Command line: --diploid --pe1-1 /N/dc2/projects/marinovg/Paramecium/variation/data/P.biaurelia-Sample_USBL-36I1/reads.end1.paired.fastq.gz --pe1-2 /N/dc2/projects/marinovg/Paramecium/variation/data/P.biaurelia-Sample_USBL-36I1/reads.end2.paired.fastq.gz -t 16 -o /N/dc2/projects/marinovg/2015-09-07-assemblies/P.biaurelia-Sample_USBL-36I1-dipSPAdes-3.5.0-trimmed/spades System information: SPAdes version: 3.5.0 Python version: 2.6.6 OS: Linux-2.6.32-573.3.1.el6.x86_64-x86_64-with-redhat-6.7-Santiago Output dir: /N/dc2/projects/marinovg/2015-09-07-assemblies/P.biaurelia-Sample_USBL-36I1-dipSPAdes-3.5.0-trimmed/spades 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 Reads: Library number: 1, library type: paired-end orientation: fr left reads: ['/N/dc2/projects/marinovg/Paramecium/variation/data/P.biaurelia-Sample_USBL-36I1/reads.end1.paired.fastq.gz'] right reads: ['/N/dc2/projects/marinovg/Paramecium/variation/data/P.biaurelia-Sample_USBL-36I1/reads.end2.paired.fastq.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 Mismatch careful mode is turned OFF Repeat resolution is enabled MismatchCorrector will be SKIPPED Coverage cutoff is turned OFF Other parameters: Dir for temp files: /N/dc2/projects/marinovg/2015-09-07-assemblies/P.biaurelia-Sample_USBL-36I1-dipSPAdes-3.5.0-trimmed/spades/tmp Threads: 16 Memory limit (in Gb): 250 ======= SPAdes pipeline started. Log can be found here: /N/dc2/projects/marinovg/2015-09-07-assemblies/P.biaurelia-Sample_USBL-36I1-dipSPAdes-3.5.0-trimmed/spades/spades.log ===== Read error correction started. == Running read error correction tool: /N/dc2/projects/marinovg/programs/SPAdes-3.5.0-Linux/bin/hammer /N/dc2/projects/marinovg/2015-09-07-assemblies/P.biaurelia-Sample_USBL-36I1-dipSPAdes-3.5.0-trimmed/spades/corrected/configs/config.info 0:00:00.000 4M / 4M INFO General (main.cpp : 82) Loading config from /N/dc2/projects/marinovg/2015-09-07-assemblies/P.biaurelia-Sample_USBL-36I1-dipSPAdes-3.5.0-trimmed/spades/corrected/configs/config.info 0:00:00.005 4M / 4M INFO General (memory_limit.hpp : 42) Memory limit set to 100 Gb 0:00:00.005 4M / 4M INFO General (main.cpp : 91) Trying to determine PHRED offset 0:00:00.041 4M / 4M INFO General (main.cpp : 97) Determined value is 33 0:00:00.041 4M / 4M INFO General (hammer_tools.cpp : 36) Hamming graph threshold tau=1, k=21, subkmer positions = [ 0 10 ] === ITERATION 0 begins === 0:00:00.043 4M / 4M INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:00:00.043 4M / 4M INFO K-mer Splitting (kmer_data.cpp : 127) Splitting kmer instances into 256 buckets. This might take a while. 0:00:00.043 4M / 4M INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:00:00.044 4M / 4M INFO K-mer Splitting (kmer_data.cpp : 145) Memory available for splitting buffers: 2.08325 Gb 0:00:00.044 4M / 4M INFO K-mer Splitting (kmer_data.cpp : 153) Using cell size of 262144 0:00:02.819 8G / 8G INFO K-mer Splitting (kmer_data.cpp : 167) Processing /N/dc2/projects/marinovg/Paramecium/variation/data/P.biaurelia-Sample_USBL-36I1/reads.end1.paired.fastq.gz 0:12:19.774 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 176) Processed 3209893 reads 0:23:05.945 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 176) Processed 6490938 reads 0:33:08.415 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 176) Processed 9305334 reads 0:33:08.417 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 167) Processing /N/dc2/projects/marinovg/Paramecium/variation/data/P.biaurelia-Sample_USBL-36I1/reads.end2.paired.fastq.gz 0:46:48.876 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 176) Processed 12879699 reads 1:00:09.861 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 176) Processed 16384990 reads 1:10:38.600 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 176) Processed 18610668 reads 1:10:38.601 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 181) Processed 18610668 reads 1:10:39.713 64M / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 1:15:18.281 64M / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 281932360 kmers in total. 1:15:18.282 64M / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 1:16:13.191 64M / 9G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 1:17:05.373 192M / 9G INFO General (kmer_index.hpp : 371) Merging final buckets. 1:17:19.853 192M / 9G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 97531009 bytes occupied (2.7675 bits per kmer). 1:17:19.855 192M / 9G INFO K-mer Counting (kmer_data.cpp : 266) Arranging kmers in hash map order 1:20:30.836 192M / 9G INFO K-mer Counting (kmer_data.cpp : 279) Done. Total swaps: 281932053 1:20:33.155 2G / 9G INFO General (main.cpp : 151) Clustering Hamming graph. 1:20:33.156 2G / 9G INFO Hamming Clustering (hamcluster.cpp : 115) Serializing sub-kmers. 1:20:33.156 2G / 9G INFO Hamming Clustering (hamcluster.cpp : 120) Serializing: [0, 10) 1:24:02.209 2G / 9G INFO Hamming Clustering (hamcluster.cpp : 120) Serializing: [10, 21) 1:27:12.428 2G / 9G INFO Hamming Clustering (hamcluster.cpp : 129) Splitting sub-kmers, pass 1. 1:31:31.006 2G / 9G INFO Hamming Clustering (hamcluster.cpp : 134) Splitting done. Processed 2 blocks. Produced 4895699 blocks. 1:31:31.007 2G / 9G INFO Hamming Clustering (hamcluster.cpp : 145) Merge sub-kmers, pass 1 1:47:39.196 2G / 9G INFO Hamming Clustering (hamcluster.cpp : 170) Merge done, total 1527195 new blocks generated. 1:47:40.943 2G / 9G INFO Hamming Clustering (hamcluster.cpp : 175) Spliting sub-kmers, pass 2. 2:13:17.120 2G / 9G INFO Hamming Clustering (hamcluster.cpp : 180) Splitting done. Processed 3054390 blocks. Produced 540983781 blocks. 2:13:17.120 2G / 9G INFO Hamming Clustering (hamcluster.cpp : 187) Merge sub-kmers, pass 2 2:25:18.268 2G / 9G INFO Hamming Clustering (hamcluster.cpp : 205) Merge done, saw 221718 big blocks out of 540983781 processed. 2:30:50.143 2G / 9G INFO General (main.cpp : 165) Clustering done. Total clusters: 140755312 2:30:50.143 2G / 9G INFO K-mer Counting (kmer_data.cpp : 284) Collecting K-mer information, this takes a while. 2:30:58.102 14G / 14G INFO K-mer Counting (kmer_data.cpp : 290) Processing /N/dc2/projects/marinovg/Paramecium/variation/data/P.biaurelia-Sample_USBL-36I1/reads.end1.paired.fastq.gz 2:33:35.110 14G / 14G INFO K-mer Counting (kmer_data.cpp : 290) Processing /N/dc2/projects/marinovg/Paramecium/variation/data/P.biaurelia-Sample_USBL-36I1/reads.end2.paired.fastq.gz 2:36:08.796 14G / 14G INFO K-mer Counting (kmer_data.cpp : 297) Collection done, postprocessing. 2:36:18.777 14G / 14G INFO K-mer Counting (kmer_data.cpp : 310) There are 281932360 kmers in total. Among them 121497424 (43.0945%) are singletons. 2:36:18.777 14G / 14G INFO General (main.cpp : 203) Subclustering Hamming graph 2:39:57.586 14G / 14G INFO Hamming Subclustering (kmer_cluster.cpp : 626) Subclustering done. Total 85329 non-read kmers were generated. 2:39:57.586 14G / 14G INFO Hamming Subclustering (kmer_cluster.cpp : 627) Subclustering statistics: 2:39:57.586 14G / 14G INFO Hamming Subclustering (kmer_cluster.cpp : 628) Total singleton hamming clusters: 86558393. Among them 69744126 (80.5747%) are good 2:39:57.586 14G / 14G INFO Hamming Subclustering (kmer_cluster.cpp : 629) Total singleton subclusters: 11162287. Among them 11162221 (99.9994%) are good 2:39:57.586 14G / 14G INFO Hamming Subclustering (kmer_cluster.cpp : 630) Total non-singleton subcluster centers: 57864066. Among them 37226065 (64.3336%) are good 2:39:57.586 14G / 14G INFO Hamming Subclustering (kmer_cluster.cpp : 631) Average size of non-trivial subcluster: 3.32406 kmers 2:39:57.586 14G / 14G INFO Hamming Subclustering (kmer_cluster.cpp : 632) Average number of sub-clusters per non-singleton cluster: 1.27362 2:39:57.586 14G / 14G INFO Hamming Subclustering (kmer_cluster.cpp : 633) Total solid k-mers: 118132412 2:39:57.586 14G / 14G INFO Hamming Subclustering (kmer_cluster.cpp : 634) Substitution probabilities: [4,4]((0.896399,0.0235533,0.0262219,0.053826),(0.0359887,0.925487,0.0133631,0.0251611),(0.0239445,0.0129916,0.926798,0.0362659),(0.0532021,0.0265416,0.0238921,0.896364)) 2:39:58.075 14G / 14G INFO General (main.cpp : 208) Finished clustering. 2:39:58.075 14G / 14G INFO General (main.cpp : 228) Starting solid k-mers expansion in 16 threads. 2:43:05.886 14G / 14G INFO General (main.cpp : 249) Solid k-mers iteration 0 produced 44293782 new k-mers. 2:46:12.787 14G / 14G INFO General (main.cpp : 249) Solid k-mers iteration 1 produced 1330444 new k-mers. 2:49:19.683 14G / 14G INFO General (main.cpp : 249) Solid k-mers iteration 2 produced 87571 new k-mers. 2:52:26.459 14G / 14G INFO General (main.cpp : 249) Solid k-mers iteration 3 produced 13108 new k-mers. 2:55:33.144 14G / 14G INFO General (main.cpp : 249) Solid k-mers iteration 4 produced 2998 new k-mers. 2:58:39.861 14G / 14G INFO General (main.cpp : 249) Solid k-mers iteration 5 produced 363 new k-mers. 3:01:46.619 14G / 14G INFO General (main.cpp : 249) Solid k-mers iteration 6 produced 34 new k-mers. 3:04:53.387 14G / 14G INFO General (main.cpp : 249) Solid k-mers iteration 7 produced 0 new k-mers. 3:04:53.388 14G / 14G INFO General (main.cpp : 253) Solid k-mers finalized 3:04:53.388 14G / 14G INFO General (hammer_tools.cpp : 210) Starting read correction in 16 threads. 3:04:53.389 14G / 14G INFO General (hammer_tools.cpp : 222) Correcting pair of reads: /N/dc2/projects/marinovg/Paramecium/variation/data/P.biaurelia-Sample_USBL-36I1/reads.end1.paired.fastq.gz and /N/dc2/projects/marinovg/Paramecium/variation/data/P.biaurelia-Sample_USBL-36I1/reads.end2.paired.fastq.gz 3:05:19.097 16G / 16G INFO General (hammer_tools.cpp : 166) Prepared batch 0 of 1600000 reads. 3:05:41.358 16G / 16G INFO General (hammer_tools.cpp : 175) Processed batch 0 3:05:58.200 16G / 16G INFO General (hammer_tools.cpp : 185) Written batch 0 3:06:22.090 16G / 16G INFO General (hammer_tools.cpp : 166) Prepared batch 1 of 1600000 reads. 3:06:44.205 16G / 16G INFO General (hammer_tools.cpp : 175) Processed batch 1 3:07:01.002 16G / 16G INFO General (hammer_tools.cpp : 185) Written batch 1 3:07:24.608 16G / 16G INFO General (hammer_tools.cpp : 166) Prepared batch 2 of 1600000 reads. 3:07:46.803 16G / 16G INFO General (hammer_tools.cpp : 175) Processed batch 2 3:08:03.646 16G / 16G INFO General (hammer_tools.cpp : 185) Written batch 2 3:08:27.094 16G / 16G INFO General (hammer_tools.cpp : 166) Prepared batch 3 of 1600000 reads. 