Command line: ./bin/plasmidspades.py --test --plasmid System information: SPAdes version: 3.8.0 Python version: 2.7.11 OS: Linux-4.5.0-2-amd64-x86_64-with-debian-stretch-sid Output dir: /home/vagrant/SPAdes-3.8.0-Linux/spades_test Mode: read error correction and assembling 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: ['/home/vagrant/SPAdes-3.8.0-Linux/share/spades/test_dataset/ecoli_1K_1.fq.gz'] right reads: ['/home/vagrant/SPAdes-3.8.0-Linux/share/spades/test_dataset/ecoli_1K_2.fq.gz'] interlaced reads: not specified single reads: not specified Read error correction parameters: Iterations: 1 PHRED offset will be auto-detected Corrected reads will be compressed (with gzip) Assembly parameters: k: automatic selection based on read length Plasmid mode is turned ON Repeat resolution is enabled Mismatch careful mode is turned OFF MismatchCorrector will be SKIPPED Coverage cutoff is turned OFF Other parameters: Dir for temp files: /home/vagrant/SPAdes-3.8.0-Linux/spades_test/tmp Threads: 16 Memory limit (in Gb): 2 ======= SPAdes pipeline started. Log can be found here: /home/vagrant/SPAdes-3.8.0-Linux/spades_test/spades.log ===== Read error correction started. == Running read error correction tool: /home/vagrant/SPAdes-3.8.0-Linux/bin/hammer /home/vagrant/SPAdes-3.8.0-Linux/spades_test/corrected/configs/config.info 0:00:00.000 4M / 4M INFO General (main.cpp : 83) Starting BayesHammer, built from refs/heads/spades_3.8.0, git revision bb97112cad669727c57d7b448952b254ce0e4d0c 0:00:00.000 4M / 4M INFO General (main.cpp : 84) Loading config from /home/vagrant/SPAdes-3.8.0-Linux/spades_test/corrected/configs/config.info 0:00:00.000 4M / 4M INFO General (memory_limit.hpp : 47) Memory limit set to 2 Gb 0:00:00.000 4M / 4M INFO General (main.cpp : 93) Trying to determine PHRED offset 0:00:00.000 4M / 4M INFO General (main.cpp : 99) Determined value is 33 0:00:00.002 4M / 4M INFO General (hammer_tools.cpp : 36) Hamming graph threshold tau=1, k=21, subkmer positions = [ 0 10 ] 0:00:00.002 4M / 4M INFO General (main.cpp : 120) Size of aux. kmer data 24 bytes === ITERATION 0 begins === 0:00:00.002 4M / 4M INFO K-mer Index Building (kmer_index.hpp : 470) Building kmer index 0:00:00.002 4M / 4M INFO K-mer Splitting (kmer_data.cpp : 141) Splitting kmer instances into 48 buckets. This might take a while. 0:00:00.002 4M / 4M INFO General (file_limit.hpp : 30) Open file limit set to 65536 0:00:00.002 4M / 4M INFO K-mer Splitting (kmer_data.cpp : 159) Memory available for splitting buffers: 0.221788 Gb 0:00:00.002 4M / 4M INFO K-mer Splitting (kmer_data.cpp : 167) Using cell size of 620164 0:00:00.003 1G / 1G INFO K-mer Splitting (kmer_data.cpp : 181) Processing /home/vagrant/SPAdes-3.8.0-Linux/share/spades/test_dataset/ecoli_1K_1.fq.gz 0:00:00.049 1G / 1G INFO K-mer Splitting (kmer_data.cpp : 181) Processing /home/vagrant/SPAdes-3.8.0-Linux/share/spades/test_dataset/ecoli_1K_2.fq.gz 0:00:00.082 1G / 1G INFO K-mer Splitting (kmer_data.cpp : 195) Processed 4108 reads 0:00:00.086 12M / 1G INFO General (kmer_index.hpp : 348) Starting k-mer counting. 0:00:00.101 12M / 1G INFO General (kmer_index.hpp : 354) K-mer counting done. There are 1974 kmers in total. 0:00:00.101 12M / 1G INFO General (kmer_index.hpp : 356) Merging temporary buckets. 0:00:00.104 12M / 1G INFO K-mer Index Building (kmer_index.hpp : 479) Building perfect hash indices 0:00:00.106 12M / 1G INFO General (kmer_index.hpp : 374) Merging final buckets. 0:00:00.107 12M / 1G INFO K-mer Index Building (kmer_index.hpp : 527) Index built. Total 792 bytes occupied (3.20973 bits per kmer). 0:00:00.107 12M / 1G INFO K-mer Counting (kmer_data.cpp : 518) Arranging kmers in hash map order 0:00:00.109 12M / 1G INFO General (main.cpp : 155) Clustering Hamming graph. 0:00:00.113 12M / 1G INFO General (main.cpp : 162) Extracting clusters 0:00:00.114 12M / 1G INFO General (main.cpp : 174) Clustering done. Total clusters: 1960 0:00:00.114 12M / 1G INFO K-mer Counting (kmer_data.cpp : 540) Collecting K-mer information, this takes a while. 0:00:00.114 12M / 1G INFO K-mer Counting (kmer_data.cpp : 546) Processing /home/vagrant/SPAdes-3.8.0-Linux/share/spades/test_dataset/ecoli_1K_1.fq.gz 0:00:00.185 12M / 1G INFO K-mer Counting (kmer_data.cpp : 546) Processing /home/vagrant/SPAdes-3.8.0-Linux/share/spades/test_dataset/ecoli_1K_2.fq.gz 0:00:00.257 12M / 1G INFO K-mer Counting (kmer_data.cpp : 553) Collection done, postprocessing. 0:00:00.257 12M / 1G INFO K-mer Counting (kmer_data.cpp : 567) There are 1974 kmers in total. Among them 0 (0%) are singletons. 0:00:00.257 12M / 1G INFO General (main.cpp : 180) Subclustering Hamming graph 0:00:00.258 12M / 1G INFO Hamming Subclustering (kmer_cluster.cpp : 647) Subclustering done. Total 0 non-read kmers were generated. 0:00:00.258 12M / 1G INFO Hamming Subclustering (kmer_cluster.cpp : 648) Subclustering statistics: 0:00:00.258 12M / 1G INFO Hamming Subclustering (kmer_cluster.cpp : 649) Total singleton hamming clusters: 1946. Among them 1946 (100%) are good 0:00:00.258 12M / 1G INFO Hamming Subclustering (kmer_cluster.cpp : 650) Total singleton subclusters: 8. Among them 8 (100%) are good 0:00:00.258 12M / 1G INFO Hamming Subclustering (kmer_cluster.cpp : 651) Total non-singleton subcluster centers: 10. Among them 10 (100%) are good 0:00:00.258 12M / 1G INFO Hamming Subclustering (kmer_cluster.cpp : 652) Average size of non-trivial subcluster: 2.8 kmers 0:00:00.258 12M / 1G INFO Hamming Subclustering (kmer_cluster.cpp : 653) Average number of sub-clusters per non-singleton cluster: 1.28571 0:00:00.258 12M / 1G INFO Hamming Subclustering (kmer_cluster.cpp : 654) Total solid k-mers: 1964 0:00:00.259 12M / 1G INFO Hamming Subclustering (kmer_cluster.cpp : 655) Substitution probabilities: [4,4]((0.875,0.125,0,0),(0,1,0,0),(0,0,1,0),(0,0,0.125,0.875)) 0:00:00.260 12M / 1G INFO General (main.cpp : 185) Finished clustering. 0:00:00.261 12M / 1G INFO General (main.cpp : 204) Starting solid k-mers expansion in 3 threads. 0:00:00.299 12M / 1G INFO General (main.cpp : 225) Solid k-mers iteration 0 produced 0 new k-mers. 0:00:00.299 12M / 1G INFO General (main.cpp : 229) Solid k-mers finalized 0:00:00.299 12M / 1G INFO General (hammer_tools.cpp : 210) Starting read correction in 3 threads. 0:00:00.299 12M / 1G INFO General (hammer_tools.cpp : 221) Correcting pair of reads: /home/vagrant/SPAdes-3.8.0-Linux/share/spades/test_dataset/ecoli_1K_1.fq.gz and /home/vagrant/SPAdes-3.8.0-Linux/share/spades/test_dataset/ecoli_1K_2.fq.gz 0:00:00.321 36M / 1G INFO General (hammer_tools.cpp : 166) Prepared batch 0 of 2054 reads. 0:00:00.343 36M / 1G INFO General (hammer_tools.cpp : 175) Processed batch 0 0:00:00.350 36M / 1G INFO General (hammer_tools.cpp : 185) Written batch 0 0:00:00.356 12M / 1G INFO General (hammer_tools.cpp : 269) Correction done. Changed 4 bases in 4 reads. 0:00:00.356 12M / 1G INFO General (hammer_tools.cpp : 270) Failed to correct 0 bases out of 353915. 