Command line: --diploid --pe1-1 /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_131/reads.end1.paired.fastq.gz --pe1-2 /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_131/reads.end2.paired.fastq.gz -t 16 -o /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_131-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_131-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_131/reads.end1.paired.fastq.gz'] right reads: ['/N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_131/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_131-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_131-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_131-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_131-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 0:00:00.053 4M / 4M INFO General (main.cpp : 97) Determined value is 33 0:00:00.053 4M / 4M INFO General (hammer_tools.cpp : 36) Hamming graph threshold tau=1, k=21, subkmer positions = [ 0 10 ] === ITERATION 0 begins === 0:00:00.055 4M / 4M INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:00:00.055 4M / 4M INFO K-mer Splitting (kmer_data.cpp : 127) Splitting kmer instances into 256 buckets. This might take a while. 0:00:00.056 4M / 4M INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:00:00.056 4M / 4M INFO K-mer Splitting (kmer_data.cpp : 145) Memory available for splitting buffers: 2.08325 Gb 0:00:00.056 4M / 4M INFO K-mer Splitting (kmer_data.cpp : 153) Using cell size of 262144 0:00:02.866 8G / 8G INFO K-mer Splitting (kmer_data.cpp : 167) Processing /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_131/reads.end1.paired.fastq.gz 0:03:48.526 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 176) Processed 3254479 reads 0:11:20.719 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 176) Processed 6501772 reads 0:17:05.405 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 176) Processed 9942240 reads 0:18:02.424 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 176) Processed 13299905 reads 0:18:04.081 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 176) Processed 13391219 reads 0:18:04.082 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 167) Processing /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_131/reads.end2.paired.fastq.gz 0:25:29.631 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 176) Processed 16885614 reads 0:30:54.354 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 176) Processed 20547644 reads 0:36:51.134 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 176) Processed 24113050 reads 0:37:36.089 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 176) Processed 26782438 reads 0:37:36.091 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 181) Processed 26782438 reads 0:37:37.242 64M / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:38:14.451 64M / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 308756626 kmers in total. 0:38:14.451 64M / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:38:30.067 64M / 9G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:39:08.516 192M / 10G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:39:57.361 192M / 10G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 106810532 bytes occupied (2.7675 bits per kmer). 0:39:57.362 192M / 10G INFO K-mer Counting (kmer_data.cpp : 266) Arranging kmers in hash map order 0:43:01.903 192M / 10G INFO K-mer Counting (kmer_data.cpp : 279) Done. Total swaps: 308756377 0:43:03.988 2G / 10G INFO General (main.cpp : 151) Clustering Hamming graph. 0:43:03.989 2G / 10G INFO Hamming Clustering (hamcluster.cpp : 115) Serializing sub-kmers. 0:43:03.989 2G / 10G INFO Hamming Clustering (hamcluster.cpp : 120) Serializing: [0, 10) 0:46:44.477 2G / 10G INFO Hamming Clustering (hamcluster.cpp : 120) Serializing: [10, 21) 0:50:10.770 2G / 10G INFO Hamming Clustering (hamcluster.cpp : 129) Splitting sub-kmers, pass 1. 0:54:31.374 2G / 10G INFO Hamming Clustering (hamcluster.cpp : 134) Splitting done. Processed 2 blocks. Produced 5187319 blocks. 0:54:31.374 2G / 10G INFO Hamming Clustering (hamcluster.cpp : 145) Merge sub-kmers, pass 1 1:10:53.223 2G / 10G INFO Hamming Clustering (hamcluster.cpp : 170) Merge done, total 1765194 new blocks generated. 1:10:54.953 2G / 10G INFO Hamming Clustering (hamcluster.cpp : 175) Spliting sub-kmers, pass 2. 1:41:24.944 2G / 10G INFO Hamming Clustering (hamcluster.cpp : 180) Splitting done. Processed 3530388 blocks. Produced 587108519 blocks. 