Command line: --diploid --pe1-1 /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_134/reads.end1.paired.fastq.gz --pe1-2 /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_134/reads.end2.paired.fastq.gz -t 16 -o /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_134-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_134-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_134/reads.end1.paired.fastq.gz'] right reads: ['/N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_134/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_134-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_134-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_134-dipSPAdes-3.5.0-trimmed/spades/corrected/configs/config.info 0:00:00.019 4M / 4M INFO General (main.cpp : 82) Loading config from /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_134-dipSPAdes-3.5.0-trimmed/spades/corrected/configs/config.info 0:00:00.166 4M / 4M INFO General (memory_limit.hpp : 42) Memory limit set to 100 Gb 0:00:00.166 4M / 4M INFO General (main.cpp : 91) Trying to determine PHRED offset 0:00:00.207 4M / 4M INFO General (main.cpp : 97) Determined value is 33 0:00:00.232 4M / 4M INFO General (hammer_tools.cpp : 36) Hamming graph threshold tau=1, k=21, subkmer positions = [ 0 10 ] === ITERATION 0 begins === 0:00:00.233 4M / 4M INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:00:00.233 4M / 4M INFO K-mer Splitting (kmer_data.cpp : 127) Splitting kmer instances into 256 buckets. This might take a while. 0:00:00.234 4M / 4M INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:00:00.234 4M / 4M INFO K-mer Splitting (kmer_data.cpp : 145) Memory available for splitting buffers: 2.08325 Gb 0:00:00.234 4M / 4M INFO K-mer Splitting (kmer_data.cpp : 153) Using cell size of 262144 0:00:03.020 8G / 8G INFO K-mer Splitting (kmer_data.cpp : 167) Processing /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_134/reads.end1.paired.fastq.gz 0:01:05.644 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 176) Processed 3213886 reads 0:02:02.532 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 176) Processed 6475849 reads 0:03:22.263 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 176) Processed 9633186 reads 0:04:47.793 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 176) Processed 11723251 reads 0:04:47.794 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 167) Processing /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_134/reads.end2.paired.fastq.gz 0:05:55.558 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 176) Processed 15055554 reads 0:06:55.903 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 176) Processed 18539373 reads 0:07:52.157 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 176) Processed 21838108 reads 0:08:19.603 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 176) Processed 23446502 reads 0:08:19.606 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 181) Processed 23446502 reads 0:08:20.757 64M / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:08:53.322 64M / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 277909756 kmers in total. 0:08:53.323 64M / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:09:05.753 64M / 9G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:09:37.951 192M / 9G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:10:09.678 192M / 9G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 96139439 bytes occupied (2.7675 bits per kmer). 0:10:09.679 192M / 9G INFO K-mer Counting (kmer_data.cpp : 266) Arranging kmers in hash map order 0:12:52.887 192M / 9G INFO K-mer Counting (kmer_data.cpp : 279) Done. Total swaps: 277909474 0:12:54.748 2G / 9G INFO General (main.cpp : 151) Clustering Hamming graph. 0:12:54.750 2G / 9G INFO Hamming Clustering (hamcluster.cpp : 115) Serializing sub-kmers. 0:12:54.750 2G / 9G INFO Hamming Clustering (hamcluster.cpp : 120) Serializing: [0, 10) 0:16:00.035 2G / 9G INFO Hamming Clustering (hamcluster.cpp : 120) Serializing: [10, 21) 0:19:07.257 2G / 9G INFO Hamming Clustering (hamcluster.cpp : 129) Splitting sub-kmers, pass 1. 0:22:54.470 2G / 9G INFO Hamming Clustering (hamcluster.cpp : 134) Splitting done. Processed 2 blocks. Produced 5049222 blocks. 0:22:54.470 2G / 9G INFO Hamming Clustering (hamcluster.cpp : 145) Merge sub-kmers, pass 1 0:37:09.409 2G / 9G INFO Hamming Clustering (hamcluster.cpp : 170) Merge done, total 1544787 new blocks generated. 0:37:10.929 2G / 9G INFO Hamming Clustering (hamcluster.cpp : 175) Spliting sub-kmers, pass 2. 0:49:01.228 2G / 9G INFO Hamming Clustering (hamcluster.cpp : 180) Splitting done. Processed 3089574 blocks. Produced 530070710 blocks. 0:49:01.228 2G / 9G INFO Hamming Clustering (hamcluster.cpp : 187) Merge sub-kmers, pass 2 0:59:56.278 2G / 9G INFO Hamming Clustering (hamcluster.cpp : 205) Merge done, saw 221912 big blocks out of 530070710 processed. 1:03:48.992 2G / 9G INFO General (main.cpp : 165) Clustering done. Total clusters: 131926205 1:03:48.992 2G / 9G INFO K-mer Counting (kmer_data.cpp : 284) Collecting K-mer information, this takes a while. 1:03:54.570 14G / 14G INFO K-mer Counting (kmer_data.cpp : 290) Processing /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_134/reads.end1.paired.fastq.gz 1:06:48.413 14G / 14G INFO K-mer Counting (kmer_data.cpp : 290) Processing /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_134/reads.end2.paired.fastq.gz 1:09:36.803 14G / 14G INFO K-mer Counting (kmer_data.cpp : 297) Collection done, postprocessing. 1:09:43.766 14G / 14G INFO K-mer Counting (kmer_data.cpp : 310) There are 277909756 kmers in total. Among them 133762474 (48.1316%) are singletons. 1:09:43.766 14G / 14G INFO General (main.cpp : 203) Subclustering Hamming graph 1:12:35.981 14G / 14G INFO Hamming Subclustering (kmer_cluster.cpp : 626) Subclustering done. Total 85787 non-read kmers were generated. 1:12:35.981 14G / 14G INFO Hamming Subclustering (kmer_cluster.cpp : 627) Subclustering statistics: 1:12:35.981 14G / 14G INFO Hamming Subclustering (kmer_cluster.cpp : 628) Total singleton hamming clusters: 75713419. Among them 57701888 (76.2109%) are good 1:12:35.981 14G / 14G INFO Hamming Subclustering (kmer_cluster.cpp : 629) Total singleton subclusters: 7734381. Among them 7734329 (99.9993%) are good 1:12:35.981 14G / 14G INFO Hamming Subclustering (kmer_cluster.cpp : 630) Total non-singleton subcluster centers: 60993451. Among them 40960721 (67.1559%) are good 1:12:35.981 14G / 14G INFO Hamming Subclustering (kmer_cluster.cpp : 631) Average size of non-trivial subcluster: 3.28771 kmers 1:12:35.981 14G / 14G INFO Hamming Subclustering (kmer_cluster.cpp : 632) Average number of sub-clusters per non-singleton cluster: 1.22264 1:12:35.981 14G / 14G INFO Hamming Subclustering (kmer_cluster.cpp : 633) Total solid k-mers: 106396938 1:12:35.981 14G / 14G INFO Hamming Subclustering (kmer_cluster.cpp : 634) Substitution probabilities: [4,4]((0.900526,0.0225903,0.0256061,0.0512776),(0.0363044,0.928795,0.0125611,0.0223393),(0.0214846,0.0122338,0.929824,0.036458),(0.0504534,0.0259145,0.0229196,0.900713)) 1:12:36.389 14G / 14G INFO General (main.cpp : 208) Finished clustering. 1:12:36.389 14G / 14G INFO General (main.cpp : 228) Starting solid k-mers expansion in 16 threads. 1:16:34.770 14G / 14G INFO General (main.cpp : 249) Solid k-mers iteration 0 produced 42082556 new k-mers. 1:20:29.597 14G / 14G INFO General (main.cpp : 249) Solid k-mers iteration 1 produced 1036195 new k-mers. 1:24:24.497 14G / 14G INFO General (main.cpp : 249) Solid k-mers iteration 2 produced 32292 new k-mers. 1:28:19.714 14G / 14G INFO General (main.cpp : 249) Solid k-mers iteration 3 produced 1555 new k-mers. 1:32:14.750 14G / 14G INFO General (main.cpp : 249) Solid k-mers iteration 4 produced 17 new k-mers. 1:36:09.952 14G / 14G INFO General (main.cpp : 249) Solid k-mers iteration 5 produced 0 new k-mers. 1:36:09.953 14G / 14G INFO General (main.cpp : 253) Solid k-mers finalized 1:36:09.953 14G / 14G INFO General (hammer_tools.cpp : 210) Starting read correction in 16 threads. 1:36:09.953 14G / 14G INFO General (hammer_tools.cpp : 222) Correcting pair of reads: /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_134/reads.end1.paired.fastq.gz and /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_134/reads.end2.paired.fastq.gz 1:36:35.570 16G / 16G INFO General (hammer_tools.cpp : 166) Prepared batch 0 of 1600000 reads. 1:36:57.041 16G / 16G INFO General (hammer_tools.cpp : 175) Processed batch 0 1:37:12.239 16G / 16G INFO General (hammer_tools.cpp : 185) Written batch 0 1:37:36.109 16G / 16G INFO General (hammer_tools.cpp : 166) Prepared batch 1 of 1600000 reads. 1:38:01.526 16G / 16G INFO General (hammer_tools.cpp : 175) Processed batch 1 1:38:36.861 16G / 16G INFO General (hammer_tools.cpp : 185) Written batch 1 1:39:00.706 16G / 16G INFO General (hammer_tools.cpp : 166) Prepared batch 2 of 1600000 reads. 1:39:26.030 16G / 16G INFO General (hammer_tools.cpp : 175) Processed batch 2 1:39:41.161 16G / 16G INFO General (hammer_tools.cpp : 185) Written batch 2 1:40:04.655 16G / 16G INFO General (hammer_tools.cpp : 166) Prepared batch 3 of 1600000 reads. 1:40:26.006 16G / 16G INFO General (hammer_tools.cpp : 175) Processed batch 3 1:40:41.141 16G / 16G INFO General (hammer_tools.cpp : 185) Written batch 3 1:41:04.571 16G / 16G INFO General (hammer_tools.cpp : 166) Prepared batch 4 of 1600000 reads. 1:41:26.019 16G / 16G INFO General (hammer_tools.cpp : 175) Processed batch 4 1:41:41.156 16G / 16G INFO General (hammer_tools.cpp : 185) Written batch 4 1:42:04.514 16G / 16G INFO General (hammer_tools.cpp : 166) Prepared batch 5 of 1600000 reads. 