Command line: --diploid --pe1-1 /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_127/reads.end1.paired.fastq.gz --pe1-2 /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_127/reads.end2.paired.fastq.gz -t 16 -o /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_127-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_127-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_127/reads.end1.paired.fastq.gz'] right reads: ['/N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_127/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_127-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_127-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_127-dipSPAdes-3.5.0-trimmed/spades/corrected/configs/config.info 0:00:00.020 4M / 4M INFO General (main.cpp : 82) Loading config from /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_127-dipSPAdes-3.5.0-trimmed/spades/corrected/configs/config.info 0:00:00.175 4M / 4M INFO General (memory_limit.hpp : 42) Memory limit set to 100 Gb 0:00:00.175 4M / 4M INFO General (main.cpp : 91) Trying to determine PHRED offset 0:00:00.225 4M / 4M INFO General (main.cpp : 97) Determined value is 33 0:00:00.249 4M / 4M INFO General (hammer_tools.cpp : 36) Hamming graph threshold tau=1, k=21, subkmer positions = [ 0 10 ] === ITERATION 0 begins === 0:00:00.250 4M / 4M INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:00:00.250 4M / 4M INFO K-mer Splitting (kmer_data.cpp : 127) Splitting kmer instances into 256 buckets. This might take a while. 0:00:00.251 4M / 4M INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:00:00.251 4M / 4M INFO K-mer Splitting (kmer_data.cpp : 145) Memory available for splitting buffers: 2.08325 Gb 0:00:00.251 4M / 4M INFO K-mer Splitting (kmer_data.cpp : 153) Using cell size of 262144 0:00:03.044 8G / 8G INFO K-mer Splitting (kmer_data.cpp : 167) Processing /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_127/reads.end1.paired.fastq.gz 0:00:52.755 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 176) Processed 2885444 reads 0:01:41.656 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 176) Processed 5758731 reads 0:02:38.266 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 176) Processed 8635774 reads 0:03:39.362 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 176) Processed 11492021 reads 0:04:27.984 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 176) Processed 14359184 reads 0:04:52.162 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 176) Processed 15790244 reads 0:04:52.163 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 167) Processing /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_127/reads.end2.paired.fastq.gz 0:08:12.372 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 176) Processed 18863186 reads 0:10:35.464 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 176) Processed 21910778 reads 0:11:28.503 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 176) Processed 25009983 reads 0:12:26.976 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 176) Processed 28433773 reads 0:13:20.085 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 181) Processed 31580488 reads 0:13:21.256 64M / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:14:08.272 64M / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 345689544 kmers in total. 0:14:08.272 64M / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:14:23.742 64M / 9G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:15:13.102 192M / 11G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:15:27.790 192M / 11G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 119587018 bytes occupied (2.7675 bits per kmer). 0:15:27.791 192M / 11G INFO K-mer Counting (kmer_data.cpp : 266) Arranging kmers in hash map order 0:18:54.614 192M / 11G INFO K-mer Counting (kmer_data.cpp : 279) Done. Total swaps: 345689241 0:18:56.906 2G / 11G INFO General (main.cpp : 151) Clustering Hamming graph. 0:18:56.909 2G / 11G INFO Hamming Clustering (hamcluster.cpp : 115) Serializing sub-kmers. 0:18:56.909 2G / 11G INFO Hamming Clustering (hamcluster.cpp : 120) Serializing: [0, 10) 0:23:05.959 2G / 11G INFO Hamming Clustering (hamcluster.cpp : 120) Serializing: [10, 21) 0:26:56.289 2G / 11G INFO Hamming Clustering (hamcluster.cpp : 129) Splitting sub-kmers, pass 1. 0:31:35.842 2G / 11G INFO Hamming Clustering (hamcluster.cpp : 134) Splitting done. Processed 2 blocks. Produced 5099635 blocks. 0:31:35.843 2G / 11G INFO Hamming Clustering (hamcluster.cpp : 145) Merge sub-kmers, pass 1 0:49:18.647 2G / 11G INFO Hamming Clustering (hamcluster.cpp : 170) Merge done, total 1707588 new blocks generated. 0:49:20.503 2G / 11G INFO Hamming Clustering (hamcluster.cpp : 175) Spliting sub-kmers, pass 2. 1:05:38.130 2G / 11G INFO Hamming Clustering (hamcluster.cpp : 180) Splitting done. Processed 3415176 blocks. Produced 619428292 blocks. 1:05:38.130 2G / 11G INFO Hamming Clustering (hamcluster.cpp : 187) Merge sub-kmers, pass 2 1:27:53.763 2G / 11G INFO Hamming Clustering (hamcluster.cpp : 205) Merge done, saw 531110 big blocks out of 619428292 processed. 1:32:55.725 2G / 11G INFO General (main.cpp : 165) Clustering done. Total clusters: 145583538 1:32:55.726 2G / 11G INFO K-mer Counting (kmer_data.cpp : 284) Collecting K-mer information, this takes a while. 1:33:02.677 18G / 18G INFO K-mer Counting (kmer_data.cpp : 290) Processing /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_127/reads.end1.paired.fastq.gz 1:37:01.476 18G / 18G INFO K-mer Counting (kmer_data.cpp : 290) Processing /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_127/reads.end2.paired.fastq.gz 1:40:53.453 18G / 18G INFO K-mer Counting (kmer_data.cpp : 297) Collection done, postprocessing. 1:41:02.002 18G / 18G INFO K-mer Counting (kmer_data.cpp : 310) There are 345689544 kmers in total. Among them 180514854 (52.2188%) are singletons. 1:41:02.002 18G / 18G INFO General (main.cpp : 203) Subclustering Hamming graph 1:46:12.936 18G / 18G INFO Hamming Subclustering (kmer_cluster.cpp : 626) Subclustering done. Total 133471 non-read kmers were generated. 1:46:12.936 18G / 18G INFO Hamming Subclustering (kmer_cluster.cpp : 627) Subclustering statistics: 1:46:12.936 18G / 18G INFO Hamming Subclustering (kmer_cluster.cpp : 628) Total singleton hamming clusters: 82168685. Among them 58042061 (70.6377%) are good 1:46:12.936 18G / 18G INFO Hamming Subclustering (kmer_cluster.cpp : 629) Total singleton subclusters: 6993312. Among them 6993102 (99.997%) are good 1:46:12.936 18G / 18G INFO Hamming Subclustering (kmer_cluster.cpp : 630) Total non-singleton subcluster centers: 70335318. Among them 50027072 (71.1265%) are good 1:46:12.937 18G / 18G INFO Hamming Subclustering (kmer_cluster.cpp : 631) Average size of non-trivial subcluster: 3.72791 kmers 1:46:12.937 18G / 18G INFO Hamming Subclustering (kmer_cluster.cpp : 632) Average number of sub-clusters per non-singleton cluster: 1.21941 1:46:12.937 18G / 18G INFO Hamming Subclustering (kmer_cluster.cpp : 633) Total solid k-mers: 115062235 1:46:12.937 18G / 18G INFO Hamming Subclustering (kmer_cluster.cpp : 634) Substitution probabilities: [4,4]((0.887639,0.0265567,0.0287728,0.0570319),(0.0390735,0.921516,0.0148545,0.0245563),(0.0232574,0.0143255,0.922808,0.0396094),(0.0564193,0.0287321,0.0272657,0.887583)) 1:46:13.415 18G / 18G INFO General (main.cpp : 208) Finished clustering. 1:46:13.415 18G / 18G INFO General (main.cpp : 228) Starting solid k-mers expansion in 16 threads. 1:51:31.360 18G / 18G INFO General (main.cpp : 249) Solid k-mers iteration 0 produced 63980645 new k-mers. 1:56:44.453 18G / 18G INFO General (main.cpp : 249) Solid k-mers iteration 1 produced 2052142 new k-mers. 2:01:57.724 18G / 18G INFO General (main.cpp : 249) Solid k-mers iteration 2 produced 97358 new k-mers. 2:07:10.852 18G / 18G INFO General (main.cpp : 249) Solid k-mers iteration 3 produced 15356 new k-mers. 2:12:24.022 18G / 18G INFO General (main.cpp : 249) Solid k-mers iteration 4 produced 5276 new k-mers. 2:17:37.002 18G / 18G INFO General (main.cpp : 249) Solid k-mers iteration 5 produced 2238 new k-mers. 2:22:50.113 18G / 18G INFO General (main.cpp : 249) Solid k-mers iteration 6 produced 1520 new k-mers. 2:28:03.416 18G / 18G INFO General (main.cpp : 249) Solid k-mers iteration 7 produced 359 new k-mers. 2:33:16.298 18G / 18G INFO General (main.cpp : 249) Solid k-mers iteration 8 produced 0 new k-mers. 2:33:16.299 18G / 18G INFO General (main.cpp : 253) Solid k-mers finalized 2:33:16.300 18G / 18G INFO General (hammer_tools.cpp : 210) Starting read correction in 16 threads. 2:33:16.300 18G / 18G INFO General (hammer_tools.cpp : 222) Correcting pair of reads: /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_127/reads.end1.paired.fastq.gz and /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_127/reads.end2.paired.fastq.gz 2:33:41.493 19G / 19G INFO General (hammer_tools.cpp : 166) Prepared batch 0 of 1600000 reads. 2:34:02.712 19G / 19G INFO General (hammer_tools.cpp : 175) Processed batch 0 2:34:17.984 19G / 19G INFO General (hammer_tools.cpp : 185) Written batch 0 2:34:41.488 19G / 19G INFO General (hammer_tools.cpp : 166) Prepared batch 1 of 1600000 reads. 2:35:02.582 19G / 19G INFO General (hammer_tools.cpp : 175) Processed batch 1 2:35:17.680 19G / 19G INFO General (hammer_tools.cpp : 185) Written batch 1 2:35:40.969 19G / 19G INFO General (hammer_tools.cpp : 166) Prepared batch 2 of 1600000 reads. 2:36:02.165 19G / 19G INFO General (hammer_tools.cpp : 175) Processed batch 2 2:36:17.251 19G / 19G INFO General (hammer_tools.cpp : 185) Written batch 2 2:36:40.335 19G / 19G INFO General (hammer_tools.cpp : 166) Prepared batch 3 of 1600000 reads. 2:37:01.143 19G / 19G INFO General (hammer_tools.cpp : 175) Processed batch 3 2:37:16.198 19G / 19G INFO General (hammer_tools.cpp : 185) Written batch 3 2:37:39.266 19G / 19G INFO General (hammer_tools.cpp : 166) Prepared batch 4 of 1600000 reads. 2:38:00.692 19G / 19G INFO General (hammer_tools.cpp : 175) Processed batch 4 2:38:15.771 19G / 19G INFO General (hammer_tools.cpp : 185) Written batch 4 2:38:38.760 19G / 19G INFO General (hammer_tools.cpp : 166) Prepared batch 5 of 1600000 reads. 2:39:04.634 19G / 19G INFO General (hammer_tools.cpp : 175) Processed batch 5 2:39:40.387 19G / 19G INFO General (hammer_tools.cpp : 185) Written batch 5 2:40:03.442 19G / 19G INFO General (hammer_tools.cpp : 166) Prepared batch 6 of 1600000 reads. 