Command line: --diploid --pe1-1 /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_132/reads.end1.paired.fastq.gz --pe1-2 /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_132/reads.end2.paired.fastq.gz -t 16 -o /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_132-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_132-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_132/reads.end1.paired.fastq.gz'] right reads: ['/N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_132/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_132-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_132-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_132-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_132-dipSPAdes-3.5.0-trimmed/spades/corrected/configs/config.info 0:00:00.071 4M / 4M INFO General (memory_limit.hpp : 42) Memory limit set to 100 Gb 0:00:00.071 4M / 4M INFO General (main.cpp : 91) Trying to determine PHRED offset 0:00:00.122 4M / 4M INFO General (main.cpp : 97) Determined value is 33 0:00:00.166 4M / 4M INFO General (hammer_tools.cpp : 36) Hamming graph threshold tau=1, k=21, subkmer positions = [ 0 10 ] === ITERATION 0 begins === 0:00:00.167 4M / 4M INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:00:00.167 4M / 4M INFO K-mer Splitting (kmer_data.cpp : 127) Splitting kmer instances into 256 buckets. This might take a while. 0:00:00.168 4M / 4M INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:00:00.168 4M / 4M INFO K-mer Splitting (kmer_data.cpp : 145) Memory available for splitting buffers: 2.08325 Gb 0:00:00.168 4M / 4M INFO K-mer Splitting (kmer_data.cpp : 153) Using cell size of 262144 0:00:02.986 8G / 8G INFO K-mer Splitting (kmer_data.cpp : 167) Processing /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_132/reads.end1.paired.fastq.gz 0:03:01.505 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 176) Processed 3317576 reads 0:03:58.377 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 176) Processed 6611242 reads 0:06:14.174 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 176) Processed 10075308 reads 0:07:11.646 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 176) Processed 10350256 reads 0:07:11.647 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 167) Processing /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_132/reads.end2.paired.fastq.gz 0:09:05.039 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 176) Processed 13901657 reads 0:12:04.974 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 176) Processed 17330281 reads 0:15:00.749 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 176) Processed 20700512 reads 0:15:00.750 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 181) Processed 20700512 reads 0:15:01.902 64M / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:15:39.250 64M / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 280104258 kmers in total. 0:15:39.250 64M / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:15:51.902 64M / 9G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:16:24.835 192M / 9G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:17:03.036 192M / 9G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 96898611 bytes occupied (2.7675 bits per kmer). 0:17:03.038 192M / 9G INFO K-mer Counting (kmer_data.cpp : 266) Arranging kmers in hash map order 0:19:49.813 192M / 9G INFO K-mer Counting (kmer_data.cpp : 279) Done. Total swaps: 280103973 0:19:51.694 2G / 9G INFO General (main.cpp : 151) Clustering Hamming graph. 0:19:51.695 2G / 9G INFO Hamming Clustering (hamcluster.cpp : 115) Serializing sub-kmers. 0:19:51.695 2G / 9G INFO Hamming Clustering (hamcluster.cpp : 120) Serializing: [0, 10) 0:22:59.255 2G / 9G INFO Hamming Clustering (hamcluster.cpp : 120) Serializing: [10, 21) 0:26:07.223 2G / 9G INFO Hamming Clustering (hamcluster.cpp : 129) Splitting sub-kmers, pass 1. 0:29:56.861 2G / 9G INFO Hamming Clustering (hamcluster.cpp : 134) Splitting done. Processed 2 blocks. Produced 5176012 blocks. 0:29:56.862 2G / 9G INFO Hamming Clustering (hamcluster.cpp : 145) Merge sub-kmers, pass 1 0:44:47.286 2G / 9G INFO Hamming Clustering (hamcluster.cpp : 170) Merge done, total 1634409 new blocks generated. 0:44:48.858 2G / 9G INFO Hamming Clustering (hamcluster.cpp : 175) Spliting sub-kmers, pass 2. 1:09:00.608 2G / 9G INFO Hamming Clustering (hamcluster.cpp : 180) Splitting done. Processed 3268818 blocks. Produced 541922967 blocks. 1:09:00.608 2G / 9G INFO Hamming Clustering (hamcluster.cpp : 187) Merge sub-kmers, pass 2 1:20:20.562 2G / 9G INFO Hamming Clustering (hamcluster.cpp : 205) Merge done, saw 212148 big blocks out of 541922967 processed. 1:24:07.395 2G / 10G INFO General (main.cpp : 165) Clustering done. Total clusters: 143845508 1:24:07.396 2G / 10G INFO K-mer Counting (kmer_data.cpp : 284) Collecting K-mer information, this takes a while. 1:24:13.076 14G / 14G INFO K-mer Counting (kmer_data.cpp : 290) Processing /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_132/reads.end1.paired.fastq.gz 1:26:47.793 14G / 14G INFO K-mer Counting (kmer_data.cpp : 290) Processing /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_132/reads.end2.paired.fastq.gz 1:29:15.592 14G / 14G INFO K-mer Counting (kmer_data.cpp : 297) Collection done, postprocessing. 1:29:22.584 14G / 14G INFO K-mer Counting (kmer_data.cpp : 310) There are 280104258 kmers in total. Among them 130112448 (46.4514%) are singletons. 1:29:22.584 14G / 14G INFO General (main.cpp : 203) Subclustering Hamming graph 1:32:36.285 14G / 14G INFO Hamming Subclustering (kmer_cluster.cpp : 626) Subclustering done. Total 77916 non-read kmers were generated. 1:32:36.285 14G / 14G INFO Hamming Subclustering (kmer_cluster.cpp : 627) Subclustering statistics: 1:32:36.285 14G / 14G INFO Hamming Subclustering (kmer_cluster.cpp : 628) Total singleton hamming clusters: 88944606. Among them 67431059 (75.8124%) are good 1:32:36.285 14G / 14G INFO Hamming Subclustering (kmer_cluster.cpp : 629) Total singleton subclusters: 8071187. Among them 8071116 (99.9991%) are good 1:32:36.285 14G / 14G INFO Hamming Subclustering (kmer_cluster.cpp : 630) Total non-singleton subcluster centers: 58820814. Among them 38380684 (65.2502%) are good 1:32:36.286 14G / 14G INFO Hamming Subclustering (kmer_cluster.cpp : 631) Average size of non-trivial subcluster: 3.21713 kmers 1:32:36.286 14G / 14G INFO Hamming Subclustering (kmer_cluster.cpp : 632) Average number of sub-clusters per non-singleton cluster: 1.21841 1:32:36.286 14G / 14G INFO Hamming Subclustering (kmer_cluster.cpp : 633) Total solid k-mers: 113882859 1:32:36.286 14G / 14G INFO Hamming Subclustering (kmer_cluster.cpp : 634) Substitution probabilities: [4,4]((0.900905,0.0224766,0.0252213,0.0513969),(0.0358534,0.928655,0.0127781,0.022714),(0.0216255,0.0123799,0.929743,0.0362511),(0.0506472,0.0254446,0.0227461,0.901162)) 1:32:36.787 14G / 14G INFO General (main.cpp : 208) Finished clustering. 1:32:36.787 14G / 14G INFO General (main.cpp : 228) Starting solid k-mers expansion in 16 threads. 1:36:09.102 14G / 14G INFO General (main.cpp : 249) Solid k-mers iteration 0 produced 40823845 new k-mers. 1:39:38.241 14G / 14G INFO General (main.cpp : 249) Solid k-mers iteration 1 produced 1072709 new k-mers. 1:43:07.858 14G / 14G INFO General (main.cpp : 249) Solid k-mers iteration 2 produced 41305 new k-mers. 1:46:37.882 14G / 14G INFO General (main.cpp : 249) Solid k-mers iteration 3 produced 4531 new k-mers. 1:50:07.801 14G / 14G INFO General (main.cpp : 249) Solid k-mers iteration 4 produced 1282 new k-mers. 1:53:37.709 14G / 14G INFO General (main.cpp : 249) Solid k-mers iteration 5 produced 230 new k-mers. 1:57:07.255 14G / 14G INFO General (main.cpp : 249) Solid k-mers iteration 6 produced 0 new k-mers. 1:57:07.256 14G / 14G INFO General (main.cpp : 253) Solid k-mers finalized 1:57:07.269 14G / 14G INFO General (hammer_tools.cpp : 210) Starting read correction in 16 threads. 1:57:07.269 14G / 14G INFO General (hammer_tools.cpp : 222) Correcting pair of reads: /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_132/reads.end1.paired.fastq.gz and /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_132/reads.end2.paired.fastq.gz 1:57:32.892 16G / 16G INFO General (hammer_tools.cpp : 166) Prepared batch 0 of 1600000 reads. 1:57:58.607 16G / 16G INFO General (hammer_tools.cpp : 175) Processed batch 0 1:58:22.712 16G / 16G INFO General (hammer_tools.cpp : 185) Written batch 0 1:58:46.853 16G / 16G INFO General (hammer_tools.cpp : 166) Prepared batch 1 of 1600000 reads. 1:59:14.745 16G / 16G INFO General (hammer_tools.cpp : 175) Processed batch 1 1:59:49.340 16G / 16G INFO General (hammer_tools.cpp : 185) Written batch 1 2:00:12.964 16G / 16G INFO General (hammer_tools.cpp : 166) Prepared batch 2 of 1600000 reads. 2:00:34.463 16G / 16G INFO General (hammer_tools.cpp : 175) Processed batch 2 2:00:50.023 16G / 16G INFO General (hammer_tools.cpp : 185) Written batch 2 2:01:13.548 16G / 16G INFO General (hammer_tools.cpp : 166) Prepared batch 3 of 1600000 reads. 2:01:35.392 16G / 16G INFO General (hammer_tools.cpp : 175) Processed batch 3 2:02:11.101 16G / 16G INFO General (hammer_tools.cpp : 185) Written batch 3 2:02:34.579 16G / 16G INFO General (hammer_tools.cpp : 166) Prepared batch 4 of 1600000 reads. 2:02:57.610 16G / 16G INFO General (hammer_tools.cpp : 175) Processed batch 4 2:03:13.307 16G / 16G INFO General (hammer_tools.cpp : 185) Written batch 4 2:03:36.333 16G / 16G INFO General (hammer_tools.cpp : 166) Prepared batch 5 of 1600000 reads. 