Command line: --diploid --pe1-1 /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_133/reads.end1.paired.fastq.gz --pe1-2 /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_133/reads.end2.paired.fastq.gz -t 16 -o /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_133-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.sexaurelia-Sample_133-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.sexaurelia-Sample_133/reads.end1.paired.fastq.gz'] right reads: ['/N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_133/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.sexaurelia-Sample_133-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.sexaurelia-Sample_133-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.sexaurelia-Sample_133-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.sexaurelia-Sample_133-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 0:00:10.112 4M / 4M INFO General (main.cpp : 97) Determined value is 33 0:00:10.112 4M / 4M INFO General (hammer_tools.cpp : 36) Hamming graph threshold tau=1, k=21, subkmer positions = [ 0 10 ] === ITERATION 0 begins === 0:00:10.114 4M / 4M INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:00:10.114 4M / 4M INFO K-mer Splitting (kmer_data.cpp : 127) Splitting kmer instances into 256 buckets. This might take a while. 0:00:10.115 4M / 4M INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:00:10.115 4M / 4M INFO K-mer Splitting (kmer_data.cpp : 145) Memory available for splitting buffers: 2.08325 Gb 0:00:10.115 4M / 4M INFO K-mer Splitting (kmer_data.cpp : 153) Using cell size of 262144 0:00:13.775 8G / 8G INFO K-mer Splitting (kmer_data.cpp : 167) Processing /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_133/reads.end1.paired.fastq.gz 0:09:33.967 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 176) Processed 3485852 reads 0:16:18.433 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 176) Processed 6500916 reads 0:24:38.649 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 176) Processed 9753271 reads 0:34:42.063 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 176) Processed 12368551 reads 0:34:42.065 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 167) Processing /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_133/reads.end2.paired.fastq.gz 0:46:44.557 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 176) Processed 15728396 reads 0:53:42.766 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 176) Processed 18873694 reads 1:03:59.587 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 176) Processed 22130474 reads 1:11:04.696 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 176) Processed 24737102 reads 1:11:04.698 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 181) Processed 24737102 reads 1:11:05.906 64M / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 1:15:41.633 64M / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 301583386 kmers in total. 1:15:41.633 64M / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 1:16:36.760 64M / 9G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 1:17:18.651 192M / 10G INFO General (kmer_index.hpp : 371) Merging final buckets. 1:17:52.179 192M / 10G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 104329036 bytes occupied (2.7675 bits per kmer). 1:17:52.181 192M / 10G INFO K-mer Counting (kmer_data.cpp : 266) Arranging kmers in hash map order 1:20:51.442 192M / 10G INFO K-mer Counting (kmer_data.cpp : 279) Done. Total swaps: 301583133 1:20:53.455 2G / 10G INFO General (main.cpp : 151) Clustering Hamming graph. 1:20:53.456 2G / 10G INFO Hamming Clustering (hamcluster.cpp : 115) Serializing sub-kmers. 1:20:53.456 2G / 10G INFO Hamming Clustering (hamcluster.cpp : 120) Serializing: [0, 10) 1:24:13.977 2G / 10G INFO Hamming Clustering (hamcluster.cpp : 120) Serializing: [10, 21) 1:27:34.807 2G / 10G INFO Hamming Clustering (hamcluster.cpp : 129) Splitting sub-kmers, pass 1. 1:32:03.378 2G / 10G INFO Hamming Clustering (hamcluster.cpp : 134) Splitting done. Processed 2 blocks. Produced 5007115 blocks. 1:32:03.378 2G / 10G INFO Hamming Clustering (hamcluster.cpp : 145) Merge sub-kmers, pass 1 1:48:32.734 2G / 10G INFO Hamming Clustering (hamcluster.cpp : 170) Merge done, total 1617502 new blocks generated. 1:48:34.752 2G / 10G INFO Hamming Clustering (hamcluster.cpp : 175) Spliting sub-kmers, pass 2. 2:29:45.894 2G / 10G INFO Hamming Clustering (hamcluster.cpp : 180) Splitting done. Processed 3235004 blocks. Produced 567497742 blocks. 2:29:45.894 2G / 10G INFO Hamming Clustering (hamcluster.cpp : 187) Merge sub-kmers, pass 2 2:44:15.185 2G / 10G INFO Hamming Clustering (hamcluster.cpp : 205) Merge done, saw 314269 big blocks out of 567497742 processed. 2:49:16.536 2G / 10G INFO General (main.cpp : 165) Clustering done. Total clusters: 138088772 2:49:16.536 2G / 10G INFO K-mer Counting (kmer_data.cpp : 284) Collecting K-mer information, this takes a while. 2:49:22.619 15G / 15G INFO K-mer Counting (kmer_data.cpp : 290) Processing /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_133/reads.end1.paired.fastq.gz 2:52:25.321 15G / 15G INFO K-mer Counting (kmer_data.cpp : 290) Processing /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_133/reads.end2.paired.fastq.gz 2:55:21.838 15G / 15G INFO K-mer Counting (kmer_data.cpp : 297) Collection done, postprocessing. 2:55:29.324 15G / 15G INFO K-mer Counting (kmer_data.cpp : 310) There are 301583386 kmers in total. Among them 147573942 (48.933%) are singletons. 2:55:29.325 15G / 15G INFO General (main.cpp : 203) Subclustering Hamming graph 2:59:19.610 15G / 15G INFO Hamming Subclustering (kmer_cluster.cpp : 626) Subclustering done. Total 99779 non-read kmers were generated. 2:59:19.610 15G / 15G INFO Hamming Subclustering (kmer_cluster.cpp : 627) Subclustering statistics: 2:59:19.610 15G / 15G INFO Hamming Subclustering (kmer_cluster.cpp : 628) Total singleton hamming clusters: 77937395. Among them 58263699 (74.7571%) are good 2:59:19.610 15G / 15G INFO Hamming Subclustering (kmer_cluster.cpp : 629) Total singleton subclusters: 7781549. Among them 7781442 (99.9986%) are good 2:59:19.610 15G / 15G INFO Hamming Subclustering (kmer_cluster.cpp : 630) Total non-singleton subcluster centers: 65554546. Among them 43308365 (66.0646%) are good 2:59:19.610 15G / 15G INFO Hamming Subclustering (kmer_cluster.cpp : 631) Average size of non-trivial subcluster: 3.38576 kmers 2:59:19.610 15G / 15G INFO Hamming Subclustering (kmer_cluster.cpp : 632) Average number of sub-clusters per non-singleton cluster: 1.21919 2:59:19.610 15G / 15G INFO Hamming Subclustering (kmer_cluster.cpp : 633) Total solid k-mers: 109353506 2:59:19.610 15G / 15G INFO Hamming Subclustering (kmer_cluster.cpp : 634) Substitution probabilities: [4,4]((0.897197,0.0238363,0.0260327,0.052934),(0.0363956,0.927362,0.0133497,0.0228928),(0.0218231,0.0129675,0.928611,0.0365989),(0.0523176,0.0263272,0.0242493,0.897106)) 2:59:20.295 15G / 15G INFO General (main.cpp : 208) Finished clustering. 2:59:20.295 15G / 15G INFO General (main.cpp : 228) Starting solid k-mers expansion in 16 threads. 3:03:28.376 15G / 15G INFO General (main.cpp : 249) Solid k-mers iteration 0 produced 48470462 new k-mers. 3:07:36.389 15G / 15G INFO General (main.cpp : 249) Solid k-mers iteration 1 produced 1396448 new k-mers. 3:11:47.467 15G / 15G INFO General (main.cpp : 249) Solid k-mers iteration 2 produced 61465 new k-mers. 3:15:55.028 15G / 15G INFO General (main.cpp : 249) Solid k-mers iteration 3 produced 5233 new k-mers. 3:20:02.456 15G / 15G INFO General (main.cpp : 249) Solid k-mers iteration 4 produced 638 new k-mers. 3:24:09.788 15G / 15G INFO General (main.cpp : 249) Solid k-mers iteration 5 produced 215 new k-mers. 3:28:17.339 15G / 15G INFO General (main.cpp : 249) Solid k-mers iteration 6 produced 7 new k-mers. 3:28:17.340 15G / 15G INFO General (main.cpp : 253) Solid k-mers finalized 3:28:17.340 15G / 15G INFO General (hammer_tools.cpp : 210) Starting read correction in 16 threads. 3:28:17.340 15G / 15G INFO General (hammer_tools.cpp : 222) Correcting pair of reads: /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_133/reads.end1.paired.fastq.gz and /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_133/reads.end2.paired.fastq.gz 3:28:42.865 17G / 17G INFO General (hammer_tools.cpp : 166) Prepared batch 0 of 1600000 reads. 3:29:03.491 17G / 17G INFO General (hammer_tools.cpp : 175) Processed batch 0 3:29:18.998 17G / 17G INFO General (hammer_tools.cpp : 185) Written batch 0 3:29:42.641 17G / 17G INFO General (hammer_tools.cpp : 166) Prepared batch 1 of 1600000 reads. 3:30:03.265 17G / 17G INFO General (hammer_tools.cpp : 175) Processed batch 1 3:30:18.639 17G / 17G INFO General (hammer_tools.cpp : 185) Written batch 1 3:30:42.016 17G / 17G INFO General (hammer_tools.cpp : 166) Prepared batch 2 of 1600000 reads. 3:31:02.649 17G / 17G INFO General (hammer_tools.cpp : 175) Processed batch 2 3:31:17.981 17G / 17G INFO General (hammer_tools.cpp : 185) Written batch 2 3:31:41.283 17G / 17G INFO General (hammer_tools.cpp : 166) Prepared batch 3 of 1600000 reads. 3:32:01.836 17G / 17G INFO General (hammer_tools.cpp : 175) Processed batch 3 3:32:18.647 17G / 17G INFO General (hammer_tools.cpp : 185) Written batch 3 3:32:42.014 17G / 17G INFO General (hammer_tools.cpp : 166) Prepared batch 4 of 1600000 reads. 3:33:02.679 17G / 17G INFO General (hammer_tools.cpp : 175) Processed batch 4 3:33:18.166 17G / 17G INFO General (hammer_tools.cpp : 185) Written batch 4 3:33:41.543 17G / 17G INFO General (hammer_tools.cpp : 166) Prepared batch 5 of 1600000 reads. 