1:42:25.474 16G / 16G INFO General (hammer_tools.cpp : 175) Processed batch 5 1:42:40.638 16G / 16G INFO General (hammer_tools.cpp : 185) Written batch 5 1:43:03.683 16G / 16G INFO General (hammer_tools.cpp : 166) Prepared batch 6 of 1600000 reads. 1:43:25.099 16G / 16G INFO General (hammer_tools.cpp : 175) Processed batch 6 1:43:40.204 16G / 16G INFO General (hammer_tools.cpp : 185) Written batch 6 1:43:47.731 16G / 16G INFO General (hammer_tools.cpp : 166) Prepared batch 7 of 523251 reads. 1:43:54.805 16G / 16G INFO General (hammer_tools.cpp : 175) Processed batch 7 1:43:59.778 16G / 16G INFO General (hammer_tools.cpp : 185) Written batch 7 1:44:02.313 14G / 16G INFO General (hammer_tools.cpp : 269) Correction done. Changed 4069178 bases in 3242243 reads. 1:44:02.313 14G / 16G INFO General (hammer_tools.cpp : 270) Failed to correct 397767760 bases out of 3499381913. 1:44:02.387 2G / 16G INFO General (main.cpp : 286) Saving corrected dataset description to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_134-dipSPAdes-3.5.0-trimmed/spades/corrected/corrected.yaml 1:44:02.391 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_134-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_134-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 0:00:00.005 4M / 4M INFO General (read_converter.hpp : 79) Converting reads to binary format (takes a while) 0:00:00.005 4M / 4M INFO General (read_converter.hpp : 81) Paired reads for library #0 0:00:01.126 80M / 80M INFO General (binary_converter.hpp : 138) 16384 reads processed 0:00:01.528 96M / 96M INFO General (binary_converter.hpp : 138) 32768 reads processed 0:00:02.328 124M / 124M INFO General (binary_converter.hpp : 138) 65536 reads processed 0:00:03.930 184M / 184M INFO General (binary_converter.hpp : 138) 131072 reads processed 0:00:07.137 300M / 300M INFO General (binary_converter.hpp : 138) 262144 reads processed 0:00:13.567 536M / 536M INFO General (binary_converter.hpp : 138) 524288 reads processed 0:00:29.188 904M / 904M INFO General (binary_converter.hpp : 138) 1048576 reads processed 0:00:57.685 904M / 904M INFO General (binary_converter.hpp : 138) 2097152 reads processed 0:01:54.915 908M / 908M INFO General (binary_converter.hpp : 138) 4194304 reads processed 0:03:52.055 908M / 908M INFO General (binary_converter.hpp : 138) 8388608 reads processed 0:05:22.117 584M / 908M INFO General (binary_converter.hpp : 158) 11621179 reads written 0:05:22.980 4M / 908M INFO General (read_converter.hpp : 91) Single reads for library #0 0:05:24.854 140M / 908M INFO General (binary_converter.hpp : 138) 16384 reads processed 0:05:25.066 144M / 908M INFO General (binary_converter.hpp : 138) 32768 reads processed 0:05:25.451 160M / 908M INFO General (binary_converter.hpp : 138) 65536 reads processed 0:05:26.064 176M / 908M INFO General (binary_converter.hpp : 158) 101831 reads written 0:05:26.262 4M / 908M INFO General (graph_construction.hpp : 129) Constructing DeBruijn graph for k=21 0:05:26.265 4M / 908M INFO General (kmer_splitters.hpp : 172) Splitting kmer instances into 256 buckets. This might take a while. 0:05:26.266 4M / 908M INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:05:26.266 4M / 908M INFO General (kmer_splitters.hpp : 190) Memory available for splitting buffers: 2.08325 Gb 0:05:26.266 4M / 908M INFO General (kmer_splitters.hpp : 199) Using cell size of 262144 0:05:59.481 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 16664785 reads 0:06:24.867 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 33329845 reads 0:06:48.680 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 46688378 reads 0:06:48.681 8G / 9G INFO General (kmer_splitters.hpp : 234) Adding contigs from previous K 0:06:48.682 8G / 9G INFO General (kmer_splitters.hpp : 245) Used 46688378 reads. Maximum read length 151 0:06:48.682 8G / 9G INFO General (kmer_splitters.hpp : 246) Average read length 149.86 0:06:50.806 64M / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:06:57.907 64M / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 112932670 kmers in total. 0:06:57.907 64M / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:07:23.226 64M / 9G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:07:23.226 64M / 9G INFO General (kmer_splitters.hpp : 379) Splitting kmer instances into 256 buckets. This might take a while. 0:07:23.227 64M / 9G INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:07:23.227 64M / 9G INFO General (kmer_splitters.hpp : 397) Memory available for splitting buffers: 2.08203 Gb 0:07:23.227 64M / 9G INFO General (kmer_splitters.hpp : 405) Using cell size of 262144 0:07:38.436 8G / 9G INFO General (kmer_splitters.hpp : 428) Processed 112932670 kmers 0:07:38.437 8G / 9G INFO General (kmer_splitters.hpp : 437) Used 112932670 kmers. 0:07:38.902 64M / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:07:42.885 64M / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 110106803 kmers in total. 0:07:42.885 64M / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:07:47.923 64M / 9G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:08:04.346 64M / 9G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:08:08.595 64M / 9G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 38090096 bytes occupied (2.7675 bits per kmer). 0:08:08.784 172M / 9G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 382) Building k-mer extensions from k+1-mers 0:08:20.130 172M / 9G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 386) Building k-mer extensions from k+1-mers finished. 0:08:20.135 172M / 9G INFO Early tip clipping (early_simplification.hpp : 236) Early tip clipping 0:13:59.981 172M / 9G INFO Early tip clipping (early_simplification.hpp : 239) 5306528 22-mers were removed by early tip clipper 0:13:59.981 172M / 9G INFO General (graph_construction.hpp : 145) Condensing graph 0:13:59.981 172M / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 337) Extracting unbranching paths 0:15:16.031 1G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 351) Extracting unbranching paths finished. 15081748 sequences extracted 0:15:24.955 1G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 311) Collecting perfect loops 0:15:58.530 1G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 326) Collecting perfect loops finished. 34 loops collected 0:16:08.884 2G / 9G INFO General (graph_construction.hpp : 150) Building index with from graph 0:16:08.885 2G / 9G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:16:08.886 2G / 9G INFO General (kmer_splitters.hpp : 289) Splitting kmer instances into 16 buckets. This might take a while. 0:16:08.886 2G / 9G INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:16:08.886 2G / 9G INFO General (kmer_splitters.hpp : 307) Memory available for splitting buffers: 32.3385 Gb 0:16:08.886 2G / 9G INFO General (kmer_splitters.hpp : 312) Using cell size of 4194304 0:16:26.174 3G / 9G INFO General (kmer_splitters.hpp : 325) Processed 9403746 edges 0:16:36.355 3G / 9G INFO General (kmer_splitters.hpp : 325) Processed 15081782 edges 0:16:36.356 3G / 9G INFO General (kmer_splitters.hpp : 330) Used 15081782 sequences. 0:16:36.409 2G / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:16:59.848 2G / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 107626142 kmers in total. 0:16:59.848 2G / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:17:04.153 2G / 9G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:19:32.612 3G / 9G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:19:37.058 3G / 9G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 37231957 bytes occupied (2.7675 bits per kmer). 0:19:38.915 5G / 9G INFO General (edge_index_builders.hpp : 21) Collecting k-mer coverage information from graph, this takes a while. 0:22:49.224 5G / 9G INFO General (graph_construction.hpp : 182) Filling coverage index 0:22:49.224 5G / 9G INFO General (edge_index_builders.hpp : 99) Collecting k-mer coverage information from reads, this takes a while. 0:26:16.325 5G / 9G INFO General (graph_construction.hpp : 184) Filling coverage and flanking coverage from index 0:26:44.265 5G / 9G INFO General (construction.cpp : 33) Figured out: read length = 151 0:26:44.281 5G / 9G INFO StageManager (stage.cpp : 125) STAGE == EC Threshold Finding 0:26:54.433 5G / 9G INFO General (kmer_coverage_model.cpp : 178) Kmer coverage valley at: 10 0:26:54.434 5G / 9G INFO General (kmer_coverage_model.cpp : 198) K-mer histogram maximum: 46 0:26:54.434 5G / 9G INFO General (kmer_coverage_model.cpp : 234) Estimated median coverage: 46. Coverage mad: 13.3434 0:26:54.435 5G / 9G INFO General (kmer_coverage_model.cpp : 261) Fitting coverage model 0:26:54.602 5G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 2 0:26:55.036 5G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 4 0:26:56.571 5G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 8 0:26:59.643 5G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 16 0:27:06.210 5G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 32 0:27:06.636 5G / 9G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 42.2624. Fitted coverage std. dev: 13.9581 0:27:06.640 5G / 9G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 0.307935 0:27:06.640 5G / 9G INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 22 0:27:06.640 5G / 9G INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 22 0:27:06.640 5G / 9G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 59965966 0:27:06.640 5G / 9G