3:08:49.629 16G / 16G INFO General (hammer_tools.cpp : 175) Processed batch 3 3:09:06.502 16G / 16G INFO General (hammer_tools.cpp : 185) Written batch 3 3:09:29.786 16G / 16G INFO General (hammer_tools.cpp : 166) Prepared batch 4 of 1600000 reads. 3:09:52.254 16G / 16G INFO General (hammer_tools.cpp : 175) Processed batch 4 3:10:09.165 16G / 16G INFO General (hammer_tools.cpp : 185) Written batch 4 3:10:27.942 16G / 16G INFO General (hammer_tools.cpp : 166) Prepared batch 5 of 1305334 reads. 3:10:46.342 16G / 16G INFO General (hammer_tools.cpp : 175) Processed batch 5 3:11:00.112 16G / 16G INFO General (hammer_tools.cpp : 185) Written batch 5 3:11:03.497 14G / 16G INFO General (hammer_tools.cpp : 269) Correction done. Changed 3543839 bases in 2778145 reads. 3:11:03.497 14G / 16G INFO General (hammer_tools.cpp : 270) Failed to correct 350583111 bases out of 2767597560. 3:11:03.608 2G / 16G INFO General (main.cpp : 286) Saving corrected dataset description to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.biaurelia-Sample_USBL-36I1-dipSPAdes-3.5.0-trimmed/spades/corrected/corrected.yaml 3:11:03.611 2G / 16G INFO General (main.cpp : 293) All done. Exiting. == Compressing corrected reads (with gzip) == Dataset description file was created: /N/dc2/projects/marinovg/2015-09-07-assemblies/P.biaurelia-Sample_USBL-36I1-dipSPAdes-3.5.0-trimmed/spades/corrected/corrected.yaml ===== Read error correction finished. ===== Assembling started. == Running assembler: K21 0:00:00.000 4M / 4M INFO General (memory_limit.hpp : 42) Memory limit set to 100 Gb 0:00:00.001 4M / 4M INFO General (main.cpp : 146) Assembling dataset (/N/dc2/projects/marinovg/2015-09-07-assemblies/P.biaurelia-Sample_USBL-36I1-dipSPAdes-3.5.0-trimmed/spades/dataset.info) with K=21 0:00:00.001 4M / 4M INFO General (launch.hpp : 28) SPAdes started 0:00:00.001 4M / 4M INFO General (launch.hpp : 29) Starting from stage: construction 0:00:00.003 4M / 4M INFO StageManager (stage.cpp : 125) STAGE == Construction 0:00:00.006 4M / 4M INFO General (read_converter.hpp : 79) Converting reads to binary format (takes a while) 0:00:00.006 4M / 4M INFO General (read_converter.hpp : 81) Paired reads for library #0 0:00:01.145 80M / 80M INFO General (binary_converter.hpp : 138) 16384 reads processed 0:00:01.552 96M / 96M INFO General (binary_converter.hpp : 138) 32768 reads processed 0:00:02.357 124M / 124M INFO General (binary_converter.hpp : 138) 65536 reads processed 0:00:03.977 184M / 184M INFO General (binary_converter.hpp : 138) 131072 reads processed 0:00:07.210 300M / 300M INFO General (binary_converter.hpp : 138) 262144 reads processed 0:00:13.697 536M / 536M INFO General (binary_converter.hpp : 138) 524288 reads processed 0:00:49.752 900M / 900M INFO General (binary_converter.hpp : 138) 1048576 reads processed 0:01:19.009 904M / 904M INFO General (binary_converter.hpp : 138) 2097152 reads processed 0:02:17.960 904M / 904M INFO General (binary_converter.hpp : 138) 4194304 reads processed 0:04:19.279 908M / 908M INFO General (binary_converter.hpp : 138) 8388608 reads processed 0:04:42.635 844M / 908M INFO General (binary_converter.hpp : 158) 9197097 reads written 0:04:44.747 4M / 908M INFO General (read_converter.hpp : 91) Single reads for library #0 0:04:46.622 140M / 908M INFO General (binary_converter.hpp : 138) 16384 reads processed 0:04:46.832 144M / 908M INFO General (binary_converter.hpp : 138) 32768 reads processed 0:04:47.221 160M / 908M INFO General (binary_converter.hpp : 138) 65536 reads processed 0:04:47.980 180M / 908M INFO General (binary_converter.hpp : 158) 108109 reads written 0:04:48.153 4M / 908M INFO General (graph_construction.hpp : 129) Constructing DeBruijn graph for k=21 0:04:48.156 4M / 908M INFO General (kmer_splitters.hpp : 172) Splitting kmer instances into 256 buckets. This might take a while. 0:04:48.157 4M / 908M INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:04:48.157 4M / 908M INFO General (kmer_splitters.hpp : 190) Memory available for splitting buffers: 2.08325 Gb 0:04:48.157 4M / 908M INFO General (kmer_splitters.hpp : 199) Using cell size of 262144 0:12:43.861 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 16713602 reads 0:19:52.862 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 33408833 reads 0:24:49.110 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 37004606 reads 0:24:49.110 8G / 9G INFO General (kmer_splitters.hpp : 234) Adding contigs from previous K 0:24:49.110 8G / 9G INFO General (kmer_splitters.hpp : 245) Used 37004606 reads. Maximum read length 151 0:24:49.110 8G / 9G INFO General (kmer_splitters.hpp : 246) Average read length 149.538 0:24:51.341 64M / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:29:20.274 64M / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 121147361 kmers in total. 0:29:20.274 64M / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:31:16.339 64M / 9G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:31:16.340 64M / 9G INFO General (kmer_splitters.hpp : 379) Splitting kmer instances into 256 buckets. This might take a while. 0:31:16.340 64M / 9G INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:31:16.340 64M / 9G INFO General (kmer_splitters.hpp : 397) Memory available for splitting buffers: 2.08203 Gb 0:31:16.340 64M / 9G INFO General (kmer_splitters.hpp : 405) Using cell size of 262144 0:40:15.822 8G / 9G INFO General (kmer_splitters.hpp : 428) Processed 121147361 kmers 0:40:15.823 8G / 9G INFO General (kmer_splitters.hpp : 437) Used 121147361 kmers. 0:40:16.398 64M / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:45:20.745 64M / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 118242511 kmers in total. 0:45:20.745 64M / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:45:53.761 64M / 9G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:46:14.521 68M / 9G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:46:19.369 68M / 9G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 40904544 bytes occupied (2.7675 bits per kmer). 0:46:19.570 184M / 9G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 382) Building k-mer extensions from k+1-mers 0:46:32.015 184M / 9G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 386) Building k-mer extensions from k+1-mers finished. 0:46:32.021 184M / 9G INFO Early tip clipping (early_simplification.hpp : 236) Early tip clipping 0:52:39.273 180M / 9G INFO Early tip clipping (early_simplification.hpp : 239) 5932571 22-mers were removed by early tip clipper 0:52:39.274 180M / 9G INFO General (graph_construction.hpp : 145) Condensing graph 0:52:39.274 180M / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 337) Extracting unbranching paths 0:54:03.287 1G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 351) Extracting unbranching paths finished. 15497735 sequences extracted 0:54:13.341 1G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 311) Collecting perfect loops 0:54:49.895 1G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 326) Collecting perfect loops finished. 24 loops collected 0:55:01.866 3G / 9G INFO General (graph_construction.hpp : 150) Building index with from graph 0:55:01.867 3G / 9G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:55:01.867 3G / 9G INFO General (kmer_splitters.hpp : 289) Splitting kmer instances into 16 buckets. This might take a while. 0:55:01.867 3G / 9G INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:55:01.867 3G / 9G INFO General (kmer_splitters.hpp : 307) Memory available for splitting buffers: 32.3086 Gb 0:55:01.867 3G / 9G INFO General (kmer_splitters.hpp : 312) Using cell size of 4194304 0:57:39.576 3G / 9G INFO General (kmer_splitters.hpp : 325) Processed 9030692 edges 1:01:15.600 3G / 9G INFO General (kmer_splitters.hpp : 325) Processed 15497759 edges 1:01:15.601 3G / 9G INFO General (kmer_splitters.hpp : 330) Used 15497759 sequences. 1:01:15.660 3G / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 1:03:03.687 3G / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 115214790 kmers in total. 1:03:03.687 3G / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 1:03:09.813 3G / 9G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 1:06:57.292 3G / 9G INFO General (kmer_index.hpp : 371) Merging final buckets. 1:07:23.411 3G / 9G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 39857150 bytes occupied (2.7675 bits per kmer). 1:07:26.029 5G / 9G INFO General (edge_index_builders.hpp : 21) Collecting k-mer coverage information from graph, this takes a while. 1:11:53.950 5G / 9G INFO General (graph_construction.hpp : 182) Filling coverage index 1:11:53.951 5G / 9G INFO General (edge_index_builders.hpp : 99) Collecting k-mer coverage information from reads, this takes a while. 