Command line: --diploid --pe1-1 /N/dc2/projects/marinovg/Paramecium/variation/data/P.tetraurelia-Sample_116/reads.end1.paired.fastq.gz --pe1-2 /N/dc2/projects/marinovg/Paramecium/variation/data/P.tetraurelia-Sample_116/reads.end2.paired.fastq.gz -t 16 -o /N/dc2/projects/marinovg/2015-09-07-assemblies/P.tetraurelia-Sample_116-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.tetraurelia-Sample_116-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.tetraurelia-Sample_116/reads.end1.paired.fastq.gz'] right reads: ['/N/dc2/projects/marinovg/Paramecium/variation/data/P.tetraurelia-Sample_116/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.tetraurelia-Sample_116-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.tetraurelia-Sample_116-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.tetraurelia-Sample_116-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.tetraurelia-Sample_116-dipSPAdes-3.5.0-trimmed/spades/corrected/configs/config.info 0:00:34.215 4M / 4M INFO General (memory_limit.hpp : 42) Memory limit set to 100 Gb 0:00:34.215 4M / 4M INFO General (main.cpp : 91) Trying to determine PHRED offset 0:00:44.520 4M / 4M INFO General (main.cpp : 97) Determined value is 33 0:00:44.521 4M / 4M INFO General (hammer_tools.cpp : 36) Hamming graph threshold tau=1, k=21, subkmer positions = [ 0 10 ] === ITERATION 0 begins === 0:00:44.526 4M / 4M INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:00:44.526 4M / 4M INFO K-mer Splitting (kmer_data.cpp : 127) Splitting kmer instances into 256 buckets. This might take a while. 0:00:44.527 4M / 4M INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:00:44.527 4M / 4M INFO K-mer Splitting (kmer_data.cpp : 145) Memory available for splitting buffers: 2.08325 Gb 0:00:44.527 4M / 4M INFO K-mer Splitting (kmer_data.cpp : 153) Using cell size of 262144 9:53:49.786 8G / 8G INFO K-mer Splitting (kmer_data.cpp : 167) Processing /N/dc2/projects/marinovg/Paramecium/variation/data/P.tetraurelia-Sample_116/reads.end1.paired.fastq.gz 11:24:08.167 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 176) Processed 2706541 reads 11:32:22.915 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 176) Processed 5819205 reads 11:40:58.064 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 176) Processed 8458363 reads 11:40:58.066 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 167) Processing /N/dc2/projects/marinovg/Paramecium/variation/data/P.tetraurelia-Sample_116/reads.end2.paired.fastq.gz 11:53:17.784 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 176) Processed 11655144 reads 12:02:28.525 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 176) Processed 14897492 reads 12:09:07.296 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 176) Processed 16916726 reads 12:09:07.296 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 181) Processed 16916726 reads 12:09:08.441 64M / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 12:12:50.167 64M / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 295824748 kmers in total. 12:12:50.167 64M / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 12:13:04.470 64M / 9G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 12:13:42.593 192M / 9G INFO General (kmer_index.hpp : 371) Merging final buckets. 12:13:56.941 192M / 9G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 102336916 bytes occupied (2.7675 bits per kmer). 12:13:56.943 192M / 9G INFO K-mer Counting (kmer_data.cpp : 266) Arranging kmers in hash map order 12:16:57.556 192M / 9G INFO K-mer Counting (kmer_data.cpp : 279) Done. Total swaps: 295824471 12:16:59.567 2G / 9G INFO General (main.cpp : 151) Clustering Hamming graph. 12:16:59.569 2G / 9G INFO Hamming Clustering (hamcluster.cpp : 115) Serializing sub-kmers. 12:16:59.570 2G / 9G INFO Hamming Clustering (hamcluster.cpp : 120) Serializing: [0, 10) 12:20:38.732 2G / 9G INFO Hamming Clustering (hamcluster.cpp : 120) Serializing: [10, 21) 12:24:17.650 2G / 9G INFO Hamming Clustering (hamcluster.cpp : 129) Splitting sub-kmers, pass 1. 12:28:25.354 2G / 9G INFO Hamming Clustering (hamcluster.cpp : 134) Splitting done. Processed 2 blocks. Produced 5234177 blocks. 12:28:25.354 2G / 9G INFO Hamming Clustering (hamcluster.cpp : 145) Merge sub-kmers, pass 1 12:44:51.526 2G / 9G INFO Hamming Clustering (hamcluster.cpp : 170) Merge done, total 2151520 new blocks generated. 12:44:53.430 2G / 9G INFO Hamming Clustering (hamcluster.cpp : 175) Spliting sub-kmers, pass 2. 13:08:37.223 2G / 9G INFO Hamming Clustering (hamcluster.cpp : 180) Splitting done. Processed 4303040 blocks. Produced 672850120 blocks. 13:08:37.223 2G / 9G INFO Hamming Clustering (hamcluster.cpp : 187) Merge sub-kmers, pass 2 13:16:55.327 2G / 9G INFO Hamming Clustering (hamcluster.cpp : 205) Merge done, saw 66167 big blocks out of 672850120 processed. 13:22:11.732 2G / 12G INFO General (main.cpp : 165) Clustering done. Total clusters: 177161610 13:22:11.732 2G / 12G INFO K-mer Counting (kmer_data.cpp : 284) Collecting K-mer information, this takes a while. 13:22:17.771 15G / 15G INFO K-mer Counting (kmer_data.cpp : 290) Processing /N/dc2/projects/marinovg/Paramecium/variation/data/P.tetraurelia-Sample_116/reads.end1.paired.fastq.gz 13:24:22.539 15G / 15G INFO K-mer Counting (kmer_data.cpp : 290) Processing /N/dc2/projects/marinovg/Paramecium/variation/data/P.tetraurelia-Sample_116/reads.end2.paired.fastq.gz 13:26:23.432 15G / 15G INFO K-mer Counting (kmer_data.cpp : 297) Collection done, postprocessing. 13:26:33.532 15G / 15G INFO K-mer Counting (kmer_data.cpp : 310) There are 295824748 kmers in total. Among them 122704804 (41.4789%) are singletons. 13:26:33.533 15G / 15G INFO General (main.cpp : 203) Subclustering Hamming graph 13:28:21.569 15G / 15G INFO Hamming Subclustering (kmer_cluster.cpp : 626) Subclustering done. Total 32000 non-read kmers were generated. 13:28:21.569 15G / 15G INFO Hamming Subclustering (kmer_cluster.cpp : 627) Subclustering statistics: 13:28:21.569 15G / 15G INFO Hamming Subclustering (kmer_cluster.cpp : 628) Total singleton hamming clusters: 116556637. Among them 93998632 (80.6463%) are good 13:28:21.569 15G / 15G INFO Hamming Subclustering (kmer_cluster.cpp : 629) Total singleton subclusters: 9483708. Among them 9483610 (99.999%) are good 13:28:21.569 15G / 15G INFO Hamming Subclustering (kmer_cluster.cpp : 630) Total non-singleton subcluster centers: 62314789. Among them 36745560 (58.9676%) are good 13:28:21.569 15G / 15G INFO Hamming Subclustering (kmer_cluster.cpp : 631) Average size of non-trivial subcluster: 2.83132 kmers 13:28:21.569 15G / 15G INFO Hamming Subclustering (kmer_cluster.cpp : 632) Average number of sub-clusters per non-singleton cluster: 1.1847 13:28:21.569 15G / 15G INFO Hamming Subclustering (kmer_cluster.cpp : 633) Total solid k-mers: 140227802 13:28:21.570 15G / 15G INFO Hamming Subclustering (kmer_cluster.cpp : 634) Substitution probabilities: [4,4]((0.922091,0.0190299,0.0212976,0.0375819),(0.0332405,0.937402,0.0106007,0.0187569),(0.0181057,0.0103343,0.93797,0.0335903),(0.0371891,0.0214414,0.0190247,0.922345)) 13:28:22.229 15G / 15G INFO General (main.cpp : 208) Finished clustering. 13:28:22.229 15G / 15G INFO General (main.cpp : 228) Starting solid k-mers expansion in 16 threads. 13:31:17.809 15G / 15G INFO General (main.cpp : 249) Solid k-mers iteration 0 produced 30400007 new k-mers. 13:34:11.713 15G / 15G INFO General (main.cpp : 249) Solid k-mers iteration 1 produced 640063 new k-mers. 13:37:04.493 15G / 15G INFO General (main.cpp : 249) Solid k-mers iteration 2 produced 25496 new k-mers. 13:39:57.249 15G / 15G INFO General (main.cpp : 249) Solid k-mers iteration 3 produced 3032 new k-mers. 13:42:49.671 15G / 15G INFO General (main.cpp : 249) Solid k-mers iteration 4 produced 421 new k-mers. 13:45:41.583 15G / 15G INFO General (main.cpp : 249) Solid k-mers iteration 5 produced 64 new k-mers. 13:48:32.873 15G / 15G INFO General (main.cpp : 249) Solid k-mers iteration 6 produced 0 new k-mers. 13:48:32.874 15G / 15G INFO General (main.cpp : 253) Solid k-mers finalized 13:48:32.874 15G / 15G INFO General (hammer_tools.cpp : 210) Starting read correction in 16 threads. 13:48:32.875 15G / 15G INFO General (hammer_tools.cpp : 222) Correcting pair of reads: /N/dc2/projects/marinovg/Paramecium/variation/data/P.tetraurelia-Sample_116/reads.end1.paired.fastq.gz and /N/dc2/projects/marinovg/Paramecium/variation/data/P.tetraurelia-Sample_116/reads.end2.paired.fastq.gz 13:48:58.686 17G / 17G INFO General (hammer_tools.cpp : 166) Prepared batch 0 of 1600000 reads. 13:49:18.906 17G / 17G INFO General (hammer_tools.cpp : 175) Processed batch 0 13:50:13.711 17G / 17G INFO General (hammer_tools.cpp : 185) Written batch 0 13:50:37.718 17G / 17G INFO General (hammer_tools.cpp : 166) Prepared batch 1 of 1600000 reads. 13:51:02.875 17G / 17G INFO General (hammer_tools.cpp : 175) Processed batch 1 13:51:19.165 17G / 17G INFO General (hammer_tools.cpp : 185) Written batch 1 13:51:42.835 17G / 17G INFO General (hammer_tools.cpp : 166) Prepared batch 2 of 1600000 reads. 13:52:03.147 17G / 17G INFO General (hammer_tools.cpp : 175) Processed batch 2 13:52:19.120 17G / 17G INFO General (hammer_tools.cpp : 185) Written batch 2 13:52:43.006 17G / 17G INFO General (hammer_tools.cpp : 166) Prepared batch 3 of 1600000 reads. 13:53:02.942 17G / 17G INFO General (hammer_tools.cpp : 175) Processed batch 3 13:53:19.624 17G / 17G INFO General (hammer_tools.cpp : 185) Written batch 3 13:53:43.136 17G / 17G INFO General (hammer_tools.cpp : 166) Prepared batch 4 of 1600000 reads. 13:54:06.732 17G / 17G INFO General (hammer_tools.cpp : 175) Processed batch 4 13:54:22.457 17G / 17G INFO General (hammer_tools.cpp : 185) Written batch 4 13:54:29.094 17G / 17G INFO General (hammer_tools.cpp : 166) Prepared batch 5 of 458363 reads. 