2:03:58.445 16G / 16G INFO General (hammer_tools.cpp : 175) Processed batch 5 2:04:14.062 16G / 16G INFO General (hammer_tools.cpp : 185) Written batch 5 2:04:24.847 16G / 16G INFO General (hammer_tools.cpp : 166) Prepared batch 6 of 750256 reads. 2:04:39.336 16G / 16G INFO General (hammer_tools.cpp : 175) Processed batch 6 2:04:46.585 16G / 16G INFO General (hammer_tools.cpp : 185) Written batch 6 2:04:49.644 14G / 16G INFO General (hammer_tools.cpp : 269) Correction done. Changed 3664633 bases in 2928897 reads. 2:04:49.644 14G / 16G INFO General (hammer_tools.cpp : 270) Failed to correct 360587053 bases out of 3081644956. 2:04:49.711 2G / 16G INFO General (main.cpp : 286) Saving corrected dataset description to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_132-dipSPAdes-3.5.0-trimmed/spades/corrected/corrected.yaml 2:04:49.714 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.sexaurelia-Sample_132-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_132-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 0:00:00.011 4M / 4M INFO General (read_converter.hpp : 79) Converting reads to binary format (takes a while) 0:00:00.011 4M / 4M INFO General (read_converter.hpp : 81) Paired reads for library #0 0:00:01.131 80M / 80M INFO General (binary_converter.hpp : 138) 16384 reads processed 0:00:01.533 96M / 96M INFO General (binary_converter.hpp : 138) 32768 reads processed 0:00:02.332 124M / 124M INFO General (binary_converter.hpp : 138) 65536 reads processed 0:00:03.935 184M / 184M INFO General (binary_converter.hpp : 138) 131072 reads processed 0:00:07.144 300M / 300M INFO General (binary_converter.hpp : 138) 262144 reads processed 0:00:13.578 536M / 536M INFO General (binary_converter.hpp : 138) 524288 reads processed 0:00:49.151 900M / 900M INFO General (binary_converter.hpp : 138) 1048576 reads processed 0:01:17.705 904M / 904M INFO General (binary_converter.hpp : 138) 2097152 reads processed 0:02:15.056 904M / 904M INFO General (binary_converter.hpp : 138) 4194304 reads processed 0:04:12.384 904M / 904M INFO General (binary_converter.hpp : 138) 8388608 reads processed 0:05:03.641 900M / 908M INFO General (binary_converter.hpp : 158) 10239067 reads written 0:05:05.375 4M / 908M INFO General (read_converter.hpp : 91) Single reads for library #0 0:05:07.220 140M / 908M INFO General (binary_converter.hpp : 138) 16384 reads processed 0:05:07.428 144M / 908M INFO General (binary_converter.hpp : 138) 32768 reads processed 0:05:07.811 160M / 908M INFO General (binary_converter.hpp : 138) 65536 reads processed 0:05:08.545 180M / 908M INFO General (binary_converter.hpp : 158) 110656 reads written 0:05:08.694 4M / 908M INFO General (graph_construction.hpp : 129) Constructing DeBruijn graph for k=21 0:05:08.697 4M / 908M INFO General (kmer_splitters.hpp : 172) Splitting kmer instances into 256 buckets. This might take a while. 0:05:08.697 4M / 908M INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:05:08.697 4M / 908M INFO General (kmer_splitters.hpp : 190) Memory available for splitting buffers: 2.08325 Gb 0:05:08.698 4M / 908M INFO General (kmer_splitters.hpp : 199) Using cell size of 262144 0:07:40.852 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 16695016 reads 0:08:13.091 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 33391286 reads 0:08:25.243 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 41177580 reads 0:08:25.245 8G / 9G INFO General (kmer_splitters.hpp : 234) Adding contigs from previous K 0:08:25.245 8G / 9G INFO General (kmer_splitters.hpp : 245) Used 41177580 reads. Maximum read length 151 0:08:25.246 8G / 9G INFO General (kmer_splitters.hpp : 246) Average read length 149.625 0:08:27.428 64M / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:08:34.766 64M / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 117424564 kmers in total. 0:08:34.766 64M / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:08:40.087 64M / 9G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:08:40.088 64M / 9G INFO General (kmer_splitters.hpp : 379) Splitting kmer instances into 256 buckets. This might take a while. 0:08:40.088 64M / 9G INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:08:40.088 64M / 9G INFO General (kmer_splitters.hpp : 397) Memory available for splitting buffers: 2.08203 Gb 0:08:40.088 64M / 9G INFO General (kmer_splitters.hpp : 405) Using cell size of 262144 0:08:56.124 8G / 9G INFO General (kmer_splitters.hpp : 428) Processed 117424564 kmers 0:08:56.125 8G / 9G INFO General (kmer_splitters.hpp : 437) Used 117424564 kmers. 0:08:56.578 64M / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:09:01.054 64M / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 114678675 kmers in total. 0:09:01.055 64M / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:09:06.574 64M / 9G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:09:19.510 64M / 9G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:09:24.315 64M / 9G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 39671684 bytes occupied (2.7675 bits per kmer). 0:09:24.512 176M / 9G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 382) Building k-mer extensions from k+1-mers 0:09:36.816 176M / 9G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 386) Building k-mer extensions from k+1-mers finished. 0:09:36.822 176M / 9G INFO Early tip clipping (early_simplification.hpp : 236) Early tip clipping 0:15:32.862 176M / 9G INFO Early tip clipping (early_simplification.hpp : 239) 5442620 22-mers were removed by early tip clipper 0:15:32.862 176M / 9G INFO General (graph_construction.hpp : 145) Condensing graph 0:15:32.862 176M / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 337) Extracting unbranching paths 0:16:55.859 1G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 351) Extracting unbranching paths finished. 14781436 sequences extracted 0:17:05.605 1G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 311) Collecting perfect loops 0:17:40.770 1G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 326) Collecting perfect loops finished. 32 loops collected 0:17:50.716 2G / 9G INFO General (graph_construction.hpp : 150) Building index with from graph 0:17:50.717 2G / 9G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:17:50.717 2G / 9G INFO General (kmer_splitters.hpp : 289) Splitting kmer instances into 16 buckets. This might take a while. 0:17:50.717 2G / 9G INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:17:50.717 2G / 9G INFO General (kmer_splitters.hpp : 307) Memory available for splitting buffers: 32.3568 Gb 0:17:50.718 2G / 9G INFO General (kmer_splitters.hpp : 312) Using cell size of 4194304 0:18:07.641 3G / 9G INFO General (kmer_splitters.hpp : 325) Processed 8861459 edges 0:18:59.223 3G / 9G INFO General (kmer_splitters.hpp : 325) Processed 14781468 edges 0:18:59.224 3G / 9G INFO General (kmer_splitters.hpp : 330) Used 14781468 sequences. 0:18:59.274 2G / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:19:43.768 2G / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 111981944 kmers in total. 0:19:43.768 2G / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:19:48.163 2G / 9G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:22:24.257 2G / 9G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:22:29.075 2G / 9G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 38738784 bytes occupied (2.7675 bits per kmer). 0:22:30.989 5G / 9G INFO General (edge_index_builders.hpp : 21) Collecting k-mer coverage information from graph, this takes a while. 0:25:49.737 5G / 9G INFO General (graph_construction.hpp : 182) Filling coverage index 0:25:49.737 5G / 9G INFO General (edge_index_builders.hpp : 99) Collecting k-mer coverage information from reads, this takes a while. 0:29:00.378 5G / 9G INFO General (graph_construction.hpp : 184) Filling coverage and flanking coverage from index 0:29:29.458 5G / 9G INFO General (construction.cpp : 33) Figured out: read length = 151 0:29:29.476 5G / 9G INFO StageManager (stage.cpp : 125) STAGE == EC Threshold Finding 0:29:39.762 5G / 9G INFO General (kmer_coverage_model.cpp : 178) Kmer coverage valley at: 10 0:29:39.763 5G / 9G INFO General (kmer_coverage_model.cpp : 198) K-mer histogram maximum: 38 0:29:39.763 5G / 9G INFO General (kmer_coverage_model.cpp : 234) Estimated median coverage: 38. Coverage mad: 11.8608 0:29:39.763 5G / 9G INFO General (kmer_coverage_model.cpp : 261) Fitting coverage model 0:29:39.876 5G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 2 0:29:40.149 5G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 4 0:29:41.370 5G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 8 0:29:43.883 5G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 16 0:29:48.189 5G / 9G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 37.3195. Fitted coverage std. dev: 10.2268 0:29:48.192 5G / 9G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 0.500685 0:29:48.193 5G / 9G INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 22 0:29:48.193 5G / 9G INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 22 0:29:48.193 5G / 9G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 60291956 0:29:48.193 5G / 9G INFO General (genomic_info_filler.cpp : 103) Mean coverage was calculated as 37.3195 0:29:48.194 5G / 9G INFO General (genomic_info_filler.cpp : 117) EC coverage threshold value was calculated as 22 0:29:48.194 5G / 9G INFO General (genomic_info_filler.cpp : 118) Trusted kmer low bound: 0 0:29:48.194 