3:34:02.065 17G / 17G INFO General (hammer_tools.cpp : 175) Processed batch 5 3:34:17.600 17G / 17G INFO General (hammer_tools.cpp : 185) Written batch 5 3:34:40.507 17G / 17G INFO General (hammer_tools.cpp : 166) Prepared batch 6 of 1600000 reads. 3:35:01.269 17G / 17G INFO General (hammer_tools.cpp : 175) Processed batch 6 3:35:16.673 17G / 17G INFO General (hammer_tools.cpp : 185) Written batch 6 3:35:33.435 17G / 17G INFO General (hammer_tools.cpp : 166) Prepared batch 7 of 1168551 reads. 3:35:48.758 17G / 17G INFO General (hammer_tools.cpp : 175) Processed batch 7 3:36:00.059 17G / 17G INFO General (hammer_tools.cpp : 185) Written batch 7 3:36:03.227 15G / 17G INFO General (hammer_tools.cpp : 269) Correction done. Changed 4606194 bases in 3614440 reads. 3:36:03.227 15G / 17G INFO General (hammer_tools.cpp : 270) Failed to correct 437490603 bases out of 3684239332. 3:36:03.328 2G / 17G INFO General (main.cpp : 286) Saving corrected dataset description to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_133-dipSPAdes-3.5.0-trimmed/spades/corrected/corrected.yaml 3:36:03.331 2G / 17G 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.sexaurelia-Sample_133-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.sexaurelia-Sample_133-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 0:00:00.002 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 0:00:01.127 80M / 80M INFO General (binary_converter.hpp : 138) 16384 reads processed 0:00:01.530 96M / 96M INFO General (binary_converter.hpp : 138) 32768 reads processed 0:00:02.330 124M / 124M INFO General (binary_converter.hpp : 138) 65536 reads processed 0:00:03.936 184M / 184M INFO General (binary_converter.hpp : 138) 131072 reads processed 0:00:07.143 300M / 300M INFO General (binary_converter.hpp : 138) 262144 reads processed 0:00:13.579 536M / 536M INFO General (binary_converter.hpp : 138) 524288 reads processed 0:00:29.121 900M / 900M INFO General (binary_converter.hpp : 138) 1048576 reads processed 0:00:57.684 904M / 904M INFO General (binary_converter.hpp : 138) 2097152 reads processed 0:01:55.059 904M / 904M INFO General (binary_converter.hpp : 138) 4194304 reads processed 0:03:52.571 904M / 904M INFO General (binary_converter.hpp : 138) 8388608 reads processed 0:05:40.788 240M / 908M INFO General (binary_converter.hpp : 158) 12244262 reads written 0:05:41.055 4M / 908M INFO General (read_converter.hpp : 91) Single reads for library #0 0:05:42.918 140M / 908M INFO General (binary_converter.hpp : 138) 16384 reads processed 0:05:43.140 144M / 908M INFO General (binary_converter.hpp : 138) 32768 reads processed 0:05:43.527 160M / 908M INFO General (binary_converter.hpp : 138) 65536 reads processed 0:05:44.428 184M / 908M INFO General (binary_converter.hpp : 158) 124135 reads written 0:05:44.590 4M / 908M INFO General (graph_construction.hpp : 129) Constructing DeBruijn graph for k=21 0:05:44.593 4M / 908M INFO General (kmer_splitters.hpp : 172) Splitting kmer instances into 256 buckets. This might take a while. 0:05:44.594 4M / 908M INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:05:44.594 4M / 908M INFO General (kmer_splitters.hpp : 190) Memory available for splitting buffers: 2.08325 Gb 0:05:44.594 4M / 908M INFO General (kmer_splitters.hpp : 199) Using cell size of 262144 0:06:32.544 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 16699720 reads 0:07:49.325 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 33387328 reads 0:08:13.495 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 49225318 reads 0:08:13.496 8G / 9G INFO General (kmer_splitters.hpp : 234) Adding contigs from previous K 0:08:13.497 8G / 9G INFO General (kmer_splitters.hpp : 245) Used 49225318 reads. Maximum read length 151 0:08:13.498 8G / 9G INFO General (kmer_splitters.hpp : 246) Average read length 149.647 0:08:15.699 64M / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:08:22.798 64M / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 124445221 kmers in total. 0:08:22.798 64M / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:08:28.986 64M / 9G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:08:28.987 64M / 9G INFO General (kmer_splitters.hpp : 379) Splitting kmer instances into 256 buckets. This might take a while. 0:08:28.987 64M / 9G INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:08:28.987 64M / 9G INFO General (kmer_splitters.hpp : 397) Memory available for splitting buffers: 2.08203 Gb 0:08:28.987 64M / 9G INFO General (kmer_splitters.hpp : 405) Using cell size of 262144 0:08:44.349 8G / 9G INFO General (kmer_splitters.hpp : 428) Processed 124445221 kmers 0:08:44.350 8G / 9G INFO General (kmer_splitters.hpp : 437) Used 124445221 kmers. 0:08:44.954 64M / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:08:48.669 64M / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 120863006 kmers in total. 0:08:48.669 64M / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:08:54.769 64M / 9G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:09:08.500 68M / 9G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:09:16.834 68M / 9G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 41811088 bytes occupied (2.7675 bits per kmer). 0:09:17.046 184M / 9G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 382) Building k-mer extensions from k+1-mers 0:09:29.325 184M / 9G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 386) Building k-mer extensions from k+1-mers finished. 0:09:29.330 184M / 9G INFO Early tip clipping (early_simplification.hpp : 236) Early tip clipping 0:15:46.201 180M / 9G INFO Early tip clipping (early_simplification.hpp : 239) 5986054 22-mers were removed by early tip clipper 0:15:46.201 180M / 9G INFO General (graph_construction.hpp : 145) Condensing graph 0:15:46.201 180M / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 337) Extracting unbranching paths 0:17:12.937 1G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 351) Extracting unbranching paths finished. 18874897 sequences extracted 0:17:23.605 1G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 311) Collecting perfect loops 0:18:01.057 1G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 326) Collecting perfect loops finished. 16 loops collected 0:18:14.236 3G / 9G INFO General (graph_construction.hpp : 150) Building index with from graph 0:18:14.237 3G / 9G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:18:14.238 3G / 9G INFO General (kmer_splitters.hpp : 289) Splitting kmer instances into 16 buckets. This might take a while. 0:18:14.238 3G / 9G INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:18:14.238 3G / 9G INFO General (kmer_splitters.hpp : 307) Memory available for splitting buffers: 32.1042 Gb 0:18:14.238 3G / 9G INFO General (kmer_splitters.hpp : 312) Using cell size of 4194304 0:18:33.050 4G / 9G INFO General (kmer_splitters.hpp : 325) Processed 10690343 edges 0:18:46.859 4G / 9G INFO General (kmer_splitters.hpp : 325) Processed 18874913 edges 0:18:46.860 4G / 9G INFO General (kmer_splitters.hpp : 330) Used 18874913 sequences. 0:18:46.944 3G / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:19:13.393 3G / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 118459167 kmers in total. 0:19:13.393 3G / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:19:38.704 3G / 9G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:22:26.280 3G / 9G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:22:31.919 3G / 9G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 40979499 bytes occupied (2.7675 bits per kmer). 0:22:34.033 6G / 9G INFO General (edge_index_builders.hpp : 21) Collecting k-mer coverage information from graph, this takes a while. 0:26:08.649 6G / 9G INFO General (graph_construction.hpp : 182) Filling coverage index 0:26:08.649 6G / 9G INFO General (edge_index_builders.hpp : 99) Collecting k-mer coverage information from reads, this takes a while. 0:29:41.395 6G / 9G INFO General (graph_construction.hpp : 184) Filling coverage and flanking coverage from index 0:30:12.549 6G / 9G INFO General (construction.cpp : 33) Figured out: read length = 151 0:30:12.567 6G / 9G INFO StageManager (stage.cpp : 125) STAGE == EC Threshold Finding 0:30:21.998 6G / 9G INFO General (kmer_coverage_model.cpp : 178) Kmer coverage valley at: 18 0:30:21.999 6G / 9G INFO General (kmer_coverage_model.cpp : 198) K-mer histogram maximum: 44 0:30:21.999 6G / 9G INFO General (kmer_coverage_model.cpp : 234) Estimated median coverage: 44. Coverage mad: 10.3782 0:30:21.999 6G / 9G INFO General (kmer_coverage_model.cpp : 261) Fitting coverage model 0:30:22.169 6G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 2 0:30:22.590 6G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 4 0:30:24.042 6G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 8 0:30:27.163 6G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 16 0:30:33.176 6G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 32 0:30:33.948 6G / 9G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 43.7484. Fitted coverage std. dev: 9.69302 0:30:33.952 6G / 9G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 0.327393 0:30:33.952 6G / 9G INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 29 0:30:33.952 6G / 9G INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 29 0:30:33.952 6G / 9G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 61294019 0:30:33.952 6G / 9G INFO General (genomic_info_filler.cpp : 103) Mean coverage was calculated as 43.7484 0:30:33.953 6G / 9G INFO General (genomic_info_filler.cpp : 117) EC coverage threshold value was calculated as 29 0:30:33.954 6G / 9G INFO General (genomic_info_filler.cpp : 118) Trusted kmer low bound: 0 0:30:33.954 6G / 9G INFO StageManager (stage.cpp : 125) STAGE == Simplification 0:30:34.252 3G / 9G INFO General (graph_simplification.hpp : 911) Graph simplification started 0:30:34.252 3G / 9G INFO General (graph_simplification.hpp : 924) Fast simplification mode enabled 0:30:34.252 3G / 9G INFO General (graph_simplification.hpp : 771) PROCEDURE == Presimplification 0:30:34.252 3G / 9G INFO General (graph_simplification.hpp : 211) Removing short low covered self-conjugate connections 0:30:35.442 3G / 9G INFO General (graph_simplification.hpp : 403) Removing isolated edges 0:30:35.444 3G / 9G INFO General (graph_simplification.hpp : 404) All edges shorter than 151 will be removed 0:30:35.445 3G / 9G INFO General (graph_simplification.hpp : 405) Also edges shorter than 0 and coverage smaller than 0 will be removed 0:30:37.023 3G / 9G INFO General (graph_simplification.hpp : 687) Non parallel mode 0:31:36.055 4G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:33:57.361 4G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:37:53.775 3G / 9G INFO General (graph_simplification.hpp : 644) Using permanent iterators 0:37:53.775 3G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 1 0:38:04.236 3G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:38:47.851 3G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:39:14.314 3G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 2 0:39:14.314 3G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:39:14.814 3G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:39:30.552 3G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 3 0:39:30.553 3G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:39:30.859 3G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:39:36.939 3G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 4 0:39:36.939 3G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:39:37.061 3G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:39:40.727 3G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 5 0:39:40.728 3G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:39:40.802 3G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:39:43.878 3G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 6 0:39:43.878 3G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:39:43.940 3G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:39:46.808 3G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 7 0:39:46.808 3G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:39:46.863 3G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:39:49.510 3G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 8 0:39:49.510 3G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:39:49.562 3G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:39:51.735 3G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 9 0:39:51.735 3G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:39:51.777 3G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:39:53.521 3G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 10 0:39:53.521 3G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:39:53.560 3G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:39:55.292 3G / 9G INFO General (graph_simplification.hpp : 796) PROCEDURE == Post simplification 0:39:55.292 3G / 9G INFO General (graph_simplification.hpp : 644) Using permanent iterators 0:39:55.292 3G / 9G INFO General (graph_simplification.hpp : 806) Iteration 0 0:39:55.292 3G / 9G INFO General (graph_simplification.hpp : 247) Removal of relatively low covered connections disabled 0:39:58.616 3G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:40:06.548 3G / 9G INFO General (graph_simplification.hpp : 806) Iteration 1 0:40:06.549 3G / 9G INFO General (graph_simplification.hpp : 247) Removal of relatively low covered connections disabled 0:40:06.549 3G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:40:09.139 3G / 9G INFO StageManager (stage.cpp : 125) STAGE == Simplification Cleanup 0:40:09.140 3G / 9G INFO General (graph_simplification.hpp : 403) Removing isolated edges 0:40:09.140 3G / 9G INFO General (graph_simplification.hpp : 404) All edges shorter than 151 will be removed 0:40:09.140 3G / 9G INFO General (graph_simplification.hpp : 405) Also edges shorter than 0 and coverage smaller than 2 will be removed 0:40:09.347 3G / 9G INFO General (simplification.cpp : 56) Removing all the edges having coverage 0 and less 0:40:15.773 3G / 9G INFO General (simplification.cpp : 68) Counting average coverage 0:40:16.525 3G / 9G INFO General (simplification.cpp : 71) Average coverage = 45.831 0:40:16.525 3G / 9G INFO StageManager (stage.cpp : 125) STAGE == Contig Output 0:40:16.525 3G / 9G INFO General (contig_output.hpp : 283) Outputting contigs to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_133-dipSPAdes-3.5.0-trimmed/spades//K21/simplified_contigs.fasta 0:41:03.186 3G / 9G INFO General (contig_output.hpp : 283) Outputting contigs to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_133-dipSPAdes-3.5.0-trimmed/spades//K21/before_rr.fasta 0:43:11.606 3G / 9G INFO General (contig_output.hpp : 283) Outputting contigs to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_133-dipSPAdes-3.5.0-trimmed/spades//K21/final_contigs.fasta 0:45:19.179 3G / 9G INFO General (launch.hpp : 82) SPAdes finished 0:45:28.876 64M / 9G INFO General (main.cpp : 166) Assembling time: 0 hours 45 minutes 28 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.sexaurelia-Sample_133-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 0:00:00.007 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=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 0:01:14.996 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 9202925 reads 0:01:35.090 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 18416601 reads 0:01:50.303 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 27617747 reads 0:02:05.338 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 36827367 reads 0:02:20.648 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 46014581 reads 0:02:26.715 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 49225318 reads 0:02:26.715 8G / 9G INFO General (kmer_splitters.hpp : 234) Adding contigs from previous K 0:02:46.729 8G / 9G INFO General (kmer_splitters.hpp : 245) Used 49225318 reads. Maximum read length 151 0:02:46.729 8G / 9G INFO General (kmer_splitters.hpp : 246) Average read length 149.647 0:02:48.990 64M / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:03:13.380 64M / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 149809798 kmers in total. 0:03:13.380 64M / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:03:27.639 64M / 9G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:03:27.639 64M / 9G INFO General (kmer_splitters.hpp : 379) Splitting kmer instances into 256 buckets. This might take a while. 0:03:27.640 64M / 9G INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:03:27.640 64M / 9G INFO General (kmer_splitters.hpp : 397) Memory available for splitting buffers: 2.08203 Gb 0:03:27.640 64M / 9G INFO General (kmer_splitters.hpp : 405) Using cell size of 131072 0:03:51.480 8G / 9G INFO General (kmer_splitters.hpp : 428) Processed 149809798 kmers 0:03:51.480 8G / 9G INFO General (kmer_splitters.hpp : 437) Used 149809798 kmers. 0:03:52.360 64M / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:04:00.830 64M / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 148169960 kmers in total. 0:04:00.830 64M / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:04:15.994 64M / 9G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:04:34.034 68M / 9G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:04:50.361 68M / 9G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 51257581 bytes occupied (2.7675 bits per kmer). 0:04:50.593 212M / 9G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 382) Building k-mer extensions from k+1-mers 0:05:07.946 212M / 9G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 386) Building k-mer extensions from k+1-mers finished. 0:05:07.951 212M / 9G INFO Early tip clipping (early_simplification.hpp : 236) Early tip clipping 0:12:49.980 212M / 9G INFO Early tip clipping (early_simplification.hpp : 239) 24527444 34-mers were removed by early tip clipper 0:12:49.980 212M / 9G INFO General (graph_construction.hpp : 145) Condensing graph 0:12:49.980 212M / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 337) Extracting unbranching paths 0:14:32.866 1G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 351) Extracting unbranching paths finished. 9629294 sequences extracted 0:14:44.257 1G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 311) Collecting perfect loops 0:15:33.023 1G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 326) Collecting perfect loops finished. 58 loops collected 0:15:43.895 2G / 9G INFO General (graph_construction.hpp : 150) Building index with from graph 0:15:43.897 2G / 9G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:15:43.897 2G / 9G INFO General (kmer_splitters.hpp : 289) Splitting kmer instances into 16 buckets. This might take a while. 0:15:43.897 2G / 9G INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:15:43.897 2G / 9G INFO General (kmer_splitters.hpp : 307) Memory available for splitting buffers: 32.6393 Gb 0:15:43.897 2G / 9G INFO General (kmer_splitters.hpp : 312) Using cell size of 2097152 0:15:52.167 2G / 9G INFO General (kmer_splitters.hpp : 325) Processed 2583347 edges 0:16:00.625 2G / 9G INFO General (kmer_splitters.hpp : 325) Processed 5163283 edges 0:16:08.679 2G / 9G INFO General (kmer_splitters.hpp : 325) Processed 7739012 edges 0:16:14.551 2G / 9G INFO General (kmer_splitters.hpp : 325) Processed 9629352 edges 0:16:14.552 2G / 9G INFO General (kmer_splitters.hpp : 330) Used 9629352 sequences. 