Command line: --diploid --pe1-1 /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_Indo1-7I/reads.end1.paired.fastq.gz --pe1-2 /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_Indo1-7I/reads.end2.paired.fastq.gz -t 16 -o /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_Indo1-7I-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_Indo1-7I-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_Indo1-7I/reads.end1.paired.fastq.gz'] right reads: ['/N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_Indo1-7I/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_Indo1-7I-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_Indo1-7I-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_Indo1-7I-dipSPAdes-3.5.0-trimmed/spades/corrected/configs/config.info 0:00:00.000 4M / 4M INFO General (main.cpp : 82) Loading config from /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_Indo1-7I-dipSPAdes-3.5.0-trimmed/spades/corrected/configs/config.info 0:00:00.005 4M / 4M INFO General (memory_limit.hpp : 42) Memory limit set to 100 Gb 0:00:00.005 4M / 4M INFO General (main.cpp : 91) Trying to determine PHRED offset 0:00:00.062 4M / 4M INFO General (main.cpp : 97) Determined value is 33 0:00:00.062 4M / 4M INFO General (hammer_tools.cpp : 36) Hamming graph threshold tau=1, k=21, subkmer positions = [ 0 10 ] === ITERATION 0 begins === 0:00:00.075 4M / 4M INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:00:00.076 4M / 4M INFO K-mer Splitting (kmer_data.cpp : 127) Splitting kmer instances into 256 buckets. This might take a while. 0:00:00.076 4M / 4M INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:00:00.076 4M / 4M INFO K-mer Splitting (kmer_data.cpp : 145) Memory available for splitting buffers: 2.08325 Gb 0:00:00.076 4M / 4M INFO K-mer Splitting (kmer_data.cpp : 153) Using cell size of 262144 0:00:02.884 8G / 8G INFO K-mer Splitting (kmer_data.cpp : 167) Processing /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_Indo1-7I/reads.end1.paired.fastq.gz 0:02:49.802 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 176) Processed 3337731 reads 0:04:19.313 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 176) Processed 6444128 reads 0:05:15.044 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 176) Processed 9684581 reads 0:06:11.317 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 176) Processed 12955138 reads 0:06:23.855 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 176) Processed 13686306 reads 0:06:23.856 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 167) Processing /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_Indo1-7I/reads.end2.paired.fastq.gz 0:09:31.694 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 176) Processed 16987007 reads 0:10:30.267 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 176) Processed 20429350 reads 0:12:01.006 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 176) Processed 23899781 reads 0:16:15.564 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 176) Processed 27372612 reads 0:16:15.566 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 181) Processed 27372612 reads 0:16:16.740 64M / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:17:13.797 64M / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 314291596 kmers in total. 0:17:13.799 64M / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:17:28.301 64M / 9G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:18:05.732 192M / 10G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:18:19.619 192M / 10G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 108725290 bytes occupied (2.7675 bits per kmer). 0:18:19.620 192M / 10G INFO K-mer Counting (kmer_data.cpp : 266) Arranging kmers in hash map order 0:21:27.851 192M / 10G INFO K-mer Counting (kmer_data.cpp : 279) Done. Total swaps: 314291326 0:21:29.985 2G / 10G INFO General (main.cpp : 151) Clustering Hamming graph. 0:21:29.986 2G / 10G INFO Hamming Clustering (hamcluster.cpp : 115) Serializing sub-kmers. 0:21:29.986 2G / 10G INFO Hamming Clustering (hamcluster.cpp : 120) Serializing: [0, 10) 0:25:00.309 2G / 10G INFO Hamming Clustering (hamcluster.cpp : 120) Serializing: [10, 21) 0:28:49.640 2G / 10G INFO Hamming Clustering (hamcluster.cpp : 129) Splitting sub-kmers, pass 1. 0:33:26.825 2G / 10G INFO Hamming Clustering (hamcluster.cpp : 134) Splitting done. Processed 2 blocks. Produced 4893324 blocks. 0:33:26.825 2G / 10G INFO Hamming Clustering (hamcluster.cpp : 145) Merge sub-kmers, pass 1 0:49:53.055 2G / 10G INFO Hamming Clustering (hamcluster.cpp : 170) Merge done, total 1639251 new blocks generated. 0:49:54.908 2G / 10G INFO Hamming Clustering (hamcluster.cpp : 175) Spliting sub-kmers, pass 2. 1:13:28.063 2G / 10G INFO Hamming Clustering (hamcluster.cpp : 180) Splitting done. Processed 3278502 blocks. Produced 582182284 blocks. 1:13:28.063 2G / 10G INFO Hamming Clustering (hamcluster.cpp : 187) Merge sub-kmers, pass 2 1:27:40.888 2G / 10G INFO Hamming Clustering (hamcluster.cpp : 205) Merge done, saw 347039 big blocks out of 582182284 processed. 1:32:00.260 2G / 10G INFO General (main.cpp : 165) Clustering done. Total clusters: 133044502 1:32:00.260 2G / 10G INFO K-mer Counting (kmer_data.cpp : 284) Collecting K-mer information, this takes a while. 1:32:06.582 16G / 16G INFO K-mer Counting (kmer_data.cpp : 290) Processing /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_Indo1-7I/reads.end1.paired.fastq.gz 1:35:26.825 16G / 16G INFO K-mer Counting (kmer_data.cpp : 290) Processing /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_Indo1-7I/reads.end2.paired.fastq.gz 1:38:37.465 16G / 16G INFO K-mer Counting (kmer_data.cpp : 297) Collection done, postprocessing. 1:38:45.175 16G / 16G INFO K-mer Counting (kmer_data.cpp : 310) There are 314291596 kmers in total. Among them 166558762 (52.995%) are singletons. 1:38:45.176 16G / 16G INFO General (main.cpp : 203) Subclustering Hamming graph 1:42:47.438 16G / 16G INFO Hamming Subclustering (kmer_cluster.cpp : 626) Subclustering done. Total 118440 non-read kmers were generated. 1:42:47.438 16G / 16G INFO Hamming Subclustering (kmer_cluster.cpp : 627) Subclustering statistics: 1:42:47.438 16G / 16G INFO Hamming Subclustering (kmer_cluster.cpp : 628) Total singleton hamming clusters: 70876639. Among them 49525863 (69.8761%) are good 1:42:47.438 16G / 16G INFO Hamming Subclustering (kmer_cluster.cpp : 629) Total singleton subclusters: 6455982. Among them 6455894 (99.9986%) are good 1:42:47.439 16G / 16G INFO Hamming Subclustering (kmer_cluster.cpp : 630) Total non-singleton subcluster centers: 69112512. Among them 45828760 (66.3104%) are good 1:42:47.439 16G / 16G INFO Hamming Subclustering (kmer_cluster.cpp : 631) Average size of non-trivial subcluster: 3.50546 kmers 1:42:47.439 16G / 16G INFO Hamming Subclustering (kmer_cluster.cpp : 632) Average number of sub-clusters per non-singleton cluster: 1.21556 1:42:47.439 16G / 16G INFO Hamming Subclustering (kmer_cluster.cpp : 633) Total solid k-mers: 101810517 1:42:47.439 16G / 16G INFO Hamming Subclustering (kmer_cluster.cpp : 634) Substitution probabilities: [4,4]((0.896519,0.0238797,0.0263847,0.0532166),(0.0360321,0.926617,0.0135384,0.0238121),(0.0227879,0.0131292,0.928043,0.0360397),(0.0527092,0.0267719,0.0242702,0.896249)) 1:42:47.916 16G / 16G INFO General (main.cpp : 208) Finished clustering. 1:42:47.916 16G / 16G INFO General (main.cpp : 228) Starting solid k-mers expansion in 16 threads. 1:47:23.397 16G / 16G INFO General (main.cpp : 249) Solid k-mers iteration 0 produced 49214488 new k-mers. 1:51:57.441 16G / 16G INFO General (main.cpp : 249) Solid k-mers iteration 1 produced 1388701 new k-mers. 1:56:31.416 16G / 16G INFO General (main.cpp : 249) Solid k-mers iteration 2 produced 56694 new k-mers. 2:01:05.196 16G / 16G INFO General (main.cpp : 249) Solid k-mers iteration 3 produced 6122 new k-mers. 2:05:38.763 16G / 16G INFO General (main.cpp : 249) Solid k-mers iteration 4 produced 1168 new k-mers. 2:10:12.395 16G / 16G INFO General (main.cpp : 249) Solid k-mers iteration 5 produced 62 new k-mers. 2:14:46.039 16G / 16G INFO General (main.cpp : 249) Solid k-mers iteration 6 produced 121 new k-mers. 2:19:19.653 16G / 16G INFO General (main.cpp : 249) Solid k-mers iteration 7 produced 0 new k-mers. 2:19:19.653 16G / 16G INFO General (main.cpp : 253) Solid k-mers finalized 2:19:19.654 16G / 16G INFO General (hammer_tools.cpp : 210) Starting read correction in 16 threads. 2:19:19.654 16G / 16G INFO General (hammer_tools.cpp : 222) Correcting pair of reads: /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_Indo1-7I/reads.end1.paired.fastq.gz and /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_Indo1-7I/reads.end2.paired.fastq.gz 2:19:45.081 18G / 18G INFO General (hammer_tools.cpp : 166) Prepared batch 0 of 1600000 reads. 2:20:04.989 18G / 18G INFO General (hammer_tools.cpp : 175) Processed batch 0 2:20:30.841 18G / 18G INFO General (hammer_tools.cpp : 185) Written batch 0 2:20:54.600 18G / 18G INFO General (hammer_tools.cpp : 166) Prepared batch 1 of 1600000 reads. 2:21:14.304 18G / 18G INFO General (hammer_tools.cpp : 175) Processed batch 1 2:21:29.830 18G / 18G INFO General (hammer_tools.cpp : 185) Written batch 1 2:21:53.397 18G / 18G INFO General (hammer_tools.cpp : 166) Prepared batch 2 of 1600000 reads. 2:22:13.292 18G / 18G INFO General (hammer_tools.cpp : 175) Processed batch 2 2:22:39.580 18G / 18G INFO General (hammer_tools.cpp : 185) Written batch 2 2:23:03.165 18G / 18G INFO General (hammer_tools.cpp : 166) Prepared batch 3 of 1600000 reads. 2:23:23.115 18G / 18G INFO General (hammer_tools.cpp : 175) Processed batch 3 2:23:39.042 18G / 18G INFO General (hammer_tools.cpp : 185) Written batch 3 2:24:02.493 18G / 18G INFO General (hammer_tools.cpp : 166) Prepared batch 4 of 1600000 reads. 