INFO General (genomic_info_filler.cpp : 103) Mean coverage was calculated as 42.2624 0:27:06.641 5G / 9G INFO General (genomic_info_filler.cpp : 117) EC coverage threshold value was calculated as 22 0:27:06.641 5G / 9G INFO General (genomic_info_filler.cpp : 118) Trusted kmer low bound: 0 0:27:06.641 5G / 9G INFO StageManager (stage.cpp : 125) STAGE == Simplification 0:27:06.853 2G / 9G INFO General (graph_simplification.hpp : 911) Graph simplification started 0:27:06.853 2G / 9G INFO General (graph_simplification.hpp : 924) Fast simplification mode enabled 0:27:06.853 2G / 9G INFO General (graph_simplification.hpp : 771) PROCEDURE == Presimplification 0:27:06.853 2G / 9G INFO General (graph_simplification.hpp : 211) Removing short low covered self-conjugate connections 0:27:07.778 2G / 9G INFO General (graph_simplification.hpp : 403) Removing isolated edges 0:27:07.778 2G / 9G INFO General (graph_simplification.hpp : 404) All edges shorter than 151 will be removed 0:27:07.778 2G / 9G INFO General (graph_simplification.hpp : 405) Also edges shorter than 0 and coverage smaller than 0 will be removed 0:27:09.177 2G / 9G INFO General (graph_simplification.hpp : 687) Non parallel mode 0:27:57.158 3G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:29:48.060 3G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:32:58.225 3G / 9G INFO General (graph_simplification.hpp : 644) Using permanent iterators 0:32:58.225 3G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 1 0:33:07.287 3G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:33:44.743 3G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:34:01.033 3G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 2 0:34:01.034 3G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:34:01.327 3G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:34:13.263 3G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 3 0:34:13.264 3G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:34:13.516 3G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:34:18.504 3G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 4 0:34:18.504 3G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:34:18.611 3G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:34:22.248 3G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 5 0:34:22.248 3G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:34:22.326 3G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:34:25.626 3G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 6 0:34:25.626 3G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:34:25.694 3G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:34:28.237 3G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 7 0:34:28.237 3G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:34:28.291 3G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:34:30.754 2G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 8 0:34:30.754 2G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:34:30.803 2G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:34:33.156 2G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 9 0:34:33.156 2G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:34:33.201 2G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:34:35.437 2G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 10 0:34:35.437 2G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:34:35.479 2G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:34:37.681 2G / 9G INFO General (graph_simplification.hpp : 796) PROCEDURE == Post simplification 0:34:37.681 2G / 9G INFO General (graph_simplification.hpp : 644) Using permanent iterators 0:34:37.681 2G / 9G INFO General (graph_simplification.hpp : 806) Iteration 0 0:34:37.681 2G / 9G INFO General (graph_simplification.hpp : 247) Removal of relatively low covered connections disabled 0:34:41.117 2G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:34:48.915 2G / 9G INFO General (graph_simplification.hpp : 806) Iteration 1 0:34:48.915 2G / 9G INFO General (graph_simplification.hpp : 247) Removal of relatively low covered connections disabled 0:34:48.915 2G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:34:51.091 2G / 9G INFO StageManager (stage.cpp : 125) STAGE == Simplification Cleanup 0:34:51.092 2G / 9G INFO General (graph_simplification.hpp : 403) Removing isolated edges 0:34:51.092 2G / 9G INFO General (graph_simplification.hpp : 404) All edges shorter than 151 will be removed 0:34:51.092 2G / 9G INFO General (graph_simplification.hpp : 405) Also edges shorter than 0 and coverage smaller than 2 will be removed 0:34:51.298 2G / 9G INFO General (simplification.cpp : 56) Removing all the edges having coverage 0 and less 0:34:57.627 2G / 9G INFO General (simplification.cpp : 68) Counting average coverage 0:34:58.349 2G / 9G INFO General (simplification.cpp : 71) Average coverage = 45.2667 0:34:58.349 2G / 9G INFO StageManager (stage.cpp : 125) STAGE == Contig Output 0:34:58.349 2G / 9G INFO General (contig_output.hpp : 283) Outputting contigs to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_134-dipSPAdes-3.5.0-trimmed/spades//K21/simplified_contigs.fasta 0:35:42.210 2G / 9G INFO General (contig_output.hpp : 283) Outputting contigs to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_134-dipSPAdes-3.5.0-trimmed/spades//K21/before_rr.fasta 0:37:42.343 2G / 9G INFO General (contig_output.hpp : 283) Outputting contigs to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_134-dipSPAdes-3.5.0-trimmed/spades//K21/final_contigs.fasta 0:39:42.922 2G / 9G INFO General (launch.hpp : 82) SPAdes finished 0:39:50.921 64M / 9G INFO General (main.cpp : 166) Assembling time: 0 hours 39 minutes 50 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_134-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 0:00:00.026 4M / 4M INFO General (graph_construction.hpp : 129) Constructing DeBruijn graph for k=33 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 131072 0:00:18.093 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 9182602 reads 0:00:33.298 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 18377182 reads 0:02:55.253 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 27561112 reads 0:03:51.062 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 36757736 reads 0:04:05.987 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 45928124 reads 0:04:08.599 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 46688378 reads 0:04:08.599 8G / 9G INFO General (kmer_splitters.hpp : 234) Adding contigs from previous K 0:05:14.652 8G / 9G INFO General (kmer_splitters.hpp : 245) Used 46688378 reads. Maximum read length 151 0:05:14.653 8G / 9G INFO General (kmer_splitters.hpp : 246) Average read length 149.86 0:05:16.832 64M / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:05:37.702 64M / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 132456666 kmers in total. 0:05:37.702 64M / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:05:49.080 64M / 9G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:05:49.080 64M / 9G INFO General (kmer_splitters.hpp : 379) Splitting kmer instances into 256 buckets. This might take a while. 0:05:49.081 64M / 9G INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:05:49.081 64M / 9G INFO General (kmer_splitters.hpp : 397) Memory available for splitting buffers: 2.08203 Gb 0:05:49.081 64M / 9G INFO General (kmer_splitters.hpp : 405) Using cell size of 131072 0:06:12.280 8G / 9G INFO General (kmer_splitters.hpp : 428) Processed 132456666 kmers 0:06:12.282 8G / 9G INFO General (kmer_splitters.hpp : 437) Used 132456666 kmers. 0:06:13.150 64M / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:06:22.162 64M / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 131199598 kmers in total. 0:06:22.163 64M / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:06:33.903 64M / 9G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:06:49.323 68M / 9G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:06:59.599 68M / 9G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 45386896 bytes occupied (2.7675 bits per kmer). 0:06:59.804 196M / 9G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 382) Building k-mer extensions from k+1-mers 0:07:15.153 196M / 9G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 386) Building k-mer extensions from k+1-mers finished. 0:07:15.159 196M / 9G INFO Early tip clipping (early_simplification.hpp : 236) Early tip clipping 0:13:54.996 196M / 9G INFO Early tip clipping (early_simplification.hpp : 239) 20114738 34-mers were removed by early tip clipper 0:13:54.996 196M / 9G INFO General (graph_construction.hpp : 145) Condensing graph 0:13:54.996 196M / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 337) Extracting unbranching paths 0:15:22.921 1G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 351) Extracting unbranching paths finished. 7545110 sequences extracted 0:15:32.865 1G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 311) Collecting perfect loops 0:16:15.682 1G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 326) Collecting perfect loops finished. 38 loops collected 0:16:21.270 1G / 9G INFO General (graph_construction.hpp : 150) Building index with from graph 0:16:21.271 1G / 9G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:16:21.271 1G / 9G INFO General (kmer_splitters.hpp : 289) Splitting kmer instances into 16 buckets. This might take a while. 