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_kmers_set_careful_assembly -t 4 -k 21,33,55,77 --careful --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_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: ['/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: [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: /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/genomics_de_novo_temp/working_dir/spades_kmers_set_careful_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_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 /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/genomics_de_novo_temp/working_dir/spades_kmers_set_careful_assembly/K21/configs/config.info 0:00:00.001 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_kmers_set_careful_assembly/K21/configs/careful_mode.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_kmers_set_careful_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 0:00:00.213 80M / 84M INFO General (binary_converter.hpp : 139) 16384 reads processed 0:00:00.328 92M / 92M INFO General (binary_converter.hpp : 139) 32768 reads processed 0:00:00.557 116M / 116M INFO General (binary_converter.hpp : 139) 65536 reads processed 0:00:01.003 164M / 164M INFO General (binary_converter.hpp : 139) 131072 reads processed 0:00:01.944 264M / 264M INFO General (binary_converter.hpp : 139) 262144 reads processed 0:00:04.095 320M / 320M INFO General (binary_converter.hpp : 139) 524288 reads processed 0:00:08.349 344M / 344M INFO General (binary_converter.hpp : 139) 1048576 reads processed 0:00:11.992 288M / 352M INFO General (binary_converter.hpp : 159) 1484726 reads written 0:00:12.174 4M / 352M INFO General (read_converter.hpp : 94) Converting single reads 0:00:12.387 132M / 352M INFO General (binary_converter.hpp : 159) 0 reads written 0:00:12.606 4M / 352M INFO General (graph_construction.hpp : 120) Constructing DeBruijn graph for k=21 0:00:12.608 4M / 352M INFO General (kmer_index_builder.hpp : 106) Splitting kmer instances into 16 buckets using 4 threads. This might take a while. 0:00:12.608 4M / 352M INFO General (file_limit.hpp : 32) Open file limit set to 1024 0:00:12.608 4M / 352M INFO General (kmer_splitters.hpp : 74) Memory available for splitting buffers: 20.833 Gb 0:00:12.608 4M / 352M INFO General (kmer_splitters.hpp : 82) Using cell size of 4194304 0:00:26.925 2G / 2G INFO General (kmer_splitters.hpp : 291) Processed 4501245 reads 0:00:31.736 2G / 2G INFO General (kmer_splitters.hpp : 291) Processed 5938904 reads 0:00:31.736 2G / 2G INFO General (kmer_splitters.hpp : 297) Adding contigs from previous K 0:00:31.946 16M / 2G INFO General (kmer_splitters.hpp : 310) Used 5938904 reads. Maximum read length 140 0:00:31.946 16M / 2G INFO General (kmer_splitters.hpp : 311) Average read length 140 0:00:31.946 16M / 2G INFO General (kmer_index_builder.hpp : 109) Starting k-mer counting. 0:00:32.387 16M / 2G INFO General (kmer_index_builder.hpp : 115) K-mer counting done. There are 10173588 kmers in total. 0:00:32.387 16M / 2G INFO General (kmer_index_builder.hpp : 121) Merging temporary buckets. 0:00:32.708 16M / 2G INFO K-mer Index Building (kmer_index_builder.hpp : 289) Building kmer index 0:00:32.708 16M / 2G INFO General (kmer_index_builder.hpp : 106) Splitting kmer instances into 64 buckets using 4 threads. This might take a while. 0:00:32.708 16M / 2G INFO General (file_limit.hpp : 32) Open file limit set to 1024 0:00:32.708 16M / 2G INFO General (kmer_splitters.hpp : 74) Memory available for splitting buffers: 20.832 Gb 0:00:32.708 16M / 2G INFO General (kmer_splitters.hpp : 82) Using cell size of 1048576 0:00:34.427 3G / 3G INFO General (kmer_splitters.hpp : 381) Processed 10173588 kmers 0:00:34.427 3G / 3G INFO General (kmer_splitters.hpp : 386) Used 10173588 kmers. 0:00:34.460 16M / 3G INFO General (kmer_index_builder.hpp : 109) Starting k-mer counting. 0:00:34.922 16M / 3G INFO General (kmer_index_builder.hpp : 115) K-mer counting done. There are 10096148 kmers in total. 0:00:34.922 16M / 3G INFO General (kmer_index_builder.hpp : 121) Merging temporary buckets. 0:00:35.603 16M / 3G INFO K-mer Index Building (kmer_index_builder.hpp : 298) Building perfect hash indices 0:00:36.177 16M / 3G INFO General (kmer_index_builder.hpp : 137) Merging final buckets. 0:00:36.379 16M / 3G INFO K-mer Index Building (kmer_index_builder.hpp : 320) Index built. Total 4689888 bytes occupied (3.71618 bits per kmer). 0:00:36.394 28M / 3G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 87) Building k-mer extensions from k+1-mers 0:00:37.313 28M / 3G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 91) Building k-mer extensions from k+1-mers finished. 0:00:37.315 28M / 3G INFO Early tip clipping (early_simplification.hpp : 181) Early tip clipping 0:00:39.601 28M / 3G INFO Early tip clipping (early_simplification.hpp : 184) 550174 22-mers were removed by early tip clipper 0:00:39.601 28M / 3G INFO General (graph_construction.hpp : 136) Condensing graph 0:00:39.611 28M / 3G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 355) Extracting unbranching paths 0:00:40.900 40M / 3G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 374) Extracting unbranching paths finished. 221440 sequences extracted 0:00:41.612 40M / 3G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 310) Collecting perfect loops 0:00:41.948 40M / 3G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 343) Collecting perfect loops finished. 2 loops collected 0:00:42.082 88M / 3G INFO General (graph_construction.hpp : 141) Building index with from graph 0:00:42.083 88M / 3G INFO K-mer Index Building (kmer_index_builder.hpp : 289) Building kmer index 0:00:42.083 88M / 3G INFO General (kmer_index_builder.hpp : 106) Splitting kmer instances into 64 buckets using 4 threads. This might take a while. 0:00:42.083 88M / 3G INFO General (file_limit.hpp : 32) Open file limit set to 1024 0:00:42.083 88M / 3G INFO General (kmer_splitters.hpp : 74) Memory available for splitting buffers: 20.8262 Gb 0:00:42.083 88M / 3G INFO General (kmer_splitters.hpp : 82) Using cell size of 1048576 0:00:42.786 3G / 3G INFO General (edge_index_builders.hpp : 75) Processed 441975 edges 0:00:42.786 3G / 3G INFO General (edge_index_builders.hpp : 80) Used 441975 sequences. 0:00:42.796 88M / 3G INFO General (kmer_index_builder.hpp : 109) Starting k-mer counting. 0:00:43.237 88M / 3G INFO General (kmer_index_builder.hpp : 115) K-mer counting done. There are 9623414 kmers in total. 0:00:43.237 88M / 3G INFO General (kmer_index_builder.hpp : 121) Merging temporary buckets. 0:00:44.286 88M / 3G INFO K-mer Index Building (kmer_index_builder.hpp : 298) Building perfect hash indices 0:00:44.816 92M / 3G INFO General (kmer_index_builder.hpp : 137) Merging final buckets. 0:00:45.026 92M / 3G INFO K-mer Index Building (kmer_index_builder.hpp : 320) Index built. Total 4470584 bytes occupied (3.71642 bits per kmer). 0:00:45.236 316M / 3G INFO General (edge_index_builders.hpp : 105) Collecting k-mer coverage information from graph, this takes a while. 0:00:46.012 316M / 3G INFO General (edge_index.hpp : 91) Index refilled 0:00:46.058 300M / 3G INFO General (graph_construction.hpp : 173) Filling coverage index 0:00:46.058 300M / 3G INFO General (edge_index_builders.hpp : 183) Collecting k-mer coverage information from reads, this takes a while. 0:01:24.410 300M / 3G INFO General (graph_construction.hpp : 175) Filling coverage and flanking coverage from index 0:01:25.583 300M / 3G INFO General (construction.cpp : 30) Figured out: read length = 140 0:01:25.585 300M / 3G INFO StageManager (stage.cpp : 126) STAGE == EC Threshold Finding 0:01:25.931 300M / 3G INFO General (kmer_coverage_model.cpp : 181) Kmer coverage valley at: 7 0:01:25.933 300M / 3G INFO General (kmer_coverage_model.cpp : 201) K-mer histogram maximum: 40 0:01:25.933 300M / 3G INFO General (kmer_coverage_model.cpp : 237) Estimated median coverage: 41. Coverage mad: 13.3434 0:01:25.933 300M / 3G INFO General (kmer_coverage_model.cpp : 259) Fitting coverage model 0:01:25.969 300M / 3G INFO General (kmer_coverage_model.cpp : 295) ... iteration 2 0:01:26.062 300M / 3G INFO General (kmer_coverage_model.cpp : 295) ... iteration 4 0:01:26.377 300M / 3G INFO General (kmer_coverage_model.cpp : 295) ... iteration 8 0:01:26.994 300M / 3G INFO General (kmer_coverage_model.cpp : 295) ... iteration 16 0:01:27.779 300M / 3G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 41.213. Fitted coverage std. dev: 11.1916 0:01:27.780 300M / 3G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 0.776085 0:01:27.780 300M / 3G INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 18 0:01:27.780 300M / 3G INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 18 0:01:27.780 300M / 3G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 8270101 0:01:27.780 300M / 3G INFO General (genomic_info_filler.cpp : 127) Mean coverage was calculated as 41.213 0:01:27.780 300M / 3G INFO General (genomic_info_filler.cpp : 141) EC coverage threshold value was calculated as 18 0:01:27.780 300M / 3G INFO General (genomic_info_filler.cpp : 142) Trusted kmer low bound: 0 0:01:27.780 300M / 3G INFO StageManager (stage.cpp : 126) STAGE == Simplification 0:01:27.807 72M / 3G INFO General (simplification.cpp : 387) Graph simplification started 0:01:27.807 72M / 3G INFO General (simplification.cpp : 77) PROCEDURE == InitialCleaning 0:01:27.807 72M / 3G INFO General (graph_simplification.hpp : 645) Flanking coverage based disconnection disabled 0:01:27.807 72M / 3G INFO General (simplification.cpp : 356) Running Self conjugate edge remover 0:01:27.844 72M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:01:27.844 72M / 3G INFO General (graph_simplification.hpp : 617) Creating parallel br instance 0:01:27.844 72M / 3G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 1 0:01:27.844 72M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:01:27.889 72M / 3G INFO General (simplification.cpp : 358) Triggered 228 times 0:01:27.889 72M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:01:28.898 76M / 3G INFO General (simplification.cpp : 358) Triggered 17425 times 0:01:28.898 76M / 3G INFO General (simplification.cpp : 356) Running Low coverage edge remover 0:01:29.984 80M / 3G INFO General (simplification.cpp : 358) Triggered 41934 times 0:01:29.984 80M / 3G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 2 0:01:29.984 80M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:01:29.994 80M / 3G INFO General (simplification.cpp : 358) Triggered 106 times 0:01:29.994 80M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:01:30.075 80M / 3G INFO General (simplification.cpp : 358) Triggered 940 times 0:01:30.075 80M / 3G INFO General (simplification.cpp : 356) Running Low coverage edge remover 0:01:30.304 80M / 3G INFO General (simplification.cpp : 358) Triggered 8284 times 0:01:30.304 80M / 3G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 3 0:01:30.304 80M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:01:30.307 80M / 3G INFO General (simplification.cpp : 358) Triggered 2 times 0:01:30.307 80M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:01:30.320 80M / 3G INFO General (simplification.cpp : 358) Triggered 145 times 0:01:30.320 80M / 3G INFO General (simplification.cpp : 356) Running Low coverage edge remover 0:01:30.343 76M / 3G INFO General (simplification.cpp : 358) Triggered 848 times 0:01:30.343 76M / 3G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 4 0:01:30.343 76M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:01:30.343 76M / 3G INFO General (simplification.cpp : 358) Triggered 1 times 0:01:30.343 76M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:01:30.345 76M / 3G INFO General (simplification.cpp : 358) Triggered 9 times 0:01:30.345 76M / 3G INFO General (simplification.cpp : 356) Running Low coverage edge remover 0:01:30.349 76M / 3G INFO General (simplification.cpp : 358) Triggered 146 times 0:01:30.349 76M / 3G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 5 0:01:30.349 76M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:01:30.349 76M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:01:30.349 76M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:01:30.350 76M / 3G INFO General (simplification.cpp : 358) Triggered 6 times 0:01:30.350 76M / 3G INFO General (simplification.cpp : 356) Running Low coverage edge remover 0:01:30.351 76M / 3G INFO General (simplification.cpp : 358) Triggered 56 times 0:01:30.351 76M / 3G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 6 0:01:30.351 76M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:01:30.351 76M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:01:30.351 76M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:01:30.352 76M / 3G INFO General (simplification.cpp : 358) Triggered 3 times 0:01:30.352 76M / 3G INFO General (simplification.cpp : 356) Running Low coverage edge remover 0:01:30.352 76M / 3G INFO General (simplification.cpp : 358) Triggered 30 times 0:01:30.352 76M / 3G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 7 0:01:30.352 76M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:01:30.352 76M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:01:30.352 76M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:01:30.352 76M / 3G INFO General (simplification.cpp : 358) Triggered 2 times 0:01:30.352 76M / 3G INFO General (simplification.cpp : 356) Running Low coverage edge remover 0:01:30.353 76M / 3G INFO General (simplification.cpp : 358) Triggered 44 times 0:01:30.353 76M / 3G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 8 0:01:30.353 76M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:01:30.353 76M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:01:30.353 76M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:01:30.354 76M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:01:30.354 76M / 3G INFO General (simplification.cpp : 356) Running Low coverage edge remover 0:01:30.354 76M / 3G INFO General (simplification.cpp : 358) Triggered 38 times 0:01:30.354 76M / 