2:24:22.414 18G / 18G INFO General (hammer_tools.cpp : 175) Processed batch 4 2:24:47.674 18G / 18G INFO General (hammer_tools.cpp : 185) Written batch 4 2:25:11.041 18G / 18G INFO General (hammer_tools.cpp : 166) Prepared batch 5 of 1600000 reads. 2:25:30.846 18G / 18G INFO General (hammer_tools.cpp : 175) Processed batch 5 2:25:46.357 18G / 18G INFO General (hammer_tools.cpp : 185) Written batch 5 2:26:09.607 18G / 18G INFO General (hammer_tools.cpp : 166) Prepared batch 6 of 1600000 reads. 2:26:29.327 18G / 18G INFO General (hammer_tools.cpp : 175) Processed batch 6 2:26:44.836 18G / 18G INFO General (hammer_tools.cpp : 185) Written batch 6 2:27:07.774 18G / 18G INFO General (hammer_tools.cpp : 166) Prepared batch 7 of 1600000 reads. 2:27:27.781 18G / 18G INFO General (hammer_tools.cpp : 175) Processed batch 7 2:27:43.200 18G / 18G INFO General (hammer_tools.cpp : 185) Written batch 7 2:27:55.898 18G / 18G INFO General (hammer_tools.cpp : 166) Prepared batch 8 of 886306 reads. 2:28:07.014 18G / 18G INFO General (hammer_tools.cpp : 175) Processed batch 8 2:28:15.553 18G / 18G INFO General (hammer_tools.cpp : 185) Written batch 8 2:28:18.044 16G / 18G INFO General (hammer_tools.cpp : 269) Correction done. Changed 5680242 bases in 4284894 reads. 2:28:18.044 16G / 18G INFO General (hammer_tools.cpp : 270) Failed to correct 529149502 bases out of 4061663438. 2:28:18.122 2G / 18G INFO General (main.cpp : 286) Saving corrected dataset description to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_Indo1-7I-dipSPAdes-3.5.0-trimmed/spades/corrected/corrected.yaml 2:28:18.128 2G / 18G 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_Indo1-7I-dipSPAdes-3.5.0-trimmed/spades/corrected/corrected.yaml ===== Read error correction finished. ===== Assembling started. == Running assembler: K21 0:00:00.004 4M / 4M INFO General (memory_limit.hpp : 42) Memory limit set to 100 Gb 0:00:00.013 4M / 4M INFO General (main.cpp : 146) Assembling dataset (/N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_Indo1-7I-dipSPAdes-3.5.0-trimmed/spades/dataset.info) with K=21 0:00:00.016 4M / 4M INFO General (launch.hpp : 28) SPAdes started 0:00:00.016 4M / 4M INFO General (launch.hpp : 29) Starting from stage: construction 0:00:00.056 4M / 4M INFO StageManager (stage.cpp : 125) STAGE == Construction 0:00:00.060 4M / 4M INFO General (read_converter.hpp : 79) Converting reads to binary format (takes a while) 0:00:00.060 4M / 4M INFO General (read_converter.hpp : 81) Paired reads for library #0 0:00:01.186 80M / 80M INFO General (binary_converter.hpp : 138) 16384 reads processed 0:00:01.588 96M / 96M INFO General (binary_converter.hpp : 138) 32768 reads processed 0:00:02.388 124M / 124M INFO General (binary_converter.hpp : 138) 65536 reads processed 0:00:03.990 184M / 184M INFO General (binary_converter.hpp : 138) 131072 reads processed 0:00:07.201 300M / 300M INFO General (binary_converter.hpp : 138) 262144 reads processed 0:00:13.643 536M / 536M INFO General (binary_converter.hpp : 138) 524288 reads processed 0:00:29.234 900M / 900M INFO General (binary_converter.hpp : 138) 1048576 reads processed 0:00:57.854 900M / 900M INFO General (binary_converter.hpp : 138) 2097152 reads processed 0:01:55.243 904M / 904M INFO General (binary_converter.hpp : 138) 4194304 reads processed 0:03:57.620 904M / 904M INFO General (binary_converter.hpp : 138) 8388608 reads processed 0:06:19.823 556M / 908M INFO General (binary_converter.hpp : 158) 13489445 reads written 0:06:20.684 4M / 908M INFO General (read_converter.hpp : 91) Single reads for library #0 0:06:22.560 140M / 908M INFO General (binary_converter.hpp : 138) 16384 reads processed 0:06:22.799 144M / 908M INFO General (binary_converter.hpp : 138) 32768 reads processed 0:06:23.218 160M / 908M INFO General (binary_converter.hpp : 138) 65536 reads processed 0:06:24.029 188M / 908M INFO General (binary_converter.hpp : 138) 131072 reads processed 0:06:25.119 216M / 908M INFO General (binary_converter.hpp : 158) 196774 reads written 0:06:25.428 4M / 908M INFO General (graph_construction.hpp : 129) Constructing DeBruijn graph for k=21 0:06:25.432 4M / 908M INFO General (kmer_splitters.hpp : 172) Splitting kmer instances into 256 buckets. This might take a while. 0:06:25.432 4M / 908M INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:06:25.433 4M / 908M INFO General (kmer_splitters.hpp : 190) Memory available for splitting buffers: 2.08325 Gb 0:06:25.433 4M / 908M INFO General (kmer_splitters.hpp : 199) Using cell size of 262144 0:09:17.876 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 16726759 reads 0:10:05.109 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 33446211 reads 0:10:30.623 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 50158715 reads 0:10:37.718 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 54351328 reads 0:10:37.718 8G / 9G INFO General (kmer_splitters.hpp : 234) Adding contigs from previous K 0:10:37.719 8G / 9G INFO General (kmer_splitters.hpp : 245) Used 54351328 reads. Maximum read length 151 0:10:37.722 8G / 9G INFO General (kmer_splitters.hpp : 246) Average read length 149.417 0:10:39.955 64M / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:10:58.573 64M / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 127124399 kmers in total. 0:10:58.575 64M / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:11:04.712 64M / 9G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:11:04.712 64M / 9G INFO General (kmer_splitters.hpp : 379) Splitting kmer instances into 256 buckets. This might take a while. 0:11:04.713 64M / 9G INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:11:04.713 64M / 9G INFO General (kmer_splitters.hpp : 397) Memory available for splitting buffers: 2.08203 Gb 0:11:04.713 64M / 9G INFO General (kmer_splitters.hpp : 405) Using cell size of 262144 0:11:20.827 8G / 9G INFO General (kmer_splitters.hpp : 428) Processed 127124399 kmers 0:11:20.827 8G / 9G INFO General (kmer_splitters.hpp : 437) Used 127124399 kmers. 0:11:21.419 64M / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:11:25.160 64M / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 123322718 kmers in total. 0:11:25.160 64M / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:11:51.283 64M / 9G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:12:05.433 68M / 9G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:12:10.576 68M / 9G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 42661990 bytes occupied (2.7675 bits per kmer). 0:12:10.788 188M / 9G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 382) Building k-mer extensions from k+1-mers 0:12:23.262 188M / 9G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 386) Building k-mer extensions from k+1-mers finished. 0:12:23.274 188M / 9G INFO Early tip clipping (early_simplification.hpp : 236) Early tip clipping 0:18:50.957 184M / 9G INFO Early tip clipping (early_simplification.hpp : 239) 7058847 22-mers were removed by early tip clipper 0:18:50.958 184M / 9G INFO General (graph_construction.hpp : 145) Condensing graph 0:18:50.958 184M / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 337) Extracting unbranching paths 0:20:18.507 1G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 351) Extracting unbranching paths finished. 19965241 sequences extracted 0:20:28.761 1G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 311) Collecting perfect loops 0:21:06.812 1G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 326) Collecting perfect loops finished. 14 loops collected 0:21:20.910 3G / 9G INFO General (graph_construction.hpp : 150) Building index with from graph 0:21:20.946 3G / 9G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:21:20.960 3G / 9G INFO General (kmer_splitters.hpp : 289) Splitting kmer instances into 16 buckets. This might take a while. 0:21:20.960 3G / 9G INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:21:20.960 3G / 9G INFO General (kmer_splitters.hpp : 307) Memory available for splitting buffers: 32.0352 Gb 0:21:20.960 3G / 9G INFO General (kmer_splitters.hpp : 312) Using cell size of 4194304 0:24:17.215 4G / 9G INFO General (kmer_splitters.hpp : 325) Processed 11155314 edges 0:25:42.308 4G / 9G INFO General (kmer_splitters.hpp : 325) Processed 19965255 edges 0:25:42.308 4G / 9G INFO General (kmer_splitters.hpp : 330) Used 19965255 sequences. 0:25:42.360 3G / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:26:27.702 3G / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 120065552 kmers in total. 0:26:27.702 3G / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:26:33.170 3G / 9G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:29:11.779 3G / 9G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:29:37.303 3G / 9G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 41535229 bytes occupied (2.7675 bits per kmer). 0:29:39.428 6G / 9G INFO General (edge_index_builders.hpp : 21) Collecting k-mer coverage information from graph, this takes a while. 0:33:21.197 6G / 9G INFO General (graph_construction.hpp : 182) Filling coverage index 0:33:21.197 6G / 9G INFO General (edge_index_builders.hpp : 99) Collecting k-mer coverage information from reads, this takes a while. 