0:00:00.356 12M / 1G INFO General (main.cpp : 262) Saving corrected dataset description to /home/vagrant/SPAdes-3.8.0-Linux/spades_test/corrected/corrected.yaml 0:00:00.357 12M / 1G INFO General (main.cpp : 269) All done. Exiting. == Compressing corrected reads (with gzip) == Dataset description file was created: /home/vagrant/SPAdes-3.8.0-Linux/spades_test/corrected/corrected.yaml ===== Read error correction finished. ===== Assembling started. == Running assembler: K21 0:00:00.000 4M / 4M INFO General (main.cpp : 73) Loading config from /home/vagrant/SPAdes-3.8.0-Linux/spades_test/K21/configs/config.info 0:00:00.000 4M / 4M INFO General (main.cpp : 73) Loading config from /home/vagrant/SPAdes-3.8.0-Linux/spades_test/K21/configs/plasmid_mode.info 0:00:00.000 4M / 4M INFO General (memory_limit.hpp : 47) Memory limit set to 2 Gb 0:00:00.000 4M / 4M INFO General (main.cpp : 86) Starting SPAdes, built from refs/heads/spades_3.8.0, git revision bb97112cad669727c57d7b448952b254ce0e4d0c 0:00:00.000 4M / 4M INFO General (main.cpp : 87) Assembling dataset (/home/vagrant/SPAdes-3.8.0-Linux/spades_test/dataset.info) with K=21 0:00:00.000 4M / 4M INFO General (launch.hpp : 29) SPAdes started 0:00:00.000 4M / 4M INFO General (launch.hpp : 36) Starting from stage: construction 0:00:00.000 4M / 4M INFO General (launch.hpp : 39) Two-step RR enabled: 0 0:00:00.000 4M / 4M INFO StageManager (stage.cpp : 126) STAGE == Construction 0:00:00.000 4M / 4M INFO General (read_converter.hpp : 80) Converting reads to binary format (takes a while) 0:00:00.000 4M / 4M INFO General (read_converter.hpp : 87) Paired reads for library #0 0:00:00.541 76M / 100M INFO General (binary_converter.hpp : 159) 2054 reads written 0:00:00.544 4M / 100M INFO General (read_converter.hpp : 98) Single reads for library #0 0:00:01.696 136M / 180M INFO General (binary_converter.hpp : 159) 0 reads written 0:00:01.701 4M / 180M INFO General (graph_construction.hpp : 119) Constructing DeBruijn graph for k=21 0:00:01.701 4M / 180M INFO General (kmer_splitters.hpp : 174) Splitting kmer instances into 9 buckets. This might take a while. 0:00:01.701 4M / 180M INFO General (file_limit.hpp : 30) Open file limit set to 65536 0:00:01.701 4M / 180M INFO General (kmer_splitters.hpp : 192) Memory available for splitting buffers: 0.221788 Gb 0:00:01.701 4M / 180M INFO General (kmer_splitters.hpp : 201) Using cell size of 3307545 0:00:01.734 768M / 788M INFO General (kmer_splitters.hpp : 236) Adding contigs from previous K 0:00:01.734 768M / 788M INFO General (kmer_splitters.hpp : 247) Used 8216 reads. Maximum read length 100 0:00:01.734 768M / 788M INFO General (kmer_splitters.hpp : 248) Average read length 86.1526 0:00:01.735 12M / 788M INFO General (kmer_index.hpp : 348) Starting k-mer counting. 0:00:01.737 12M / 788M INFO General (kmer_index.hpp : 354) K-mer counting done. There are 984 kmers in total. 0:00:01.737 12M / 788M INFO General (kmer_index.hpp : 356) Merging temporary buckets. 0:00:01.737 12M / 788M INFO K-mer Index Building (kmer_index.hpp : 470) Building kmer index 0:00:01.737 12M / 788M INFO General (kmer_splitters.hpp : 381) Splitting kmer instances into 48 buckets. This might take a while. 0:00:01.738 12M / 788M INFO General (file_limit.hpp : 30) Open file limit set to 65536 0:00:01.738 12M / 788M INFO General (kmer_splitters.hpp : 399) Memory available for splitting buffers: 0.22092 Gb 0:00:01.738 12M / 788M INFO General (kmer_splitters.hpp : 407) Using cell size of 617737 0:00:01.741 1G / 1G INFO General (kmer_splitters.hpp : 439) Used 984 kmers. 0:00:01.743 12M / 1G INFO General (kmer_index.hpp : 348) Starting k-mer counting. 0:00:01.758 12M / 1G INFO General (kmer_index.hpp : 354) K-mer counting done. There are 985 kmers in total. 0:00:01.758 12M / 1G INFO General (kmer_index.hpp : 356) Merging temporary buckets. 0:00:01.761 12M / 1G INFO K-mer Index Building (kmer_index.hpp : 479) Building perfect hash indices 0:00:01.764 12M / 1G INFO General (kmer_index.hpp : 374) Merging final buckets. 0:00:01.765 12M / 1G INFO K-mer Index Building (kmer_index.hpp : 527) Index built. Total 512 bytes occupied (4.15838 bits per kmer). 0:00:01.765 12M / 1G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 390) Building k-mer extensions from k+1-mers 0:00:01.766 12M / 1G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 394) Building k-mer extensions from k+1-mers finished. 0:00:01.766 12M / 1G INFO Early tip clipping (early_simplification.hpp : 259) Early tip clipping 0:00:01.767 12M / 1G INFO Early tip clipping (early_simplification.hpp : 262) 5 22-mers were removed by early tip clipper 0:00:01.767 12M / 1G INFO General (graph_construction.hpp : 135) Condensing graph 0:00:01.767 12M / 1G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 337) Extracting unbranching paths 0:00:01.769 12M / 1G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 351) Extracting unbranching paths finished. 2 sequences extracted 0:00:01.769 12M / 1G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 311) Collecting perfect loops 0:00:01.770 12M / 1G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 326) Collecting perfect loops finished. 0 loops collected 0:00:01.770 12M / 1G INFO General (graph_construction.hpp : 140) Building index with from graph 0:00:01.771 12M / 1G INFO K-mer Index Building (kmer_index.hpp : 470) Building kmer index 0:00:01.771 12M / 1G INFO General (kmer_splitters.hpp : 291) Splitting kmer instances into 16 buckets. This might take a while. 0:00:01.771 12M / 1G INFO General (file_limit.hpp : 30) Open file limit set to 65536 0:00:01.771 12M / 1G INFO General (kmer_splitters.hpp : 309) Memory available for splitting buffers: 0.66276 Gb 0:00:01.771 12M / 1G INFO General (kmer_splitters.hpp : 314) Using cell size of 4194304 0:00:01.773 588M / 1G INFO General (kmer_splitters.hpp : 332) Used 2 sequences. 0:00:01.773 12M / 1G INFO General (kmer_index.hpp : 348) Starting k-mer counting. 0:00:01.775 12M / 1G INFO General (kmer_index.hpp : 354) K-mer counting done. There are 979 kmers in total. 0:00:01.776 12M / 1G INFO General (kmer_index.hpp : 356) Merging temporary buckets. 0:00:01.777 12M / 1G INFO K-mer Index Building (kmer_index.hpp : 479) Building perfect hash indices 0:00:01.777 12M / 1G INFO General (kmer_index.hpp : 374) Merging final buckets. 0:00:01.778 12M / 1G INFO K-mer Index Building (kmer_index.hpp : 527) Index built. Total 504 bytes occupied (4.11849 bits per kmer). 0:00:01.779 12M / 1G INFO General (edge_index_builders.hpp : 28) Collecting k-mer coverage information from graph, this takes a while. 0:00:01.780 12M / 1G INFO General (edge_index.hpp : 100) Index refilled 0:00:01.780 12M / 1G INFO General (graph_construction.hpp : 172) Filling coverage index 0:00:01.780 12M / 1G INFO General (edge_index_builders.hpp : 106) Collecting k-mer coverage information from reads, this takes a while. 0:00:01.826 12M / 1G INFO General (graph_construction.hpp : 174) Filling coverage and flanking coverage from index 0:00:01.826 12M / 1G INFO General (construction.cpp : 30) Figured out: read length = 100 0:00:01.826 12M / 1G INFO StageManager (stage.cpp : 126) STAGE == EC Threshold Finding 0:00:01.826 12M / 1G INFO General (kmer_coverage_model.cpp : 180) Kmer coverage valley at: 0 0:00:01.826 12M / 1G INFO General (kmer_coverage_model.cpp : 200) K-mer histogram maximum: 348 0:00:01.826 12M / 1G INFO General (kmer_coverage_model.cpp : 236) Estimated median coverage: 348. Coverage mad: 62.2692 0:00:01.826 12M / 1G INFO General (kmer_coverage_model.cpp : 275) Fitting coverage model 0:00:01.902 12M / 1G INFO General (kmer_coverage_model.cpp : 311) ... iteration 2 0:00:02.063 12M / 1G INFO General (kmer_coverage_model.cpp : 311) ... iteration 4 0:00:02.503 12M / 1G INFO General (kmer_coverage_model.cpp : 311) ... iteration 8 0:00:03.328 12M / 1G INFO General (kmer_coverage_model.cpp : 311) ... iteration 16 0:00:04.667 12M / 1G INFO General (kmer_coverage_model.cpp : 311) ... iteration 32 0:00:06.961 12M / 1G INFO General (kmer_coverage_model.cpp : 311) ... iteration 64 0:00:08.598 12M / 1G INFO General (kmer_coverage_model.cpp : 325) Fitted mean coverage: 343.199. Fitted coverage std. dev: 68.1396 0:00:08.599 12M / 1G INFO General (kmer_coverage_model.cpp : 350) Probability of erroneous kmer at valley: 0.999995 0:00:08.599 12M / 1G INFO General (kmer_coverage_model.cpp : 374) Preliminary threshold calculated as: 360 0:00:08.599 12M / 1G INFO General (kmer_coverage_model.cpp : 378) Threshold adjusted to: 171 0:00:08.599 12M / 1G INFO General (kmer_coverage_model.cpp : 391) Estimated genome size (ignoring repeats): 749 0:00:08.599 12M / 1G INFO General (genomic_info_filler.cpp : 133) Mean coverage was calculated as 343.199 0:00:08.599 12M / 1G INFO General (genomic_info_filler.cpp : 147) EC