13:54:34.944 17G / 17G INFO General (hammer_tools.cpp : 175) Processed batch 5 13:54:39.484 17G / 17G INFO General (hammer_tools.cpp : 185) Written batch 5 13:54:42.551 15G / 17G INFO General (hammer_tools.cpp : 269) Correction done. Changed 2979681 bases in 2561670 reads. 13:54:42.552 15G / 17G INFO General (hammer_tools.cpp : 270) Failed to correct 314175332 bases out of 2491980890. 13:54:42.625 2G / 17G INFO General (main.cpp : 286) Saving corrected dataset description to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.tetraurelia-Sample_116-dipSPAdes-3.5.0-trimmed/spades/corrected/corrected.yaml 13:54:42.631 2G / 17G INFO General (main.cpp : 293) All done. Exiting. == Compressing corrected reads (with gzip) == Dataset description file was created: /N/dc2/projects/marinovg/2015-09-07-assemblies/P.tetraurelia-Sample_116-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.tetraurelia-Sample_116-dipSPAdes-3.5.0-trimmed/spades/dataset.info) with K=21 0:00:00.001 4M / 4M INFO General (launch.hpp : 28) SPAdes started 0:00:00.001 4M / 4M INFO General (launch.hpp : 29) Starting from stage: construction 0:00:00.002 4M / 4M INFO StageManager (stage.cpp : 125) STAGE == Construction 0:00:00.006 4M / 4M INFO General (read_converter.hpp : 79) Converting reads to binary format (takes a while) 0:00:00.006 4M / 4M INFO General (read_converter.hpp : 81) Paired reads for library #0 0:00:01.137 80M / 80M INFO General (binary_converter.hpp : 138) 16384 reads processed 0:00:01.542 96M / 96M INFO General (binary_converter.hpp : 138) 32768 reads processed 0:00:02.350 124M / 124M INFO General (binary_converter.hpp : 138) 65536 reads processed 0:00:03.982 184M / 184M INFO General (binary_converter.hpp : 138) 131072 reads processed 0:00:07.248 300M / 300M INFO General (binary_converter.hpp : 138) 262144 reads processed 0:00:13.807 536M / 536M INFO General (binary_converter.hpp : 138) 524288 reads processed 0:00:49.846 900M / 900M INFO General (binary_converter.hpp : 138) 1048576 reads processed 0:01:19.187 900M / 900M INFO General (binary_converter.hpp : 138) 2097152 reads processed 0:02:18.809 900M / 900M INFO General (binary_converter.hpp : 138) 4194304 reads processed 0:04:16.864 840M / 904M INFO General (binary_converter.hpp : 158) 8281837 reads written 0:04:18.864 4M / 904M INFO General (read_converter.hpp : 91) Single reads for library #0 0:04:20.737 140M / 904M INFO General (binary_converter.hpp : 138) 16384 reads processed 0:04:20.957 144M / 904M INFO General (binary_converter.hpp : 138) 32768 reads processed 0:04:21.355 160M / 904M INFO General (binary_converter.hpp : 138) 65536 reads processed 0:04:22.141 188M / 904M INFO General (binary_converter.hpp : 138) 131072 reads processed 0:04:23.007 208M / 904M INFO General (binary_converter.hpp : 158) 176055 reads written 0:04:23.252 4M / 904M INFO General (graph_construction.hpp : 129) Constructing DeBruijn graph for k=21 0:04:23.256 4M / 904M INFO General (kmer_splitters.hpp : 172) Splitting kmer instances into 256 buckets. This might take a while. 0:04:23.257 4M / 904M INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:04:23.257 4M / 904M INFO General (kmer_splitters.hpp : 190) Memory available for splitting buffers: 2.08325 Gb 0:04:23.257 4M / 904M INFO General (kmer_splitters.hpp : 199) Using cell size of 262144 0:09:09.328 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 16798711 reads 0:12:23.697 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 33479458 reads 0:12:23.698 8G / 9G INFO General (kmer_splitters.hpp : 234) Adding contigs from previous K 0:12:23.699 8G / 9G INFO General (kmer_splitters.hpp : 245) Used 33479458 reads. Maximum read length 151 0:12:23.699 8G / 9G INFO General (kmer_splitters.hpp : 246) Average read length 148.807 0:12:25.876 64M / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:15:34.233 64M / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 124044174 kmers in total. 0:15:34.233 64M / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:16:18.197 64M / 9G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:16:18.197 64M / 9G INFO General (kmer_splitters.hpp : 379) Splitting kmer instances into 256 buckets. This might take a while. 0:16:18.198 64M / 9G INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:16:18.198 64M / 9G INFO General (kmer_splitters.hpp : 397) Memory available for splitting buffers: 2.08203 Gb 0:16:18.198 64M / 9G INFO General (kmer_splitters.hpp : 405) Using cell size of 262144 0:19:32.158 8G / 9G INFO General (kmer_splitters.hpp : 428) Processed 124044174 kmers 0:19:32.158 8G / 9G INFO General (kmer_splitters.hpp : 437) Used 124044174 kmers. 0:19:32.789 64M / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:19:37.463 64M / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 122232646 kmers in total. 0:19:37.463 64M / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:19:44.386 64M / 9G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:20:05.604 68M / 9G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:20:12.266 68M / 9G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 42284897 bytes occupied (2.7675 bits per kmer). 0:20:12.481 188M / 9G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 382) Building k-mer extensions from k+1-mers 0:20:24.454 188M / 9G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 386) Building k-mer extensions from k+1-mers finished. 0:20:24.463 188M / 9G INFO Early tip clipping (early_simplification.hpp : 236) Early tip clipping 0:26:57.034 188M / 9G INFO Early tip clipping (early_simplification.hpp : 239) 6439442 22-mers were removed by early tip clipper 0:26:57.034 188M / 9G INFO General (graph_construction.hpp : 145) Condensing graph 0:26:57.034 188M / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 337) Extracting unbranching paths 0:28:17.823 1G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 351) Extracting unbranching paths finished. 10162065 sequences extracted 0:28:27.870 1G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 311) Collecting perfect loops 0:29:05.720 1G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 326) Collecting perfect loops finished. 90 loops collected 0:29:13.127 2G / 9G INFO General (graph_construction.hpp : 150) Building index with from graph 0:29:13.134 2G / 9G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:29:13.134 2G / 9G INFO General (kmer_splitters.hpp : 289) Splitting kmer instances into 16 buckets. This might take a while. 0:29:13.134 2G / 9G INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:29:13.134 2G / 9G INFO General (kmer_splitters.hpp : 307) Memory available for splitting buffers: 32.6289 Gb 0:29:13.134 2G / 9G INFO General (kmer_splitters.hpp : 312) Using cell size of 4194304 0:32:19.491 2G / 9G INFO General (kmer_splitters.hpp : 325) Processed 5797480 edges 0:34:44.239 2G / 9G INFO General (kmer_splitters.hpp : 325) Processed 10162155 edges 0:34:44.240 2G / 9G INFO General (kmer_splitters.hpp : 330) Used 10162155 sequences. 0:34:44.280 2G / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:36:10.768 2G / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 117604732 kmers in total. 0:36:10.768 2G / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:36:16.619 2G / 9G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:39:26.400 2G / 9G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:39:34.527 2G / 9G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 40683923 bytes occupied (2.7675 bits per kmer). 0:39:36.882 4G / 9G INFO General (edge_index_builders.hpp : 21) Collecting k-mer coverage information from graph, this takes a while. 0:43:43.815 4G / 9G INFO General (graph_construction.hpp : 182) Filling coverage index 0:43:43.815 4G / 9G INFO General (edge_index_builders.hpp : 99) Collecting k-mer coverage information from reads, this takes a while. 0:46:09.689 4G / 9G INFO General (graph_construction.hpp : 184) Filling coverage and flanking coverage from index 0:46:43.251 4G / 9G INFO General (construction.cpp : 33) Figured out: read length = 151 0:46:43.269 4G / 9G INFO StageManager (stage.cpp : 125) STAGE == EC Threshold Finding 0:46:54.587 4G / 9G INFO General (kmer_coverage_model.cpp : 178) Kmer coverage valley at: 12 0:46:54.588 4G / 9G INFO General (kmer_coverage_model.cpp : 198) K-mer histogram maximum: 26 0:46:54.588 4G / 9G INFO General (kmer_coverage_model.cpp : 234) Estimated median coverage: 27. Coverage mad: 7.413 0:46:54.588 4G / 9G INFO General (kmer_coverage_model.cpp : 261) Fitting coverage model 0:46:54.670 4G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 2 0:46:54.854 4G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 4 0:46:55.538 4G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 8 0:46:56.806 4G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 16 0:46:58.188 4G / 9G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 26.363. Fitted coverage std. dev: 6.816 0:46:58.190 4G / 9G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 0.244336 0:46:58.190 4G / 9G INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 19 0:46:58.190 4G / 9G INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 19 0:46:58.191 4G / 9G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 62351609 0:46:58.191 4G / 9G INFO General (genomic_info_filler.cpp : 103) Mean coverage was calculated as 26.363 0:46:58.191 4G / 9G INFO General (genomic_info_filler.cpp : 117) EC coverage threshold value was calculated as 19 0:46:58.191 4G / 9G INFO General (genomic_info_filler.cpp : 118) Trusted kmer low bound: 0 0:46:58.191 4G / 9G INFO StageManager (stage.cpp : 125) STAGE == Simplification 0:46:58.375 1G / 9G INFO General (graph_simplification.hpp : 911) Graph simplification started 0:46:58.375 1G / 9G INFO General (graph_simplification.hpp : 924) Fast