3G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 9 0:01:30.354 76M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:01:30.354 76M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:01:30.354 76M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:01:30.354 76M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:01:30.354 76M / 3G INFO General (simplification.cpp : 356) Running Low coverage edge remover 0:01:30.355 76M / 3G INFO General (simplification.cpp : 358) Triggered 42 times 0:01:30.355 76M / 3G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 10 0:01:30.355 76M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:01:30.360 76M / 3G INFO General (simplification.cpp : 358) Triggered 10 times 0:01:30.360 76M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:01:30.381 76M / 3G INFO General (simplification.cpp : 358) Triggered 10 times 0:01:30.381 76M / 3G INFO General (simplification.cpp : 356) Running Low coverage edge remover 0:01:30.386 76M / 3G INFO General (simplification.cpp : 358) Triggered 57 times 0:01:30.386 76M / 3G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 11 0:01:30.386 76M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:01:30.386 76M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:01:30.386 76M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:01:30.387 76M / 3G INFO General (simplification.cpp : 358) Triggered 1 times 0:01:30.387 76M / 3G INFO General (simplification.cpp : 356) Running Low coverage edge remover 0:01:30.387 76M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:01:30.387 76M / 3G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 12 0:01:30.387 76M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:01:30.387 76M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:01:30.387 76M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:01:30.387 76M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:01:30.387 76M / 3G INFO General (simplification.cpp : 356) Running Low coverage edge remover 0:01:30.387 76M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:01:30.387 76M / 3G INFO General (simplification.cpp : 167) PROCEDURE == Post simplification 0:01:30.387 76M / 3G INFO General (graph_simplification.hpp : 447) Disconnection of relatively low covered edges disabled 0:01:30.387 76M / 3G INFO General (graph_simplification.hpp : 477) Complex tip clipping disabled 0:01:30.387 76M / 3G INFO General (graph_simplification.hpp : 617) Creating parallel br instance 0:01:30.387 76M / 3G INFO General (simplification.cpp : 301) Iteration 1 0:01:30.387 76M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:01:30.389 76M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:01:30.389 76M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:01:30.406 76M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:01:30.406 76M / 3G INFO General (simplification.cpp : 301) Iteration 2 0:01:30.406 76M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:01:30.408 76M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:01:30.408 76M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:01:30.425 76M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:01:30.425 76M / 3G INFO General (simplification.cpp : 333) Disrupting self-conjugate edges 0:01:30.436 76M / 3G INFO StageManager (stage.cpp : 126) STAGE == Simplification Cleanup 0:01:30.436 76M / 3G INFO General (simplification.cpp : 547) Removing isolated edges 0:01:30.439 76M / 3G INFO General (simplification.cpp : 570) Counting average coverage 0:01:30.443 76M / 3G INFO General (simplification.cpp : 575) Average coverage = 41.7495 0:01:30.443 76M / 3G INFO StageManager (stage.cpp : 126) STAGE == Contig Output 0:01:30.443 76M / 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_kmers_set_careful_assembly//K21/assembly_graph_with_scaffolds.gfa 0:01:30.512 76M / 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_kmers_set_careful_assembly//K21/before_rr.fasta 0:01:30.633 76M / 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_kmers_set_careful_assembly//K21/assembly_graph.fastg 0:01:30.917 76M / 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_kmers_set_careful_assembly//K21/simplified_contigs.fasta 0:01:31.041 76M / 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_kmers_set_careful_assembly//K21/final_contigs.fasta 0:01:31.173 76M / 3G INFO StageManager (stage.cpp : 126) STAGE == Contig Output 0:01:31.173 76M / 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_kmers_set_careful_assembly//K21/assembly_graph_with_scaffolds.gfa 0:01:31.237 76M / 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_kmers_set_careful_assembly//K21/before_rr.fasta 0:01:31.348 76M / 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_kmers_set_careful_assembly//K21/assembly_graph.fastg 0:01:31.640 76M / 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_kmers_set_careful_assembly//K21/simplified_contigs.fasta 0:01:31.765 76M / 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_kmers_set_careful_assembly//K21/final_contigs.fasta 0:01:31.908 76M / 3G INFO General (launch.hpp : 137) SPAdes finished 0:01:31.995 16M / 3G INFO General (main.cpp : 110) Assembling time: 0 hours 1 minutes 32 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_kmers_set_careful_assembly/K33/configs/config.info 0:00:00.001 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_kmers_set_careful_assembly/K33/configs/careful_mode.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_kmers_set_careful_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 0:00:00.002 4M / 4M INFO StageManager (stage.cpp : 126) STAGE == Construction 0:00:00.007 4M / 4M INFO General (read_converter.hpp : 67) Binary reads detected 0:00:00.008 4M / 4M INFO General (graph_construction.hpp : 120) Constructing DeBruijn graph for k=33 0:00:00.010 4M / 4M INFO General (kmer_index_builder.hpp : 106) Splitting kmer instances into 16 buckets using 4 threads. This might take a while. 0:00:00.010 4M / 4M INFO General (file_limit.hpp : 32) Open file limit set to 1024 0:00:00.010 4M / 4M INFO General (kmer_splitters.hpp : 74) Memory available for splitting buffers: 20.833 Gb 0:00:00.010 4M / 4M INFO General (kmer_splitters.hpp : 82) Using cell size of 2097152 0:00:09.203 2G / 2G INFO General (kmer_splitters.hpp : 291) Processed 2500256 reads 0:00:17.786 2G / 2G INFO General (kmer_splitters.hpp : 291) Processed 5002200 reads 0:00:21.061 2G / 2G INFO General (kmer_splitters.hpp : 291) Processed 5938904 reads 0:00:21.061 2G / 2G INFO General (kmer_splitters.hpp : 297) Adding contigs from previous K 0:00:22.419 16M / 2G INFO General (kmer_splitters.hpp : 310) Used 5938904 reads. Maximum read length 140 0:00:22.419 16M / 2G INFO General (kmer_splitters.hpp : 311) Average read length 140 0:00:22.419 16M / 2G INFO General (kmer_index_builder.hpp : 109) Starting k-mer counting. 0:00:24.168 16M / 2G INFO General (kmer_index_builder.hpp : 115) K-mer counting done. There are 10745075 kmers in total. 0:00:24.168 16M / 2G INFO General (kmer_index_builder.hpp : 121) Merging temporary buckets. 0:00:24.750 16M / 2G INFO K-mer Index Building (kmer_index_builder.hpp : 289) Building kmer index 0:00:24.750 16M / 2G INFO General (kmer_index_builder.hpp : 106) Splitting kmer instances into 64 buckets using 4 threads. This might take a while. 0:00:24.750 16M / 2G INFO General (file_limit.hpp : 32) Open file limit set to 1024 0:00:24.750 16M / 2G INFO General (kmer_splitters.hpp : 74) Memory available for splitting buffers: 20.832 Gb 0:00:24.750 16M / 2G INFO General (kmer_splitters.hpp : 82) Using cell size of 524288 0:00:26.543 3G / 3G INFO General (kmer_splitters.hpp : 381) Processed 10745075 kmers 0:00:26.543 3G / 3G INFO General (kmer_splitters.hpp : 386) Used 10745075 kmers. 0:00:26.591 16M / 3G INFO General (kmer_index_builder.hpp : 109) Starting k-mer counting. 0:00:27.319 16M / 3G INFO General (kmer_index_builder.hpp : 115) K-mer counting done. There are 10709395 kmers in total. 0:00:27.319 16M / 3G INFO General (kmer_index_builder.hpp : 121) Merging temporary buckets. 0:00:28.145 16M / 3G INFO K-mer Index Building (kmer_index_builder.hpp : 298) Building perfect hash indices 0:00:28.806 16M / 3G INFO General (kmer_index_builder.hpp : 137) Merging final buckets. 0:00:29.235 16M / 3G INFO K-mer Index Building (kmer_index_builder.hpp : 320) Index built. Total 4973872 bytes occupied (3.71552 bits per kmer). 0:00:29.252 28M / 3G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 87) Building k-mer extensions from k+1-mers 0:00:30.288 28M / 3G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 91) Building k-mer extensions from k+1-mers finished. 0:00:30.291 28M / 3G INFO Early tip clipping (early_simplification.hpp : 181) Early tip clipping 0:00:32.701 28M / 3G INFO Early tip clipping (early_simplification.hpp : 184) 1082335 34-mers were removed by early tip clipper 0:00:32.701 28M / 3G INFO General (graph_construction.hpp : 136) Condensing graph 0:00:32.719 28M / 3G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 355) Extracting unbranching paths 0:00:33.950 32M / 3G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 374) Extracting unbranching paths finished. 108471 sequences extracted 0:00:34.857 32M / 3G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 310) Collecting perfect loops 0:00:35.269 32M / 3G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 343) Collecting perfect loops finished. 0 loops collected 0:00:35.343 60M / 3G INFO General (graph_construction.hpp : 141) Building index with from graph 0:00:35.344 60M / 3G INFO K-mer Index Building (kmer_index_builder.hpp : 289) Building kmer index 0:00:35.344 60M / 3G INFO General (kmer_index_builder.hpp : 106) Splitting kmer instances into 64 buckets using 4 threads. This might take a while. 0:00:35.344 60M / 3G INFO General (file_limit.hpp : 32) Open file limit set to 1024 0:00:35.344 60M / 3G INFO General (kmer_splitters.hpp : 74) Memory available for splitting buffers: 20.8285 Gb 0:00:35.344 60M / 3G INFO General (kmer_splitters.hpp : 82) Using cell size of 524288 0:00:36.242 3G / 3G INFO General (edge_index_builders.hpp : 75) Processed 216629 edges 0:00:36.242 3G / 3G INFO General (edge_index_builders.hpp : 80) Used 216629 sequences. 0:00:36.262 60M / 3G INFO General (kmer_index_builder.hpp : 109) Starting k-mer counting. 0:00:36.930 60M / 3G INFO General (kmer_index_builder.hpp : 115) K-mer counting done. There are 9662740 kmers in total. 0:00:36.930 60M / 3G INFO General (kmer_index_builder.hpp : 121) Merging temporary buckets. 0:00:37.800 60M / 3G INFO K-mer Index Building (kmer_index_builder.hpp : 298) Building perfect hash indices 0:00:38.364 64M / 3G INFO General (kmer_index_builder.hpp : 137) Merging final buckets. 0:00:38.763 64M / 3G INFO K-mer Index Building (kmer_index_builder.hpp : 320) Index built. Total 4488744 bytes occupied (3.71633 bits per kmer). 0:00:39.028 288M / 3G INFO General (edge_index_builders.hpp : 105) Collecting k-mer coverage information from graph, this takes a while. 0:00:39.934 288M / 3G INFO General (edge_index.hpp : 91) Index refilled 0:00:40.011 276M / 3G INFO General (graph_construction.hpp : 173) Filling coverage index 0:00:40.011 276M / 3G INFO General (edge_index_builders.hpp : 183) Collecting k-mer coverage information from reads, this takes a while. 0:01:15.633 272M / 3G INFO General (graph_construction.hpp : 175) Filling coverage and flanking coverage from index 0:01:16.025 272M / 3G INFO General (construction.cpp : 30) Figured out: read length = 140 0:01:16.026 272M / 3G INFO StageManager (stage.cpp : 126) STAGE == EC Threshold Finding 0:01:16.323 272M / 3G INFO General (kmer_coverage_model.cpp : 181) Kmer coverage valley at: 5 0:01:16.323 272M / 3G INFO General (kmer_coverage_model.cpp : 201) K-mer histogram maximum: 35 0:01:16.323 272M / 3G INFO General (kmer_coverage_model.cpp : 237) Estimated median coverage: 37. Coverage mad: 11.8608 0:01:16.323 272M / 3G INFO General (kmer_coverage_model.cpp : 259) Fitting coverage model 0:01:16.353 272M / 3G INFO General (kmer_coverage_model.cpp : 295) ... iteration 2 0:01:16.428 272M / 3G INFO General (kmer_coverage_model.cpp : 295) ... iteration 4 0:01:16.687 272M / 3G INFO General (kmer_coverage_model.cpp : 295) ... iteration 8 0:01:17.219 272M / 3G INFO General (kmer_coverage_model.cpp : 295) ... iteration 16 0:01:17.717 272M / 3G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 37.0004. Fitted coverage std. dev: 10.2607 0:01:17.719 272M / 3G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 0.906114 0:01:17.719 272M / 3G INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 17 0:01:17.719 272M / 3G INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 17 0:01:17.719 272M / 3G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 8243812 0:01:17.719 272M / 3G INFO General (genomic_info_filler.cpp : 127) Mean coverage was calculated as 37.0004 0:01:17.719 272M / 3G INFO General (genomic_info_filler.cpp : 141) EC coverage threshold value was calculated as 17 0:01:17.719 272M / 3G INFO General (genomic_info_filler.cpp : 142) Trusted kmer low bound: 0 0:01:17.719 272M / 3G INFO StageManager (stage.cpp : 126) STAGE == Simplification 0:01:17.741 44M / 3G INFO General (simplification.cpp : 387) Graph simplification started 0:01:17.741 44M / 3G INFO General (simplification.cpp : 77) PROCEDURE == InitialCleaning 0:01:17.741 44M / 3G INFO General (graph_simplification.hpp : 645) Flanking coverage based disconnection disabled 0:01:17.741 44M / 3G INFO General (simplification.cpp : 356) Running Self conjugate edge remover 0:01:17.754 44M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:01:17.754 44M / 3G INFO General (graph_simplification.hpp : 617) Creating parallel br instance 0:01:17.754 44M / 3G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 1 0:01:17.754 44M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:01:17.777 40M / 3G INFO General (simplification.cpp : 358) Triggered 606 times 0:01:17.777 40M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:01:18.364 44M / 3G INFO General (simplification.cpp : 358) Triggered 19740 