2:40:29.269 19G / 19G INFO General (hammer_tools.cpp : 175) Processed batch 6 2:41:04.598 19G / 19G INFO General (hammer_tools.cpp : 185) Written batch 6 2:41:27.524 19G / 19G INFO General (hammer_tools.cpp : 166) Prepared batch 7 of 1600000 reads. 2:41:53.420 19G / 19G INFO General (hammer_tools.cpp : 175) Processed batch 7 2:42:08.503 19G / 19G INFO General (hammer_tools.cpp : 185) Written batch 7 2:42:31.117 19G / 19G INFO General (hammer_tools.cpp : 166) Prepared batch 8 of 1600000 reads. 2:42:52.346 19G / 19G INFO General (hammer_tools.cpp : 175) Processed batch 8 2:43:07.433 19G / 19G INFO General (hammer_tools.cpp : 185) Written batch 8 2:43:27.136 19G / 19G INFO General (hammer_tools.cpp : 166) Prepared batch 9 of 1390244 reads. 2:43:47.057 19G / 19G INFO General (hammer_tools.cpp : 175) Processed batch 9 2:44:00.217 19G / 19G INFO General (hammer_tools.cpp : 185) Written batch 9 2:44:02.737 18G / 19G INFO General (hammer_tools.cpp : 269) Correction done. Changed 5238661 bases in 4226642 reads. 2:44:02.737 18G / 19G INFO General (hammer_tools.cpp : 270) Failed to correct 428130048 bases out of 4715957914. 2:44:02.820 2G / 19G INFO General (main.cpp : 286) Saving corrected dataset description to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_127-dipSPAdes-3.5.0-trimmed/spades/corrected/corrected.yaml 2:44:02.845 2G / 19G 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_127-dipSPAdes-3.5.0-trimmed/spades/corrected/corrected.yaml ===== Read error correction finished. ===== Assembling started. == Running assembler: K21 0:00:00.016 4M / 4M INFO General (memory_limit.hpp : 42) Memory limit set to 100 Gb 0:00:00.065 4M / 4M INFO General (main.cpp : 146) Assembling dataset (/N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_127-dipSPAdes-3.5.0-trimmed/spades/dataset.info) with K=21 0:00:00.072 4M / 4M INFO General (launch.hpp : 28) SPAdes started 0:00:00.072 4M / 4M INFO General (launch.hpp : 29) Starting from stage: construction 0:00:00.129 4M / 4M INFO StageManager (stage.cpp : 125) STAGE == Construction 0:00:00.139 4M / 4M INFO General (read_converter.hpp : 79) Converting reads to binary format (takes a while) 0:00:00.139 4M / 4M INFO General (read_converter.hpp : 81) Paired reads for library #0 0:00:01.275 80M / 80M INFO General (binary_converter.hpp : 138) 16384 reads processed 0:00:01.676 96M / 96M INFO General (binary_converter.hpp : 138) 32768 reads processed 0:00:02.473 124M / 124M INFO General (binary_converter.hpp : 138) 65536 reads processed 0:00:04.072 184M / 184M INFO General (binary_converter.hpp : 138) 131072 reads processed 0:00:07.274 300M / 300M INFO General (binary_converter.hpp : 138) 262144 reads processed 0:00:13.685 536M / 536M INFO General (binary_converter.hpp : 138) 524288 reads processed 0:00:29.194 904M / 904M INFO General (binary_converter.hpp : 138) 1048576 reads processed 0:00:57.725 904M / 904M INFO General (binary_converter.hpp : 138) 2097152 reads processed 0:01:54.933 908M / 908M INFO General (binary_converter.hpp : 138) 4194304 reads processed 0:04:11.987 908M / 908M INFO General (binary_converter.hpp : 138) 8388608 reads processed 0:07:33.656 832M / 908M INFO General (binary_converter.hpp : 158) 15682481 reads written 0:07:35.147 4M / 908M INFO General (read_converter.hpp : 91) Single reads for library #0 0:07:37.016 140M / 908M INFO General (binary_converter.hpp : 138) 16384 reads processed 0:07:37.240 144M / 908M INFO General (binary_converter.hpp : 138) 32768 reads processed 0:07:37.624 160M / 908M INFO General (binary_converter.hpp : 138) 65536 reads processed 0:07:38.307 176M / 908M INFO General (binary_converter.hpp : 158) 107490 reads written 0:07:38.478 4M / 908M INFO General (graph_construction.hpp : 129) Constructing DeBruijn graph for k=21 0:07:38.490 4M / 908M INFO General (kmer_splitters.hpp : 172) Splitting kmer instances into 256 buckets. This might take a while. 0:07:38.495 4M / 908M INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:07:38.499 4M / 908M INFO General (kmer_splitters.hpp : 190) Memory available for splitting buffers: 2.08325 Gb 0:07:38.499 4M / 908M INFO General (kmer_splitters.hpp : 199) Using cell size of 262144 0:08:07.549 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 16671313 reads 0:08:42.768 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 33344212 reads 0:09:07.869 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 50021720 reads 0:09:27.497 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 62944904 reads 0:09:27.497 8G / 9G INFO General (kmer_splitters.hpp : 234) Adding contigs from previous K 0:09:27.498 8G / 9G INFO General (kmer_splitters.hpp : 245) Used 62944904 reads. Maximum read length 151 0:09:27.499 8G / 9G INFO General (kmer_splitters.hpp : 246) Average read length 149.804 0:09:29.527 64M / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:09:39.662 64M / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 143094750 kmers in total. 0:09:39.663 64M / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:09:46.682 64M / 9G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:09:46.707 64M / 9G INFO General (kmer_splitters.hpp : 379) Splitting kmer instances into 256 buckets. This might take a while. 0:09:46.707 64M / 9G INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:09:46.707 64M / 9G INFO General (kmer_splitters.hpp : 397) Memory available for splitting buffers: 2.08203 Gb 0:09:46.708 64M / 9G INFO General (kmer_splitters.hpp : 405) Using cell size of 262144 0:10:06.045 8G / 9G INFO General (kmer_splitters.hpp : 428) Processed 143094750 kmers 0:10:06.045 8G / 9G INFO General (kmer_splitters.hpp : 437) Used 143094750 kmers. 0:10:06.500 64M / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:10:11.410 64M / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 137459387 kmers in total. 0:10:11.411 64M / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:10:38.065 64M / 9G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:10:59.713 68M / 9G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:11:17.122 68M / 9G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 47552390 bytes occupied (2.7675 bits per kmer). 0:11:17.355 200M / 9G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 382) Building k-mer extensions from k+1-mers 0:11:36.877 200M / 9G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 386) Building k-mer extensions from k+1-mers finished. 0:11:36.899 200M / 9G INFO Early tip clipping (early_simplification.hpp : 236) Early tip clipping 0:19:16.059 200M / 9G INFO Early tip clipping (early_simplification.hpp : 239) 7236740 22-mers were removed by early tip clipper 0:19:16.059 200M / 9G INFO General (graph_construction.hpp : 145) Condensing graph 0:19:16.125 200M / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 337) Extracting unbranching paths 0:21:10.146 3G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 351) Extracting unbranching paths finished. 29398948 sequences extracted 0:21:22.317 3G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 311) Collecting perfect loops 0:22:04.581 3G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 326) Collecting perfect loops finished. 14 loops collected 0:22:25.867 5G / 9G INFO General (graph_construction.hpp : 150) Building index with from graph 0:22:25.929 5G / 9G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:22:25.949 5G / 9G INFO General (kmer_splitters.hpp : 289) Splitting kmer instances into 16 buckets. This might take a while. 0:22:25.949 5G / 9G INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:22:25.969 5G / 9G INFO General (kmer_splitters.hpp : 307) Memory available for splitting buffers: 31.4518 Gb 0:22:25.969 5G / 9G INFO General (kmer_splitters.hpp : 312) Using cell size of 4194304 0:23:07.746 6G / 9G INFO General (kmer_splitters.hpp : 325) Processed 14519562 edges 0:23:55.994 6G / 9G INFO General (kmer_splitters.hpp : 325) Processed 29043815 edges 0:23:58.445 6G / 9G INFO General (kmer_splitters.hpp : 325) Processed 29398962 edges 0:23:58.446 6G / 9G INFO General (kmer_splitters.hpp : 330) Used 29398962 sequences. 0:23:58.538 5G / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:24:46.907 5G / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 135858010 kmers in total. 0:24:46.907 5G / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:24:52.333 5G / 9G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:28:04.273 5G / 9G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:28:30.319 5G / 9G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 46998415 bytes occupied (2.7675 bits per kmer). 0:28:32.592 8G / 9G INFO General (edge_index_builders.hpp : 21) Collecting k-mer coverage information from graph, this takes a while. 0:32:53.636 8G / 9G INFO General (graph_construction.hpp : 182) Filling coverage index 0:32:53.636 8G / 9G INFO General (edge_index_builders.hpp : 99) Collecting k-mer coverage information from reads, this takes a while. 