simplification mode enabled 0:46:58.375 1G / 9G INFO General (graph_simplification.hpp : 771) PROCEDURE == Presimplification 0:46:58.375 1G / 9G INFO General (graph_simplification.hpp : 211) Removing short low covered self-conjugate connections 0:46:59.143 1G / 9G INFO General (graph_simplification.hpp : 403) Removing isolated edges 0:46:59.144 1G / 9G INFO General (graph_simplification.hpp : 404) All edges shorter than 151 will be removed 0:46:59.145 1G / 9G INFO General (graph_simplification.hpp : 405) Also edges shorter than 0 and coverage smaller than 0 will be removed 0:47:00.420 1G / 9G INFO General (graph_simplification.hpp : 687) Non parallel mode 0:47:34.785 2G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:48:55.320 2G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:51:03.816 2G / 9G INFO General (graph_simplification.hpp : 644) Using permanent iterators 0:51:03.816 2G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 1 0:51:12.166 2G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:51:46.087 2G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:52:01.885 2G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 2 0:52:01.885 2G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:52:02.122 2G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:52:11.058 2G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 3 0:52:11.058 2G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:52:11.226 2G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:52:16.848 2G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 4 0:52:16.849 2G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:52:16.955 2G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:52:20.546 2G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 5 0:52:20.547 2G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:52:20.618 2G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:52:23.581 2G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 6 0:52:23.581 2G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:52:23.637 2G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:52:26.105 2G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 7 0:52:26.105 2G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:52:26.148 2G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:52:28.158 2G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 8 0:52:28.158 2G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:52:28.197 2G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:52:29.796 2G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 9 0:52:29.796 2G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:52:29.831 2G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:52:31.470 2G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 10 0:52:31.471 2G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:52:31.509 2G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:52:33.701 2G / 9G INFO General (graph_simplification.hpp : 796) PROCEDURE == Post simplification 0:52:33.701 2G / 9G INFO General (graph_simplification.hpp : 644) Using permanent iterators 0:52:33.701 2G / 9G INFO General (graph_simplification.hpp : 806) Iteration 0 0:52:33.701 2G / 9G INFO General (graph_simplification.hpp : 247) Removal of relatively low covered connections disabled 0:52:36.990 2G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:52:44.274 2G / 9G INFO General (graph_simplification.hpp : 806) Iteration 1 0:52:44.274 2G / 9G INFO General (graph_simplification.hpp : 247) Removal of relatively low covered connections disabled 0:52:44.274 2G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:52:46.517 2G / 9G INFO StageManager (stage.cpp : 125) STAGE == Simplification Cleanup 0:52:46.521 2G / 9G INFO General (graph_simplification.hpp : 403) Removing isolated edges 0:52:46.521 2G / 9G INFO General (graph_simplification.hpp : 404) All edges shorter than 151 will be removed 0:52:46.521 2G / 9G INFO General (graph_simplification.hpp : 405) Also edges shorter than 0 and coverage smaller than 2 will be removed 0:52:46.729 2G / 9G INFO General (simplification.cpp : 56) Removing all the edges having coverage 0 and less 0:52:52.702 2G / 9G INFO General (simplification.cpp : 68) Counting average coverage 0:52:53.466 2G / 9G INFO General (simplification.cpp : 71) Average coverage = 25.4044 0:52:53.466 2G / 9G INFO StageManager (stage.cpp : 125) STAGE == Contig Output 0:52:53.466 2G / 9G INFO General (contig_output.hpp : 283) Outputting contigs to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.tetraurelia-Sample_116-dipSPAdes-3.5.0-trimmed/spades//K21/simplified_contigs.fasta 0:53:36.996 2G / 9G INFO General (contig_output.hpp : 283) Outputting contigs to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.tetraurelia-Sample_116-dipSPAdes-3.5.0-trimmed/spades//K21/before_rr.fasta 0:55:54.212 2G / 9G INFO General (contig_output.hpp : 283) Outputting contigs to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.tetraurelia-Sample_116-dipSPAdes-3.5.0-trimmed/spades//K21/final_contigs.fasta 0:57:55.683 2G / 9G INFO General (launch.hpp : 82) SPAdes finished 0:58:01.940 64M / 9G INFO General (main.cpp : 166) Assembling time: 0 hours 58 minutes 1 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.tetraurelia-Sample_116-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 0:00:00.003 4M / 4M INFO StageManager (stage.cpp : 125) STAGE == Construction 0:00:00.003 4M / 4M INFO General (construction.cpp : 44) Contigs from previous K will be used 0:00:00.009 4M / 4M INFO General (read_converter.hpp : 49) Binary reads detected 0:00:00.032 4M / 4M INFO General (graph_construction.hpp : 129) Constructing DeBruijn graph for k=33 0:00:00.034 4M / 4M INFO General (kmer_splitters.hpp : 172) Splitting kmer instances into 256 buckets. This might take a while. 0:00:00.035 4M / 4M INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:00:00.035 4M / 4M INFO General (kmer_splitters.hpp : 190) Memory available for splitting buffers: 2.08325 Gb 0:00:00.035 4M / 4M INFO General (kmer_splitters.hpp : 199) Using cell size of 131072 0:07:37.828 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 9266356 reads 0:12:20.720 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 18536221 reads 0:18:22.520 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 27809640 reads 0:22:37.882 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 33479458 reads 0:22:37.884 8G / 9G INFO General (kmer_splitters.hpp : 234) Adding contigs from previous K 0:23:02.580 8G / 9G INFO General (kmer_splitters.hpp : 245) Used 33479458 reads. Maximum read length 151 0:23:02.580 8G / 9G INFO General (kmer_splitters.hpp : 246) Average read length 148.807 0:23:04.816 64M / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:23:24.892 64M / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 136916945 kmers in total. 0:23:24.893 64M / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:23:37.968 64M / 9G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:23:37.968 64M / 9G INFO General (kmer_splitters.hpp : 379) Splitting kmer instances into 256 buckets. This might take a while. 0:23:37.969 64M / 9G INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:23:37.969 64M / 9G INFO General (kmer_splitters.hpp : 397) Memory available for splitting buffers: 2.08203 Gb 0:23:37.969 64M / 9G INFO General (kmer_splitters.hpp : 405) Using cell size of 131072 0:24:01.960 8G / 9G INFO General (kmer_splitters.hpp : 428) Processed 136916945 kmers 0:24:01.960 8G / 9G INFO General (kmer_splitters.hpp : 437) Used 136916945 kmers. 0:24:02.772 64M / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:24:12.455 64M / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 136115198 kmers in total. 0:24:12.456 64M / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:24:25.344 64M / 9G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:24:48.476 68M / 9G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:25:04.458 68M / 9G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 47087389 bytes occupied (2.7675 bits per kmer). 0:25:04.672 200M / 9G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 382) Building k-mer extensions from k+1-mers 0:25:22.865 200M / 9G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 386) Building k-mer extensions from k+1-mers finished. 0:25:22.878 200M / 9G INFO Early tip clipping (early_simplification.hpp : 236) Early tip clipping 0:32:41.608 200M / 9G INFO Early tip clipping (early_simplification.hpp : 239) 15644633 34-mers were removed by early tip clipper 0:32:41.608 200M / 9G INFO General (graph_construction.hpp : 145) Condensing graph 0:32:41.608 200M / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 337) Extracting unbranching paths 0:34:08.875 772M / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 351) Extracting unbranching paths finished. 5367374 sequences extracted 0:34:19.728 768M / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 311) Collecting perfect loops 0:35:05.006 768M / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 326) Collecting perfect loops finished. 106 loops collected 0:35:09.155 1G / 9G INFO General (graph_construction.hpp : 150) Building index with from graph 0:35:09.162 1G / 9G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:35:09.162 1G / 9G INFO General (kmer_splitters.hpp : 289) Splitting kmer instances into 16 buckets. This might take a while. 0:35:09.162 1G / 9G INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:35:09.162 1G / 9G INFO General (kmer_splitters.hpp : 307) Memory available for splitting buffers: 32.9089 Gb 0:35:09.162 1G / 9G INFO General (kmer_splitters.hpp : 312) Using cell size of 2097152 0:35:16.717 1G / 9G INFO General (kmer_splitters.hpp : 325) Processed 1487501 edges 0:35:24.338 1G / 9G INFO General (kmer_splitters.hpp : 325) Processed 2971029 edges 0:35:31.709 1G / 9G INFO General (kmer_splitters.hpp : 325) Processed 4454500 edges 0:35:36.220 1G / 9G INFO General (kmer_splitters.hpp : 325) Processed 5367480 edges 0:35:36.220 1G / 9G INFO General (kmer_splitters.hpp : 330) Used 5367480 sequences. 