0:37:23.943 6G / 9G INFO General (graph_construction.hpp : 184) Filling coverage and flanking coverage from index 0:37:53.177 6G / 9G INFO General (construction.cpp : 33) Figured out: read length = 151 0:37:53.217 6G / 9G INFO StageManager (stage.cpp : 125) STAGE == EC Threshold Finding 0:38:02.828 6G / 9G INFO General (kmer_coverage_model.cpp : 178) Kmer coverage valley at: 17 0:38:02.857 6G / 9G INFO General (kmer_coverage_model.cpp : 198) K-mer histogram maximum: 50 0:38:02.857 6G / 9G INFO General (kmer_coverage_model.cpp : 234) Estimated median coverage: 50. Coverage mad: 11.8608 0:38:02.858 6G / 9G INFO General (kmer_coverage_model.cpp : 261) Fitting coverage model 0:38:03.339 6G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 2 0:38:03.832 6G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 4 0:38:05.385 6G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 8 0:38:09.023 6G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 16 0:38:15.124 6G / 9G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 49.4842. Fitted coverage std. dev: 11.1075 0:38:15.170 6G / 9G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 0.459347 0:38:15.170 6G / 9G INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 31 0:38:15.170 6G / 9G INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 31 0:38:15.170 6G / 9G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 61006318 0:38:15.196 6G / 9G INFO General (genomic_info_filler.cpp : 103) Mean coverage was calculated as 49.4842 0:38:15.197 6G / 9G INFO General (genomic_info_filler.cpp : 117) EC coverage threshold value was calculated as 31 0:38:15.197 6G / 9G INFO General (genomic_info_filler.cpp : 118) Trusted kmer low bound: 0 0:38:15.197 6G / 9G INFO StageManager (stage.cpp : 125) STAGE == Simplification 0:38:15.776 3G / 9G INFO General (graph_simplification.hpp : 911) Graph simplification started 0:38:15.796 3G / 9G INFO General (graph_simplification.hpp : 924) Fast simplification mode enabled 0:38:15.805 3G / 9G INFO General (graph_simplification.hpp : 771) PROCEDURE == Presimplification 0:38:15.814 3G / 9G INFO General (graph_simplification.hpp : 211) Removing short low covered self-conjugate connections 0:38:17.184 3G / 9G INFO General (graph_simplification.hpp : 403) Removing isolated edges 0:38:17.185 3G / 9G INFO General (graph_simplification.hpp : 404) All edges shorter than 151 will be removed 0:38:17.185 3G / 9G INFO General (graph_simplification.hpp : 405) Also edges shorter than 0 and coverage smaller than 0 will be removed 0:38:18.975 3G / 9G INFO General (graph_simplification.hpp : 687) Non parallel mode 0:39:16.860 4G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:41:39.448 4G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:45:48.572 4G / 9G INFO General (graph_simplification.hpp : 644) Using permanent iterators 0:45:48.595 4G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 1 0:45:59.385 4G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:46:47.095 4G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:47:23.784 3G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 2 0:47:23.784 3G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:47:24.458 3G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:47:37.554 3G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 3 0:47:37.554 3G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:47:37.826 3G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:47:43.049 3G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 4 0:47:43.049 3G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:47:43.160 3G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:47:46.453 3G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 5 0:47:46.453 3G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:47:46.526 3G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:47:49.415 3G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 6 0:47:49.416 3G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:47:49.480 3G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:47:52.307 3G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 7 0:47:52.307 3G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:47:52.367 3G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:47:55.195 3G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 8 0:47:55.195 3G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:47:55.252 3G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:47:57.635 3G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 9 0:47:57.636 3G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:47:57.687 3G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:47:59.566 3G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 10 0:47:59.566 3G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:47:59.609 3G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:48:01.505 3G / 9G INFO General (graph_simplification.hpp : 796) PROCEDURE == Post simplification 0:48:01.506 3G / 9G INFO General (graph_simplification.hpp : 644) Using permanent iterators 0:48:01.506 3G / 9G INFO General (graph_simplification.hpp : 806) Iteration 0 0:48:01.506 3G / 9G INFO General (graph_simplification.hpp : 247) Removal of relatively low covered connections disabled 0:48:04.997 3G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:48:13.131 3G / 9G INFO General (graph_simplification.hpp : 806) Iteration 1 0:48:13.131 3G / 9G INFO General (graph_simplification.hpp : 247) Removal of relatively low covered connections disabled 0:48:13.131 3G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:48:16.035 3G / 9G INFO StageManager (stage.cpp : 125) STAGE == Simplification Cleanup 0:48:16.039 3G / 9G INFO General (graph_simplification.hpp : 403) Removing isolated edges 0:48:16.040 3G / 9G INFO General (graph_simplification.hpp : 404) All edges shorter than 151 will be removed 0:48:16.040 3G / 9G INFO General (graph_simplification.hpp : 405) Also edges shorter than 0 and coverage smaller than 2 will be removed 0:48:16.302 3G / 9G INFO General (simplification.cpp : 56) Removing all the edges having coverage 0 and less 0:48:22.916 3G / 9G INFO General (simplification.cpp : 68) Counting average coverage 0:48:23.678 3G / 9G INFO General (simplification.cpp : 71) Average coverage = 51.6796 0:48:23.678 3G / 9G INFO StageManager (stage.cpp : 125) STAGE == Contig Output 0:48:23.678 3G / 9G INFO General (contig_output.hpp : 283) Outputting contigs to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_Indo1-7I-dipSPAdes-3.5.0-trimmed/spades//K21/simplified_contigs.fasta 0:49:20.120 3G / 9G INFO General (contig_output.hpp : 283) Outputting contigs to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_Indo1-7I-dipSPAdes-3.5.0-trimmed/spades//K21/before_rr.fasta 0:51:43.391 3G / 9G INFO General (contig_output.hpp : 283) Outputting contigs to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_Indo1-7I-dipSPAdes-3.5.0-trimmed/spades//K21/final_contigs.fasta 0:53:54.349 3G / 9G INFO General (launch.hpp : 82) SPAdes finished 0:54:04.732 64M / 9G INFO General (main.cpp : 166) Assembling time: 0 hours 54 minutes 4 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_Indo1-7I-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 0:00:00.008 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 0:01:41.953 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 9216648 reads 0:03:12.956 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 18450493 reads 0:03:28.106 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 27673554 reads 0:03:43.380 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 36890996 reads 0:03:58.441 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 46114626 reads 0:04:12.008 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 54351328 reads 0:04:12.008 8G / 9G INFO General (kmer_splitters.hpp : 234) Adding contigs from previous K 0:04:32.992 8G / 9G INFO General (kmer_splitters.hpp : 245) Used 54351328 reads. Maximum read length 151 0:04:32.993 8G / 9G INFO General (kmer_splitters.hpp : 246) Average read length 149.417 0:04:35.274 64M / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:04:59.976 64M / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 151683323 kmers in total. 0:04:59.976 64M / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:05:14.522 64M / 9G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:05:14.522 64M / 9G INFO General (kmer_splitters.hpp : 379) Splitting kmer instances into 256 buckets. This might take a while. 0:05:14.523 64M / 9G INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:05:14.523 64M / 9G INFO General (kmer_splitters.hpp : 397) Memory available for splitting buffers: 2.08203 Gb 0:05:14.523 64M / 9G INFO General (kmer_splitters.hpp : 405) Using cell size of 131072 0:05:38.441 8G / 9G INFO General (kmer_splitters.hpp : 428) Processed 151683323 kmers 0:05:38.441 8G / 9G INFO General (kmer_splitters.hpp : 437) Used 151683323 kmers. 0:05:39.328 64M / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:05:47.858 64M / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 150132107 kmers in total. 0:05:47.858 64M / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:06:49.345 64M / 9G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:07:08.814 68M / 9G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:07:41.121 68M / 9G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 51936365 bytes occupied (2.7675 bits per kmer). 0:07:41.378 212M / 9G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 382) Building k-mer extensions from k+1-mers 0:07:58.954 212M / 9G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 386) Building k-mer extensions from k+1-mers finished. 0:07:58.965 212M / 9G INFO Early tip clipping (early_simplification.hpp : 236) Early tip clipping 0:16:33.460 212M / 9G INFO Early tip clipping (early_simplification.hpp : 239) 28233140 34-mers were removed by early tip clipper 0:16:33.460 212M / 9G INFO General (graph_construction.hpp : 145) Condensing graph 0:16:33.460 212M / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 337) Extracting unbranching paths 0:18:26.749 1G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 351) Extracting unbranching paths finished. 9410748 sequences extracted 0:18:38.637 1G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 311) Collecting perfect loops 0:19:30.116 1G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 326) Collecting perfect loops finished. 