0:16:21.271 1G / 9G INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:16:21.271 1G / 9G INFO General (kmer_splitters.hpp : 307) Memory available for splitting buffers: 32.7799 Gb 0:16:21.271 1G / 9G INFO General (kmer_splitters.hpp : 312) Using cell size of 2097152 0:16:29.415 2G / 9G INFO General (kmer_splitters.hpp : 325) Processed 2253921 edges 0:16:37.162 2G / 9G INFO General (kmer_splitters.hpp : 325) Processed 4508614 edges 0:16:44.924 2G / 9G INFO General (kmer_splitters.hpp : 325) Processed 6762214 edges 0:16:47.658 2G / 9G INFO General (kmer_splitters.hpp : 325) Processed 7545148 edges 0:16:47.660 2G / 9G INFO General (kmer_splitters.hpp : 330) Used 7545148 sequences. 0:16:47.708 1G / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:17:20.782 1G / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 112341928 kmers in total. 0:17:20.783 1G / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:17:29.873 1G / 9G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:19:56.120 1G / 9G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:20:05.527 1G / 9G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 38863317 bytes occupied (2.7675 bits per kmer). 0:20:07.445 4G / 9G INFO General (edge_index_builders.hpp : 21) Collecting k-mer coverage information from graph, this takes a while. 0:23:29.655 4G / 9G INFO General (graph_construction.hpp : 182) Filling coverage index 0:23:29.655 4G / 9G INFO General (edge_index_builders.hpp : 99) Collecting k-mer coverage information from reads, this takes a while. 0:26:48.444 4G / 9G INFO General (graph_construction.hpp : 184) Filling coverage and flanking coverage from index 0:27:15.062 4G / 9G INFO General (construction.cpp : 33) Figured out: read length = 151 0:27:15.080 4G / 9G INFO StageManager (stage.cpp : 125) STAGE == EC Threshold Finding 0:27:27.599 4G / 9G INFO General (kmer_coverage_model.cpp : 178) Kmer coverage valley at: 9 0:27:27.600 4G / 9G INFO General (kmer_coverage_model.cpp : 198) K-mer histogram maximum: 42 0:27:27.600 4G / 9G INFO General (kmer_coverage_model.cpp : 234) Estimated median coverage: 42. Coverage mad: 13.3434 0:27:27.600 4G / 9G INFO General (kmer_coverage_model.cpp : 261) Fitting coverage model 0:27:27.747 4G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 2 0:27:28.123 4G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 4 0:27:29.465 4G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 8 0:27:32.713 4G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 16 0:27:38.449 4G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 32 0:27:38.817 4G / 9G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 37.9574. Fitted coverage std. dev: 12.9932 0:27:38.820 4G / 9G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 0.288305 0:27:38.820 4G / 9G INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 19 0:27:38.820 4G / 9G INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 19 0:27:38.820 4G / 9G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 61084596 0:27:38.820 4G / 9G INFO General (genomic_info_filler.cpp : 103) Mean coverage was calculated as 37.9574 0:27:38.821 4G / 9G INFO General (genomic_info_filler.cpp : 117) EC coverage threshold value was calculated as 19 0:27:38.821 4G / 9G INFO General (genomic_info_filler.cpp : 118) Trusted kmer low bound: 0 0:27:38.821 4G / 9G INFO StageManager (stage.cpp : 125) STAGE == Simplification 0:27:39.035 1G / 9G INFO General (graph_simplification.hpp : 911) Graph simplification started 0:27:39.035 1G / 9G INFO General (graph_simplification.hpp : 924) Fast simplification mode enabled 0:27:39.035 1G / 9G INFO General (graph_simplification.hpp : 771) PROCEDURE == Presimplification 0:27:39.035 1G / 9G INFO General (graph_simplification.hpp : 211) Removing short low covered self-conjugate connections 0:27:39.547 1G / 9G INFO General (graph_simplification.hpp : 403) Removing isolated edges 0:27:39.547 1G / 9G INFO General (graph_simplification.hpp : 404) All edges shorter than 151 will be removed 0:27:39.547 1G / 9G INFO General (graph_simplification.hpp : 405) Also edges shorter than 0 and coverage smaller than 0 will be removed 0:27:40.803 1G / 9G INFO General (graph_simplification.hpp : 687) Non parallel mode 0:28:01.647 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:28:52.408 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:30:31.678 1G / 9G INFO General (graph_simplification.hpp : 644) Using permanent iterators 0:30:31.679 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 1 0:30:34.039 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:30:43.919 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:30:53.661 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 2 0:30:53.661 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:30:53.734 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:30:57.691 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 3 0:30:57.691 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:30:57.740 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:30:59.705 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 4 0:30:59.705 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:30:59.728 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:31:01.060 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 5 0:31:01.060 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:31:01.075 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:31:02.089 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 6 0:31:02.089 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:31:02.099 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:31:02.992 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 7 0:31:02.992 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:31:03.000 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:31:03.854 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 8 0:31:03.854 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:31:03.860 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:31:04.719 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 9 0:31:04.719 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:31:04.724 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:31:05.648 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 10 0:31:05.648 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:31:05.653 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:31:06.428 1G / 9G INFO General (graph_simplification.hpp : 796) PROCEDURE == Post simplification 0:31:06.428 1G / 9G INFO General (graph_simplification.hpp : 644) Using permanent iterators 0:31:06.429 1G / 9G INFO General (graph_simplification.hpp : 806) Iteration 0 0:31:06.429 1G / 9G INFO General (graph_simplification.hpp : 247) Removal of relatively low covered connections disabled 0:31:06.882 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:31:07.919 1G / 9G INFO General (graph_simplification.hpp : 806) Iteration 1 0:31:07.919 1G / 9G INFO General (graph_simplification.hpp : 247) Removal of relatively low covered connections disabled 0:31:07.919 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:31:08.279 1G / 9G INFO StageManager (stage.cpp : 125) STAGE == Simplification Cleanup 0:31:08.280 1G / 9G INFO General (graph_simplification.hpp : 403) Removing isolated edges 0:31:08.280 1G / 9G INFO General (graph_simplification.hpp : 404) All edges shorter than 151 will be removed 0:31:08.280 1G / 9G INFO General (graph_simplification.hpp : 405) Also edges shorter than 0 and coverage smaller than 2 will be removed 0:31:08.327 1G / 9G INFO General (simplification.cpp : 56) Removing all the edges having coverage 0 and less 0:31:09.156 1G / 9G INFO General (simplification.cpp : 68) Counting average coverage 0:31:09.295 1G / 9G INFO General (simplification.cpp : 71) Average coverage = 37.7516 0:31:09.296 1G / 9G INFO StageManager (stage.cpp : 125) STAGE == Contig Output 0:31:09.296 1G / 9G INFO General (contig_output.hpp : 283) Outputting contigs to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_134-dipSPAdes-3.5.0-trimmed/spades//K33/simplified_contigs.fasta 0:31:28.477 1G / 9G INFO General (contig_output.hpp : 283) Outputting contigs to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_134-dipSPAdes-3.5.0-trimmed/spades//K33/before_rr.fasta 0:32:23.467 1G / 9G INFO General (contig_output.hpp : 283) Outputting contigs to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_134-dipSPAdes-3.5.0-trimmed/spades//K33/final_contigs.fasta 0:33:18.505 1G / 9G INFO General (launch.hpp : 82) SPAdes finished 0:33:21.176 64M / 9G INFO General (main.cpp : 166) Assembling time: 0 hours 33 minutes 21 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_134-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 0:00:00.028 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 131072 0:00:21.169 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 11308441 reads 0:00:38.881 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 22630834 reads 0:00:56.593 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 33945865 reads 0:01:12.519 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 45247688 reads 0:01:15.947 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 46688378 reads 0:01:15.947 8G / 9G INFO General (kmer_splitters.hpp : 234) Adding contigs from previous K 0:02:00.851 8G / 9G INFO General (kmer_splitters.hpp : 245) Used 46688378 reads. Maximum read length 151 0:02:00.852 8G / 9G INFO General (kmer_splitters.hpp : 246) Average read length 149.86 0:02:03.037 64M / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:03:22.857 64M / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 150475665 kmers in total. 