1:14:52.614 5G / 9G INFO General (graph_construction.hpp : 184) Filling coverage and flanking coverage from index 1:15:30.097 5G / 9G INFO General (construction.cpp : 33) Figured out: read length = 151 1:15:30.114 5G / 9G INFO StageManager (stage.cpp : 125) STAGE == EC Threshold Finding 1:15:39.635 5G / 9G INFO General (kmer_coverage_model.cpp : 178) Kmer coverage valley at: 12 1:15:39.636 5G / 9G INFO General (kmer_coverage_model.cpp : 198) K-mer histogram maximum: 31 1:15:39.636 5G / 9G INFO General (kmer_coverage_model.cpp : 234) Estimated median coverage: 32. Coverage mad: 8.8956 1:15:39.636 5G / 9G INFO General (kmer_coverage_model.cpp : 261) Fitting coverage model 1:15:39.758 5G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 2 1:15:40.060 5G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 4 1:15:41.113 5G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 8 1:15:42.835 5G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 16 1:15:43.227 5G / 9G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 32.1497. Fitted coverage std. dev: 7.10489 1:15:43.230 5G / 9G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 0.650742 1:15:43.230 5G / 9G INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 22 1:15:43.230 5G / 9G INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 22 1:15:43.230 5G / 9G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 61188588 1:15:43.230 5G / 9G INFO General (genomic_info_filler.cpp : 103) Mean coverage was calculated as 32.1497 1:15:43.231 5G / 9G INFO General (genomic_info_filler.cpp : 117) EC coverage threshold value was calculated as 22 1:15:43.231 5G / 9G INFO General (genomic_info_filler.cpp : 118) Trusted kmer low bound: 0 1:15:43.231 5G / 9G INFO StageManager (stage.cpp : 125) STAGE == Simplification 1:15:43.473 2G / 9G INFO General (graph_simplification.hpp : 911) Graph simplification started 1:15:43.473 2G / 9G INFO General (graph_simplification.hpp : 924) Fast simplification mode enabled 1:15:43.473 2G / 9G INFO General (graph_simplification.hpp : 771) PROCEDURE == Presimplification 1:15:43.473 2G / 9G INFO General (graph_simplification.hpp : 211) Removing short low covered self-conjugate connections 1:15:44.586 2G / 9G INFO General (graph_simplification.hpp : 403) Removing isolated edges 1:15:44.589 2G / 9G INFO General (graph_simplification.hpp : 404) All edges shorter than 151 will be removed 1:15:44.589 2G / 9G INFO General (graph_simplification.hpp : 405) Also edges shorter than 0 and coverage smaller than 0 will be removed 1:15:46.117 2G / 9G INFO General (graph_simplification.hpp : 687) Non parallel mode 1:16:45.877 3G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 1:19:03.154 3G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 1:22:33.944 3G / 9G INFO General (graph_simplification.hpp : 644) Using permanent iterators 1:22:33.944 3G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 1 1:22:48.908 3G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 1:23:49.138 3G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 1:24:12.280 3G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 2 1:24:12.280 3G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 1:24:12.808 3G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 1:24:32.960 3G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 3 1:24:32.960 3G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 1:24:33.371 3G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 1:24:40.961 3G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 4 1:24:40.961 3G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 1:24:41.129 3G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 1:24:45.481 3G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 5 1:24:45.481 3G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 1:24:45.580 3G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 1:24:49.491 3G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 6 1:24:49.491 3G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 1:24:49.579 3G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 1:24:52.752 3G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 7 1:24:52.752 3G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 1:24:52.821 3G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 1:24:55.550 3G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 8 1:24:55.550 3G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 1:24:55.611 3G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 1:24:57.948 3G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 9 1:24:57.948 3G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 1:24:58.003 3G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 1:25:00.413 3G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 10 1:25:00.413 3G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 1:25:00.472 3G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 1:25:03.906 3G / 9G INFO General (graph_simplification.hpp : 796) PROCEDURE == Post simplification 1:25:03.906 3G / 9G INFO General (graph_simplification.hpp : 644) Using permanent iterators 1:25:03.906 3G / 9G INFO General (graph_simplification.hpp : 806) Iteration 0 1:25:03.907 3G / 9G INFO General (graph_simplification.hpp : 247) Removal of relatively low covered connections disabled 1:25:10.271 3G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 1:25:24.383 3G / 9G INFO General (graph_simplification.hpp : 806) Iteration 1 1:25:24.383 3G / 9G INFO General (graph_simplification.hpp : 247) Removal of relatively low covered connections disabled 1:25:24.383 3G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 1:25:28.537 3G / 9G INFO StageManager (stage.cpp : 125) STAGE == Simplification Cleanup 1:25:28.538 3G / 9G INFO General (graph_simplification.hpp : 403) Removing isolated edges 1:25:28.538 3G / 9G INFO General (graph_simplification.hpp : 404) All edges shorter than 151 will be removed 1:25:28.538 3G / 9G INFO General (graph_simplification.hpp : 405) Also edges shorter than 0 and coverage smaller than 2 will be removed 1:25:28.868 3G / 9G INFO General (simplification.cpp : 56) Removing all the edges having coverage 0 and less 1:25:40.179 3G / 9G INFO General (simplification.cpp : 68) Counting average coverage 1:25:41.523 3G / 9G INFO General (simplification.cpp : 71) Average coverage = 32.9242 1:25:41.523 3G / 9G INFO StageManager (stage.cpp : 125) STAGE == Contig Output 1:25:41.523 3G / 9G INFO General (contig_output.hpp : 283) Outputting contigs to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.biaurelia-Sample_USBL-36I1-dipSPAdes-3.5.0-trimmed/spades//K21/simplified_contigs.fasta 1:26:45.344 3G / 9G INFO General (contig_output.hpp : 283) Outputting contigs to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.biaurelia-Sample_USBL-36I1-dipSPAdes-3.5.0-trimmed/spades//K21/before_rr.fasta 1:29:40.841 3G / 9G INFO General (contig_output.hpp : 283) Outputting contigs to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.biaurelia-Sample_USBL-36I1-dipSPAdes-3.5.0-trimmed/spades//K21/final_contigs.fasta 1:32:52.486 3G / 9G INFO General (launch.hpp : 82) SPAdes finished 1:33:03.469 64M / 9G INFO General (main.cpp : 166) Assembling time: 1 hours 33 minutes 3 seconds == Warning == Default k-mer sizes were set to [21, 33, 55, 77] because estimated read length (151) is equal to or greater than 150 == Running assembler: K33 0:00:00.000 4M / 4M INFO General (memory_limit.hpp : 42) Memory limit set to 100 Gb 0:00:00.001 4M / 4M INFO General (main.cpp : 146) Assembling dataset (/N/dc2/projects/marinovg/2015-09-07-assemblies/P.biaurelia-Sample_USBL-36I1-dipSPAdes-3.5.0-trimmed/spades/dataset.info) with K=33 0:00:00.001 4M / 4M INFO General (launch.hpp : 28) SPAdes started 0:00:00.001 4M / 4M INFO General (launch.hpp : 29) Starting from stage: construction 0:00:00.002 4M / 4M INFO StageManager (stage.cpp : 125) STAGE == Construction 0:00:00.002 4M / 4M INFO General (construction.cpp : 44) Contigs from previous K will be used 0:00:00.008 4M / 4M INFO General (read_converter.hpp : 49) Binary reads detected 0:00:00.027 4M / 4M INFO General (graph_construction.hpp : 129) Constructing DeBruijn graph for k=33 0:00:00.030 4M / 4M INFO General (kmer_splitters.hpp : 172) Splitting kmer instances into 256 buckets. This might take a while. 0:00:00.031 4M / 4M INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:00:00.031 4M / 4M INFO General (kmer_splitters.hpp : 190) Memory available for splitting buffers: 2.08325 Gb 0:00:00.031 4M / 4M INFO General (kmer_splitters.hpp : 199) Using cell size of 131072 0:12:27.836 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 9215134 reads 0:24:58.776 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 18431135 reads 0:37:49.634 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 27645687 reads 0:50:16.657 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 36843764 reads 0:51:40.355 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 37004606 reads 0:51:40.355 8G / 9G INFO General (kmer_splitters.hpp : 234) Adding contigs from previous K 0:58:55.879 8G / 9G INFO General (kmer_splitters.hpp : 245) Used 37004606 reads. Maximum read length 151 0:58:55.880 8G / 9G INFO General (kmer_splitters.hpp : 246) Average read length 149.538 0:58:58.141 64M / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 1:06:13.667 64M / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 140727330 kmers in total. 1:06:13.667 64M / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 1:08:26.707 64M / 9G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 1:08:26.707 64M / 9G INFO General (kmer_splitters.hpp : 379) Splitting kmer instances into 256 buckets. This might take a while. 1:08:26.708 64M / 9G INFO General (file_limit.hpp : 29) Open file limit set to 32768 1:08:26.708 64M / 9G INFO General (kmer_splitters.hpp : 397) Memory available for splitting buffers: 2.08203 Gb 1:08:26.708 64M / 9G INFO General (kmer_splitters.hpp : 405) Using cell size of 131072 1:56:10.660 8G / 9G INFO General (kmer_splitters.hpp : 428) Processed 140727330 kmers 1:56:10.660 8G / 9G INFO General (kmer_splitters.hpp : 437) Used 140727330 kmers. 1:56:11.635 64M / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 2:05:36.969 64M / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 139488622 kmers in total. 2:05:36.969 64M / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 2:06:14.230 64M / 9G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 2:06:39.022 68M / 9G INFO General (kmer_index.hpp : 371) Merging final buckets. 2:06:50.665 68M / 9G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 48254386 bytes occupied (2.7675 bits per kmer). 2:06:50.885 204M / 9G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 382) Building k-mer extensions from k+1-mers 2:07:07.448 204M / 9G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 386) Building k-mer extensions from k+1-mers finished. 2:07:07.455 204M / 9G INFO Early tip clipping (early_simplification.hpp : 236) Early tip clipping 2:14:18.463 204M / 9G INFO Early tip clipping (early_simplification.hpp : 239) 19537480 34-mers were removed by early tip clipper 2:14:18.463 204M / 9G INFO General (graph_construction.hpp : 145) Condensing graph 2:14:18.464 204M / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 337) Extracting unbranching paths 2:15:50.424 1G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 351) Extracting unbranching paths finished. 7550693 sequences extracted 2:16:02.268 1G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 311) Collecting perfect loops 2:16:48.167 1G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 326) Collecting perfect loops finished. 