0:35:36.276 1G / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:36:15.128 1G / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 121272312 kmers in total. 0:36:15.128 1G / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:36:27.612 1G / 9G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:39:53.071 1G / 9G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:40:08.112 1G / 9G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 41952674 bytes occupied (2.7675 bits per kmer). 0:40:10.625 4G / 9G INFO General (edge_index_builders.hpp : 21) Collecting k-mer coverage information from graph, this takes a while. 0:44:34.586 3G / 9G INFO General (graph_construction.hpp : 182) Filling coverage index 0:44:34.586 3G / 9G INFO General (edge_index_builders.hpp : 99) Collecting k-mer coverage information from reads, this takes a while. 0:47:58.604 3G / 9G INFO General (graph_construction.hpp : 184) Filling coverage and flanking coverage from index 0:48:32.290 3G / 9G INFO General (construction.cpp : 33) Figured out: read length = 151 0:48:32.309 3G / 9G INFO StageManager (stage.cpp : 125) STAGE == EC Threshold Finding 0:48:44.461 3G / 9G INFO General (kmer_coverage_model.cpp : 178) Kmer coverage valley at: 10 0:48:44.461 3G / 9G INFO General (kmer_coverage_model.cpp : 198) K-mer histogram maximum: 23 0:48:44.461 3G / 9G INFO General (kmer_coverage_model.cpp : 234) Estimated median coverage: 24. Coverage mad: 7.413 0:48:44.461 3G / 9G INFO General (kmer_coverage_model.cpp : 261) Fitting coverage model 0:48:44.549 3G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 2 0:48:44.775 3G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 4 0:48:45.507 3G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 8 0:48:46.660 3G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 16 0:48:47.691 3G / 9G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 23.5677. Fitted coverage std. dev: 6.53146 0:48:47.692 3G / 9G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 0.254321 0:48:47.692 3G / 9G INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 16 0:48:47.692 3G / 9G INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 16 0:48:47.693 3G / 9G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 64480688 0:48:47.693 3G / 9G INFO General (genomic_info_filler.cpp : 103) Mean coverage was calculated as 23.5677 0:48:47.693 3G / 9G INFO General (genomic_info_filler.cpp : 117) EC coverage threshold value was calculated as 16 0:48:47.693 3G / 9G INFO General (genomic_info_filler.cpp : 118) Trusted kmer low bound: 0 0:48:47.693 3G / 9G INFO StageManager (stage.cpp : 125) STAGE == Simplification 0:48:47.985 1G / 9G INFO General (graph_simplification.hpp : 911) Graph simplification started 0:48:47.985 1G / 9G INFO General (graph_simplification.hpp : 924) Fast simplification mode enabled 0:48:47.985 1G / 9G INFO General (graph_simplification.hpp : 771) PROCEDURE == Presimplification 0:48:47.985 1G / 9G INFO General (graph_simplification.hpp : 211) Removing short low covered self-conjugate connections 0:48:48.432 1G / 9G INFO General (graph_simplification.hpp : 403) Removing isolated edges 0:48:48.432 1G / 9G INFO General (graph_simplification.hpp : 404) All edges shorter than 151 will be removed 0:48:48.433 1G / 9G INFO General (graph_simplification.hpp : 405) Also edges shorter than 0 and coverage smaller than 0 will be removed 0:48:50.010 1G / 9G INFO General (graph_simplification.hpp : 687) Non parallel mode 0:49:05.121 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:49:41.632 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:50:47.117 1G / 9G INFO General (graph_simplification.hpp : 644) Using permanent iterators 0:50:47.118 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 1 0:50:49.976 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:51:01.940 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:51:11.755 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 2 0:51:11.755 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:51:11.845 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:51:15.352 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 3 0:51:15.353 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:51:15.410 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:51:17.678 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 4 0:51:17.678 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:51:17.714 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:51:19.411 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 5 0:51:19.411 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:51:19.435 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:51:21.022 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 6 0:51:21.022 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:51:21.040 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:51:22.521 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 7 0:51:22.521 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:51:22.535 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:51:23.862 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 8 0:51:23.862 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:51:23.872 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:51:24.830 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 9 0:51:24.830 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:51:24.838 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:51:25.495 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 10 0:51:25.495 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:51:25.506 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:51:26.008 1G / 9G INFO General (graph_simplification.hpp : 796) PROCEDURE == Post simplification 0:51:26.008 1G / 9G INFO General (graph_simplification.hpp : 644) Using permanent iterators 0:51:26.008 1G / 9G INFO General (graph_simplification.hpp : 806) Iteration 0 0:51:26.008 1G / 9G INFO General (graph_simplification.hpp : 247) Removal of relatively low covered connections disabled 0:51:26.719 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:51:28.305 1G / 9G INFO General (graph_simplification.hpp : 806) Iteration 1 0:51:28.306 1G / 9G INFO General (graph_simplification.hpp : 247) Removal of relatively low covered connections disabled 0:51:28.306 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:51:28.933 1G / 9G INFO StageManager (stage.cpp : 125) STAGE == Simplification Cleanup 0:51:28.935 1G / 9G INFO General (graph_simplification.hpp : 403) Removing isolated edges 0:51:28.935 1G / 9G INFO General (graph_simplification.hpp : 404) All edges shorter than 151 will be removed 0:51:28.935 1G / 9G INFO General (graph_simplification.hpp : 405) Also edges shorter than 0 and coverage smaller than 2 will be removed 0:51:29.030 1G / 9G INFO General (simplification.cpp : 56) Removing all the edges having coverage 0 and less 0:51:30.259 1G / 9G INFO General (simplification.cpp : 68) Counting average coverage 0:51:30.486 1G / 9G INFO General (simplification.cpp : 71) Average coverage = 21.7228 0:51:30.486 1G / 9G INFO StageManager (stage.cpp : 125) STAGE == Contig Output 0:51:30.486 1G / 9G INFO General (contig_output.hpp : 283) Outputting contigs to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.tetraurelia-Sample_116-dipSPAdes-3.5.0-trimmed/spades//K33/simplified_contigs.fasta 0:51:54.933 1G / 9G INFO General (contig_output.hpp : 283) Outputting contigs to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.tetraurelia-Sample_116-dipSPAdes-3.5.0-trimmed/spades//K33/before_rr.fasta 0:53:04.101 1G / 9G INFO General (contig_output.hpp : 283) Outputting contigs to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.tetraurelia-Sample_116-dipSPAdes-3.5.0-trimmed/spades//K33/final_contigs.fasta 0:54:13.820 1G / 9G INFO General (launch.hpp : 82) SPAdes finished 0:54:16.636 64M / 9G INFO General (main.cpp : 166) Assembling time: 0 hours 54 minutes 16 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.tetraurelia-Sample_116-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 0:00:00.003 4M / 4M INFO General (launch.hpp : 44) Will need read mapping, kmer mapper will be attached 0:00:00.003 4M / 4M INFO StageManager (stage.cpp : 125) STAGE == Construction 0:00:00.003 4M / 4M INFO General (construction.cpp : 44) Contigs from previous K will be used 0:00:00.008 4M / 4M INFO General (read_converter.hpp : 49) Binary reads detected 0:00:00.027 4M / 4M INFO General (graph_construction.hpp : 129) Constructing DeBruijn graph for k=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 0:00:22.736 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 11432118 reads 0:00:41.376 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 22864404 reads 0:00:56.252 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 33479458 reads 0:00:56.253 8G / 9G INFO General (kmer_splitters.hpp : 234) Adding contigs from previous K 0:01:18.961 8G / 9G INFO General (kmer_splitters.hpp : 245) Used 33479458 reads. Maximum read length 151 0:01:18.961 8G / 9G INFO General (kmer_splitters.hpp : 246) Average read length 148.807 0:01:21.155 64M / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:01:37.863 64M / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 147150250 kmers in total. 0:01:37.865 64M / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:01:51.896 64M / 9G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:01:51.896 64M / 9G INFO General (kmer_splitters.hpp : 379) Splitting kmer instances into 256 buckets. This might take a while. 