1:41:24.945 2G / 10G INFO Hamming Clustering (hamcluster.cpp : 187) Merge sub-kmers, pass 2 1:53:46.373 2G / 10G INFO Hamming Clustering (hamcluster.cpp : 205) Merge done, saw 283362 big blocks out of 587108519 processed. 1:59:06.405 2G / 10G INFO General (main.cpp : 165) Clustering done. Total clusters: 147767228 1:59:06.405 2G / 10G INFO K-mer Counting (kmer_data.cpp : 284) Collecting K-mer information, this takes a while. 1:59:12.911 16G / 16G INFO K-mer Counting (kmer_data.cpp : 290) Processing /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_131/reads.end1.paired.fastq.gz 2:02:29.495 16G / 16G INFO K-mer Counting (kmer_data.cpp : 290) Processing /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_131/reads.end2.paired.fastq.gz 2:05:39.361 16G / 16G INFO K-mer Counting (kmer_data.cpp : 297) Collection done, postprocessing. 2:05:47.600 16G / 16G INFO K-mer Counting (kmer_data.cpp : 310) There are 308756626 kmers in total. Among them 152405856 (49.3612%) are singletons. 2:05:47.600 16G / 16G INFO General (main.cpp : 203) Subclustering Hamming graph 2:09:03.097 16G / 16G INFO Hamming Subclustering (kmer_cluster.cpp : 626) Subclustering done. Total 99022 non-read kmers were generated. 2:09:03.097 16G / 16G INFO Hamming Subclustering (kmer_cluster.cpp : 627) Subclustering statistics: 2:09:03.097 16G / 16G INFO Hamming Subclustering (kmer_cluster.cpp : 628) Total singleton hamming clusters: 88261745. Among them 64684563 (73.2872%) are good 2:09:03.097 16G / 16G INFO Hamming Subclustering (kmer_cluster.cpp : 629) Total singleton subclusters: 7755973. Among them 7755867 (99.9986%) are good 2:09:03.097 16G / 16G INFO Hamming Subclustering (kmer_cluster.cpp : 630) Total non-singleton subcluster centers: 64926595. Among them 44318224 (68.259%) are good 2:09:03.097 16G / 16G INFO Hamming Subclustering (kmer_cluster.cpp : 631) Average size of non-trivial subcluster: 3.37021 kmers 2:09:03.097 16G / 16G INFO Hamming Subclustering (kmer_cluster.cpp : 632) Average number of sub-clusters per non-singleton cluster: 1.22144 2:09:03.097 16G / 16G INFO Hamming Subclustering (kmer_cluster.cpp : 633) Total solid k-mers: 116758654 2:09:03.098 16G / 16G INFO Hamming Subclustering (kmer_cluster.cpp : 634) Substitution probabilities: [4,4]((0.897375,0.0231015,0.0263757,0.053148),(0.037351,0.925979,0.0131627,0.0235074),(0.0224433,0.0126472,0.927264,0.0376458),(0.0523305,0.026688,0.0234171,0.897564)) 2:09:03.589 16G / 16G INFO General (main.cpp : 208) Finished clustering. 2:09:03.589 16G / 16G INFO General (main.cpp : 228) Starting solid k-mers expansion in 16 threads. 2:13:34.072 16G / 16G INFO General (main.cpp : 249) Solid k-mers iteration 0 produced 46148473 new k-mers. 2:18:04.009 16G / 16G INFO General (main.cpp : 249) Solid k-mers iteration 1 produced 1181854 new k-mers. 2:22:31.676 16G / 16G INFO General (main.cpp : 249) Solid k-mers iteration 2 produced 43679 new k-mers. 2:26:58.724 16G / 16G INFO General (main.cpp : 249) Solid k-mers iteration 3 produced 2541 new k-mers. 2:31:25.433 16G / 16G INFO General (main.cpp : 249) Solid k-mers iteration 4 produced 318 new k-mers. 2:35:53.105 16G / 16G INFO General (main.cpp : 249) Solid k-mers iteration 5 produced 1 new k-mers. 2:35:53.106 16G / 16G INFO General (main.cpp : 253) Solid k-mers finalized 2:35:53.106 16G / 16G INFO General (hammer_tools.cpp : 210) Starting read correction in 16 threads. 2:35:53.106 16G / 16G INFO General (hammer_tools.cpp : 222) Correcting pair of reads: /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_131/reads.end1.paired.fastq.gz and /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_131/reads.end2.paired.fastq.gz 2:36:18.493 17G / 17G INFO General (hammer_tools.cpp : 166) Prepared batch 0 of 1600000 reads. 2:36:39.241 17G / 17G INFO General (hammer_tools.cpp : 175) Processed batch 0 2:37:15.010 17G / 17G INFO General (hammer_tools.cpp : 185) Written batch 0 2:37:38.676 17G / 17G INFO General (hammer_tools.cpp : 166) Prepared batch 1 of 1600000 reads. 2:37:59.596 17G / 17G INFO General (hammer_tools.cpp : 175) Processed batch 1 2:38:15.200 17G / 17G INFO General (hammer_tools.cpp : 185) Written batch 1 2:38:38.669 17G / 17G INFO General (hammer_tools.cpp : 166) Prepared batch 2 of 1600000 reads. 2:38:59.872 17G / 17G INFO General (hammer_tools.cpp : 175) Processed batch 2 2:39:15.904 17G / 17G INFO General (hammer_tools.cpp : 185) Written batch 2 2:39:39.280 17G / 17G INFO General (hammer_tools.cpp : 166) Prepared batch 3 of 1600000 reads. 