times 0:01:18.364 44M / 3G INFO General (simplification.cpp : 356) Running Low coverage edge remover 0:01:18.736 48M / 3G INFO General (simplification.cpp : 358) Triggered 13192 times 0:01:18.736 48M / 3G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 2 0:01:18.736 48M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:01:18.743 48M / 3G INFO General (simplification.cpp : 358) Triggered 141 times 0:01:18.743 48M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:01:18.780 48M / 3G INFO General (simplification.cpp : 358) Triggered 537 times 0:01:18.780 48M / 3G INFO General (simplification.cpp : 356) Running Low coverage edge remover 0:01:18.879 44M / 3G INFO General (simplification.cpp : 358) Triggered 1259 times 0:01:18.879 44M / 3G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 3 0:01:18.879 44M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:01:18.880 40M / 3G INFO General (simplification.cpp : 358) Triggered 3 times 0:01:18.880 40M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:01:18.885 40M / 3G INFO General (simplification.cpp : 358) Triggered 54 times 0:01:18.885 40M / 3G INFO General (simplification.cpp : 356) Running Low coverage edge remover 0:01:18.889 40M / 3G INFO General (simplification.cpp : 358) Triggered 64 times 0:01:18.889 40M / 3G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 4 0:01:18.889 40M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:01:18.889 40M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:01:18.889 40M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:01:18.889 40M / 3G INFO General (simplification.cpp : 358) Triggered 2 times 0:01:18.889 40M / 3G INFO General (simplification.cpp : 356) Running Low coverage edge remover 0:01:18.890 40M / 3G INFO General (simplification.cpp : 358) Triggered 18 times 0:01:18.890 40M / 3G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 5 0:01:18.890 40M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:01:18.890 40M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:01:18.890 40M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:01:18.890 40M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:01:18.890 40M / 3G INFO General (simplification.cpp : 356) Running Low coverage edge remover 0:01:18.892 40M / 3G INFO General (simplification.cpp : 358) Triggered 16 times 0:01:18.892 40M / 3G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 6 0:01:18.892 40M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:01:18.892 40M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:01:18.892 40M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:01:18.892 40M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:01:18.892 40M / 3G INFO General (simplification.cpp : 356) Running Low coverage edge remover 0:01:18.892 40M / 3G INFO General (simplification.cpp : 358) Triggered 2 times 0:01:18.892 40M / 3G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 7 0:01:18.892 40M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:01:18.892 40M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:01:18.892 40M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:01:18.892 40M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:01:18.892 40M / 3G INFO General (simplification.cpp : 356) Running Low coverage edge remover 0:01:18.893 40M / 3G INFO General (simplification.cpp : 358) Triggered 10 times 0:01:18.893 40M / 3G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 8 0:01:18.893 40M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:01:18.893 40M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:01:18.893 40M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:01:18.893 40M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:01:18.893 40M / 3G INFO General (simplification.cpp : 356) Running Low coverage edge remover 0:01:18.893 40M / 3G INFO General (simplification.cpp : 358) Triggered 9 times 0:01:18.893 40M / 3G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 9 0:01:18.893 40M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:01:18.893 40M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:01:18.893 40M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:01:18.893 40M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:01:18.893 40M / 3G INFO General (simplification.cpp : 356) Running Low coverage edge remover 0:01:18.894 40M / 3G INFO General (simplification.cpp : 358) Triggered 11 times 0:01:18.894 40M / 3G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 10 0:01:18.894 40M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:01:18.896 40M / 3G INFO General (simplification.cpp : 358) Triggered 6 times 0:01:18.896 40M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:01:18.902 40M / 3G INFO General (simplification.cpp : 358) Triggered 3 times 0:01:18.902 40M / 3G INFO General (simplification.cpp : 356) Running Low coverage edge remover 0:01:18.904 40M / 3G INFO General (simplification.cpp : 358) Triggered 17 times 0:01:18.904 40M / 3G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 11 0:01:18.904 40M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:01:18.904 40M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:01:18.904 40M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:01:18.904 40M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:01:18.904 40M / 3G INFO General (simplification.cpp : 356) Running Low coverage edge remover 0:01:18.904 40M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:01:18.904 40M / 3G INFO General (simplification.cpp : 167) PROCEDURE == Post simplification 0:01:18.904 40M / 3G INFO General (graph_simplification.hpp : 447) Disconnection of relatively low covered edges disabled 0:01:18.904 40M / 3G INFO General (graph_simplification.hpp : 477) Complex tip clipping disabled 0:01:18.904 40M / 3G INFO General (graph_simplification.hpp : 617) Creating parallel br instance 0:01:18.904 40M / 3G INFO General (simplification.cpp : 301) Iteration 1 0:01:18.904 40M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:01:18.905 40M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:01:18.905 40M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:01:18.909 40M / 3G INFO General (simplification.cpp : 358) Triggered 1 times 0:01:18.909 40M / 3G INFO General (simplification.cpp : 301) Iteration 2 0:01:18.909 40M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:01:18.909 40M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:01:18.909 40M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:01:18.913 40M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:01:18.913 40M / 3G INFO General (simplification.cpp : 333) Disrupting self-conjugate edges 0:01:18.915 40M / 3G INFO StageManager (stage.cpp : 126) STAGE == Simplification Cleanup 0:01:18.915 40M / 3G INFO General (simplification.cpp : 547) Removing isolated edges 0:01:18.917 40M / 3G INFO General (simplification.cpp : 570) Counting average coverage 0:01:18.917 40M / 3G INFO General (simplification.cpp : 575) Average coverage = 37.3251 0:01:18.917 40M / 3G INFO StageManager (stage.cpp : 126) STAGE == Contig Output 0:01:18.917 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_kmers_set_careful_assembly//K33/assembly_graph_with_scaffolds.gfa 0:01:18.945 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_kmers_set_careful_assembly//K33/before_rr.fasta 0:01:19.007 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_kmers_set_careful_assembly//K33/assembly_graph.fastg 0:01:19.149 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_kmers_set_careful_assembly//K33/simplified_contigs.fasta 0:01:19.210 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_kmers_set_careful_assembly//K33/final_contigs.fasta 0:01:19.284 40M / 3G INFO StageManager (stage.cpp : 126) STAGE == Contig Output 0:01:19.284 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_kmers_set_careful_assembly//K33/assembly_graph_with_scaffolds.gfa 0:01:19.316 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_kmers_set_careful_assembly//K33/before_rr.fasta 0:01:19.376 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_kmers_set_careful_assembly//K33/assembly_graph.fastg 0:01:19.517 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_kmers_set_careful_assembly//K33/simplified_contigs.fasta 0:01:19.581 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_kmers_set_careful_assembly//K33/final_contigs.fasta 0:01:19.658 40M / 3G INFO General (launch.hpp : 137) SPAdes finished 0:01:19.726 20M / 3G INFO General (main.cpp : 110) Assembling time: 0 hours 1 minutes 19 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_kmers_set_careful_assembly/K55/configs/config.info 0:00:00.001 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_kmers_set_careful_assembly/K55/configs/careful_mode.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_kmers_set_careful_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 0:00:08.546 2G / 2G INFO General (kmer_splitters.hpp : 291) Processed 3142047 reads 0:00:16.564 2G / 2G INFO General (kmer_splitters.hpp : 291) Processed 5938904 reads 0:00:16.564 2G / 2G INFO General (kmer_splitters.hpp : 297) Adding contigs from previous K 0:00:17.875 16M / 2G INFO General (kmer_splitters.hpp : 310) Used 5938904 reads. Maximum read length 140 0:00:17.875 16M / 2G INFO General (kmer_splitters.hpp : 311) Average read length 140 0:00:17.875 16M / 2G INFO General (kmer_index_builder.hpp : 109) Starting k-mer counting. 0:00:18.830 16M / 2G INFO General (kmer_index_builder.hpp : 115) K-mer counting done. There are 11239275 kmers in total. 0:00:18.830 16M / 2G INFO General (kmer_index_builder.hpp : 121) Merging temporary buckets. 0:00:19.389 16M / 2G INFO K-mer Index Building (kmer_index_builder.hpp : 289) Building kmer index 0:00:19.389 16M / 2G INFO General (kmer_index_builder.hpp : 106) Splitting kmer instances into 64 buckets using 4 threads. This might take a while. 0:00:19.389 16M / 2G INFO General (file_limit.hpp : 32) Open file limit set to 1024 0:00:19.389 16M / 2G INFO General (kmer_splitters.hpp : 74) Memory available for splitting buffers: 20.832 Gb 0:00:19.390 16M / 2G INFO General (kmer_splitters.hpp : 82) Using cell size of 524288 0:00:21.466 3G / 3G INFO General (kmer_splitters.hpp : 381) Processed 11239275 kmers 0:00:21.466 3G / 3G INFO General (kmer_splitters.hpp : 386) Used 11239275 kmers. 0:00:21.512 16M / 3G INFO General (kmer_index_builder.hpp : 109) Starting k-mer counting. 0:00:22.153 16M / 3G INFO General (kmer_index_builder.hpp : 115) K-mer counting done. There are 11225939 kmers in total. 0:00:22.153 16M / 3G INFO General (kmer_index_builder.hpp : 121) Merging temporary buckets. 0:00:22.990 16M / 3G INFO K-mer Index Building (kmer_index_builder.hpp : 298) Building perfect hash indices 0:00:23.638 16M / 3G INFO General (kmer_index_builder.hpp : 137) Merging final buckets. 0:00:24.081 16M / 3G INFO K-mer Index Building (kmer_index_builder.hpp : 320) Index built. Total 5213488 bytes occupied (3.71532 bits per kmer). 0:00:24.097 28M / 3G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 87) Building k-mer extensions from k+1-mers 0:00:25.670 28M / 3G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 91) Building k-mer extensions from k+1-mers finished. 0:00:25.671 28M / 3G INFO General (graph_construction.hpp : 136) Condensing graph 0:00:25.705 28M / 3G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 355) Extracting unbranching paths 0:00:27.175 52M / 3G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 374) Extracting unbranching paths finished. 260722 sequences extracted 0:00:28.137 52M / 3G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 310) Collecting perfect loops 0:00:28.541 52M / 3G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 343) Collecting perfect loops finished. 0 loops collected 0:00:28.721 112M / 3G INFO General (graph_construction.hpp : 141) Building index with from graph 0:00:28.722 112M / 3G INFO K-mer Index Building (kmer_index_builder.hpp : 289) Building kmer index 0:00:28.722 112M / 3G INFO General (kmer_index_builder.hpp : 106) Splitting kmer instances into 64 buckets using 4 threads. This might take a while. 0:00:28.722 112M / 3G INFO General (file_limit.hpp : 32) Open file limit set to 1024 0:00:28.722 112M / 3G INFO General (kmer_splitters.hpp : 74) Memory available for splitting buffers: 20.8242 Gb 0:00:28.722 112M / 3G INFO General (kmer_splitters.hpp : 82) Using cell size of 524288 0:00:29.700 3G / 3G INFO General (edge_index_builders.hpp : 75) Processed 521402 edges 0:00:29.700 3G / 3G INFO General (edge_index_builders.hpp : 80) Used 521402 sequences. 0:00:29.738 112M / 3G INFO General (kmer_index_builder.hpp : 109) Starting k-mer counting. 0:00:30.379 112M / 3G INFO General (kmer_index_builder.hpp : 115) K-mer counting done. There are 11239275 kmers in total. 0:00:30.379 112M / 3G INFO General (kmer_index_builder.hpp : 121) Merging temporary buckets. 0:00:31.180 112M / 3G INFO K-mer Index Building (kmer_index_builder.hpp : 298) Building perfect hash indices 0:00:31.859 120M / 3G INFO General (kmer_index_builder.hpp : 137) Merging final buckets. 0:00:32.252 120M / 3G INFO K-mer Index Building (kmer_index_builder.hpp : 320) Index built. Total 5219760 bytes occupied (3.71537 bits per kmer). 0:00:32.485 380M / 3G INFO General (edge_index_builders.hpp : 105) Collecting k-mer coverage information from graph, this takes a while. 0:00:33.291 380M / 3G INFO General (edge_index.hpp : 91) Index refilled 0:00:33.340 360M / 3G INFO General (graph_construction.hpp : 173) Filling coverage index 0:00:33.340 360M / 3G INFO General (edge_index_builders.hpp : 183) Collecting k-mer coverage information from reads, this takes a while. 