0:37:20.171 8G / 9G INFO General (graph_construction.hpp : 184) Filling coverage and flanking coverage from index 0:37:59.270 8G / 9G INFO General (construction.cpp : 33) Figured out: read length = 151 0:37:59.299 8G / 9G INFO StageManager (stage.cpp : 125) STAGE == EC Threshold Finding 0:38:13.457 8G / 9G INFO General (kmer_coverage_model.cpp : 178) Kmer coverage valley at: 26 0:38:13.476 8G / 9G INFO General (kmer_coverage_model.cpp : 198) K-mer histogram maximum: 56 0:38:13.476 8G / 9G INFO General (kmer_coverage_model.cpp : 234) Estimated median coverage: 57. Coverage mad: 11.8608 0:38:13.478 8G / 9G INFO General (kmer_coverage_model.cpp : 261) Fitting coverage model 0:38:13.828 8G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 2 0:38:14.348 8G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 4 0:38:16.207 8G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 8 0:38:18.967 8G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 16 0:38:20.193 8G / 9G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 56.7069. Fitted coverage std. dev: 11.3206 0:38:20.198 8G / 9G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 0.409909 0:38:20.198 8G / 9G INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 38 0:38:20.198 8G / 9G INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 38 0:38:20.198 8G / 9G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 61535141 0:38:20.221 8G / 9G INFO General (genomic_info_filler.cpp : 103) Mean coverage was calculated as 56.7069 0:38:20.222 8G / 9G INFO General (genomic_info_filler.cpp : 117) EC coverage threshold value was calculated as 38 0:38:20.222 8G / 9G INFO General (genomic_info_filler.cpp : 118) Trusted kmer low bound: 0 0:38:20.222 8G / 9G INFO StageManager (stage.cpp : 125) STAGE == Simplification 0:38:20.511 5G / 9G INFO General (graph_simplification.hpp : 911) Graph simplification started 0:38:20.527 5G / 9G INFO General (graph_simplification.hpp : 924) Fast simplification mode enabled 0:38:20.531 5G / 9G INFO General (graph_simplification.hpp : 771) PROCEDURE == Presimplification 0:38:20.535 5G / 9G INFO General (graph_simplification.hpp : 211) Removing short low covered self-conjugate connections 0:38:22.522 5G / 9G INFO General (graph_simplification.hpp : 403) Removing isolated edges 0:38:22.522 5G / 9G INFO General (graph_simplification.hpp : 404) All edges shorter than 151 will be removed 0:38:22.522 5G / 9G INFO General (graph_simplification.hpp : 405) Also edges shorter than 0 and coverage smaller than 0 will be removed 0:38:25.127 5G / 9G INFO General (graph_simplification.hpp : 687) Non parallel mode 0:40:10.107 6G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:44:21.252 6G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:51:30.728 5G / 9G INFO General (graph_simplification.hpp : 644) Using permanent iterators 0:51:30.749 5G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 1 0:51:46.112 5G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:52:48.663 5G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:53:41.648 5G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 2 0:53:41.648 5G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:53:42.618 5G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:54:00.174 5G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 3 0:54:00.174 5G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:54:00.510 5G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:54:07.557 5G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 4 0:54:07.557 5G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:54:07.697 5G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:54:12.478 5G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 5 0:54:12.478 5G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:54:12.567 5G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:54:16.245 5G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 6 0:54:16.245 5G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:54:16.315 5G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:54:19.513 5G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 7 0:54:19.513 5G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:54:19.575 5G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:54:22.466 5G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 8 0:54:22.466 5G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:54:22.519 5G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:54:24.737 5G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 9 0:54:24.737 5G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:54:24.780 5G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:54:26.648 5G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 10 0:54:26.649 5G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:54:26.688 5G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:54:28.896 4G / 9G INFO General (graph_simplification.hpp : 796) PROCEDURE == Post simplification 0:54:28.896 4G / 9G INFO General (graph_simplification.hpp : 644) Using permanent iterators 0:54:28.896 4G / 9G INFO General (graph_simplification.hpp : 806) Iteration 0 0:54:28.901 4G / 9G INFO General (graph_simplification.hpp : 247) Removal of relatively low covered connections disabled 0:54:33.525 4G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:54:43.954 4G / 9G INFO General (graph_simplification.hpp : 806) Iteration 1 0:54:43.954 4G / 9G INFO General (graph_simplification.hpp : 247) Removal of relatively low covered connections disabled 0:54:43.954 4G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:54:46.869 4G / 9G INFO StageManager (stage.cpp : 125) STAGE == Simplification Cleanup 0:54:46.870 4G / 9G INFO General (graph_simplification.hpp : 403) Removing isolated edges 0:54:46.870 4G / 9G INFO General (graph_simplification.hpp : 404) All edges shorter than 151 will be removed 0:54:46.870 4G / 9G INFO General (graph_simplification.hpp : 405) Also edges shorter than 0 and coverage smaller than 2 will be removed 0:54:47.156 4G / 9G INFO General (simplification.cpp : 56) Removing all the edges having coverage 0 and less 0:54:55.819 4G / 9G INFO General (simplification.cpp : 68) Counting average coverage 0:54:56.779 4G / 9G INFO General (simplification.cpp : 71) Average coverage = 57.9407 0:54:56.779 4G / 9G INFO StageManager (stage.cpp : 125) STAGE == Contig Output 0:54:56.887 4G / 9G INFO General (contig_output.hpp : 283) Outputting contigs to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_127-dipSPAdes-3.5.0-trimmed/spades//K21/simplified_contigs.fasta 0:55:47.558 4G / 9G INFO General (contig_output.hpp : 283) Outputting contigs to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_127-dipSPAdes-3.5.0-trimmed/spades//K21/before_rr.fasta 0:58:08.014 4G / 9G INFO General (contig_output.hpp : 283) Outputting contigs to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_127-dipSPAdes-3.5.0-trimmed/spades//K21/final_contigs.fasta 1:00:28.306 4G / 9G INFO General (launch.hpp : 82) SPAdes finished 1:00:42.472 64M / 9G INFO General (main.cpp : 166) Assembling time: 1 hours 0 minutes 42 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 0:00:00.002 4M / 4M INFO General (main.cpp : 146) Assembling dataset (/N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_127-dipSPAdes-3.5.0-trimmed/spades/dataset.info) with K=33 0:00:00.002 4M / 4M INFO General (launch.hpp : 28) SPAdes started 0:00:00.002 4M / 4M INFO General (launch.hpp : 29) Starting from stage: construction 0:00:00.011 4M / 4M INFO StageManager (stage.cpp : 125) STAGE == Construction 0:00:00.011 4M / 4M INFO General (construction.cpp : 44) Contigs from previous K will be used 0:00:00.017 4M / 4M INFO General (read_converter.hpp : 49) Binary reads detected 0:00:00.039 4M / 4M INFO General (graph_construction.hpp : 129) Constructing DeBruijn graph for k=33 0:00:00.041 4M / 4M INFO General (kmer_splitters.hpp : 172) Splitting kmer instances into 256 buckets. This might take a while. 0:00:00.042 4M / 4M INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:00:00.042 4M / 4M INFO General (kmer_splitters.hpp : 190) Memory available for splitting buffers: 2.08325 Gb 0:00:00.042 4M / 4M INFO General (kmer_splitters.hpp : 199) Using cell size of 131072 0:01:06.962 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 9183737 reads 0:01:24.240 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 18384779 reads 0:01:57.155 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 27578748 reads 0:02:19.806 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 36765617 reads 0:03:33.827 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 45962063 reads 0:04:41.710 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 55148854 reads 0:04:54.309 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 62944904 reads 0:04:54.311 8G / 9G INFO General (kmer_splitters.hpp : 234) Adding contigs from previous K 0:05:15.481 8G / 9G INFO General (kmer_splitters.hpp : 245) Used 62944904 reads. Maximum read length 151 0:05:15.481 8G / 9G INFO General (kmer_splitters.hpp : 246) Average read length 149.804 0:05:17.730 64M / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:05:47.533 64M / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 188616861 kmers in total. 0:05:47.533 64M / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:06:05.101 64M / 9G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:06:05.101 64M / 9G INFO General (kmer_splitters.hpp : 379) Splitting kmer instances into 256 buckets. This might take a while. 0:06:05.102 64M / 9G INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:06:05.102 64M / 9G INFO General (kmer_splitters.hpp : 397) Memory available for splitting buffers: 2.08203 Gb 0:06:05.102 64M / 9G INFO General (kmer_splitters.hpp : 405) Using cell size of 131072 0:07:03.186 8G / 9G INFO General (kmer_splitters.hpp : 428) Processed 188616861 kmers 0:07:03.186 8G / 9G INFO General (kmer_splitters.hpp : 437) Used 188616861 kmers. 0:07:04.236 64M / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:07:17.309 64M / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 185707495 kmers in total. 0:07:17.310 64M / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:07:34.006 64M / 9G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:07:57.681 68M / 9G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:08:11.956 68M / 9G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 64243224 bytes occupied (2.7675 bits per kmer). 0:08:12.247 248M / 9G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 382) Building k-mer extensions from k+1-mers 0:08:37.741 248M / 9G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 386) Building k-mer extensions from k+1-mers finished. 0:08:37.746 248M / 9G INFO Early tip clipping (early_simplification.hpp : 236) Early tip clipping 0:19:12.613 248M / 9G INFO Early tip clipping (early_simplification.hpp : 239) 35679716 34-mers were removed by early tip clipper 0:19:12.613 248M / 9G INFO General (graph_construction.hpp : 145) Condensing graph 0:19:12.613 248M / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 337) Extracting unbranching paths 0:21:36.982 2G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 351) Extracting unbranching paths finished. 16369356 sequences extracted 0:21:51.662 2G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 311) Collecting perfect loops 0:22:58.922 2G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 326) Collecting perfect loops finished. 28 loops collected 0:23:10.629 3G / 9G INFO General (graph_construction.hpp : 150) Building index with from graph 0:23:10.630 3G / 9G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:23:10.631 3G / 9G INFO General (kmer_splitters.hpp : 289) Splitting kmer instances into 16 buckets. This might take a while. 