2:40:00.812 17G / 17G INFO General (hammer_tools.cpp : 175) Processed batch 3 2:40:41.870 17G / 17G INFO General (hammer_tools.cpp : 185) Written batch 3 2:41:05.104 17G / 17G INFO General (hammer_tools.cpp : 166) Prepared batch 4 of 1600000 reads. 2:41:26.909 17G / 17G INFO General (hammer_tools.cpp : 175) Processed batch 4 2:42:01.759 17G / 17G INFO General (hammer_tools.cpp : 185) Written batch 4 2:42:25.018 17G / 17G INFO General (hammer_tools.cpp : 166) Prepared batch 5 of 1600000 reads. 2:42:46.429 17G / 17G INFO General (hammer_tools.cpp : 175) Processed batch 5 2:43:12.785 17G / 17G INFO General (hammer_tools.cpp : 185) Written batch 5 2:43:35.935 17G / 17G INFO General (hammer_tools.cpp : 166) Prepared batch 6 of 1600000 reads. 2:43:58.506 17G / 17G INFO General (hammer_tools.cpp : 175) Processed batch 6 2:44:33.821 17G / 17G INFO General (hammer_tools.cpp : 185) Written batch 6 2:44:56.671 17G / 17G INFO General (hammer_tools.cpp : 166) Prepared batch 7 of 1600000 reads. 2:45:18.763 17G / 17G INFO General (hammer_tools.cpp : 175) Processed batch 7 2:45:34.530 17G / 17G INFO General (hammer_tools.cpp : 185) Written batch 7 2:45:42.965 17G / 17G INFO General (hammer_tools.cpp : 166) Prepared batch 8 of 591219 reads. 2:45:51.515 17G / 17G INFO General (hammer_tools.cpp : 175) Processed batch 8 2:45:57.230 17G / 17G INFO General (hammer_tools.cpp : 185) Written batch 8 2:46:00.081 16G / 17G INFO General (hammer_tools.cpp : 269) Correction done. Changed 4609844 bases in 3608526 reads. 2:46:00.081 16G / 17G INFO General (hammer_tools.cpp : 270) Failed to correct 441939691 bases out of 3991196955. 2:46:00.160 2G / 17G INFO General (main.cpp : 286) Saving corrected dataset description to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_131-dipSPAdes-3.5.0-trimmed/spades/corrected/corrected.yaml 2:46:00.163 2G / 17G INFO General (main.cpp : 293) All done. Exiting. == Compressing corrected reads (with gzip) == Dataset description file was created: /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_131-dipSPAdes-3.5.0-trimmed/spades/corrected/corrected.yaml ===== Read error correction finished. ===== Assembling started. == Running assembler: K21 0:00:00.000 4M / 4M INFO General (memory_limit.hpp : 42) Memory limit set to 100 Gb 0:00:00.001 4M / 4M INFO General (main.cpp : 146) Assembling dataset (/N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_131-dipSPAdes-3.5.0-trimmed/spades/dataset.info) with K=21 0:00:00.001 4M / 4M INFO General (launch.hpp : 28) SPAdes started 0:00:00.001 4M / 4M INFO General (launch.hpp : 29) Starting from stage: construction 0:00:00.002 4M / 4M INFO StageManager (stage.cpp : 125) STAGE == Construction 0:00:00.005 4M / 4M INFO General (read_converter.hpp : 79) Converting reads to binary format (takes a while) 0:00:00.005 4M / 4M INFO General (read_converter.hpp : 81) Paired reads for library #0 0:00:01.124 80M / 80M INFO General (binary_converter.hpp : 138) 16384 reads processed 0:00:01.525 96M / 96M INFO General (binary_converter.hpp : 138) 32768 reads processed 0:00:02.323 124M / 124M INFO General (binary_converter.hpp : 138) 65536 reads processed 0:00:03.924 184M / 184M INFO General (binary_converter.hpp : 138) 131072 reads processed 0:00:07.129 300M / 300M INFO General (binary_converter.hpp : 138) 262144 reads processed 0:00:13.556 536M / 536M INFO General (binary_converter.hpp : 138) 524288 reads processed 0:00:29.113 904M / 904M INFO General (binary_converter.hpp : 138) 1048576 reads processed 0:00:57.705 904M / 904M INFO General (binary_converter.hpp : 138) 2097152 reads processed 0:01:55.282 904M / 904M INFO General (binary_converter.hpp : 138) 4194304 reads processed 0:04:07.257 904M / 904M INFO General (binary_converter.hpp : 138) 8388608 reads processed 0:06:23.181 300M / 908M INFO General (binary_converter.hpp : 158) 13248663 reads written 0:06:23.558 4M / 908M INFO General (read_converter.hpp : 91) Single reads for library #0 0:06:25.403 140M / 908M INFO General (binary_converter.hpp : 138) 16384 reads processed 0:06:25.627 144M / 908M INFO General (binary_converter.hpp : 138) 32768 reads processed 0:06:26.006 160M / 908M INFO General (binary_converter.hpp : 138) 65536 reads processed 0:06:26.755 188M / 908M INFO General (binary_converter.hpp : 138) 131072 reads processed 0:06:27.107 192M / 908M INFO General (binary_converter.hpp : 158) 142196 reads written 0:06:27.280 4M / 908M INFO General (graph_construction.hpp : 129) Constructing DeBruijn graph for k=21 0:06:27.283 4M / 908M INFO General (kmer_splitters.hpp : 172) Splitting kmer instances into 256 buckets. This might take a while. 