0:01:07.920 360M / 3G INFO General (graph_construction.hpp : 175) Filling coverage and flanking coverage from index 0:01:08.824 360M / 3G INFO General (construction.cpp : 30) Figured out: read length = 140 0:01:08.824 360M / 3G INFO StageManager (stage.cpp : 126) STAGE == EC Threshold Finding 0:01:09.126 360M / 3G INFO General (kmer_coverage_model.cpp : 181) Kmer coverage valley at: 4 0:01:09.126 360M / 3G INFO General (kmer_coverage_model.cpp : 201) K-mer histogram maximum: 27 0:01:09.126 360M / 3G INFO General (kmer_coverage_model.cpp : 237) Estimated median coverage: 29. Coverage mad: 10.3782 0:01:09.126 360M / 3G INFO General (kmer_coverage_model.cpp : 259) Fitting coverage model 0:01:09.151 360M / 3G INFO General (kmer_coverage_model.cpp : 295) ... iteration 2 0:01:09.215 360M / 3G INFO General (kmer_coverage_model.cpp : 295) ... iteration 4 0:01:09.434 360M / 3G INFO General (kmer_coverage_model.cpp : 295) ... iteration 8 0:01:09.881 360M / 3G INFO General (kmer_coverage_model.cpp : 295) ... iteration 16 0:01:10.375 360M / 3G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 29.2949. Fitted coverage std. dev: 8.56469 0:01:10.376 360M / 3G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 0.892381 0:01:10.376 360M / 3G INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 14 0:01:10.376 360M / 3G INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 14 0:01:10.376 360M / 3G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 8179565 0:01:10.376 360M / 3G INFO General (genomic_info_filler.cpp : 127) Mean coverage was calculated as 29.2949 0:01:10.376 360M / 3G INFO General (genomic_info_filler.cpp : 141) EC coverage threshold value was calculated as 14 0:01:10.376 360M / 3G INFO General (genomic_info_filler.cpp : 142) Trusted kmer low bound: 0 0:01:10.376 360M / 3G INFO StageManager (stage.cpp : 126) STAGE == Gap Closer 0:01:10.377 360M / 3G INFO General (gap_closer.cpp : 159) Preparing shift maps 0:01:10.582 376M / 3G INFO General (gap_closer.cpp : 119) Processing paired reads (takes a while) 0:01:13.102 380M / 3G INFO General (gap_closer.cpp : 138) Used 1484726 paired reads 0:01:13.102 380M / 3G INFO General (gap_closer.cpp : 140) Merging paired indices 0:01:13.153 364M / 3G INFO GapCloser (gap_closer.cpp : 346) Closing short gaps 0:01:13.528 364M / 3G INFO GapCloser (gap_closer.cpp : 380) Closing short gaps complete: filled 11 gaps after checking 180 candidates 0:01:13.547 360M / 3G INFO StageManager (stage.cpp : 126) STAGE == Simplification 0:01:13.569 92M / 3G INFO General (simplification.cpp : 387) Graph simplification started 0:01:13.569 92M / 3G INFO General (simplification.cpp : 77) PROCEDURE == InitialCleaning 0:01:13.569 92M / 3G INFO General (graph_simplification.hpp : 645) Flanking coverage based disconnection disabled 0:01:13.569 92M / 3G INFO General (simplification.cpp : 356) Running Self conjugate edge remover 0:01:13.605 92M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:01:13.605 92M / 3G INFO General (graph_simplification.hpp : 617) Creating parallel br instance 0:01:13.605 92M / 3G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 1 0:01:13.605 92M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:01:14.837 100M / 3G INFO General (simplification.cpp : 358) Triggered 109413 times 0:01:14.837 100M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:01:16.918 136M / 3G INFO General (simplification.cpp : 358) Triggered 10497 times 0:01:16.918 136M / 3G INFO General (simplification.cpp : 356) Running Low coverage edge remover 0:01:17.082 128M / 3G INFO General (simplification.cpp : 358) Triggered 2480 times 0:01:17.082 128M / 3G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 2 0:01:17.082 128M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:01:17.096 128M / 3G INFO General (simplification.cpp : 358) Triggered 152 times 0:01:17.096 128M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:01:17.179 132M / 3G INFO General (simplification.cpp : 358) Triggered 218 times 0:01:17.179 132M / 3G INFO General (simplification.cpp : 356) Running Low coverage edge remover 0:01:17.248 132M / 3G INFO General (simplification.cpp : 358) Triggered 391 times 0:01:17.248 132M / 3G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 3 0:01:17.248 132M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:01:17.254 128M / 3G INFO General (simplification.cpp : 358) Triggered 28 times 0:01:17.254 128M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:01:17.266 128M / 3G INFO General (simplification.cpp : 358) Triggered 19 times 0:01:17.266 128M / 3G INFO General (simplification.cpp : 356) Running Low coverage edge remover 0:01:17.268 128M / 3G INFO General (simplification.cpp : 358) Triggered 25 times 0:01:17.268 128M / 3G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 4 0:01:17.268 128M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:01:17.268 128M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:01:17.269 128M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:01:17.269 128M / 3G INFO General (simplification.cpp : 358) Triggered 1 times 0:01:17.269 128M / 3G INFO General (simplification.cpp : 356) Running Low coverage edge remover 0:01:17.269 128M / 3G INFO General (simplification.cpp : 358) Triggered 4 times 0:01:17.269 128M / 3G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 5 0:01:17.269 128M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:01:17.269 128M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:01:17.269 128M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:01:17.269 128M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:01:17.269 128M / 3G INFO General (simplification.cpp : 356) Running Low coverage edge remover 0:01:17.270 128M / 3G INFO General (simplification.cpp : 358) Triggered 2 times 0:01:17.270 128M / 3G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 6 0:01:17.270 128M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:01:17.270 128M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:01:17.270 128M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:01:17.270 128M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:01:17.270 128M / 3G INFO General (simplification.cpp : 356) Running Low coverage edge remover 0:01:17.272 128M / 3G INFO General (simplification.cpp : 358) Triggered 8 times 0:01:17.272 128M / 3G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 7 0:01:17.272 128M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:01:17.272 128M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:01:17.272 128M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:01:17.272 128M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:01:17.272 128M / 3G INFO General (simplification.cpp : 356) Running Low coverage edge remover 0:01:17.273 128M / 3G INFO General (simplification.cpp : 358) Triggered 5 times 0:01:17.273 128M / 3G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 8 0:01:17.273 128M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:01:17.273 128M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:01:17.273 128M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:01:17.273 128M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:01:17.273 128M / 3G INFO General (simplification.cpp : 356) Running Low coverage edge remover 0:01:17.274 128M / 3G INFO General (simplification.cpp : 358) Triggered 2 times 0:01:17.274 128M / 3G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 9 0:01:17.274 128M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:01:17.274 128M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:01:17.274 128M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:01:17.274 128M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:01:17.274 128M / 3G INFO General (simplification.cpp : 356) Running Low coverage edge remover 0:01:17.274 128M / 3G INFO General (simplification.cpp : 358) Triggered 7 times 0:01:17.274 128M / 3G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 10 0:01:17.274 128M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:01:17.275 128M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:01:17.275 128M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:01:17.277 128M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:01:17.277 128M / 3G INFO General (simplification.cpp : 356) Running Low coverage edge remover 0:01:17.278 128M / 3G INFO General (simplification.cpp : 358) Triggered 9 times 0:01:17.278 128M / 3G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 11 0:01:17.278 128M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:01:17.278 128M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:01:17.278 128M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:01:17.278 128M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:01:17.278 128M / 3G INFO General (simplification.cpp : 356) Running Low coverage edge remover 0:01:17.278 128M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:01:17.278 128M / 3G INFO General (simplification.cpp : 167) PROCEDURE == Post simplification 0:01:17.278 128M / 3G INFO General (graph_simplification.hpp : 447) Disconnection of relatively low covered edges disabled 0:01:17.278 128M / 3G INFO General (graph_simplification.hpp : 477) Complex tip clipping disabled 0:01:17.278 128M / 3G INFO General (graph_simplification.hpp : 617) Creating parallel br instance 0:01:17.278 128M / 3G INFO General (simplification.cpp : 301) Iteration 1 0:01:17.278 128M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:01:17.278 128M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:01:17.278 128M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:01:17.280 128M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:01:17.280 128M / 3G INFO General (simplification.cpp : 301) Iteration 2 0:01:17.280 128M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:01:17.280 128M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:01:17.280 128M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:01:17.282 128M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:01:17.282 128M / 3G INFO General (simplification.cpp : 333) Disrupting self-conjugate edges 0:01:17.283 128M / 3G INFO StageManager (stage.cpp : 126) STAGE == Gap Closer 0:01:17.283 128M / 3G INFO General (graph_pack.hpp : 99) Index refill 0:01:17.285 128M / 3G INFO K-mer Index Building (kmer_index_builder.hpp : 289) Building kmer index 0:01:17.285 128M / 3G INFO General (kmer_index_builder.hpp : 106) Splitting kmer instances into 64 buckets using 4 threads. This might take a while. 0:01:17.285 128M / 3G INFO General (file_limit.hpp : 32) Open file limit set to 1024 0:01:17.285 128M / 3G INFO General (kmer_splitters.hpp : 74) Memory available for splitting buffers: 20.8229 Gb 0:01:17.285 128M / 3G INFO General (kmer_splitters.hpp : 82) Using cell size of 524288 0:01:18.045 3G / 3G INFO General (edge_index_builders.hpp : 75) Processed 3668 edges 0:01:18.045 3G / 3G INFO General (edge_index_builders.hpp : 80) Used 3668 sequences. 0:01:18.067 128M / 3G INFO General (kmer_index_builder.hpp : 109) Starting k-mer counting. 0:01:18.642 128M / 3G INFO General (kmer_index_builder.hpp : 115) K-mer counting done. There are 8534796 kmers in total. 0:01:18.642 128M / 3G INFO General (kmer_index_builder.hpp : 121) Merging temporary buckets. 0:01:19.419 128M / 3G INFO K-mer Index Building (kmer_index_builder.hpp : 298) Building perfect hash indices 0:01:19.950 132M / 3G INFO General (kmer_index_builder.hpp : 137) Merging final buckets. 0:01:20.302 132M / 3G INFO K-mer Index Building (kmer_index_builder.hpp : 320) Index built. Total 3965776 bytes occupied (3.71728 bits per kmer). 0:01:20.477 328M / 3G INFO General (edge_index_builders.hpp : 105) Collecting k-mer coverage information from graph, this takes a while. 0:01:21.085 328M / 3G INFO General (edge_index.hpp : 91) Index refilled 0:01:21.085 328M / 3G INFO General (gap_closer.cpp : 159) Preparing shift maps 0:01:21.088 328M / 3G INFO General (gap_closer.cpp : 119) Processing paired reads (takes a while) 0:01:23.691 328M / 3G INFO General (gap_closer.cpp : 138) Used 1484726 paired reads 0:01:23.691 328M / 3G INFO General (gap_closer.cpp : 140) Merging paired indices 0:01:23.692 328M / 3G INFO GapCloser (gap_closer.cpp : 346) Closing short gaps 0:01:23.700 328M / 3G INFO GapCloser (gap_closer.cpp : 380) Closing short gaps complete: filled 6 gaps after checking 111 candidates 0:01:24.032 328M / 3G INFO StageManager (stage.cpp : 126) STAGE == Simplification Cleanup 0:01:24.032 328M / 3G INFO General (simplification.cpp : 547) Removing isolated edges 0:01:24.064 324M / 3G INFO General (simplification.cpp : 570) Counting average coverage 0:01:24.064 324M / 3G INFO General (simplification.cpp : 575) Average coverage = 29.4677 0:01:24.064 324M / 3G INFO StageManager (stage.cpp : 126) STAGE == Contig Output 0:01:24.064 324M / 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_kmers_set_careful_assembly//K55/assembly_graph_with_scaffolds.gfa 0:01:24.087 324M / 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_kmers_set_careful_assembly//K55/before_rr.fasta 0:01:24.140 324M / 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_kmers_set_careful_assembly//K55/assembly_graph.fastg 0:01:24.253 324M / 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_kmers_set_careful_assembly//K55/simplified_contigs.fasta 0:01:24.305 324M / 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_kmers_set_careful_assembly//K55/final_contigs.fasta 0:01:24.370 324M / 3G INFO StageManager (stage.cpp : 126) STAGE == Contig Output 0:01:24.370 324M / 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_kmers_set_careful_assembly//K55/assembly_graph_with_scaffolds.gfa 0:01:24.403 324M / 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_kmers_set_careful_assembly//K55/before_rr.fasta 0:01:24.779 324M / 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_kmers_set_careful_assembly//K55/assembly_graph.fastg 0:01:24.984 324M / 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_kmers_set_careful_assembly//K55/simplified_contigs.fasta 0:01:25.049 324M / 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_kmers_set_careful_assembly//K55/final_contigs.fasta 0:01:25.118 324M / 3G INFO General (launch.hpp : 137) SPAdes finished 0:01:25.442 24M / 3G INFO General (main.cpp : 110) Assembling time: 0 hours 1 minutes 25 seconds == Running assembler: K77 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_kmers_set_careful_assembly/K77/configs/config.info 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_kmers_set_careful_assembly/K77/configs/careful_mode.