24 loops collected 0:19:37.001 2G / 9G INFO General (graph_construction.hpp : 150) Building index with from graph 0:19:37.006 2G / 9G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:19:37.007 2G / 9G INFO General (kmer_splitters.hpp : 289) Splitting kmer instances into 16 buckets. This might take a while. 0:19:37.007 2G / 9G INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:19:37.007 2G / 9G INFO General (kmer_splitters.hpp : 307) Memory available for splitting buffers: 32.6549 Gb 0:19:37.007 2G / 9G INFO General (kmer_splitters.hpp : 312) Using cell size of 2097152 0:21:21.583 2G / 9G INFO General (kmer_splitters.hpp : 325) Processed 2558916 edges 0:23:03.745 2G / 9G INFO General (kmer_splitters.hpp : 325) Processed 5117313 edges 0:23:44.041 2G / 9G INFO General (kmer_splitters.hpp : 325) Processed 7672286 edges 0:23:49.659 2G / 9G INFO General (kmer_splitters.hpp : 325) Processed 9410772 edges 0:23:49.660 2G / 9G INFO General (kmer_splitters.hpp : 330) Used 9410772 sequences. 0:23:49.733 2G / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:24:27.673 2G / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 123450183 kmers in total. 0:24:27.673 2G / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:24:37.974 2G / 9G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:27:21.618 2G / 9G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:27:31.994 2G / 9G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 42706087 bytes occupied (2.7675 bits per kmer). 0:27:34.151 4G / 9G INFO General (edge_index_builders.hpp : 21) Collecting k-mer coverage information from graph, this takes a while. 0:31:25.125 4G / 9G INFO General (graph_construction.hpp : 182) Filling coverage index 0:31:25.126 4G / 9G INFO General (edge_index_builders.hpp : 99) Collecting k-mer coverage information from reads, this takes a while. 0:35:16.074 4G / 9G INFO General (graph_construction.hpp : 184) Filling coverage and flanking coverage from index 0:35:46.225 4G / 9G INFO General (construction.cpp : 33) Figured out: read length = 151 0:35:46.243 4G / 9G INFO StageManager (stage.cpp : 125) STAGE == EC Threshold Finding 0:35:56.190 4G / 9G INFO General (kmer_coverage_model.cpp : 178) Kmer coverage valley at: 13 0:35:56.190 4G / 9G INFO General (kmer_coverage_model.cpp : 198) K-mer histogram maximum: 45 0:35:56.190 4G / 9G INFO General (kmer_coverage_model.cpp : 234) Estimated median coverage: 45. Coverage mad: 11.8608 0:35:56.190 4G / 9G INFO General (kmer_coverage_model.cpp : 261) Fitting coverage model 0:35:56.356 4G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 2 0:35:56.786 4G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 4 0:35:58.182 4G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 8 0:36:01.529 4G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 16 0:36:07.381 4G / 9G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 44.0604. Fitted coverage std. dev: 10.95 0:36:07.385 4G / 9G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 0.473474 0:36:07.385 4G / 9G INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 27 0:36:07.385 4G / 9G INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 27 0:36:07.385 4G / 9G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 61714132 0:36:07.386 4G / 9G INFO General (genomic_info_filler.cpp : 103) Mean coverage was calculated as 44.0604 0:36:07.386 4G / 9G INFO General (genomic_info_filler.cpp : 117) EC coverage threshold value was calculated as 27 0:36:07.386 4G / 9G INFO General (genomic_info_filler.cpp : 118) Trusted kmer low bound: 0 0:36:07.386 4G / 9G INFO StageManager (stage.cpp : 125) STAGE == Simplification 0:36:07.626 1G / 9G INFO General (graph_simplification.hpp : 911) Graph simplification started 0:36:07.626 1G / 9G INFO General (graph_simplification.hpp : 924) Fast simplification mode enabled 0:36:07.626 1G / 9G INFO General (graph_simplification.hpp : 771) PROCEDURE == Presimplification 0:36:07.626 1G / 9G INFO General (graph_simplification.hpp : 211) Removing short low covered self-conjugate connections 0:36:08.196 1G / 9G INFO General (graph_simplification.hpp : 403) Removing isolated edges 0:36:08.197 1G / 9G INFO General (graph_simplification.hpp : 404) All edges shorter than 151 will be removed 0:36:08.197 1G / 9G INFO General (graph_simplification.hpp : 405) Also edges shorter than 0 and coverage smaller than 0 will be removed 0:36:09.743 1G / 9G INFO General (graph_simplification.hpp : 687) Non parallel mode 0:36:36.830 2G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:37:41.768 2G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:39:45.207 1G / 9G INFO General (graph_simplification.hpp : 644) Using permanent iterators 0:39:45.208 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 1 0:39:48.440 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:40:02.012 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:40:18.925 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 2 0:40:18.926 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:40:19.078 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:40:24.113 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 3 0:40:24.114 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:40:24.179 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:40:26.418 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 4 0:40:26.418 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:40:26.449 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:40:27.883 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 5 0:40:27.883 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:40:27.902 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:40:29.229 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 6 0:40:29.229 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:40:29.243 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:40:30.891 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 7 0:40:30.891 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:40:30.900 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:40:32.542 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 8 0:40:32.542 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:40:32.553 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:40:34.044 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 9 0:40:34.044 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:40:34.053 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:40:35.104 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 10 0:40:35.104 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:40:35.113 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:40:35.656 1G / 9G INFO General (graph_simplification.hpp : 796) PROCEDURE == Post simplification 0:40:35.657 1G / 9G INFO General (graph_simplification.hpp : 644) Using permanent iterators 0:40:35.657 1G / 9G INFO General (graph_simplification.hpp : 806) Iteration 0 0:40:35.657 1G / 9G INFO General (graph_simplification.hpp : 247) Removal of relatively low covered connections disabled 0:40:36.035 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:40:36.888 1G / 9G INFO General (graph_simplification.hpp : 806) Iteration 1 0:40:36.888 1G / 9G INFO General (graph_simplification.hpp : 247) Removal of relatively low covered connections disabled 0:40:36.888 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:40:37.231 1G / 9G INFO StageManager (stage.cpp : 125) STAGE == Simplification Cleanup 0:40:37.233 1G / 9G INFO General (graph_simplification.hpp : 403) Removing isolated edges 0:40:37.233 1G / 9G INFO General (graph_simplification.hpp : 404) All edges shorter than 151 will be removed 0:40:37.233 1G / 9G INFO General (graph_simplification.hpp : 405) Also edges shorter than 0 and coverage smaller than 2 will be removed 0:40:37.268 1G / 9G INFO General (simplification.cpp : 56) Removing all the edges having coverage 0 and less 0:40:37.959 1G / 9G INFO General (simplification.cpp : 68) Counting average coverage 0:40:38.078 1G / 9G INFO General (simplification.cpp : 71) Average coverage = 43.4221 0:40:38.078 1G / 9G INFO StageManager (stage.cpp : 125) STAGE == Contig Output 0:40:38.078 1G / 9G INFO General (contig_output.hpp : 283) Outputting contigs to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_Indo1-7I-dipSPAdes-3.5.0-trimmed/spades//K33/simplified_contigs.fasta 0:40:56.187 1G / 9G INFO General (contig_output.hpp : 283) Outputting contigs to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_Indo1-7I-dipSPAdes-3.5.0-trimmed/spades//K33/before_rr.fasta 0:41:48.709 1G / 9G INFO General (contig_output.hpp : 283) Outputting contigs to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_Indo1-7I-dipSPAdes-3.5.0-trimmed/spades//K33/final_contigs.fasta 0:42:41.445 1G / 9G INFO General (launch.hpp : 82) SPAdes finished 0:42:44.438 64M / 9G INFO General (main.cpp : 166) Assembling time: 0 hours 42 minutes 44 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_Indo1-7I-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 0:00:00.029 4M / 4M INFO General (graph_construction.hpp : 129) Constructing DeBruijn graph for k=55 0:00:00.032 4M / 4M INFO General (kmer_splitters.hpp : 172) Splitting kmer instances into 256 buckets. This might take a while. 0:00:00.032 4M / 4M INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:00:00.032 4M / 4M INFO General (kmer_splitters.hpp : 190) Memory available for splitting buffers: 2.08325 Gb 0:00:00.033 4M / 4M INFO General (kmer_splitters.hpp : 199) Using cell size of 131072 0:03:13.726 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 11360316 reads 0:03:36.478 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 22736020 reads 0:03:52.039 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 34098492 reads 0:04:17.932 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 45465804 reads 0:05:11.688 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 54351328 reads 0:05:11.690 8G / 9G INFO General (kmer_splitters.hpp : 234) Adding contigs from previous K 0:05:46.134 8G / 9G INFO General (kmer_splitters.hpp : 245) Used 54351328 reads. Maximum read length 151 0:05:46.134 8G / 9G INFO General (kmer_splitters.hpp : 246) Average read length 149.417 0:05:48.420 64M / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:07:41.178 64M / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 173967006 kmers in total. 