coverage threshold value was calculated as 171 0:00:08.600 12M / 1G INFO General (genomic_info_filler.cpp : 148) Trusted kmer low bound: 0 0:00:08.600 12M / 1G INFO StageManager (stage.cpp : 126) STAGE == Simplification 0:00:08.600 12M / 1G INFO General (simplification.cpp : 349) Graph simplification started 0:00:08.600 12M / 1G INFO General (simplification.cpp : 98) PROCEDURE == InitialCleaning 0:00:08.600 12M / 1G INFO General (graph_simplification.hpp : 577) Removing isolated edges 0:00:08.600 12M / 1G INFO General (graph_simplification.hpp : 578) All isolated edges shorter than 100 will be removed 0:00:08.600 12M / 1G INFO General (graph_simplification.hpp : 579) Also isolated edges shorter than 0 and coverage smaller than 0 will be removed 0:00:08.600 12M / 1G INFO General (graph_simplification.hpp : 794) Flanking coverage based disconnection disabled 0:00:08.600 12M / 1G INFO General (simplification.cpp : 326) Running Self conjugate edge remover 0:00:08.604 12M / 1G INFO General (simplification.cpp : 326) Running Initial isolated edge remover 0:00:08.607 12M / 1G INFO General (simplification.cpp : 326) Running Initial tip clipper 0:00:08.610 12M / 1G INFO General (simplification.cpp : 326) Running Initial ec remover 0:00:08.610 12M / 1G INFO General (graph_simplification.hpp : 707) Creating parallel br instance 0:00:08.610 12M / 1G INFO General (simplification.cpp : 372) PROCEDURE == Simplification cycle, iteration 1 0:00:08.610 12M / 1G INFO General (simplification.cpp : 326) Running Tip clipper 0:00:08.610 12M / 1G INFO General (simplification.cpp : 326) Running Bulge remover 0:00:08.610 12M / 1G INFO General (simplification.cpp : 326) Running Low coverage edge remover 0:00:08.610 12M / 1G INFO General (simplification.cpp : 372) PROCEDURE == Simplification cycle, iteration 2 0:00:08.610 12M / 1G INFO General (simplification.cpp : 326) Running Tip clipper 0:00:08.610 12M / 1G INFO General (simplification.cpp : 326) Running Bulge remover 0:00:08.610 12M / 1G INFO General (simplification.cpp : 326) Running Low coverage edge remover 0:00:08.610 12M / 1G INFO General (simplification.cpp : 372) PROCEDURE == Simplification cycle, iteration 3 0:00:08.610 12M / 1G INFO General (simplification.cpp : 326) Running Tip clipper 0:00:08.610 12M / 1G INFO General (simplification.cpp : 326) Running Bulge remover 0:00:08.610 12M / 1G INFO General (simplification.cpp : 326) Running Low coverage edge remover 0:00:08.610 12M / 1G INFO General (simplification.cpp : 372) PROCEDURE == Simplification cycle, iteration 4 0:00:08.610 12M / 1G INFO General (simplification.cpp : 326) Running Tip clipper 0:00:08.610 12M / 1G INFO General (simplification.cpp : 326) Running Bulge remover 0:00:08.610 12M / 1G INFO General (simplification.cpp : 326) Running Low coverage edge remover 0:00:08.611 12M / 1G INFO General (simplification.cpp : 372) PROCEDURE == Simplification cycle, iteration 5 0:00:08.611 12M / 1G INFO General (simplification.cpp : 326) Running Tip clipper 0:00:08.611 12M / 1G INFO General (simplification.cpp : 326) Running Bulge remover 0:00:08.611 12M / 1G INFO General (simplification.cpp : 326) Running Low coverage edge remover 0:00:08.611 12M / 1G INFO General (simplification.cpp : 372) PROCEDURE == Simplification cycle, iteration 6 0:00:08.611 12M / 1G INFO General (simplification.cpp : 326) Running Tip clipper 0:00:08.611 12M / 1G INFO General (simplification.cpp : 326) Running Bulge remover 0:00:08.611 12M / 1G INFO General (simplification.cpp : 326) Running Low coverage edge remover 0:00:08.611 12M / 1G INFO General (simplification.cpp : 372) PROCEDURE == Simplification cycle, iteration 7 0:00:08.611 12M / 1G INFO General (simplification.cpp : 326) Running Tip clipper 0:00:08.611 12M / 1G INFO General (simplification.cpp : 326) Running Bulge remover 0:00:08.611 12M / 1G INFO General (simplification.cpp : 326) Running Low coverage edge remover 0:00:08.611 12M / 1G INFO General (simplification.cpp : 372) PROCEDURE == Simplification cycle, iteration 8 0:00:08.611 12M / 1G INFO General (simplification.cpp : 326) Running Tip clipper 0:00:08.611 12M / 1G INFO General (simplification.cpp : 326) Running Bulge remover 0:00:08.611 12M / 1G INFO General (simplification.cpp : 326) Running Low coverage edge remover 0:00:08.611 12M / 1G INFO General (simplification.cpp : 372) PROCEDURE == Simplification cycle, iteration 9 0:00:08.611 12M / 1G INFO General (simplification.cpp : 326) Running Tip clipper 0:00:08.611 12M / 1G INFO General (simplification.cpp : 326) Running Bulge remover 0:00:08.611 12M / 1G INFO General (simplification.cpp : 326) Running Low coverage edge remover 0:00:08.611 12M / 1G INFO General (simplification.cpp : 372) PROCEDURE == Simplification cycle, iteration 10 0:00:08.611 12M / 1G INFO General (simplification.cpp : 326) Running Tip clipper 0:00:08.611 12M / 1G INFO General (simplification.cpp : 326) Running Bulge remover 0:00:08.611 12M / 1G INFO General (simplification.cpp : 326) Running Low coverage edge remover 0:00:08.611 12M / 1G INFO General (simplification.cpp : 213) PROCEDURE == Post simplification 0:00:08.611 12M / 1G INFO General (graph_simplification.hpp : 707) Creating parallel br instance 0:00:08.611 12M / 1G INFO General (simplification.cpp : 268) Iteration 0 0:00:08.611 12M / 1G INFO General (graph_simplification.hpp : 463) Removal of relatively low covered connections disabled 0:00:08.611 12M / 1G INFO General (graph_simplification.hpp : 480) Disconnection of relatively low covered edges disabled 0:00:08.611 12M / 1G INFO General (graph_simplification.hpp : 536) Complex tip clipping disabled 0:00:08.611 12M / 1G INFO General (simplification.cpp : 326) Running Tip clipper 0:00:08.611 12M / 1G INFO General (simplification.cpp : 326) Running Bulge remover 0:00:08.611 12M / 1G INFO General (simplification.cpp : 296) Disrupting self-conjugate edges 0:00:08.611 12M / 1G INFO StageManager (stage.cpp : 126) STAGE == Simplification Cleanup 0:00:08.611 12M / 1G INFO General (graph_simplification.hpp : 577) Removing isolated edges 0:00:08.611 12M / 1G INFO General (graph_simplification.hpp : 578) All isolated edges shorter than 150 will be removed 0:00:08.611 12M / 1G INFO General (graph_simplification.hpp : 579) Also isolated edges shorter than 0 and coverage smaller than 2 will be removed 0:00:08.611 12M / 1G INFO General (simplification.cpp : 457) Counting average coverage 0:00:08.611 12M / 1G INFO General (simplification.cpp : 462) Average coverage = 273.35 0:00:08.611 12M / 1G INFO StageManager (stage.cpp : 126) STAGE == Contig Output 0:00:08.611 12M / 1G INFO General (contig_output.hpp : 305) Outputting contigs to /home/vagrant/SPAdes-3.8.0-Linux/spades_test//K21/simplified_contigs.fasta 0:00:08.611 12M / 1G INFO General (contig_output.hpp : 305) Outputting contigs to /home/vagrant/SPAdes-3.8.0-Linux/spades_test//K21/before_rr.fasta 0:00:08.611 12M / 1G INFO General (contig_output.hpp : 338) Outputting graph to /home/vagrant/SPAdes-3.8.0-Linux/spades_test//K21/assembly_graph.fastg 0:00:08.611 12M / 1G INFO General (contig_output.hpp : 305) Outputting contigs to /home/vagrant/SPAdes-3.8.0-Linux/spades_test//K21/final_contigs.fasta 0:00:08.612 12M / 1G INFO General (launch.hpp : 117) SPAdes finished 0:00:08.612 12M / 1G INFO General (main.cpp : 106) Assembling time: 0 hours 0 minutes 8 seconds == Running assembler: K33 0:00:00.000 4M / 4M INFO General (main.cpp : 73) Loading config from /home/vagrant/SPAdes-3.8.0-Linux/spades_test/K33/configs/config.info 0:00:00.000 4M / 4M INFO General (main.cpp : 73) Loading config from /home/vagrant/SPAdes-3.8.0-Linux/spades_test/K33/configs/plasmid_mode.info 0:00:00.000 4M / 4M INFO General (memory_limit.hpp : 47) Memory limit set to 2 Gb 0:00:00.000 4M / 4M INFO General (main.cpp : 86) Starting SPAdes, built from refs/heads/spades_3.8.0, git revision bb97112cad669727c57d7b448952b254ce0e4d0c 0:00:00.000 4M / 4M INFO General (main.cpp : 87) Assembling dataset (/home/vagrant/SPAdes-3.8.0-Linux/spades_test/dataset.info) with K=33 0:00:00.000 4M / 4M INFO General (launch.hpp : 29) SPAdes started 0:00:00.000 4M / 4M INFO General (launch.hpp : 36) Starting from stage: construction 0:00:00.000 4M / 4M INFO General (launch.hpp : 39) Two-step RR enabled: 0 0:00:00.000 4M / 4M INFO StageManager (stage.cpp : 126) STAGE == Construction 0:00:00.000 4M / 4M INFO General (construction.cpp : 41) Contigs from previous K will be used 0:00:00.000 4M / 4M INFO General (read_converter.hpp : 49) Binary reads detected 0:00:00.000 4M / 4M INFO General (graph_construction.hpp : 119) Constructing DeBruijn graph for k=33 0:00:00.000 4M / 4M INFO General (kmer_splitters.hpp : 174) Splitting kmer instances into 9 buckets. This might take a while. 