0:23:10.631 3G / 9G INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:23:10.631 3G / 9G INFO General (kmer_splitters.hpp : 307) Memory available for splitting buffers: 32.2044 Gb 0:23:10.631 3G / 9G INFO General (kmer_splitters.hpp : 312) Using cell size of 2097152 0:24:23.062 3G / 9G INFO General (kmer_splitters.hpp : 325) Processed 3591351 edges 0:25:05.285 3G / 9G INFO General (kmer_splitters.hpp : 325) Processed 7183696 edges 0:25:34.526 3G / 9G INFO General (kmer_splitters.hpp : 325) Processed 10773642 edges 0:25:47.796 3G / 9G INFO General (kmer_splitters.hpp : 325) Processed 14363269 edges 0:26:15.816 3G / 9G INFO General (kmer_splitters.hpp : 325) Processed 16369384 edges 0:26:15.816 3G / 9G INFO General (kmer_splitters.hpp : 330) Used 16369384 sequences. 0:26:15.889 3G / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:27:22.240 3G / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 152937145 kmers in total. 0:27:22.240 3G / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:27:34.949 3G / 9G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:31:22.519 3G / 9G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:31:38.745 3G / 9G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 52906732 bytes occupied (2.7675 bits per kmer). 0:31:41.355 6G / 9G INFO General (edge_index_builders.hpp : 21) Collecting k-mer coverage information from graph, this takes a while. 0:36:39.270 6G / 9G INFO General (graph_construction.hpp : 182) Filling coverage index 0:36:39.270 6G / 9G INFO General (edge_index_builders.hpp : 99) Collecting k-mer coverage information from reads, this takes a while. 0:40:59.817 6G / 9G INFO General (graph_construction.hpp : 184) Filling coverage and flanking coverage from index 0:41:40.410 6G / 9G INFO General (construction.cpp : 33) Figured out: read length = 151 0:41:40.428 6G / 9G INFO StageManager (stage.cpp : 125) STAGE == EC Threshold Finding 0:41:54.702 6G / 9G INFO General (kmer_coverage_model.cpp : 178) Kmer coverage valley at: 23 0:41:54.704 6G / 9G INFO General (kmer_coverage_model.cpp : 198) K-mer histogram maximum: 50 0:41:54.704 6G / 9G INFO General (kmer_coverage_model.cpp : 234) Estimated median coverage: 51. Coverage mad: 11.8608 0:41:54.705 6G / 9G INFO General (kmer_coverage_model.cpp : 261) Fitting coverage model 0:41:54.897 6G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 2 0:41:55.381 6G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 4 0:41:57.080 6G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 8 0:41:59.616 6G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 16 0:42:00.820 6G / 9G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 50.8399. Fitted coverage std. dev: 10.9176 0:42:00.824 6G / 9G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 0.334577 0:42:00.824 6G / 9G INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 34 0:42:00.824 6G / 9G INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 34 0:42:00.824 6G / 9G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 61807925 0:42:00.825 6G / 9G INFO General (genomic_info_filler.cpp : 103) Mean coverage was calculated as 50.8399 0:42:00.826 6G / 9G INFO General (genomic_info_filler.cpp : 117) EC coverage threshold value was calculated as 34 0:42:00.826 6G / 9G INFO General (genomic_info_filler.cpp : 118) Trusted kmer low bound: 0 0:42:00.826 6G / 9G INFO StageManager (stage.cpp : 125) STAGE == Simplification 0:42:01.123 3G / 9G INFO General (graph_simplification.hpp : 911) Graph simplification started 0:42:01.123 3G / 9G INFO General (graph_simplification.hpp : 924) Fast simplification mode enabled 0:42:01.123 3G / 9G INFO General (graph_simplification.hpp : 771) PROCEDURE == Presimplification 0:42:01.123 3G / 9G INFO General (graph_simplification.hpp : 211) Removing short low covered self-conjugate connections 0:42:02.347 3G / 9G INFO General (graph_simplification.hpp : 403) Removing isolated edges 0:42:02.348 3G / 9G INFO General (graph_simplification.hpp : 404) All edges shorter than 151 will be removed 0:42:02.348 3G / 9G INFO General (graph_simplification.hpp : 405) Also edges shorter than 0 and coverage smaller than 0 will be removed 0:42:04.360 3G / 9G INFO General (graph_simplification.hpp : 687) Non parallel mode 0:42:59.976 3G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:45:05.372 3G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:49:07.973 3G / 9G INFO General (graph_simplification.hpp : 644) Using permanent iterators 0:49:07.974 3G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 1 0:49:12.340 3G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:49:30.469 3G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:49:56.225 2G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 2 0:49:56.225 2G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:49:56.480 2G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:50:04.248 2G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 3 0:50:04.249 2G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:50:04.348 2G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:50:07.308 2G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 4 0:50:07.308 2G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:50:07.350 2G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:50:09.242 2G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 5 0:50:09.242 2G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:50:09.265 2G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:50:10.802 2G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 6 0:50:10.802 2G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:50:10.817 2G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:50:12.494 2G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 7 0:50:12.494 2G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:50:12.505 2G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:50:14.159 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 8 0:50:14.159 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:50:14.167 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:50:15.122 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 9 0:50:15.122 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:50:15.128 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:50:15.636 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 10 0:50:15.636 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:50:15.641 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:50:16.098 1G / 9G INFO General (graph_simplification.hpp : 796) PROCEDURE == Post simplification 0:50:16.098 1G / 9G INFO General (graph_simplification.hpp : 644) Using permanent iterators 0:50:16.098 1G / 9G INFO General (graph_simplification.hpp : 806) Iteration 0 0:50:16.098 1G / 9G INFO General (graph_simplification.hpp : 247) Removal of relatively low covered connections disabled 0:50:16.568 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:50:17.603 1G / 9G INFO General (graph_simplification.hpp : 806) Iteration 1 0:50:17.603 1G / 9G INFO General (graph_simplification.hpp : 247) Removal of relatively low covered connections disabled 0:50:17.603 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:50:18.181 1G / 9G INFO StageManager (stage.cpp : 125) STAGE == Simplification Cleanup 0:50:18.182 1G / 9G INFO General (graph_simplification.hpp : 403) Removing isolated edges 0:50:18.182 1G / 9G INFO General (graph_simplification.hpp : 404) All edges shorter than 151 will be removed 0:50:18.182 1G / 9G INFO General (graph_simplification.hpp : 405) Also edges shorter than 0 and coverage smaller than 2 will be removed 0:50:18.265 1G / 9G INFO General (simplification.cpp : 56) Removing all the edges having coverage 0 and less 0:50:19.120 1G / 9G INFO General (simplification.cpp : 68) Counting average coverage 0:50:19.276 1G / 9G INFO General (simplification.cpp : 71) Average coverage = 48.6012 0:50:19.276 1G / 9G INFO StageManager (stage.cpp : 125) STAGE == Contig Output 0:50:19.276 1G / 9G INFO General (contig_output.hpp : 283) Outputting contigs to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_127-dipSPAdes-3.5.0-trimmed/spades//K33/simplified_contigs.fasta 0:50:38.392 1G / 9G INFO General (contig_output.hpp : 283) Outputting contigs to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_127-dipSPAdes-3.5.0-trimmed/spades//K33/before_rr.fasta 0:51:33.840 1G / 9G INFO General (contig_output.hpp : 283) Outputting contigs to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_127-dipSPAdes-3.5.0-trimmed/spades//K33/final_contigs.fasta 0:52:47.868 1G / 9G INFO General (launch.hpp : 82) SPAdes finished 0:52:52.180 64M / 9G INFO General (main.cpp : 166) Assembling time: 0 hours 52 minutes 52 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_127-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 0:00:00.010 4M / 4M INFO General (launch.hpp : 44) Will need read mapping, kmer mapper will be attached 0:00:00.010 4M / 4M INFO StageManager (stage.cpp : 125) STAGE == Construction 0:00:00.010 4M / 4M INFO General (construction.cpp : 44) Contigs from previous K will be used 0:00:00.014 4M / 4M INFO General (read_converter.hpp : 49) Binary reads detected 0:00:00.035 4M / 4M INFO General (graph_construction.hpp : 129) Constructing DeBruijn graph for k=55 0:00:00.038 4M / 4M INFO General (kmer_splitters.hpp : 172) Splitting kmer instances into 256 buckets. This might take a while. 0:00:00.039 4M / 4M INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:00:00.039 4M / 4M INFO General (kmer_splitters.hpp : 190) Memory available for splitting buffers: 2.08325 Gb 0:00:00.039 4M / 4M INFO General (kmer_splitters.hpp : 199) Using cell size of 131072 0:00:54.718 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 11313337 reads 0:01:09.822 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 22646336 reads 0:02:17.378 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 33966158 reads 0:06:03.756 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 45290353 reads 0:06:18.747 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 56604424 reads 0:06:27.473 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 62944904 reads 0:06:27.474 8G / 9G INFO General (kmer_splitters.hpp : 234) Adding contigs from previous K 0:07:09.272 8G / 9G INFO General (kmer_splitters.hpp : 245) Used 62944904 reads. Maximum read length 151 0:07:09.273 8G / 9G INFO General (kmer_splitters.hpp : 246) Average read length 149.804 0:07:11.509 64M / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:07:59.595 64M / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 228439044 kmers in total. 