0:01:51.897 64M / 9G INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:01:51.897 64M / 9G INFO General (kmer_splitters.hpp : 397) Memory available for splitting buffers: 2.08203 Gb 0:01:51.897 64M / 9G INFO General (kmer_splitters.hpp : 405) Using cell size of 131072 0:02:20.988 8G / 9G INFO General (kmer_splitters.hpp : 428) Processed 147150250 kmers 0:02:20.988 8G / 9G INFO General (kmer_splitters.hpp : 437) Used 147150250 kmers. 0:02:21.836 64M / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:02:32.176 64M / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 146942838 kmers in total. 0:02:32.176 64M / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:02:45.716 64M / 9G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:03:13.029 68M / 9G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:03:25.761 68M / 9G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 50833080 bytes occupied (2.7675 bits per kmer). 0:03:25.991 212M / 9G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 382) Building k-mer extensions from k+1-mers 0:03:50.466 212M / 9G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 386) Building k-mer extensions from k+1-mers finished. 0:03:50.478 212M / 9G INFO General (graph_construction.hpp : 145) Condensing graph 0:03:50.478 212M / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 337) Extracting unbranching paths 0:05:21.491 1G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 351) Extracting unbranching paths finished. 6631645 sequences extracted 0:05:35.125 1G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 311) Collecting perfect loops 0:06:25.025 1G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 326) Collecting perfect loops finished. 6 loops collected 0:06:31.583 1G / 9G INFO General (graph_construction.hpp : 150) Building index with from graph 0:06:31.589 1G / 9G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:06:31.589 1G / 9G INFO General (kmer_splitters.hpp : 289) Splitting kmer instances into 16 buckets. This might take a while. 0:06:31.589 1G / 9G INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:06:31.589 1G / 9G INFO General (kmer_splitters.hpp : 307) Memory available for splitting buffers: 32.7643 Gb 0:06:31.589 1G / 9G INFO General (kmer_splitters.hpp : 312) Using cell size of 2097152 0:06:39.842 2G / 9G INFO General (kmer_splitters.hpp : 325) Processed 1511438 edges 0:06:48.164 2G / 9G INFO General (kmer_splitters.hpp : 325) Processed 3022830 edges 0:06:56.666 2G / 9G INFO General (kmer_splitters.hpp : 325) Processed 4536605 edges 0:07:05.169 2G / 9G INFO General (kmer_splitters.hpp : 325) Processed 6048616 edges 0:07:08.339 2G / 9G INFO General (kmer_splitters.hpp : 325) Processed 6631651 edges 0:07:08.339 2G / 9G INFO General (kmer_splitters.hpp : 330) Used 6631651 sequences. 0:07:08.425 1G / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:07:54.011 1G / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 147150250 kmers in total. 0:07:54.011 1G / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:08:08.965 1G / 9G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:12:49.342 1G / 9G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:13:04.018 1G / 9G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 50904832 bytes occupied (2.7675 bits per kmer). 0:13:07.125 5G / 9G INFO General (edge_index_builders.hpp : 21) Collecting k-mer coverage information from graph, this takes a while. 0:18:48.368 4G / 9G INFO General (graph_construction.hpp : 182) Filling coverage index 0:18:48.368 4G / 9G INFO General (edge_index_builders.hpp : 99) Collecting k-mer coverage information from reads, this takes a while. 0:21:03.347 4G / 9G INFO General (graph_construction.hpp : 184) Filling coverage and flanking coverage from index 0:21:38.505 4G / 9G INFO General (construction.cpp : 33) Figured out: read length = 151 0:21:38.526 4G / 9G INFO StageManager (stage.cpp : 125) STAGE == EC Threshold Finding 0:21:49.725 4G / 9G INFO General (kmer_coverage_model.cpp : 178) Kmer coverage valley at: 7 0:21:49.726 4G / 9G INFO General (kmer_coverage_model.cpp : 198) K-mer histogram maximum: 18 0:21:49.726 4G / 9G INFO General (kmer_coverage_model.cpp : 234) Estimated median coverage: 19. Coverage mad: 7.413 0:21:49.726 4G / 9G INFO General (kmer_coverage_model.cpp : 261) Fitting coverage model 0:21:49.797 4G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 2 0:21:49.980 4G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 4 0:21:50.611 4G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 8 0:21:51.699 4G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 16 0:21:52.968 4G / 9G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 18.6315. Fitted coverage std. dev: 5.90058 0:21:52.969 4G / 9G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 0.246563 0:21:52.969 4G / 9G INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 13 0:21:52.969 4G / 9G INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 12 0:21:52.969 4G / 9G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 65578038 0:21:52.970 4G / 9G INFO General (genomic_info_filler.cpp : 103) Mean coverage was calculated as 18.6315 0:21:52.970 4G / 9G INFO General (genomic_info_filler.cpp : 117) EC coverage threshold value was calculated as 12 0:21:52.970 4G / 9G INFO General (genomic_info_filler.cpp : 118) Trusted kmer low bound: 0 0:21:52.970 4G / 9G INFO StageManager (stage.cpp : 125) STAGE == Gap Closer 0:21:52.986 4G / 9G INFO General (gap_closer.cpp : 157) Preparing shift maps 0:21:59.782 5G / 9G INFO General (gap_closer.cpp : 117) Processing paired reads (takes a while) 0:22:23.386 5G / 9G INFO General (gap_closer.cpp : 136) Used 16563674 paired reads 0:22:23.387 5G / 9G INFO General (gap_closer.cpp : 138) Merging paired indices 0:22:25.875 4G / 9G INFO GapCloser (gap_closer.cpp : 395) Closing short gaps 0:22:42.023 4G / 9G INFO GapCloser (gap_closer.cpp : 424) Closing short gaps complete: filled 1649 gaps after checking 21112 candidates 0:22:45.006 4G / 9G INFO StageManager (stage.cpp : 125) STAGE == Simplification 0:22:45.294 1G / 9G INFO General (graph_simplification.hpp : 911) Graph simplification started 0:22:45.294 1G / 9G INFO General (graph_simplification.hpp : 924) Fast simplification mode enabled 0:22:45.294 1G / 9G INFO General (graph_simplification.hpp : 771) PROCEDURE == Presimplification 0:22:45.294 1G / 9G INFO General (graph_simplification.hpp : 211) Removing short low covered self-conjugate connections 0:22:45.900 1G / 9G INFO General (graph_simplification.hpp : 403) Removing isolated edges 0:22:45.900 1G / 9G INFO General (graph_simplification.hpp : 404) All edges shorter than 151 will be removed 0:22:45.900 1G / 9G INFO General (graph_simplification.hpp : 405) Also edges shorter than 0 and coverage smaller than 0 will be removed 0:22:48.344 1G / 9G INFO General (graph_simplification.hpp : 687) Non parallel mode 0:23:06.800 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:24:04.615 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:24:31.083 1G / 9G INFO General (graph_simplification.hpp : 644) Using permanent iterators 0:24:31.083 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 1 0:24:32.106 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:24:36.381 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:24:37.908 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 2 0:24:37.908 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:24:37.925 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:24:38.956 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 3 0:24:38.956 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:24:38.985 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:24:40.347 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 4 0:24:40.347 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:24:40.372 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:24:41.517 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 5 0:24:41.517 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:24:41.531 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:24:42.812 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 6 0:24:42.812 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:24:42.824 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:24:44.209 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 7 0:24:44.209 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:24:44.219 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:24:45.511 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 8 0:24:45.511 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:24:45.520 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:24:46.613 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 9 0:24:46.613 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:24:46.621 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:24:47.503 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 10 0:24:47.503 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:24:47.508 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:24:47.993 1G / 9G INFO General (graph_simplification.hpp : 796) PROCEDURE == Post simplification 0:24:47.993 1G / 9G INFO General (graph_simplification.hpp : 644) Using permanent iterators 0:24:47.993 1G / 9G INFO General (graph_simplification.hpp : 806) Iteration 0 0:24:47.993 1G / 9G INFO General (graph_simplification.hpp : 247) Removal of relatively low covered connections disabled 0:24:48.269 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:24:48.866 1G / 9G INFO General (graph_simplification.hpp : 806) Iteration 1 0:24:48.866 1G / 9G INFO General (graph_simplification.hpp : 247) Removal of relatively low covered connections disabled 0:24:48.866 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:24:49.070 1G / 9G INFO StageManager (stage.cpp : 125) STAGE == Gap Closer 0:24:49.070 1G / 9G INFO General (graph_pack.hpp : 84) Index refill 0:24:49.076 1G / 9G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:24:49.076 1G / 9G INFO General (kmer_splitters.hpp : 289) Splitting kmer instances into 16 buckets. This might take a while. 