0:16:14.628 2G / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:16:53.025 2G / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 125282354 kmers in total. 0:16:53.025 2G / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:17:05.585 2G / 9G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:20:08.279 2G / 9G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:20:21.136 2G / 9G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 43339903 bytes occupied (2.7675 bits per kmer). 0:20:23.343 4G / 9G INFO General (edge_index_builders.hpp : 21) Collecting k-mer coverage information from graph, this takes a while. 0:24:37.812 4G / 9G INFO General (graph_construction.hpp : 182) Filling coverage index 0:24:37.812 4G / 9G INFO General (edge_index_builders.hpp : 99) Collecting k-mer coverage information from reads, this takes a while. 0:27:54.413 4G / 9G INFO General (graph_construction.hpp : 184) Filling coverage and flanking coverage from index 0:28:26.331 4G / 9G INFO General (construction.cpp : 33) Figured out: read length = 151 0:28:26.347 4G / 9G INFO StageManager (stage.cpp : 125) STAGE == EC Threshold Finding 0:28:37.688 4G / 9G INFO General (kmer_coverage_model.cpp : 178) Kmer coverage valley at: 14 0:28:37.688 4G / 9G INFO General (kmer_coverage_model.cpp : 198) K-mer histogram maximum: 39 0:28:37.689 4G / 9G INFO General (kmer_coverage_model.cpp : 234) Estimated median coverage: 40. Coverage mad: 10.3782 0:28:37.689 4G / 9G INFO General (kmer_coverage_model.cpp : 261) Fitting coverage model 0:28:37.838 4G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 2 0:28:38.223 4G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 4 0:28:39.543 4G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 8 0:28:42.523 4G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 16 0:28:47.981 4G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 32 0:28:48.338 4G / 9G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 39.0404. Fitted coverage std. dev: 9.43478 0:28:48.341 4G / 9G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 0.377461 0:28:48.341 4G / 9G INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 25 0:28:48.341 4G / 9G INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 25 0:28:48.341 4G / 9G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 62186673 0:28:48.341 4G / 9G INFO General (genomic_info_filler.cpp : 103) Mean coverage was calculated as 39.0404 0:28:48.342 4G / 9G INFO General (genomic_info_filler.cpp : 117) EC coverage threshold value was calculated as 25 0:28:48.342 4G / 9G INFO General (genomic_info_filler.cpp : 118) Trusted kmer low bound: 0 0:28:48.342 4G / 9G INFO StageManager (stage.cpp : 125) STAGE == Simplification 0:28:48.605 1G / 9G INFO General (graph_simplification.hpp : 911) Graph simplification started 0:28:48.605 1G / 9G INFO General (graph_simplification.hpp : 924) Fast simplification mode enabled 0:28:48.605 1G / 9G INFO General (graph_simplification.hpp : 771) PROCEDURE == Presimplification 0:28:48.605 1G / 9G INFO General (graph_simplification.hpp : 211) Removing short low covered self-conjugate connections 0:28:49.320 1G / 9G INFO General (graph_simplification.hpp : 403) Removing isolated edges 0:28:49.320 1G / 9G INFO General (graph_simplification.hpp : 404) All edges shorter than 151 will be removed 0:28:49.321 1G / 9G INFO General (graph_simplification.hpp : 405) Also edges shorter than 0 and coverage smaller than 0 will be removed 0:28:50.913 1G / 9G INFO General (graph_simplification.hpp : 687) Non parallel mode 0:29:20.172 2G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:30:29.128 2G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:32:41.919 1G / 9G INFO General (graph_simplification.hpp : 644) Using permanent iterators 0:32:41.919 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 1 0:32:45.338 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:32:59.210 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:33:14.962 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 2 0:33:14.962 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:33:15.108 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:33:21.329 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 3 0:33:21.329 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:33:21.407 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:33:23.912 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 4 0:33:23.912 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:33:23.942 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:33:25.525 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 5 0:33:25.525 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:33:25.541 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:33:26.980 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 6 0:33:26.980 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:33:26.991 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:33:28.705 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 7 0:33:28.705 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:33:28.713 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:33:30.380 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 8 0:33:30.380 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:33:30.388 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:33:31.721 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 9 0:33:31.721 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:33:31.727 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:33:32.582 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 10 0:33:32.582 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:33:32.587 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:33:32.989 1G / 9G INFO General (graph_simplification.hpp : 796) PROCEDURE == Post simplification 0:33:32.989 1G / 9G INFO General (graph_simplification.hpp : 644) Using permanent iterators 0:33:32.989 1G / 9G INFO General (graph_simplification.hpp : 806) Iteration 0 0:33:32.989 1G / 9G INFO General (graph_simplification.hpp : 247) Removal of relatively low covered connections disabled 0:33:33.401 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:33:34.320 1G / 9G INFO General (graph_simplification.hpp : 806) Iteration 1 0:33:34.320 1G / 9G INFO General (graph_simplification.hpp : 247) Removal of relatively low covered connections disabled 0:33:34.320 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:33:34.780 1G / 9G INFO StageManager (stage.cpp : 125) STAGE == Simplification Cleanup 0:33:34.780 1G / 9G INFO General (graph_simplification.hpp : 403) Removing isolated edges 0:33:34.780 1G / 9G INFO General (graph_simplification.hpp : 404) All edges shorter than 151 will be removed 0:33:34.780 1G / 9G INFO General (graph_simplification.hpp : 405) Also edges shorter than 0 and coverage smaller than 2 will be removed 0:33:34.831 1G / 9G INFO General (simplification.cpp : 56) Removing all the edges having coverage 0 and less 0:33:35.572 1G / 9G INFO General (simplification.cpp : 68) Counting average coverage 0:33:35.707 1G / 9G INFO General (simplification.cpp : 71) Average coverage = 38.1622 0:33:35.707 1G / 9G INFO StageManager (stage.cpp : 125) STAGE == Contig Output 0:33:35.707 1G / 9G INFO General (contig_output.hpp : 283) Outputting contigs to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_133-dipSPAdes-3.5.0-trimmed/spades//K33/simplified_contigs.fasta 0:33:54.540 1G / 9G INFO General (contig_output.hpp : 283) Outputting contigs to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_133-dipSPAdes-3.5.0-trimmed/spades//K33/before_rr.fasta 0:34:49.070 1G / 9G INFO General (contig_output.hpp : 283) Outputting contigs to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_133-dipSPAdes-3.5.0-trimmed/spades//K33/final_contigs.fasta 0:35:43.310 1G / 9G INFO General (launch.hpp : 82) SPAdes finished 0:35:46.315 64M / 9G INFO General (main.cpp : 166) Assembling time: 0 hours 35 minutes 46 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.sexaurelia-Sample_133-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 0:00:00.006 4M / 4M INFO General (read_converter.hpp : 49) Binary reads detected 0:00:00.025 4M / 4M INFO General (graph_construction.hpp : 129) Constructing DeBruijn graph for k=55 0:00:00.027 4M / 4M INFO General (kmer_splitters.hpp : 172) Splitting kmer instances into 256 buckets. This might take a while. 0:00:00.028 4M / 4M INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:00:00.028 4M / 4M INFO General (kmer_splitters.hpp : 190) Memory available for splitting buffers: 2.08325 Gb 0:00:00.028 4M / 4M INFO General (kmer_splitters.hpp : 199) Using cell size of 131072 0:00:19.060 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 11340357 reads 0:00:34.733 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 22691494 reads 0:00:50.318 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 34022793 reads 0:01:05.820 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 45349835 reads 0:01:12.935 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 49225318 reads 0:01:12.936 8G / 9G INFO General (kmer_splitters.hpp : 234) Adding contigs from previous K 0:01:30.523 8G / 9G INFO General (kmer_splitters.hpp : 245) Used 49225318 reads. Maximum read length 151 0:01:30.523 8G / 9G INFO General (kmer_splitters.hpp : 246) Average read length 149.647 0:01:32.777 64M / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:01:56.716 64M / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 173489723 kmers in total. 0:01:56.716 64M / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:02:17.112 64M / 9G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:02:17.112 64M / 9G INFO General (kmer_splitters.hpp : 379) Splitting kmer instances into 256 buckets. This might take a while. 