5G / 9G INFO StageManager (stage.cpp : 125) STAGE == Simplification 0:29:48.410 2G / 9G INFO General (graph_simplification.hpp : 911) Graph simplification started 0:29:48.411 2G / 9G INFO General (graph_simplification.hpp : 924) Fast simplification mode enabled 0:29:48.411 2G / 9G INFO General (graph_simplification.hpp : 771) PROCEDURE == Presimplification 0:29:48.411 2G / 9G INFO General (graph_simplification.hpp : 211) Removing short low covered self-conjugate connections 0:29:49.333 2G / 9G INFO General (graph_simplification.hpp : 403) Removing isolated edges 0:29:49.333 2G / 9G INFO General (graph_simplification.hpp : 404) All edges shorter than 151 will be removed 0:29:49.333 2G / 9G INFO General (graph_simplification.hpp : 405) Also edges shorter than 0 and coverage smaller than 0 will be removed 0:29:50.871 2G / 9G INFO General (graph_simplification.hpp : 687) Non parallel mode 0:30:38.329 3G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:32:26.725 3G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:35:30.025 3G / 9G INFO General (graph_simplification.hpp : 644) Using permanent iterators 0:35:30.026 3G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 1 0:35:39.097 3G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:36:16.546 3G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:36:33.475 2G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 2 0:36:33.475 2G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:36:33.780 2G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:36:47.270 2G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 3 0:36:47.270 2G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:36:47.533 2G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:36:52.607 2G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 4 0:36:52.608 2G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:36:52.708 2G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:36:55.808 2G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 5 0:36:55.808 2G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:36:55.872 2G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:36:58.726 2G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 6 0:36:58.726 2G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:36:58.784 2G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:37:01.107 2G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 7 0:37:01.108 2G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:37:01.154 2G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:37:03.501 2G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 8 0:37:03.501 2G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:37:03.546 2G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:37:05.834 2G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 9 0:37:05.834 2G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:37:05.878 2G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:37:07.995 2G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 10 0:37:07.995 2G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:37:08.036 2G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:37:10.188 2G / 9G INFO General (graph_simplification.hpp : 796) PROCEDURE == Post simplification 0:37:10.188 2G / 9G INFO General (graph_simplification.hpp : 644) Using permanent iterators 0:37:10.188 2G / 9G INFO General (graph_simplification.hpp : 806) Iteration 0 0:37:10.188 2G / 9G INFO General (graph_simplification.hpp : 247) Removal of relatively low covered connections disabled 0:37:13.548 2G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:37:21.167 2G / 9G INFO General (graph_simplification.hpp : 806) Iteration 1 0:37:21.168 2G / 9G INFO General (graph_simplification.hpp : 247) Removal of relatively low covered connections disabled 0:37:21.168 2G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:37:23.263 2G / 9G INFO StageManager (stage.cpp : 125) STAGE == Simplification Cleanup 0:37:23.264 2G / 9G INFO General (graph_simplification.hpp : 403) Removing isolated edges 0:37:23.264 2G / 9G INFO General (graph_simplification.hpp : 404) All edges shorter than 151 will be removed 0:37:23.264 2G / 9G INFO General (graph_simplification.hpp : 405) Also edges shorter than 0 and coverage smaller than 2 will be removed 0:37:23.483 2G / 9G INFO General (simplification.cpp : 56) Removing all the edges having coverage 0 and less 0:37:29.689 2G / 9G INFO General (simplification.cpp : 68) Counting average coverage 0:37:30.403 2G / 9G INFO General (simplification.cpp : 71) Average coverage = 37.6804 0:37:30.403 2G / 9G INFO StageManager (stage.cpp : 125) STAGE == Contig Output 0:37:30.404 2G / 9G INFO General (contig_output.hpp : 283) Outputting contigs to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_132-dipSPAdes-3.5.0-trimmed/spades//K21/simplified_contigs.fasta 0:38:14.759 2G / 9G INFO General (contig_output.hpp : 283) Outputting contigs to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_132-dipSPAdes-3.5.0-trimmed/spades//K21/before_rr.fasta 0:40:17.751 2G / 9G INFO General (contig_output.hpp : 283) Outputting contigs to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_132-dipSPAdes-3.5.0-trimmed/spades//K21/final_contigs.fasta 0:42:57.318 2G / 9G INFO General (launch.hpp : 82) SPAdes finished 0:43:05.288 64M / 9G INFO General (main.cpp : 166) Assembling time: 0 hours 43 minutes 5 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_132-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 0:00:00.006 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. 0:00:00.030 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 0:02:35.887 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 9200997 reads 0:02:50.633 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 18413252 reads 0:03:05.298 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 27614191 reads 0:03:19.964 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 36817061 reads 0:03:27.304 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 41177580 reads 0:03:27.304 8G / 9G INFO General (kmer_splitters.hpp : 234) Adding contigs from previous K 0:03:47.991 8G / 9G INFO General (kmer_splitters.hpp : 245) Used 41177580 reads. Maximum read length 151 0:03:47.991 8G / 9G INFO General (kmer_splitters.hpp : 246) Average read length 149.625 0:03:50.250 64M / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:04:11.966 64M / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 136531827 kmers in total. 0:04:11.966 64M / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:04:23.633 64M / 9G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:04:23.633 64M / 9G INFO General (kmer_splitters.hpp : 379) Splitting kmer instances into 256 buckets. This might take a while. 0:04:23.634 64M / 9G INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:04:23.634 64M / 9G INFO General (kmer_splitters.hpp : 397) Memory available for splitting buffers: 2.08203 Gb 0:04:23.634 64M / 9G INFO General (kmer_splitters.hpp : 405) Using cell size of 131072 0:04:45.250 8G / 9G INFO General (kmer_splitters.hpp : 428) Processed 136531827 kmers 0:04:45.250 8G / 9G INFO General (kmer_splitters.hpp : 437) Used 136531827 kmers. 0:04:45.982 64M / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:04:55.845 64M / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 135303581 kmers in total. 0:04:55.846 64M / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:05:07.809 64M / 9G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:05:23.877 68M / 9G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:05:35.618 68M / 9G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 46806615 bytes occupied (2.7675 bits per kmer). 0:05:35.830 200M / 9G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 382) Building k-mer extensions from k+1-mers 0:05:52.248 200M / 9G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 386) Building k-mer extensions from k+1-mers finished. 0:05:52.253 200M / 9G INFO Early tip clipping (early_simplification.hpp : 236) Early tip clipping 0:12:40.996 200M / 9G INFO Early tip clipping (early_simplification.hpp : 239) 19284172 34-mers were removed by early tip clipper 0:12:40.996 200M / 9G INFO General (graph_construction.hpp : 145) Condensing graph 0:12:40.997 200M / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 337) Extracting unbranching paths 0:14:11.330 1G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 351) Extracting unbranching paths finished. 7530994 sequences extracted 0:14:23.130 1G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 311) Collecting perfect loops 0:15:07.300 1G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 326) Collecting perfect loops finished. 66 loops collected 0:15:12.786 1G / 9G INFO General (graph_construction.hpp : 150) Building index with from graph 0:15:12.787 1G / 9G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:15:12.787 1G / 9G INFO General (kmer_splitters.hpp : 289) Splitting kmer instances into 16 buckets. This might take a while. 0:15:12.787 1G / 9G INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:15:12.787 1G / 9G INFO General (kmer_splitters.hpp : 307) Memory available for splitting buffers: 32.776 Gb 0:15:12.787 1G / 9G INFO General (kmer_splitters.hpp : 312) Using cell size of 2097152 0:15:51.273 2G / 9G INFO General (kmer_splitters.hpp : 325) Processed 2155527 edges 0:16:59.784 2G / 9G INFO General (kmer_splitters.hpp : 325) Processed 4309922 edges 0:18:30.930 2G / 9G INFO General (kmer_splitters.hpp : 325) Processed 6465882 edges 0:20:56.952 2G / 9G INFO General (kmer_splitters.hpp : 325) Processed 7531060 edges 0:20:56.953 2G / 9G INFO General (kmer_splitters.hpp : 330) Used 7531060 sequences. 