / 3G INFO General (gap_closer.cpp : 140) Merging paired indices 0:01:17.409 360M / 3G INFO GapCloser (gap_closer.cpp : 346) Closing short gaps 0:01:17.762 360M / 3G INFO GapCloser (gap_closer.cpp : 380) Closing short gaps complete: filled 11 gaps after checking 176 candidates 0:01:17.780 360M / 3G INFO StageManager (stage.cpp : 126) STAGE == Simplification 0:01:17.809 96M / 3G INFO General (simplification.cpp : 387) Graph simplification started 0:01:17.809 96M / 3G INFO General (simplification.cpp : 77) PROCEDURE == InitialCleaning 0:01:17.809 96M / 3G INFO General (graph_simplification.hpp : 645) Flanking coverage based disconnection disabled 0:01:17.809 96M / 3G INFO General (simplification.cpp : 356) Running Self conjugate edge remover 0:01:17.845 96M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:01:17.845 96M / 3G INFO General (simplification.cpp : 356) Running Initial isolated edge remover 0:01:17.898 96M / 3G INFO General (simplification.cpp : 358) Triggered 593 times 0:01:17.898 96M / 3G INFO General (simplification.cpp : 356) Running Initial tip clipper 0:01:19.257 100M / 3G INFO General (simplification.cpp : 358) Triggered 109413 times 0:01:19.257 100M / 3G INFO General (simplification.cpp : 356) Running Initial ec remover 0:01:19.558 92M / 3G INFO General (simplification.cpp : 358) Triggered 9266 times 0:01:19.561 88M / 3G INFO General (graph_simplification.hpp : 617) Creating parallel br instance 0:01:19.561 88M / 3G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 1 0:01:19.561 88M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:01:19.567 88M / 3G INFO General (simplification.cpp : 358) Triggered 163 times 0:01:19.567 88M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:01:20.278 84M / 3G INFO General (simplification.cpp : 358) Triggered 4190 times 0:01:20.278 84M / 3G INFO General (simplification.cpp : 356) Running Low coverage edge remover 0:01:20.340 76M / 3G INFO General (simplification.cpp : 358) Triggered 277 times 0:01:20.340 76M / 3G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 2 0:01:20.340 76M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:01:20.343 76M / 3G INFO General (simplification.cpp : 358) Triggered 16 times 0:01:20.343 76M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:01:20.343 76M / 3G INFO General (simplification.cpp : 358) Triggered 4 times 0:01:20.343 76M / 3G INFO General (simplification.cpp : 356) Running Low coverage edge remover 0:01:20.368 72M / 3G INFO General (simplification.cpp : 358) Triggered 82 times 0:01:20.368 72M / 3G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 3 0:01:20.368 72M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:01:20.369 72M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:01:20.369 72M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:01:20.369 72M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:01:20.369 72M / 3G INFO General (simplification.cpp : 356) Running Low coverage edge remover 0:01:20.371 72M / 3G INFO General (simplification.cpp : 358) Triggered 16 times 0:01:20.371 72M / 3G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 4 0:01:20.371 72M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:01:20.371 72M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:01:20.371 72M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:01:20.372 72M / 3G INFO General (simplification.cpp : 358) Triggered 3 times 0:01:20.372 72M / 3G INFO General (simplification.cpp : 356) Running Low coverage edge remover 0:01:20.372 72M / 3G INFO General (simplification.cpp : 358) Triggered 3 times 0:01:20.372 72M / 3G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 5 0:01:20.372 72M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:01:20.372 72M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:01:20.372 72M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:01:20.372 72M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:01:20.372 72M / 3G INFO General (simplification.cpp : 356) Running Low coverage edge remover 0:01:20.372 72M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:01:20.372 72M / 3G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 