0:02:17.112 64M / 9G INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:02:17.112 64M / 9G INFO General (kmer_splitters.hpp : 397) Memory available for splitting buffers: 2.08203 Gb 0:02:17.112 64M / 9G INFO General (kmer_splitters.hpp : 405) Using cell size of 131072 0:02:47.246 8G / 9G INFO General (kmer_splitters.hpp : 428) Processed 173489723 kmers 0:02:47.247 8G / 9G INFO General (kmer_splitters.hpp : 437) Used 173489723 kmers. 0:02:48.240 64M / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:02:58.016 64M / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 172869303 kmers in total. 0:02:58.016 64M / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:03:15.138 64M / 9G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:03:36.750 68M / 9G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:04:14.442 68M / 9G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 59802011 bytes occupied (2.7675 bits per kmer). 0:04:14.720 236M / 9G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 382) Building k-mer extensions from k+1-mers 0:04:37.616 236M / 9G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 386) Building k-mer extensions from k+1-mers finished. 0:04:37.622 236M / 9G INFO General (graph_construction.hpp : 145) Condensing graph 0:04:37.622 236M / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 337) Extracting unbranching paths 0:06:28.312 1G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 351) Extracting unbranching paths finished. 12379367 sequences extracted 0:06:44.618 1G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 311) Collecting perfect loops 0:07:43.222 1G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 326) Collecting perfect loops finished. 2 loops collected 0:07:54.096 2G / 9G INFO General (graph_construction.hpp : 150) Building index with from graph 0:07:54.097 2G / 9G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:07:54.097 2G / 9G INFO General (kmer_splitters.hpp : 289) Splitting kmer instances into 16 buckets. This might take a while. 0:07:54.097 2G / 9G INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:07:54.098 2G / 9G INFO General (kmer_splitters.hpp : 307) Memory available for splitting buffers: 32.3424 Gb 0:07:54.098 2G / 9G INFO General (kmer_splitters.hpp : 312) Using cell size of 2097152 0:09:02.433 3G / 9G INFO General (kmer_splitters.hpp : 325) Processed 2394187 edges 0:09:59.945 3G / 9G INFO General (kmer_splitters.hpp : 325) Processed 4788964 edges 0:10:44.982 3G / 9G INFO General (kmer_splitters.hpp : 325) Processed 7181603 edges 0:12:14.094 3G / 9G INFO General (kmer_splitters.hpp : 325) Processed 9574535 edges 0:12:42.252 3G / 9G INFO General (kmer_splitters.hpp : 325) Processed 11972377 edges 0:12:43.807 3G / 9G INFO General (kmer_splitters.hpp : 325) Processed 12379369 edges 0:12:43.808 3G / 9G INFO General (kmer_splitters.hpp : 330) Used 12379369 sequences. 0:12:43.886 2G / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:13:45.967 2G / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 173489723 kmers in total. 0:13:45.967 2G / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:14:17.468 2G / 9G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:18:27.206 3G / 9G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:18:44.806 3G / 9G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 60016641 bytes occupied (2.7675 bits per kmer). 0:18:47.855 6G / 9G INFO General (edge_index_builders.hpp : 21) Collecting k-mer coverage information from graph, this takes a while. 0:24:20.826 6G / 9G INFO General (graph_construction.hpp : 182) Filling coverage index 0:24:20.826 6G / 9G INFO General (edge_index_builders.hpp : 99) Collecting k-mer coverage information from reads, this takes a while. 0:27:24.387 6G / 9G INFO General (graph_construction.hpp : 184) Filling coverage and flanking coverage from index 0:28:06.403 6G / 9G INFO General (construction.cpp : 33) Figured out: read length = 151 0:28:06.420 6G / 9G INFO StageManager (stage.cpp : 125) STAGE == EC Threshold Finding 0:28:17.018 6G / 9G INFO General (kmer_coverage_model.cpp : 178) Kmer coverage valley at: 10 0:28:17.018 6G / 9G INFO General (kmer_coverage_model.cpp : 198) K-mer histogram maximum: 31 0:28:17.018 6G / 9G INFO General (kmer_coverage_model.cpp : 234) Estimated median coverage: 32. Coverage mad: 8.8956 0:28:17.018 6G / 9G INFO General (kmer_coverage_model.cpp : 261) Fitting coverage model 0:28:17.134 6G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 2 0:28:17.440 6G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 4 0:28:18.441 6G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 8 0:28:21.075 6G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 16 0:28:25.403 6G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 32 0:28:27.008 6G / 9G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 30.9235. Fitted coverage std. dev: 8.5215 0:28:27.011 6G / 9G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 0.36525 0:28:27.011 6G / 9G INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 19 0:28:27.011 6G / 9G INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 19 0:28:27.011 6G / 9G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 62476020 0:28:27.011 6G / 9G INFO General (genomic_info_filler.cpp : 103) Mean coverage was calculated as 30.9235 0:28:27.011 6G / 9G INFO General (genomic_info_filler.cpp : 117) EC coverage threshold value was calculated as 19 0:28:27.012 6G / 9G INFO General (genomic_info_filler.cpp : 118) Trusted kmer low bound: 0 0:28:27.012 6G / 9G INFO StageManager (stage.cpp : 125) STAGE == Gap Closer 0:28:27.022 6G / 9G INFO General (gap_closer.cpp : 157) Preparing shift maps 0:28:37.941 7G / 9G INFO General (gap_closer.cpp : 117) Processing paired reads (takes a while) 0:29:17.077 7G / 9G INFO General (gap_closer.cpp : 136) Used 24488524 paired reads 0:29:17.078 7G / 9G INFO General (gap_closer.cpp : 138) Merging paired indices 0:29:22.955 6G / 9G INFO GapCloser (gap_closer.cpp : 395) Closing short gaps 0:29:55.673 6G / 9G INFO GapCloser (gap_closer.cpp : 424) Closing short gaps complete: filled 900 gaps after checking 13301 candidates 0:29:59.554 6G / 9G INFO StageManager (stage.cpp : 125) STAGE == Simplification 0:29:59.886 2G / 9G INFO General (graph_simplification.hpp : 911) Graph simplification started 0:29:59.886 2G / 9G INFO General (graph_simplification.hpp : 924) Fast simplification mode enabled 0:29:59.887 2G / 9G INFO General (graph_simplification.hpp : 771) PROCEDURE == Presimplification 0:29:59.887 2G / 9G INFO General (graph_simplification.hpp : 211) Removing short low covered self-conjugate connections 0:30:01.008 2G / 9G INFO General (graph_simplification.hpp : 403) Removing isolated edges 0:30:01.008 2G / 9G INFO General (graph_simplification.hpp : 404) All edges shorter than 151 will be removed 0:30:01.009 2G / 9G INFO General (graph_simplification.hpp : 405) Also edges shorter than 0 and coverage smaller than 0 will be removed 0:30:03.585 2G / 9G INFO General (graph_simplification.hpp : 687) Non parallel mode 0:30:39.343 3G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:32:27.766 2G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:33:25.228 2G / 9G INFO General (graph_simplification.hpp : 644) Using permanent iterators 0:33:25.229 2G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 1 0:33:26.436 2G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:33:31.538 2G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:33:34.557 2G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 2 0:33:34.557 2G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:33:34.598 2G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:33:37.614 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 3 0:33:37.614 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:33:37.658 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:33:39.258 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 4 0:33:39.258 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:33:39.275 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:33:40.339 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 5 0:33:40.339 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:33:40.349 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:33:41.592 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 6 0:33:41.592 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:33:41.598 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:33:43.147 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 7 0:33:43.147 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:33:43.152 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:33:44.986 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 8 0:33:44.986 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:33:44.989 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:33:46.725 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 9 0:33:46.725 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:33:46.728 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:33:48.022 912M / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 10 0:33:48.022 912M / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:33:48.025 912M / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:33:48.850 844M / 9G INFO General (graph_simplification.hpp : 796) PROCEDURE == Post simplification 0:33:48.850 844M / 9G INFO General (graph_simplification.hpp : 644) Using permanent iterators 0:33:48.850 844M / 9G INFO General (graph_simplification.hpp : 806) Iteration 0 0:33:48.850 844M / 9G INFO General (graph_simplification.hpp : 247) Removal of relatively low covered connections disabled 0:33:48.992 840M / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:33:49.271 840M / 9G INFO General (graph_simplification.hpp : 806) Iteration 1 0:33:49.271 840M / 9G INFO General (graph_simplification.hpp : 247) Removal of relatively low covered connections disabled 0:33:49.271 840M / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:33:49.455 804M / 9G INFO StageManager (stage.cpp : 125) STAGE == Gap Closer 0:33:49.455 804M / 9G INFO General (graph_pack.hpp : 84) Index refill 0:33:49.456 804M / 9G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:33:49.456 804M / 9G INFO General (kmer_splitters.hpp : 289) Splitting kmer instances into 16 buckets. This might take a while. 