0:06:27.284 4M / 908M INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:06:27.284 4M / 908M INFO General (kmer_splitters.hpp : 190) Memory available for splitting buffers: 2.08325 Gb 0:06:27.284 4M / 908M INFO General (kmer_splitters.hpp : 199) Using cell size of 262144 0:08:44.709 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 16667272 reads 0:09:16.418 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 33334464 reads 0:09:53.188 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 50000546 reads 0:10:00.025 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 53279044 reads 0:10:00.027 8G / 9G INFO General (kmer_splitters.hpp : 234) Adding contigs from previous K 0:10:00.027 8G / 9G INFO General (kmer_splitters.hpp : 245) Used 53279044 reads. Maximum read length 151 0:10:00.027 8G / 9G INFO General (kmer_splitters.hpp : 246) Average read length 149.776 0:10:02.274 64M / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:10:11.102 64M / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 126331332 kmers in total. 0:10:11.102 64M / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:10:17.480 64M / 9G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:10:17.480 64M / 9G INFO General (kmer_splitters.hpp : 379) Splitting kmer instances into 256 buckets. This might take a while. 0:10:17.481 64M / 9G INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:10:17.481 64M / 9G INFO General (kmer_splitters.hpp : 397) Memory available for splitting buffers: 2.08203 Gb 0:10:17.481 64M / 9G INFO General (kmer_splitters.hpp : 405) Using cell size of 262144 0:11:52.470 8G / 9G INFO General (kmer_splitters.hpp : 428) Processed 126331332 kmers 0:11:52.471 8G / 9G INFO General (kmer_splitters.hpp : 437) Used 126331332 kmers. 0:11:52.973 64M / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:15:25.165 64M / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 123129266 kmers in total. 0:15:25.165 64M / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:16:11.670 64M / 9G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:16:26.091 68M / 9G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:16:31.832 68M / 9G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 42595068 bytes occupied (2.7675 bits per kmer). 0:16:32.045 188M / 9G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 382) Building k-mer extensions from k+1-mers 0:16:45.210 188M / 9G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 386) Building k-mer extensions from k+1-mers finished. 0:16:45.217 188M / 9G INFO Early tip clipping (early_simplification.hpp : 236) Early tip clipping 0:23:54.544 184M / 9G INFO Early tip clipping (early_simplification.hpp : 239) 6512982 22-mers were removed by early tip clipper 0:23:54.545 184M / 9G INFO General (graph_construction.hpp : 145) Condensing graph 0:23:54.545 184M / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 337) Extracting unbranching paths 0:25:27.646 1G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 351) Extracting unbranching paths finished. 17127905 sequences extracted 0:25:37.880 1G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 311) Collecting perfect loops 0:26:16.885 1G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 326) Collecting perfect loops finished. 52 loops collected 0:26:28.940 3G / 9G INFO General (graph_construction.hpp : 150) Building index with from graph 0:26:28.942 3G / 9G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:26:28.942 3G / 9G INFO General (kmer_splitters.hpp : 289) Splitting kmer instances into 16 buckets. This might take a while. 0:26:28.942 3G / 9G INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:26:28.942 3G / 9G INFO General (kmer_splitters.hpp : 307) Memory available for splitting buffers: 32.2044 Gb 0:26:28.942 3G / 9G INFO General (kmer_splitters.hpp : 312) Using cell size of 4194304 0:31:21.496 3G / 9G INFO General (kmer_splitters.hpp : 325) Processed 9592753 edges 0:33:43.964 3G / 9G INFO General (kmer_splitters.hpp : 325) Processed 17127957 edges 0:33:43.965 3G / 9G INFO General (kmer_splitters.hpp : 330) Used 17127957 sequences. 0:33:44.008 3G / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:35:11.128 3G / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 119818350 kmers in total. 0:35:11.128 3G / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:35:15.885 3G / 9G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:37:45.924 3G / 9G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:38:04.412 3G / 9G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 41449707 bytes occupied (2.7675 bits per kmer). 