0:07:41.178 64M / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:08:37.378 64M / 9G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:08:37.378 64M / 9G INFO General (kmer_splitters.hpp : 379) Splitting kmer instances into 256 buckets. This might take a while. 0:08:37.378 64M / 9G INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:08:37.379 64M / 9G INFO General (kmer_splitters.hpp : 397) Memory available for splitting buffers: 2.08203 Gb 0:08:37.379 64M / 9G INFO General (kmer_splitters.hpp : 405) Using cell size of 131072 0:09:49.150 8G / 9G INFO General (kmer_splitters.hpp : 428) Processed 173967006 kmers 0:09:49.150 8G / 9G INFO General (kmer_splitters.hpp : 437) Used 173967006 kmers. 0:09:50.175 64M / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:11:01.417 64M / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 173384790 kmers in total. 0:11:01.417 64M / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:11:16.903 64M / 9G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:11:38.579 68M / 9G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:11:54.227 68M / 9G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 59980333 bytes occupied (2.7675 bits per kmer). 0:11:54.496 236M / 9G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 382) Building k-mer extensions from k+1-mers 0:12:16.826 236M / 9G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 386) Building k-mer extensions from k+1-mers finished. 0:12:16.836 236M / 9G INFO General (graph_construction.hpp : 145) Condensing graph 0:12:16.836 236M / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 337) Extracting unbranching paths 0:14:07.730 1G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 351) Extracting unbranching paths finished. 12549681 sequences extracted 0:14:24.086 1G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 311) Collecting perfect loops 0:15:22.560 1G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 326) Collecting perfect loops finished. 4 loops collected 0:15:34.187 3G / 9G INFO General (graph_construction.hpp : 150) Building index with from graph 0:15:34.192 3G / 9G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:15:34.192 3G / 9G INFO General (kmer_splitters.hpp : 289) Splitting kmer instances into 16 buckets. This might take a while. 0:15:34.192 3G / 9G INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:15:34.192 3G / 9G INFO General (kmer_splitters.hpp : 307) Memory available for splitting buffers: 32.3268 Gb 0:15:34.192 3G / 9G INFO General (kmer_splitters.hpp : 312) Using cell size of 2097152 0:15:42.860 3G / 9G INFO General (kmer_splitters.hpp : 325) Processed 2417947 edges 0:15:51.280 3G / 9G INFO General (kmer_splitters.hpp : 325) Processed 4838690 edges 0:15:59.782 3G / 9G INFO General (kmer_splitters.hpp : 325) Processed 7259972 edges 0:16:08.245 3G / 9G INFO General (kmer_splitters.hpp : 325) Processed 9681925 edges 0:16:16.651 3G / 9G INFO General (kmer_splitters.hpp : 325) Processed 12103992 edges 0:16:18.275 3G / 9G INFO General (kmer_splitters.hpp : 325) Processed 12549685 edges 0:16:18.275 3G / 9G INFO General (kmer_splitters.hpp : 330) Used 12549685 sequences. 0:16:18.347 3G / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:17:11.293 3G / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 173967006 kmers in total. 0:17:11.294 3G / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:17:25.582 3G / 9G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:21:47.431 3G / 9G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:22:03.153 3G / 9G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 60181752 bytes occupied (2.7675 bits per kmer). 0:22:06.251 6G / 9G INFO General (edge_index_builders.hpp : 21) Collecting k-mer coverage information from graph, this takes a while. 0:27:47.431 6G / 9G INFO General (graph_construction.hpp : 182) Filling coverage index 0:27:47.431 6G / 9G INFO General (edge_index_builders.hpp : 99) Collecting k-mer coverage information from reads, this takes a while. 0:31:15.988 6G / 9G INFO General (graph_construction.hpp : 184) Filling coverage and flanking coverage from index 0:32:01.371 6G / 9G INFO General (construction.cpp : 33) Figured out: read length = 151 0:32:01.388 6G / 9G INFO StageManager (stage.cpp : 125) STAGE == EC Threshold Finding 0:32:14.589 6G / 9G INFO General (kmer_coverage_model.cpp : 178) Kmer coverage valley at: 10 0:32:14.589 6G / 9G INFO General (kmer_coverage_model.cpp : 198) K-mer histogram maximum: 35 0:32:14.589 6G / 9G INFO General (kmer_coverage_model.cpp : 234) Estimated median coverage: 36. Coverage mad: 10.3782 0:32:14.590 6G / 9G INFO General (kmer_coverage_model.cpp : 261) Fitting coverage model 0:32:14.713 6G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 2 0:32:15.048 6G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 4 0:32:16.190 6G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 8 0:32:19.080 6G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 16 0:32:23.848 6G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 32 0:32:24.438 6G / 9G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 34.8972. Fitted coverage std. dev: 9.96979 0:32:24.441 6G / 9G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 0.396703 0:32:24.441 6G / 9G INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 21 0:32:24.441 6G / 9G INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 21 0:32:24.441 6G / 9G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 61642000 0:32:24.441 6G / 9G INFO General (genomic_info_filler.cpp : 103) Mean coverage was calculated as 34.8972 0:32:24.442 6G / 9G INFO General (genomic_info_filler.cpp : 117) EC coverage threshold value was calculated as 21 0:32:24.442 6G / 9G INFO General (genomic_info_filler.cpp : 118) Trusted kmer low bound: 0 0:32:24.442 6G / 9G INFO StageManager (stage.cpp : 125) STAGE == Gap Closer 0:32:24.509 6G / 9G INFO General (gap_closer.cpp : 157) Preparing shift maps 0:32:35.745 7G / 9G INFO General (gap_closer.cpp : 117) Processing paired reads (takes a while) 0:33:18.739 7G / 9G INFO General (gap_closer.cpp : 136) Used 26978890 paired reads 0:33:18.741 7G / 9G INFO General (gap_closer.cpp : 138) Merging paired indices 0:33:23.263 6G / 9G INFO GapCloser (gap_closer.cpp : 395) Closing short gaps 0:33:55.543 6G / 9G INFO GapCloser (gap_closer.cpp : 424) Closing short gaps complete: filled 724 gaps after checking 10214 candidates 0:33:58.811 6G / 9G INFO StageManager (stage.cpp : 125) STAGE == Simplification 0:33:59.118 2G / 9G INFO General (graph_simplification.hpp : 911) Graph simplification started 0:33:59.118 2G / 9G INFO General (graph_simplification.hpp : 924) Fast simplification mode enabled 0:33:59.118 2G / 9G INFO General (graph_simplification.hpp : 771) PROCEDURE == Presimplification 0:33:59.118 2G / 9G INFO General (graph_simplification.hpp : 211) Removing short low covered self-conjugate connections 0:34:00.088 2G / 9G INFO General (graph_simplification.hpp : 403) Removing isolated edges 0:34:00.090 2G / 9G INFO General (graph_simplification.hpp : 404) All edges shorter than 151 will be removed 0:34:00.092 2G / 9G INFO General (graph_simplification.hpp : 405) Also edges shorter than 0 and coverage smaller than 0 will be removed 0:34:03.005 2G / 9G INFO General (graph_simplification.hpp : 687) Non parallel mode 0:34:40.075 3G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:36:32.260 3G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:37:31.498 2G / 9G INFO General (graph_simplification.hpp : 644) Using permanent iterators 0:37:31.498 2G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 1 0:37:32.813 2G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:37:38.298 2G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:37:41.787 2G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 2 0:37:41.787 2G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:37:41.837 2G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:37:44.927 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 3 0:37:44.927 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:37:44.971 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:37:46.432 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 4 0:37:46.432 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:37:46.449 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:37:47.590 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 5 0:37:47.591 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:37:47.604 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:37:48.886 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 6 0:37:48.886 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:37:48.896 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:37:50.564 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 7 0:37:50.564 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:37:50.573 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:37:52.505 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 8 0:37:52.505 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:37:52.513 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:37:54.383 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 9 0:37:54.383 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:37:54.387 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:37:55.976 888M / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 10 0:37:55.976 888M / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:37:55.980 888M / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:37:56.951 784M / 9G INFO General (graph_simplification.hpp : 796) PROCEDURE == Post simplification 0:37:56.951 784M / 9G INFO General (graph_simplification.hpp : 644) Using permanent iterators 0:37:56.951 784M / 9G INFO General (graph_simplification.hpp : 806) Iteration 0 0:37:56.951 784M / 9G INFO General (graph_simplification.hpp : 247) Removal of relatively low covered connections disabled 0:37:57.076 784M / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:37:57.320 784M / 9G INFO General (graph_simplification.hpp : 806) Iteration 1 0:37:57.321 784M / 9G INFO General (graph_simplification.hpp : 247) Removal of relatively low covered connections disabled 0:37:57.321 784M / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:37:57.495 744M / 9G INFO StageManager (stage.cpp : 125) STAGE == Gap Closer 0:37:57.495 744M / 9G INFO General (graph_pack.hpp : 84) Index refill 0:37:57.498 744M / 9G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:37:57.498 744M / 9G INFO General (kmer_splitters.hpp : 289) Splitting kmer instances into 16 buckets. This might take a while. 