0:00:00.000 4M / 4M INFO General (file_limit.hpp : 30) Open file limit set to 65536 0:00:00.000 4M / 4M INFO General (kmer_splitters.hpp : 192) Memory available for splitting buffers: 0.221788 Gb 0:00:00.000 4M / 4M INFO General (kmer_splitters.hpp : 201) Using cell size of 1653772 0:00:00.035 768M / 788M INFO General (kmer_splitters.hpp : 236) Adding contigs from previous K 0:00:00.040 768M / 788M INFO General (kmer_splitters.hpp : 247) Used 8216 reads. Maximum read length 100 0:00:00.040 768M / 788M INFO General (kmer_splitters.hpp : 248) Average read length 86.1526 0:00:00.040 12M / 788M INFO General (kmer_index.hpp : 348) Starting k-mer counting. 0:00:00.045 12M / 788M INFO General (kmer_index.hpp : 354) K-mer counting done. There are 972 kmers in total. 0:00:00.045 12M / 788M INFO General (kmer_index.hpp : 356) Merging temporary buckets. 0:00:00.046 12M / 788M INFO K-mer Index Building (kmer_index.hpp : 470) Building kmer index 0:00:00.046 12M / 788M INFO General (kmer_splitters.hpp : 381) Splitting kmer instances into 48 buckets. This might take a while. 0:00:00.046 12M / 788M INFO General (file_limit.hpp : 30) Open file limit set to 65536 0:00:00.046 12M / 788M INFO General (kmer_splitters.hpp : 399) Memory available for splitting buffers: 0.22092 Gb 0:00:00.046 12M / 788M INFO General (kmer_splitters.hpp : 407) Using cell size of 308868 0:00:00.054 1G / 1G INFO General (kmer_splitters.hpp : 439) Used 972 kmers. 0:00:00.055 12M / 1G INFO General (kmer_index.hpp : 348) Starting k-mer counting. 0:00:00.066 12M / 1G INFO General (kmer_index.hpp : 354) K-mer counting done. There are 973 kmers in total. 0:00:00.066 12M / 1G INFO General (kmer_index.hpp : 356) Merging temporary buckets. 0:00:00.069 12M / 1G INFO K-mer Index Building (kmer_index.hpp : 479) Building perfect hash indices 0:00:00.071 12M / 1G INFO General (kmer_index.hpp : 374) Merging final buckets. 0:00:00.072 12M / 1G INFO K-mer Index Building (kmer_index.hpp : 527) Index built. Total 504 bytes occupied (4.14388 bits per kmer). 0:00:00.072 12M / 1G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 390) Building k-mer extensions from k+1-mers 0:00:00.075 12M / 1G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 394) Building k-mer extensions from k+1-mers finished. 0:00:00.075 12M / 1G INFO Early tip clipping (early_simplification.hpp : 259) Early tip clipping 0:00:00.081 12M / 1G INFO Early tip clipping (early_simplification.hpp : 262) 5 34-mers were removed by early tip clipper 0:00:00.081 12M / 1G INFO General (graph_construction.hpp : 135) Condensing graph 0:00:00.081 12M / 1G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 337) Extracting unbranching paths 0:00:00.084 12M / 1G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 351) Extracting unbranching paths finished. 2 sequences extracted 0:00:00.087 12M / 1G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 311) Collecting perfect loops 0:00:00.087 12M / 1G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 326) Collecting perfect loops finished. 0 loops collected 0:00:00.093 12M / 1G INFO General (graph_construction.hpp : 140) Building index with from graph 0:00:00.094 12M / 1G INFO K-mer Index Building (kmer_index.hpp : 470) Building kmer index 0:00:00.094 12M / 1G INFO General (kmer_splitters.hpp : 291) Splitting kmer instances into 16 buckets. This might take a while. 0:00:00.094 12M / 1G INFO General (file_limit.hpp : 30) Open file limit set to 65536 0:00:00.094 12M / 1G INFO General (kmer_splitters.hpp : 309) Memory available for splitting buffers: 0.66276 Gb 0:00:00.094 12M / 1G INFO General (kmer_splitters.hpp : 314) Using cell size of 2097152 0:00:00.098 588M / 1G INFO General (kmer_splitters.hpp : 332) Used 2 sequences. 0:00:00.099 12M / 1G INFO General (kmer_index.hpp : 348) Starting k-mer counting. 0:00:00.101 12M / 1G INFO General (kmer_index.hpp : 354) K-mer counting done. There are 967 kmers in total. 0:00:00.101 12M / 1G INFO General (kmer_index.hpp : 356) Merging temporary buckets. 0:00:00.102 12M / 1G INFO K-mer Index Building (kmer_index.hpp : 479) Building perfect hash indices 0:00:00.104 12M / 1G INFO General (kmer_index.hpp : 374) Merging final buckets. 0:00:00.105 12M / 1G INFO K-mer Index Building (kmer_index.hpp : 527) Index built. Total 504 bytes occupied (4.1696 bits per kmer). 0:00:00.105 12M / 1G INFO General (edge_index_builders.hpp : 28) Collecting k-mer coverage information from graph, this takes a while. 0:00:00.106 12M / 1G INFO General (edge_index.hpp : 100) Index refilled 0:00:00.106 12M / 1G INFO General (graph_construction.hpp : 172) Filling coverage index 0:00:00.106 12M / 1G INFO General (edge_index_builders.hpp : 106) Collecting k-mer coverage information from reads, this takes a while. 0:00:00.143 12M / 1G INFO General (graph_construction.hpp : 174) Filling coverage and flanking coverage from index 0:00:00.143 12M / 1G INFO General (construction.cpp : 30) Figured out: read length = 100 0:00:00.143 12M / 1G INFO StageManager (stage.cpp : 126) STAGE == EC Threshold Finding 0:00:00.144 12M / 1G INFO General (kmer_coverage_model.cpp : 180) Kmer coverage valley at: 0 0:00:00.144 12M / 1G INFO General (kmer_coverage_model.cpp : 200) K-mer histogram maximum: 17 0:00:00.144 12M / 1G INFO General (kmer_coverage_model.cpp : 236) Estimated median coverage: 17. Coverage mad: 11.8608 0:00:00.144 12M / 1G INFO General (kmer_coverage_model.cpp : 275) Fitting coverage model 0:00:00.171 12M / 1G INFO General (kmer_coverage_model.cpp : 311) ... iteration 2 0:00:00.236 12M / 1G INFO General (kmer_coverage_model.cpp : 311) ... iteration 4 0:00:00.417 12M / 1G INFO General (kmer_coverage_model.cpp : 311) ... iteration 8 0:00:00.615 12M / 1G INFO General (kmer_coverage_model.cpp : 311) ... iteration 16 0:00:01.022 12M / 1G INFO General (kmer_coverage_model.cpp : 311) ... iteration 32 0:00:01.754 12M / 1G INFO General (kmer_coverage_model.cpp : 311) ... iteration 64 0:00:02.323 12M / 1G INFO General (kmer_coverage_model.cpp : 325) Fitted mean coverage: 109.191. Fitted coverage std. dev: 64.5753 0:00:02.324 12M / 1G INFO General (kmer_coverage_model.cpp : 350) Probability of erroneous kmer at valley: 3.97345e-06 0:00:02.324 12M / 1G INFO General (kmer_coverage_model.cpp : 374) Preliminary threshold calculated as: 1 0:00:02.324 12M / 1G INFO General (kmer_coverage_model.cpp : 378) Threshold adjusted to: 1 0:00:02.324 12M / 1G INFO General (kmer_coverage_model.cpp : 391) Estimated genome size (ignoring repeats): 397 0:00:02.324 12M / 1G INFO General (genomic_info_filler.cpp : 133) Mean coverage was calculated as 109.191 0:00:02.324 12M / 1G INFO General (genomic_info_filler.cpp : 147) EC coverage threshold value was calculated as 1 0:00:02.324 12M / 1G INFO General (genomic_info_filler.cpp : 148) Trusted kmer low bound: 0 0:00:02.324 12M / 1G INFO StageManager (stage.cpp : 126) STAGE == Simplification 0:00:02.324 12M / 1G INFO General (simplification.cpp : 349) Graph simplification started 0:00:02.324 12M / 1G INFO General (simplification.cpp : 98) PROCEDURE == InitialCleaning 0:00:02.324 12M / 1G INFO General (graph_simplification.hpp : 577) Removing isolated edges 0:00:02.324 12M / 1G INFO General (graph_simplification.hpp : 578) All isolated edges shorter than 100 will be removed 0:00:02.324 12M / 1G INFO General (graph_simplification.hpp : 579) Also isolated edges shorter than 0 and coverage smaller than 0 will be removed 0:00:02.324 12M / 1G INFO General (graph_simplification.hpp : 794) Flanking coverage based disconnection disabled 0:00:02.324 12M / 1G INFO General (simplification.cpp : 326) Running Self conjugate edge remover 0:00:02.329 12M / 1G INFO General (simplification.cpp : 326) Running Initial isolated edge remover 0:00:02.333 12M / 1G INFO General (simplification.cpp : 326) Running Initial tip clipper 0:00:02.336 12M / 1G INFO General (simplification.cpp : 326) Running Initial ec remover 0:00:02.340 12M / 1G INFO General (graph_simplification.hpp : 707) Creating parallel br instance 0:00:02.340 12M / 1G INFO General (simplification.cpp : 372) PROCEDURE == Simplification cycle, iteration 1 0:00:02.340 12M / 1G INFO General (simplification.cpp : 326) Running Tip clipper 0:00:02.342 12M / 1G INFO General (simplification.cpp : 326) Running Bulge remover 0:00:02.349 12M / 1G INFO General (simplification.cpp : 326) Running Low coverage edge remover 0:00:02.352 12M / 1G INFO General (simplification.cpp : 372) PROCEDURE == Simplification cycle, iteration 2 0:00:02.352 12M / 1G INFO General (simplification.cpp : 326) Running Tip clipper 0:00:02.352 12M / 1G INFO General (simplification.cpp : 326) Running Bulge remover 0:00:02.357 12M / 1G INFO General (simplification.cpp : 326) Running Low coverage edge remover 0:00:02.357 12M / 1G INFO General (simplification.cpp : 372) PROCEDURE == Simplification cycle, iteration 3 0:00:02.357 12M / 1G INFO General (simplification.cpp : 326) Running Tip clipper 0:00:02.357 12M / 1G INFO General (simplification.cpp : 326) Running Bulge remover 0:00:02.361 12M / 1G INFO General (simplification.cpp : 326) Running Low coverage edge remover 0:00:02.362 12M / 1G INFO General (simplification.cpp : 372) PROCEDURE == Simplification cycle, iteration 4 0:00:02.362 12M / 1G INFO General (simplification.cpp : 326) Running Tip clipper 0:00:02.362 12M / 1G INFO General (simplification.cpp : 326) Running Bulge remover 0:00:02.367 12M / 1G INFO General (simplification.cpp : 326) Running Low coverage edge remover 0:00:02.367 12M / 1G INFO General (simplification.cpp : 372) PROCEDURE == Simplification cycle, iteration 5 0:00:02.367 12M / 1G INFO General (simplification.cpp : 326) Running Tip clipper 0:00:02.367 12M / 1G INFO General (simplification.cpp : 326) Running Bulge remover 0:00:02.371 12M / 1G INFO General (simplification.cpp : 326) Running Low coverage edge remover 0:00:02.371 12M / 1G INFO General (simplification.cpp : 372) PROCEDURE == Simplification cycle, iteration 6 0:00:02.371 12M / 1G INFO General (simplification.cpp : 326) Running Tip clipper 0:00:02.371 12M / 1G INFO General (simplification.cpp : 326) Running Bulge remover 0:00:02.375 12M / 1G INFO General (simplification.cpp : 326) Running Low coverage edge remover 0:00:02.375 12M / 1G INFO General (simplification.cpp : 372) PROCEDURE == Simplification cycle, iteration 7 0:00:02.375 12M / 1G INFO General (simplification.cpp : 326) Running Tip clipper 0:00:02.375 12M / 1G INFO General (simplification.cpp : 326) Running Bulge remover 0:00:02.379 12M / 1G INFO General (simplification.cpp : 326) Running Low coverage edge remover 0:00:02.380 12M / 1G INFO General (simplification.cpp : 372) PROCEDURE == Simplification cycle, iteration 8 0:00:02.380 12M / 1G INFO General (simplification.cpp : 326) Running Tip clipper 0:00:02.380 12M / 1G INFO General (simplification.cpp : 326) Running Bulge remover 0:00:02.384 12M / 1G INFO General (simplification.cpp : 326) Running Low coverage edge remover 0:00:02.384 12M / 1G INFO General (simplification.cpp : 372) PROCEDURE == Simplification cycle, iteration 9 0:00:02.384 12M / 1G INFO General (simplification.cpp : 326) Running Tip clipper 0:00:02.384 12M / 1G INFO General (simplification.cpp : 326) Running Bulge remover 0:00:02.388 12M / 1G INFO General (simplification.cpp : 326) Running Low coverage edge remover 0:00:02.388 12M / 1G INFO General (simplification.cpp : 372) PROCEDURE == Simplification cycle, iteration 10 0:00:02.388 12M / 1G INFO General (simplification.cpp : 326) Running Tip clipper 0:00:02.388 12M / 1G INFO General (simplification.cpp : 326) Running Bulge remover 0:00:02.392 12M / 1G INFO General (simplification.cpp : 326) Running Low coverage edge remover 0:00:02.392 12M / 1G INFO General (simplification.cpp : 213) PROCEDURE == Post simplification 0:00:02.392 12M / 1G INFO General (graph_simplification.hpp : 707) Creating parallel br instance 0:00:02.392 12M / 1G INFO General (simplification.cpp : 268) Iteration 0 0:00:02.392 12M / 1G INFO General (graph_simplification.hpp : 463) Removal of relatively low covered connections disabled 0:00:02.392 12M / 1G INFO General (graph_simplification.hpp : 480) Disconnection of relatively low covered edges disabled 0:00:02.392 12M / 1G INFO General (graph_simplification.hpp : 536) Complex tip clipping disabled 0:00:02.392 12M / 1G INFO General (simplification.cpp : 326) Running Tip clipper 0:00:02.397 12M / 1G INFO General (simplification.cpp : 326) Running Bulge remover 0:00:02.404 12M / 1G INFO General (simplification.cpp : 296) Disrupting self-conjugate edges 0:00:02.404 12M / 1G INFO StageManager (stage.cpp : 126) STAGE == Simplification Cleanup 0:00:02.404 12M / 1G INFO General (graph_simplification.hpp : 577) Removing isolated edges 0:00:02.404 12M / 1G INFO General (graph_simplification.hpp : 578) All isolated edges shorter than 150 will be removed 0:00:02.404 12M / 1G INFO General (graph_simplification.hpp : 579) Also isolated edges shorter than 0 and coverage smaller than 2 will be removed 0:00:02.408 12M / 1G INFO General (simplification.cpp : 457) Counting average coverage 0:00:02.408 12M / 1G INFO General (simplification.cpp : 462) Average coverage = 225.839 0:00:02.408 12M / 1G INFO StageManager (stage.cpp : 126) STAGE == Contig Output 0:00:02.408 12M / 1G INFO General (contig_output.hpp : 305) Outputting contigs to /home/vagrant/SPAdes-3.8.0-Linux/spades_test//K33/simplified_contigs.fasta 0:00:02.408 12M / 1G INFO General (contig_output.hpp : 305) Outputting contigs to /home/vagrant/SPAdes-3.8.0-Linux/spades_test//K33/before_rr.fasta 0:00:02.408 12M / 1G INFO General (contig_output.hpp : 338) Outputting graph to /home/vagrant/SPAdes-3.8.0-Linux/spades_test//K33/assembly_graph.fastg 0:00:02.409 12M / 1G INFO General (contig_output.hpp : 305) Outputting contigs to /home/vagrant/SPAdes-3.8.0-Linux/spades_test//K33/final_contigs.fasta 0:00:02.409 12M / 1G INFO General (launch.hpp : 117) SPAdes finished 0:00:02.409 12M / 1G INFO General (main.cpp : 106) Assembling time: 0 hours 0 minutes 2 seconds == Running assembler: K55 0:00:00.000 4M / 4M INFO General (main.cpp : 73) Loading config from /home/vagrant/SPAdes-3.8.0-Linux/spades_test/K55/configs/config.info 0:00:00.000 4M / 4M INFO General (main.cpp : 73) Loading config from /home/vagrant/SPAdes-3.8.0-Linux/spades_test/K55/configs/plasmid_mode.info 0:00:00.000 4M / 4M INFO General (memory_limit.hpp : 47) Memory limit set to 2 Gb 0:00:00.000 4M / 4M INFO General (main.cpp : 86) Starting SPAdes, built from refs/heads/spades_3.8.0, git revision bb97112cad669727c57d7b448952b254ce0e4d0c 0:00:00.000 4M / 4M INFO General (main.cpp : 87) Assembling dataset (/home/vagrant/SPAdes-3.8.0-Linux/spades_test/dataset.info) with K=55 0:00:00.000 4M / 4M INFO General (launch.hpp : 29) SPAdes started 0:00:00.000 4M / 4M INFO General (launch.hpp : 36) Starting from stage: construction 0:00:00.000 4M / 4M INFO General (launch.hpp : 39) Two-step RR enabled: 0 0:00:00.001 4M / 4M INFO General (launch.hpp : 58) Will need read mapping, kmer mapper will be attached 0:00:00.001 4M / 4M INFO StageManager (stage.cpp : 126) STAGE == Construction 0:00:00.001 4M / 4M INFO General (construction.cpp : 41) Contigs from previous K will be used 0:00:00.001 4M / 4M INFO General (read_converter.hpp : 49) Binary reads detected 0:00:00.002 4M / 4M INFO General (graph_construction.hpp : 119) Constructing DeBruijn graph for k=55 0:00:00.002 4M / 4M INFO General (kmer_splitters.hpp : 174) Splitting kmer instances into 9 buckets. This might take a while. 