0:38:06.472 6G / 9G INFO General (edge_index_builders.hpp : 21) Collecting k-mer coverage information from graph, this takes a while. 0:41:50.108 5G / 9G INFO General (graph_construction.hpp : 182) Filling coverage index 0:41:50.109 5G / 9G INFO General (edge_index_builders.hpp : 99) Collecting k-mer coverage information from reads, this takes a while. 0:45:48.386 5G / 9G INFO General (graph_construction.hpp : 184) Filling coverage and flanking coverage from index 0:46:20.278 5G / 9G INFO General (construction.cpp : 33) Figured out: read length = 151 0:46:20.296 5G / 9G INFO StageManager (stage.cpp : 125) STAGE == EC Threshold Finding 0:46:31.462 5G / 9G INFO General (kmer_coverage_model.cpp : 178) Kmer coverage valley at: 13 0:46:31.463 5G / 9G INFO General (kmer_coverage_model.cpp : 198) K-mer histogram maximum: 51 0:46:31.463 5G / 9G INFO General (kmer_coverage_model.cpp : 234) Estimated median coverage: 51. Coverage mad: 13.3434 0:46:31.463 5G / 9G INFO General (kmer_coverage_model.cpp : 261) Fitting coverage model 0:46:31.656 5G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 2 0:46:32.143 5G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 4 0:46:33.762 5G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 8 0:46:37.290 5G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 16 0:46:43.958 5G / 9G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 48.0465. Fitted coverage std. dev: 12.9244 0:46:43.963 5G / 9G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 0.51794 0:46:43.963 5G / 9G INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 30 0:46:43.963 5G / 9G INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 30 0:46:43.963 5G / 9G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 59316289 0:46:43.963 5G / 9G INFO General (genomic_info_filler.cpp : 103) Mean coverage was calculated as 48.0465 0:46:43.964 5G / 9G INFO General (genomic_info_filler.cpp : 117) EC coverage threshold value was calculated as 30 0:46:43.964 5G / 9G INFO General (genomic_info_filler.cpp : 118) Trusted kmer low bound: 0 0:46:43.964 5G / 9G INFO StageManager (stage.cpp : 125) STAGE == Simplification 0:46:44.161 3G / 9G INFO General (graph_simplification.hpp : 911) Graph simplification started 0:46:44.161 3G / 9G INFO General (graph_simplification.hpp : 924) Fast simplification mode enabled 0:46:44.161 3G / 9G INFO General (graph_simplification.hpp : 771) PROCEDURE == Presimplification 0:46:44.161 3G / 9G INFO General (graph_simplification.hpp : 211) Removing short low covered self-conjugate connections 0:46:45.367 3G / 9G INFO General (graph_simplification.hpp : 403) Removing isolated edges 0:46:45.369 3G / 9G INFO General (graph_simplification.hpp : 404) All edges shorter than 151 will be removed 0:46:45.370 3G / 9G INFO General (graph_simplification.hpp : 405) Also edges shorter than 0 and coverage smaller than 0 will be removed 0:46:47.068 3G / 9G INFO General (graph_simplification.hpp : 687) Non parallel mode 0:47:39.261 4G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:49:47.531 4G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:53:23.775 3G / 9G INFO General (graph_simplification.hpp : 644) Using permanent iterators 0:53:23.775 3G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 1 0:53:34.714 3G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:54:19.840 3G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:54:47.463 3G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 2 0:54:47.463 3G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:54:47.990 3G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:55:00.019 3G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 3 0:55:00.019 3G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:55:00.270 3G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:55:05.993 3G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 4 0:55:05.993 3G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:55:06.111 3G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:55:09.947 3G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 5 0:55:09.947 3G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:55:10.030 3G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:55:13.129 3G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 6 0:55:13.129 3G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:55:13.196 3G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:55:16.142 