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_kmers_set_careful_assembly/dataset.info) with K=77 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 0:00:00.004 4M / 4M INFO General (read_converter.hpp : 67) Binary reads detected 0:00:00.004 4M / 4M INFO General (graph_construction.hpp : 120) Constructing DeBruijn graph for k=77 0:00:00.006 4M / 4M INFO General (kmer_index_builder.hpp : 106) Splitting kmer instances into 16 buckets using 4 threads. This might take a while. 0:00:00.006 4M / 4M INFO General (file_limit.hpp : 32) Open file limit set to 1024 0:00:00.006 4M / 4M INFO General (kmer_splitters.hpp : 74) Memory available for splitting buffers: 20.833 Gb 0:00:00.006 4M / 4M INFO General (kmer_splitters.hpp : 82) Using cell size of 1398101 0:00:06.773 2G / 2G INFO General (kmer_splitters.hpp : 291) Processed 2830375 reads 0:00:13.320 2G / 2G INFO General (kmer_splitters.hpp : 291) Processed 5662465 reads 0:00:14.066 2G / 2G INFO General (kmer_splitters.hpp : 291) Processed 5938904 reads 0:00:14.066 2G / 2G INFO General (kmer_splitters.hpp : 297) Adding contigs from previous K 0:00:15.473 16M / 2G INFO General (kmer_splitters.hpp : 310) Used 5938904 reads. Maximum read length 140 0:00:15.473 16M / 2G INFO General (kmer_splitters.hpp : 311) Average read length 140 0:00:15.473 16M / 2G INFO General (kmer_index_builder.hpp : 109) Starting k-mer counting. 0:00:16.978 16M / 2G INFO General (kmer_index_builder.hpp : 115) K-mer counting done. There are 11356793 kmers in total. 0:00:16.978 16M / 2G INFO General (kmer_index_builder.hpp : 121) Merging temporary buckets. 0:00:18.060 16M / 2G INFO K-mer Index Building (kmer_index_builder.hpp : 289) Building kmer index 0:00:18.060 16M / 2G INFO General (kmer_index_builder.hpp : 106) Splitting kmer instances into 64 buckets using 4 threads. This might take a while. 0:00:18.060 16M / 2G INFO General (file_limit.hpp : 32) Open file limit set to 1024 0:00:18.060 16M / 2G INFO General (kmer_splitters.hpp : 74) Memory available for splitting buffers: 20.832 Gb 0:00:18.060 16M / 2G INFO General (kmer_splitters.hpp : 82) Using cell size of 349525 0:00:20.301 3G / 3G INFO General (kmer_splitters.hpp : 381) Processed 11356793 kmers 0:00:20.301 3G / 3G INFO General (kmer_splitters.hpp : 386) Used 11356793 kmers. 0:00:20.362 16M / 3G INFO General (kmer_index_builder.hpp : 109) Starting k-mer counting. 0:00:21.254 16M / 3G INFO General (kmer_index_builder.hpp : 115) K-mer counting done. There are 11358688 kmers in total. 0:00:21.254 16M / 3G INFO General (kmer_index_builder.hpp : 121) Merging temporary buckets. 0:00:22.367 16M / 3G INFO K-mer Index Building (kmer_index_builder.hpp : 298) Building perfect hash indices 0:00:23.184 16M / 3G INFO General (kmer_index_builder.hpp : 137) Merging final buckets. 0:00:23.826 16M / 3G INFO K-mer Index Building (kmer_index_builder.hpp : 320) Index built. Total 5275224 bytes occupied (3.71538 bits per kmer). 0:00:23.842 28M / 3G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 87) Building k-mer extensions from k+1-mers 0:00:25.324 28M / 3G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 91) Building k-mer extensions from k+1-mers finished. 0:00:25.326 28M / 3G INFO General (graph_construction.hpp : 136) Condensing graph 0:00:25.375 28M / 3G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 355) Extracting unbranching paths 0:00:26.907 52M / 3G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 374) Extracting unbranching paths finished. 246417 sequences extracted 0:00:27.987 52M / 3G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 310) Collecting perfect loops 0:00:28.424 52M / 3G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 343) Collecting perfect loops finished. 0 loops collected 0:00:28.621 104M / 3G INFO General (graph_construction.hpp : 141) Building index with from graph 0:00:28.622 104M / 3G INFO K-mer Index Building (kmer_index_builder.hpp : 289) Building kmer index 0:00:28.622 104M / 3G INFO General (kmer_index_builder.hpp : 106) Splitting kmer instances into 64 buckets using 4 threads. This might take a while. 0:00:28.622 104M / 3G INFO General (file_limit.hpp : 32) Open file limit set to 1024 0:00:28.622 104M / 3G INFO General (kmer_splitters.hpp : 74) Memory available for splitting buffers: 20.8249 Gb 0:00:28.622 104M / 3G INFO General (kmer_splitters.hpp : 82) Using cell size of 349525 0:00:30.151 3G / 3G INFO General (edge_index_builders.hpp : 75) Processed 492830 edges 0:00:30.151 3G / 3G INFO General (edge_index_builders.hpp : 80) Used 492830 sequences. 0:00:30.183 104M / 3G INFO General (kmer_index_builder.hpp : 109) Starting k-mer counting. 0:00:31.051 104M / 3G INFO General (kmer_index_builder.hpp : 115) K-mer counting done. There are 11356793 kmers in total. 0:00:31.051 104M / 3G INFO General (kmer_index_builder.hpp : 121) Merging temporary buckets. 0:00:32.090 104M / 3G INFO K-mer Index Building (kmer_index_builder.hpp : 298) Building perfect hash indices 0:00:32.931 116M / 3G INFO General (kmer_index_builder.hpp : 137) Merging final buckets. 0:00:33.583 116M / 3G INFO K-mer Index Building (kmer_index_builder.hpp : 320) Index built. Total 5274312 bytes occupied (3.71535 bits per kmer). 0:00:33.839 376M / 3G INFO General (edge_index_builders.hpp : 105) Collecting k-mer coverage information from graph, this takes a while. 0:00:34.806 376M / 3G INFO General (edge_index.hpp : 91) Index refilled 0:00:34.887 364M / 3G INFO General (graph_construction.hpp : 173) Filling coverage index 0:00:34.887 364M / 3G INFO General (edge_index_builders.hpp : 183) Collecting k-mer coverage information from reads, this takes a while. 0:01:05.661 352M / 3G INFO General (graph_construction.hpp : 175) Filling coverage and flanking coverage from index 0:01:06.780 352M / 3G INFO General (construction.cpp : 30) Figured out: read length = 140 0:01:06.780 352M / 3G INFO StageManager (stage.cpp : 126) STAGE == EC Threshold Finding 0:01:07.043 352M / 3G INFO General (kmer_coverage_model.cpp : 181) Kmer coverage valley at: 4 0:01:07.043 352M / 3G INFO General (kmer_coverage_model.cpp : 201) K-mer histogram maximum: 20 0:01:07.043 352M / 3G INFO General (kmer_coverage_model.cpp : 237) Estimated median coverage: 21. Coverage mad: 8.8956 0:01:07.043 352M / 3G INFO General (kmer_coverage_model.cpp : 259) Fitting coverage model 0:01:07.061 352M / 3G INFO General (kmer_coverage_model.cpp : 295) ... iteration 2 0:01:07.121 352M / 3G INFO General (kmer_coverage_model.cpp : 295) ... iteration 4 0:01:07.303 352M / 3G INFO General (kmer_coverage_model.cpp : 295) ... iteration 8 0:01:07.660 352M / 3G INFO General (kmer_coverage_model.cpp : 295) ... iteration 16 0:01:07.987 352M / 3G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 21.6619. Fitted coverage std. dev: 6.82922 0:01:07.988 352M / 3G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 0.685717 0:01:07.988 352M / 3G INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 11 0:01:07.988 352M / 3G INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 11 0:01:07.988 352M / 3G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 8033755 0:01:07.988 352M / 3G INFO General (genomic_info_filler.cpp : 127) Mean coverage was calculated as 21.6619 0:01:07.988 352M / 3G INFO General (genomic_info_filler.cpp : 141) EC coverage threshold value was calculated as 11 0:01:07.988 352M / 3G INFO General (genomic_info_filler.cpp : 142) Trusted kmer low bound: 0 0:01:07.988 352M / 3G INFO StageManager (stage.cpp : 126) STAGE == Gap Closer 0:01:07.990 352M / 3G INFO General (gap_closer.cpp : 159) Preparing shift maps 0:01:08.206 368M / 3G INFO General (gap_closer.cpp : 119) Processing paired reads (takes a while) 0:01:10.457 384M / 3G INFO General (gap_closer.cpp : 138) Used 1484726 paired reads 0:01:10.457 384M / 3G INFO General (gap_closer.cpp : 140) Merging paired indices 0:01:10.504 360M / 3G INFO GapCloser (gap_closer.cpp : 346) Closing short gaps 0:01:10.847 360M / 3G INFO GapCloser (gap_closer.cpp : 380) Closing short gaps complete: filled 13 gaps after checking 253 candidates 0:01:10.862 352M / 3G INFO StageManager (stage.cpp : 126) STAGE == Simplification 0:01:10.882 92M / 3G INFO General (simplification.cpp : 387) Graph simplification started 0:01:10.882 92M / 3G INFO General (simplification.cpp : 77) PROCEDURE == InitialCleaning 0:01:10.882 92M / 3G INFO General (simplification.cpp : 50) Most init cleaning disabled on main iteration 0:01:10.882 92M / 3G INFO General (simplification.cpp : 356) Running Self conjugate edge remover 0:01:10.913 92M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:01:10.913 92M / 3G INFO General (graph_simplification.hpp : 617) Creating parallel br instance 0:01:10.913 92M / 3G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 1 0:01:10.913 92M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:01:12.410 88M / 3G INFO General (simplification.cpp : 358) Triggered 116285 times 0:01:12.410 88M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:01:13.081 100M / 3G INFO General (simplification.cpp : 358) Triggered 2718 times 0:01:13.081 100M / 3G INFO General (simplification.cpp : 356) Running Low coverage edge remover 0:01:13.105 100M / 3G INFO General (simplification.cpp : 358) Triggered 96 times 0:01:13.105 100M / 3G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 2 0:01:13.105 100M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:01:13.116 100M / 3G INFO General (simplification.cpp : 358) Triggered 81 times 0:01:13.116 100M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:01:13.127 100M / 3G INFO General (simplification.cpp : 358) Triggered 24 times 0:01:13.127 100M / 3G INFO General (simplification.cpp : 356) Running Low coverage edge remover 0:01:13.167 100M / 3G INFO General (simplification.cpp : 358) Triggered 102 times 0:01:13.167 100M / 3G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 3 0:01:13.167 100M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:01:13.169 100M / 3G INFO General (simplification.cpp : 358) Triggered 12 times 0:01:13.169 100M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:01:13.172 100M / 3G INFO General (simplification.cpp : 358) Triggered 5 times 0:01:13.172 100M / 3G INFO General (simplification.cpp : 356) Running Low coverage edge remover 0:01:13.173 100M / 3G INFO General (simplification.cpp : 358) Triggered 9 times 0:01:13.173 100M / 3G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 4 0:01:13.173 100M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:01:13.173 100M / 3G INFO General (simplification.cpp : 358) Triggered 1 times 0:01:13.173 100M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:01:13.174 100M / 3G INFO General (simplification.cpp : 358) Triggered 2 times 0:01:13.174 100M / 3G INFO General (simplification.cpp : 356) Running Low coverage edge remover 0:01:13.174 100M / 3G INFO General (simplification.cpp : 358) Triggered 3 times 0:01:13.174 100M / 3G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 5 0:01:13.174 100M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:01:13.174 100M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:01:13.174 100M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:01:13.174 100M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:01:13.174 100M / 3G INFO General (simplification.cpp : 356) Running Low coverage edge remover 0:01:13.174 100M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:01:13.174 100M / 3G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 6 0:01:13.175 100M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:01:13.175 100M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:01:13.175 100M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:01:13.175 100M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:01:13.175 100M / 3G INFO General (simplification.cpp : 356) Running Low coverage edge remover 0:01:13.175 100M / 3G INFO General (simplification.cpp : 358) Triggered 2 times 0:01:13.175 100M / 3G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 7 0:01:13.175 100M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:01:13.175 100M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:01:13.175 100M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:01:13.175 100M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:01:13.175 100M / 3G INFO General (simplification.cpp : 356) Running Low coverage edge remover 0:01:13.176 100M / 3G INFO General (simplification.cpp : 358) Triggered 1 times 0:01:13.176 100M / 3G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 8 0:01:13.176 100M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:01:13.176 100M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:01:13.176 100M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:01:13.176 100M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:01:13.176 100M / 3G INFO General (simplification.cpp : 356) Running Low coverage edge remover 0:01:13.176 100M / 3G INFO General (simplification.cpp : 358) Triggered 1 times 0:01:13.176 100M / 3G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 9 0:01:13.176 100M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:01:13.176 100M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:01:13.176 100M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:01:13.176 100M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:01:13.176 100M / 3G INFO General (simplification.cpp : 356) Running Low coverage edge remover 0:01:13.176 100M / 3G INFO General (simplification.cpp : 358) Triggered 4 times 0:01:13.176 100M / 3G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 10 0:01:13.176 100M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:01:13.177 100M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:01:13.177 100M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:01:13.179 100M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:01:13.179 100M / 3G INFO General (simplification.cpp : 356) Running Low coverage edge remover 0:01:13.181 100M / 3G INFO General (simplification.cpp : 358) Triggered 7 times 0:01:13.181 100M / 3G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 11 0:01:13.181 100M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:01:13.181 100M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:01:13.181 100M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:01:13.181 100M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:01:13.181 100M / 3G INFO General (simplification.cpp : 356) Running Low coverage edge remover 0:01:13.181 100M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:01:13.181 100M / 3G INFO General (simplification.cpp : 167) PROCEDURE == Post simplification 0:01:13.181 100M / 3G INFO General (graph_simplification.hpp : 447) Disconnection of relatively low covered edges disabled 0:01:13.181 100M / 3G INFO General (graph_simplification.hpp : 477) Complex tip clipping disabled 0:01:13.181 100M / 3G INFO General (graph_simplification.hpp : 617) Creating parallel br instance 0:01:13.181 100M / 3G INFO General (simplification.cpp : 301) Iteration 1 0:01:13.181 100M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:01:13.182 100M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:01:13.182 100M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:01:13.184 100M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:01:13.184 100M / 3G INFO General (simplification.cpp : 301) Iteration 2 0:01:13.184 100M / 3G INFO General (simplification.cpp : 356) Running Tip clipper 0:01:13.185 100M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:01:13.185 100M / 3G INFO General (simplification.cpp : 356) Running Bulge remover 0:01:13.187 100M / 3G INFO General (simplification.cpp : 358) Triggered 0 times 0:01:13.187 100M / 3G INFO General (simplification.cpp : 333) Disrupting self-conjugate edges 0:01:13.190 100M / 3G INFO StageManager (stage.cpp : 126) STAGE == Gap Closer 0:01:13.190 100M / 3G INFO General (graph_pack.hpp : 99) Index refill 0:01:13.192 100M / 3G INFO K-mer Index Building (kmer_index_builder.hpp : 289) Building kmer index 0:01:13.192 100M / 3G INFO General (kmer_index_builder.hpp : 106) Splitting kmer instances into 64 buckets using 4 threads. This might take a while. 