0:20:57.000 1G / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:22:12.699 1G / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 117247655 kmers in total. 0:22:12.700 1G / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:22:21.729 1G / 9G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:24:52.657 1G / 9G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:25:04.013 1G / 9G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 40560405 bytes occupied (2.7675 bits per kmer). 0:25:06.021 4G / 9G INFO General (edge_index_builders.hpp : 21) Collecting k-mer coverage information from graph, this takes a while. 0:28:37.226 4G / 9G INFO General (graph_construction.hpp : 182) Filling coverage index 0:28:37.226 4G / 9G INFO General (edge_index_builders.hpp : 99) Collecting k-mer coverage information from reads, this takes a while. 0:31:38.035 4G / 9G INFO General (graph_construction.hpp : 184) Filling coverage and flanking coverage from index 0:32:05.667 4G / 9G INFO General (construction.cpp : 33) Figured out: read length = 151 0:32:05.684 4G / 9G INFO StageManager (stage.cpp : 125) STAGE == EC Threshold Finding 0:32:15.287 4G / 9G INFO General (kmer_coverage_model.cpp : 178) Kmer coverage valley at: 9 0:32:15.288 4G / 9G INFO General (kmer_coverage_model.cpp : 198) K-mer histogram maximum: 34 0:32:15.288 4G / 9G INFO General (kmer_coverage_model.cpp : 234) Estimated median coverage: 34. Coverage mad: 10.3782 0:32:15.288 4G / 9G INFO General (kmer_coverage_model.cpp : 261) Fitting coverage model 0:32:15.416 4G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 2 0:32:15.741 4G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 4 0:32:16.838 4G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 8 0:32:19.356 4G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 16 0:32:23.718 4G / 9G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 33.45. Fitted coverage std. dev: 9.68987 0:32:23.721 4G / 9G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 0.43922 0:32:23.721 4G / 9G INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 20 0:32:23.721 4G / 9G INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 20 0:32:23.721 4G / 9G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 60468580 0:32:23.721 4G / 9G INFO General (genomic_info_filler.cpp : 103) Mean coverage was calculated as 33.45 0:32:23.722 4G / 9G INFO General (genomic_info_filler.cpp : 117) EC coverage threshold value was calculated as 20 0:32:23.722 4G / 9G INFO General (genomic_info_filler.cpp : 118) Trusted kmer low bound: 0 0:32:23.722 4G / 9G INFO StageManager (stage.cpp : 125) STAGE == Simplification 0:32:23.947 1G / 9G INFO General (graph_simplification.hpp : 911) Graph simplification started 0:32:23.947 1G / 9G INFO General (graph_simplification.hpp : 924) Fast simplification mode enabled 0:32:23.947 1G / 9G INFO General (graph_simplification.hpp : 771) PROCEDURE == Presimplification 0:32:23.947 1G / 9G INFO General (graph_simplification.hpp : 211) Removing short low covered self-conjugate connections 0:32:24.455 1G / 9G INFO General (graph_simplification.hpp : 403) Removing isolated edges 0:32:24.456 1G / 9G INFO General (graph_simplification.hpp : 404) All edges shorter than 151 will be removed 0:32:24.456 1G / 9G INFO General (graph_simplification.hpp : 405) Also edges shorter than 0 and coverage smaller than 0 will be removed 0:32:25.873 1G / 9G INFO General (graph_simplification.hpp : 687) Non parallel mode 0:32:46.740 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:33:36.984 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:35:14.831 1G / 9G INFO General (graph_simplification.hpp : 644) Using permanent iterators 0:35:14.831 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 1 0:35:17.329 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:35:27.639 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:35:37.522 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 2 0:35:37.522 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:35:37.607 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:35:42.685 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 3 0:35:42.685 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:35:42.749 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:35:44.705 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 4 0:35:44.705 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:35:44.727 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:35:45.960 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 5 0:35:45.960 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:35:45.972 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:35:47.065 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 6 0:35:47.065 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:35:47.073 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:35:48.189 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 7 0:35:48.189 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:35:48.195 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:35:49.346 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 8 0:35:49.346 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:35:49.351 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:35:50.432 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 9 0:35:50.433 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:35:50.438 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:35:51.213 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 10 0:35:51.213 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:35:51.217 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:35:51.701 1G / 9G INFO General (graph_simplification.hpp : 796) PROCEDURE == Post simplification 0:35:51.701 1G / 9G INFO General (graph_simplification.hpp : 644) Using permanent iterators 0:35:51.701 1G / 9G INFO General (graph_simplification.hpp : 806) Iteration 0 0:35:51.702 1G / 9G INFO General (graph_simplification.hpp : 247) Removal of relatively low covered connections disabled 0:35:52.141 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:35:53.129 1G / 9G INFO General (graph_simplification.hpp : 806) Iteration 1 0:35:53.129 1G / 9G INFO General (graph_simplification.hpp : 247) Removal of relatively low covered connections disabled 0:35:53.129 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:35:53.471 1G / 9G INFO StageManager (stage.cpp : 125) STAGE == Simplification Cleanup 0:35:53.472 1G / 9G INFO General (graph_simplification.hpp : 403) Removing isolated edges 0:35:53.473 1G / 9G INFO General (graph_simplification.hpp : 404) All edges shorter than 151 will be removed 0:35:53.473 1G / 9G INFO General (graph_simplification.hpp : 405) Also edges shorter than 0 and coverage smaller than 2 will be removed 0:35:53.532 1G / 9G INFO General (simplification.cpp : 56) Removing all the edges having coverage 0 and less 0:35:54.324 1G / 9G INFO General (simplification.cpp : 68) Counting average coverage 0:35:54.464 1G / 9G INFO General (simplification.cpp : 71) Average coverage = 31.5721 0:35:54.464 1G / 9G INFO StageManager (stage.cpp : 125) STAGE == Contig Output 0:35:54.464 1G / 9G INFO General (contig_output.hpp : 283) Outputting contigs to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_132-dipSPAdes-3.5.0-trimmed/spades//K33/simplified_contigs.fasta 0:36:14.108 1G / 9G INFO General (contig_output.hpp : 283) Outputting contigs to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_132-dipSPAdes-3.5.0-trimmed/spades//K33/before_rr.fasta 0:37:10.855 1G / 9G INFO General (contig_output.hpp : 283) Outputting contigs to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_132-dipSPAdes-3.5.0-trimmed/spades//K33/final_contigs.fasta 0:38:07.067 1G / 9G INFO General (launch.hpp : 82) SPAdes finished 0:38:09.751 64M / 9G INFO General (main.cpp : 166) Assembling time: 0 hours 38 minutes 9 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_132-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 0:00:00.026 4M / 4M INFO General (graph_construction.hpp : 129) Constructing DeBruijn graph for k=55 0:00:00.029 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 0:01:51.740 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 11340712 reads 0:02:06.809 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 22679642 reads 0:02:21.860 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 34025988 reads 0:02:31.656 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 41177580 reads 0:02:31.656 8G / 9G INFO General (kmer_splitters.hpp : 234) Adding contigs from previous K 0:02:50.552 8G / 9G INFO General (kmer_splitters.hpp : 245) Used 41177580 reads. Maximum read length 151 0:02:50.553 8G / 9G INFO General (kmer_splitters.hpp : 246) Average read length 149.625 0:02:52.808 64M / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:03:35.825 64M / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 154143811 kmers in total. 0:03:35.825 64M / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:04:09.780 64M / 9G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:04:09.780 64M / 9G INFO General (kmer_splitters.hpp : 379) Splitting kmer instances into 256 buckets. This might take a while. 