6 0:01:20.372 72M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:01:20.372 72M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:01:20.372 72M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:01:20.372 72M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:01:20.372 72M / 3G INFO General (simplification.cpp : 356) Running Low coverage edge remover 0:01:20.373 72M / 3G INFO General (simplification.cpp : 358) Triggered 4 times 0:01:20.373 72M / 3G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 7 0:01:20.373 72M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:01:20.373 72M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:01:20.373 72M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:01:20.373 72M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:01:20.373 72M / 3G INFO General (simplification.cpp : 356) Running Low coverage edge remover 0:01:20.375 72M / 3G INFO General (simplification.cpp : 358) Triggered 5 times 0:01:20.375 72M / 3G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 8 0:01:20.375 72M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:01:20.375 72M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:01:20.375 72M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:01:20.375 72M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:01:20.375 72M / 3G INFO General (simplification.cpp : 356) Running Low coverage edge remover 0:01:20.375 72M / 3G INFO General (simplification.cpp : 358) Triggered 3 times 0:01:20.375 72M / 3G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 9 0:01:20.375 72M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:01:20.375 72M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:01:20.375 72M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:01:20.375 72M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:01:20.375 72M / 3G INFO General (simplification.cpp : 356) Running Low coverage edge remover 0:01:20.376 72M / 3G INFO General (simplification.cpp : 358) Triggered 4 times 0:01:20.376 72M / 3G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 10 0:01:20.376 72M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:01:20.376 72M / 3G INFO General (simplification.cpp : 358) Triggered 1 times 0:01:20.376 72M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:01:20.377 72M / 3G INFO General (simplification.cpp : 358) Triggered 3 times 0:01:20.377 72M / 3G INFO General (simplification.cpp : 356) Running Low coverage edge remover 0:01:20.377 72M / 3G INFO General (simplification.cpp : 358) Triggered 2 times 0:01:20.377 72M / 3G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 11 0:01:20.377 72M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:01:20.377 72M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:01:20.377 72M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:01:20.377 72M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:01:20.377 72M / 3G INFO General (simplification.cpp : 356) Running Low coverage edge remover 0:01:20.377 72M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:01:20.377 72M / 3G INFO General (simplification.cpp : 167) PROCEDURE == Post simplification 0:01:20.377 72M / 3G INFO General (graph_simplification.hpp : 447) Disconnection of relatively low covered edges disabled 0:01:20.377 72M / 3G INFO General (graph_simplification.hpp : 477) Complex tip clipping disabled 0:01:20.377 72M / 3G INFO General (graph_simplification.hpp : 617) Creating parallel br instance 0:01:20.377 72M / 3G INFO General (simplification.cpp : 301) Iteration 1 0:01:20.377 72M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:01:20.377 72M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:01:20.378 72M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:01:20.378 72M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:01:20.378 72M / 3G INFO General (simplification.cpp : 301) Iteration 2 0:01:20.378 72M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:01:20.378 72M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:01:20.378 72M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:01:20.378 72M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:01:20.378 72M / 3G INFO General (simplification.cpp : 333) Disrupting self-conjugate edges 0:01:20.379 72M / 3G INFO StageManager (stage.cpp : 126) STAGE == Gap Closer 0:01:20.379 72M / 3G INFO General (graph_pack.hpp : 99) Index refill 0:01:20.381 72M / 3G INFO K-mer Index Building (kmer_index_builder.hpp : 289) Building kmer index 0:01:20.381 72M / 3G INFO General (kmer_index_builder.hpp : 106) Splitting kmer instances into 64 buckets using 4 threads. This might take a while. 