0:07:59.596 64M / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:08:20.291 64M / 9G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:08:20.291 64M / 9G INFO General (kmer_splitters.hpp : 379) Splitting kmer instances into 256 buckets. This might take a while. 0:08:20.291 64M / 9G INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:08:20.291 64M / 9G INFO General (kmer_splitters.hpp : 397) Memory available for splitting buffers: 2.08203 Gb 0:08:20.292 64M / 9G INFO General (kmer_splitters.hpp : 405) Using cell size of 131072 0:08:59.302 8G / 9G INFO General (kmer_splitters.hpp : 428) Processed 228439044 kmers 0:08:59.303 8G / 9G INFO General (kmer_splitters.hpp : 437) Used 228439044 kmers. 0:09:00.937 64M / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:09:16.908 64M / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 227578204 kmers in total. 0:09:16.908 64M / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:09:35.684 64M / 9G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:10:08.784 192M / 9G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:10:26.545 192M / 9G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 78727873 bytes occupied (2.7675 bits per kmer). 0:10:26.898 412M / 9G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 382) Building k-mer extensions from k+1-mers 0:10:58.982 412M / 9G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 386) Building k-mer extensions from k+1-mers finished. 0:10:58.986 412M / 9G INFO General (graph_construction.hpp : 145) Condensing graph 0:10:58.987 412M / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 337) Extracting unbranching paths 0:13:55.124 2G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 351) Extracting unbranching paths finished. 22099629 sequences extracted 0:14:18.489 2G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 311) Collecting perfect loops 0:15:40.730 2G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 326) Collecting perfect loops finished. 4 loops collected 0:16:01.631 5G / 9G INFO General (graph_construction.hpp : 150) Building index with from graph 0:16:01.633 5G / 9G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:16:01.633 5G / 9G INFO General (kmer_splitters.hpp : 289) Splitting kmer instances into 16 buckets. This might take a while. 0:16:01.633 5G / 9G INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:16:01.633 5G / 9G INFO General (kmer_splitters.hpp : 307) Memory available for splitting buffers: 31.5885 Gb 0:16:01.633 5G / 9G INFO General (kmer_splitters.hpp : 312) Using cell size of 2097152 0:16:51.923 5G / 9G INFO General (kmer_splitters.hpp : 325) Processed 3243974 edges 0:18:59.356 5G / 9G INFO General (kmer_splitters.hpp : 325) Processed 6490841 edges 0:20:24.970 5G / 9G INFO General (kmer_splitters.hpp : 325) Processed 9736698 edges 0:21:45.207 6G / 9G INFO General (kmer_splitters.hpp : 325) Processed 12985723 edges 0:22:17.178 6G / 9G INFO General (kmer_splitters.hpp : 325) Processed 16231674 edges 0:22:46.707 6G / 9G INFO General (kmer_splitters.hpp : 325) Processed 19474329 edges 0:24:05.254 6G / 9G INFO General (kmer_splitters.hpp : 325) Processed 22099633 edges 0:24:05.254 6G / 9G INFO General (kmer_splitters.hpp : 330) Used 22099633 sequences. 0:24:05.297 5G / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:25:57.808 5G / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 228439044 kmers in total. 0:25:57.808 5G / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:26:58.635 5G / 9G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:32:59.226 5G / 9G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:33:17.197 5G / 9G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 79025680 bytes occupied (2.7675 bits per kmer). 0:33:21.074 10G / 10G INFO General (edge_index_builders.hpp : 21) Collecting k-mer coverage information from graph, this takes a while. 0:41:33.678 10G / 10G INFO General (graph_construction.hpp : 182) Filling coverage index 0:41:33.678 10G / 10G INFO General (edge_index_builders.hpp : 99) Collecting k-mer coverage information from reads, this takes a while. 0:45:31.901 10G / 10G INFO General (graph_construction.hpp : 184) Filling coverage and flanking coverage from index 0:46:32.280 10G / 10G INFO General (construction.cpp : 33) Figured out: read length = 151 0:46:32.296 10G / 10G INFO StageManager (stage.cpp : 125) STAGE == EC Threshold Finding 0:46:46.980 10G / 10G INFO General (kmer_coverage_model.cpp : 178) Kmer coverage valley at: 14 0:46:46.980 10G / 10G INFO General (kmer_coverage_model.cpp : 198) K-mer histogram maximum: 39 0:46:46.980 10G / 10G INFO General (kmer_coverage_model.cpp : 234) Estimated median coverage: 40. Coverage mad: 10.3782 0:46:46.981 10G / 10G INFO General (kmer_coverage_model.cpp : 261) Fitting coverage model 0:46:47.124 10G / 10G INFO General (kmer_coverage_model.cpp : 296) ... iteration 2 0:46:47.508 10G / 10G INFO General (kmer_coverage_model.cpp : 296) ... iteration 4 0:46:48.892 10G / 10G INFO General (kmer_coverage_model.cpp : 296) ... iteration 8 0:46:51.457 10G / 10G INFO General (kmer_coverage_model.cpp : 296) ... iteration 16 0:46:53.942 10G / 10G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 40.3057. Fitted coverage std. dev: 10.0381 0:46:53.945 10G / 10G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 0.507058 0:46:53.945 10G / 10G INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 25 0:46:53.945 10G / 10G INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 25 0:46:53.945 10G / 10G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 62522227 0:46:53.946 10G / 10G INFO General (genomic_info_filler.cpp : 103) Mean coverage was calculated as 40.3057 0:46:53.946 10G / 10G INFO General (genomic_info_filler.cpp : 117) EC coverage threshold value was calculated as 25 0:46:53.946 10G / 10G INFO General (genomic_info_filler.cpp : 118) Trusted kmer low bound: 0 0:46:53.946 10G / 10G INFO StageManager (stage.cpp : 125) STAGE == Gap Closer 0:46:53.974 10G / 10G INFO General (gap_closer.cpp : 157) Preparing shift maps 0:47:15.375 10G / 10G INFO General (gap_closer.cpp : 117) Processing paired reads (takes a while) 0:48:21.901 12G / 12G INFO General (gap_closer.cpp : 136) Used 31364962 paired reads 0:48:21.901 12G / 12G INFO General (gap_closer.cpp : 138) Merging paired indices 0:48:43.345 10G / 12G INFO GapCloser (gap_closer.cpp : 395) Closing short gaps 0:49:51.151 10G / 12G INFO GapCloser (gap_closer.cpp : 424) Closing short gaps complete: filled 377 gaps after checking 38563 candidates 0:50:01.041 10G / 12G INFO StageManager (stage.cpp : 125) STAGE == Simplification 0:50:01.471 4G / 12G INFO General (graph_simplification.hpp : 911) Graph simplification started 0:50:01.471 4G / 12G INFO General (graph_simplification.hpp : 924) Fast simplification mode enabled 0:50:01.471 4G / 12G INFO General (graph_simplification.hpp : 771) PROCEDURE == Presimplification 0:50:01.471 4G / 12G INFO General (graph_simplification.hpp : 211) Removing short low covered self-conjugate connections 0:50:03.653 4G / 12G INFO General (graph_simplification.hpp : 403) Removing isolated edges 0:50:03.654 4G / 12G INFO General (graph_simplification.hpp : 404) All edges shorter than 151 will be removed 0:50:03.654 4G / 12G INFO General (graph_simplification.hpp : 405) Also edges shorter than 0 and coverage smaller than 0 will be removed 0:50:07.996 4G / 12G INFO General (graph_simplification.hpp : 687) Non parallel mode 0:51:27.324 5G / 12G INFO General (graph_simplification.hpp : 93) Clipping tips 0:55:13.878 5G / 12G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:56:42.822 3G / 12G INFO General (graph_simplification.hpp : 644) Using permanent iterators 0:56:42.822 3G / 12G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 1 0:56:44.611 3G / 12G INFO General (graph_simplification.hpp : 93) Clipping tips 0:56:52.407 3G / 12G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:56:59.181 2G / 12G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 2 0:56:59.181 2G / 12G INFO General (graph_simplification.hpp : 93) Clipping tips 0:56:59.266 2G / 12G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:57:04.204 2G / 12G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 3 0:57:04.204 2G / 12G INFO General (graph_simplification.hpp : 93) Clipping tips 0:57:04.263 2G / 12G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:57:06.460 2G / 12G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 4 0:57:06.460 2G / 12G INFO General (graph_simplification.hpp : 93) Clipping tips 0:57:06.483 2G / 12G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:57:07.926 1G / 12G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 5 0:57:07.926 1G / 12G INFO General (graph_simplification.hpp : 93) Clipping tips 0:57:07.939 1G / 12G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:57:09.191 1G / 12G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 6 0:57:09.191 1G / 12G INFO General (graph_simplification.hpp : 93) Clipping tips 0:57:09.200 1G / 12G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:57:10.934 1G / 12G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 7 0:57:10.934 1G / 12G INFO General (graph_simplification.hpp : 93) Clipping tips 0:57:10.940 1G / 12G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:57:12.812 1G / 12G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 8 0:57:12.812 1G / 12G INFO General (graph_simplification.hpp : 93) Clipping tips 0:57:12.817 1G / 12G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:57:14.444 1G / 12G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 9 0:57:14.445 1G / 12G INFO General (graph_simplification.hpp : 93) Clipping tips 0:57:14.449 1G / 12G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:57:15.577 1G / 12G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 10 0:57:15.577 1G / 12G INFO General (graph_simplification.hpp : 93) Clipping tips 0:57:15.580 1G / 12G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:57:16.112 1G / 12G INFO General (graph_simplification.hpp : 796) PROCEDURE == Post simplification 0:57:16.112 1G / 12G INFO General (graph_simplification.hpp : 644) Using permanent iterators 0:57:16.112 1G / 12G INFO General (graph_simplification.hpp : 806) Iteration 0 0:57:16.112 1G / 12G INFO General (graph_simplification.hpp : 247) Removal of relatively low covered connections disabled 0:57:16.304 1G / 12G INFO General (graph_simplification.hpp : 93) Clipping tips 0:57:16.706 1G / 12G INFO General (graph_simplification.hpp : 806) Iteration 1 0:57:16.706 1G / 12G INFO General (graph_simplification.hpp : 247) Removal of relatively low covered connections disabled 0:57:16.706 1G / 12G INFO General (graph_simplification.hpp : 93) Clipping tips 0:57:17.000 1020M / 12G INFO StageManager (stage.cpp : 125) STAGE == Gap Closer 0:57:17.000 1020M / 12G INFO General (graph_pack.hpp : 84) Index refill 0:57:17.001 1020M / 12G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:57:17.001 1020M / 12G INFO General (kmer_splitters.hpp : 289) Splitting kmer instances into 16 buckets. This might take a while. 