0:24:49.076 1G / 9G INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:24:49.076 1G / 9G INFO General (kmer_splitters.hpp : 307) Memory available for splitting buffers: 32.9844 Gb 0:24:49.076 1G / 9G INFO General (kmer_splitters.hpp : 312) Using cell size of 2097152 0:24:55.574 1G / 9G INFO General (kmer_splitters.hpp : 325) Processed 54693 edges 0:25:01.955 1G / 9G INFO General (kmer_splitters.hpp : 325) Processed 110311 edges 0:25:05.710 1G / 9G INFO General (kmer_splitters.hpp : 325) Processed 142650 edges 0:25:05.711 1G / 9G INFO General (kmer_splitters.hpp : 330) Used 142650 sequences. 0:25:05.773 1G / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:25:31.786 1G / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 87186791 kmers in total. 0:25:31.786 1G / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:25:39.861 1G / 9G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:27:54.802 1G / 9G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:28:02.492 1G / 9G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 30161218 bytes occupied (2.7675 bits per kmer). 0:28:04.214 3G / 9G INFO General (edge_index_builders.hpp : 21) Collecting k-mer coverage information from graph, this takes a while. 0:30:40.032 3G / 9G INFO General (gap_closer.cpp : 157) Preparing shift maps 0:30:40.231 3G / 9G INFO General (gap_closer.cpp : 117) Processing paired reads (takes a while) 0:31:18.313 3G / 9G INFO General (gap_closer.cpp : 136) Used 16563674 paired reads 0:31:18.314 3G / 9G INFO General (gap_closer.cpp : 138) Merging paired indices 0:31:18.643 3G / 9G INFO GapCloser (gap_closer.cpp : 395) Closing short gaps 0:31:19.145 3G / 9G INFO GapCloser (gap_closer.cpp : 424) Closing short gaps complete: filled 264 gaps after checking 11490 candidates 0:31:20.756 3G / 9G INFO StageManager (stage.cpp : 125) STAGE == Simplification Cleanup 0:31:20.760 3G / 9G INFO General (graph_simplification.hpp : 403) Removing isolated edges 0:31:20.760 3G / 9G INFO General (graph_simplification.hpp : 404) All edges shorter than 151 will be removed 0:31:20.760 3G / 9G INFO General (graph_simplification.hpp : 405) Also edges shorter than 0 and coverage smaller than 2 will be removed 0:31:21.435 2G / 9G INFO General (simplification.cpp : 56) Removing all the edges having coverage 0 and less 0:31:21.906 2G / 9G INFO General (simplification.cpp : 68) Counting average coverage 0:31:22.018 2G / 9G INFO General (simplification.cpp : 71) Average coverage = 17.1913 0:31:22.018 2G / 9G INFO StageManager (stage.cpp : 125) STAGE == Contig Output 0:31:22.018 2G / 9G INFO General (contig_output.hpp : 283) Outputting contigs to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.tetraurelia-Sample_116-dipSPAdes-3.5.0-trimmed/spades//K55/simplified_contigs.fasta 0:31:42.065 2G / 9G INFO General (contig_output.hpp : 283) Outputting contigs to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.tetraurelia-Sample_116-dipSPAdes-3.5.0-trimmed/spades//K55/before_rr.fasta 0:32:39.654 2G / 9G INFO General (contig_output.hpp : 283) Outputting contigs to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.tetraurelia-Sample_116-dipSPAdes-3.5.0-trimmed/spades//K55/final_contigs.fasta 0:33:37.689 2G / 9G INFO General (launch.hpp : 82) SPAdes finished 0:33:41.106 64M / 9G INFO General (main.cpp : 166) Assembling time: 0 hours 33 minutes 41 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.tetraurelia-Sample_116-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 0:00:00.007 4M / 4M INFO General (launch.hpp : 44) Will need read mapping, kmer mapper will be attached 0:00:00.007 4M / 4M INFO StageManager (stage.cpp : 125) STAGE == Construction 0:00:00.007 4M / 4M INFO General (construction.cpp : 44) Contigs from previous K will be used 0:00:00.012 4M / 4M INFO General (read_converter.hpp : 49) Binary reads detected 0:00:00.033 4M / 4M INFO General (graph_construction.hpp : 129) Constructing DeBruijn graph for k=77 0:00:00.035 4M / 4M INFO General (kmer_splitters.hpp : 172) Splitting kmer instances into 256 buckets. This might take a while. 0:00:00.036 4M / 4M INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:00:00.036 4M / 4M INFO General (kmer_splitters.hpp : 190) Memory available for splitting buffers: 2.08325 Gb 0:00:00.036 4M / 4M INFO General (kmer_splitters.hpp : 199) Using cell size of 87381 0:00:20.422 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 9924067 reads 0:00:34.021 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 19851848 reads 0:08:29.753 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 29774218 reads 0:16:11.361 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 33479458 reads 0:16:11.361 8G / 9G INFO General (kmer_splitters.hpp : 234) Adding contigs from previous K 0:26:21.026 8G / 9G INFO General (kmer_splitters.hpp : 245) Used 33479458 reads. Maximum read length 151 0:26:21.027 8G / 9G INFO General (kmer_splitters.hpp : 246) Average read length 148.807 0:26:23.258 64M / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:26:51.421 64M / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 146806260 kmers in total. 0:26:51.421 64M / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:27:13.316 64M / 9G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:27:13.317 64M / 9G INFO General (kmer_splitters.hpp : 379) Splitting kmer instances into 256 buckets. This might take a while. 0:27:13.317 64M / 9G INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:27:13.317 64M / 9G INFO General (kmer_splitters.hpp : 397) Memory available for splitting buffers: 2.08203 Gb 0:27:13.317 64M / 9G INFO General (kmer_splitters.hpp : 405) Using cell size of 87381 0:27:49.200 8G / 9G INFO General (kmer_splitters.hpp : 428) Processed 146806260 kmers 0:27:49.201 8G / 9G INFO General (kmer_splitters.hpp : 437) Used 146806260 kmers. 0:27:50.411 64M / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:28:05.381 64M / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 146997450 kmers in total. 0:28:05.382 64M / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:28:26.184 64M / 9G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:28:53.337 68M / 9G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:29:19.690 68M / 9G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 50851962 bytes occupied (2.7675 bits per kmer). 0:29:19.949 212M / 9G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 382) Building k-mer extensions from k+1-mers 0:29:43.926 212M / 9G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 386) Building k-mer extensions from k+1-mers finished. 0:29:43.940 212M / 9G INFO General (graph_construction.hpp : 145) Condensing graph 0:29:43.940 212M / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 337) Extracting unbranching paths 0:31:17.231 888M / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 351) Extracting unbranching paths finished. 5606272 sequences extracted 0:31:31.407 888M / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 311) Collecting perfect loops 0:32:25.368 888M / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 326) Collecting perfect loops finished. 8 loops collected 0:32:31.765 1G / 9G INFO General (graph_construction.hpp : 150) Building index with from graph 0:32:31.771 1G / 9G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:32:31.771 1G / 9G INFO General (kmer_splitters.hpp : 289) Splitting kmer instances into 16 buckets. This might take a while. 0:32:31.772 1G / 9G INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:32:31.772 1G / 9G INFO General (kmer_splitters.hpp : 307) Memory available for splitting buffers: 32.8047 Gb 0:32:31.772 1G / 9G INFO General (kmer_splitters.hpp : 312) Using cell size of 1398101 0:32:38.197 2G / 9G INFO General (kmer_splitters.hpp : 325) Processed 852929 edges 0:32:44.619 2G / 9G INFO General (kmer_splitters.hpp : 325) Processed 1705511 edges 0:32:51.169 2G / 9G INFO General (kmer_splitters.hpp : 325) Processed 2561598 edges 0:32:57.741 2G / 9G INFO General (kmer_splitters.hpp : 325) Processed 3415486 edges 0:33:04.266 2G / 9G INFO General (kmer_splitters.hpp : 325) Processed 4270502 edges 0:33:10.680 2G / 9G INFO General (kmer_splitters.hpp : 325) Processed 5124894 edges 0:33:14.353 2G / 9G INFO General (kmer_splitters.hpp : 325) Processed 5606280 edges 0:33:14.354 2G / 9G INFO General (kmer_splitters.hpp : 330) Used 5606280 sequences. 0:33:14.431 1G / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:34:15.320 1G / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 146806260 kmers in total. 0:34:15.321 1G / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:34:36.651 1G / 9G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:39:06.604 1G / 9G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:39:28.570 1G / 9G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 50785826 bytes occupied (2.7675 bits per kmer). 0:39:31.667 4G / 9G INFO General (edge_index_builders.hpp : 21) Collecting k-mer coverage information from graph, this takes a while. 0:45:40.317 4G / 9G INFO General (graph_construction.hpp : 182) Filling coverage index 0:45:40.317 4G / 9G INFO General (edge_index_builders.hpp : 99) Collecting k-mer coverage information from reads, this takes a while. 