0:04:09.781 64M / 9G INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:04:09.781 64M / 9G INFO General (kmer_splitters.hpp : 397) Memory available for splitting buffers: 2.08203 Gb 0:04:09.781 64M / 9G INFO General (kmer_splitters.hpp : 405) Using cell size of 131072 0:11:10.896 8G / 9G INFO General (kmer_splitters.hpp : 428) Processed 154143811 kmers 0:11:10.897 8G / 9G INFO General (kmer_splitters.hpp : 437) Used 154143811 kmers. 0:11:11.724 64M / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:11:52.388 64M / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 153710896 kmers in total. 0:11:52.389 64M / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:12:05.754 64M / 9G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:12:24.982 68M / 9G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:12:38.797 68M / 9G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 53174401 bytes occupied (2.7675 bits per kmer). 0:12:39.037 216M / 9G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 382) Building k-mer extensions from k+1-mers 0:12:59.732 216M / 9G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 386) Building k-mer extensions from k+1-mers finished. 0:12:59.737 216M / 9G INFO General (graph_construction.hpp : 145) Condensing graph 0:12:59.737 216M / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 337) Extracting unbranching paths 0:14:34.816 1G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 351) Extracting unbranching paths finished. 9608188 sequences extracted 0:14:49.008 1G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 311) Collecting perfect loops 0:15:40.085 1G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 326) Collecting perfect loops finished. 10 loops collected 0:15:48.653 2G / 9G INFO General (graph_construction.hpp : 150) Building index with from graph 0:15:48.654 2G / 9G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:15:48.654 2G / 9G INFO General (kmer_splitters.hpp : 289) Splitting kmer instances into 16 buckets. This might take a while. 0:15:48.654 2G / 9G INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:15:48.654 2G / 9G INFO General (kmer_splitters.hpp : 307) Memory available for splitting buffers: 32.5482 Gb 0:15:48.654 2G / 9G INFO General (kmer_splitters.hpp : 312) Using cell size of 2097152 0:16:27.478 2G / 9G INFO General (kmer_splitters.hpp : 325) Processed 2089179 edges 0:16:35.692 2G / 9G INFO General (kmer_splitters.hpp : 325) Processed 4181010 edges 0:17:24.232 2G / 9G INFO General (kmer_splitters.hpp : 325) Processed 6274855 edges 0:18:12.798 2G / 9G INFO General (kmer_splitters.hpp : 325) Processed 8366802 edges 0:20:49.560 2G / 9G INFO General (kmer_splitters.hpp : 325) Processed 9608198 edges 0:20:49.561 2G / 9G INFO General (kmer_splitters.hpp : 330) Used 9608198 sequences. 0:20:49.625 2G / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:21:37.570 2G / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 154143811 kmers in total. 0:21:37.570 2G / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:22:11.863 2G / 9G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:26:03.278 2G / 9G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:26:20.535 2G / 9G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 53324163 bytes occupied (2.7675 bits per kmer). 0:26:23.186 5G / 9G INFO General (edge_index_builders.hpp : 21) Collecting k-mer coverage information from graph, this takes a while. 0:31:39.565 5G / 9G INFO General (graph_construction.hpp : 182) Filling coverage index 0:31:39.565 5G / 9G INFO General (edge_index_builders.hpp : 99) Collecting k-mer coverage information from reads, this takes a while. 0:34:25.809 5G / 9G INFO General (graph_construction.hpp : 184) Filling coverage and flanking coverage from index 0:35:06.044 5G / 9G INFO General (construction.cpp : 33) Figured out: read length = 151 0:35:06.062 5G / 9G INFO StageManager (stage.cpp : 125) STAGE == EC Threshold Finding 0:35:16.156 5G / 9G INFO General (kmer_coverage_model.cpp : 178) Kmer coverage valley at: 7 0:35:16.157 5G / 9G INFO General (kmer_coverage_model.cpp : 198) K-mer histogram maximum: 27 0:35:16.157 5G / 9G INFO General (kmer_coverage_model.cpp : 234) Estimated median coverage: 27. Coverage mad: 8.8956 0:35:16.157 5G / 9G INFO General (kmer_coverage_model.cpp : 261) Fitting coverage model 0:35:16.241 5G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 2 0:35:16.467 5G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 4 0:35:17.284 5G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 8 0:35:19.047 5G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 16 0:35:23.017 5G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 32 0:35:24.336 5G / 9G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 26.6731. Fitted coverage std. dev: 8.48137 0:35:24.338 5G / 9G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 0.401596 0:35:24.338 5G / 9G INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 15 0:35:24.338 5G / 9G INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 15 0:35:24.338 5G / 9G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 61159266 0:35:24.338 5G / 9G INFO General (genomic_info_filler.cpp : 103) Mean coverage was calculated as 26.6731 0:35:24.339 5G / 9G INFO General (genomic_info_filler.cpp : 117) EC coverage threshold value was calculated as 15 0:35:24.339 5G / 9G INFO General (genomic_info_filler.cpp : 118) Trusted kmer low bound: 0 0:35:24.339 5G / 9G INFO StageManager (stage.cpp : 125) STAGE == Gap Closer 0:35:24.350 5G / 9G INFO General (gap_closer.cpp : 157) Preparing shift maps 0:35:33.844 5G / 9G INFO General (gap_closer.cpp : 117) Processing paired reads (takes a while) 0:36:22.485 6G / 9G INFO General (gap_closer.cpp : 136) Used 20478134 paired reads 0:36:22.486 6G / 9G INFO General (gap_closer.cpp : 138) Merging paired indices 0:36:27.052 5G / 9G INFO GapCloser (gap_closer.cpp : 395) Closing short gaps 0:36:52.001 5G / 9G INFO GapCloser (gap_closer.cpp : 424) Closing short gaps complete: filled 1463 gaps after checking 19808 candidates 0:36:55.574 5G / 9G INFO StageManager (stage.cpp : 125) STAGE == Simplification 0:36:55.872 2G / 9G INFO General (graph_simplification.hpp : 911) Graph simplification started 0:36:55.873 2G / 9G INFO General (graph_simplification.hpp : 924) Fast simplification mode enabled 0:36:55.873 2G / 9G INFO General (graph_simplification.hpp : 771) PROCEDURE == Presimplification 0:36:55.873 2G / 9G INFO General (graph_simplification.hpp : 211) Removing short low covered self-conjugate connections 0:36:56.816 2G / 9G INFO General (graph_simplification.hpp : 403) Removing isolated edges 0:36:56.817 2G / 9G INFO General (graph_simplification.hpp : 404) All edges shorter than 151 will be removed 0:36:56.817 2G / 9G INFO General (graph_simplification.hpp : 405) Also edges shorter than 0 and coverage smaller than 0 will be removed 0:36:59.744 2G / 9G INFO General (graph_simplification.hpp : 687) Non parallel mode 0:37:32.151 2G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:39:07.119 2G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:39:56.400 1G / 9G INFO General (graph_simplification.hpp : 644) Using permanent iterators 0:39:56.400 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 1 0:39:57.500 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:40:02.161 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:40:04.242 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 2 0:40:04.242 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:40:04.268 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:40:06.088 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 3 0:40:06.088 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:40:06.118 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:40:07.465 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 4 0:40:07.465 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:40:07.480 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:40:08.446 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 5 0:40:08.446 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:40:08.454 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:40:09.365 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 6 0:40:09.365 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:40:09.371 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:40:10.562 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 7 0:40:10.562 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:40:10.566 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:40:11.772 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 8 0:40:11.772 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:40:11.775 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:40:13.083 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 9 0:40:13.083 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:40:13.086 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:40:14.231 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 10 0:40:14.231 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:40:14.233 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:40:15.065 1016M / 9G INFO General (graph_simplification.hpp : 796) PROCEDURE == Post simplification 0:40:15.066 1016M / 9G INFO General (graph_simplification.hpp : 644) Using permanent iterators 0:40:15.066 1016M / 9G INFO General (graph_simplification.hpp : 806) Iteration 0 0:40:15.066 1016M / 9G INFO General (graph_simplification.hpp : 247) Removal of relatively low covered connections disabled 0:40:15.267 1016M / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:40:15.676 1016M / 9G INFO General (graph_simplification.hpp : 806) Iteration 1 0:40:15.676 1016M / 9G INFO General (graph_simplification.hpp : 247) Removal of relatively low covered connections disabled 0:40:15.677 1016M / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:40:15.923 996M / 9G INFO StageManager (stage.cpp : 125) STAGE == Gap Closer 0:40:15.923 996M / 9G INFO General (graph_pack.hpp : 84) Index refill 0:40:15.924 996M / 9G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:40:15.924 996M / 9G INFO General (kmer_splitters.hpp : 289) Splitting kmer instances into 16 buckets. This might take a while. 