56 loops collected 2:16:53.815 1G / 9G INFO General (graph_construction.hpp : 150) Building index with from graph 2:16:53.816 1G / 9G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 2:16:53.816 1G / 9G INFO General (kmer_splitters.hpp : 289) Splitting kmer instances into 16 buckets. This might take a while. 2:16:53.816 1G / 9G INFO General (file_limit.hpp : 29) Open file limit set to 32768 2:16:53.816 1G / 9G INFO General (kmer_splitters.hpp : 307) Memory available for splitting buffers: 32.7708 Gb 2:16:53.816 1G / 9G INFO General (kmer_splitters.hpp : 312) Using cell size of 2097152 2:18:23.053 2G / 9G INFO General (kmer_splitters.hpp : 325) Processed 2089487 edges 2:21:53.622 2G / 9G INFO General (kmer_splitters.hpp : 325) Processed 4184620 edges 2:25:44.069 2G / 9G INFO General (kmer_splitters.hpp : 325) Processed 6272330 edges 2:29:52.177 2G / 9G INFO General (kmer_splitters.hpp : 325) Processed 7550749 edges 2:29:52.177 2G / 9G INFO General (kmer_splitters.hpp : 330) Used 7550749 sequences. 2:29:52.235 1G / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 2:31:09.221 1G / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 121189850 kmers in total. 2:31:09.221 1G / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 2:31:18.783 1G / 9G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 2:34:12.081 1G / 9G INFO General (kmer_index.hpp : 371) Merging final buckets. 2:34:21.292 1G / 9G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 41924139 bytes occupied (2.7675 bits per kmer). 2:34:23.355 4G / 9G INFO General (edge_index_builders.hpp : 21) Collecting k-mer coverage information from graph, this takes a while. 2:38:05.015 4G / 9G INFO General (graph_construction.hpp : 182) Filling coverage index 2:38:05.015 4G / 9G INFO General (edge_index_builders.hpp : 99) Collecting k-mer coverage information from reads, this takes a while. 2:40:43.514 4G / 9G INFO General (graph_construction.hpp : 184) Filling coverage and flanking coverage from index 2:41:15.107 4G / 9G INFO General (construction.cpp : 33) Figured out: read length = 151 2:41:15.126 4G / 9G INFO StageManager (stage.cpp : 125) STAGE == EC Threshold Finding 2:41:25.004 4G / 9G INFO General (kmer_coverage_model.cpp : 178) Kmer coverage valley at: 10 2:41:25.005 4G / 9G INFO General (kmer_coverage_model.cpp : 198) K-mer histogram maximum: 28 2:41:25.005 4G / 9G INFO General (kmer_coverage_model.cpp : 234) Estimated median coverage: 29. Coverage mad: 8.8956 2:41:25.005 4G / 9G INFO General (kmer_coverage_model.cpp : 261) Fitting coverage model 2:41:25.100 4G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 2 2:41:25.354 4G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 4 2:41:26.273 4G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 8 2:41:28.274 4G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 16 2:41:31.427 4G / 9G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 28.6652. Fitted coverage std. dev: 6.95857 2:41:31.430 4G / 9G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 0.540147 2:41:31.430 4G / 9G INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 20 2:41:31.430 4G / 9G INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 19 2:41:31.430 4G / 9G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 62931600 2:41:31.430 4G / 9G INFO General (genomic_info_filler.cpp : 103) Mean coverage was calculated as 28.6652 2:41:31.431 4G / 9G INFO General (genomic_info_filler.cpp : 117) EC coverage threshold value was calculated as 19 2:41:31.431 4G / 9G INFO General (genomic_info_filler.cpp : 118) Trusted kmer low bound: 0 2:41:31.431 4G / 9G INFO StageManager (stage.cpp : 125) STAGE == Simplification 2:41:31.663 1G / 9G INFO General (graph_simplification.hpp : 911) Graph simplification started 2:41:31.663 1G / 9G INFO General (graph_simplification.hpp : 924) Fast simplification mode enabled 2:41:31.663 1G / 9G INFO General (graph_simplification.hpp : 771) PROCEDURE == Presimplification 2:41:31.663 1G / 9G INFO General (graph_simplification.hpp : 211) Removing short low covered self-conjugate connections 2:41:32.131 1G / 9G INFO General (graph_simplification.hpp : 403) Removing isolated edges 2:41:32.132 1G / 9G INFO General (graph_simplification.hpp : 404) All edges shorter than 151 will be removed 2:41:32.132 1G / 9G INFO General (graph_simplification.hpp : 405) Also edges shorter than 0 and coverage smaller than 0 will be removed 2:41:33.608 1G / 9G INFO General (graph_simplification.hpp : 687) Non parallel mode 2:41:57.786 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 2:42:57.202 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 2:44:41.510 1G / 9G INFO General (graph_simplification.hpp : 644) Using permanent iterators 2:44:41.510 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 1 2:44:45.722 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 2:45:03.072 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 2:45:14.445 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 2 2:45:14.445 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 2:45:14.612 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 2:45:21.280 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 3 2:45:21.280 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 2:45:21.390 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 2:45:24.318 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 4 2:45:24.318 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 2:45:24.364 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 2:45:26.157 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 5 2:45:26.157 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 2:45:26.184 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 2:45:27.882 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 6 2:45:27.882 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 2:45:27.902 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 2:45:29.608 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 7 2:45:29.608 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 2:45:29.624 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 2:45:31.247 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 8 2:45:31.247 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 2:45:31.260 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 2:45:32.332 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 9 2:45:32.332 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 2:45:32.343 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 2:45:33.029 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 10 2:45:33.030 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 2:45:33.039 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 2:45:33.582 1G / 9G INFO General (graph_simplification.hpp : 796) PROCEDURE == Post simplification 2:45:33.582 1G / 9G INFO General (graph_simplification.hpp : 644) Using permanent iterators 2:45:33.582 1G / 9G INFO General (graph_simplification.hpp : 806) Iteration 0 2:45:33.583 1G / 9G INFO General (graph_simplification.hpp : 247) Removal of relatively low covered connections disabled 2:45:34.767 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 2:45:37.466 1G / 9G INFO General (graph_simplification.hpp : 806) Iteration 1 2:45:37.466 1G / 9G INFO General (graph_simplification.hpp : 247) Removal of relatively low covered connections disabled 2:45:37.466 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 2:45:38.407 1G / 9G INFO StageManager (stage.cpp : 125) STAGE == Simplification Cleanup 2:45:38.408 1G / 9G INFO General (graph_simplification.hpp : 403) Removing isolated edges 2:45:38.408 1G / 9G INFO General (graph_simplification.hpp : 404) All edges shorter than 151 will be removed 2:45:38.408 1G / 9G INFO General (graph_simplification.hpp : 405) Also edges shorter than 0 and coverage smaller than 2 will be removed 2:45:38.529 1G / 9G INFO General (simplification.cpp : 56) Removing all the edges having coverage 0 and less 2:45:40.639 1G / 9G INFO General (simplification.cpp : 68) Counting average coverage 2:45:41.005 1G / 9G INFO General (simplification.cpp : 71) Average coverage = 26.5507 2:45:41.005 1G / 9G INFO StageManager (stage.cpp : 125) STAGE == Contig Output 2:45:41.006 1G / 9G INFO General (contig_output.hpp : 283) Outputting contigs to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.biaurelia-Sample_USBL-36I1-dipSPAdes-3.5.0-trimmed/spades//K33/simplified_contigs.fasta 2:46:39.285 1G / 9G INFO General (contig_output.hpp : 283) Outputting contigs to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.biaurelia-Sample_USBL-36I1-dipSPAdes-3.5.0-trimmed/spades//K33/before_rr.fasta 2:47:56.301 1G / 9G INFO General (contig_output.hpp : 283) Outputting contigs to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.biaurelia-Sample_USBL-36I1-dipSPAdes-3.5.0-trimmed/spades//K33/final_contigs.fasta 2:49:50.585 1G / 9G INFO General (launch.hpp : 82) SPAdes finished 2:49:54.695 64M / 9G INFO General (main.cpp : 166) Assembling time: 2 hours 49 minutes 54 seconds == Running assembler: K55 0:00:00.000 4M / 4M INFO General (memory_limit.hpp : 42) Memory limit set to 100 Gb 0:00:00.001 4M / 4M INFO General (main.cpp : 146) Assembling dataset (/N/dc2/projects/marinovg/2015-09-07-assemblies/P.biaurelia-Sample_USBL-36I1-dipSPAdes-3.5.0-trimmed/spades/dataset.info) with K=55 0:00:00.001 4M / 4M INFO General (launch.hpp : 28) SPAdes started 0:00:00.001 4M / 4M INFO General (launch.hpp : 29) Starting from stage: construction 0:00:00.002 4M / 4M INFO General (launch.hpp : 44) Will need read mapping, kmer mapper will be attached 0:00:00.002 4M / 4M INFO StageManager (stage.cpp : 125) STAGE == Construction 0:00:00.002 4M / 4M INFO General (construction.cpp : 44) Contigs from previous K will be used 0:00:00.007 4M / 4M INFO General (read_converter.hpp : 49) Binary reads detected 0:00:00.027 4M / 4M INFO General (graph_construction.hpp : 129) Constructing DeBruijn graph for k=55 0:00:00.030 4M / 4M INFO General (kmer_splitters.hpp : 172) Splitting kmer instances into 256 buckets. This might take a while. 