0:01:13.192 100M / 3G INFO General (file_limit.hpp : 32) Open file limit set to 1024 0:01:13.192 100M / 3G INFO General (kmer_splitters.hpp : 74) Memory available for splitting buffers: 20.8252 Gb 0:01:13.192 100M / 3G INFO General (kmer_splitters.hpp : 82) Using cell size of 349525 0:01:14.052 3G / 3G INFO General (edge_index_builders.hpp : 75) Processed 11512 edges 0:01:14.052 3G / 3G INFO General (edge_index_builders.hpp : 80) Used 11512 sequences. 0:01:14.073 100M / 3G INFO General (kmer_index_builder.hpp : 109) Starting k-mer counting. 0:01:14.789 100M / 3G INFO General (kmer_index_builder.hpp : 115) K-mer counting done. There are 8807354 kmers in total. 0:01:14.789 100M / 3G INFO General (kmer_index_builder.hpp : 121) Merging temporary buckets. 0:01:15.658 100M / 3G INFO K-mer Index Building (kmer_index_builder.hpp : 298) Building perfect hash indices 0:01:16.330 100M / 3G INFO General (kmer_index_builder.hpp : 137) Merging final buckets. 0:01:16.910 100M / 3G INFO K-mer Index Building (kmer_index_builder.hpp : 320) Index built. Total 4092232 bytes occupied (3.7171 bits per kmer). 0:01:17.092 304M / 3G INFO General (edge_index_builders.hpp : 105) Collecting k-mer coverage information from graph, this takes a while. 0:01:17.689 304M / 3G INFO General (edge_index.hpp : 91) Index refilled 0:01:17.689 304M / 3G INFO General (gap_closer.cpp : 159) Preparing shift maps 0:01:17.698 308M / 3G INFO General (gap_closer.cpp : 119) Processing paired reads (takes a while) 0:01:20.042 308M / 3G INFO General (gap_closer.cpp : 138) Used 1484726 paired reads 0:01:20.042 308M / 3G INFO General (gap_closer.cpp : 140) Merging paired indices 0:01:20.048 304M / 3G INFO GapCloser (gap_closer.cpp : 346) Closing short gaps 0:01:20.066 304M / 3G INFO GapCloser (gap_closer.cpp : 380) Closing short gaps complete: filled 3 gaps after checking 164 candidates 0:01:20.350 304M / 3G INFO StageManager (stage.cpp : 126) STAGE == Simplification Cleanup 0:01:20.350 304M / 3G INFO General (simplification.cpp : 547) Removing isolated edges 0:01:20.621 288M / 3G INFO General (simplification.cpp : 570) Counting average coverage 0:01:20.621 288M / 3G INFO General (simplification.cpp : 575) Average coverage = 21.6667 0:01:20.621 288M / 3G INFO StageManager (stage.cpp : 126) STAGE == Mismatch Correction 0:01:20.621 288M / 3G INFO General (graph_pack.hpp : 108) Normalizing k-mer map. Total 432464 kmers to process 0:01:20.963 288M / 3G INFO General (graph_pack.hpp : 110) Normalizing done 0:01:28.825 288M / 3G INFO General (mismatch_shall_not_pass.hp: 187) Finished collecting potential mismatches positions 0:01:28.900 288M / 3G INFO General (mismatch_shall_not_pass.hp: 284) All edges processed 0:01:28.901 288M / 3G INFO General (mismatch_correction.cpp : 26) Corrected 0 nucleotides 0:01:28.901 288M / 3G INFO StageManager (stage.cpp : 126) STAGE == Contig Output 0:01:28.901 288M / 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_kmers_set_careful_assembly//K77/assembly_graph_with_scaffolds.gfa 0:01:28.930 288M / 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_kmers_set_careful_assembly//K77/before_rr.fasta 0:01:28.983 288M / 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_kmers_set_careful_assembly//K77/assembly_graph.fastg 0:01:29.111 288M / 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_kmers_set_careful_assembly//K77/simplified_contigs.fasta 0:01:29.164 288M / 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_kmers_set_careful_assembly//K77/intermediate_contigs.fasta 0:01:29.231 288M / 3G INFO StageManager (stage.cpp : 126) STAGE == Paired Information Counting 0:01:29.234 288M / 3G INFO General (graph_pack.hpp : 108) Normalizing k-mer map. Total 432464 kmers to process 0:01:29.234 288M / 3G INFO General (graph_pack.hpp : 110) Normalizing done 0:01:29.234 288M / 3G INFO General (pair_info_count.cpp : 317) Min edge length for estimation: 114373 0:01:29.234 288M / 3G INFO General (pair_info_count.cpp : 328) Estimating insert size for library #0 0:01:29.234 288M / 3G INFO General (pair_info_count.cpp : 176) Estimating insert size (takes a while) 0:01:29.314 368M / 3G INFO General (short_read_mapper.hpp : 88) Selecting usual mapper 0:01:30.840 368M / 3G INFO General (sequence_mapper_notifier.h: 81) Processed 200000 reads 0:01:30.867 368M / 3G INFO General (sequence_mapper_notifier.h: 81) Processed 400000 reads 0:01:30.963 368M / 3G INFO General (sequence_mapper_notifier.h: 81) Processed 600000 reads 0:01:31.089 368M / 3G INFO General (sequence_mapper_notifier.h: 81) Processed 800000 reads 0:01:32.554 368M / 3G INFO General (sequence_mapper_notifier.h: 99) Total 1484726 reads processed 0:01:32.752 368M / 3G INFO General (pair_info_count.cpp : 194) Edge pairs: 67108864 (rough upper limit) 0:01:32.752 368M / 3G INFO General (pair_info_count.cpp : 198) 751521 paired reads (50.6168% of all) aligned to long edges 0:01:32.762 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 0:01:32.946 480M / 3G INFO General (pair_info_count.cpp : 368) Filtering data for library #0 0:01:32.947 480M / 3G INFO General (short_read_mapper.hpp : 88) Selecting usual mapper 0:01:34.535 480M / 3G INFO General (sequence_mapper_notifier.h: 81) Processed 200000 reads 0:01:34.545 480M / 3G INFO General (sequence_mapper_notifier.h: 81) Processed 400000 reads 0:01:34.551 480M / 3G INFO General (sequence_mapper_notifier.h: 81) Processed 600000 reads 0:01:34.573 480M / 3G INFO General (sequence_mapper_notifier.h: 81) Processed 800000 reads 0:01:35.912 480M / 3G INFO General (sequence_mapper_notifier.h: 99) Total 1484726 reads processed 0:01:35.912 480M / 3G INFO General (pair_info_count.cpp : 380) Mapping library #0 0:01:35.912 480M / 3G INFO General (pair_info_count.cpp : 382) Mapping paired reads (takes a while) 0:01:35.912 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 0:01:35.926 492M / 3G INFO General (short_read_mapper.hpp : 88) Selecting usual mapper 0:01:37.755 492M / 3G INFO General (sequence_mapper_notifier.h: 81) Processed 200000 reads 0:01:37.766 492M / 3G INFO General (sequence_mapper_notifier.h: 81) Processed 400000 reads 0:01:37.789 492M / 3G INFO General (sequence_mapper_notifier.h: 81) Processed 600000 reads 0:01:37.826 492M / 3G INFO General (sequence_mapper_notifier.h: 81) Processed 800000 reads 0:01:39.521 492M / 3G INFO General (sequence_mapper_notifier.h: 99) Total 1484726 reads processed 0:01:39.556 288M / 3G INFO StageManager (stage.cpp : 126) STAGE == Distance Estimation 0:01:39.557 288M / 3G INFO General (distance_estimation.cpp : 224) Processing library #0 0:01:39.557 288M / 3G INFO General (distance_estimation.cpp : 130) Weight Filter Done 0:01:39.557 288M / 3G INFO DistanceEstimator (distance_estimation.hpp : 116) Using SIMPLE distance estimator 0:01:39.565 288M / 3G INFO General (distance_estimation.cpp : 35) Filtering info 0:01:39.565 288M / 3G INFO General (pair_info_filters.hpp : 242) Start filtering; index size: 6424 0:01:39.566 288M / 3G INFO General (pair_info_filters.hpp : 263) Done filtering 0:01:39.566 288M / 3G INFO General (distance_estimation.cpp : 172) Refining clustered pair information 0:01:39.567 288M / 3G INFO General (distance_estimation.cpp : 174) The refining of clustered pair information has been finished 0:01:39.568 288M / 3G INFO General (distance_estimation.cpp : 176) Improving paired information 0:01:39.577 288M / 3G INFO PairInfoImprover (pair_info_improver.hpp : 103) Paired info stats: missing = 240; contradictional = 90 0:01:39.585 288M / 3G INFO PairInfoImprover (pair_info_improver.hpp : 103) Paired info stats: missing = 9; contradictional = 12 0:01:39.585 288M / 3G INFO General (distance_estimation.cpp : 183) Filling scaffolding index 0:01:39.585 288M / 3G INFO DistanceEstimator (distance_estimation.hpp : 116) Using SMOOTHING distance estimator 0:01:39.642 288M / 3G INFO General (distance_estimation.cpp : 35) Filtering info 0:01:39.642 288M / 3G INFO General (pair_info_filters.hpp : 242) Start filtering; index size: 1603 0:01:39.643 288M / 3G INFO General (pair_info_filters.hpp : 263) Done filtering 0:01:39.643 288M / 3G INFO General (distance_estimation.cpp : 228) Clearing raw paired index 0:01:39.645 288M / 3G INFO StageManager (stage.cpp : 126) STAGE == Repeat Resolving 0:01:39.645 288M / 3G INFO General (repeat_resolving.cpp : 69) Using Path-Extend repeat resolving 0:01:39.645 288M / 3G INFO General (launcher.cpp : 478) ExSPAnder repeat resolving tool started 0:01:39.651 292M / 3G INFO General (launcher.cpp : 393) Creating main extenders, unique edge length = 2000 0:01:39.651 292M / 3G INFO General (extenders_logic.cpp : 275) Estimated coverage of library #0 is 21.6667 0:01:39.652 292M / 3G INFO General (extenders_logic.cpp : 275) Estimated coverage of library #0 is 21.6667 0:01:39.653 292M / 3G INFO General (extenders_logic.cpp : 472) Using 1 paired-end library 0:01:39.653 292M / 3G INFO General (extenders_logic.cpp : 473) Using 1 paired-end scaffolding library 0:01:39.653 292M / 3G INFO General (extenders_logic.cpp : 474) Using 0 single read libraries 0:01:39.653 292M / 3G INFO General (launcher.cpp : 421) Total number of extenders is 3 0:01:39.653 292M / 3G INFO General (path_extender.hpp : 867) Processed 0 paths from 720 (0%) 0:01:39.782 292M / 3G INFO General (path_extender.hpp : 867) Processed 73 paths from 720 (10%) 0:01:39.811 292M / 3G INFO General (path_extender.hpp : 865) Processed 128 paths from 720 (17%) 0:01:39.820 292M / 3G INFO General (path_extender.hpp : 867) Processed 146 paths from 720 (20%) 0:01:39.823 292M / 3G INFO General (path_extender.hpp : 867) Processed 219 paths from 720 (30%) 0:01:39.828 292M / 3G INFO General (path_extender.hpp : 865) Processed 256 paths from 720 (35%) 0:01:39.830 292M / 3G INFO General (path_extender.hpp : 867) Processed 292 paths from 720 (40%) 0:01:39.831 296M / 3G INFO General (path_extender.hpp : 867) Processed 365 paths from 720 (50%) 0:01:39.832 296M / 3G INFO General (path_extender.hpp : 867) Processed 438 paths from 720 (60%) 0:01:39.832 296M / 3G INFO General (path_extender.hpp : 867) Processed 511 paths from 720 (70%) 0:01:39.832 296M / 3G INFO General (path_extender.hpp : 865) Processed 512 paths from 720 (71%) 0:01:39.838 296M / 3G INFO General (path_extender.hpp : 867) Processed 584 paths from 720 (81%) 0:01:39.838 296M / 3G INFO General (path_extender.hpp : 867) Processed 657 paths from 720 (91%) 0:01:39.838 296M / 3G INFO General (launcher.cpp : 234) Finalizing paths 0:01:39.838 296M / 3G INFO General (launcher.cpp : 236) Deduplicating paths 0:01:39.839 296M / 3G INFO General (launcher.cpp : 240) Paths deduplicated 0:01:39.839 296M / 3G INFO PEResolver (pe_resolver.hpp : 299) Removing overlaps 0:01:39.839 296M / 3G INFO PEResolver (pe_resolver.hpp : 302) Sorting paths 0:01:39.839 296M / 3G INFO PEResolver (pe_resolver.hpp : 309) Marking overlaps 0:01:39.839 296M / 3G INFO OverlapRemover (pe_resolver.hpp : 132) Marking start/end overlaps 0:01:39.840 296M / 3G INFO OverlapRemover (pe_resolver.hpp : 135) Marking remaining overlaps 0:01:39.841 296M / 3G INFO PEResolver (pe_resolver.hpp : 312) Splitting paths 0:01:39.841 296M / 3G INFO PEResolver (pe_resolver.hpp : 317) Deduplicating paths 0:01:39.842 296M / 3G INFO PEResolver (pe_resolver.hpp : 319) Overlaps removed 0:01:39.842 296M / 3G INFO General (launcher.cpp : 257) Paths finalized 0:01:39.842 296M / 3G INFO General (launcher.cpp : 287) Traversing tandem repeats 0:01:39.844 296M / 3G INFO General (launcher.cpp : 297) Traversed 3 loops 0:01:39.844 296M / 3G INFO General (launcher.cpp : 428) Closing gaps in paths 0:01:39.845 296M / 3G INFO General (launcher.cpp : 456) Gap closing completed 0:01:39.846 296M / 3G INFO General (launcher.cpp : 234) Finalizing paths 0:01:39.846 296M / 3G INFO General (launcher.cpp : 236) Deduplicating paths 0:01:39.846 296M / 3G INFO General (launcher.cpp : 240) Paths deduplicated 0:01:39.846 296M / 3G INFO PEResolver (pe_resolver.hpp : 299) Removing overlaps 0:01:39.846 296M / 3G INFO PEResolver (pe_resolver.hpp : 302) Sorting paths 0:01:39.846 296M / 3G INFO PEResolver (pe_resolver.hpp : 309) Marking overlaps 0:01:39.846 296M / 3G INFO OverlapRemover (pe_resolver.hpp : 132) Marking start/end overlaps 0:01:39.846 296M / 3G INFO OverlapRemover (pe_resolver.hpp : 135) Marking remaining overlaps 0:01:39.846 296M / 3G INFO PEResolver (pe_resolver.hpp : 312) Splitting paths 0:01:39.846 296M / 3G INFO PEResolver (pe_resolver.hpp : 317) Deduplicating paths 0:01:39.846 296M / 3G INFO PEResolver (pe_resolver.hpp : 319) Overlaps removed 0:01:39.847 296M / 3G INFO General (launcher.cpp : 257) Paths finalized 0:01:39.847 296M / 3G INFO General (launcher.cpp : 531) ExSPAnder repeat resolving tool finished 0:01:39.850 292M / 3G INFO StageManager (stage.cpp : 126) STAGE == Contig Output 0:01:39.850 292M / 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_kmers_set_careful_assembly//K77/assembly_graph_with_scaffolds.gfa 0:01:39.874 292M / 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_kmers_set_careful_assembly//K77/before_rr.fasta 0:01:39.930 292M / 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_kmers_set_careful_assembly//K77/assembly_graph.fastg 0:01:40.049 292M / 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_kmers_set_careful_assembly//K77/final_contigs.paths 0:01:40.116 292M / 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_kmers_set_careful_assembly//K77/scaffolds.paths 0:01:40.206 292M / 3G INFO General (launch.hpp : 137) SPAdes finished 0:01:40.442 24M / 3G INFO General (main.cpp : 110) Assembling time: 0 hours 1 minutes 40 seconds ===== Assembling finished. Used k-mer sizes: 21, 33, 55, 77 ===== Mismatch correction started. == Processing of contigs == Running contig polishing tool: /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/conda/anaconda3/envs/de_novo_example/share/spades-3.11.1-4/bin/corrector /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/genomics_de_novo_temp/working_dir/spades_kmers_set_careful_assembly/mismatch_corrector/contigs/configs/corrector.info /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/genomics_de_novo_temp/working_dir/spades_kmers_set_careful_assembly/misc/assembled_contigs.fasta == Dataset description file was created: /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/genomics_de_novo_temp/working_dir/spades_kmers_set_careful_assembly/mismatch_corrector/contigs/configs/corrector.info /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/genomics_de_novo_temp/working_dir/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: /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/genomics_de_novo_temp/working_dir/spades_kmers_set_careful_assembly/misc/assembled_contigs.fasta 0:00:00.521 4M / 8M INFO DatasetProcessor (dataset_processor.cpp : 203) Processing paired sublib of number 0 0:00:00.521 4M / 8M INFO DatasetProcessor (dataset_processor.cpp : 206) /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/genomics_de_novo_temp/working_dir/BCep_R1_QCd_err_cor.fastq.gz /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/genomics_de_novo_temp/working_dir/BCep_R2_QCd_err_cor.fastq.gz 0:00:00.522 4M / 8M INFO DatasetProcessor (dataset_processor.cpp : 140) Running bwa index ...: /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/conda/anaconda3/envs/de_novo_example/share/spades-3.11.1-4/bin/bwa-spades index -a is /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/genomics_de_novo_temp/working_dir/spades_kmers_set_careful_assembly/misc/assembled_contigs.fasta [bwa_index] Pack FASTA... 0.06 sec [bwa_index] Construct BWT for the packed sequence... [bwa_index] 3.80 seconds elapse. [bwa_index] Update BWT... 0.06 sec [bwa_index] Pack forward-only FASTA... 0.02 sec [bwa_index] Construct SA from BWT and Occ... 0.91 sec [main] Version: 0.7.12-r1039 [main] CMD: /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/conda/anaconda3/envs/de_novo_example/share/spades-3.11.1-4/bin/bwa-spades index -a is /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/genomics_de_novo_temp/working_dir/spades_kmers_set_careful_assembly/misc/assembled_contigs.fasta [main] Real time: 4.930 sec; CPU: 4.890 sec 0:00:05.543 4M / 8M INFO DatasetProcessor (dataset_processor.cpp : 149) Running bwa mem ...:/nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/conda/anaconda3/envs/de_novo_example/share/spades-3.11.1-4/bin/bwa-spades mem -v 1 -t 4 /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/genomics_de_novo_temp/working_dir/spades_kmers_set_careful_assembly/misc/assembled_contigs.fasta /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/genomics_de_novo_temp/working_dir/BCep_R1_QCd_err_cor.fastq.gz /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/genomics_de_novo_temp/working_dir/BCep_R2_QCd_err_cor.fastq.gz > /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/genomics_de_novo_temp/working_dir/spades_kmers_set_careful_assembly/tmp/corrector_kilcnfmy/lib0_MaeeuE/tmp.sam [main] Version: 0.7.12-r1039 [main] CMD: /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/conda/anaconda3/envs/de_novo_example/share/spades-3.11.1-4/bin/bwa-spades mem -v 1 -t 4 /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/genomics_de_novo_temp/working_dir/spades_kmers_set_careful_assembly/misc/assembled_contigs.fasta /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/genomics_de_novo_temp/working_dir/BCep_R1_QCd_err_cor.fastq.gz /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/genomics_de_novo_temp/working_dir/BCep_R2_QCd_err_cor.fastq.gz [main] Real time: 35.928 sec; CPU: 145.594 sec 0:00:41.550 4M / 8M INFO DatasetProcessor (dataset_processor.cpp : 209) Adding samfile /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/genomics_de_novo_temp/working_dir/spades_kmers_set_careful_assembly/tmp/corrector_kilcnfmy/lib0_MaeeuE/tmp.sam 0:00:48.780 52M / 52M INFO DatasetProcessor (dataset_processor.cpp : 105) processed 1000000reads, flushing 0:00:54.485 52M / 52M INFO DatasetProcessor (dataset_processor.cpp : 105) processed 2000000reads, flushing 0:01:00.337 52M / 52M INFO DatasetProcessor (dataset_processor.cpp : 105) processed 3000000reads, flushing 0:01:06.480 52M / 52M INFO DatasetProcessor (dataset_processor.cpp : 105) processed 4000000reads, flushing 0:01:09.536 8M / 52M INFO DatasetProcessor (dataset_processor.cpp : 235) Processing contigs 0:01:15.070 280M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_4_length_364479_cov_21.546089 processed with 3 changes in thread 2 0:01:15.769 276M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_3_length_440862_cov_21.072605 processed with 4 changes in thread 0 0:01:16.118 256M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_2_length_472579_cov_19.238748 processed with 4 changes in thread 1 0:01:19.730 248M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_6_length_306432_cov_19.636862 processed with 3 changes in thread 0 0:01:20.987 240M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_5_length_344685_cov_25.459394 processed with 5 changes in thread 2 0:01:21.195 228M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_7_length_299227_cov_24.655313 processed with 2 changes in thread 1 0:01:22.619 220M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_1_length_961949_cov_19.621119 processed with 6 changes in thread 3 0:01:23.862 140M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_8_length_268954_cov_23.278852 processed with 1 changes in thread 0 0:01:24.423 132M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_9_length_234109_cov_21.678835 processed with 0 changes in thread 2 0:01:24.587 132M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_10_length_233751_cov_21.940400 processed with 4 changes in thread 1 0:01:25.771 132M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_11_length_230050_cov_22.620221 processed with 0 changes in thread 3 0:01:26.763 132M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_12_length_217699_cov_21.270837 processed with 2 changes in thread 0 0:01:27.161 124M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_14_length_197116_cov_20.332609 processed with 4 changes in thread 1 0:01:27.270 116M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_13_length_198969_cov_21.176749 processed with 2 changes in thread 2 0:01:28.505 108M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_15_length_187413_cov_22.794412 processed with 1 changes in thread 3 0:01:29.421 104M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_18_length_158486_cov_20.793945 processed with 0 changes in thread 2 0:01:29.513 100M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_16_length_185852_cov_22.792948 processed with 0 changes in thread 0 0:01:29.967 88M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_17_length_169218_cov_25.408121 processed with 6 changes in thread 1 0:01:30.726 84M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_19_length_143955_cov_24.086900 processed with 1 changes in thread 3 0:01:31.509 76M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_21_length_132351_cov_23.399875 processed with 1 changes in thread 0 0:01:31.539 76M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_20_length_137841_cov_23.290054 processed with 0 changes in thread 2 0:01:31.705 72M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_22_length_110696_cov_23.729631 processed with 0 changes in thread 1 0:01:32.323 72M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_23_length_110572_cov_22.487307 processed with 0 changes in thread 3 0:01:33.046 72M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_25_length_108332_cov_21.130054 processed with 0 changes in thread 2 0:01:33.135 72M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_24_length_110289_cov_22.734357 processed with 0 changes in thread 0 0:01:33.193 72M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_26_length_107910_cov_20.836618 processed with 0 changes in thread 1 0:01:33.780 68M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_27_length_98944_cov_23.022151 processed with 4 changes in thread 3 0:01:34.357 64M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_28_length_97291_cov_20.455418 processed with 1 changes in thread 2 0:01:34.474 60M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_29_length_96001_cov_21.316803 processed with 0 changes in thread 0 0:01:34.587 56M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_30_length_95246_cov_22.232229 processed with 0 changes in thread 1 0:01:34.975 56M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_31_length_92827_cov_19.998857 processed with 0 changes in thread 3 0:01:35.558 56M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_33_length_79870_cov_21.181206 processed with 0 changes in thread 0 0:01:35.614 56M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_32_length_90163_cov_21.067780 processed with 0 changes in thread 2 0:01:35.784 56M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_34_length_79606_cov_22.817488 processed with 1 changes in thread 1 0:01:36.154 56M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_35_length_78062_cov_23.423812 processed with 0 changes in thread 3 0:01:36.659 56M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_37_length_73714_cov_22.161889 processed with 1 changes in thread 2 0:01:36.732 56M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_36_length_75123_cov_24.300229 processed with 0 changes in thread 0 0:01:36.775 56M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_38_length_68531_cov_22.212829 processed with 0 changes in thread 1 0:01:36.953 56M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_39_length_55189_cov_22.543312 processed with 0 changes in thread 3 0:01:37.354 56M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_43_length_50921_cov_12.211785 processed with 0 changes in thread 3 0:01:37.362 56M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_40_length_55064_cov_20.018459 processed with 0 changes in thread 2 0:01:37.468 52M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_42_length_51172_cov_20.956963 processed with 0 changes in thread 1 0:01:37.492 48M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_41_length_51580_cov_23.217832 processed with 0 changes in thread 0 0:01:37.932 40M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_45_length_44894_cov_19.954839 processed with 0 changes in thread 2 0:01:38.013 40M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_46_length_42523_cov_19.967300 processed with 0 changes in thread 1 0:01:38.015 36M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_44_length_49790_cov_20.959065 processed with 0 changes in thread 3 0:01:38.084 36M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_47_length_41288_cov_22.147655 processed with 0 changes in thread 0 0:01:38.264 36M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_48_length_38254_cov_13.331849 processed with 2 changes in thread 2 0:01:38.499 32M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_50_length_34581_cov_21.672850 processed with 0 changes in thread 3 0:01:38.516 28M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_49_length_36434_cov_21.153946 processed with 0 changes in thread 1 0:01:38.550 24M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_51_length_32176_cov_22.353500 processed with 0 changes in thread 0 0:01:38.670 28M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_52_length_31930_cov_20.079302 processed with 0 changes in thread 2 0:01:38.890 28M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_53_length_31095_cov_20.054646 processed with 0 changes in thread 3 0:01:38.954 28M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_54_length_30188_cov_23.285211 processed with 0 changes in thread 1 0:01:38.955 24M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_55_length_28221_cov_23.648238 processed with 0 changes in thread 0 0:01:39.044 24M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_56_length_27922_cov_22.091183 processed with 0 changes in thread 2 0:01:39.177 24M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_58_length_25618_cov_12.825026 processed with 0 changes in thread 1 0:01:39.248 24M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_59_length_22905_cov_20.985719 processed with 0 changes in thread 0 0:01:39.285 24M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_57_length_27126_cov_23.426596 processed with 0 changes in thread 3 0:01:39.365 24M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_60_length_22537_cov_23.265227 processed with 0 changes in thread 2 0:01:40.203 20M / 284M INFO DatasetProcessor (dataset_processor.cpp : 255) Gluing processed contigs 0:01:40.390 16M / 284M INFO General (main.cpp : 71) Correcting time: 0 hours 1 minutes 40 seconds == Processing of scaffolds == Running contig polishing tool: /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/conda/anaconda3/envs/de_novo_example/share/spades-3.11.1-4/bin/corrector /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/genomics_de_novo_temp/working_dir/spades_kmers_set_careful_assembly/mismatch_corrector/scaffolds/configs/corrector.info /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/genomics_de_novo_temp/working_dir/spades_kmers_set_careful_assembly/misc/assembled_scaffolds.fasta == Dataset description file was created: /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/genomics_de_novo_temp/working_dir/spades_kmers_set_careful_assembly/mismatch_corrector/scaffolds/configs/corrector.info /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/genomics_de_novo_temp/working_dir/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 0:00:00.001 4M / 4M INFO DatasetProcessor (dataset_processor.cpp : 195) Splitting assembly... 