3G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 7 0:55:16.142 3G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:55:16.204 3G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:55:19.109 3G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 8 0:55:19.109 3G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:55:19.167 3G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:55:21.857 3G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 9 0:55:21.857 3G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:55:21.912 3G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:55:24.251 3G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 10 0:55:24.251 3G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:55:24.297 3G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:55:26.319 3G / 9G INFO General (graph_simplification.hpp : 796) PROCEDURE == Post simplification 0:55:26.319 3G / 9G INFO General (graph_simplification.hpp : 644) Using permanent iterators 0:55:26.319 3G / 9G INFO General (graph_simplification.hpp : 806) Iteration 0 0:55:26.319 3G / 9G INFO General (graph_simplification.hpp : 247) Removal of relatively low covered connections disabled 0:55:29.810 3G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:55:37.715 3G / 9G INFO General (graph_simplification.hpp : 806) Iteration 1 0:55:37.715 3G / 9G INFO General (graph_simplification.hpp : 247) Removal of relatively low covered connections disabled 0:55:37.715 3G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:55:40.222 3G / 9G INFO StageManager (stage.cpp : 125) STAGE == Simplification Cleanup 0:55:40.223 3G / 9G INFO General (graph_simplification.hpp : 403) Removing isolated edges 0:55:40.223 3G / 9G INFO General (graph_simplification.hpp : 404) All edges shorter than 151 will be removed 0:55:40.223 3G / 9G INFO General (graph_simplification.hpp : 405) Also edges shorter than 0 and coverage smaller than 2 will be removed 0:55:40.472 3G / 9G INFO General (simplification.cpp : 56) Removing all the edges having coverage 0 and less 0:55:47.104 3G / 9G INFO General (simplification.cpp : 68) Counting average coverage 0:55:47.878 3G / 9G INFO General (simplification.cpp : 71) Average coverage = 47.3618 0:55:47.879 3G / 9G INFO StageManager (stage.cpp : 125) STAGE == Contig Output 0:55:47.879 3G / 9G INFO General (contig_output.hpp : 283) Outputting contigs to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_131-dipSPAdes-3.5.0-trimmed/spades//K21/simplified_contigs.fasta 0:57:00.032 3G / 9G INFO General (contig_output.hpp : 283) Outputting contigs to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_131-dipSPAdes-3.5.0-trimmed/spades//K21/before_rr.fasta 0:59:21.745 3G / 9G INFO General (contig_output.hpp : 283) Outputting contigs to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_131-dipSPAdes-3.5.0-trimmed/spades//K21/final_contigs.fasta 1:01:26.377 3G / 9G INFO General (launch.hpp : 82) SPAdes finished 1:01:35.541 64M / 9G INFO General (main.cpp : 166) Assembling time: 1 hours 1 minutes 35 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_131-dipSPAdes-3.5.0-trimmed/spades/dataset.info) with K=33 0:00:00.001 4M / 4M INFO General (launch.hpp : 28) SPAdes started 0:00:00.001 4M / 4M INFO General (launch.hpp : 29) Starting from stage: construction 0:00:00.002 4M / 4M INFO StageManager (stage.cpp : 125) STAGE == Construction 0:00:00.002 4M / 4M INFO General (construction.cpp : 44) Contigs from previous K will be used 0:00:00.007 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 0:00:00.029 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 0:04:04.189 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 9181944 reads 0:04:19.868 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 18379390 reads 0:08:05.795 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 27570839 reads 0:08:21.380 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 36756683 reads 0:08:36.916 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 45948085 reads 0:08:49.479 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 53279044 reads 0:08:49.480 8G / 9G INFO General (kmer_splitters.hpp : 234) Adding contigs from previous K 0:09:09.461 8G / 9G INFO General (kmer_splitters.hpp : 245) Used 53279044 reads. Maximum read length 151 0:09:09.461 8G / 9G INFO General (kmer_splitters.hpp : 246) Average read length 149.776 0:09:11.775 64M / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:09:37.758 64M / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 148136149 kmers in total. 