0:00:00.002 4M / 4M INFO General (file_limit.hpp : 30) Open file limit set to 65536 0:00:00.002 4M / 4M INFO General (kmer_splitters.hpp : 192) Memory available for splitting buffers: 0.221788 Gb 0:00:00.002 4M / 4M INFO General (kmer_splitters.hpp : 201) Using cell size of 1653772 0:00:00.017 768M / 788M INFO General (kmer_splitters.hpp : 236) Adding contigs from previous K 0:00:00.018 768M / 788M INFO General (kmer_splitters.hpp : 247) Used 8216 reads. Maximum read length 100 0:00:00.018 768M / 788M INFO General (kmer_splitters.hpp : 248) Average read length 86.1526 0:00:00.020 12M / 788M INFO General (kmer_index.hpp : 348) Starting k-mer counting. 0:00:00.025 12M / 788M INFO General (kmer_index.hpp : 354) K-mer counting done. There are 949 kmers in total. 0:00:00.025 12M / 788M INFO General (kmer_index.hpp : 356) Merging temporary buckets. 0:00:00.026 12M / 788M INFO K-mer Index Building (kmer_index.hpp : 470) Building kmer index 0:00:00.026 12M / 788M INFO General (kmer_splitters.hpp : 381) Splitting kmer instances into 48 buckets. This might take a while. 0:00:00.026 12M / 788M INFO General (file_limit.hpp : 30) Open file limit set to 65536 0:00:00.026 12M / 788M INFO General (kmer_splitters.hpp : 399) Memory available for splitting buffers: 0.22092 Gb 0:00:00.026 12M / 788M INFO General (kmer_splitters.hpp : 407) Using cell size of 308868 0:00:00.035 1G / 1G INFO General (kmer_splitters.hpp : 439) Used 949 kmers. 0:00:00.039 12M / 1G INFO General (kmer_index.hpp : 348) Starting k-mer counting. 0:00:00.063 12M / 1G INFO General (kmer_index.hpp : 354) K-mer counting done. There are 951 kmers in total. 0:00:00.063 12M / 1G INFO General (kmer_index.hpp : 356) Merging temporary buckets. 0:00:00.068 12M / 1G INFO K-mer Index Building (kmer_index.hpp : 479) Building perfect hash indices 0:00:00.072 12M / 1G INFO General (kmer_index.hpp : 374) Merging final buckets. 0:00:00.073 12M / 1G INFO K-mer Index Building (kmer_index.hpp : 527) Index built. Total 504 bytes occupied (4.23975 bits per kmer). 0:00:00.073 12M / 1G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 390) Building k-mer extensions from k+1-mers 0:00:00.075 12M / 1G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 394) Building k-mer extensions from k+1-mers finished. 0:00:00.075 12M / 1G INFO General (graph_construction.hpp : 135) Condensing graph 0:00:00.075 12M / 1G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 337) Extracting unbranching paths 0:00:00.077 12M / 1G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 351) Extracting unbranching paths finished. 8 sequences extracted 0:00:00.078 12M / 1G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 311) Collecting perfect loops 0:00:00.078 12M / 1G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 326) Collecting perfect loops finished. 0 loops collected 0:00:00.079 12M / 1G INFO General (graph_construction.hpp : 140) Building index with from graph 0:00:00.079 12M / 1G INFO K-mer Index Building (kmer_index.hpp : 470) Building kmer index 0:00:00.079 12M / 1G INFO General (kmer_splitters.hpp : 291) Splitting kmer instances into 16 buckets. This might take a while. 0:00:00.079 12M / 1G INFO General (file_limit.hpp : 30) Open file limit set to 65536 0:00:00.079 12M / 1G INFO General (kmer_splitters.hpp : 309) Memory available for splitting buffers: 0.66276 Gb 0:00:00.079 12M / 1G INFO General (kmer_splitters.hpp : 314) Using cell size of 2097152 0:00:00.083 588M / 1G INFO General (kmer_splitters.hpp : 332) Used 8 sequences. 0:00:00.084 12M / 1G INFO General (kmer_index.hpp : 348) Starting k-mer counting. 0:00:00.086 12M / 1G INFO General (kmer_index.hpp : 354) K-mer counting done. There are 949 kmers in total. 0:00:00.086 12M / 1G INFO General (kmer_index.hpp : 356) Merging temporary buckets. 0:00:00.087 12M / 1G INFO K-mer Index Building (kmer_index.hpp : 479) Building perfect hash indices 0:00:00.088 12M / 1G INFO General (kmer_index.hpp : 374) Merging final buckets. 0:00:00.089 12M / 1G INFO K-mer Index Building (kmer_index.hpp : 527) Index built. Total 504 bytes occupied (4.24868 bits per kmer). 0:00:00.089 12M / 1G INFO General (edge_index_builders.hpp : 28) Collecting k-mer coverage information from graph, this takes a while. 0:00:00.091 12M / 1G INFO General (edge_index.hpp : 100) Index refilled 0:00:00.092 12M / 1G INFO General (graph_construction.hpp : 172) Filling coverage index 0:00:00.092 12M / 1G INFO General (edge_index_builders.hpp : 106) Collecting k-mer coverage information from reads, this takes a while. 0:00:00.122 12M / 1G INFO General (graph_construction.hpp : 174) Filling coverage and flanking coverage from index 0:00:00.122 12M / 1G INFO General (construction.cpp : 30) Figured out: read length = 100 0:00:00.122 12M / 1G INFO StageManager (stage.cpp : 126) STAGE == EC Threshold Finding 0:00:00.122 12M / 1G INFO General (kmer_coverage_model.cpp : 180) Kmer coverage valley at: 0 0:00:00.122 12M / 1G INFO General (kmer_coverage_model.cpp : 200) K-mer histogram maximum: 6 0:00:00.122 12M / 1G INFO General (kmer_coverage_model.cpp : 236) Estimated median coverage: 6. Coverage mad: 4.4478 0:00:00.122 12M / 1G INFO General (kmer_coverage_model.cpp : 275) Fitting coverage model 0:00:00.132 12M / 1G INFO General (kmer_coverage_model.cpp : 311) ... iteration 2 0:00:00.169 12M / 1G INFO General (kmer_coverage_model.cpp : 311) ... iteration 4 0:00:00.270 12M / 1G INFO General (kmer_coverage_model.cpp : 311) ... iteration 8 0:00:00.410 12M / 1G INFO General (kmer_coverage_model.cpp : 311) ... iteration 16 0:00:00.536 12M / 1G INFO General (kmer_coverage_model.cpp : 325) Fitted mean coverage: 13.7375. Fitted coverage std. dev: 9.60863 0:00:00.537 12M / 1G INFO General (kmer_coverage_model.cpp : 350) Probability of erroneous kmer at valley: 2.02732e-07 0:00:00.537 12M / 1G INFO General (kmer_coverage_model.cpp : 374) Preliminary threshold calculated as: 1 0:00:00.537 12M / 1G INFO General (kmer_coverage_model.cpp : 378) Threshold adjusted to: 1 0:00:00.537 12M / 1G INFO General (kmer_coverage_model.cpp : 391) Estimated genome size (ignoring repeats): 238 0:00:00.537 12M / 1G INFO General (genomic_info_filler.cpp : 133) Mean coverage was calculated as 13.7375 0:00:00.537 12M / 1G INFO General (genomic_info_filler.cpp : 147) EC coverage threshold value was calculated as 1 0:00:00.537 12M / 1G INFO General (genomic_info_filler.cpp : 148) Trusted kmer low bound: 0 0:00:00.537 12M / 1G INFO StageManager (stage.cpp : 126) STAGE == Gap Closer 0:00:00.537 12M / 1G INFO General (gap_closer.cpp : 162) Preparing shift maps 0:00:00.537 12M / 1G INFO General (gap_closer.cpp : 122) Processing paired reads (takes a while) 0:00:00.545 12M / 1G INFO General (gap_closer.cpp : 141) Used 2054 paired reads 0:00:00.545 12M / 1G INFO General (gap_closer.cpp : 143) Merging paired indices 0:00:00.545 12M / 1G INFO GapCloser (gap_closer.cpp : 402) Closing short gaps 0:00:00.545 12M / 1G INFO GapCloser (gap_closer.cpp : 436) Closing short gaps complete: filled 0 gaps after checking 4 candidates 0:00:00.549 12M / 1G INFO StageManager (stage.cpp : 126) STAGE == Simplification 0:00:00.549 12M / 1G INFO General (simplification.cpp : 349) Graph simplification started 0:00:00.549 12M / 1G INFO General (simplification.cpp : 98) PROCEDURE == InitialCleaning 0:00:00.549 12M / 1G INFO General (graph_simplification.hpp : 577) Removing isolated edges 0:00:00.549 12M / 1G INFO General (graph_simplification.hpp : 578) All isolated edges shorter than 100 will be removed 0:00:00.549 12M / 1G INFO General (graph_simplification.hpp : 579) Also isolated edges shorter than 0 and coverage smaller than 0 will be removed 0:00:00.549 12M / 1G INFO General (graph_simplification.hpp : 794) Flanking coverage based disconnection disabled 0:00:00.549 12M / 1G INFO General (simplification.cpp : 326) Running Self conjugate edge remover 0:00:00.553 12M / 1G INFO General (simplification.cpp : 326) Running Initial isolated edge remover 0:00:00.556 12M / 1G INFO General (simplification.cpp : 326) Running Initial tip clipper 0:00:00.557 12M / 1G INFO General (simplification.cpp : 326) Running Initial ec remover 0:00:00.557 12M / 1G INFO General (graph_simplification.hpp : 707) Creating parallel br instance 0:00:00.557 12M / 1G INFO General (simplification.cpp : 372) PROCEDURE == Simplification cycle, iteration 1 0:00:00.557 12M / 1G INFO General (simplification.cpp : 326) Running Tip clipper 0:00:00.557 12M / 1G INFO General (simplification.cpp : 326) Running Bulge remover 0:00:00.557 12M / 1G INFO General (simplification.cpp : 326) Running Low coverage edge remover 0:00:00.557 12M / 1G INFO General (simplification.cpp : 372) PROCEDURE == Simplification cycle, iteration 2 0:00:00.557 12M / 1G INFO General (simplification.cpp : 326) Running Tip clipper 0:00:00.557 12M / 1G INFO General (simplification.cpp : 326) Running Bulge remover 0:00:00.557 12M / 1G INFO General (simplification.cpp : 326) Running Low coverage edge remover 0:00:00.557 12M / 1G INFO General (simplification.cpp : 372) PROCEDURE == Simplification cycle, iteration 3 0:00:00.557 12M / 1G INFO General (simplification.cpp : 326) Running Tip clipper 0:00:00.557 12M / 1G INFO General (simplification.cpp : 326) Running Bulge remover 0:00:00.557 12M / 1G INFO General (simplification.cpp : 326) Running Low coverage edge remover 0:00:00.558 12M / 1G INFO General (simplification.cpp : 372) PROCEDURE == Simplification cycle, iteration 4 0:00:00.558 12M / 1G INFO General (simplification.cpp : 326) Running Tip clipper 0:00:00.558 12M / 1G INFO General (simplification.cpp : 326) Running Bulge remover 0:00:00.558 12M / 1G INFO General (simplification.cpp : 326) Running Low coverage edge remover 0:00:00.558 12M / 1G INFO General (simplification.cpp : 372) PROCEDURE == Simplification cycle, iteration 5 0:00:00.558 12M / 1G INFO General (simplification.cpp : 326) Running Tip clipper 0:00:00.558 12M / 1G INFO General (simplification.cpp : 326) Running Bulge remover 0:00:00.558 12M / 1G INFO General (simplification.cpp : 326) Running Low coverage edge remover 0:00:00.558 12M / 1G INFO General (simplification.cpp : 372) PROCEDURE == Simplification cycle, iteration 6 0:00:00.558 12M / 1G INFO General (simplification.cpp : 326) Running Tip clipper 0:00:00.558 12M / 1G INFO General (simplification.cpp : 326) Running Bulge remover 0:00:00.558 12M / 1G INFO General (simplification.cpp : 326) Running Low coverage edge remover 0:00:00.558 12M / 1G INFO General (simplification.cpp : 372) PROCEDURE == Simplification cycle, iteration 7 0:00:00.558 12M / 1G INFO General (simplification.cpp : 326) Running Tip clipper 0:00:00.558 12M / 1G INFO General (simplification.cpp : 326) Running Bulge remover 0:00:00.558 12M / 1G INFO General (simplification.cpp : 326) Running Low coverage edge remover 0:00:00.558 12M / 1G INFO General (simplification.cpp : 372) PROCEDURE == Simplification cycle, iteration 8 0:00:00.558 12M / 1G INFO General (simplification.cpp : 326) Running Tip clipper 0:00:00.558 12M / 1G INFO General (simplification.cpp : 326) Running Bulge remover 0:00:00.558 12M / 1G INFO General (simplification.cpp : 326) Running Low coverage edge remover 0:00:00.558 12M / 1G INFO General (simplification.cpp : 372) PROCEDURE == Simplification cycle, iteration 9 0:00:00.558 12M / 1G INFO General (simplification.cpp : 326) Running Tip clipper 0:00:00.558 12M / 1G INFO General (simplification.cpp : 326) Running Bulge remover 0:00:00.558 12M / 1G INFO General (simplification.cpp : 326) Running Low coverage edge remover 0:00:00.558 12M / 1G INFO General (simplification.cpp : 372) PROCEDURE == Simplification cycle, iteration 10 0:00:00.558 12M / 1G INFO General (simplification.cpp : 326) Running Tip clipper 0:00:00.558 12M / 1G INFO General (simplification.cpp : 326) Running Bulge remover 0:00:00.558 12M / 1G INFO General (simplification.cpp : 326) Running Low coverage edge remover 0:00:00.558 12M / 1G INFO General (simplification.cpp : 213) PROCEDURE == Post simplification 0:00:00.558 12M / 1G INFO General (graph_simplification.hpp : 707) Creating parallel br instance 0:00:00.558 12M / 1G INFO General (simplification.cpp : 268) Iteration 0 0:00:00.558 12M / 1G INFO General (graph_simplification.hpp : 463) Removal of relatively low covered connections disabled 0:00:00.558 12M / 1G INFO General (graph_simplification.hpp : 480) Disconnection of relatively low covered edges disabled 0:00:00.558 12M / 1G INFO General (graph_simplification.hpp : 536) Complex tip clipping disabled 0:00:00.558 12M / 1G INFO General (simplification.cpp : 326) Running Tip clipper 0:00:00.558 12M / 1G INFO General (simplification.cpp : 326) Running Bulge remover 0:00:00.558 12M / 1G INFO General (simplification.cpp : 296) Disrupting self-conjugate edges 0:00:00.558 12M / 1G INFO StageManager (stage.cpp : 126) STAGE == Gap Closer 0:00:00.558 12M / 1G INFO General (graph_pack.hpp : 93) Index refill 0:00:00.558 12M / 1G INFO K-mer Index Building (kmer_index.hpp : 470) Building kmer index 0:00:00.558 12M / 1G INFO General (kmer_splitters.hpp : 291) Splitting kmer instances into 16 buckets. This might take a while. 0:00:00.558 12M / 1G INFO General (file_limit.hpp : 30) Open file limit set to 65536 0:00:00.558 12M / 1G INFO General (kmer_splitters.hpp : 309) Memory available for splitting buffers: 0.66276 Gb 0:00:00.558 12M / 1G INFO General (kmer_splitters.hpp : 314) Using cell size of 2097152 0:00:00.560 588M / 1G INFO General (kmer_splitters.hpp : 332) Used 2 sequences. 0:00:00.560 12M / 1G INFO General (kmer_index.hpp : 348) Starting k-mer counting. 0:00:00.563 12M / 1G INFO General (kmer_index.hpp : 354) K-mer counting done. There are 945 kmers in total. 0:00:00.563 12M / 1G INFO General (kmer_index.hpp : 356) Merging temporary buckets. 0:00:00.564 12M / 1G INFO K-mer Index Building (kmer_index.hpp : 479) Building perfect hash indices 0:00:00.565 12M / 1G INFO General (kmer_index.hpp : 374) Merging final buckets. 0:00:00.566 12M / 1G INFO K-mer Index Building (kmer_index.hpp : 527) Index built. Total 496 bytes occupied (4.19894 bits per kmer). 0:00:00.566 12M / 1G INFO General (edge_index_builders.hpp : 28) Collecting k-mer coverage information from graph, this takes a while. 