0:03:22.857 64M / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:03:37.038 64M / 9G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:03:37.038 64M / 9G INFO General (kmer_splitters.hpp : 379) Splitting kmer instances into 256 buckets. This might take a while. 0:03:37.038 64M / 9G INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:03:37.038 64M / 9G INFO General (kmer_splitters.hpp : 397) Memory available for splitting buffers: 2.08203 Gb 0:03:37.039 64M / 9G INFO General (kmer_splitters.hpp : 405) Using cell size of 131072 0:04:16.501 8G / 9G INFO General (kmer_splitters.hpp : 428) Processed 150475665 kmers 0:04:16.502 8G / 9G INFO General (kmer_splitters.hpp : 437) Used 150475665 kmers. 0:04:17.308 64M / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:05:48.392 64M / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 149997154 kmers in total. 0:05:48.392 64M / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:06:01.981 64M / 9G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:06:27.489 68M / 9G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:06:40.430 68M / 9G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 51889673 bytes occupied (2.7675 bits per kmer). 0:06:40.664 212M / 9G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 382) Building k-mer extensions from k+1-mers 0:07:01.317 212M / 9G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 386) Building k-mer extensions from k+1-mers finished. 0:07:01.322 212M / 9G INFO General (graph_construction.hpp : 145) Condensing graph 0:07:01.322 212M / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 337) Extracting unbranching paths 0:08:35.526 1G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 351) Extracting unbranching paths finished. 9842960 sequences extracted 0:08:49.269 1G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 311) Collecting perfect loops 0:09:38.778 1G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 326) Collecting perfect loops finished. 6 loops collected 0:09:47.590 2G / 9G INFO General (graph_construction.hpp : 150) Building index with from graph 0:09:47.592 2G / 9G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:09:47.592 2G / 9G INFO General (kmer_splitters.hpp : 289) Splitting kmer instances into 16 buckets. This might take a while. 0:09:47.592 2G / 9G INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:09:47.592 2G / 9G INFO General (kmer_splitters.hpp : 307) Memory available for splitting buffers: 32.5339 Gb 0:09:47.592 2G / 9G INFO General (kmer_splitters.hpp : 312) Using cell size of 2097152 0:09:56.140 2G / 9G INFO General (kmer_splitters.hpp : 325) Processed 2197118 edges 0:10:04.486 2G / 9G INFO General (kmer_splitters.hpp : 325) Processed 4394192 edges 0:10:12.698 2G / 9G INFO General (kmer_splitters.hpp : 325) Processed 6585790 edges 0:10:27.729 2G / 9G INFO General (kmer_splitters.hpp : 325) Processed 8778970 edges 0:10:32.495 2G / 9G INFO General (kmer_splitters.hpp : 325) Processed 9842966 edges 0:10:32.496 2G / 9G INFO General (kmer_splitters.hpp : 330) Used 9842966 sequences. 0:10:32.562 2G / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:11:48.001 2G / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 150475665 kmers in total. 0:11:48.001 2G / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:11:59.881 2G / 9G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:15:43.533 2G / 9G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:15:55.776 2G / 9G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 52055210 bytes occupied (2.7675 bits per kmer). 0:15:58.342 5G / 9G INFO General (edge_index_builders.hpp : 21) Collecting k-mer coverage information from graph, this takes a while. 0:20:44.417 5G / 9G INFO General (graph_construction.hpp : 182) Filling coverage index 0:20:44.417 5G / 9G INFO General (edge_index_builders.hpp : 99) Collecting k-mer coverage information from reads, this takes a while. 0:23:40.736 5G / 9G INFO General (graph_construction.hpp : 184) Filling coverage and flanking coverage from index 0:24:17.638 5G / 9G INFO General (construction.cpp : 33) Figured out: read length = 151 0:24:17.653 5G / 9G INFO StageManager (stage.cpp : 125) STAGE == EC Threshold Finding 0:24:32.028 5G / 9G INFO General (kmer_coverage_model.cpp : 178) Kmer coverage valley at: 8 0:24:32.028 5G / 9G INFO General (kmer_coverage_model.cpp : 198) K-mer histogram maximum: 33 0:24:32.028 5G / 9G INFO General (kmer_coverage_model.cpp : 234) Estimated median coverage: 33. Coverage mad: 11.8608 0:24:32.028 5G / 9G INFO General (kmer_coverage_model.cpp : 261) Fitting coverage model 0:24:32.146 5G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 2 0:24:32.456 5G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 4 0:24:33.483 5G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 8 0:24:34.999 5G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 16 0:24:38.980 5G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 32 0:24:39.399 5G / 9G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 30.5945. Fitted coverage std. dev: 10.8508 0:24:39.401 5G / 9G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 0.289899 0:24:39.401 5G / 9G INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 17 0:24:39.402 5G / 9G INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 17 0:24:39.402 5G / 9G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 59447081 0:24:39.402 5G / 9G INFO General (genomic_info_filler.cpp : 103) Mean coverage was calculated as 30.5945 0:24:39.402 5G / 9G INFO General (genomic_info_filler.cpp : 117) EC coverage threshold value was calculated as 17 0:24:39.402 5G / 9G INFO General (genomic_info_filler.cpp : 118) Trusted kmer low bound: 0 0:24:39.402 5G / 9G INFO StageManager (stage.cpp : 125) STAGE == Gap Closer 0:24:39.412 5G / 9G INFO General (gap_closer.cpp : 157) Preparing shift maps 0:24:48.030 5G / 9G INFO General (gap_closer.cpp : 117) Processing paired reads (takes a while) 0:25:35.509 6G / 9G INFO General (gap_closer.cpp : 136) Used 23242358 paired reads 0:25:35.509 6G / 9G INFO General (gap_closer.cpp : 138) Merging paired indices 0:25:39.945 5G / 9G INFO GapCloser (gap_closer.cpp : 395) Closing short gaps 0:26:06.125 5G / 9G INFO GapCloser (gap_closer.cpp : 424) Closing short gaps complete: filled 393 gaps after checking 8866 candidates 0:26:08.766 5G / 9G INFO StageManager (stage.cpp : 125) STAGE == Simplification 0:26:09.022 2G / 9G INFO General (graph_simplification.hpp : 911) Graph simplification started 0:26:09.022 2G / 9G INFO General (graph_simplification.hpp : 924) Fast simplification mode enabled 0:26:09.022 2G / 9G INFO General (graph_simplification.hpp : 771) PROCEDURE == Presimplification 0:26:09.022 2G / 9G INFO General (graph_simplification.hpp : 211) Removing short low covered self-conjugate connections 0:26:09.802 2G / 9G INFO General (graph_simplification.hpp : 403) Removing isolated edges 0:26:09.803 2G / 9G INFO General (graph_simplification.hpp : 404) All edges shorter than 151 will be removed 0:26:09.803 2G / 9G INFO General (graph_simplification.hpp : 405) Also edges shorter than 0 and coverage smaller than 0 will be removed 0:26:11.888 2G / 9G INFO General (graph_simplification.hpp : 687) Non parallel mode 0:26:39.829 2G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:28:04.681 2G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:28:49.511 1G / 9G INFO General (graph_simplification.hpp : 644) Using permanent iterators 0:28:49.511 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 1 0:28:50.427 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:28:54.216 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:28:56.413 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 2 0:28:56.413 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:28:56.440 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:28:58.237 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 3 0:28:58.237 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:28:58.261 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:28:59.495 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 4 0:28:59.495 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:28:59.508 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:29:00.633 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 5 0:29:00.633 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:29:00.641 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:29:01.494 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 6 0:29:01.494 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:29:01.500 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:29:02.552 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 7 0:29:02.552 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:29:02.556 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:29:03.645 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 8 0:29:03.646 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:29:03.649 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:29:04.707 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 9 0:29:04.708 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:29:04.710 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:29:05.807 932M / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 10 0:29:05.807 932M / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:29:05.809 932M / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:29:06.753 832M / 9G INFO General (graph_simplification.hpp : 796) PROCEDURE == Post simplification 0:29:06.753 832M / 9G INFO General (graph_simplification.hpp : 644) Using permanent iterators 0:29:06.753 832M / 9G INFO General (graph_simplification.hpp : 806) Iteration 0 0:29:06.753 832M / 9G INFO General (graph_simplification.hpp : 247) Removal of relatively low covered connections disabled 0:29:06.901 832M / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:29:07.204 832M / 9G INFO General (graph_simplification.hpp : 806) Iteration 1 0:29:07.204 832M / 9G INFO General (graph_simplification.hpp : 247) Removal of relatively low covered connections disabled 0:29:07.204 832M / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:29:07.396 804M / 9G INFO StageManager (stage.cpp : 125) STAGE == Gap Closer 0:29:07.396 804M / 9G INFO General (graph_pack.hpp : 84) Index refill 0:29:07.397 804M / 9G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:29:07.397 804M / 9G INFO General (kmer_splitters.hpp : 289) Splitting kmer instances into 16 buckets. This might take a while. 