0:40:15.925 996M / 9G INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:40:15.925 996M / 9G INFO General (kmer_splitters.hpp : 307) Memory available for splitting buffers: 33.0091 Gb 0:40:15.925 996M / 9G INFO General (kmer_splitters.hpp : 312) Using cell size of 2097152 0:42:34.183 1G / 9G INFO General (kmer_splitters.hpp : 325) Processed 45337 edges 0:44:32.231 1G / 9G INFO General (kmer_splitters.hpp : 325) Processed 91539 edges 0:45:15.985 1G / 9G INFO General (kmer_splitters.hpp : 325) Processed 101122 edges 0:45:15.985 1G / 9G INFO General (kmer_splitters.hpp : 330) Used 101122 sequences. 0:45:16.076 988M / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:45:38.001 988M / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 74157930 kmers in total. 0:45:38.002 988M / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:45:44.035 988M / 9G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:47:20.464 1016M / 9G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:47:27.640 1016M / 9G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 25654051 bytes occupied (2.7675 bits per kmer). 0:47:28.931 2G / 9G INFO General (edge_index_builders.hpp : 21) Collecting k-mer coverage information from graph, this takes a while. 0:49:34.996 2G / 9G INFO General (gap_closer.cpp : 157) Preparing shift maps 0:49:35.133 2G / 9G INFO General (gap_closer.cpp : 117) Processing paired reads (takes a while) 0:50:11.381 2G / 9G INFO General (gap_closer.cpp : 136) Used 20478134 paired reads 0:50:11.381 2G / 9G INFO General (gap_closer.cpp : 138) Merging paired indices 0:50:11.598 2G / 9G INFO GapCloser (gap_closer.cpp : 395) Closing short gaps 0:50:11.913 2G / 9G INFO GapCloser (gap_closer.cpp : 424) Closing short gaps complete: filled 105 gaps after checking 6238 candidates 0:50:12.685 2G / 9G INFO StageManager (stage.cpp : 125) STAGE == Simplification Cleanup 0:50:12.686 2G / 9G INFO General (graph_simplification.hpp : 403) Removing isolated edges 0:50:12.686 2G / 9G INFO General (graph_simplification.hpp : 404) All edges shorter than 151 will be removed 0:50:12.686 2G / 9G INFO General (graph_simplification.hpp : 405) Also edges shorter than 0 and coverage smaller than 2 will be removed 0:50:13.215 2G / 9G INFO General (simplification.cpp : 56) Removing all the edges having coverage 0 and less 0:50:13.536 2G / 9G INFO General (simplification.cpp : 68) Counting average coverage 0:50:13.608 2G / 9G INFO General (simplification.cpp : 71) Average coverage = 24.9895 0:50:13.608 2G / 9G INFO StageManager (stage.cpp : 125) STAGE == Contig Output 0:50:13.608 2G / 9G INFO General (contig_output.hpp : 283) Outputting contigs to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_132-dipSPAdes-3.5.0-trimmed/spades//K55/simplified_contigs.fasta 0:50:30.062 2G / 9G INFO General (contig_output.hpp : 283) Outputting contigs to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_132-dipSPAdes-3.5.0-trimmed/spades//K55/before_rr.fasta 0:51:18.078 2G / 9G INFO General (contig_output.hpp : 283) Outputting contigs to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_132-dipSPAdes-3.5.0-trimmed/spades//K55/final_contigs.fasta 0:52:09.199 2G / 9G INFO General (launch.hpp : 82) SPAdes finished 0:52:12.325 64M / 9G INFO General (main.cpp : 166) Assembling time: 0 hours 52 minutes 12 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_132-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 0:00:00.028 4M / 4M INFO General (graph_construction.hpp : 129) Constructing DeBruijn graph for k=77 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 87381 0:01:16.395 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 9832272 reads 0:01:28.828 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 19674230 reads 0:01:41.257 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 29511580 reads 0:01:53.372 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 39334591 reads 0:01:58.044 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 41177580 reads 0:01:58.044 8G / 9G INFO General (kmer_splitters.hpp : 234) Adding contigs from previous K 0:02:19.669 8G / 9G INFO General (kmer_splitters.hpp : 245) Used 41177580 reads. Maximum read length 151 0:02:19.670 8G / 9G INFO General (kmer_splitters.hpp : 246) Average read length 149.625 0:02:21.905 64M / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:02:55.545 64M / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 156321677 kmers in total. 0:02:55.546 64M / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:03:21.699 64M / 9G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:03:21.700 64M / 9G INFO General (kmer_splitters.hpp : 379) Splitting kmer instances into 256 buckets. This might take a while. 0:03:21.700 64M / 9G INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:03:21.700 64M / 9G INFO General (kmer_splitters.hpp : 397) Memory available for splitting buffers: 2.08203 Gb 0:03:21.700 64M / 9G INFO General (kmer_splitters.hpp : 405) Using cell size of 87381 0:03:56.753 8G / 9G INFO General (kmer_splitters.hpp : 428) Processed 156321677 kmers 0:03:56.753 8G / 9G INFO General (kmer_splitters.hpp : 437) Used 156321677 kmers. 0:03:57.977 64M / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:04:14.409 64M / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 156493052 kmers in total. 0:04:14.409 64M / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:05:18.283 64M / 9G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:05:38.627 68M / 9G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:06:50.612 68M / 9G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 54136850 bytes occupied (2.7675 bits per kmer). 0:06:50.855 220M / 9G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 382) Building k-mer extensions from k+1-mers 0:07:14.306 220M / 9G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 386) Building k-mer extensions from k+1-mers finished. 0:07:14.311 220M / 9G INFO General (graph_construction.hpp : 145) Condensing graph 0:07:14.311 220M / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 337) Extracting unbranching paths 0:08:53.620 1G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 351) Extracting unbranching paths finished. 8271144 sequences extracted 0:09:09.150 1G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 311) Collecting perfect loops 0:10:06.119 1G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 326) Collecting perfect loops finished. 10 loops collected 0:10:14.361 2G / 9G INFO General (graph_construction.hpp : 150) Building index with from graph 0:10:14.363 2G / 9G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:10:14.363 2G / 9G INFO General (kmer_splitters.hpp : 289) Splitting kmer instances into 16 buckets. This might take a while. 0:10:14.363 2G / 9G INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:10:14.363 2G / 9G INFO General (kmer_splitters.hpp : 307) Memory available for splitting buffers: 32.5977 Gb 0:10:14.363 2G / 9G INFO General (kmer_splitters.hpp : 312) Using cell size of 1398101 0:11:11.686 2G / 9G INFO General (kmer_splitters.hpp : 325) Processed 1184662 edges 0:12:38.940 2G / 9G INFO General (kmer_splitters.hpp : 325) Processed 2367258 edges 0:14:46.442 2G / 9G INFO General (kmer_splitters.hpp : 325) Processed 3549380 edges 0:16:03.402 2G / 9G INFO General (kmer_splitters.hpp : 325) Processed 4735470 edges 0:17:10.517 2G / 9G INFO General (kmer_splitters.hpp : 325) Processed 5918571 edges 0:20:23.844 2G / 9G INFO General (kmer_splitters.hpp : 325) Processed 7101788 edges 0:20:29.918 2G / 9G INFO General (kmer_splitters.hpp : 325) Processed 8271154 edges 0:20:29.918 2G / 9G INFO General (kmer_splitters.hpp : 330) Used 8271154 sequences. 0:20:29.972 2G / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:21:30.582 2G / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 156321677 kmers in total. 0:21:30.583 2G / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:22:15.514 2G / 9G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:26:09.728 2G / 9G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:26:53.465 2G / 9G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 54077571 bytes occupied (2.7675 bits per kmer). 0:26:56.114 5G / 9G INFO General (edge_index_builders.hpp : 21) Collecting k-mer coverage information from graph, this takes a while. 0:32:33.967 5G / 9G INFO General (graph_construction.hpp : 182) Filling coverage index 0:32:33.967 5G / 9G INFO General (edge_index_builders.hpp : 99) Collecting k-mer coverage information from reads, this takes a while. 