0:33:49.456 804M / 9G INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:33:49.456 804M / 9G INFO General (kmer_splitters.hpp : 307) Memory available for splitting buffers: 33.0716 Gb 0:33:49.456 804M / 9G INFO General (kmer_splitters.hpp : 312) Using cell size of 2097152 0:35:54.401 1G / 9G INFO General (kmer_splitters.hpp : 325) Processed 33680 edges 0:36:49.032 1G / 9G INFO General (kmer_splitters.hpp : 325) Processed 67963 edges 0:37:11.538 1G / 9G INFO General (kmer_splitters.hpp : 325) Processed 74766 edges 0:37:11.538 1G / 9G INFO General (kmer_splitters.hpp : 330) Used 74766 sequences. 0:37:11.566 784M / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:37:34.012 784M / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 73579492 kmers in total. 0:37:34.012 784M / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:37:40.770 784M / 9G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:39:15.533 808M / 9G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:39:22.724 808M / 9G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 25453937 bytes occupied (2.7675 bits per kmer). 0:39:24.000 2G / 9G INFO General (edge_index_builders.hpp : 21) Collecting k-mer coverage information from graph, this takes a while. 0:41:22.542 2G / 9G INFO General (gap_closer.cpp : 157) Preparing shift maps 0:41:22.618 2G / 9G INFO General (gap_closer.cpp : 117) Processing paired reads (takes a while) 0:42:04.038 2G / 9G INFO General (gap_closer.cpp : 136) Used 24488524 paired reads 0:42:04.038 2G / 9G INFO General (gap_closer.cpp : 138) Merging paired indices 0:42:04.137 2G / 9G INFO GapCloser (gap_closer.cpp : 395) Closing short gaps 0:42:04.310 2G / 9G INFO GapCloser (gap_closer.cpp : 424) Closing short gaps complete: filled 35 gaps after checking 2176 candidates 0:42:04.867 2G / 9G INFO StageManager (stage.cpp : 125) STAGE == Simplification Cleanup 0:42:04.867 2G / 9G INFO General (graph_simplification.hpp : 403) Removing isolated edges 0:42:04.867 2G / 9G INFO General (graph_simplification.hpp : 404) All edges shorter than 151 will be removed 0:42:04.868 2G / 9G INFO General (graph_simplification.hpp : 405) Also edges shorter than 0 and coverage smaller than 2 will be removed 0:42:05.178 2G / 9G INFO General (simplification.cpp : 56) Removing all the edges having coverage 0 and less 0:42:05.411 2G / 9G INFO General (simplification.cpp : 68) Counting average coverage 0:42:05.457 2G / 9G INFO General (simplification.cpp : 71) Average coverage = 29.9143 0:42:05.457 2G / 9G INFO StageManager (stage.cpp : 125) STAGE == Contig Output 0:42:05.457 2G / 9G INFO General (contig_output.hpp : 283) Outputting contigs to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_133-dipSPAdes-3.5.0-trimmed/spades//K55/simplified_contigs.fasta 0:42:21.482 2G / 9G INFO General (contig_output.hpp : 283) Outputting contigs to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_133-dipSPAdes-3.5.0-trimmed/spades//K55/before_rr.fasta 0:43:18.026 2G / 9G INFO General (contig_output.hpp : 283) Outputting contigs to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_133-dipSPAdes-3.5.0-trimmed/spades//K55/final_contigs.fasta 0:44:07.077 2G / 9G INFO General (launch.hpp : 82) SPAdes finished 0:44:10.155 68M / 9G INFO General (main.cpp : 166) Assembling time: 0 hours 44 minutes 10 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.sexaurelia-Sample_133-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 0:00:00.006 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 0:05:38.057 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 9833510 reads 0:07:36.870 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 19681307 reads 0:10:28.489 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 29511108 reads 0:11:23.331 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 39355879 reads 0:15:21.245 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 49177159 reads 0:15:21.733 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 49225318 reads 0:15:21.733 8G / 9G INFO General (kmer_splitters.hpp : 234) Adding contigs from previous K 0:15:43.620 8G / 9G INFO General (kmer_splitters.hpp : 245) Used 49225318 reads. Maximum read length 151 0:15:43.621 8G / 9G INFO General (kmer_splitters.hpp : 246) Average read length 149.647 0:15:45.879 64M / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:16:21.793 64M / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 177641494 kmers in total. 0:16:21.794 64M / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:16:47.014 64M / 9G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:16:47.014 64M / 9G INFO General (kmer_splitters.hpp : 379) Splitting kmer instances into 256 buckets. This might take a while. 0:16:47.015 64M / 9G INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:16:47.015 64M / 9G INFO General (kmer_splitters.hpp : 397) Memory available for splitting buffers: 2.08203 Gb 0:16:47.015 64M / 9G INFO General (kmer_splitters.hpp : 405) Using cell size of 87381 0:17:25.757 8G / 9G INFO General (kmer_splitters.hpp : 428) Processed 177641494 kmers 0:17:25.758 8G / 9G INFO General (kmer_splitters.hpp : 437) Used 177641494 kmers. 0:17:27.288 64M / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:18:22.984 64M / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 177799096 kmers in total. 0:18:22.984 64M / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:18:46.997 64M / 9G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:19:10.849 68M / 9G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:19:56.269 68M / 9G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 61507415 bytes occupied (2.7675 bits per kmer). 0:19:56.571 240M / 9G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 382) Building k-mer extensions from k+1-mers 0:20:22.635 240M / 9G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 386) Building k-mer extensions from k+1-mers finished. 0:20:22.641 240M / 9G INFO General (graph_construction.hpp : 145) Condensing graph 0:20:22.641 240M / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 337) Extracting unbranching paths 0:22:29.228 1G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 351) Extracting unbranching paths finished. 10705895 sequences extracted 0:22:47.646 1G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 311) Collecting perfect loops 0:23:57.504 1G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 326) Collecting perfect loops finished. 2 loops collected 0:24:07.853 2G / 9G INFO General (graph_construction.hpp : 150) Building index with from graph 0:24:07.854 2G / 9G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:24:07.855 2G / 9G INFO General (kmer_splitters.hpp : 289) Splitting kmer instances into 16 buckets. This might take a while. 0:24:07.855 2G / 9G INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:24:07.855 2G / 9G INFO General (kmer_splitters.hpp : 307) Memory available for splitting buffers: 32.4023 Gb 0:24:07.855 2G / 9G INFO General (kmer_splitters.hpp : 312) Using cell size of 1398101 0:25:53.745 3G / 9G INFO General (kmer_splitters.hpp : 325) Processed 1348380 edges 0:28:05.149 3G / 9G INFO General (kmer_splitters.hpp : 325) Processed 2696399 edges 0:29:44.813 3G / 9G INFO General (kmer_splitters.hpp : 325) Processed 4044081 edges 0:31:09.124 3G / 9G INFO General (kmer_splitters.hpp : 325) Processed 5393512 edges 0:32:40.306 3G / 9G INFO General (kmer_splitters.hpp : 325) Processed 6740517 edges 0:33:20.004 3G / 9G INFO General (kmer_splitters.hpp : 325) Processed 8089210 edges 0:34:02.592 3G / 9G INFO General (kmer_splitters.hpp : 325) Processed 9438050 edges 0:35:07.398 3G / 9G INFO General (kmer_splitters.hpp : 325) Processed 10705897 edges 0:35:07.398 3G / 9G INFO General (kmer_splitters.hpp : 330) Used 10705897 sequences. 0:35:07.487 2G / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:37:38.179 2G / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 177641494 kmers in total. 0:37:38.179 2G / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:38:02.094 2G / 9G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:42:40.628 2G / 9G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:43:03.753 2G / 9G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 61452894 bytes occupied (2.7675 bits per kmer). 0:43:06.814 6G / 9G INFO General (edge_index_builders.hpp : 21) Collecting k-mer coverage information from graph, this takes a while. 0:49:39.034 6G / 9G INFO General (graph_construction.hpp : 182) Filling coverage index 0:49:39.034 6G / 9G INFO General (edge_index_builders.hpp : 99) Collecting k-mer coverage information from reads, this takes a while. 