0:57:17.001 1020M / 12G INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:57:17.001 1020M / 12G INFO General (kmer_splitters.hpp : 307) Memory available for splitting buffers: 33.0013 Gb 0:57:17.001 1020M / 12G INFO General (kmer_splitters.hpp : 312) Using cell size of 2097152 0:57:50.593 1G / 12G INFO General (kmer_splitters.hpp : 325) Processed 38309 edges 0:58:08.001 1G / 12G INFO General (kmer_splitters.hpp : 325) Processed 78487 edges 0:58:23.903 1G / 12G INFO General (kmer_splitters.hpp : 325) Processed 85650 edges 0:58:23.903 1G / 12G INFO General (kmer_splitters.hpp : 330) Used 85650 sequences. 0:58:23.993 1016M / 12G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:58:46.188 1016M / 12G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 73223039 kmers in total. 0:58:46.188 1016M / 12G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:58:53.061 1016M / 12G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 1:00:26.681 1G / 12G INFO General (kmer_index.hpp : 371) Merging final buckets. 1:00:33.113 1G / 12G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 25330636 bytes occupied (2.7675 bits per kmer). 1:00:34.412 2G / 12G INFO General (edge_index_builders.hpp : 21) Collecting k-mer coverage information from graph, this takes a while. 1:02:36.455 2G / 12G INFO General (gap_closer.cpp : 157) Preparing shift maps 1:02:36.573 2G / 12G INFO General (gap_closer.cpp : 117) Processing paired reads (takes a while) 1:03:39.125 2G / 12G INFO General (gap_closer.cpp : 136) Used 31364962 paired reads 1:03:39.125 2G / 12G INFO General (gap_closer.cpp : 138) Merging paired indices 1:03:39.230 2G / 12G INFO GapCloser (gap_closer.cpp : 395) Closing short gaps 1:03:39.405 2G / 12G INFO GapCloser (gap_closer.cpp : 424) Closing short gaps complete: filled 6 gaps after checking 522 candidates 1:03:39.806 2G / 12G INFO StageManager (stage.cpp : 125) STAGE == Simplification Cleanup 1:03:39.806 2G / 12G INFO General (graph_simplification.hpp : 403) Removing isolated edges 1:03:39.806 2G / 12G INFO General (graph_simplification.hpp : 404) All edges shorter than 151 will be removed 1:03:39.807 2G / 12G INFO General (graph_simplification.hpp : 405) Also edges shorter than 0 and coverage smaller than 2 will be removed 1:03:40.635 2G / 12G INFO General (simplification.cpp : 56) Removing all the edges having coverage 0 and less 1:03:40.909 2G / 12G INFO General (simplification.cpp : 68) Counting average coverage 1:03:40.974 2G / 12G INFO General (simplification.cpp : 71) Average coverage = 38.2313 1:03:40.974 2G / 12G INFO StageManager (stage.cpp : 125) STAGE == Contig Output 1:03:40.974 2G / 12G INFO General (contig_output.hpp : 283) Outputting contigs to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_127-dipSPAdes-3.5.0-trimmed/spades//K55/simplified_contigs.fasta 1:03:56.629 2G / 12G INFO General (contig_output.hpp : 283) Outputting contigs to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_127-dipSPAdes-3.5.0-trimmed/spades//K55/before_rr.fasta 1:05:00.399 2G / 12G INFO General (contig_output.hpp : 283) Outputting contigs to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_127-dipSPAdes-3.5.0-trimmed/spades//K55/final_contigs.fasta 1:05:46.618 2G / 12G INFO General (launch.hpp : 82) SPAdes finished 1:05:50.414 64M / 12G INFO General (main.cpp : 166) Assembling time: 1 hours 5 minutes 50 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_127-dipSPAdes-3.5.0-trimmed/spades/dataset.info) with K=77 0:00:00.001 4M / 4M INFO General (launch.hpp : 28) SPAdes started 0:00:00.001 4M / 4M INFO General (launch.hpp : 29) Starting from stage: construction 0:00:00.002 4M / 4M INFO General (launch.hpp : 44) Will need read mapping, kmer mapper will be attached 0:00:00.002 4M / 4M INFO StageManager (stage.cpp : 125) STAGE == Construction 0:00:00.002 4M / 4M INFO General (construction.cpp : 44) Contigs from previous K will be used 0:00:00.006 4M / 4M INFO General (read_converter.hpp : 49) Binary reads detected 0:00:00.027 4M / 4M INFO General (graph_construction.hpp : 129) Constructing DeBruijn graph for k=77 0:00:00.030 4M / 4M INFO General (kmer_splitters.hpp : 172) Splitting kmer instances into 256 buckets. This might take a while. 0:00:00.030 4M / 4M INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:00:00.031 4M / 4M INFO General (kmer_splitters.hpp : 190) Memory available for splitting buffers: 2.08325 Gb 0:00:00.031 4M / 4M INFO General (kmer_splitters.hpp : 199) Using cell size of 87381 0:03:22.311 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 9806317 reads 0:03:35.115 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 19642306 reads 0:03:47.844 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 29463324 reads 0:09:38.655 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 39276675 reads 0:11:32.694 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 49113692 reads 0:11:56.166 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 58910121 reads 0:13:01.539 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 62944904 reads 0:13:01.540 8G / 9G INFO General (kmer_splitters.hpp : 234) Adding contigs from previous K 0:13:22.430 8G / 9G INFO General (kmer_splitters.hpp : 245) Used 62944904 reads. Maximum read length 151 0:13:22.430 8G / 9G INFO General (kmer_splitters.hpp : 246) Average read length 149.804 0:13:24.667 64M / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:15:04.227 64M / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 233963734 kmers in total. 0:15:04.227 64M / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:15:37.327 64M / 9G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:15:37.327 64M / 9G INFO General (kmer_splitters.hpp : 379) Splitting kmer instances into 256 buckets. This might take a while. 0:15:37.328 64M / 9G INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:15:37.328 64M / 9G INFO General (kmer_splitters.hpp : 397) Memory available for splitting buffers: 2.08203 Gb 0:15:37.328 64M / 9G INFO General (kmer_splitters.hpp : 405) Using cell size of 87381 0:16:19.142 8G / 9G INFO General (kmer_splitters.hpp : 428) Processed 178956288 kmers 0:16:34.405 8G / 9G INFO General (kmer_splitters.hpp : 428) Processed 233963734 kmers 0:16:34.406 8G / 9G INFO General (kmer_splitters.hpp : 437) Used 233963734 kmers. 0:16:36.312 64M / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:17:03.245 64M / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 234154389 kmers in total. 0:17:03.245 64M / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:17:35.742 64M / 9G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:18:13.143 192M / 9G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:19:02.861 192M / 9G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 81002822 bytes occupied (2.7675 bits per kmer). 0:19:03.264 416M / 9G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 382) Building k-mer extensions from k+1-mers 0:19:40.179 416M / 9G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 386) Building k-mer extensions from k+1-mers finished. 0:19:40.183 416M / 9G INFO General (graph_construction.hpp : 145) Condensing graph 0:19:40.183 416M / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 337) Extracting unbranching paths 0:22:41.790 2G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 351) Extracting unbranching paths finished. 19985536 sequences extracted 0:23:07.243 2G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 311) Collecting perfect loops 0:24:44.481 2G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 326) Collecting perfect loops finished. 12 loops collected 0:25:05.256 5G / 9G INFO General (graph_construction.hpp : 150) Building index with from graph 0:25:05.263 5G / 9G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:25:05.263 5G / 9G INFO General (kmer_splitters.hpp : 289) Splitting kmer instances into 16 buckets. This might take a while. 0:25:05.263 5G / 9G INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:25:05.263 5G / 9G INFO General (kmer_splitters.hpp : 307) Memory available for splitting buffers: 31.6302 Gb 0:25:05.263 5G / 9G INFO General (kmer_splitters.hpp : 312) Using cell size of 1398101 0:25:53.199 5G / 9G INFO General (kmer_splitters.hpp : 325) Processed 1912363 edges 0:27:33.944 5G / 9G INFO General (kmer_splitters.hpp : 325) Processed 3824394 edges 0:28:56.830 5G / 9G INFO General (kmer_splitters.hpp : 325) Processed 5734063 edges 0:29:29.200 5G / 9G INFO General (kmer_splitters.hpp : 325) Processed 7644077 edges 0:30:16.666 5G / 9G INFO General (kmer_splitters.hpp : 325) Processed 9555124 edges 0:30:23.624 5G / 9G INFO General (kmer_splitters.hpp : 325) Processed 11468137 edges 0:30:30.578 5G / 9G INFO General (kmer_splitters.hpp : 325) Processed 13379297 edges 0:30:37.644 5G / 9G INFO General (kmer_splitters.hpp : 325) Processed 15290619 edges 0:30:44.678 6G / 9G INFO General (kmer_splitters.hpp : 325) Processed 17198855 edges 0:30:51.525 6G / 9G INFO General (kmer_splitters.hpp : 325) Processed 19109347 edges 0:30:54.717 6G / 9G INFO General (kmer_splitters.hpp : 325) Processed 19985548 edges 0:30:54.718 6G / 9G INFO General (kmer_splitters.hpp : 330) Used 19985548 sequences. 0:30:54.786 5G / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:32:47.611 5G / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 233963734 kmers in total. 0:32:47.611 5G / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:33:15.871 5G / 9G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:39:34.605 5G / 9G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:40:05.144 5G / 9G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 80936866 bytes occupied (2.7675 bits per kmer). 