0:34:53.512 5G / 9G INFO General (graph_construction.hpp : 184) Filling coverage and flanking coverage from index 0:35:31.780 5G / 9G INFO General (construction.cpp : 33) Figured out: read length = 151 0:35:31.799 5G / 9G INFO StageManager (stage.cpp : 125) STAGE == EC Threshold Finding 0:35:41.632 5G / 9G INFO General (kmer_coverage_model.cpp : 178) Kmer coverage valley at: 4 0:35:41.632 5G / 9G INFO General (kmer_coverage_model.cpp : 198) K-mer histogram maximum: 20 0:35:41.632 5G / 9G INFO General (kmer_coverage_model.cpp : 234) Estimated median coverage: 20. Coverage mad: 8.8956 0:35:41.633 5G / 9G INFO General (kmer_coverage_model.cpp : 261) Fitting coverage model 0:35:41.704 5G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 2 0:35:41.891 5G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 4 0:35:42.544 5G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 8 0:35:43.694 5G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 16 0:35:45.175 5G / 9G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 20.2012. Fitted coverage std. dev: 7.09194 0:35:45.177 5G / 9G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 0.564402 0:35:45.177 5G / 9G INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 12 0:35:45.177 5G / 9G INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 12 0:35:45.177 5G / 9G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 59422925 0:35:45.177 5G / 9G INFO General (genomic_info_filler.cpp : 103) Mean coverage was calculated as 20.2012 0:35:45.177 5G / 9G INFO General (genomic_info_filler.cpp : 117) EC coverage threshold value was calculated as 12 0:35:45.177 5G / 9G INFO General (genomic_info_filler.cpp : 118) Trusted kmer low bound: 0 0:35:45.178 5G / 9G INFO StageManager (stage.cpp : 125) STAGE == Gap Closer 0:35:45.188 5G / 9G INFO General (gap_closer.cpp : 157) Preparing shift maps 0:35:54.189 5G / 9G INFO General (gap_closer.cpp : 117) Processing paired reads (takes a while) 0:36:21.374 6G / 9G INFO General (gap_closer.cpp : 136) Used 20478134 paired reads 0:36:21.375 6G / 9G INFO General (gap_closer.cpp : 138) Merging paired indices 0:36:27.422 5G / 9G INFO GapCloser (gap_closer.cpp : 395) Closing short gaps 0:36:49.182 5G / 9G INFO GapCloser (gap_closer.cpp : 424) Closing short gaps complete: filled 1300 gaps after checking 21993 candidates 0:36:52.738 5G / 9G INFO StageManager (stage.cpp : 125) STAGE == Simplification 0:36:52.962 2G / 9G INFO General (graph_simplification.hpp : 911) Graph simplification started 0:36:52.962 2G / 9G INFO General (graph_simplification.hpp : 924) Fast simplification mode enabled 0:36:52.962 2G / 9G INFO General (graph_simplification.hpp : 771) PROCEDURE == Presimplification 0:36:52.962 2G / 9G INFO General (graph_simplification.hpp : 211) Removing short low covered self-conjugate connections 0:36:53.747 2G / 9G INFO General (graph_simplification.hpp : 403) Removing isolated edges 0:36:53.750 2G / 9G INFO General (graph_simplification.hpp : 404) All edges shorter than 151 will be removed 0:36:53.750 2G / 9G INFO General (graph_simplification.hpp : 405) Also edges shorter than 0 and coverage smaller than 0 will be removed 0:36:57.534 2G / 9G INFO General (graph_simplification.hpp : 687) Non parallel mode 0:37:20.142 2G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:38:41.057 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:38:45.849 1G / 9G INFO General (graph_simplification.hpp : 644) Using permanent iterators 0:38:45.850 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 1 0:38:46.377 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:38:48.565 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:38:48.648 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 2 0:38:48.649 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:38:48.650 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:38:49.161 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 3 0:38:49.161 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:38:49.168 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:38:49.835 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 4 0:38:49.836 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:38:49.845 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:38:50.548 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 5 0:38:50.548 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:38:50.560 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:38:51.475 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 6 0:38:51.475 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:38:51.479 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:38:52.562 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 7 0:38:52.562 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:38:52.565 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:38:53.887 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 8 0:38:53.887 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:38:53.890 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:38:55.217 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 9 0:38:55.217 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:38:55.219 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:38:56.322 948M / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 10 0:38:56.322 948M / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:38:56.324 948M / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:38:57.297 868M / 9G INFO General (graph_simplification.hpp : 796) PROCEDURE == Post simplification 0:38:57.297 868M / 9G INFO General (graph_simplification.hpp : 644) Using permanent iterators 0:38:57.297 868M / 9G INFO General (graph_simplification.hpp : 806) Iteration 0 0:38:57.297 868M / 9G INFO General (graph_simplification.hpp : 247) Removal of relatively low covered connections disabled 0:38:57.440 868M / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:38:57.732 868M / 9G INFO General (graph_simplification.hpp : 806) Iteration 1 0:38:57.732 868M / 9G INFO General (graph_simplification.hpp : 247) Removal of relatively low covered connections disabled 0:38:57.732 868M / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:38:57.835 852M / 9G INFO StageManager (stage.cpp : 125) STAGE == Gap Closer 0:38:57.835 852M / 9G INFO General (graph_pack.hpp : 84) Index refill 0:38:57.836 852M / 9G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:38:57.836 852M / 9G INFO General (kmer_splitters.hpp : 289) Splitting kmer instances into 16 buckets. This might take a while. 0:38:57.837 852M / 9G INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:38:57.837 852M / 9G INFO General (kmer_splitters.hpp : 307) Memory available for splitting buffers: 33.056 Gb 0:38:57.837 852M / 9G INFO General (kmer_splitters.hpp : 312) Using cell size of 1398101 0:40:22.743 1G / 9G INFO General (kmer_splitters.hpp : 325) Processed 21947 edges 0:41:18.210 1G / 9G INFO General (kmer_splitters.hpp : 325) Processed 44202 edges 0:43:44.919 1G / 9G INFO General (kmer_splitters.hpp : 325) Processed 66111 edges 0:44:57.612 1G / 9G INFO General (kmer_splitters.hpp : 325) Processed 73135 edges 0:44:57.613 1G / 9G INFO General (kmer_splitters.hpp : 330) Used 73135 sequences. 0:44:57.694 852M / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:46:05.407 852M / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 74308851 kmers in total. 0:46:05.407 852M / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:46:16.111 852M / 9G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:47:56.904 876M / 9G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:48:33.141 876M / 9G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 25706251 bytes occupied (2.7675 bits per kmer). 0:48:34.282 2G / 9G INFO General (edge_index_builders.hpp : 21) Collecting k-mer coverage information from graph, this takes a while. 0:50:48.513 2G / 9G INFO General (gap_closer.cpp : 157) Preparing shift maps 0:50:48.638 2G / 9G INFO General (gap_closer.cpp : 117) Processing paired reads (takes a while) 0:51:23.250 2G / 9G INFO General (gap_closer.cpp : 136) Used 20478134 paired reads 0:51:23.251 2G / 9G INFO General (gap_closer.cpp : 138) Merging paired indices 0:51:23.488 2G / 9G INFO GapCloser (gap_closer.cpp : 395) Closing short gaps 0:51:23.849 2G / 9G INFO GapCloser (gap_closer.cpp : 424) Closing short gaps complete: filled 84 gaps after checking 6579 candidates 0:51:24.927 2G / 9G INFO StageManager (stage.cpp : 125) STAGE == Simplification Cleanup 0:51:24.928 2G / 9G INFO General (graph_simplification.hpp : 403) Removing isolated edges 0:51:24.928 2G / 9G INFO General (graph_simplification.hpp : 404) All edges shorter than 151 will be removed 0:51:24.928 2G / 9G INFO General (graph_simplification.hpp : 405) Also edges shorter than 0 and coverage smaller than 2 will be removed 0:51:26.047 2G / 9G INFO General (simplification.cpp : 56) Removing all the edges having coverage 0 and less 0:51:26.262 2G / 9G INFO General (simplification.cpp : 68) Counting average coverage 0:51:26.319 2G / 9G INFO General (simplification.cpp : 71) Average coverage = 18.9085 0:51:26.319 2G / 9G INFO StageManager (stage.cpp : 125) STAGE == Mismatch Correction 0:52:03.223 2G / 9G INFO General (mismatch_shall_not_pass.hp: 188) Finished collecting potential mismatches positions 0:52:03.313 2G / 9G INFO General (mismatch_shall_not_pass.hp: 291) All edges processed 0:52:03.316 2G / 9G INFO General (mismatch_correction.cpp : 18) Corrected 0 nucleotides 0:52:03.335 2G / 9G INFO StageManager (stage.cpp : 125) STAGE == Paired Information Counting 0:52:03.578 2G / 9G INFO General (pair_info_count.cpp : 150) Graph N50: 22167 0:52:03.578 2G / 9G INFO General (pair_info_count.cpp : 152) Estimating insert size for library #0 0:52:03.578 2G / 9G INFO General (pair_info_count.cpp : 31) Estimating insert size (takes a while) 0:52:03.589 2G / 9G INFO