0:00:00.001 4M / 4M INFO DatasetProcessor (dataset_processor.cpp : 196) Assembly file: /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/genomics_de_novo_temp/working_dir/spades_kmers_set_careful_assembly/misc/assembled_scaffolds.fasta 0:00:00.440 4M / 8M INFO DatasetProcessor (dataset_processor.cpp : 203) Processing paired sublib of number 0 0:00:00.440 4M / 8M INFO DatasetProcessor (dataset_processor.cpp : 206) /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/genomics_de_novo_temp/working_dir/BCep_R1_QCd_err_cor.fastq.gz /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/genomics_de_novo_temp/working_dir/BCep_R2_QCd_err_cor.fastq.gz 0:00:00.441 4M / 8M INFO DatasetProcessor (dataset_processor.cpp : 140) Running bwa index ...: /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/conda/anaconda3/envs/de_novo_example/share/spades-3.11.1-4/bin/bwa-spades index -a is /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/genomics_de_novo_temp/working_dir/spades_kmers_set_careful_assembly/misc/assembled_scaffolds.fasta [bwa_index] Pack FASTA... 0.06 sec [bwa_index] Construct BWT for the packed sequence... [bwa_index] 5.07 seconds elapse. [bwa_index] Update BWT... 0.05 sec [bwa_index] Pack forward-only FASTA... 0.03 sec [bwa_index] Construct SA from BWT and Occ... 0.93 sec [main] Version: 0.7.12-r1039 [main] CMD: /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/conda/anaconda3/envs/de_novo_example/share/spades-3.11.1-4/bin/bwa-spades index -a is /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/genomics_de_novo_temp/working_dir/spades_kmers_set_careful_assembly/misc/assembled_scaffolds.fasta [main] Real time: 6.230 sec; CPU: 6.186 sec 0:00:06.756 4M / 8M INFO DatasetProcessor (dataset_processor.cpp : 149) Running bwa mem ...:/nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/conda/anaconda3/envs/de_novo_example/share/spades-3.11.1-4/bin/bwa-spades mem -v 1 -t 4 /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/genomics_de_novo_temp/working_dir/spades_kmers_set_careful_assembly/misc/assembled_scaffolds.fasta /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/genomics_de_novo_temp/working_dir/BCep_R1_QCd_err_cor.fastq.gz /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/genomics_de_novo_temp/working_dir/BCep_R2_QCd_err_cor.fastq.gz > /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/genomics_de_novo_temp/working_dir/spades_kmers_set_careful_assembly/tmp/corrector_qxxhze0v/lib0_bBqail/tmp.sam [main] Version: 0.7.12-r1039 [main] CMD: /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/conda/anaconda3/envs/de_novo_example/share/spades-3.11.1-4/bin/bwa-spades mem -v 1 -t 4 /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/genomics_de_novo_temp/working_dir/spades_kmers_set_careful_assembly/misc/assembled_scaffolds.fasta /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/genomics_de_novo_temp/working_dir/BCep_R1_QCd_err_cor.fastq.gz /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/genomics_de_novo_temp/working_dir/BCep_R2_QCd_err_cor.fastq.gz [main] Real time: 35.498 sec; CPU: 143.163 sec 0:00:42.326 4M / 8M INFO DatasetProcessor (dataset_processor.cpp : 209) Adding samfile /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/genomics_de_novo_temp/working_dir/spades_kmers_set_careful_assembly/tmp/corrector_qxxhze0v/lib0_bBqail/tmp.sam 0:00:48.002 52M / 52M INFO DatasetProcessor (dataset_processor.cpp : 105) processed 1000000reads, flushing 0:00:53.901 52M / 52M INFO DatasetProcessor (dataset_processor.cpp : 105) processed 2000000reads, flushing 0:01:00.134 52M / 52M INFO DatasetProcessor (dataset_processor.cpp : 105) processed 3000000reads, flushing 0:01:06.360 52M / 52M INFO DatasetProcessor (dataset_processor.cpp : 105) processed 4000000reads, flushing 0:01:09.629 8M / 52M INFO DatasetProcessor (dataset_processor.cpp : 235) Processing contigs 0:01:15.101 280M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_4_length_364479_cov_21.546089 processed with 3 changes in thread 2 0:01:15.445 276M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_2_length_472579_cov_19.238748 processed with 4 changes in thread 0 0:01:15.932 256M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_3_length_440862_cov_21.072605 processed with 4 changes in thread 3 0:01:19.555 248M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_6_length_306432_cov_19.636862 processed with 3 changes in thread 0 0:01:20.919 244M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_7_length_299227_cov_24.655313 processed with 2 changes in thread 3 0:01:20.933 236M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_5_length_344685_cov_25.459394 processed with 5 changes in thread 2 0:01:23.105 232M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_1_length_961949_cov_19.621119 processed with 6 changes in thread 1 0:01:23.948 148M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_8_length_288984_cov_22.507994 processed with 10 changes in thread 0 0:01:24.423 136M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_10_length_234109_cov_21.678835 processed with 0 changes in thread 2 0:01:25.139 136M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_9_length_268954_cov_23.278852 processed with 1 changes in thread 3 0:01:26.382 132M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_11_length_233751_cov_21.940400 processed with 4 changes in thread 1 0:01:27.377 136M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_12_length_230050_cov_22.620221 processed with 0 changes in thread 0 0:01:27.532 128M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_13_length_217699_cov_21.270837 processed with 2 changes in thread 2 0:01:27.934 120M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_14_length_209358_cov_20.199010 processed with 3 changes in thread 3 0:01:29.097 112M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_15_length_198969_cov_21.176749 processed with 2 changes in thread 1 0:01:30.084 104M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_18_length_158486_cov_20.793945 processed with 0 changes in thread 3 0:01:30.207 96M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_16_length_187413_cov_22.794412 processed with 1 changes in thread 0 0:01:30.362 88M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_17_length_169218_cov_25.408121 processed with 0 changes in thread 2 0:01:31.326 84M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_19_length_143955_cov_24.086900 processed with 1 changes in thread 1 0:01:32.122 80M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_22_length_127106_cov_20.994009 processed with 0 changes in thread 2 0:01:32.194 76M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_20_length_137841_cov_23.290054 processed with 0 changes in thread 3 0:01:32.252 72M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_21_length_132351_cov_23.399875 processed with 1 changes in thread 0 0:01:33.164 76M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_23_length_120680_cov_22.522450 processed with 1 changes in thread 1 0:01:33.742 72M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_26_length_108332_cov_21.130054 processed with 0 changes in thread 0 0:01:33.822 72M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_25_length_110572_cov_22.487307 processed with 0 changes in thread 3 0:01:33.841 72M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_24_length_110696_cov_23.729631 processed with 0 changes in thread 2 0:01:34.626 68M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_27_length_107910_cov_20.836618 processed with 0 changes in thread 1 0:01:35.135 64M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_29_length_97291_cov_20.455418 processed with 1 changes in thread 3 0:01:35.229 60M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_28_length_98944_cov_23.022151 processed with 4 changes in thread 0 0:01:35.249 56M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_30_length_95246_cov_22.232229 processed with 0 changes in thread 2 0:01:35.830 56M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_31_length_92827_cov_19.998857 processed with 0 changes in thread 1 0:01:36.336 56M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_33_length_79870_cov_21.181206 processed with 0 changes in thread 0 0:01:36.392 56M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_32_length_90163_cov_21.067780 processed with 0 changes in thread 3 0:01:36.447 56M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_34_length_79606_cov_22.817488 processed with 1 changes in thread 2 0:01:37.013 56M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_35_length_78062_cov_23.423812 processed with 0 changes in thread 1 0:01:37.284 56M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_38_length_55189_cov_22.543312 processed with 0 changes in thread 2 0:01:37.446 56M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_37_length_73714_cov_22.161889 processed with 1 changes in thread 3 0:01:37.521 56M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_36_length_75123_cov_24.300229 processed with 0 changes in thread 0 0:01:37.720 52M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_39_length_55064_cov_20.018459 processed with 0 changes in thread 1 0:01:37.924 52M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_42_length_50921_cov_12.211785 processed with 0 changes in thread 0 0:01:38.048 52M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_40_length_51580_cov_23.217832 processed with 0 changes in thread 2 0:01:38.135 48M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_41_length_51172_cov_20.956963 processed with 4 changes in thread 3 0:01:38.416 44M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_43_length_50891_cov_20.787421 processed with 19 changes in thread 1 0:01:38.592 40M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_44_length_49790_cov_20.959065 processed with 0 changes in thread 0 0:01:38.616 36M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_45_length_44894_cov_19.954839 processed with 0 changes in thread 2 0:01:38.683 32M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_46_length_42523_cov_19.967300 processed with 0 changes in thread 3 0:01:38.950 32M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_48_length_38254_cov_13.331849 processed with 5 changes in thread 0 0:01:39.007 36M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_47_length_41288_cov_22.147655 processed with 0 changes in thread 1 0:01:39.088 32M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_49_length_32176_cov_22.353500 processed with 0 changes in thread 2 0:01:39.094 32M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_50_length_31930_cov_20.079302 processed with 0 changes in thread 3 0:01:39.403 24M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_51_length_30188_cov_23.285211 processed with 0 changes in thread 0 0:01:39.427 24M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_52_length_28221_cov_23.648238 processed with 0 changes in thread 1 0:01:39.479 24M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_53_length_27922_cov_22.091183 processed with 0 changes in thread 2 0:01:39.510 24M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_54_length_27126_cov_23.426596 processed with 0 changes in thread 3 0:01:39.613 24M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_55_length_25618_cov_12.825026 processed with 0 changes in thread 0 0:01:39.730 24M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_56_length_22905_cov_20.985719 processed with 0 changes in thread 1 0:01:39.810 20M / 284M INFO DatasetProcessor (dataset_processor.cpp : 251) Contig NODE_57_length_22537_cov_23.265227 processed with 0 changes in thread 2 0:01:40.478 20M / 284M INFO DatasetProcessor (dataset_processor.cpp : 255) Gluing processed contigs 0:01:40.656 16M / 284M INFO General (main.cpp : 71) Correcting time: 0 hours 1 minutes 40 seconds ===== Mismatch correction finished. * Assembled contigs are in /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/genomics_de_novo_temp/working_dir/spades_kmers_set_careful_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_kmers_set_careful_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_kmers_set_careful_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_kmers_set_careful_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_kmers_set_careful_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_kmers_set_careful_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_kmers_set_careful_assembly/spades.log Thank you for using SPAdes!