0:29:07.397 804M / 9G INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:29:07.397 804M / 9G INFO General (kmer_splitters.hpp : 307) Memory available for splitting buffers: 33.0716 Gb 0:29:07.397 804M / 9G INFO General (kmer_splitters.hpp : 312) Using cell size of 2097152 0:30:14.971 1G / 9G INFO General (kmer_splitters.hpp : 325) Processed 39760 edges 0:30:44.785 1G / 9G INFO General (kmer_splitters.hpp : 325) Processed 78468 edges 0:30:56.885 1G / 9G INFO General (kmer_splitters.hpp : 325) Processed 82405 edges 0:30:56.886 1G / 9G INFO General (kmer_splitters.hpp : 330) Used 82405 sequences. 0:30:56.917 792M / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:31:28.888 792M / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 70650220 kmers in total. 0:31:28.888 792M / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:31:34.598 792M / 9G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:32:51.742 816M / 9G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:32:57.447 816M / 9G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 24440594 bytes occupied (2.7675 bits per kmer). 0:32:58.622 2G / 9G INFO General (edge_index_builders.hpp : 21) Collecting k-mer coverage information from graph, this takes a while. 0:34:51.449 2G / 9G INFO General (gap_closer.cpp : 157) Preparing shift maps 0:34:51.524 2G / 9G INFO General (gap_closer.cpp : 117) Processing paired reads (takes a while) 0:35:33.168 2G / 9G INFO General (gap_closer.cpp : 136) Used 23242358 paired reads 0:35:33.168 2G / 9G INFO General (gap_closer.cpp : 138) Merging paired indices 0:35:33.278 2G / 9G INFO GapCloser (gap_closer.cpp : 395) Closing short gaps 0:35:33.480 2G / 9G INFO GapCloser (gap_closer.cpp : 424) Closing short gaps complete: filled 25 gaps after checking 4574 candidates 0:35:33.766 2G / 9G INFO StageManager (stage.cpp : 125) STAGE == Simplification Cleanup 0:35:33.767 2G / 9G INFO General (graph_simplification.hpp : 403) Removing isolated edges 0:35:33.767 2G / 9G INFO General (graph_simplification.hpp : 404) All edges shorter than 151 will be removed 0:35:33.767 2G / 9G INFO General (graph_simplification.hpp : 405) Also edges shorter than 0 and coverage smaller than 2 will be removed 0:35:33.952 2G / 9G INFO General (simplification.cpp : 56) Removing all the edges having coverage 0 and less 0:35:34.207 2G / 9G INFO General (simplification.cpp : 68) Counting average coverage 0:35:34.253 2G / 9G INFO General (simplification.cpp : 71) Average coverage = 29.9129 0:35:34.253 2G / 9G INFO StageManager (stage.cpp : 125) STAGE == Contig Output 0:35:34.253 2G / 9G INFO General (contig_output.hpp : 283) Outputting contigs to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_134-dipSPAdes-3.5.0-trimmed/spades//K55/simplified_contigs.fasta 0:35:49.576 2G / 9G INFO General (contig_output.hpp : 283) Outputting contigs to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_134-dipSPAdes-3.5.0-trimmed/spades//K55/before_rr.fasta 0:36:35.079 2G / 9G INFO General (contig_output.hpp : 283) Outputting contigs to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_134-dipSPAdes-3.5.0-trimmed/spades//K55/final_contigs.fasta 0:37:20.394 2G / 9G INFO General (launch.hpp : 82) SPAdes finished 0:37:23.039 64M / 9G INFO General (main.cpp : 166) Assembling time: 0 hours 37 minutes 23 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_134-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 0:01:44.121 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 9798977 reads 0:02:07.040 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 19618498 reads 0:03:51.278 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 29425248 reads 0:05:40.470 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 39237688 reads 0:07:29.496 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 46688378 reads 0:07:29.496 8G / 9G INFO General (kmer_splitters.hpp : 234) Adding contigs from previous K 0:08:06.522 8G / 9G INFO General (kmer_splitters.hpp : 245) Used 46688378 reads. Maximum read length 151 0:08:06.522 8G / 9G INFO General (kmer_splitters.hpp : 246) Average read length 149.86 0:08:08.690 64M / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:08:39.086 64M / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 153769411 kmers in total. 0:08:39.088 64M / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:08:59.797 64M / 9G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:08:59.797 64M / 9G INFO General (kmer_splitters.hpp : 379) Splitting kmer instances into 256 buckets. This might take a while. 0:08:59.798 64M / 9G INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:08:59.798 64M / 9G INFO General (kmer_splitters.hpp : 397) Memory available for splitting buffers: 2.08203 Gb 0:08:59.798 64M / 9G INFO General (kmer_splitters.hpp : 405) Using cell size of 87381 0:09:36.161 8G / 9G INFO General (kmer_splitters.hpp : 428) Processed 153769411 kmers 0:09:36.162 8G / 9G INFO General (kmer_splitters.hpp : 437) Used 153769411 kmers. 0:09:37.351 64M / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:09:52.308 64M / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 153891290 kmers in total. 0:09:52.308 64M / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:10:11.503 64M / 9G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:10:32.384 68M / 9G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:10:51.038 68M / 9G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 53236809 bytes occupied (2.7675 bits per kmer). 0:10:51.278 216M / 9G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 382) Building k-mer extensions from k+1-mers 0:11:16.766 216M / 9G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 386) Building k-mer extensions from k+1-mers finished. 0:11:16.771 216M / 9G INFO General (graph_construction.hpp : 145) Condensing graph 0:11:16.771 216M / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 337) Extracting unbranching paths 0:12:54.025 1G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 351) Extracting unbranching paths finished. 8539139 sequences extracted 0:13:08.890 1G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 311) Collecting perfect loops 0:14:05.414 1G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 326) Collecting perfect loops finished. 6 loops collected 0:14:13.990 2G / 9G INFO General (graph_construction.hpp : 150) Building index with from graph 0:14:13.991 2G / 9G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:14:13.991 2G / 9G INFO General (kmer_splitters.hpp : 289) Splitting kmer instances into 16 buckets. This might take a while. 0:14:13.991 2G / 9G INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:14:13.991 2G / 9G INFO General (kmer_splitters.hpp : 307) Memory available for splitting buffers: 32.5807 Gb 0:14:13.991 2G / 9G INFO General (kmer_splitters.hpp : 312) Using cell size of 1398101 0:14:20.588 2G / 9G INFO General (kmer_splitters.hpp : 325) Processed 1241463 edges 0:14:26.823 2G / 9G INFO General (kmer_splitters.hpp : 325) Processed 2483197 edges 0:14:33.667 2G / 9G INFO General (kmer_splitters.hpp : 325) Processed 3725584 edges 0:14:40.233 2G / 9G INFO General (kmer_splitters.hpp : 325) Processed 4968630 edges 0:14:46.807 2G / 9G INFO General (kmer_splitters.hpp : 325) Processed 6210998 edges 0:14:53.332 2G / 9G INFO General (kmer_splitters.hpp : 325) Processed 7453025 edges 0:14:59.155 2G / 9G INFO General (kmer_splitters.hpp : 325) Processed 8539145 edges 0:14:59.155 2G / 9G INFO General (kmer_splitters.hpp : 330) Used 8539145 sequences. 0:14:59.229 2G / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:16:11.397 2G / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 153769411 kmers in total. 0:16:11.398 2G / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:16:29.365 2G / 9G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:20:08.518 2G / 9G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:20:25.525 2G / 9G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 53194642 bytes occupied (2.7675 bits per kmer). 0:20:28.182 5G / 9G INFO General (edge_index_builders.hpp : 21) Collecting k-mer coverage information from graph, this takes a while. 0:25:59.012 5G / 9G INFO General (graph_construction.hpp : 182) Filling coverage index 0:25:59.012 5G / 9G INFO General (edge_index_builders.hpp : 99) Collecting k-mer coverage information from reads, this takes a while. 