0:01:20.382 72M / 3G INFO General (file_limit.hpp : 32) Open file limit set to 1024 0:01:20.382 72M / 3G INFO General (kmer_splitters.hpp : 74) Memory available for splitting buffers: 20.8275 Gb 0:01:20.382 72M / 3G INFO General (kmer_splitters.hpp : 82) Using cell size of 524288 0:01:21.343 3G / 3G INFO General (edge_index_builders.hpp : 75) Processed 1514 edges 0:01:21.343 3G / 3G INFO General (edge_index_builders.hpp : 80) Used 1514 sequences. 0:01:21.364 72M / 3G INFO General (kmer_index_builder.hpp : 109) Starting k-mer counting. 0:01:21.892 72M / 3G INFO General (kmer_index_builder.hpp : 115) K-mer counting done. There are 8470296 kmers in total. 0:01:21.892 72M / 3G INFO General (kmer_index_builder.hpp : 121) Merging temporary buckets. 0:01:22.608 72M / 3G INFO K-mer Index Building (kmer_index_builder.hpp : 298) Building perfect hash indices 0:01:23.118 80M / 3G INFO General (kmer_index_builder.hpp : 137) Merging final buckets. 0:01:23.466 80M / 3G INFO K-mer Index Building (kmer_index_builder.hpp : 320) Index built. Total 3935920 bytes occupied (3.71739 bits per kmer). 0:01:23.641 276M / 3G INFO General (edge_index_builders.hpp : 105) Collecting k-mer coverage information from graph, this takes a while. 0:01:24.216 276M / 3G INFO General (edge_index.hpp : 91) Index refilled 0:01:24.216 276M / 3G INFO General (gap_closer.cpp : 159) Preparing shift maps 0:01:24.218 276M / 3G INFO General (gap_closer.cpp : 119) Processing paired reads (takes a while) 0:01:26.505 276M / 3G INFO General (gap_closer.cpp : 138) Used 1484726 paired reads 0:01:26.505 276M / 3G INFO General (gap_closer.cpp : 140) Merging paired indices 0:01:26.505 276M / 3G INFO GapCloser (gap_closer.cpp : 346) Closing short gaps 0:01:26.507 276M / 3G INFO GapCloser (gap_closer.cpp : 380) Closing short gaps complete: filled 6 gaps after checking 105 candidates 0:01:26.850 276M / 3G INFO StageManager (stage.cpp : 126) STAGE == Simplification Cleanup 0:01:26.850 276M / 3G INFO General (simplification.cpp : 547) Removing isolated edges 0:01:26.852 276M / 3G INFO General (simplification.cpp : 570) Counting average coverage 0:01:26.852 276M / 3G INFO General (simplification.cpp : 575) Average coverage = 29.4548 0:01:26.852 276M / 3G INFO StageManager (stage.cpp : 126) STAGE == Mismatch Correction 0:01:26.852 276M / 3G INFO General (graph_pack.hpp : 108) Normalizing k-mer map. Total 499374 kmers to process 0:01:27.052 276M / 3G INFO General (graph_pack.hpp : 110) Normalizing done 0:01:35.616 276M / 3G INFO General (mismatch_shall_not_pass.hp: 187) Finished collecting potential mismatches positions 0:01:35.708 276M / 3G INFO General (mismatch_shall_not_pass.hp: 284) All edges processed 0:01:35.709 276M / 3G INFO General (mismatch_correction.cpp : 26) Corrected 0 nucleotides 0:01:35.709 276M / 3G INFO StageManager (stage.cpp : 126) STAGE == Contig Output 0:01:35.709 276M / 3G INFO General (contig_output_stage.cpp : 40) Writing GFA to /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/genomics_de_novo_temp/working_dir/spades_default_assembly//K55/assembly_graph_with_scaffolds.gfa 0:01:35.731 276M / 3G INFO General (contig_output.hpp : 22) Outputting contigs to /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/genomics_de_novo_temp/working_dir/spades_default_assembly//K55/before_rr.fasta 0:01:35.782 276M / 3G INFO General (contig_output_stage.cpp : 50) Outputting FastG graph to /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/genomics_de_novo_temp/working_dir/spades_default_assembly//K55/assembly_graph.fastg 0:01:35.897 276M / 3G INFO General (contig_output.hpp : 22) Outputting contigs to /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/genomics_de_novo_temp/working_dir/spades_default_assembly//K55/simplified_contigs.fasta 0:01:35.947 276M / 3G INFO General (contig_output.hpp : 22) Outputting contigs to /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/genomics_de_novo_temp/working_dir/spades_default_assembly//K55/intermediate_contigs.fasta 0:01:36.011 276M / 3G INFO StageManager (stage.cpp : 126) STAGE == Paired Information Counting 0:01:36.012 276M / 3G INFO General (graph_pack.hpp : 108) Normalizing k-mer map. Total 499374 kmers to process 0:01:36.012 276M / 3G INFO General (graph_pack.hpp : 110) Normalizing done 0:01:36.013 276M / 3G INFO General (pair_info_count.cpp : 317) Min edge length for estimation: 63359 0:01:36.013 276M / 3G INFO General (pair_info_count.cpp : 328) Estimating insert size for library #0 0:01:36.013 276M / 3G INFO General (pair_info_count.cpp : 176) Estimating insert size (takes a while) 0:01:36.059 356M / 3G INFO General (short_read_mapper.hpp : 88) Selecting usual mapper 0:01:37.629 356M / 3G INFO General (sequence_mapper_notifier.h: 81) Processed 200000 reads 0:01:37.654 356M / 3G INFO General (sequence_mapper_notifier.h: 81) Processed 400000 reads 0:01:37.674 356M / 3G INFO General (sequence_mapper_notifier.h: 81) Processed 600000 reads 0:01:37.722 356M / 3G INFO General (sequence_mapper_notifier.h: 81) Processed 800000 reads 0:01:39.223 356M / 3G INFO General (sequence_mapper_notifier.h: 99) Total 1484726 reads processed 0:01:39.448 356M / 3G INFO General (pair_info_count.cpp : 194) Edge pairs: 67108864 (rough upper limit) 0:01:39.448 356M / 3G INFO General (pair_info_count.cpp : 198) 733713 paired reads (49.4174% of all) aligned to long edges 0:01:39.454 276M / 3G INFO General (pair_info_count.cpp : 351) Insert size = 375.197, deviation = 112.039, left quantile = 234, right quantile = 521, read length = 140 0:01:39.585 468M / 3G INFO General (pair_info_count.cpp : 368) Filtering data for library #0 0:01:39.585 468M / 3G INFO General (short_read_mapper.hpp : 88) Selecting usual mapper 0:01:41.165 468M / 3G INFO General (sequence_mapper_notifier.h: 81) Processed 200000 reads 0:01:41.169 468M / 3G INFO General (sequence_mapper_notifier.h: 81) Processed 400000 reads 0:01:41.186 468M / 3G INFO General (sequence_mapper_notifier.h: 81) Processed 600000 reads 0:01:41.200 468M / 3G INFO General (sequence_mapper_notifier.h: 81) Processed 800000 reads 0:01:42.589 468M / 3G INFO General (sequence_mapper_notifier.h: 99) Total 1484726 reads processed 0:01:42.589 468M / 3G INFO General (pair_info_count.cpp : 380) Mapping library #0 0:01:42.589 468M / 3G INFO General (pair_info_count.cpp : 382) Mapping paired reads (takes a while) 0:01:42.590 468M / 3G INFO General (pair_info_count.cpp : 275) Left insert size quantile 234, right insert size quantile 521, filtering threshold 2, rounding threshold 0 0:01:42.607 480M / 3G INFO General (short_read_mapper.hpp : 88) Selecting usual mapper 0:01:44.520 480M / 3G INFO General (sequence_mapper_notifier.h: 81) Processed 200000 reads 0:01:44.551 480M / 3G INFO General (sequence_mapper_notifier.h: 81) Processed 400000 reads 0:01:44.613 480M / 3G INFO General (sequence_mapper_notifier.h: 81) Processed 600000 reads 0:01:44.615 480M / 3G INFO General (sequence_mapper_notifier.h: 81) Processed 800000 reads 0:01:46.360 480M / 3G INFO General (sequence_mapper_notifier.h: 99) Total 1484726 reads processed 0:01:46.390 276M / 3G INFO StageManager (stage.cpp : 126) STAGE == Distance Estimation 0:01:46.390 276M / 3G INFO General (distance_estimation.cpp : 224) Processing library #0 0:01:46.390 276M / 3G INFO General (distance_estimation.cpp : 130) Weight Filter Done 0:01:46.390 276M / 3G INFO DistanceEstimator (distance_estimation.hpp : 116) Using SIMPLE distance estimator 0:01:46.397 276M / 3G INFO General (distance_estimation.cpp : 35) Filtering info 0:01:46.397 276M / 3G INFO General (pair_info_filters.hpp : 242) Start filtering; index size: 5506 0:01:46.398 276M / 3G INFO General (pair_info_filters.hpp : 263) Done filtering 0:01:46.398 276M / 3G INFO General (distance_estimation.cpp : 172) Refining clustered pair