0:52:25.009 6G / 9G INFO General (graph_construction.hpp : 184) Filling coverage and flanking coverage from index 0:53:10.621 6G / 9G INFO General (construction.cpp : 33) Figured out: read length = 151 0:53:10.638 6G / 9G INFO StageManager (stage.cpp : 125) STAGE == EC Threshold Finding 0:53:21.180 6G / 9G INFO General (kmer_coverage_model.cpp : 178) Kmer coverage valley at: 7 0:53:21.180 6G / 9G INFO General (kmer_coverage_model.cpp : 198) K-mer histogram maximum: 23 0:53:21.180 6G / 9G INFO General (kmer_coverage_model.cpp : 234) Estimated median coverage: 24. Coverage mad: 8.8956 0:53:21.180 6G / 9G INFO General (kmer_coverage_model.cpp : 261) Fitting coverage model 0:53:21.268 6G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 2 0:53:21.501 6G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 4 0:53:22.255 6G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 8 0:53:23.294 6G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 16 0:53:26.825 6G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 32 0:53:28.463 6G / 9G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 23.2365. Fitted coverage std. dev: 7.24259 0:53:28.465 6G / 9G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 0.332589 0:53:28.465 6G / 9G INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 14 0:53:28.465 6G / 9G INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 14 0:53:28.465 6G / 9G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 62241221 0:53:28.465 6G / 9G INFO General (genomic_info_filler.cpp : 103) Mean coverage was calculated as 23.2365 0:53:28.466 6G / 9G INFO General (genomic_info_filler.cpp : 117) EC coverage threshold value was calculated as 14 0:53:28.466 6G / 9G INFO General (genomic_info_filler.cpp : 118) Trusted kmer low bound: 0 0:53:28.466 6G / 9G INFO StageManager (stage.cpp : 125) STAGE == Gap Closer 0:53:28.477 6G / 9G INFO General (gap_closer.cpp : 157) Preparing shift maps 0:53:41.545 7G / 9G INFO General (gap_closer.cpp : 117) Processing paired reads (takes a while) 0:54:13.550 7G / 9G INFO General (gap_closer.cpp : 136) Used 24488524 paired reads 0:54:13.552 7G / 9G INFO General (gap_closer.cpp : 138) Merging paired indices 0:54:22.021 6G / 9G INFO GapCloser (gap_closer.cpp : 395) Closing short gaps 0:54:51.301 6G / 9G INFO GapCloser (gap_closer.cpp : 424) Closing short gaps complete: filled 1200 gaps after checking 18628 candidates 0:54:55.665 6G / 9G INFO StageManager (stage.cpp : 125) STAGE == Simplification 0:54:55.974 2G / 9G INFO General (graph_simplification.hpp : 911) Graph simplification started 0:54:55.974 2G / 9G INFO General (graph_simplification.hpp : 924) Fast simplification mode enabled 0:54:55.974 2G / 9G INFO General (graph_simplification.hpp : 771) PROCEDURE == Presimplification 0:54:55.974 2G / 9G INFO General (graph_simplification.hpp : 211) Removing short low covered self-conjugate connections 0:54:56.958 2G / 9G INFO General (graph_simplification.hpp : 403) Removing isolated edges 0:54:56.959 2G / 9G INFO General (graph_simplification.hpp : 404) All edges shorter than 151 will be removed 0:54:56.960 2G / 9G INFO General (graph_simplification.hpp : 405) Also edges shorter than 0 and coverage smaller than 0 will be removed 0:55:01.756 2G / 9G INFO General (graph_simplification.hpp : 687) Non parallel mode 0:55:35.798 2G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:57:29.529 2G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:57:36.417 1G / 9G INFO General (graph_simplification.hpp : 644) Using permanent iterators 0:57:36.417 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 1 0:57:37.019 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:57:39.517 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:57:39.623 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 2 0:57:39.624 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:57:39.626 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:57:40.631 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 3 0:57:40.632 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:57:40.650 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:57:41.421 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 4 0:57:41.421 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:57:41.434 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:57:42.232 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 5 0:57:42.232 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:57:42.238 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:57:43.167 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 6 0:57:43.168 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:57:43.172 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:57:44.569 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 7 0:57:44.569 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:57:44.572 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:57:46.289 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 8 0:57:46.289 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:57:46.292 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:57:48.050 964M / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 9 0:57:48.050 964M / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:57:48.053 964M / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:57:49.684 808M / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 10 0:57:49.684 808M / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:57:49.686 808M / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:57:50.710 716M / 9G INFO General (graph_simplification.hpp : 796) PROCEDURE == Post simplification 0:57:50.710 716M / 9G INFO General (graph_simplification.hpp : 644) Using permanent iterators 0:57:50.710 716M / 9G INFO General (graph_simplification.hpp : 806) Iteration 0 0:57:50.710 716M / 9G INFO General (graph_simplification.hpp : 247) Removal of relatively low covered connections disabled 0:57:50.815 716M / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:57:51.015 716M / 9G INFO General (graph_simplification.hpp : 806) Iteration 1 0:57:51.016 716M / 9G INFO General (graph_simplification.hpp : 247) Removal of relatively low covered connections disabled 0:57:51.016 716M / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:57:51.168 692M / 9G INFO StageManager (stage.cpp : 125) STAGE == Gap Closer 0:57:51.168 692M / 9G INFO General (graph_pack.hpp : 84) Index refill 0:57:51.169 692M / 9G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:57:51.169 692M / 9G INFO General (kmer_splitters.hpp : 289) Splitting kmer instances into 16 buckets. This might take a while. 0:57:51.169 692M / 9G INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:57:51.169 692M / 9G INFO General (kmer_splitters.hpp : 307) Memory available for splitting buffers: 33.1081 Gb 0:57:51.169 692M / 9G INFO General (kmer_splitters.hpp : 312) Using cell size of 1398101 0:59:45.466 1G / 9G INFO General (kmer_splitters.hpp : 325) Processed 16833 edges 1:01:16.493 1G / 9G INFO General (kmer_splitters.hpp : 325) Processed 33493 edges 1:02:04.596 1G / 9G INFO General (kmer_splitters.hpp : 325) Processed 50096 edges 1:02:43.926 1G / 9G INFO General (kmer_splitters.hpp : 325) Processed 55145 edges 1:02:43.927 1G / 9G INFO General (kmer_splitters.hpp : 330) Used 55145 sequences. 1:02:43.982 688M / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 1:03:33.051 688M / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 74279705 kmers in total. 1:03:33.051 688M / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 1:04:05.480 688M / 9G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 1:05:43.085 712M / 9G INFO General (kmer_index.hpp : 371) Merging final buckets. 1:05:52.778 712M / 9G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 25696171 bytes occupied (2.7675 bits per kmer). 1:05:54.042 2G / 9G INFO General (edge_index_builders.hpp : 21) Collecting k-mer coverage information from graph, this takes a while. 1:08:08.371 2G / 9G INFO General (gap_closer.cpp : 157) Preparing shift maps 1:08:08.446 2G / 9G INFO General (gap_closer.cpp : 117) Processing paired reads (takes a while) 1:09:00.343 2G / 9G INFO General (gap_closer.cpp : 136) Used 24488524 paired reads 1:09:00.343 2G / 9G INFO General (gap_closer.cpp : 138) Merging paired indices 1:09:00.499 2G / 9G INFO GapCloser (gap_closer.cpp : 395) Closing short gaps 1:09:00.712 2G / 9G INFO GapCloser (gap_closer.cpp : 424) Closing short gaps complete: filled 66 gaps after checking 3364 candidates 1:09:01.766 2G / 9G INFO StageManager (stage.cpp : 125) STAGE == Simplification Cleanup 1:09:01.767 2G / 9G INFO General (graph_simplification.hpp : 403) Removing isolated edges 1:09:01.767 2G / 9G INFO General (graph_simplification.hpp : 404) All edges shorter than 151 will be removed 1:09:01.767 2G / 9G INFO General (graph_simplification.hpp : 405) Also edges shorter than 0 and coverage smaller than 2 will be removed 1:09:02.608 2G / 9G INFO General (simplification.cpp : 56) Removing all the edges having coverage 0 and less 1:09:02.759 2G / 9G INFO General (simplification.cpp : 68) Counting average coverage 1:09:02.779 2G / 9G INFO General (simplification.cpp : 71) Average coverage = 22.4509 1:09:02.779 2G / 9G INFO StageManager (stage.cpp : 125) STAGE == Mismatch Correction 1:09:51.494 2G / 9G INFO General (mismatch_shall_not_pass.hp: 188) Finished collecting potential mismatches positions 1:09:51.558 2G / 9G INFO General (mismatch_shall_not_pass.hp: 291) All edges processed 1:09:51.562 2G / 9G INFO General (mismatch_correction.cpp : 18) Corrected 0 nucleotides 1:09:51.579 2G / 9G INFO StageManager (stage.cpp : 125) STAGE == Paired Information Counting 1:09:51.722 2G / 9G INFO General (pair_info_count.cpp : 150) Graph N50: 24544 1:09:51.722 2G / 9G INFO General (pair_info_count.cpp : 152) Estimating insert size for library #0 1:09:51.722 2G / 9G INFO General (pair_info_count.cpp : 31) Estimating insert size (takes a while) 1:09:51.734 2G / 9G INFO