0:40:09.125 10G / 10G INFO General (edge_index_builders.hpp : 21) Collecting k-mer coverage information from graph, this takes a while. 0:48:46.540 10G / 10G INFO General (graph_construction.hpp : 182) Filling coverage index 0:48:46.540 10G / 10G INFO General (edge_index_builders.hpp : 99) Collecting k-mer coverage information from reads, this takes a while. 0:52:16.881 10G / 10G INFO General (graph_construction.hpp : 184) Filling coverage and flanking coverage from index 0:53:20.851 10G / 10G INFO General (construction.cpp : 33) Figured out: read length = 151 0:53:20.869 10G / 10G INFO StageManager (stage.cpp : 125) STAGE == EC Threshold Finding 0:53:34.657 10G / 10G INFO General (kmer_coverage_model.cpp : 178) Kmer coverage valley at: 9 0:53:34.657 10G / 10G INFO General (kmer_coverage_model.cpp : 198) K-mer histogram maximum: 29 0:53:34.657 10G / 10G INFO General (kmer_coverage_model.cpp : 234) Estimated median coverage: 30. Coverage mad: 10.3782 0:53:34.657 10G / 10G INFO General (kmer_coverage_model.cpp : 261) Fitting coverage model 0:53:34.763 10G / 10G INFO General (kmer_coverage_model.cpp : 296) ... iteration 2 0:53:35.050 10G / 10G INFO General (kmer_coverage_model.cpp : 296) ... iteration 4 0:53:36.100 10G / 10G INFO General (kmer_coverage_model.cpp : 296) ... iteration 8 0:53:37.920 10G / 10G INFO General (kmer_coverage_model.cpp : 296) ... iteration 16 0:53:40.209 10G / 10G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 30.0955. Fitted coverage std. dev: 8.74528 0:53:40.211 10G / 10G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 0.457959 0:53:40.211 10G / 10G INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 18 0:53:40.211 10G / 10G INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 18 0:53:40.211 10G / 10G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 62476964 0:53:40.211 10G / 10G INFO General (genomic_info_filler.cpp : 103) Mean coverage was calculated as 30.0955 0:53:40.212 10G / 10G INFO General (genomic_info_filler.cpp : 117) EC coverage threshold value was calculated as 18 0:53:40.212 10G / 10G INFO General (genomic_info_filler.cpp : 118) Trusted kmer low bound: 0 0:53:40.212 10G / 10G INFO StageManager (stage.cpp : 125) STAGE == Gap Closer 0:53:40.222 10G / 10G INFO General (gap_closer.cpp : 157) Preparing shift maps 0:54:03.839 10G / 10G INFO General (gap_closer.cpp : 117) Processing paired reads (takes a while) 0:54:54.846 13G / 13G INFO General (gap_closer.cpp : 136) Used 31364962 paired reads 0:54:54.846 13G / 13G INFO General (gap_closer.cpp : 138) Merging paired indices 0:55:22.029 10G / 13G INFO GapCloser (gap_closer.cpp : 395) Closing short gaps 0:56:26.144 10G / 13G INFO GapCloser (gap_closer.cpp : 424) Closing short gaps complete: filled 781 gaps after checking 43544 candidates 0:56:37.020 10G / 13G INFO StageManager (stage.cpp : 125) STAGE == Simplification 0:56:37.464 4G / 13G INFO General (graph_simplification.hpp : 911) Graph simplification started 0:56:37.464 4G / 13G INFO General (graph_simplification.hpp : 924) Fast simplification mode enabled 0:56:37.464 4G / 13G INFO General (graph_simplification.hpp : 771) PROCEDURE == Presimplification 0:56:37.464 4G / 13G INFO General (graph_simplification.hpp : 211) Removing short low covered self-conjugate connections 0:56:39.243 4G / 13G INFO General (graph_simplification.hpp : 403) Removing isolated edges 0:56:39.245 4G / 13G INFO General (graph_simplification.hpp : 404) All edges shorter than 151 will be removed 0:56:39.246 4G / 13G INFO General (graph_simplification.hpp : 405) Also edges shorter than 0 and coverage smaller than 0 will be removed 0:56:45.706 4G / 13G INFO General (graph_simplification.hpp : 687) Non parallel mode 0:57:48.544 5G / 13G INFO General (graph_simplification.hpp : 93) Clipping tips 1:01:20.894 3G / 13G INFO General (graph_simplification.hpp : 187) Removing low covered connections 1:01:34.992 2G / 13G INFO General (graph_simplification.hpp : 644) Using permanent iterators 1:01:34.992 2G / 13G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 1 1:01:35.730 2G / 13G INFO General (graph_simplification.hpp : 93) Clipping tips 1:01:38.992 2G / 13G INFO General (graph_simplification.hpp : 187) Removing low covered connections 1:01:39.522 2G / 13G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 2 1:01:39.522 2G / 13G INFO General (graph_simplification.hpp : 93) Clipping tips 1:01:39.529 2G / 13G INFO General (graph_simplification.hpp : 187) Removing low covered connections 1:01:41.984 2G / 13G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 3 1:01:41.984 2G / 13G INFO General (graph_simplification.hpp : 93) Clipping tips 1:01:42.032 2G / 13G INFO General (graph_simplification.hpp : 187) Removing low covered connections 1:01:43.369 1G / 13G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 4 1:01:43.370 1G / 13G INFO General (graph_simplification.hpp : 93) Clipping tips 1:01:43.389 1G / 13G INFO General (graph_simplification.hpp : 187) Removing low covered connections 1:01:44.455 1G / 13G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 5 1:01:44.455 1G / 13G INFO General (graph_simplification.hpp : 93) Clipping tips 1:01:44.464 1G / 13G INFO General (graph_simplification.hpp : 187) Removing low covered connections 1:01:45.384 1G / 13G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 6 1:01:45.384 1G / 13G INFO General (graph_simplification.hpp : 93) Clipping tips 1:01:45.390 1G / 13G INFO General (graph_simplification.hpp : 187) Removing low covered connections 1:01:46.772 1G / 13G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 7 1:01:46.772 1G / 13G INFO General (graph_simplification.hpp : 93) Clipping tips 1:01:46.777 1G / 13G INFO General (graph_simplification.hpp : 187) Removing low covered connections 1:01:48.465 1G / 13G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 8 1:01:48.465 1G / 13G INFO General (graph_simplification.hpp : 93) Clipping tips 1:01:48.469 1G / 13G INFO General (graph_simplification.hpp : 187) Removing low covered connections 1:01:50.177 1G / 13G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 9 1:01:50.177 1G / 13G INFO General (graph_simplification.hpp : 93) Clipping tips 1:01:50.179 1G / 13G INFO General (graph_simplification.hpp : 187) Removing low covered connections 1:01:51.523 1004M / 13G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 10 1:01:51.523 1004M / 13G INFO General (graph_simplification.hpp : 93) Clipping tips 1:01:51.525 1004M / 13G INFO General (graph_simplification.hpp : 187) Removing low covered connections 1:01:52.461 928M / 13G INFO General (graph_simplification.hpp : 796) PROCEDURE == Post simplification 1:01:52.461 928M / 13G INFO General (graph_simplification.hpp : 644) Using permanent iterators 1:01:52.461 928M / 13G INFO General (graph_simplification.hpp : 806) Iteration 0 1:01:52.461 928M / 13G INFO General (graph_simplification.hpp : 247) Removal of relatively low covered connections disabled 1:01:52.600 928M / 13G INFO General (graph_simplification.hpp : 93) Clipping tips 1:01:52.870 928M / 13G INFO General (graph_simplification.hpp : 806) Iteration 1 1:01:52.871 928M / 13G INFO General (graph_simplification.hpp : 247) Removal of relatively low covered connections disabled 1:01:52.871 928M / 13G INFO General (graph_simplification.hpp : 93) Clipping tips 1:01:52.986 904M / 13G INFO StageManager (stage.cpp : 125) STAGE == Gap Closer 1:01:52.986 904M / 13G INFO General (graph_pack.hpp : 84) Index refill 1:01:52.987 904M / 13G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 1:01:52.987 904M / 13G INFO General (kmer_splitters.hpp : 289) Splitting kmer instances into 16 buckets. This might take a while. 1:01:52.987 904M / 13G INFO General (file_limit.hpp : 29) Open file limit set to 32768 1:01:52.988 904M / 13G INFO General (kmer_splitters.hpp : 307) Memory available for splitting buffers: 33.0391 Gb 1:01:52.988 904M / 13G INFO General (kmer_splitters.hpp : 312) Using cell size of 1398101 1:03:41.185 1G / 13G INFO General (kmer_splitters.hpp : 325) Processed 19417 edges 1:05:05.480 1G / 13G INFO General (kmer_splitters.hpp : 325) Processed 39627 edges 1:05:50.881 1G / 13G INFO General (kmer_splitters.hpp : 325) Processed 59373 edges 1:06:21.561 1G / 13G INFO General (kmer_splitters.hpp : 325) Processed 65486 edges 1:06:21.561 1G / 13G INFO General (kmer_splitters.hpp : 330) Used 65486 sequences. 1:06:21.645 900M / 13G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 1:06:49.400 900M / 13G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 73623501 kmers in total. 1:06:49.400 900M / 13G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 1:06:58.280 900M / 13G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 1:08:37.781 924M / 13G INFO General (kmer_index.hpp : 371) Merging final buckets. 1:08:47.522 924M / 13G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 25469166 bytes occupied (2.7675 bits per kmer). 1:08:48.814 2G / 13G INFO General (edge_index_builders.hpp : 21) Collecting k-mer coverage information from graph, this takes a while. 