0:00:00.030 4M / 4M INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:00:00.030 4M / 4M INFO General (kmer_splitters.hpp : 190) Memory available for splitting buffers: 2.08325 Gb 0:00:00.030 4M / 4M INFO General (kmer_splitters.hpp : 199) Using cell size of 131072 0:14:48.402 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 11357891 reads 0:27:32.137 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 22707442 reads 0:41:02.119 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 34049458 reads 0:47:38.111 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 37004606 reads 0:47:38.112 8G / 9G INFO General (kmer_splitters.hpp : 234) Adding contigs from previous K 0:57:10.503 8G / 9G INFO General (kmer_splitters.hpp : 245) Used 37004606 reads. Maximum read length 151 0:57:10.504 8G / 9G INFO General (kmer_splitters.hpp : 246) Average read length 149.538 0:57:12.675 64M / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 1:04:33.042 64M / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 158168333 kmers in total. 1:04:33.042 64M / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 1:04:50.354 64M / 9G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 1:04:50.354 64M / 9G INFO General (kmer_splitters.hpp : 379) Splitting kmer instances into 256 buckets. This might take a while. 1:04:50.354 64M / 9G INFO General (file_limit.hpp : 29) Open file limit set to 32768 1:04:50.354 64M / 9G INFO General (kmer_splitters.hpp : 397) Memory available for splitting buffers: 2.08203 Gb 1:04:50.354 64M / 9G INFO General (kmer_splitters.hpp : 405) Using cell size of 131072 1:56:23.151 8G / 9G INFO General (kmer_splitters.hpp : 428) Processed 158168333 kmers 1:56:23.151 8G / 9G INFO General (kmer_splitters.hpp : 437) Used 158168333 kmers. 1:56:24.132 64M / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 2:05:12.477 64M / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 157723135 kmers in total. 2:05:12.478 64M / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 2:07:28.576 64M / 9G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 2:07:58.064 68M / 9G INFO General (kmer_index.hpp : 371) Merging final buckets. 2:08:34.929 68M / 9G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 54562383 bytes occupied (2.7675 bits per kmer). 2:08:35.208 220M / 9G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 382) Building k-mer extensions from k+1-mers 2:08:56.990 220M / 9G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 386) Building k-mer extensions from k+1-mers finished. 2:08:56.994 220M / 9G INFO General (graph_construction.hpp : 145) Condensing graph 2:08:56.994 220M / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 337) Extracting unbranching paths 2:10:45.745 1G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 351) Extracting unbranching paths finished. 9279972 sequences extracted 2:11:02.771 1G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 311) Collecting perfect loops 2:11:56.386 1G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 326) Collecting perfect loops finished. 8 loops collected 2:12:05.688 2G / 9G INFO General (graph_construction.hpp : 150) Building index with from graph 2:12:05.689 2G / 9G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 2:12:05.689 2G / 9G INFO General (kmer_splitters.hpp : 289) Splitting kmer instances into 16 buckets. This might take a while. 2:12:05.689 2G / 9G INFO General (file_limit.hpp : 29) Open file limit set to 32768 2:12:05.689 2G / 9G INFO General (kmer_splitters.hpp : 307) Memory available for splitting buffers: 32.5703 Gb 2:12:05.689 2G / 9G INFO General (kmer_splitters.hpp : 312) Using cell size of 2097152 2:17:11.359 2G / 9G INFO General (kmer_splitters.hpp : 325) Processed 1969247 edges 2:20:42.636 2G / 9G INFO General (kmer_splitters.hpp : 325) Processed 3937649 edges 2:24:34.617 2G / 9G INFO General (kmer_splitters.hpp : 325) Processed 5906935 edges 2:28:46.846 2G / 9G INFO General (kmer_splitters.hpp : 325) Processed 7874414 edges 2:33:16.606 2G / 9G INFO General (kmer_splitters.hpp : 325) Processed 9279980 edges 2:33:16.606 2G / 9G INFO General (kmer_splitters.hpp : 330) Used 9279980 sequences. 2:33:16.678 2G / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 2:35:32.473 2G / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 158168333 kmers in total. 2:35:32.473 2G / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 2:36:08.323 2G / 9G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 2:41:39.428 2G / 9G INFO General (kmer_index.hpp : 371) Merging final buckets. 2:42:56.379 2G / 9G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 54716393 bytes occupied (2.7675 bits per kmer). 2:42:59.893 5G / 9G INFO General (edge_index_builders.hpp : 21) Collecting k-mer coverage information from graph, this takes a while. 2:49:44.296 5G / 9G INFO General (graph_construction.hpp : 182) Filling coverage index 2:49:44.296 5G / 9G INFO General (edge_index_builders.hpp : 99) Collecting k-mer coverage information from reads, this takes a while. 2:52:20.235 5G / 9G INFO General (graph_construction.hpp : 184) Filling coverage and flanking coverage from index 2:53:08.714 5G / 9G INFO General (construction.cpp : 33) Figured out: read length = 151 2:53:08.731 5G / 9G INFO StageManager (stage.cpp : 125) STAGE == EC Threshold Finding 2:53:16.911 5G / 9G INFO General (kmer_coverage_model.cpp : 178) Kmer coverage valley at: 7 2:53:16.911 5G / 9G INFO General (kmer_coverage_model.cpp : 198) K-mer histogram maximum: 22 2:53:16.911 5G / 9G INFO General (kmer_coverage_model.cpp : 234) Estimated median coverage: 23. Coverage mad: 7.413 2:53:16.911 5G / 9G INFO General (kmer_coverage_model.cpp : 261) Fitting coverage model 2:53:16.995 5G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 2 2:53:17.213 5G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 4 2:53:17.990 5G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 8 2:53:19.255 5G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 16 2:53:19.795 5G / 9G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 22.85. Fitted coverage std. dev: 6.23641 2:53:19.797 5G / 9G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 0.570766 2:53:19.797 5G / 9G INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 15 2:53:19.797 5G / 9G INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 14 2:53:19.797 5G / 9G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 64355654 2:53:19.797 5G / 9G INFO General (genomic_info_filler.cpp : 103) Mean coverage was calculated as 22.85 2:53:19.798 5G / 9G INFO General (genomic_info_filler.cpp : 117) EC coverage threshold value was calculated as 14 2:53:19.798 5G / 9G INFO General (genomic_info_filler.cpp : 118) Trusted kmer low bound: 0 2:53:19.798 5G / 9G INFO StageManager (stage.cpp : 125) STAGE == Gap Closer 2:53:19.808 5G / 9G INFO General (gap_closer.cpp : 157) Preparing shift maps 2:53:30.862 5G / 9G INFO General (gap_closer.cpp : 117) Processing paired reads (takes a while) 2:53:57.557 6G / 9G INFO General (gap_closer.cpp : 136) Used 18394194 paired reads 2:53:57.558 6G / 9G INFO General (gap_closer.cpp : 138) Merging paired indices 2:54:01.860 5G / 9G INFO GapCloser (gap_closer.cpp : 395) Closing short gaps 2:54:30.231 5G / 9G INFO GapCloser (gap_closer.cpp : 424) Closing short gaps complete: filled 2548 gaps after checking 20406 candidates 2:54:34.600 5G / 9G INFO StageManager (stage.cpp : 125) STAGE == Simplification 2:54:34.907 2G / 9G INFO General (graph_simplification.hpp : 911) Graph simplification started 2:54:34.907 2G / 9G INFO General (graph_simplification.hpp : 924) Fast simplification mode enabled 2:54:34.907 2G / 9G INFO General (graph_simplification.hpp : 771) PROCEDURE == Presimplification 2:54:34.907 2G / 9G INFO General (graph_simplification.hpp : 211) Removing short low covered self-conjugate connections 2:54:35.822 2G / 9G INFO General (graph_simplification.hpp : 403) Removing isolated edges 2:54:35.822 2G / 9G INFO General (graph_simplification.hpp : 404) All edges shorter than 151 will be removed 2:54:35.823 2G / 9G INFO General (graph_simplification.hpp : 405) Also edges shorter than 0 and coverage smaller than 0 will be removed 2:54:38.796 2G / 9G INFO General (graph_simplification.hpp : 687) Non parallel mode 2:55:13.407 2G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 2:56:49.711 2G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 2:57:38.593 1G / 9G INFO General (graph_simplification.hpp : 644) Using permanent iterators 2:57:38.593 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 1 2:57:40.181 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 2:57:46.660 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 2:57:48.790 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 2 2:57:48.790 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 2:57:48.827 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 2:57:51.208 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 3 2:57:51.208 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 2:57:51.262 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 2:57:53.040 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 4 2:57:53.040 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 2:57:53.071 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 2:57:54.255 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 5 2:57:54.255 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 2:57:54.268 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 2:57:55.604 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 6 2:57:55.604 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 2:57:55.614 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 2:57:57.272 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 7 2:57:57.272 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 2:57:57.279 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 2:57:58.800 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 8 2:57:58.800 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 2:57:58.806 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 2:58:00.166 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 9 2:58:00.166 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 2:58:00.172 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 2:58:01.151 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 10 2:58:01.151 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 2:58:01.155 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 2:58:01.737 1G / 9G INFO General (graph_simplification.hpp : 796) PROCEDURE == Post simplification 2:58:01.737 1G / 9G INFO General (graph_simplification.hpp : 644) Using permanent iterators 2:58:01.737 1G / 9G INFO General (graph_simplification.hpp : 806) Iteration 0 2:58:01.737 1G / 9G INFO General (graph_simplification.hpp : 247) Removal of relatively low covered connections disabled 2:58:02.152 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 2:58:03.035 1G / 9G INFO General (graph_simplification.hpp : 806) Iteration 1 2:58:03.035 1G / 9G INFO General (graph_simplification.hpp : 247) Removal of relatively low covered connections disabled 2:58:03.035 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 2:58:03.383 1G / 9G INFO StageManager (stage.cpp : 125) STAGE == Gap Closer 2:58:03.383 1G / 9G INFO General (graph_pack.hpp : 84) Index refill 2:58:03.384 1G / 9G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 2:58:03.384 1G / 9G INFO General (kmer_splitters.hpp : 289) Splitting kmer instances into 16 buckets. This might take a while. 