0:09:37.758 64M / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:09:50.918 64M / 9G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:09:50.918 64M / 9G INFO General (kmer_splitters.hpp : 379) Splitting kmer instances into 256 buckets. This might take a while. 0:09:50.919 64M / 9G INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:09:50.919 64M / 9G INFO General (kmer_splitters.hpp : 397) Memory available for splitting buffers: 2.08203 Gb 0:09:50.919 64M / 9G INFO General (kmer_splitters.hpp : 405) Using cell size of 131072 0:39:25.590 8G / 9G INFO General (kmer_splitters.hpp : 428) Processed 148136149 kmers 0:39:25.591 8G / 9G INFO General (kmer_splitters.hpp : 437) Used 148136149 kmers. 0:39:26.411 64M / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:44:22.165 64M / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 146739395 kmers in total. 0:44:22.166 64M / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:44:37.826 64M / 9G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:44:56.052 68M / 9G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:45:34.755 68M / 9G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 50762689 bytes occupied (2.7675 bits per kmer). 0:45:35.011 208M / 9G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 382) Building k-mer extensions from k+1-mers 0:45:53.874 208M / 9G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 386) Building k-mer extensions from k+1-mers finished. 0:45:53.883 208M / 9G INFO Early tip clipping (early_simplification.hpp : 236) Early tip clipping 0:53:46.886 208M / 9G INFO Early tip clipping (early_simplification.hpp : 239) 22771393 34-mers were removed by early tip clipper 0:53:46.886 208M / 9G INFO General (graph_construction.hpp : 145) Condensing graph 0:53:46.886 208M / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 337) Extracting unbranching paths 0:55:33.671 1G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 351) Extracting unbranching paths finished. 8550005 sequences extracted 0:55:46.065 1G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 311) Collecting perfect loops 0:56:39.653 1G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 326) Collecting perfect loops finished. 60 loops collected 0:56:45.990 1G / 9G INFO General (graph_construction.hpp : 150) Building index with from graph 0:56:45.991 1G / 9G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:56:45.992 1G / 9G INFO General (kmer_splitters.hpp : 289) Splitting kmer instances into 16 buckets. This might take a while. 0:56:45.992 1G / 9G INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:56:45.992 1G / 9G INFO General (kmer_splitters.hpp : 307) Memory available for splitting buffers: 32.7057 Gb 0:56:45.992 1G / 9G INFO General (kmer_splitters.hpp : 312) Using cell size of 2097152 1:01:33.975 2G / 9G INFO General (kmer_splitters.hpp : 325) Processed 2288493 edges 1:04:24.155 2G / 9G INFO General (kmer_splitters.hpp : 325) Processed 4577399 edges 1:08:35.603 2G / 9G INFO General (kmer_splitters.hpp : 325) Processed 6864571 edges 1:12:36.444 2G / 9G INFO General (kmer_splitters.hpp : 325) Processed 8550065 edges 1:12:36.444 2G / 9G INFO General (kmer_splitters.hpp : 330) Used 8550065 sequences. 1:12:36.477 1G / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 1:16:23.498 1G / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 125364756 kmers in total. 1:16:23.498 1G / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 1:16:56.152 1G / 9G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 1:19:32.730 1G / 9G INFO General (kmer_index.hpp : 371) Merging final buckets. 1:20:03.869 1G / 9G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 43368408 bytes occupied (2.7675 bits per kmer). 1:20:06.028 4G / 9G INFO General (edge_index_builders.hpp : 21) Collecting k-mer coverage information from graph, this takes a while. 1:23:56.663 4G / 9G INFO General (graph_construction.hpp : 182) Filling coverage index 1:23:56.663 4G / 9G INFO General (edge_index_builders.hpp : 99) Collecting k-mer coverage information from reads, this takes a while. 