0:28:36.662 5G / 9G INFO General (graph_construction.hpp : 184) Filling coverage and flanking coverage from index 0:29:15.166 5G / 9G INFO General (construction.cpp : 33) Figured out: read length = 151 0:29:15.182 5G / 9G INFO StageManager (stage.cpp : 125) STAGE == EC Threshold Finding 0:29:23.732 5G / 9G INFO General (kmer_coverage_model.cpp : 178) Kmer coverage valley at: 5 0:29:23.732 5G / 9G INFO General (kmer_coverage_model.cpp : 198) K-mer histogram maximum: 24 0:29:23.732 5G / 9G INFO General (kmer_coverage_model.cpp : 234) Estimated median coverage: 24. Coverage mad: 10.3782 0:29:23.732 5G / 9G INFO General (kmer_coverage_model.cpp : 261) Fitting coverage model 0:29:23.817 5G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 2 0:29:24.040 5G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 4 0:29:24.691 5G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 8 0:29:25.625 5G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 16 0:29:26.683 5G / 9G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 23.3332. Fitted coverage std. dev: 8.63995 0:29:26.684 5G / 9G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 0.431317 0:29:26.684 5G / 9G INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 13 0:29:26.684 5G / 9G INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 13 0:29:26.684 5G / 9G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 58959850 0:29:26.684 5G / 9G INFO General (genomic_info_filler.cpp : 103) Mean coverage was calculated as 23.3332 0:29:26.685 5G / 9G INFO General (genomic_info_filler.cpp : 117) EC coverage threshold value was calculated as 13 0:29:26.685 5G / 9G INFO General (genomic_info_filler.cpp : 118) Trusted kmer low bound: 0 0:29:26.685 5G / 9G INFO StageManager (stage.cpp : 125) STAGE == Gap Closer 0:29:26.695 5G / 9G INFO General (gap_closer.cpp : 157) Preparing shift maps 0:29:35.794 5G / 9G INFO General (gap_closer.cpp : 117) Processing paired reads (takes a while) 0:30:07.007 6G / 9G INFO General (gap_closer.cpp : 136) Used 23242358 paired reads 0:30:07.007 6G / 9G INFO General (gap_closer.cpp : 138) Merging paired indices 0:30:13.675 5G / 9G INFO GapCloser (gap_closer.cpp : 395) Closing short gaps 0:30:37.663 5G / 9G INFO GapCloser (gap_closer.cpp : 424) Closing short gaps complete: filled 548 gaps after checking 10826 candidates 0:30:40.829 5G / 9G INFO StageManager (stage.cpp : 125) STAGE == Simplification 0:30:41.090 2G / 9G INFO General (graph_simplification.hpp : 911) Graph simplification started 0:30:41.091 2G / 9G INFO General (graph_simplification.hpp : 924) Fast simplification mode enabled 0:30:41.091 2G / 9G INFO General (graph_simplification.hpp : 771) PROCEDURE == Presimplification 0:30:41.091 2G / 9G INFO General (graph_simplification.hpp : 211) Removing short low covered self-conjugate connections 0:30:41.883 2G / 9G INFO General (graph_simplification.hpp : 403) Removing isolated edges 0:30:41.883 2G / 9G INFO General (graph_simplification.hpp : 404) All edges shorter than 151 will be removed 0:30:41.883 2G / 9G INFO General (graph_simplification.hpp : 405) Also edges shorter than 0 and coverage smaller than 0 will be removed 0:30:45.329 2G / 9G INFO General (graph_simplification.hpp : 687) Non parallel mode 0:31:10.839 2G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:32:39.788 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:32:44.827 1G / 9G INFO General (graph_simplification.hpp : 644) Using permanent iterators 0:32:44.827 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 1 0:32:45.304 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:32:47.298 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:32:47.358 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 2 0:32:47.358 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:32:47.360 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:32:47.990 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 3 0:32:47.990 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:32:47.999 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:32:48.838 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 4 0:32:48.838 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:32:48.849 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:32:49.568 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 5 0:32:49.568 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:32:49.581 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:32:50.415 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 6 0:32:50.415 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:32:50.420 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:32:51.285 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 7 0:32:51.285 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:32:51.288 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:32:52.347 1016M / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 8 0:32:52.347 1016M / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:32:52.350 1016M / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:32:53.520 896M / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 9 0:32:53.520 896M / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:32:53.522 896M / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:32:54.660 776M / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 10 0:32:54.660 776M / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:32:54.662 776M / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:32:55.681 676M / 9G INFO General (graph_simplification.hpp : 796) PROCEDURE == Post simplification 0:32:55.681 676M / 9G INFO General (graph_simplification.hpp : 644) Using permanent iterators 0:32:55.681 676M / 9G INFO General (graph_simplification.hpp : 806) Iteration 0 0:32:55.681 676M / 9G INFO General (graph_simplification.hpp : 247) Removal of relatively low covered connections disabled 0:32:55.784 676M / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:32:55.982 676M / 9G INFO General (graph_simplification.hpp : 806) Iteration 1 0:32:55.982 676M / 9G INFO General (graph_simplification.hpp : 247) Removal of relatively low covered connections disabled 0:32:55.982 676M / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:32:56.127 660M / 9G INFO StageManager (stage.cpp : 125) STAGE == Gap Closer 0:32:56.128 660M / 9G INFO General (graph_pack.hpp : 84) Index refill 0:32:56.129 660M / 9G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:32:56.129 660M / 9G INFO General (kmer_splitters.hpp : 289) Splitting kmer instances into 16 buckets. This might take a while. 0:32:56.129 660M / 9G INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:32:56.129 660M / 9G INFO General (kmer_splitters.hpp : 307) Memory available for splitting buffers: 33.1185 Gb 0:32:56.129 660M / 9G INFO General (kmer_splitters.hpp : 312) Using cell size of 1398101 0:33:01.295 1G / 9G INFO General (kmer_splitters.hpp : 325) Processed 17958 edges 0:33:06.204 1G / 9G INFO General (kmer_splitters.hpp : 325) Processed 35926 edges 0:33:11.125 1G / 9G INFO General (kmer_splitters.hpp : 325) Processed 54576 edges 0:33:12.008 1G / 9G INFO General (kmer_splitters.hpp : 325) Processed 57885 edges 0:33:12.008 1G / 9G INFO General (kmer_splitters.hpp : 330) Used 57885 sequences. 0:33:12.087 648M / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:33:37.204 648M / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 70925408 kmers in total. 0:33:37.204 648M / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:33:45.311 648M / 9G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:35:16.877 672M / 9G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:35:25.410 672M / 9G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 24535794 bytes occupied (2.7675 bits per kmer). 0:35:26.493 2G / 9G INFO General (edge_index_builders.hpp : 21) Collecting k-mer coverage information from graph, this takes a while. 0:37:28.390 2G / 9G INFO General (gap_closer.cpp : 157) Preparing shift maps 0:37:28.454 2G / 9G INFO General (gap_closer.cpp : 117) Processing paired reads (takes a while) 0:38:04.460 2G / 9G INFO General (gap_closer.cpp : 136) Used 23242358 paired reads 0:38:04.460 2G / 9G INFO General (gap_closer.cpp : 138) Merging paired indices 0:38:04.598 2G / 9G INFO GapCloser (gap_closer.cpp : 395) Closing short gaps 0:38:04.772 2G / 9G INFO GapCloser (gap_closer.cpp : 424) Closing short gaps complete: filled 25 gaps after checking 2590 candidates 0:38:05.228 2G / 9G INFO StageManager (stage.cpp : 125) STAGE == Simplification Cleanup 0:38:05.228 2G / 9G INFO General (graph_simplification.hpp : 403) Removing isolated edges 0:38:05.228 2G / 9G INFO General (graph_simplification.hpp : 404) All edges shorter than 151 will be removed 0:38:05.229 2G / 9G INFO General (graph_simplification.hpp : 405) Also edges shorter than 0 and coverage smaller than 2 will be removed 0:38:05.679 2G / 9G INFO General (simplification.cpp : 56) Removing all the edges having coverage 0 and less 0:38:05.845 2G / 9G INFO General (simplification.cpp : 68) Counting average coverage 0:38:05.867 2G / 9G INFO General (simplification.cpp : 71) Average coverage = 22.6042 0:38:05.867 2G / 9G INFO StageManager (stage.cpp : 125) STAGE == Mismatch Correction 0:39:02.004 2G / 9G INFO General (mismatch_shall_not_pass.hp: 188) Finished collecting potential mismatches positions 0:39:02.068 2G / 9G INFO General (mismatch_shall_not_pass.hp: 291) All edges processed 0:39:02.071 2G / 9G INFO General (mismatch_correction.cpp : 18) Corrected 0 nucleotides 0:39:02.087 2G / 9G INFO StageManager (stage.cpp : 125) STAGE == Paired Information Counting 0:39:02.245 2G / 9G INFO General (pair_info_count.cpp : 150) Graph N50: 14209 0:39:02.246 2G / 9G INFO General (pair_info_count.cpp : 152) Estimating insert size for library #0 0:39:02.246 2G / 9G INFO General (pair_info_count.cpp : 31) Estimating