2:58:03.384 1G / 9G INFO General (file_limit.hpp : 29) Open file limit set to 32768 2:58:03.384 1G / 9G INFO General (kmer_splitters.hpp : 307) Memory available for splitting buffers: 32.8997 Gb 2:58:03.384 1G / 9G INFO General (kmer_splitters.hpp : 312) Using cell size of 2097152 3:02:13.680 1G / 9G INFO General (kmer_splitters.hpp : 325) Processed 78059 edges 3:06:03.219 1G / 9G INFO General (kmer_splitters.hpp : 325) Processed 156153 edges 3:09:08.353 1G / 9G INFO General (kmer_splitters.hpp : 325) Processed 186673 edges 3:09:08.354 1G / 9G INFO General (kmer_splitters.hpp : 330) Used 186673 sequences. 3:09:08.455 1G / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 3:11:55.242 1G / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 80241173 kmers in total. 3:11:55.242 1G / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 3:12:01.987 1G / 9G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 3:13:46.426 1G / 9G INFO General (kmer_index.hpp : 371) Merging final buckets. 3:13:52.709 1G / 9G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 27758476 bytes occupied (2.7675 bits per kmer). 3:13:54.078 3G / 9G INFO General (edge_index_builders.hpp : 21) Collecting k-mer coverage information from graph, this takes a while. 3:16:10.153 3G / 9G INFO General (gap_closer.cpp : 157) Preparing shift maps 3:16:10.374 3G / 9G INFO General (gap_closer.cpp : 117) Processing paired reads (takes a while) 3:16:43.742 3G / 9G INFO General (gap_closer.cpp : 136) Used 18394194 paired reads 3:16:43.743 3G / 9G INFO General (gap_closer.cpp : 138) Merging paired indices 3:16:44.034 3G / 9G INFO GapCloser (gap_closer.cpp : 395) Closing short gaps 3:16:44.551 3G / 9G INFO GapCloser (gap_closer.cpp : 424) Closing short gaps complete: filled 176 gaps after checking 9216 candidates 3:16:45.641 3G / 9G INFO StageManager (stage.cpp : 125) STAGE == Simplification Cleanup 3:16:45.642 3G / 9G INFO General (graph_simplification.hpp : 403) Removing isolated edges 3:16:45.642 3G / 9G INFO General (graph_simplification.hpp : 404) All edges shorter than 151 will be removed 3:16:45.642 3G / 9G INFO General (graph_simplification.hpp : 405) Also edges shorter than 0 and coverage smaller than 2 will be removed 3:16:46.356 3G / 9G INFO General (simplification.cpp : 56) Removing all the edges having coverage 0 and less 3:16:47.008 3G / 9G INFO General (simplification.cpp : 68) Counting average coverage 3:16:47.143 3G / 9G INFO General (simplification.cpp : 71) Average coverage = 20.591 3:16:47.144 3G / 9G INFO StageManager (stage.cpp : 125) STAGE == Contig Output 3:16:47.144 3G / 9G INFO General (contig_output.hpp : 283) Outputting contigs to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.biaurelia-Sample_USBL-36I1-dipSPAdes-3.5.0-trimmed/spades//K55/simplified_contigs.fasta 3:17:07.185 3G / 9G INFO General (contig_output.hpp : 283) Outputting contigs to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.biaurelia-Sample_USBL-36I1-dipSPAdes-3.5.0-trimmed/spades//K55/before_rr.fasta 3:18:04.516 3G / 9G INFO General (contig_output.hpp : 283) Outputting contigs to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.biaurelia-Sample_USBL-36I1-dipSPAdes-3.5.0-trimmed/spades//K55/final_contigs.fasta 3:19:01.902 3G / 9G INFO General (launch.hpp : 82) SPAdes finished 3:19:05.887 64M / 9G INFO General (main.cpp : 166) Assembling time: 3 hours 19 minutes 5 seconds == Running assembler: K77 0:00:00.000 4M / 4M INFO General (memory_limit.hpp : 42) Memory limit set to 100 Gb 0:00:00.001 4M / 4M INFO General (main.cpp : 146) Assembling dataset (/N/dc2/projects/marinovg/2015-09-07-assemblies/P.biaurelia-Sample_USBL-36I1-dipSPAdes-3.5.0-trimmed/spades/dataset.info) with K=77 0:00:00.001 4M / 4M INFO General (launch.hpp : 28) SPAdes started 0:00:00.001 4M / 4M INFO General (launch.hpp : 29) Starting from stage: construction 0:00:00.002 4M / 4M INFO General (launch.hpp : 44) Will need read mapping, kmer mapper will be attached 0:00:00.002 4M / 4M INFO StageManager (stage.cpp : 125) STAGE == Construction 0:00:00.002 4M / 4M INFO General (construction.cpp : 44) Contigs from previous K will be used 0:00:00.007 4M / 4M INFO General (read_converter.hpp : 49) Binary reads detected 0:00:00.026 4M / 4M INFO General (graph_construction.hpp : 129) Constructing DeBruijn graph for k=77 0:00:00.028 4M / 4M INFO General (kmer_splitters.hpp : 172) Splitting kmer instances into 256 buckets. This might take a while. 0:00:00.029 4M / 4M INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:00:00.029 4M / 4M INFO General (kmer_splitters.hpp : 190) Memory available for splitting buffers: 2.08325 Gb 0:00:00.029 4M / 4M INFO General (kmer_splitters.hpp : 199) Using cell size of 87381 0:42:29.623 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 9853668 reads 1:29:36.857 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 19702720 reads 2:11:13.772 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 29555648 reads 2:28:12.089 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 37004606 reads 2:28:12.090 8G / 9G INFO General (kmer_splitters.hpp : 234) Adding contigs from previous K 2:44:08.468 8G / 9G INFO General (kmer_splitters.hpp : 245) Used 37004606 reads. Maximum read length 151 2:44:08.468 8G / 9G INFO General (kmer_splitters.hpp : 246) Average read length 149.538 2:44:10.750 64M / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 2:52:23.358 64M / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 160606134 kmers in total. 2:52:23.358 64M / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 2:53:03.964 64M / 9G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 2:53:03.964 64M / 9G INFO General (kmer_splitters.hpp : 379) Splitting kmer instances into 256 buckets. This might take a while. 2:53:03.965 64M / 9G INFO General (file_limit.hpp : 29) Open file limit set to 32768 2:53:03.965 64M / 9G INFO General (kmer_splitters.hpp : 397) Memory available for splitting buffers: 2.08203 Gb 2:53:03.965 64M / 9G INFO General (kmer_splitters.hpp : 405) Using cell size of 87381 3:54:14.227 8G / 9G INFO General (kmer_splitters.hpp : 428) Processed 160606134 kmers 3:54:14.227 8G / 9G INFO General (kmer_splitters.hpp : 437) Used 160606134 kmers. 3:54:15.652 64M / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 4:05:04.110 64M / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 160768140 kmers in total. 4:05:04.110 64M / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 4:06:58.871 64M / 9G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 4:07:29.398 68M / 9G INFO General (kmer_index.hpp : 371) Merging final buckets. 4:08:15.317 68M / 9G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 55615778 bytes occupied (2.7675 bits per kmer). 4:08:15.605 224M / 9G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 382) Building k-mer extensions from k+1-mers 4:08:40.214 224M / 9G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 386) Building k-mer extensions from k+1-mers finished. 4:08:40.221 224M / 9G INFO General (graph_construction.hpp : 145) Condensing graph 4:08:40.221 224M / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 337) Extracting unbranching paths 4:10:30.662 1G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 351) Extracting unbranching paths finished. 7852775 sequences extracted 4:10:48.036 1G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 311) Collecting perfect loops 4:11:48.928 1G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 326) Collecting perfect loops finished. 8 loops collected 4:11:56.947 2G / 9G INFO General (graph_construction.hpp : 150) Building index with from graph 4:11:56.949 2G / 9G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 4:11:56.949 2G / 9G INFO General (kmer_splitters.hpp : 289) Splitting kmer instances into 16 buckets. This might take a while. 4:11:56.949 2G / 9G INFO General (file_limit.hpp : 29) Open file limit set to 32768 4:11:56.949 2G / 9G INFO General (kmer_splitters.hpp : 307) Memory available for splitting buffers: 32.6263 Gb 4:11:56.949 2G / 9G INFO General (kmer_splitters.hpp : 312) Using cell size of 1398101 4:16:14.563 2G / 9G INFO General (kmer_splitters.hpp : 325) Processed 1095330 edges 4:20:03.778 2G / 9G INFO General (kmer_splitters.hpp : 325) Processed 2187915 edges 4:24:25.239 2G / 9G INFO General (kmer_splitters.hpp : 325) Processed 3278524 edges 4:29:55.699 2G / 9G INFO General (kmer_splitters.hpp : 325) Processed 4374803 edges 4:34:05.349 2G / 9G INFO General (kmer_splitters.hpp : 325) Processed 5468189 edges 4:36:12.854 2G / 9G INFO General (kmer_splitters.hpp : 325) Processed 6561859 edges 4:41:02.811 2G / 9G INFO General (kmer_splitters.hpp : 325) Processed 7657156 edges 4:42:39.349 2G / 9G INFO General (kmer_splitters.hpp : 325) Processed 7852783 edges 4:42:39.350 2G / 9G INFO General (kmer_splitters.hpp : 330) Used 7852783 sequences. 4:42:39.418 2G / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 4:44:09.200 2G / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 160606134 kmers in total. 4:44:09.200 2G / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 4:44:29.799 2G / 9G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 4:48:34.917 2G / 9G INFO General (kmer_index.hpp : 371) Merging final buckets. 4:48:56.314 2G / 9G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 55559718 bytes occupied (2.7675 bits per kmer). 