information 0:01:46.399 276M / 3G INFO General (distance_estimation.cpp : 174) The refining of clustered pair information has been finished 0:01:46.399 276M / 3G INFO General (distance_estimation.cpp : 176) Improving paired information 0:01:46.406 276M / 3G INFO PairInfoImprover (pair_info_improver.hpp : 103) Paired info stats: missing = 117; contradictional = 112 0:01:46.413 276M / 3G INFO PairInfoImprover (pair_info_improver.hpp : 103) Paired info stats: missing = 2; contradictional = 4 0:01:46.413 276M / 3G INFO General (distance_estimation.cpp : 183) Filling scaffolding index 0:01:46.413 276M / 3G INFO DistanceEstimator (distance_estimation.hpp : 116) Using SMOOTHING distance estimator 0:01:46.489 276M / 3G INFO General (distance_estimation.cpp : 35) Filtering info 0:01:46.489 276M / 3G INFO General (pair_info_filters.hpp : 242) Start filtering; index size: 1627 0:01:46.490 276M / 3G INFO General (pair_info_filters.hpp : 263) Done filtering 0:01:46.490 276M / 3G INFO General (distance_estimation.cpp : 228) Clearing raw paired index 0:01:46.494 276M / 3G INFO StageManager (stage.cpp : 126) STAGE == Repeat Resolving 0:01:46.494 276M / 3G INFO General (repeat_resolving.cpp : 69) Using Path-Extend repeat resolving 0:01:46.494 276M / 3G INFO General (launcher.cpp : 478) ExSPAnder repeat resolving tool started 0:01:46.500 280M / 3G INFO General (launcher.cpp : 393) Creating main extenders, unique edge length = 2000 0:01:46.500 280M / 3G INFO General (extenders_logic.cpp : 275) Estimated coverage of library #0 is 29.4548 0:01:46.500 280M / 3G INFO General (extenders_logic.cpp : 275) Estimated coverage of library #0 is 29.4548 0:01:46.501 280M / 3G INFO General (extenders_logic.cpp : 472) Using 1 paired-end library 0:01:46.501 280M / 3G INFO General (extenders_logic.cpp : 473) Using 1 paired-end scaffolding library 0:01:46.501 280M / 3G INFO General (extenders_logic.cpp : 474) Using 0 single read libraries 0:01:46.501 280M / 3G INFO General (launcher.cpp : 421) Total number of extenders is 3 0:01:46.501 280M / 3G INFO General (path_extender.hpp : 867) Processed 0 paths from 696 (0%) 0:01:46.575 280M / 3G INFO General (path_extender.hpp : 867) Processed 70 paths from 696 (10%) 0:01:46.616 280M / 3G INFO General (path_extender.hpp : 865) Processed 128 paths from 696 (18%) 0:01:46.618 280M / 3G INFO General (path_extender.hpp : 867) Processed 140 paths from 696 (20%) 0:01:46.641 280M / 3G INFO General (path_extender.hpp : 867) Processed 210 paths from 696 (30%) 0:01:46.647 280M / 3G INFO General (path_extender.hpp : 865) Processed 256 paths from 696 (36%) 0:01:46.649 280M / 3G INFO General (path_extender.hpp : 867) Processed 280 paths from 696 (40%) 0:01:46.651 280M / 3G INFO General (path_extender.hpp : 867) Processed 350 paths from 696 (50%) 0:01:46.652 280M / 3G INFO General (path_extender.hpp : 867) Processed 420 paths from 696 (60%) 0:01:46.654 280M / 3G INFO General (path_extender.hpp : 867) Processed 490 paths from 696 (70%) 0:01:46.658 280M / 3G INFO General (path_extender.hpp : 865) Processed 512 paths from 696 (73%) 0:01:46.662 280M / 3G INFO General (path_extender.hpp : 867) Processed 560 paths from 696 (80%) 0:01:46.665 280M / 3G INFO General (path_extender.hpp : 867) Processed 630 paths from 696 (90%) 0:01:46.665 280M / 3G INFO General (launcher.cpp : 234) Finalizing paths 0:01:46.665 280M / 3G INFO General (launcher.cpp : 236) Deduplicating paths 0:01:46.666 280M / 3G INFO General (launcher.cpp : 240) Paths deduplicated 0:01:46.666 280M / 3G INFO PEResolver (pe_resolver.hpp : 299) Removing overlaps 0:01:46.666 280M / 3G INFO PEResolver (pe_resolver.hpp : 302) Sorting paths 0:01:46.666 280M / 3G INFO PEResolver (pe_resolver.hpp : 309) Marking overlaps 0:01:46.666 280M / 3G INFO OverlapRemover (pe_resolver.hpp : 132) Marking start/end overlaps 0:01:46.667 280M / 3G INFO OverlapRemover (pe_resolver.hpp : 135) Marking remaining overlaps 0:01:46.668 280M / 3G INFO PEResolver (pe_resolver.hpp : 312) Splitting paths 0:01:46.668 280M / 3G INFO PEResolver (pe_resolver.hpp : 317) Deduplicating paths 0:01:46.669 280M / 3G INFO PEResolver (pe_resolver.hpp : 319) Overlaps