insert size (takes a while) 0:39:02.257 2G / 9G INFO General (short_read_mapper.hpp : 91) Selecting usual mapper 0:39:07.571 2G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 200000 reads 0:39:07.623 2G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 400000 reads 0:39:07.632 2G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 600000 reads 0:39:07.634 2G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 800000 reads 0:39:07.641 2G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 1000000 reads 0:39:07.651 2G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 1200000 reads 0:39:07.925 2G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 2200000 reads 0:39:13.190 2G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 4200000 reads 0:39:19.543 2G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 8400000 reads 0:39:23.387 2G / 9G INFO General (sequence_mapper_notifier.h: 89) Processed 11621179 reads 0:39:23.388 2G / 9G INFO General (pair_info_count.cpp : 41) 5616857 paired reads (48.3329% of all) aligned to long edges 0:39:23.399 2G / 9G INFO General (pair_info_count.cpp : 170) Estimated insert size for paired library #0 0:39:23.399 2G / 9G INFO General (pair_info_count.cpp : 175) Insert size = 313.086, deviation = 90.6616, left quantile = 201, right quantile = 431, read length = 151 0:39:23.399 2G / 9G INFO General (pair_info_count.cpp : 187) Mapping library #0 0:39:23.399 2G / 9G INFO General (pair_info_count.cpp : 189) Mapping paired reads (takes a while) 0:39:23.399 2G / 9G INFO General (pair_info_count.cpp : 73) Left insert size qauntile 201, right insert size quantile 431 0:39:23.409 2G / 9G INFO General (short_read_mapper.hpp : 91) Selecting usual mapper 0:39:30.801 4G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 200000 reads 0:39:31.559 4G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 400000 reads 0:39:32.441 4G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 600000 reads 0:39:33.483 4G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 800000 reads 0:39:34.644 4G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 1000000 reads 0:39:35.954 4G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 1200000 reads 0:39:42.991 4G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 2200000 reads 0:39:58.532 4G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 4200000 reads 0:40:33.456 4G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 8400000 reads 0:41:47.567 5G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 16800000 reads 0:42:49.341 3G / 9G INFO General (sequence_mapper_notifier.h: 89) Processed 23242358 reads 0:44:54.496 3G / 9G INFO General (split_graph_pair_info.hpp : 344) Threshold for paired information 0.0608241 0:44:57.999 2G / 9G INFO StageManager (stage.cpp : 125) STAGE == Distance Estimation 0:44:57.999 2G / 9G INFO General (distance_estimation.cpp : 234) Processing library #0 0:44:57.999 2G / 9G INFO General (distance_estimation.cpp : 136) Weight Filter Done 0:44:57.999 2G / 9G INFO DistanceEstimator (distance_estimation.hpp : 187) Using SIMPLE distance estimator 0:45:05.673 2G / 9G INFO DistanceEstimator (distance_estimation.hpp : 208) Merging maps 0:45:06.443 2G / 9G INFO General (distance_estimation.cpp : 38) Filtering info 0:45:07.580 2G / 9G INFO General (pair_info_filters.hpp : 354) Pruning the index 0:45:07.625 2G / 9G INFO General (distance_estimation.cpp : 184) Refining clustered pair information 0:45:07.727 2G / 9G INFO General (distance_estimation.cpp : 186) The refining of clustered pair information has been finished 0:45:07.727 2G / 9G INFO General (distance_estimation.cpp : 188) Filling paired information 0:45:09.644 2G / 9G INFO PairInfoImprover (pair_info_improver.hpp : 61) Paired info stats: missing = 39275; contradictional = 7412 0:45:11.582 2G / 9G INFO PairInfoImprover (pair_info_improver.hpp : 61) Paired info stats: missing = 6315; contradictional = 0 0:45:11.582 2G / 9G INFO General (distance_estimation.cpp : 193) Filling scaffolding index 0:45:11.582 2G / 9G INFO DistanceEstimator (distance_estimation.hpp : 187) Using SMOOTHING distance estimator 0:45:20.855 2G / 9G INFO DistanceEstimator (distance_estimation.hpp : 208) Merging maps 0:45:20.934 2G / 9G INFO General (distance_estimation.cpp : 38) Filtering info 0:45:21.216 2G / 9G INFO General (pair_info_filters.hpp : 354) Pruning the index 0:45:21.677 2G / 9G INFO StageManager (stage.cpp : 125) STAGE == Repeat Resolving 0:45:21.678 2G / 9G INFO General (contig_output.hpp : 283) Outputting contigs to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_134-dipSPAdes-3.5.0-trimmed/spades//K77/before_rr.fasta 0:46:04.822 2G / 9G INFO General (repeat_resolving.cpp : 59) Using Path-Extend repeat resolving 0:46:04.823 2G / 9G INFO General (path_extend_launch.hpp : 459) Threshold for library #0 is 0.0608241 0:46:04.823 2G / 9G INFO General (path_extend_launch.hpp : 298) Path-Extend repeat resolving tool started 0:46:04.867 2G / 9G INFO General (path_extend_launch.hpp : 316) Using 1 paired-end library 0:46:04.867 2G / 9G INFO General (path_extend_launch.hpp : 317) Using 1 paired-end scaffolding library 0:46:04.867 2G / 9G INFO General (path_extend_launch.hpp : 318) Using 0 mate-pair libraries 0:46:04.867 2G / 9G INFO General (path_extend_launch.hpp : 319) Using 0 single read libraries 0:46:04.867 2G / 9G INFO General (path_extend_launch.hpp : 320) Scaffolder is on 0:46:05.179 2G / 9G INFO General (path_extend_launch.hpp : 332) Growing paths using paired-end and long single reads 0:46:05.180 2G / 9G INFO PathExtender (path_extender.hpp : 611) Processed 0 paths from 26471 (0%) 0:46:05.275 2G / 9G INFO PathExtender (path_extender.hpp : 609) Processed 128 paths from 26471 (0%) 0:46:05.414 2G / 9G INFO PathExtender (path_extender.hpp : 609) Processed 256 paths from 26471 (0%) 0:46:05.656 2G / 9G INFO PathExtender (path_extender.hpp : 609) Processed 512 paths from 26471 (1%) 0:46:06.037 2G / 9G INFO PathExtender (path_extender.hpp : 609) Processed 1024 paths from 26471 (3%) 0:46:06.877 2G / 9G INFO PathExtender (path_extender.hpp : 609) Processed 2048 paths from 26471 (7%) 0:46:07.348 2G / 9G INFO PathExtender (path_extender.hpp : 611) Processed 2648 paths from 26471 (10%) 0:46:07.948 2G / 9G INFO PathExtender (path_extender.hpp : 609) Processed 4096 paths from 26471 (15%) 0:46:08.638 2G / 9G INFO PathExtender (path_extender.hpp : 611) Processed 5296 paths from 26471 (20%) 0:46:09.932 2G / 9G INFO PathExtender (path_extender.hpp : 611) Processed 7944 paths from 26471 (30%) 0:46:09.974 2G / 9G INFO PathExtender (path_extender.hpp : 609) Processed 8192 paths from 26471 (30%) 0:46:10.798 2G / 9G INFO PathExtender (path_extender.hpp : 611) Processed 10592 paths from 26471 (40%) 0:46:11.020 2G / 9G INFO PathExtender (path_extender.hpp : 611) Processed 13240 paths from 26471 (50%) 0:46:13.021 2G / 9G INFO PathExtender (path_extender.hpp : 611) Processed 15888 paths from 26471 (60%) 0:46:13.325 2G / 9G INFO PathExtender (path_extender.hpp : 609) Processed 16384 paths from 26471 (61%) 0:46:15.424 2G / 9G INFO PathExtender (path_extender.hpp : 611) Processed 18536 paths from 26471 (70%) 0:46:17.669 2G / 9G INFO PathExtender (path_extender.hpp : 611) Processed 21184 paths from 26471 (80%) 0:46:19.774 2G / 9G INFO PathExtender (path_extender.hpp : 611) Processed 23832 paths from 26471 (90%) 0:46:21.371 2G / 9G INFO PathExtendIO (pe_io.hpp : 339) Constructing FASTG file from paths 0:46:21.911 2G / 9G INFO PathExtendIO (pe_io.hpp : 342) Writing contigs in FASTG to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_134-dipSPAdes-3.5.0-trimmed/spades//K77/final_contigs.fastg 0:46:21.911 2G / 9G INFO PathExtendIO (pe_io.hpp : 343) Writing contigs in FASTA to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_134-dipSPAdes-3.5.0-trimmed/spades//K77/final_contigs.fasta 0:47:03.772 2G / 9G INFO PathExtendIO (pe_io.hpp : 339) Constructing FASTG file from paths 0:47:04.332 2G / 9G INFO PathExtendIO (pe_io.hpp : 342) Writing contigs in FASTG to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_134-dipSPAdes-3.5.0-trimmed/spades//K77/path_extend/pe_before_traversal.fastg 0:47:04.332 2G / 9G INFO PathExtendIO (pe_io.hpp : 343) Writing contigs in FASTA to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_134-dipSPAdes-3.5.0-trimmed/spades//K77/path_extend/pe_before_traversal.fasta 0:47:46.591 2G / 9G INFO General (path_extend_launch.hpp : 281) Traversing tandem repeats 0:47:47.886 2G / 9G INFO PathExtendIO (pe_io.hpp : 339) Constructing FASTG file from paths 0:47:48.327 2G / 9G INFO PathExtendIO (pe_io.hpp : 342) Writing contigs in FASTG to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_134-dipSPAdes-3.5.0-trimmed/spades//K77/scaffolds.fastg 0:47:48.327 2G / 9G INFO PathExtendIO (pe_io.hpp : 343) Writing contigs in FASTA to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_134-dipSPAdes-3.5.0-trimmed/spades//K77/scaffolds.fasta 0:48:30.189 2G / 9G INFO General (launch.hpp : 82) SPAdes finished 0:48:33.127 328M / 9G INFO General (main.cpp : 166) Assembling time: 0 hours 48 minutes 33 seconds ===== Assembling finished. * Corrected reads are in /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_134-dipSPAdes-3.5.0-trimmed/spades/corrected/ * Assembled contigs are in /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_134-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_134-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_134-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_134-dipSPAdes-3.5.0-trimmed/spades/spades.log Thank you for using SPAdes!