1:11:09.052 2G / 13G INFO General (gap_closer.cpp : 157) Preparing shift maps 1:11:09.159 2G / 13G INFO General (gap_closer.cpp : 117) Processing paired reads (takes a while) 1:12:09.313 2G / 13G INFO General (gap_closer.cpp : 136) Used 31364962 paired reads 1:12:09.314 2G / 13G INFO General (gap_closer.cpp : 138) Merging paired indices 1:12:09.514 2G / 13G INFO GapCloser (gap_closer.cpp : 395) Closing short gaps 1:12:09.676 2G / 13G INFO GapCloser (gap_closer.cpp : 424) Closing short gaps complete: filled 6 gaps after checking 598 candidates 1:12:10.148 2G / 13G INFO StageManager (stage.cpp : 125) STAGE == Simplification Cleanup 1:12:10.148 2G / 13G INFO General (graph_simplification.hpp : 403) Removing isolated edges 1:12:10.149 2G / 13G INFO General (graph_simplification.hpp : 404) All edges shorter than 151 will be removed 1:12:10.149 2G / 13G INFO General (graph_simplification.hpp : 405) Also edges shorter than 0 and coverage smaller than 2 will be removed 1:12:11.942 2G / 13G INFO General (simplification.cpp : 56) Removing all the edges having coverage 0 and less 1:12:12.118 2G / 13G INFO General (simplification.cpp : 68) Counting average coverage 1:12:12.162 2G / 13G INFO General (simplification.cpp : 71) Average coverage = 28.7663 1:12:12.163 2G / 13G INFO StageManager (stage.cpp : 125) STAGE == Mismatch Correction 1:13:16.210 2G / 13G INFO General (mismatch_shall_not_pass.hp: 188) Finished collecting potential mismatches positions 1:13:16.354 2G / 13G INFO General (mismatch_shall_not_pass.hp: 291) All edges processed 1:13:16.358 2G / 13G INFO General (mismatch_correction.cpp : 18) Corrected 0 nucleotides 1:13:16.371 2G / 13G INFO StageManager (stage.cpp : 125) STAGE == Paired Information Counting 1:13:16.576 2G / 13G INFO General (pair_info_count.cpp : 150) Graph N50: 29515 1:13:16.598 2G / 13G INFO General (pair_info_count.cpp : 152) Estimating insert size for library #0 1:13:16.598 2G / 13G INFO General (pair_info_count.cpp : 31) Estimating insert size (takes a while) 1:13:16.607 2G / 13G INFO General (short_read_mapper.hpp : 91) Selecting usual mapper 1:13:23.067 2G / 13G INFO General (sequence_mapper_notifier.h: 81) Processed 200000 reads 1:13:23.079 2G / 13G INFO General (sequence_mapper_notifier.h: 81) Processed 400000 reads 1:13:23.086 2G / 13G INFO General (sequence_mapper_notifier.h: 81) Processed 600000 reads 1:13:23.087 2G / 13G INFO General (sequence_mapper_notifier.h: 81) Processed 800000 reads 1:13:23.100 2G / 13G INFO General (sequence_mapper_notifier.h: 81) Processed 1000000 reads 1:13:23.112 2G / 13G INFO General (sequence_mapper_notifier.h: 81) Processed 1200000 reads 1:13:23.524 2G / 13G INFO General (sequence_mapper_notifier.h: 81) Processed 2200000 reads 1:13:29.968 2G / 13G INFO General (sequence_mapper_notifier.h: 81) Processed 4200000 reads 1:13:37.911 2G / 13G INFO General (sequence_mapper_notifier.h: 81) Processed 8400000 reads 1:13:52.887 2G / 13G INFO General (sequence_mapper_notifier.h: 89) Processed 15682481 reads 1:13:52.888 2G / 13G INFO General (pair_info_count.cpp : 41) 7854515 paired reads (50.0846% of all) aligned to long edges 1:13:52.897 2G / 13G INFO General (pair_info_count.cpp : 170) Estimated insert size for paired library #0 1:13:52.897 2G / 13G INFO General (pair_info_count.cpp : 175) Insert size = 211.342, deviation = 56.2116, left quantile = 147, right quantile = 285, read length = 151 1:13:52.897 2G / 13G INFO General (pair_info_count.cpp : 187) Mapping library #0 1:13:52.897 2G / 13G INFO General (pair_info_count.cpp : 189) Mapping paired reads (takes a while) 1:13:52.897 2G / 13G INFO General (pair_info_count.cpp : 73) Left insert size qauntile 147, right insert size quantile 285 1:13:52.906 2G / 13G INFO General (short_read_mapper.hpp : 91) Selecting usual mapper 1:14:01.073 4G / 13G INFO General (sequence_mapper_notifier.h: 81) Processed 200000 reads 1:14:01.789 4G / 13G INFO General (sequence_mapper_notifier.h: 81) Processed 400000 reads 1:14:02.755 4G / 13G INFO General (sequence_mapper_notifier.h: 81) Processed 600000 reads 1:14:03.806 4G / 13G INFO General (sequence_mapper_notifier.h: 81) Processed 800000 reads 1:14:04.975 4G / 13G INFO General (sequence_mapper_notifier.h: 81) Processed 1000000 reads 1:14:06.366 4G / 13G INFO General (sequence_mapper_notifier.h: 81) Processed 1200000 reads 1:14:13.149 4G / 13G INFO General (sequence_mapper_notifier.h: 81) Processed 2200000 reads 1:14:27.339 4G / 13G INFO General (sequence_mapper_notifier.h: 81) Processed 4200000 reads 1:14:58.028 4G / 13G INFO General (sequence_mapper_notifier.h: 81) Processed 8400000 reads 1:16:01.278 4G / 13G INFO General (sequence_mapper_notifier.h: 81) Processed 16800000 reads 1:17:57.271 3G / 13G INFO General (sequence_mapper_notifier.h: 89) Processed 31364962 reads 1:19:02.907 3G / 13G INFO General (split_graph_pair_info.hpp : 344) Threshold for paired information 0.0615734 1:19:06.274 2G / 13G INFO StageManager (stage.cpp : 125) STAGE == Distance Estimation 1:19:06.286 2G / 13G INFO General (distance_estimation.cpp : 234) Processing library #0 1:19:06.286 2G / 13G INFO General (distance_estimation.cpp : 136) Weight Filter Done 1:19:06.286 2G / 13G INFO DistanceEstimator (distance_estimation.hpp : 187) Using SIMPLE distance estimator 1:19:07.955 2G / 13G INFO DistanceEstimator (distance_estimation.hpp : 208) Merging maps 1:19:08.832 2G / 13G INFO General (distance_estimation.cpp : 38) Filtering info 1:19:10.126 2G / 13G INFO General (pair_info_filters.hpp : 354) Pruning the index 1:19:10.171 2G / 13G INFO General (distance_estimation.cpp : 184) Refining clustered pair information 1:19:10.276 2G / 13G INFO General (distance_estimation.cpp : 186) The refining of clustered pair information has been finished 1:19:10.276 2G / 13G INFO General (distance_estimation.cpp : 188) Filling paired information 1:19:11.053 2G / 13G INFO PairInfoImprover (pair_info_improver.hpp : 61) Paired info stats: missing = 17651; contradictional = 3560 1:19:11.779 2G / 13G INFO PairInfoImprover (pair_info_improver.hpp : 61) Paired info stats: missing = 1802; contradictional = 0 1:19:11.779 2G / 13G INFO General (distance_estimation.cpp : 193) Filling scaffolding index 1:19:11.779 2G / 13G INFO DistanceEstimator (distance_estimation.hpp : 187) Using SMOOTHING distance estimator 1:19:16.992 2G / 13G INFO DistanceEstimator (distance_estimation.hpp : 208) Merging maps 1:19:17.030 2G / 13G INFO General (distance_estimation.cpp : 38) Filtering info 1:19:17.193 2G / 13G INFO General (pair_info_filters.hpp : 354) Pruning the index 1:19:17.569 2G / 13G INFO StageManager (stage.cpp : 125) STAGE == Repeat Resolving 1:19:17.569 2G / 13G INFO General (contig_output.hpp : 283) Outputting contigs to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_127-dipSPAdes-3.5.0-trimmed/spades//K77/before_rr.fasta 1:20:02.270 2G / 13G INFO General (repeat_resolving.cpp : 59) Using Path-Extend repeat resolving 1:20:02.270 2G / 13G INFO General (path_extend_launch.hpp : 459) Threshold for library #0 is 0.0615734 1:20:02.270 2G / 13G INFO General (path_extend_launch.hpp : 298) Path-Extend repeat resolving tool started 1:20:02.325 2G / 13G INFO General (path_extend_launch.hpp : 316) Using 1 paired-end library 1:20:02.325 2G / 13G INFO General (path_extend_launch.hpp : 317) Using 1 paired-end scaffolding library 1:20:02.326 2G / 13G INFO General (path_extend_launch.hpp : 318) Using 0 mate-pair libraries 1:20:02.326 2G / 13G INFO General (path_extend_launch.hpp : 319) Using 0 single read libraries 1:20:02.326 2G / 13G INFO General (path_extend_launch.hpp : 320) Scaffolder is on 1:20:02.644 2G / 13G INFO General (path_extend_launch.hpp : 332) Growing paths using paired-end and long single reads 1:20:02.644 2G / 13G INFO PathExtender (path_extender.hpp : 611) Processed 0 paths from 24574 (0%) 1:20:03.081 2G / 13G INFO PathExtender (path_extender.hpp : 609) Processed 128 paths from 24574 (0%) 1:20:03.400 2G / 13G INFO PathExtender (path_extender.hpp : 609) Processed 256 paths from 24574 (1%) 1:20:03.960 2G / 13G INFO PathExtender (path_extender.hpp : 609) Processed 512 paths from 24574 (2%) 1:20:04.839 2G / 13G INFO PathExtender (path_extender.hpp : 609) Processed 1024 paths from 24574 (4%) 1:20:05.768 2G / 13G INFO PathExtender (path_extender.hpp : 609) Processed 2048 paths from 24574 (8%) 1:20:05.890 2G / 13G INFO PathExtender (path_extender.hpp : 611) Processed 2458 paths from 24574 (10%) 1:20:06.767 2G / 13G INFO PathExtender (path_extender.hpp : 609) Processed 4096 paths from 24574 (16%) 1:20:07.100 2G / 13G INFO PathExtender (path_extender.hpp : 611) Processed 4916 paths from 24574 (20%) 1:20:07.863 2G / 13G INFO PathExtender (path_extender.hpp : 611) Processed 7374 paths from 24574 (30%) 1:20:08.071 2G / 13G INFO PathExtender (path_extender.hpp : 609) Processed 8192 paths from 24574 (33%) 1:20:08.303 2G / 13G INFO PathExtender (path_extender.hpp : 611) Processed 9832 paths from 24574 (40%) 1:20:08.595 2G / 13G INFO PathExtender (path_extender.hpp : 611) Processed 12290 paths from 24574 (50%) 1:20:08.791 2G / 13G INFO PathExtender (path_extender.hpp : 611) Processed 14748 paths from 24574 (60%) 1:20:10.516 2G / 13G INFO PathExtender (path_extender.hpp : 609) Processed 16384 paths from 24574 (66%) 1:20:11.324 2G / 13G INFO PathExtender (path_extender.hpp : 611) Processed 17206 paths from 24574 (70%) 1:20:13.587 2G / 13G INFO PathExtender (path_extender.hpp : 611) Processed 19664 paths from 24574 (80%) 1:20:17.344 2G / 13G INFO PathExtender (path_extender.hpp : 611) Processed 22122 paths from 24574 (90%) 1:20:19.229 2G / 13G INFO PathExtendIO (pe_io.hpp : 339) Constructing FASTG file from paths 1:20:19.745 2G / 13G INFO PathExtendIO (pe_io.hpp : 342) Writing contigs in FASTG to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_127-dipSPAdes-3.5.0-trimmed/spades//K77/final_contigs.fastg 1:20:19.745 2G / 13G INFO PathExtendIO (pe_io.hpp : 343) Writing contigs in FASTA to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_127-dipSPAdes-3.5.0-trimmed/spades//K77/final_contigs.fasta 1:21:02.783 2G / 13G INFO PathExtendIO (pe_io.hpp : 339) Constructing FASTG file from paths 1:21:03.274 2G / 13G INFO PathExtendIO (pe_io.hpp : 342) Writing contigs in FASTG to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_127-dipSPAdes-3.5.0-trimmed/spades//K77/path_extend/pe_before_traversal.fastg 1:21:03.274 2G / 13G INFO PathExtendIO (pe_io.hpp : 343) Writing contigs in FASTA to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_127-dipSPAdes-3.5.0-trimmed/spades//K77/path_extend/pe_before_traversal.fasta 1:21:46.123 2G / 13G INFO General (path_extend_launch.hpp : 281) Traversing tandem repeats 1:21:46.978 2G / 13G INFO PathExtendIO (pe_io.hpp : 339) Constructing FASTG file from paths 1:21:47.438 2G / 13G INFO PathExtendIO (pe_io.hpp : 342) Writing contigs in FASTG to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_127-dipSPAdes-3.5.0-trimmed/spades//K77/scaffolds.fastg 1:21:47.439 2G / 13G INFO PathExtendIO (pe_io.hpp : 343) Writing contigs in FASTA to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_127-dipSPAdes-3.5.0-trimmed/spades//K77/scaffolds.fasta 1:22:31.012 2G / 13G INFO General (launch.hpp : 82) SPAdes finished 1:22:35.333 272M / 13G INFO General (main.cpp : 166) Assembling time: 1 hours 22 minutes 35 seconds ===== Assembling finished. * Corrected reads are in /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_127-dipSPAdes-3.5.0-trimmed/spades/corrected/ * Assembled contigs are in /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_127-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_127-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_127-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_127-dipSPAdes-3.5.0-trimmed/spades/spades.log Thank you for using SPAdes!