0:00:00.568 12M / 1G INFO General (edge_index.hpp : 100) Index refilled 0:00:00.568 12M / 1G INFO General (gap_closer.cpp : 162) Preparing shift maps 0:00:00.568 12M / 1G INFO General (gap_closer.cpp : 122) Processing paired reads (takes a while) 0:00:00.578 12M / 1G INFO General (gap_closer.cpp : 141) Used 2054 paired reads 0:00:00.578 12M / 1G INFO General (gap_closer.cpp : 143) Merging paired indices 0:00:00.578 12M / 1G INFO GapCloser (gap_closer.cpp : 402) Closing short gaps 0:00:00.578 12M / 1G INFO GapCloser (gap_closer.cpp : 436) Closing short gaps complete: filled 0 gaps after checking 0 candidates 0:00:00.581 12M / 1G INFO StageManager (stage.cpp : 126) STAGE == Simplification Cleanup 0:00:00.581 12M / 1G INFO General (graph_simplification.hpp : 577) Removing isolated edges 0:00:00.581 12M / 1G INFO General (graph_simplification.hpp : 578) All isolated edges shorter than 150 will be removed 0:00:00.581 12M / 1G INFO General (graph_simplification.hpp : 579) Also isolated edges shorter than 0 and coverage smaller than 2 will be removed 0:00:00.585 12M / 1G INFO General (simplification.cpp : 457) Counting average coverage 0:00:00.585 12M / 1G INFO General (simplification.cpp : 462) Average coverage = 140.62 0:00:00.585 12M / 1G INFO StageManager (stage.cpp : 126) STAGE == Mismatch Correction 0:00:00.585 12M / 1G INFO General (graph_pack.hpp : 102) Normalizing k-mer map. Total 0 kmers to process 0:00:00.585 12M / 1G INFO General (graph_pack.hpp : 104) Normalizing done 0:00:00.611 12M / 1G INFO General (mismatch_shall_not_pass.hp: 192) Finished collecting potential mismatches positions 0:00:00.611 12M / 1G INFO General (mismatch_shall_not_pass.hp: 296) All edges processed 0:00:00.611 12M / 1G INFO General (mismatch_correction.cpp : 24) Corrected 0 nucleotides 0:00:00.611 12M / 1G INFO StageManager (stage.cpp : 126) STAGE == Chromosome Removal 0:00:00.611 12M / 1G INFO General (contig_output.hpp : 305) Outputting contigs to /home/vagrant/SPAdes-3.8.0-Linux/spades_test//K55/before_chromosome_removal.fasta 0:00:00.611 12M / 1G INFO General (chromosome_removal.cpp : 168) Before iteration 0, 4 vertices in graph 0:00:00.611 12M / 1G INFO General (chromosome_removal.cpp : 92) Removing of long chromosomal edges started 0:00:00.611 12M / 1G WARN General (chromosome_removal.cpp : 105) plasmid detection failed, not enough long edges 0:00:00.611 12M / 1G INFO General (chromosome_removal.cpp : 176) Before iteration 1 4 vertices in graph 0:00:00.611 12M / 1G INFO General (chromosome_removal.cpp : 92) Removing of long chromosomal edges started 0:00:00.611 12M / 1G WARN General (chromosome_removal.cpp : 105) plasmid detection failed, not enough long edges 0:00:00.611 12M / 1G INFO General (chromosome_removal.cpp : 178) Before dead_end simplification 0 4 vertices in graph 0:00:00.611 12M / 1G INFO General (chromosome_removal.cpp : 183) Iteration 0 graph was not changed 0:00:00.611 12M / 1G INFO General (chromosome_removal.cpp : 184) 4 vertices left 0:00:00.612 12M / 1G INFO General (chromosome_removal.cpp : 232) Iteration 1 of small components additional filtering graph was not changed 0:00:00.612 12M / 1G INFO General (chromosome_removal.cpp : 233) After plasmidSPAdes subroutine 0 vertices left 0:00:00.612 12M / 1G INFO General (chromosome_removal.cpp : 237) Counting average coverage after genomic edge removal 0:00:00.612 12M / 1G INFO General (chromosome_removal.cpp : 240) Average coverage = 0 0:00:00.612 12M / 1G INFO StageManager (stage.cpp : 126) STAGE == Paired Information Counting 0:00:00.612 12M / 1G INFO General (graph_pack.hpp : 102) Normalizing k-mer map. Total 0 kmers to process 0:00:00.612 12M / 1G INFO General (graph_pack.hpp : 104) Normalizing done 0:00:00.612 12M / 1G INFO General (pair_info_count.cpp : 173) Min edge length for estimation: 0 0:00:00.612 12M / 1G INFO General (pair_info_count.cpp : 187) Estimating insert size for library #0 0:00:00.612 12M / 1G INFO General (pair_info_count.cpp : 24) Estimating insert size (takes a while) 0:00:00.612 12M / 1G INFO General (short_read_mapper.hpp : 93) Selecting usual mapper 0:00:00.642 12M / 1G INFO General (sequence_mapper_notifier.h: 91) Total 0 reads processed 0:00:00.642 12M / 1G INFO General (pair_info_count.cpp : 36) 0 paired reads (0% of all) aligned to long edges 0:00:00.642 12M / 1G WARN General (pair_info_count.cpp : 195) Unable to estimate insert size for paired library #0 0:00:00.642 12M / 1G WARN General (pair_info_count.cpp : 201) None of paired reads aligned properly. Please, check orientation of your read pairs. 0:00:00.642 12M / 1G INFO General (pair_info_count.cpp : 231) Mapping library #0 0:00:00.642 12M / 1G INFO General (pair_info_count.cpp : 246) Mapping single reads (takes a while) 0:00:00.642 12M / 1G INFO General (short_read_mapper.hpp : 93) Selecting usual mapper 0:00:00.663 12M / 1G INFO General (sequence_mapper_notifier.h: 91) Total 0 reads processed 0:00:00.663 12M / 1G INFO General (pair_info_count.cpp : 251) Total paths obtained from single reads: 0 0:00:00.663 12M / 1G INFO StageManager (stage.cpp : 126) STAGE == Distance Estimation 0:00:00.663 12M / 1G INFO StageManager (stage.cpp : 126) STAGE == Repeat Resolving 0:00:00.663 12M / 1G INFO General (contig_output.hpp : 305) Outputting contigs to /home/vagrant/SPAdes-3.8.0-Linux/spades_test//K55/before_rr.fasta 0:00:00.663 12M / 1G INFO General (contig_output.hpp : 338) Outputting graph to /home/vagrant/SPAdes-3.8.0-Linux/spades_test//K55/assembly_graph.fastg 0:00:00.663 12M / 1G INFO General (repeat_resolving.cpp : 72) Using Path-Extend repeat resolving 0:00:00.663 12M / 1G INFO General (path_extend_launch.hpp : 793) ExSPAnder repeat resolving tool started 0:00:00.663 12M / 1G INFO General (path_extend_launch.hpp : 825) SUBSTAGE = paired-end libraries 0:00:00.663 12M / 1G INFO General (path_extend_launch.hpp : 330) resolvable_repeat_length_bound set to 10000 0:00:00.663 12M / 1G INFO General (path_extend_launch.hpp : 613) Using 0 paired-end libraries 0:00:00.663 12M / 1G INFO General (path_extend_launch.hpp : 614) Using 0 paired-end scaffolding libraries 0:00:00.663 12M / 1G INFO General (path_extend_launch.hpp : 615) Using 0 mate-pair libraries 0:00:00.663 12M / 1G INFO General (path_extend_launch.hpp : 616) Using 1 single read library 0:00:00.663 12M / 1G INFO General (path_extend_launch.hpp : 617) Scaffolder is on 0:00:00.664 12M / 1G INFO General (path_extend_launch.hpp : 843) Growing paths using paired-end and long single reads 0:00:00.664 12M / 1G INFO General (path_extend_launch.hpp : 330) resolvable_repeat_length_bound set to 10000 0:00:00.664 12M / 1G INFO General (path_extend_launch.hpp : 613) Using 0 paired-end libraries 0:00:00.664 12M / 1G INFO General (path_extend_launch.hpp : 614) Using 0 paired-end scaffolding libraries 0:00:00.664 12M / 1G INFO General (path_extend_launch.hpp : 615) Using 0 mate-pair libraries 0:00:00.664 12M / 1G INFO General (path_extend_launch.hpp : 616) Using 1 single read library 0:00:00.664 12M / 1G INFO General (path_extend_launch.hpp : 617) Scaffolder is on 0:00:00.664 12M / 1G INFO PathExtendIO (pe_io.hpp : 187) Writing contigs to /home/vagrant/SPAdes-3.8.0-Linux/spades_test//K55/final_contigs 0:00:00.664 12M / 1G INFO General (path_extend_launch.hpp : 217) Traversing tandem repeats 0:00:00.664 12M / 1G INFO PathExtendIO (pe_io.hpp : 187) Writing contigs to /home/vagrant/SPAdes-3.8.0-Linux/spades_test//K55/scaffolds 0:00:00.664 12M / 1G INFO General (launch.hpp : 117) SPAdes finished 0:00:00.664 12M / 1G INFO General (main.cpp : 106) Assembling time: 0 hours 0 minutes 0 seconds ===== Assembling finished. * Corrected reads are in /home/vagrant/SPAdes-3.8.0-Linux/spades_test/corrected/ * Assembled contigs are in /home/vagrant/SPAdes-3.8.0-Linux/spades_test/contigs.fasta * Assembled scaffolds are in /home/vagrant/SPAdes-3.8.0-Linux/spades_test/scaffolds.fasta * Assembly graph is in /home/vagrant/SPAdes-3.8.0-Linux/spades_test/assembly_graph.fastg * Paths in the assembly graph corresponding to the contigs are in /home/vagrant/SPAdes-3.8.0-Linux/spades_test/contigs.paths * Paths in the assembly graph corresponding to the scaffolds are in /home/vagrant/SPAdes-3.8.0-Linux/spades_test/scaffolds.paths ======= SPAdes pipeline finished WITH WARNINGS! === Error correction and assembling warnings: * 0:00:00.611 12M / 1G WARN General (chromosome_removal.cpp : 105) plasmid detection failed, not enough long edges * 0:00:00.642 12M / 1G WARN General (pair_info_count.cpp : 195) Unable to estimate insert size for paired library #0 * 0:00:00.642 12M / 1G WARN General (pair_info_count.cpp : 201) None of paired reads aligned properly. Please, check orientation of your read pairs. ======= Warnings saved to /home/vagrant/SPAdes-3.8.0-Linux/spades_test/warnings.log