0:48:25.739 4G / 9G INFO General (graph_construction.hpp : 184) Filling coverage and flanking coverage from index 0:49:06.604 4G / 9G INFO General (construction.cpp : 33) Figured out: read length = 151 0:49:06.622 4G / 9G INFO StageManager (stage.cpp : 125) STAGE == EC Threshold Finding 0:49:16.946 4G / 9G INFO General (kmer_coverage_model.cpp : 178) Kmer coverage valley at: 4 0:49:16.946 4G / 9G INFO General (kmer_coverage_model.cpp : 198) K-mer histogram maximum: 13 0:49:16.946 4G / 9G INFO General (kmer_coverage_model.cpp : 234) Estimated median coverage: 14. Coverage mad: 5.9304 0:49:16.946 4G / 9G INFO General (kmer_coverage_model.cpp : 261) Fitting coverage model 0:49:16.999 4G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 2 0:49:17.135 4G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 4 0:49:17.600 4G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 8 0:49:18.492 4G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 16 0:49:19.837 4G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 32 0:49:19.837 4G / 9G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 14.0679. Fitted coverage std. dev: 5.00212 0:49:19.838 4G / 9G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 0.370618 0:49:19.838 4G / 9G INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 9 0:49:19.838 4G / 9G INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 9 0:49:19.838 4G / 9G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 64993665 0:49:19.838 4G / 9G INFO General (genomic_info_filler.cpp : 103) Mean coverage was calculated as 14.0679 0:49:19.838 4G / 9G INFO General (genomic_info_filler.cpp : 117) EC coverage threshold value was calculated as 9 0:49:19.838 4G / 9G INFO General (genomic_info_filler.cpp : 118) Trusted kmer low bound: 0 0:49:19.839 4G / 9G INFO StageManager (stage.cpp : 125) STAGE == Gap Closer 0:49:19.853 4G / 9G INFO General (gap_closer.cpp : 157) Preparing shift maps 0:49:27.424 4G / 9G INFO General (gap_closer.cpp : 117) Processing paired reads (takes a while) 0:49:46.365 5G / 9G INFO General (gap_closer.cpp : 136) Used 16563674 paired reads 0:49:46.366 5G / 9G INFO General (gap_closer.cpp : 138) Merging paired indices 0:49:49.820 4G / 9G INFO GapCloser (gap_closer.cpp : 395) Closing short gaps 0:50:04.713 4G / 9G INFO GapCloser (gap_closer.cpp : 424) Closing short gaps complete: filled 1078 gaps after checking 21629 candidates 0:50:07.422 4G / 9G INFO StageManager (stage.cpp : 125) STAGE == Simplification 0:50:07.769 1G / 9G INFO General (graph_simplification.hpp : 911) Graph simplification started 0:50:07.769 1G / 9G INFO General (graph_simplification.hpp : 924) Fast simplification mode enabled 0:50:07.769 1G / 9G INFO General (graph_simplification.hpp : 771) PROCEDURE == Presimplification 0:50:07.770 1G / 9G INFO General (graph_simplification.hpp : 211) Removing short low covered self-conjugate connections 0:50:08.405 1G / 9G INFO General (graph_simplification.hpp : 403) Removing isolated edges 0:50:08.407 1G / 9G INFO General (graph_simplification.hpp : 404) All edges shorter than 151 will be removed 0:50:08.408 1G / 9G INFO General (graph_simplification.hpp : 405) Also edges shorter than 0 and coverage smaller than 0 will be removed 0:50:12.466 1G / 9G INFO General (graph_simplification.hpp : 687) Non parallel mode 0:50:29.411 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:51:30.260 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:51:32.717 1G / 9G INFO General (graph_simplification.hpp : 644) Using permanent iterators 0:51:32.718 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 1 0:51:33.368 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:51:35.995 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:51:36.029 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 2 0:51:36.029 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:51:36.032 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:51:36.218 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 3 0:51:36.218 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:51:36.223 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:51:36.907 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 4 0:51:36.907 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:51:36.921 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:51:37.775 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 5 0:51:37.775 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:51:37.789 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:51:38.867 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 6 0:51:38.867 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:51:38.877 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:51:40.261 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 7 0:51:40.261 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:51:40.270 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:51:41.605 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 8 0:51:41.606 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:51:41.614 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:51:42.912 1016M / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 9 0:51:42.912 1016M / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:51:42.921 1016M / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:51:43.900 964M / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 10 0:51:43.900 964M / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:51:43.904 964M / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:51:44.552 928M / 9G INFO General (graph_simplification.hpp : 796) PROCEDURE == Post simplification 0:51:44.553 928M / 9G INFO General (graph_simplification.hpp : 644) Using permanent iterators 0:51:44.553 928M / 9G INFO General (graph_simplification.hpp : 806) Iteration 0 0:51:44.553 928M / 9G INFO General (graph_simplification.hpp : 247) Removal of relatively low covered connections disabled 0:51:44.766 928M / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:51:45.196 928M / 9G INFO General (graph_simplification.hpp : 806) Iteration 1 0:51:45.196 928M / 9G INFO General (graph_simplification.hpp : 247) Removal of relatively low covered connections disabled 0:51:45.196 928M / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:51:45.433 912M / 9G INFO StageManager (stage.cpp : 125) STAGE == Gap Closer 0:51:45.433 912M / 9G INFO General (graph_pack.hpp : 84) Index refill 0:51:45.438 912M / 9G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:51:45.438 912M / 9G INFO General (kmer_splitters.hpp : 289) Splitting kmer instances into 16 buckets. This might take a while. 0:51:45.438 912M / 9G INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:51:45.439 912M / 9G INFO General (kmer_splitters.hpp : 307) Memory available for splitting buffers: 33.0365 Gb 0:51:45.439 912M / 9G INFO General (kmer_splitters.hpp : 312) Using cell size of 1398101 0:51:50.734 1G / 9G INFO General (kmer_splitters.hpp : 325) Processed 25475 edges 0:51:55.829 1G / 9G INFO General (kmer_splitters.hpp : 325) Processed 50529 edges 0:52:00.665 1G / 9G INFO General (kmer_splitters.hpp : 325) Processed 75991 edges 0:52:05.081 1G / 9G INFO General (kmer_splitters.hpp : 325) Processed 99333 edges 0:52:05.082 1G / 9G INFO General (kmer_splitters.hpp : 330) Used 99333 sequences. 0:52:05.169 904M / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:52:39.540 904M / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 87359023 kmers in total. 0:52:39.540 904M / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:52:51.855 904M / 9G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:54:56.755 932M / 9G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:55:10.861 932M / 9G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 30220803 bytes occupied (2.7675 bits per kmer). 0:55:12.413 2G / 9G INFO General (edge_index_builders.hpp : 21) Collecting k-mer coverage information from graph, this takes a while. 0:58:10.884 2G / 9G INFO General (gap_closer.cpp : 157) Preparing shift maps 0:58:11.046 2G / 9G INFO General (gap_closer.cpp : 117) Processing paired reads (takes a while) 0:58:36.561 2G / 9G INFO General (gap_closer.cpp : 136) Used 16563674 paired reads 0:58:36.564 2G / 9G INFO General (gap_closer.cpp : 138) Merging paired indices 0:58:36.955 2G / 9G INFO GapCloser (gap_closer.cpp : 395) Closing short gaps 0:58:37.515 2G / 9G INFO GapCloser (gap_closer.cpp : 424) Closing short gaps complete: filled 107 gaps after checking 12348 candidates 0:58:39.202 2G / 9G INFO StageManager (stage.cpp : 125) STAGE == Simplification Cleanup 0:58:39.205 2G / 9G INFO General (graph_simplification.hpp : 403) Removing isolated edges 0:58:39.205 2G / 9G INFO General (graph_simplification.hpp : 404) All edges shorter than 151 will be removed 0:58:39.205 2G / 9G INFO General (graph_simplification.hpp : 405) Also edges shorter than 0 and coverage smaller than 2 will be removed 0:58:40.208 2G / 9G INFO General (simplification.cpp : 56) Removing all the edges having coverage 0 and less 0:58:40.509 2G / 9G INFO General (simplification.cpp : 68) Counting average coverage 0:58:40.581 2G / 9G INFO General (simplification.cpp : 71) Average coverage = 13.0282 0:58:40.581 2G / 9G INFO StageManager (stage.cpp : 125) STAGE == Mismatch Correction 0:59:08.399 2G / 9G INFO General (mismatch_shall_not_pass.hp: 188) Finished collecting potential mismatches positions 0:59:08.523 2G / 9G INFO General (mismatch_shall_not_pass.hp: 291) All edges processed 0:59:08.528 2G / 9G INFO General (mismatch_correction.cpp : 18) Corrected 0 nucleotides 0:59:08.548 2G / 9G INFO StageManager (stage.cpp : 125) STAGE == Paired Information Counting 0:59:08.913 2G / 9G INFO General (pair_info_count.cpp : 150) Graph N50: 17578 0:59:08.913 2G / 9G INFO General (pair_info_count.cpp : 152) Estimating insert size for library #0 0:59:08.913 2G / 9G INFO General (pair_info_count.cpp : 31) Estimating insert size (takes a while) 0:59:08.929 2G / 9G INFO General (short_read_mapper.hpp : 91) Selecting usual mapper 0:59:14.597 2G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 200000 reads 0:59:14.622 2G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 400000 reads 0:59:14.636 2G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 600000 reads 0:59:14.643 2G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 800000 reads 0:59:14.644 2G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 1000000 reads 0:59:14.650 2G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 1200000 reads 0:59:14.787 2G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 2200000 reads 0:59:20.607 2G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 4200000 reads 0:59:24.086 2G / 9G INFO General (sequence_mapper_notifier.h: 89) Processed 8281837 reads 0:59:24.086 2G / 9G INFO General (pair_info_count.cpp : 41) 3989168 paired reads (48.1677% of all) aligned to long edges 0:59:24.099 2G / 9G INFO General (pair_info_count.cpp : 170) Estimated insert size for paired library #0 0:59:24.099 2G / 9G INFO General (pair_info_count.cpp : 175) Insert size = 360.268, deviation = 110.667, left quantile = 230, right quantile = 507, read length = 151 0:59:24.099 2G / 9G INFO General (pair_info_count.cpp : 187) Mapping library #0 0:59:24.099 2G / 9G INFO General (pair_info_count.cpp : 189) Mapping paired reads (takes a while) 0:59:24.100 2G / 9G INFO General (pair_info_count.cpp : 73) Left insert size qauntile 230, right insert size quantile 507 0:59:24.115 2G / 9G INFO General (short_read_mapper.hpp : 91) Selecting usual mapper 0:59:32.360 5G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 200000 reads 0:59:33.220 5G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 400000 reads 0:59:34.172 5G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 600000 reads 0:59:35.273 5G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 800000 reads 0:59:36.483 5G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 1000000 reads 0:59:37.775 5G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 1200000 reads 0:59:44.955 5G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 2200000 reads 1:00:01.040 5G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 4200000 reads 1:00:36.968 5G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 8400000 reads 1:01:54.850 3G / 9G INFO General (sequence_mapper_notifier.h: 89) Processed 16563674 reads 1:05:07.813 4G / 9G INFO General (split_graph_pair_info.hpp : 344) Threshold for paired information 0.0349104 1:05:12.159 2G / 9G INFO StageManager (stage.cpp : 125) STAGE == Distance Estimation 1:05:12.159 2G / 9G INFO General (distance_estimation.cpp : 234) Processing library #0 1:05:12.159 2G / 9G INFO General (distance_estimation.cpp : 136) Weight Filter Done 1:05:12.159 2G / 9G INFO DistanceEstimator (distance_estimation.hpp : 187) Using SIMPLE distance estimator 1:06:05.241 3G / 9G INFO DistanceEstimator (distance_estimation.hpp : 208) Merging maps 1:06:07.419 3G / 9G INFO General (distance_estimation.cpp : 38) Filtering info 1:06:10.840 3G / 9G INFO General (pair_info_filters.hpp : 354) Pruning the index 1:06:11.018 3G / 9G INFO General (distance_estimation.cpp : 184) Refining clustered pair information 1:06:11.238 3G / 9G INFO General (distance_estimation.cpp : 186) The refining of clustered pair information has been finished 1:06:11.239 3G / 9G INFO General (distance_estimation.cpp : 188) Filling paired information 1:06:26.857 3G / 9G INFO PairInfoImprover (pair_info_improver.hpp : 61) Paired info stats: missing = 101174; contradictional = 5306 1:06:42.292 3G / 9G INFO PairInfoImprover (pair_info_improver.hpp : 61) Paired info stats: missing = 29848; contradictional = 0 1:06:42.293 3G / 9G INFO General (distance_estimation.cpp : 193) Filling scaffolding index 1:06:42.293 3G / 9G INFO DistanceEstimator (distance_estimation.hpp : 187) Using SMOOTHING distance estimator 1:07:25.548 3G / 9G INFO DistanceEstimator (distance_estimation.hpp : 208) Merging maps 1:07:25.587 3G / 9G INFO General (distance_estimation.cpp : 38) Filtering info 1:07:25.869 3G / 9G INFO General (pair_info_filters.hpp : 354) Pruning the index 1:07:26.436 2G / 9G INFO StageManager (stage.cpp : 125) STAGE == Repeat Resolving 1:07:26.436 2G / 9G INFO General (contig_output.hpp : 283) Outputting contigs to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.tetraurelia-Sample_116-dipSPAdes-3.5.0-trimmed/spades//K77/before_rr.fasta 1:08:21.896 2G / 9G INFO General (repeat_resolving.cpp : 59) Using Path-Extend repeat resolving 1:08:21.897 2G / 9G INFO General (path_extend_launch.hpp : 459) Threshold for library #0 is 0.0349104 1:08:21.897 2G / 9G INFO General (path_extend_launch.hpp : 298) Path-Extend repeat resolving tool started 1:08:21.995 2G / 9G INFO General (path_extend_launch.hpp : 316) Using 1 paired-end library 1:08:21.995 2G / 9G INFO General (path_extend_launch.hpp : 317) Using 1 paired-end scaffolding library 1:08:21.995 2G / 9G INFO General (path_extend_launch.hpp : 318) Using 0 mate-pair libraries 1:08:21.995 2G / 9G INFO General (path_extend_launch.hpp : 319) Using 0 single read libraries 1:08:21.995 2G / 9G INFO General (path_extend_launch.hpp : 320) Scaffolder is on 1:08:22.587 3G / 9G INFO General (path_extend_launch.hpp : 332) Growing paths using paired-end and long single reads 1:08:22.587 3G / 9G INFO PathExtender (path_extender.hpp : 611) Processed 0 paths from 44421 (0%) 1:08:23.866 3G / 9G INFO PathExtender (path_extender.hpp : 609) Processed 128 paths from 44421 (0%) 1:08:25.544 3G / 9G INFO PathExtender (path_extender.hpp : 609) Processed 256 paths from 44421 (0%) 1:08:28.971 3G / 9G INFO PathExtender (path_extender.hpp : 609) Processed 512 paths from 44421 (1%) 1:08:33.221 3G / 9G INFO PathExtender (path_extender.hpp : 609) Processed 1024 paths from 44421 (2%) 1:08:37.858 3G / 9G INFO PathExtender (path_extender.hpp : 609) Processed 2048 paths from 44421 (4%) 1:08:40.640 3G / 9G INFO PathExtender (path_extender.hpp : 609) Processed 4096 paths from 44421 (9%) 1:08:41.055 3G / 9G INFO PathExtender (path_extender.hpp : 611) Processed 4443 paths from 44421 (10%) 1:08:43.306 3G / 9G INFO PathExtender (path_extender.hpp : 609) Processed 8192 paths from 44421 (18%) 1:08:43.482 3G / 9G INFO PathExtender (path_extender.hpp : 611) Processed 8886 paths from 44421 (20%) 1:08:44.009 3G / 9G INFO PathExtender (path_extender.hpp : 611) Processed 13329 paths from 44421 (30%) 1:08:45.095 3G / 9G INFO PathExtender (path_extender.hpp : 609) Processed 16384 paths from 44421 (36%) 1:08:45.515 3G / 9G INFO PathExtender (path_extender.hpp : 611) Processed 17772 paths from 44421 (40%) 1:08:46.335 3G / 9G INFO PathExtender (path_extender.hpp : 611) Processed 22215 paths from 44421 (50%) 1:08:46.766 3G / 9G INFO PathExtender (path_extender.hpp : 611) Processed 26658 paths from 44421 (60%) 1:08:48.601 3G / 9G INFO PathExtender (path_extender.hpp : 611) Processed 31101 paths from 44421 (70%) 1:08:51.614 3G / 9G INFO PathExtender (path_extender.hpp : 609) Processed 32768 paths from 44421 (73%) 1:08:58.050 3G / 9G INFO PathExtender (path_extender.hpp : 611) Processed 35544 paths from 44421 (80%) 1:09:00.477 3G / 9G INFO PathExtender (path_extender.hpp : 611) Processed 39987 paths from 44421 (90%) 1:09:03.061 3G / 9G INFO PathExtendIO (pe_io.hpp : 339) Constructing FASTG file from paths 1:09:03.907 3G / 9G INFO PathExtendIO (pe_io.hpp : 342) Writing contigs in FASTG to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.tetraurelia-Sample_116-dipSPAdes-3.5.0-trimmed/spades//K77/final_contigs.fastg 1:09:03.908 3G / 9G INFO PathExtendIO (pe_io.hpp : 343) Writing contigs in FASTA to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.tetraurelia-Sample_116-dipSPAdes-3.5.0-trimmed/spades//K77/final_contigs.fasta 1:09:56.675 3G / 9G INFO PathExtendIO (pe_io.hpp : 339) Constructing FASTG file from paths 1:09:57.525 3G / 9G INFO PathExtendIO (pe_io.hpp : 342) Writing contigs in FASTG to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.tetraurelia-Sample_116-dipSPAdes-3.5.0-trimmed/spades//K77/path_extend/pe_before_traversal.fastg 1:09:57.525 3G / 9G INFO PathExtendIO (pe_io.hpp : 343) Writing contigs in FASTA to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.tetraurelia-Sample_116-dipSPAdes-3.5.0-trimmed/spades//K77/path_extend/pe_before_traversal.fasta 1:10:49.845 3G / 9G INFO General (path_extend_launch.hpp : 281) Traversing tandem repeats 1:10:51.353 3G / 9G INFO PathExtendIO (pe_io.hpp : 339) Constructing FASTG file from paths 1:10:52.180 3G / 9G INFO PathExtendIO (pe_io.hpp : 342) Writing contigs in FASTG to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.tetraurelia-Sample_116-dipSPAdes-3.5.0-trimmed/spades//K77/scaffolds.fastg 1:10:52.180 3G / 9G INFO PathExtendIO (pe_io.hpp : 343) Writing contigs in FASTA to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.tetraurelia-Sample_116-dipSPAdes-3.5.0-trimmed/spades//K77/scaffolds.fasta 1:11:45.866 3G / 9G INFO General (launch.hpp : 82) SPAdes finished 1:11:50.145 408M / 9G INFO General (main.cpp : 166) Assembling time: 1 hours 11 minutes 50 seconds ===== Assembling finished. * Corrected reads are in /N/dc2/projects/marinovg/2015-09-07-assemblies/P.tetraurelia-Sample_116-dipSPAdes-3.5.0-trimmed/spades/corrected/ * Assembled contigs are in /N/dc2/projects/marinovg/2015-09-07-assemblies/P.tetraurelia-Sample_116-dipSPAdes-3.5.0-trimmed/spades/contigs.fasta (contigs.fastg) * Assembled scaffolds are in /N/dc2/projects/marinovg/2015-09-07-assemblies/P.tetraurelia-Sample_116-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.tetraurelia-Sample_116-dipSPAdes-3.5.0-trimmed/spades/warnings.log SPAdes log can be found here: /N/dc2/projects/marinovg/2015-09-07-assemblies/P.tetraurelia-Sample_116-dipSPAdes-3.5.0-trimmed/spades/spades.log Thank you for using SPAdes!