General (short_read_mapper.hpp : 91) Selecting usual mapper 1:09:57.647 2G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 200000 reads 1:09:57.651 2G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 400000 reads 1:09:57.664 2G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 600000 reads 1:09:57.670 2G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 800000 reads 1:09:57.683 2G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 1000000 reads 1:09:57.712 2G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 1200000 reads 1:09:58.123 2G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 2200000 reads 1:10:03.839 2G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 4200000 reads 1:10:11.070 2G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 8400000 reads 1:10:16.159 2G / 9G INFO General (sequence_mapper_notifier.h: 89) Processed 12244262 reads 1:10:16.159 2G / 9G INFO General (pair_info_count.cpp : 41) 6045010 paired reads (49.3701% of all) aligned to long edges 1:10:16.171 2G / 9G INFO General (pair_info_count.cpp : 170) Estimated insert size for paired library #0 1:10:16.171 2G / 9G INFO General (pair_info_count.cpp : 175) Insert size = 279.833, deviation = 79.1279, left quantile = 182, right quantile = 383, read length = 151 1:10:16.171 2G / 9G INFO General (pair_info_count.cpp : 187) Mapping library #0 1:10:16.171 2G / 9G INFO General (pair_info_count.cpp : 189) Mapping paired reads (takes a while) 1:10:16.171 2G / 9G INFO General (pair_info_count.cpp : 73) Left insert size qauntile 182, right insert size quantile 383 1:10:16.182 2G / 9G INFO General (short_read_mapper.hpp : 91) Selecting usual mapper 1:10:23.913 4G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 200000 reads 1:10:24.678 4G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 400000 reads 1:10:25.560 4G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 600000 reads 1:10:26.609 4G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 800000 reads 1:10:27.782 4G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 1000000 reads 1:10:29.029 4G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 1200000 reads 1:10:36.046 4G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 2200000 reads 1:10:51.211 4G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 4200000 reads 1:11:24.813 4G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 8400000 reads 1:12:34.411 5G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 16800000 reads 1:13:42.308 3G / 9G INFO General (sequence_mapper_notifier.h: 89) Processed 24488524 reads 1:16:10.267 3G / 9G INFO General (split_graph_pair_info.hpp : 344) Threshold for paired information 0.0696265 1:16:13.789 2G / 9G INFO StageManager (stage.cpp : 125) STAGE == Distance Estimation 1:16:13.789 2G / 9G INFO General (distance_estimation.cpp : 234) Processing library #0 1:16:13.789 2G / 9G INFO General (distance_estimation.cpp : 136) Weight Filter Done 1:16:13.789 2G / 9G INFO DistanceEstimator (distance_estimation.hpp : 187) Using SIMPLE distance estimator 1:16:22.381 2G / 9G INFO DistanceEstimator (distance_estimation.hpp : 208) Merging maps 1:16:23.148 2G / 9G INFO General (distance_estimation.cpp : 38) Filtering info 1:16:24.261 2G / 9G INFO General (pair_info_filters.hpp : 354) Pruning the index 1:16:24.305 2G / 9G INFO General (distance_estimation.cpp : 184) Refining clustered pair information 1:16:24.407 2G / 9G INFO General (distance_estimation.cpp : 186) The refining of clustered pair information has been finished 1:16:24.408 2G / 9G INFO General (distance_estimation.cpp : 188) Filling paired information 1:16:25.536 2G / 9G INFO PairInfoImprover (pair_info_improver.hpp : 61) Paired info stats: missing = 35612; contradictional = 4898 1:16:26.656 2G / 9G INFO PairInfoImprover (pair_info_improver.hpp : 61) Paired info stats: missing = 3006; contradictional = 0 1:16:26.657 2G / 9G INFO General (distance_estimation.cpp : 193) Filling scaffolding index 1:16:26.657 2G / 9G INFO DistanceEstimator (distance_estimation.hpp : 187) Using SMOOTHING distance estimator 1:16:37.095 2G / 9G INFO DistanceEstimator (distance_estimation.hpp : 208) Merging maps 1:16:37.147 2G / 9G INFO General (distance_estimation.cpp : 38) Filtering info 1:16:37.343 2G / 9G INFO General (pair_info_filters.hpp : 354) Pruning the index 1:16:37.790 2G / 9G INFO StageManager (stage.cpp : 125) STAGE == Repeat Resolving 1:16:37.790 2G / 9G INFO General (contig_output.hpp : 283) Outputting contigs to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_133-dipSPAdes-3.5.0-trimmed/spades//K77/before_rr.fasta 1:17:26.391 2G / 9G INFO General (repeat_resolving.cpp : 59) Using Path-Extend repeat resolving 1:17:26.392 2G / 9G INFO General (path_extend_launch.hpp : 459) Threshold for library #0 is 0.0696265 1:17:26.392 2G / 9G INFO General (path_extend_launch.hpp : 298) Path-Extend repeat resolving tool started 1:17:26.437 2G / 9G INFO General (path_extend_launch.hpp : 316) Using 1 paired-end library 1:17:26.437 2G / 9G INFO General (path_extend_launch.hpp : 317) Using 1 paired-end scaffolding library 1:17:26.437 2G / 9G INFO General (path_extend_launch.hpp : 318) Using 0 mate-pair libraries 1:17:26.437 2G / 9G INFO General (path_extend_launch.hpp : 319) Using 0 single read libraries 1:17:26.437 2G / 9G INFO General (path_extend_launch.hpp : 320) Scaffolder is on 1:17:26.710 2G / 9G INFO General (path_extend_launch.hpp : 332) Growing paths using paired-end and long single reads 1:17:26.711 2G / 9G INFO PathExtender (path_extender.hpp : 611) Processed 0 paths from 23053 (0%) 1:17:27.040 2G / 9G INFO PathExtender (path_extender.hpp : 609) Processed 128 paths from 23053 (0%) 1:17:27.296 2G / 9G INFO PathExtender (path_extender.hpp : 609) Processed 256 paths from 23053 (1%) 1:17:27.844 2G / 9G INFO PathExtender (path_extender.hpp : 609) Processed 512 paths from 23053 (2%) 1:17:29.320 2G / 9G INFO PathExtender (path_extender.hpp : 609) Processed 1024 paths from 23053 (4%) 1:17:30.375 2G / 9G INFO PathExtender (path_extender.hpp : 609) Processed 2048 paths from 23053 (8%) 1:17:30.656 2G / 9G INFO PathExtender (path_extender.hpp : 611) Processed 2306 paths from 23053 (10%) 1:17:31.436 2G / 9G INFO PathExtender (path_extender.hpp : 609) Processed 4096 paths from 23053 (17%) 1:17:31.699 2G / 9G INFO PathExtender (path_extender.hpp : 611) Processed 4612 paths from 23053 (20%) 1:17:32.237 2G / 9G INFO PathExtender (path_extender.hpp : 611) Processed 6918 paths from 23053 (30%) 1:17:32.855 2G / 9G INFO PathExtender (path_extender.hpp : 609) Processed 8192 paths from 23053 (35%) 1:17:33.076 2G / 9G INFO PathExtender (path_extender.hpp : 611) Processed 9224 paths from 23053 (40%) 1:17:33.364 2G / 9G INFO PathExtender (path_extender.hpp : 611) Processed 11530 paths from 23053 (50%) 1:17:34.060 2G / 9G INFO PathExtender (path_extender.hpp : 611) Processed 13836 paths from 23053 (60%) 1:17:36.406 2G / 9G INFO PathExtender (path_extender.hpp : 611) Processed 16142 paths from 23053 (70%) 1:17:36.568 2G / 9G INFO PathExtender (path_extender.hpp : 609) Processed 16384 paths from 23053 (71%) 1:17:38.197 2G / 9G INFO PathExtender (path_extender.hpp : 611) Processed 18448 paths from 23053 (80%) 1:17:39.640 2G / 9G INFO PathExtender (path_extender.hpp : 611) Processed 20754 paths from 23053 (90%) 1:17:40.855 2G / 9G INFO PathExtendIO (pe_io.hpp : 339) Constructing FASTG file from paths 1:17:41.253 2G / 9G INFO PathExtendIO (pe_io.hpp : 342) Writing contigs in FASTG to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_133-dipSPAdes-3.5.0-trimmed/spades//K77/final_contigs.fastg 1:17:41.254 2G / 9G INFO PathExtendIO (pe_io.hpp : 343) Writing contigs in FASTA to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_133-dipSPAdes-3.5.0-trimmed/spades//K77/final_contigs.fasta 1:18:28.181 2G / 9G INFO PathExtendIO (pe_io.hpp : 339) Constructing FASTG file from paths 1:18:28.591 2G / 9G INFO PathExtendIO (pe_io.hpp : 342) Writing contigs in FASTG to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_133-dipSPAdes-3.5.0-trimmed/spades//K77/path_extend/pe_before_traversal.fastg 1:18:28.591 2G / 9G INFO PathExtendIO (pe_io.hpp : 343) Writing contigs in FASTA to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_133-dipSPAdes-3.5.0-trimmed/spades//K77/path_extend/pe_before_traversal.fasta 1:19:14.915 2G / 9G INFO General (path_extend_launch.hpp : 281) Traversing tandem repeats 1:19:15.996 2G / 9G INFO PathExtendIO (pe_io.hpp : 339) Constructing FASTG file from paths 1:19:16.351 2G / 9G INFO PathExtendIO (pe_io.hpp : 342) Writing contigs in FASTG to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_133-dipSPAdes-3.5.0-trimmed/spades//K77/scaffolds.fastg 1:19:16.351 2G / 9G INFO PathExtendIO (pe_io.hpp : 343) Writing contigs in FASTA to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_133-dipSPAdes-3.5.0-trimmed/spades//K77/scaffolds.fasta 1:20:03.275 2G / 9G INFO General (launch.hpp : 82) SPAdes finished 1:20:06.762 264M / 9G INFO General (main.cpp : 166) Assembling time: 1 hours 20 minutes 6 seconds ===== Assembling finished. * Corrected reads are in /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_133-dipSPAdes-3.5.0-trimmed/spades/corrected/ * Assembled contigs are in /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_133-dipSPAdes-3.5.0-trimmed/spades/contigs.fasta (contigs.fastg) * Assembled scaffolds are in /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_133-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.sexaurelia-Sample_133-dipSPAdes-3.5.0-trimmed/spades/warnings.log SPAdes log can be found here: /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_133-dipSPAdes-3.5.0-trimmed/spades/spades.log Thank you for using SPAdes!