removed 0:01:46.669 280M / 3G INFO General (launcher.cpp : 257) Paths finalized 0:01:46.669 280M / 3G INFO General (launcher.cpp : 287) Traversing tandem repeats 0:01:46.671 280M / 3G INFO General (launcher.cpp : 297) Traversed 4 loops 0:01:46.671 280M / 3G INFO General (launcher.cpp : 428) Closing gaps in paths 0:01:46.672 284M / 3G INFO General (launcher.cpp : 456) Gap closing completed 0:01:46.673 284M / 3G INFO General (launcher.cpp : 234) Finalizing paths 0:01:46.673 284M / 3G INFO General (launcher.cpp : 236) Deduplicating paths 0:01:46.673 284M / 3G INFO General (launcher.cpp : 240) Paths deduplicated 0:01:46.673 284M / 3G INFO PEResolver (pe_resolver.hpp : 299) Removing overlaps 0:01:46.673 284M / 3G INFO PEResolver (pe_resolver.hpp : 302) Sorting paths 0:01:46.673 284M / 3G INFO PEResolver (pe_resolver.hpp : 309) Marking overlaps 0:01:46.673 284M / 3G INFO OverlapRemover (pe_resolver.hpp : 132) Marking start/end overlaps 0:01:46.673 284M / 3G INFO OverlapRemover (pe_resolver.hpp : 135) Marking remaining overlaps 0:01:46.674 284M / 3G INFO PEResolver (pe_resolver.hpp : 312) Splitting paths 0:01:46.674 284M / 3G INFO PEResolver (pe_resolver.hpp : 317) Deduplicating paths 0:01:46.674 284M / 3G INFO PEResolver (pe_resolver.hpp : 319) Overlaps removed 0:01:46.674 284M / 3G INFO General (launcher.cpp : 257) Paths finalized 0:01:46.675 284M / 3G INFO General (launcher.cpp : 531) ExSPAnder repeat resolving tool finished 0:01:46.680 280M / 3G INFO StageManager (stage.cpp : 126) STAGE == Contig Output 0:01:46.680 280M / 3G INFO General (contig_output_stage.cpp : 40) Writing GFA to /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/genomics_de_novo_temp/working_dir/spades_default_assembly//K55/assembly_graph_with_scaffolds.gfa 0:01:46.708 280M / 3G INFO General (contig_output.hpp : 22) Outputting contigs to /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/genomics_de_novo_temp/working_dir/spades_default_assembly//K55/before_rr.fasta 0:01:46.762 280M / 3G INFO General (contig_output_stage.cpp : 50) Outputting FastG graph to /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/genomics_de_novo_temp/working_dir/spades_default_assembly//K55/assembly_graph.fastg 0:01:46.879 280M / 3G INFO General (contig_output_stage.cpp : 20) Outputting FastG paths to /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/genomics_de_novo_temp/working_dir/spades_default_assembly//K55/final_contigs.paths 0:01:46.945 280M / 3G INFO General (contig_output_stage.cpp : 20) Outputting FastG paths to /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/genomics_de_novo_temp/working_dir/spades_default_assembly//K55/scaffolds.paths 0:01:47.027 280M / 3G INFO General (launch.hpp : 137) SPAdes finished 0:01:47.221 24M / 3G INFO General (main.cpp : 110) Assembling time: 0 hours 1 minutes 47 seconds ===== Assembling finished. Used k-mer sizes: 21, 33, 55 * Assembled contigs are in /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/genomics_de_novo_temp/working_dir/spades_default_assembly/contigs.fasta * Assembled scaffolds are in /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/genomics_de_novo_temp/working_dir/spades_default_assembly/scaffolds.fasta * Assembly graph is in /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/genomics_de_novo_temp/working_dir/spades_default_assembly/assembly_graph.fastg * Assembly graph in GFA format is in /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/genomics_de_novo_temp/working_dir/spades_default_assembly/assembly_graph_with_scaffolds.gfa * Paths in the assembly graph corresponding to the contigs are in /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/genomics_de_novo_temp/working_dir/spades_default_assembly/contigs.paths * Paths in the assembly graph corresponding to the scaffolds are in /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/genomics_de_novo_temp/working_dir/spades_default_assembly/scaffolds.paths ======= SPAdes pipeline finished. SPAdes log can be found here: /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/genomics_de_novo_temp/working_dir/spades_default_assembly/spades.log Thank you for using SPAdes!