0:37:57.498 744M / 9G INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:37:57.498 744M / 9G INFO General (kmer_splitters.hpp : 307) Memory available for splitting buffers: 33.0911 Gb 0:37:57.498 744M / 9G INFO General (kmer_splitters.hpp : 312) Using cell size of 2097152 0:40:45.967 1G / 9G INFO General (kmer_splitters.hpp : 325) Processed 33012 edges 0:41:50.837 1G / 9G INFO General (kmer_splitters.hpp : 325) Processed 65251 edges 0:42:11.178 1G / 9G INFO General (kmer_splitters.hpp : 325) Processed 68750 edges 0:42:11.178 1G / 9G INFO General (kmer_splitters.hpp : 330) Used 68750 sequences. 0:42:11.197 740M / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:42:53.177 740M / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 71103084 kmers in total. 0:42:53.178 740M / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:42:59.263 740M / 9G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:44:30.047 764M / 9G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:44:56.179 764M / 9G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 24597255 bytes occupied (2.7675 bits per kmer). 0:44:57.355 2G / 9G INFO General (edge_index_builders.hpp : 21) Collecting k-mer coverage information from graph, this takes a while. 0:46:49.931 2G / 9G INFO General (gap_closer.cpp : 157) Preparing shift maps 0:46:50.007 2G / 9G INFO General (gap_closer.cpp : 117) Processing paired reads (takes a while) 0:47:34.823 2G / 9G INFO General (gap_closer.cpp : 136) Used 26978890 paired reads 0:47:34.824 2G / 9G INFO General (gap_closer.cpp : 138) Merging paired indices 0:47:34.926 2G / 9G INFO GapCloser (gap_closer.cpp : 395) Closing short gaps 0:47:35.185 2G / 9G INFO GapCloser (gap_closer.cpp : 424) Closing short gaps complete: filled 66 gaps after checking 3028 candidates 0:47:35.999 2G / 9G INFO StageManager (stage.cpp : 125) STAGE == Simplification Cleanup 0:47:36.003 2G / 9G INFO General (graph_simplification.hpp : 403) Removing isolated edges 0:47:36.003 2G / 9G INFO General (graph_simplification.hpp : 404) All edges shorter than 151 will be removed 0:47:36.003 2G / 9G INFO General (graph_simplification.hpp : 405) Also edges shorter than 0 and coverage smaller than 2 will be removed 0:47:36.251 2G / 9G INFO General (simplification.cpp : 56) Removing all the edges having coverage 0 and less 0:47:36.462 2G / 9G INFO General (simplification.cpp : 68) Counting average coverage 0:47:36.497 2G / 9G INFO General (simplification.cpp : 71) Average coverage = 34.1605 0:47:36.497 2G / 9G INFO StageManager (stage.cpp : 125) STAGE == Contig Output 0:47:36.497 2G / 9G INFO General (contig_output.hpp : 283) Outputting contigs to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_Indo1-7I-dipSPAdes-3.5.0-trimmed/spades//K55/simplified_contigs.fasta 0:47:51.753 2G / 9G INFO General (contig_output.hpp : 283) Outputting contigs to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_Indo1-7I-dipSPAdes-3.5.0-trimmed/spades//K55/before_rr.fasta 0:48:36.463 2G / 9G INFO General (contig_output.hpp : 283) Outputting contigs to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_Indo1-7I-dipSPAdes-3.5.0-trimmed/spades//K55/final_contigs.fasta 0:49:21.196 2G / 9G INFO General (launch.hpp : 82) SPAdes finished 0:49:23.940 68M / 9G INFO General (main.cpp : 166) Assembling time: 0 hours 49 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_Indo1-7I-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 0:00:00.003 4M / 4M INFO General (construction.cpp : 44) Contigs from previous K will be used 0:00:00.007 4M / 4M INFO General (read_converter.hpp : 49) Binary reads detected 0:00:00.027 4M / 4M INFO General (graph_construction.hpp : 129) Constructing DeBruijn graph for k=77 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 87381 0:02:45.865 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 9852837 reads 0:05:46.596 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 19724502 reads 0:05:59.629 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 29581753 reads 0:14:43.481 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 39447094 reads 0:16:39.750 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 49285856 reads 0:18:04.961 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 54351328 reads 0:18:04.961 8G / 9G INFO General (kmer_splitters.hpp : 234) Adding contigs from previous K 0:23:03.881 8G / 9G INFO General (kmer_splitters.hpp : 245) Used 54351328 reads. Maximum read length 151 0:23:03.881 8G / 9G INFO General (kmer_splitters.hpp : 246) Average read length 149.417 0:23:06.156 64M / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:23:56.767 64M / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 177568963 kmers in total. 0:23:56.767 64M / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:24:24.467 64M / 9G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:24:24.467 64M / 9G INFO General (kmer_splitters.hpp : 379) Splitting kmer instances into 256 buckets. This might take a while. 0:24:24.468 64M / 9G INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:24:24.468 64M / 9G INFO General (kmer_splitters.hpp : 397) Memory available for splitting buffers: 2.08203 Gb 0:24:24.468 64M / 9G INFO General (kmer_splitters.hpp : 405) Using cell size of 87381 0:28:29.749 8G / 9G INFO General (kmer_splitters.hpp : 428) Processed 177568963 kmers 0:28:29.750 8G / 9G INFO General (kmer_splitters.hpp : 437) Used 177568963 kmers. 0:28:31.404 64M / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:29:02.899 64M / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 177754123 kmers in total. 0:29:02.899 64M / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:29:44.937 64M / 9G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:30:12.750 68M / 9G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:30:56.753 68M / 9G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 61491852 bytes occupied (2.7675 bits per kmer). 0:30:57.065 240M / 9G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 382) Building k-mer extensions from k+1-mers 0:31:25.644 240M / 9G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 386) Building k-mer extensions from k+1-mers finished. 0:31:25.655 240M / 9G INFO General (graph_construction.hpp : 145) Condensing graph 0:31:25.655 240M / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 337) Extracting unbranching paths 0:33:44.206 1G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 351) Extracting unbranching paths finished. 10770295 sequences extracted 0:34:03.564 1G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 311) Collecting perfect loops 0:35:13.500 1G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 326) Collecting perfect loops finished. 12 loops collected 0:35:24.733 2G / 9G INFO General (graph_construction.hpp : 150) Building index with from graph 0:35:24.738 2G / 9G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:35:24.739 2G / 9G INFO General (kmer_splitters.hpp : 289) Splitting kmer instances into 16 buckets. This might take a while. 0:35:24.739 2G / 9G INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:35:24.739 2G / 9G INFO General (kmer_splitters.hpp : 307) Memory available for splitting buffers: 32.3958 Gb 0:35:24.739 2G / 9G INFO General (kmer_splitters.hpp : 312) Using cell size of 1398101 0:36:19.435 3G / 9G INFO General (kmer_splitters.hpp : 325) Processed 1356664 edges 0:37:10.713 3G / 9G INFO General (kmer_splitters.hpp : 325) Processed 2713118 edges 0:37:48.360 3G / 9G INFO General (kmer_splitters.hpp : 325) Processed 4068690 edges 0:39:01.953 3G / 9G INFO General (kmer_splitters.hpp : 325) Processed 5424549 edges 0:39:59.996 3G / 9G INFO General (kmer_splitters.hpp : 325) Processed 6783061 edges 0:40:06.493 3G / 9G INFO General (kmer_splitters.hpp : 325) Processed 8141067 edges 0:40:13.304 3G / 9G INFO General (kmer_splitters.hpp : 325) Processed 9497581 edges 0:40:19.737 3G / 9G INFO General (kmer_splitters.hpp : 325) Processed 10770307 edges 0:40:19.737 3G / 9G INFO General (kmer_splitters.hpp : 330) Used 10770307 sequences. 0:40:19.818 2G / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:43:41.746 2G / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 177568963 kmers in total. 0:43:41.746 2G / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:44:06.311 2G / 9G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:48:45.173 2G / 9G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:49:07.971 2G / 9G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 61427802 bytes occupied (2.7675 bits per kmer). 