General (short_read_mapper.hpp : 91) Selecting usual mapper 0:52:09.333 2G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 200000 reads 0:52:09.334 2G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 400000 reads 0:52:09.342 2G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 600000 reads 0:52:09.352 2G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 800000 reads 0:52:09.368 2G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 1000000 reads 0:52:09.370 2G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 1200000 reads 0:52:09.559 2G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 2200000 reads 0:52:15.208 2G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 4200000 reads 0:52:21.410 2G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 8400000 reads 0:52:24.155 2G / 9G INFO General (sequence_mapper_notifier.h: 89) Processed 10239067 reads 0:52:24.156 2G / 9G INFO General (pair_info_count.cpp : 41) 5171683 paired reads (50.5093% of all) aligned to long edges 0:52:24.167 2G / 9G INFO General (pair_info_count.cpp : 170) Estimated insert size for paired library #0 0:52:24.167 2G / 9G INFO General (pair_info_count.cpp : 175) Insert size = 305.049, deviation = 89.6803, left quantile = 194, right quantile = 422, read length = 151 0:52:24.167 2G / 9G INFO General (pair_info_count.cpp : 187) Mapping library #0 0:52:24.167 2G / 9G INFO General (pair_info_count.cpp : 189) Mapping paired reads (takes a while) 0:52:24.167 2G / 9G INFO General (pair_info_count.cpp : 73) Left insert size qauntile 194, right insert size quantile 422 0:52:24.178 2G / 9G INFO General (short_read_mapper.hpp : 91) Selecting usual mapper 0:52:31.928 4G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 200000 reads 0:52:32.633 4G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 400000 reads 0:52:33.479 4G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 600000 reads 0:52:34.502 4G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 800000 reads 0:52:35.645 4G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 1000000 reads 0:52:36.883 4G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 1200000 reads 0:52:43.936 4G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 2200000 reads 0:52:59.231 4G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 4200000 reads 0:53:33.332 5G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 8400000 reads 0:54:44.780 5G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 16800000 reads 0:55:20.138 3G / 9G INFO General (sequence_mapper_notifier.h: 89) Processed 20478134 reads 0:57:12.165 3G / 9G INFO General (split_graph_pair_info.hpp : 344) Threshold for paired information 0.0561561 0:57:15.689 2G / 9G INFO StageManager (stage.cpp : 125) STAGE == Distance Estimation 0:57:15.689 2G / 9G INFO General (distance_estimation.cpp : 234) Processing library #0 0:57:15.689 2G / 9G INFO General (distance_estimation.cpp : 136) Weight Filter Done 0:57:15.689 2G / 9G INFO DistanceEstimator (distance_estimation.hpp : 187) Using SIMPLE distance estimator 0:57:24.205 2G / 9G INFO DistanceEstimator (distance_estimation.hpp : 208) Merging maps 0:57:25.029 2G / 9G INFO General (distance_estimation.cpp : 38) Filtering info 0:57:26.291 2G / 9G INFO General (pair_info_filters.hpp : 354) Pruning the index 0:57:26.345 2G / 9G INFO General (distance_estimation.cpp : 184) Refining clustered pair information 0:57:26.452 2G / 9G INFO General (distance_estimation.cpp : 186) The refining of clustered pair information has been finished 0:57:26.452 2G / 9G INFO General (distance_estimation.cpp : 188) Filling paired information 0:57:27.995 2G / 9G INFO PairInfoImprover (pair_info_improver.hpp : 61) Paired info stats: missing = 43341; contradictional = 5508 0:57:29.512 2G / 9G INFO PairInfoImprover (pair_info_improver.hpp : 61) Paired info stats: missing = 5861; contradictional = 0 0:57:29.512 2G / 9G INFO General (distance_estimation.cpp : 193) Filling scaffolding index 0:57:29.512 2G / 9G INFO DistanceEstimator (distance_estimation.hpp : 187) Using SMOOTHING distance estimator 0:57:39.203 2G / 9G INFO DistanceEstimator (distance_estimation.hpp : 208) Merging maps 0:57:39.251 2G / 9G INFO General (distance_estimation.cpp : 38) Filtering info 0:57:39.496 2G / 9G INFO General (pair_info_filters.hpp : 354) Pruning the index 0:57:39.896 2G / 9G INFO StageManager (stage.cpp : 125) STAGE == Repeat Resolving 0:57:39.897 2G / 9G INFO General (contig_output.hpp : 283) Outputting contigs to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_132-dipSPAdes-3.5.0-trimmed/spades//K77/before_rr.fasta 0:58:26.462 2G / 9G INFO General (repeat_resolving.cpp : 59) Using Path-Extend repeat resolving 0:58:26.463 2G / 9G INFO General (path_extend_launch.hpp : 459) Threshold for library #0 is 0.0561561 0:58:26.463 2G / 9G INFO General (path_extend_launch.hpp : 298) Path-Extend repeat resolving tool started 0:58:26.532 2G / 9G INFO General (path_extend_launch.hpp : 316) Using 1 paired-end library 0:58:26.532 2G / 9G INFO General (path_extend_launch.hpp : 317) Using 1 paired-end scaffolding library 0:58:26.532 2G / 9G INFO General (path_extend_launch.hpp : 318) Using 0 mate-pair libraries 0:58:26.532 2G / 9G INFO General (path_extend_launch.hpp : 319) Using 0 single read libraries 0:58:26.532 2G / 9G INFO General (path_extend_launch.hpp : 320) Scaffolder is on 0:58:26.933 2G / 9G INFO General (path_extend_launch.hpp : 332) Growing paths using paired-end and long single reads 0:58:26.934 2G / 9G INFO PathExtender (path_extender.hpp : 611) Processed 0 paths from 31108 (0%) 0:58:27.168 2G / 9G INFO PathExtender (path_extender.hpp : 609) Processed 128 paths from 31108 (0%) 0:58:27.487 2G / 9G INFO PathExtender (path_extender.hpp : 609) Processed 256 paths from 31108 (0%) 0:58:27.894 2G / 9G INFO PathExtender (path_extender.hpp : 609) Processed 512 paths from 31108 (1%) 0:58:28.676 2G / 9G INFO PathExtender (path_extender.hpp : 609) Processed 1024 paths from 31108 (3%) 0:58:29.730 2G / 9G INFO PathExtender (path_extender.hpp : 609) Processed 2048 paths from 31108 (6%) 0:58:30.590 2G / 9G INFO PathExtender (path_extender.hpp : 611) Processed 3111 paths from 31108 (10%) 0:58:31.090 2G / 9G INFO PathExtender (path_extender.hpp : 609) Processed 4096 paths from 31108 (13%) 0:58:31.597 2G / 9G INFO PathExtender (path_extender.hpp : 611) Processed 6222 paths from 31108 (20%) 0:58:31.839 2G / 9G INFO PathExtender (path_extender.hpp : 609) Processed 8192 paths from 31108 (26%) 0:58:32.274 2G / 9G INFO PathExtender (path_extender.hpp : 611) Processed 9333 paths from 31108 (30%) 0:58:32.579 2G / 9G INFO PathExtender (path_extender.hpp : 611) Processed 12444 paths from 31108 (40%) 0:58:32.960 2G / 9G INFO PathExtender (path_extender.hpp : 611) Processed 15555 paths from 31108 (50%) 0:58:33.085 2G / 9G INFO PathExtender (path_extender.hpp : 609) Processed 16384 paths from 31108 (52%) 0:58:33.348 2G / 9G INFO PathExtender (path_extender.hpp : 611) Processed 18666 paths from 31108 (60%) 0:58:34.029 2G / 9G INFO PathExtender (path_extender.hpp : 611) Processed 21777 paths from 31108 (70%) 0:58:36.626 2G / 9G INFO PathExtender (path_extender.hpp : 611) Processed 24888 paths from 31108 (80%) 0:58:39.016 2G / 9G INFO PathExtender (path_extender.hpp : 611) Processed 27999 paths from 31108 (90%) 0:58:40.925 2G / 9G INFO PathExtendIO (pe_io.hpp : 339) Constructing FASTG file from paths 0:58:41.656 2G / 9G INFO PathExtendIO (pe_io.hpp : 342) Writing contigs in FASTG to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_132-dipSPAdes-3.5.0-trimmed/spades//K77/final_contigs.fastg 0:58:41.657 2G / 9G INFO PathExtendIO (pe_io.hpp : 343) Writing contigs in FASTA to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_132-dipSPAdes-3.5.0-trimmed/spades//K77/final_contigs.fasta 0:59:26.884 2G / 9G INFO PathExtendIO (pe_io.hpp : 339) Constructing FASTG file from paths 0:59:27.627 2G / 9G INFO PathExtendIO (pe_io.hpp : 342) Writing contigs in FASTG to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_132-dipSPAdes-3.5.0-trimmed/spades//K77/path_extend/pe_before_traversal.fastg 0:59:27.627 2G / 9G INFO PathExtendIO (pe_io.hpp : 343) Writing contigs in FASTA to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_132-dipSPAdes-3.5.0-trimmed/spades//K77/path_extend/pe_before_traversal.fasta 1:00:12.828 2G / 9G INFO General (path_extend_launch.hpp : 281) Traversing tandem repeats 1:00:14.172 2G / 9G INFO PathExtendIO (pe_io.hpp : 339) Constructing FASTG file from paths 1:00:14.829 2G / 9G INFO PathExtendIO (pe_io.hpp : 342) Writing contigs in FASTG to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_132-dipSPAdes-3.5.0-trimmed/spades//K77/scaffolds.fastg 1:00:14.829 2G / 9G INFO PathExtendIO (pe_io.hpp : 343) Writing contigs in FASTA to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_132-dipSPAdes-3.5.0-trimmed/spades//K77/scaffolds.fasta 1:01:00.447 2G / 9G INFO General (launch.hpp : 82) SPAdes finished 1:01:03.945 336M / 9G INFO General (main.cpp : 166) Assembling time: 1 hours 1 minutes 3 seconds ===== Assembling finished. * Corrected reads are in /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_132-dipSPAdes-3.5.0-trimmed/spades/corrected/ * Assembled contigs are in /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_132-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_132-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_132-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_132-dipSPAdes-3.5.0-trimmed/spades/spades.log Thank you for using SPAdes!