4:48:59.036 5G / 9G INFO General (edge_index_builders.hpp : 21) Collecting k-mer coverage information from graph, this takes a while. 4:54:52.939 5G / 9G INFO General (graph_construction.hpp : 182) Filling coverage index 4:54:52.939 5G / 9G INFO General (edge_index_builders.hpp : 99) Collecting k-mer coverage information from reads, this takes a while. 4:57:01.295 5G / 9G INFO General (graph_construction.hpp : 184) Filling coverage and flanking coverage from index 4:57:44.091 5G / 9G INFO General (construction.cpp : 33) Figured out: read length = 151 4:57:44.116 5G / 9G INFO StageManager (stage.cpp : 125) STAGE == EC Threshold Finding 4:57:54.066 5G / 9G INFO General (kmer_coverage_model.cpp : 178) Kmer coverage valley at: 5 4:57:54.066 5G / 9G INFO General (kmer_coverage_model.cpp : 198) K-mer histogram maximum: 16 4:57:54.066 5G / 9G INFO General (kmer_coverage_model.cpp : 234) Estimated median coverage: 17. Coverage mad: 7.413 4:57:54.066 5G / 9G INFO General (kmer_coverage_model.cpp : 261) Fitting coverage model 4:57:54.123 5G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 2 4:57:54.275 5G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 4 4:57:54.798 5G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 8 4:57:56.001 5G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 16 4:57:57.222 5G / 9G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 17.0996. Fitted coverage std. dev: 5.45268 4:57:57.224 5G / 9G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 0.409244 4:57:57.224 5G / 9G INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 11 4:57:57.224 5G / 9G INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 11 4:57:57.224 5G / 9G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 62640652 4:57:57.224 5G / 9G INFO General (genomic_info_filler.cpp : 103) Mean coverage was calculated as 17.0996 4:57:57.224 5G / 9G INFO General (genomic_info_filler.cpp : 117) EC coverage threshold value was calculated as 11 4:57:57.224 5G / 9G INFO General (genomic_info_filler.cpp : 118) Trusted kmer low bound: 0 4:57:57.224 5G / 9G INFO StageManager (stage.cpp : 125) STAGE == Gap Closer 4:57:57.235 5G / 9G INFO General (gap_closer.cpp : 157) Preparing shift maps 4:58:06.189 5G / 9G INFO General (gap_closer.cpp : 117) Processing paired reads (takes a while) 4:58:27.905 6G / 9G INFO General (gap_closer.cpp : 136) Used 18394194 paired reads 4:58:27.907 6G / 9G INFO General (gap_closer.cpp : 138) Merging paired indices 4:58:33.140 5G / 9G INFO GapCloser (gap_closer.cpp : 395) Closing short gaps 4:58:54.007 5G / 9G INFO GapCloser (gap_closer.cpp : 424) Closing short gaps complete: filled 2655 gaps after checking 27323 candidates 4:58:58.238 5G / 9G INFO StageManager (stage.cpp : 125) STAGE == Simplification 4:58:58.589 1G / 9G INFO General (graph_simplification.hpp : 911) Graph simplification started 4:58:58.589 1G / 9G INFO General (graph_simplification.hpp : 924) Fast simplification mode enabled 4:58:58.589 1G / 9G INFO General (graph_simplification.hpp : 771) PROCEDURE == Presimplification 4:58:58.589 1G / 9G INFO General (graph_simplification.hpp : 211) Removing short low covered self-conjugate connections 4:58:59.284 1G / 9G INFO General (graph_simplification.hpp : 403) Removing isolated edges 4:58:59.286 1G / 9G INFO General (graph_simplification.hpp : 404) All edges shorter than 151 will be removed 4:58:59.286 1G / 9G INFO General (graph_simplification.hpp : 405) Also edges shorter than 0 and coverage smaller than 0 will be removed 4:59:03.286 1G / 9G INFO General (graph_simplification.hpp : 687) Non parallel mode 4:59:26.626 2G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 5:00:47.451 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 5:00:52.552 1G / 9G INFO General (graph_simplification.hpp : 644) Using permanent iterators 5:00:52.552 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 1 5:00:53.268 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 5:00:56.251 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 5:00:56.312 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 2 5:00:56.312 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 5:00:56.314 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 5:00:56.832 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 3 5:00:56.832 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 5:00:56.844 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 5:00:57.616 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 4 5:00:57.616 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 5:00:57.635 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 5:00:58.446 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 5 5:00:58.447 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 5:00:58.456 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 5:00:59.593 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 6 5:00:59.593 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 5:00:59.598 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 5:01:01.078 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 7 5:01:01.078 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 5:01:01.082 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 5:01:02.565 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 8 5:01:02.565 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 5:01:02.569 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 5:01:03.917 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 9 5:01:03.917 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 5:01:03.920 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 5:01:04.812 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 10 5:01:04.812 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 5:01:04.815 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 5:01:05.349 1G / 9G INFO General (graph_simplification.hpp : 796) PROCEDURE == Post simplification 5:01:05.349 1G / 9G INFO General (graph_simplification.hpp : 644) Using permanent iterators 5:01:05.349 1G / 9G INFO General (graph_simplification.hpp : 806) Iteration 0 5:01:05.349 1G / 9G INFO General (graph_simplification.hpp : 247) Removal of relatively low covered connections disabled 5:01:05.579 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 5:01:06.068 1G / 9G INFO General (graph_simplification.hpp : 806) Iteration 1 5:01:06.068 1G / 9G INFO General (graph_simplification.hpp : 247) Removal of relatively low covered connections disabled 5:01:06.068 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 5:01:06.237 1G / 9G INFO StageManager (stage.cpp : 125) STAGE == Gap Closer 5:01:06.237 1G / 9G INFO General (graph_pack.hpp : 84) Index refill 5:01:06.239 1G / 9G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 5:01:06.239 1G / 9G INFO General (kmer_splitters.hpp : 289) Splitting kmer instances into 16 buckets. This might take a while. 5:01:06.239 1G / 9G INFO General (file_limit.hpp : 29) Open file limit set to 32768 5:01:06.239 1G / 9G INFO General (kmer_splitters.hpp : 307) Memory available for splitting buffers: 32.9792 Gb 5:01:06.239 1G / 9G INFO General (kmer_splitters.hpp : 312) Using cell size of 1398101 5:04:05.539 1G / 9G INFO General (kmer_splitters.hpp : 325) Processed 31272 edges 5:08:13.351 1G / 9G INFO General (kmer_splitters.hpp : 325) Processed 64161 edges 5:12:21.463 1G / 9G INFO General (kmer_splitters.hpp : 325) Processed 95899 edges 5:17:07.506 1G / 9G INFO General (kmer_splitters.hpp : 325) Processed 116580 edges 5:17:07.506 1G / 9G INFO General (kmer_splitters.hpp : 330) Used 116580 sequences. 5:17:07.580 1G / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 5:18:20.647 1G / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 81323223 kmers in total. 5:18:20.647 1G / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 5:18:30.700 1G / 9G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 5:20:19.582 1G / 9G INFO General (kmer_index.hpp : 371) Merging final buckets. 5:20:29.844 1G / 9G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 28132781 bytes occupied (2.7675 bits per kmer). 5:20:31.228 2G / 9G INFO General (edge_index_builders.hpp : 21) Collecting k-mer coverage information from graph, this takes a while. 5:23:03.461 2G / 9G INFO General (gap_closer.cpp : 157) Preparing shift maps 5:23:03.622 2G / 9G INFO General (gap_closer.cpp : 117) Processing paired reads (takes a while) 5:23:36.458 2G / 9G INFO General (gap_closer.cpp : 136) Used 18394194 paired reads 5:23:36.460 2G / 9G INFO General (gap_closer.cpp : 138) Merging paired indices 5:23:36.854 2G / 9G INFO GapCloser (gap_closer.cpp : 395) Closing short gaps 5:23:37.414 2G / 9G INFO GapCloser (gap_closer.cpp : 424) Closing short gaps complete: filled 175 gaps after checking 11744 candidates 5:23:38.358 2G / 9G INFO StageManager (stage.cpp : 125) STAGE == Simplification Cleanup 5:23:38.358 2G / 9G INFO General (graph_simplification.hpp : 403) Removing isolated edges 5:23:38.359 2G / 9G INFO General (graph_simplification.hpp : 404) All edges shorter than 151 will be removed 5:23:38.359 2G / 9G INFO General (graph_simplification.hpp : 405) Also edges shorter than 0 and coverage smaller than 2 will be removed 5:23:39.783 2G / 9G INFO General (simplification.cpp : 56) Removing all the edges having coverage 0 and less 5:23:40.123 2G / 9G INFO General (simplification.cpp : 68) Counting average coverage 5:23:40.197 2G / 9G INFO General (simplification.cpp : 71) Average coverage = 15.419 5:23:40.197 2G / 9G INFO StageManager (stage.cpp : 125) STAGE == Mismatch Correction 5:24:14.936 2G / 9G INFO General (mismatch_shall_not_pass.hp: 188) Finished collecting potential mismatches positions 5:24:15.068 2G / 9G INFO General (mismatch_shall_not_pass.hp: 291) All edges processed 5:24:15.074 2G / 9G INFO General (mismatch_correction.cpp : 18) Corrected 0 nucleotides 5:24:15.091 2G / 9G INFO StageManager (stage.cpp : 125) STAGE == Paired Information Counting 5:24:15.485 2G / 9G INFO General (pair_info_count.cpp : 150) Graph N50: 11215 5:24:15.485 2G / 9G INFO General (pair_info_count.cpp : 152) Estimating insert size for library #0 5:24:15.485 2G / 9G INFO General (pair_info_count.cpp : 31) Estimating insert size (takes a while) 5:24:15.496 2G / 9G INFO General (short_read_mapper.hpp : 91) Selecting usual mapper 5:24:21.738 2G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 200000 reads 5:24:21.747 2G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 400000 reads 5:24:21.777 2G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 600000 reads 5:24:21.785 2G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 800000 reads 5:24:21.797 2G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 1000000 reads 5:24:21.811 2G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 1200000 reads 5:24:22.293 2G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 2200000 reads 5:24:28.321 2G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 4200000 reads 5:24:35.017 2G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 8497824 reads 5:24:35.277 2G / 9G INFO General (sequence_mapper_notifier.h: 89) Processed 9197097 reads 5:24:35.278 2G / 9G INFO General (pair_info_count.cpp : 41) 4679229 paired reads (50.8772% of all) aligned to long edges 5:24:35.290 2G / 9G INFO General (pair_info_count.cpp : 170) Estimated insert size for paired library #0 5:24:35.290 2G / 9G INFO General (pair_info_count.cpp : 175) Insert size = 303.686, deviation = 87.9397, left quantile = 197, right quantile = 420, read length = 151 5:24:35.290 2G / 9G INFO General (pair_info_count.cpp : 187) Mapping library #0 5:24:35.290 2G / 9G INFO General (pair_info_count.cpp : 189) Mapping paired reads (takes a while) 5:24:35.290 2G / 9G INFO General (pair_info_count.cpp : 73) Left insert size qauntile 197, right insert size quantile 420 5:24:35.299 2G / 9G INFO General (short_read_mapper.hpp : 91) Selecting usual mapper 5:24:44.207 5G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 200000 reads 5:24:45.056 5G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 400000 reads 5:24:45.947 5G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 600000 reads 5:24:46.998 5G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 800000 reads 5:24:48.176 5G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 1000000 reads 5:24:49.423 5G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 1200000 reads 5:24:56.851 5G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 2200000 reads 5:25:13.801 5G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 4200000 reads 5:25:50.890 5G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 8400000 reads 5:27:12.438 5G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 16897826 reads 5:27:28.903 3G / 9G INFO General (sequence_mapper_notifier.h: 89) Processed 18394194 reads 5:29:19.972 3G / 9G INFO General (split_graph_pair_info.hpp : 344) Threshold for paired information 0.0508546 5:29:23.870 3G / 9G INFO StageManager (stage.cpp : 125) STAGE == Distance Estimation 5:29:23.870 3G / 9G INFO General (distance_estimation.cpp : 234) Processing library #0 5:29:23.870 3G / 9G INFO General (distance_estimation.cpp : 136) Weight Filter Done 5:29:23.871 3G / 9G INFO DistanceEstimator (distance_estimation.hpp : 187) Using SIMPLE distance estimator 5:29:34.329 3G / 9G INFO DistanceEstimator (distance_estimation.hpp : 208) Merging maps 5:29:36.110 3G / 9G INFO General (distance_estimation.cpp : 38) Filtering info 5:29:39.096 3G / 9G INFO General (pair_info_filters.hpp : 354) Pruning the index 5:29:39.196 3G / 9G INFO General (distance_estimation.cpp : 184) Refining clustered pair information 5:29:39.391 3G / 9G INFO General (distance_estimation.cpp : 186) The refining of clustered pair information has been finished 5:29:39.391 3G / 9G INFO General (distance_estimation.cpp : 188) Filling paired information 5:29:42.090 3G / 9G INFO PairInfoImprover (pair_info_improver.hpp : 61) Paired info stats: missing = 77122; contradictional = 3792 5:29:45.054 3G / 9G INFO PairInfoImprover (pair_info_improver.hpp : 61) Paired info stats: missing = 14429; contradictional = 0 5:29:45.054 3G / 9G INFO General (distance_estimation.cpp : 193) Filling scaffolding index 5:29:45.054 3G / 9G INFO DistanceEstimator (distance_estimation.hpp : 187) Using SMOOTHING distance estimator 5:29:58.620 3G / 9G INFO DistanceEstimator (distance_estimation.hpp : 208) Merging maps 5:29:58.687 3G / 9G INFO General (distance_estimation.cpp : 38) Filtering info 5:29:59.067 3G / 9G INFO General (pair_info_filters.hpp : 354) Pruning the index 5:29:59.686 2G / 9G INFO StageManager (stage.cpp : 125) STAGE == Repeat Resolving 5:29:59.686 2G / 9G INFO General (contig_output.hpp : 283) Outputting contigs to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.biaurelia-Sample_USBL-36I1-dipSPAdes-3.5.0-trimmed/spades//K77/before_rr.fasta 5:31:09.920 2G / 9G INFO General (repeat_resolving.cpp : 59) Using Path-Extend repeat resolving 5:31:09.921 2G / 9G INFO General (path_extend_launch.hpp : 459) Threshold for library #0 is 0.0508546 5:31:09.921 2G / 9G INFO General (path_extend_launch.hpp : 298) Path-Extend repeat resolving tool started 5:31:10.015 2G / 9G INFO General (path_extend_launch.hpp : 316) Using 1 paired-end library 5:31:10.015 2G / 9G INFO General (path_extend_launch.hpp : 317) Using 1 paired-end scaffolding library 5:31:10.015 2G / 9G INFO General (path_extend_launch.hpp : 318) Using 0 mate-pair libraries 5:31:10.016 2G / 9G INFO General (path_extend_launch.hpp : 319) Using 0 single read libraries 5:31:10.016 2G / 9G INFO General (path_extend_launch.hpp : 320) Scaffolder is on 5:31:10.660 3G / 9G INFO General (path_extend_launch.hpp : 332) Growing paths using paired-end and long single reads 5:31:10.660 3G / 9G INFO PathExtender (path_extender.hpp : 611) Processed 0 paths from 50960 (0%) 5:31:14.439 3G / 9G INFO PathExtender (path_extender.hpp : 609) Processed 128 paths from 50960 (0%) 5:31:17.474 3G / 9G INFO PathExtender (path_extender.hpp : 609) Processed 256 paths from 50960 (0%) 5:31:24.092 3G / 9G INFO PathExtender (path_extender.hpp : 609) Processed 512 paths from 50960 (1%) 5:31:30.919 3G / 9G INFO PathExtender (path_extender.hpp : 609) Processed 1024 paths from 50960 (2%) 5:31:37.185 3G / 9G INFO PathExtender (path_extender.hpp : 609) Processed 2048 paths from 50960 (4%) 5:31:40.473 3G / 9G INFO PathExtender (path_extender.hpp : 609) Processed 4096 paths from 50960 (8%) 5:31:41.149 3G / 9G INFO PathExtender (path_extender.hpp : 611) Processed 5097 paths from 50960 (10%) 5:31:42.740 3G / 9G INFO PathExtender (path_extender.hpp : 609) Processed 8192 paths from 50960 (16%) 5:31:43.344 3G / 9G INFO PathExtender (path_extender.hpp : 611) Processed 10194 paths from 50960 (20%) 5:31:44.781 3G / 9G INFO PathExtender (path_extender.hpp : 611) Processed 15291 paths from 50960 (30%) 5:31:44.897 3G / 9G INFO PathExtender (path_extender.hpp : 609) Processed 16384 paths from 50960 (32%) 5:31:45.613 3G / 9G INFO PathExtender (path_extender.hpp : 611) Processed 20388 paths from 50960 (40%) 5:31:46.484 3G / 9G INFO PathExtender (path_extender.hpp : 611) Processed 25485 paths from 50960 (50%) 5:31:47.249 3G / 9G INFO PathExtender (path_extender.hpp : 611) Processed 30582 paths from 50960 (60%) 5:31:47.609 3G / 9G INFO PathExtender (path_extender.hpp : 609) Processed 32768 paths from 50960 (64%) 5:31:49.043 3G / 9G INFO PathExtender (path_extender.hpp : 611) Processed 35679 paths from 50960 (70%) 5:31:57.218 3G / 9G INFO PathExtender (path_extender.hpp : 611) Processed 40776 paths from 50960 (80%) 5:31:58.789 3G / 9G INFO PathExtender (path_extender.hpp : 611) Processed 45873 paths from 50960 (90%) 5:32:01.157 3G / 9G INFO PathExtendIO (pe_io.hpp : 339) Constructing FASTG file from paths 5:32:01.914 3G / 9G INFO PathExtendIO (pe_io.hpp : 342) Writing contigs in FASTG to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.biaurelia-Sample_USBL-36I1-dipSPAdes-3.5.0-trimmed/spades//K77/final_contigs.fastg 5:32:01.914 3G / 9G INFO PathExtendIO (pe_io.hpp : 343) Writing contigs in FASTA to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.biaurelia-Sample_USBL-36I1-dipSPAdes-3.5.0-trimmed/spades//K77/final_contigs.fasta 5:33:09.079 3G / 9G INFO PathExtendIO (pe_io.hpp : 339) Constructing FASTG file from paths 5:33:09.843 3G / 9G INFO PathExtendIO (pe_io.hpp : 342) Writing contigs in FASTG to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.biaurelia-Sample_USBL-36I1-dipSPAdes-3.5.0-trimmed/spades//K77/path_extend/pe_before_traversal.fastg 5:33:09.844 3G / 9G INFO PathExtendIO (pe_io.hpp : 343) Writing contigs in FASTA to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.biaurelia-Sample_USBL-36I1-dipSPAdes-3.5.0-trimmed/spades//K77/path_extend/pe_before_traversal.fasta 5:33:58.766 3G / 9G INFO General (path_extend_launch.hpp : 281) Traversing tandem repeats 5:34:00.388 3G / 9G INFO PathExtendIO (pe_io.hpp : 339) Constructing FASTG file from paths 5:34:01.129 3G / 9G INFO PathExtendIO (pe_io.hpp : 342) Writing contigs in FASTG to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.biaurelia-Sample_USBL-36I1-dipSPAdes-3.5.0-trimmed/spades//K77/scaffolds.fastg 5:34:01.129 3G / 9G INFO PathExtendIO (pe_io.hpp : 343) Writing contigs in FASTA to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.biaurelia-Sample_USBL-36I1-dipSPAdes-3.5.0-trimmed/spades//K77/scaffolds.fasta 5:34:51.303 3G / 9G INFO General (launch.hpp : 82) SPAdes finished 5:34:55.294 424M / 9G INFO General (main.cpp : 166) Assembling time: 5 hours 34 minutes 55 seconds ===== Assembling finished. * Corrected reads are in /N/dc2/projects/marinovg/2015-09-07-assemblies/P.biaurelia-Sample_USBL-36I1-dipSPAdes-3.5.0-trimmed/spades/corrected/ * Assembled contigs are in /N/dc2/projects/marinovg/2015-09-07-assemblies/P.biaurelia-Sample_USBL-36I1-dipSPAdes-3.5.0-trimmed/spades/contigs.fasta (contigs.fastg) * Assembled scaffolds are in /N/dc2/projects/marinovg/2015-09-07-assemblies/P.biaurelia-Sample_USBL-36I1-dipSPAdes-3.5.0-trimmed/spades/scaffolds.fasta (scaffolds.fastg) ======= SPAdes pipeline finished WITH WARNINGS! === Pipeline warnings: * Default k-mer sizes were set to [21, 33, 55, 77] because estimated read length (151) is equal to or greater than 150 ======= Warnings saved to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.biaurelia-Sample_USBL-36I1-dipSPAdes-3.5.0-trimmed/spades/warnings.log SPAdes log can be found here: /N/dc2/projects/marinovg/2015-09-07-assemblies/P.biaurelia-Sample_USBL-36I1-dipSPAdes-3.5.0-trimmed/spades/spades.log Thank you for using SPAdes!