0:49:11.043 6G / 9G INFO General (edge_index_builders.hpp : 21) Collecting k-mer coverage information from graph, this takes a while. 0:55:49.171 6G / 9G INFO General (graph_construction.hpp : 182) Filling coverage index 0:55:49.171 6G / 9G INFO General (edge_index_builders.hpp : 99) Collecting k-mer coverage information from reads, this takes a while. 0:59:20.125 6G / 9G INFO General (graph_construction.hpp : 184) Filling coverage and flanking coverage from index 1:00:06.267 6G / 9G INFO General (construction.cpp : 33) Figured out: read length = 151 1:00:06.283 6G / 9G INFO StageManager (stage.cpp : 125) STAGE == EC Threshold Finding 1:00:18.595 6G / 9G INFO General (kmer_coverage_model.cpp : 178) Kmer coverage valley at: 7 1:00:18.595 6G / 9G INFO General (kmer_coverage_model.cpp : 198) K-mer histogram maximum: 26 1:00:18.596 6G / 9G INFO General (kmer_coverage_model.cpp : 234) Estimated median coverage: 27. Coverage mad: 8.8956 1:00:18.596 6G / 9G INFO General (kmer_coverage_model.cpp : 261) Fitting coverage model 1:00:18.690 6G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 2 1:00:18.941 6G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 4 1:00:19.831 6G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 8 1:00:22.009 6G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 16 1:00:25.619 6G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 32 1:00:26.365 6G / 9G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 26.2171. Fitted coverage std. dev: 8.52754 1:00:26.368 6G / 9G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 0.368667 1:00:26.368 6G / 9G INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 15 1:00:26.368 6G / 9G INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 15 1:00:26.368 6G / 9G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 61907169 1:00:26.368 6G / 9G INFO General (genomic_info_filler.cpp : 103) Mean coverage was calculated as 26.2171 1:00:26.368 6G / 9G INFO General (genomic_info_filler.cpp : 117) EC coverage threshold value was calculated as 15 1:00:26.369 6G / 9G INFO General (genomic_info_filler.cpp : 118) Trusted kmer low bound: 0 1:00:26.369 6G / 9G INFO StageManager (stage.cpp : 125) STAGE == Gap Closer 1:00:26.382 6G / 9G INFO General (gap_closer.cpp : 157) Preparing shift maps 1:00:39.504 7G / 9G INFO General (gap_closer.cpp : 117) Processing paired reads (takes a while) 1:01:18.459 7G / 9G INFO General (gap_closer.cpp : 136) Used 26978890 paired reads 1:01:18.460 7G / 9G INFO General (gap_closer.cpp : 138) Merging paired indices 1:01:25.382 6G / 9G INFO GapCloser (gap_closer.cpp : 395) Closing short gaps 1:01:56.777 6G / 9G INFO GapCloser (gap_closer.cpp : 424) Closing short gaps complete: filled 979 gaps after checking 14478 candidates 1:02:01.246 6G / 9G INFO StageManager (stage.cpp : 125) STAGE == Simplification 1:02:01.573 2G / 9G INFO General (graph_simplification.hpp : 911) Graph simplification started 1:02:01.573 2G / 9G INFO General (graph_simplification.hpp : 924) Fast simplification mode enabled 1:02:01.573 2G / 9G INFO General (graph_simplification.hpp : 771) PROCEDURE == Presimplification 1:02:01.573 2G / 9G INFO General (graph_simplification.hpp : 211) Removing short low covered self-conjugate connections 1:02:02.545 2G / 9G INFO General (graph_simplification.hpp : 403) Removing isolated edges 1:02:02.545 2G / 9G INFO General (graph_simplification.hpp : 404) All edges shorter than 151 will be removed 1:02:02.545 2G / 9G INFO General (graph_simplification.hpp : 405) Also edges shorter than 0 and coverage smaller than 0 will be removed 1:02:07.823 2G / 9G INFO General (graph_simplification.hpp : 687) Non parallel mode 1:02:43.201 3G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 1:04:44.588 2G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 1:04:51.379 1G / 9G INFO General (graph_simplification.hpp : 644) Using permanent iterators 1:04:51.380 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 1 1:04:52.109 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 1:04:55.113 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 1:04:55.235 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 2 1:04:55.235 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 1:04:55.242 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 1:04:56.452 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 3 1:04:56.452 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 1:04:56.480 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 1:04:57.410 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 4 1:04:57.410 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 1:04:57.425 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 1:04:58.182 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 5 1:04:58.182 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 1:04:58.193 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 1:04:59.264 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 6 1:04:59.264 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 1:04:59.272 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 1:05:00.590 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 7 1:05:00.590 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 1:05:00.598 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 1:05:02.520 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 8 1:05:02.520 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 1:05:02.527 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 1:05:04.470 1020M / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 9 1:05:04.470 1020M / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 1:05:04.476 1020M / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 1:05:06.285 836M / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 10 1:05:06.285 836M / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 1:05:06.290 836M / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 1:05:07.770 696M / 9G INFO General (graph_simplification.hpp : 796) PROCEDURE == Post simplification 1:05:07.770 696M / 9G INFO General (graph_simplification.hpp : 644) Using permanent iterators 1:05:07.770 696M / 9G INFO General (graph_simplification.hpp : 806) Iteration 0 1:05:07.770 696M / 9G INFO General (graph_simplification.hpp : 247) Removal of relatively low covered connections disabled 1:05:07.885 696M / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 1:05:08.223 672M / 9G INFO StageManager (stage.cpp : 125) STAGE == Gap Closer 1:05:08.224 672M / 9G INFO General (graph_pack.hpp : 84) Index refill 1:05:08.229 672M / 9G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 1:05:08.229 672M / 9G INFO General (kmer_splitters.hpp : 289) Splitting kmer instances into 16 buckets. This might take a while. 1:05:08.229 672M / 9G INFO General (file_limit.hpp : 29) Open file limit set to 32768 1:05:08.229 672M / 9G INFO General (kmer_splitters.hpp : 307) Memory available for splitting buffers: 33.1146 Gb 1:05:08.229 672M / 9G INFO General (kmer_splitters.hpp : 312) Using cell size of 1398101 1:06:31.517 1G / 9G INFO General (kmer_splitters.hpp : 325) Processed 17399 edges 1:06:59.916 1G / 9G INFO General (kmer_splitters.hpp : 325) Processed 34942 edges 1:07:16.056 1G / 9G INFO General (kmer_splitters.hpp : 325) Processed 52683 edges 1:07:33.748 1G / 9G INFO General (kmer_splitters.hpp : 325) Processed 56459 edges 1:07:33.749 1G / 9G INFO General (kmer_splitters.hpp : 330) Used 56459 sequences. 1:07:33.834 668M / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 1:08:02.106 668M / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 71779712 kmers in total. 1:08:02.106 668M / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 1:08:11.795 668M / 9G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 1:09:48.307 692M / 9G INFO General (kmer_index.hpp : 371) Merging final buckets. 1:09:58.071 692M / 9G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 24831332 bytes occupied (2.7675 bits per kmer). 1:09:59.376 2G / 9G INFO General (edge_index_builders.hpp : 21) Collecting k-mer coverage information from graph, this takes a while. 1:12:09.534 2G / 9G INFO General (gap_closer.cpp : 157) Preparing shift maps 1:12:09.600 2G / 9G INFO General (gap_closer.cpp : 117) Processing paired reads (takes a while) 1:13:00.857 2G / 9G INFO General (gap_closer.cpp : 136) Used 26978890 paired reads 1:13:00.858 2G / 9G INFO General (gap_closer.cpp : 138) Merging paired indices 1:13:00.958 2G / 9G INFO GapCloser (gap_closer.cpp : 395) Closing short gaps 1:13:01.159 2G / 9G INFO GapCloser (gap_closer.cpp : 424) Closing short gaps complete: filled 53 gaps after checking 3725 candidates 1:13:01.839 2G / 9G INFO StageManager (stage.cpp : 125) STAGE == Simplification Cleanup 1:13:01.843 2G / 9G INFO General (graph_simplification.hpp : 403) Removing isolated edges 1:13:01.843 2G / 9G INFO General (graph_simplification.hpp : 404) All edges shorter than 151 will be removed 1:13:01.843 2G / 9G INFO General (graph_simplification.hpp : 405) Also edges shorter than 0 and coverage smaller than 2 will be removed 1:13:02.691 2G / 9G INFO General (simplification.cpp : 56) Removing all the edges having coverage 0 and less 1:13:02.849 2G / 9G INFO General (simplification.cpp : 68) Counting average coverage 1:13:02.868 2G / 9G INFO General (simplification.cpp : 71) Average coverage = 25.6511 1:13:02.868 2G / 9G INFO StageManager (stage.cpp : 125) STAGE == Mismatch Correction 1:13:54.385 2G / 9G INFO General (mismatch_shall_not_pass.hp: 188) Finished collecting potential mismatches positions 1:13:54.447 2G / 9G INFO General (mismatch_shall_not_pass.hp: 291) All edges processed 1:13:54.450 2G / 9G INFO General (mismatch_correction.cpp : 18) Corrected 0 nucleotides 1:13:54.466 2G / 9G INFO StageManager (stage.cpp : 125) STAGE == Paired Information Counting 1:13:54.611 2G / 9G INFO General (pair_info_count.cpp : 150) Graph N50: 19042 1:13:54.611 2G / 9G INFO General (pair_info_count.cpp : 152) Estimating insert size for library #0 1:13:54.611 2G / 9G INFO General (pair_info_count.cpp : 31) Estimating insert size (takes a while) 1:13:54.625 2G / 9G INFO General (short_read_mapper.hpp : 91) Selecting usual mapper 1:14:00.561 2G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 200000 reads 1:14:00.582 2G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 400000 reads 1:14:00.587 2G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 600000 reads 1:14:00.592 2G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 800000 reads 1:14:00.601 2G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 1000000 reads 1:14:00.603 2G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 1200000 reads 1:14:01.266 2G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 2200000 reads 1:14:07.082 2G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 4200000 reads 1:14:15.631 2G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 8400000 reads 1:14:24.761 2G / 9G INFO General (sequence_mapper_notifier.h: 89) Processed 13489445 reads 1:14:24.761 2G / 9G INFO General (pair_info_count.cpp : 41) 6335359 paired reads (46.9653% of all) aligned to long edges 1:14:24.772 2G / 9G INFO General (pair_info_count.cpp : 170) Estimated insert size for paired library #0 1:14:24.772 2G / 9G INFO General (pair_info_count.cpp : 175) Insert size = 332.805, deviation = 97.9765, left quantile = 213, right quantile = 460, read length = 151 1:14:24.772 2G / 9G INFO General (pair_info_count.cpp : 187) Mapping library #0 1:14:24.772 2G / 9G INFO General (pair_info_count.cpp : 189) Mapping paired reads (takes a while) 1:14:24.772 2G / 9G INFO General (pair_info_count.cpp : 73) Left insert size qauntile 213, right insert size quantile 460 1:14:24.786 2G / 9G INFO General (short_read_mapper.hpp : 91) Selecting usual mapper 1:14:32.347 4G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 200000 reads 1:14:33.127 4G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 400000 reads 1:14:34.027 4G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 600000 reads 1:14:35.105 4G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 800000 reads 1:14:36.370 4G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 1000000 reads 1:14:37.643 4G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 1200000 reads 1:14:44.998 4G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 2200000 reads 1:15:02.439 4G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 4200000 reads 1:15:40.056 4G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 8400000 reads 1:16:58.858 5G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 16800000 reads 1:18:39.858 3G / 9G INFO General (sequence_mapper_notifier.h: 89) Processed 26978890 reads 1:22:07.705 3G / 9G INFO General (split_graph_pair_info.hpp : 344) Threshold for paired information 0.0537276 1:22:12.132 2G / 9G INFO StageManager (stage.cpp : 125) STAGE == Distance Estimation 1:22:12.132 2G / 9G INFO General (distance_estimation.cpp : 234) Processing library #0 1:22:12.132 2G / 9G INFO General (distance_estimation.cpp : 136) Weight Filter Done 1:22:12.133 2G / 9G INFO DistanceEstimator (distance_estimation.hpp : 187) Using SIMPLE distance estimator 1:22:21.162 2G / 9G INFO DistanceEstimator (distance_estimation.hpp : 208) Merging maps 1:22:22.265 2G / 9G INFO General (distance_estimation.cpp : 38) Filtering info 1:22:24.009 2G / 9G INFO General (pair_info_filters.hpp : 354) Pruning the index 1:22:24.068 2G / 9G INFO General (distance_estimation.cpp : 184) Refining clustered pair information 1:22:24.209 2G / 9G INFO General (distance_estimation.cpp : 186) The refining of clustered pair information has been finished 1:22:24.209 2G / 9G INFO General (distance_estimation.cpp : 188) Filling paired information 1:22:26.736 2G / 9G INFO PairInfoImprover (pair_info_improver.hpp : 61) Paired info stats: missing = 64589; contradictional = 8004 1:22:29.229 2G / 9G INFO PairInfoImprover (pair_info_improver.hpp : 61) Paired info stats: missing = 10184; contradictional = 0 1:22:29.229 2G / 9G INFO General (distance_estimation.cpp : 193) Filling scaffolding index 1:22:29.230 2G / 9G INFO DistanceEstimator (distance_estimation.hpp : 187) Using SMOOTHING distance estimator 1:22:42.054 2G / 9G INFO DistanceEstimator (distance_estimation.hpp : 208) Merging maps 1:22:42.116 2G / 9G INFO General (distance_estimation.cpp : 38) Filtering info 1:22:42.406 2G / 9G INFO General (pair_info_filters.hpp : 354) Pruning the index 1:22:42.979 2G / 9G INFO StageManager (stage.cpp : 125) STAGE == Repeat Resolving 1:22:42.979 2G / 9G INFO General (contig_output.hpp : 283) Outputting contigs to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_Indo1-7I-dipSPAdes-3.5.0-trimmed/spades//K77/before_rr.fasta 1:23:44.443 2G / 9G INFO General (repeat_resolving.cpp : 59) Using Path-Extend repeat resolving 1:23:44.444 2G / 9G INFO General (path_extend_launch.hpp : 459) Threshold for library #0 is 0.0537276 1:23:44.444 2G / 9G INFO General (path_extend_launch.hpp : 298) Path-Extend repeat resolving tool started 1:23:44.503 2G / 9G INFO General (path_extend_launch.hpp : 316) Using 1 paired-end library 1:23:44.503 2G / 9G INFO General (path_extend_launch.hpp : 317) Using 1 paired-end scaffolding library 1:23:44.503 2G / 9G INFO General (path_extend_launch.hpp : 318) Using 0 mate-pair libraries 1:23:44.503 2G / 9G INFO General (path_extend_launch.hpp : 319) Using 0 single read libraries 1:23:44.503 2G / 9G INFO General (path_extend_launch.hpp : 320) Scaffolder is on 1:23:44.927 2G / 9G INFO General (path_extend_launch.hpp : 332) Growing paths using paired-end and long single reads 1:23:44.927 2G / 9G INFO PathExtender (path_extender.hpp : 611) Processed 0 paths from 24156 (0%) 1:23:45.237 2G / 9G INFO PathExtender (path_extender.hpp : 609) Processed 128 paths from 24156 (0%) 1:23:45.502 2G / 9G INFO PathExtender (path_extender.hpp : 609) Processed 256 paths from 24156 (1%) 1:23:46.183 2G / 9G INFO PathExtender (path_extender.hpp : 609) Processed 512 paths from 24156 (2%) 1:23:46.990 2G / 9G INFO PathExtender (path_extender.hpp : 609) Processed 1024 paths from 24156 (4%) 1:23:48.222 2G / 9G INFO PathExtender (path_extender.hpp : 609) Processed 2048 paths from 24156 (8%) 1:23:48.568 2G / 9G INFO PathExtender (path_extender.hpp : 611) Processed 2416 paths from 24156 (10%) 1:23:49.583 2G / 9G INFO PathExtender (path_extender.hpp : 609) Processed 4096 paths from 24156 (16%) 1:23:49.933 2G / 9G INFO PathExtender (path_extender.hpp : 611) Processed 4832 paths from 24156 (20%) 1:23:51.037 2G / 9G INFO PathExtender (path_extender.hpp : 611) Processed 7248 paths from 24156 (30%) 1:23:51.422 2G / 9G INFO PathExtender (path_extender.hpp : 609) Processed 8192 paths from 24156 (33%) 1:23:51.720 2G / 9G INFO PathExtender (path_extender.hpp : 611) Processed 9664 paths from 24156 (40%) 1:23:52.362 2G / 9G INFO PathExtender (path_extender.hpp : 611) Processed 12080 paths from 24156 (50%) 1:23:54.859 2G / 9G INFO PathExtender (path_extender.hpp : 611) Processed 14496 paths from 24156 (60%) 1:23:57.729 2G / 9G INFO PathExtender (path_extender.hpp : 609) Processed 16384 paths from 24156 (67%) 1:23:58.415 2G / 9G INFO PathExtender (path_extender.hpp : 611) Processed 16912 paths from 24156 (70%) 1:24:01.230 2G / 9G INFO PathExtender (path_extender.hpp : 611) Processed 19328 paths from 24156 (80%) 1:24:03.181 2G / 9G INFO PathExtender (path_extender.hpp : 611) Processed 21744 paths from 24156 (90%) 1:24:05.006 2G / 9G INFO PathExtendIO (pe_io.hpp : 339) Constructing FASTG file from paths 1:24:05.527 2G / 9G INFO PathExtendIO (pe_io.hpp : 342) Writing contigs in FASTG to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_Indo1-7I-dipSPAdes-3.5.0-trimmed/spades//K77/final_contigs.fastg 1:24:05.527 2G / 9G INFO PathExtendIO (pe_io.hpp : 343) Writing contigs in FASTA to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_Indo1-7I-dipSPAdes-3.5.0-trimmed/spades//K77/final_contigs.fasta 1:25:15.600 2G / 9G INFO PathExtendIO (pe_io.hpp : 339) Constructing FASTG file from paths 1:25:16.157 2G / 9G INFO PathExtendIO (pe_io.hpp : 342) Writing contigs in FASTG to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_Indo1-7I-dipSPAdes-3.5.0-trimmed/spades//K77/path_extend/pe_before_traversal.fastg 1:25:16.157 2G / 9G INFO PathExtendIO (pe_io.hpp : 343) Writing contigs in FASTA to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_Indo1-7I-dipSPAdes-3.5.0-trimmed/spades//K77/path_extend/pe_before_traversal.fasta 1:26:04.012 2G / 9G INFO General (path_extend_launch.hpp : 281) Traversing tandem repeats 1:26:06.039 2G / 9G INFO PathExtendIO (pe_io.hpp : 339) Constructing FASTG file from paths 1:26:06.530 2G / 9G INFO PathExtendIO (pe_io.hpp : 342) Writing contigs in FASTG to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_Indo1-7I-dipSPAdes-3.5.0-trimmed/spades//K77/scaffolds.fastg 1:26:06.530 2G / 9G INFO PathExtendIO (pe_io.hpp : 343) Writing contigs in FASTA to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_Indo1-7I-dipSPAdes-3.5.0-trimmed/spades//K77/scaffolds.fasta 1:26:56.026 2G / 9G INFO General (launch.hpp : 82) SPAdes finished 1:27:00.175 300M / 9G INFO General (main.cpp : 166) Assembling time: 1 hours 27 minutes 0 seconds ===== Assembling finished. * Corrected reads are in /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_Indo1-7I-dipSPAdes-3.5.0-trimmed/spades/corrected/ * Assembled contigs are in /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_Indo1-7I-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_Indo1-7I-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_Indo1-7I-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_Indo1-7I-dipSPAdes-3.5.0-trimmed/spades/spades.log Thank you for using SPAdes!