1:27:57.643 4G / 9G INFO General (graph_construction.hpp : 184) Filling coverage and flanking coverage from index 1:28:27.744 4G / 9G INFO General (construction.cpp : 33) Figured out: read length = 151 1:28:27.765 4G / 9G INFO StageManager (stage.cpp : 125) STAGE == EC Threshold Finding 1:28:37.920 4G / 9G INFO General (kmer_coverage_model.cpp : 178) Kmer coverage valley at: 12 1:28:37.920 4G / 9G INFO General (kmer_coverage_model.cpp : 198) K-mer histogram maximum: 45 1:28:37.920 4G / 9G INFO General (kmer_coverage_model.cpp : 234) Estimated median coverage: 45. Coverage mad: 11.8608 1:28:37.921 4G / 9G INFO General (kmer_coverage_model.cpp : 261) Fitting coverage model 1:28:38.092 4G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 2 1:28:38.519 4G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 4 1:28:39.950 4G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 8 1:28:43.441 4G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 16 1:28:49.518 4G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 32 1:28:49.907 4G / 9G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 43.0849. Fitted coverage std. dev: 12.2138 1:28:49.911 4G / 9G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 0.447177 1:28:49.911 4G / 9G INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 27 1:28:49.911 4G / 9G INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 27 1:28:49.911 4G / 9G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 59719966 1:28:49.911 4G / 9G INFO General (genomic_info_filler.cpp : 103) Mean coverage was calculated as 43.0849 1:28:49.912 4G / 9G INFO General (genomic_info_filler.cpp : 117) EC coverage threshold value was calculated as 27 1:28:49.912 4G / 9G INFO General (genomic_info_filler.cpp : 118) Trusted kmer low bound: 0 1:28:49.912 4G / 9G INFO StageManager (stage.cpp : 125) STAGE == Simplification 1:28:50.161 1G / 9G INFO General (graph_simplification.hpp : 911) Graph simplification started 1:28:50.161 1G / 9G INFO General (graph_simplification.hpp : 924) Fast simplification mode enabled 1:28:50.161 1G / 9G INFO General (graph_simplification.hpp : 771) PROCEDURE == Presimplification 1:28:50.161 1G / 9G INFO General (graph_simplification.hpp : 211) Removing short low covered self-conjugate connections 1:28:50.812 1G / 9G INFO General (graph_simplification.hpp : 403) Removing isolated edges 1:28:50.812 1G / 9G INFO General (graph_simplification.hpp : 404) All edges shorter than 151 will be removed 1:28:50.812 1G / 9G INFO General (graph_simplification.hpp : 405) Also edges shorter than 0 and coverage smaller than 0 will be removed 1:28:52.519 1G / 9G INFO General (graph_simplification.hpp : 687) Non parallel mode 1:29:17.982 2G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 1:30:18.007 2G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 1:32:13.642 1G / 9G INFO General (graph_simplification.hpp : 644) Using permanent iterators 1:32:13.643 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 1 1:32:16.866 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 1:32:30.327 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 1:32:45.096 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 2 1:32:45.096 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 1:32:45.229 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 1:32:50.870 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 3 1:32:50.870 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 1:32:50.941 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 1:32:53.557 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 4 1:32:53.557 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 1:32:53.590 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 1:32:55.205 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 5 1:32:55.205 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 1:32:55.224 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 1:32:56.518 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 6 1:32:56.518 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 1:32:56.531 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 1:32:57.830 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 7 1:32:57.830 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 1:32:57.839 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 1:32:59.298 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 8 1:32:59.298 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 1:32:59.306 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 1:33:00.648 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 9 1:33:00.649 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 1:33:00.655 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 1:33:01.539 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 10 1:33:01.539 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 1:33:01.545 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 1:33:02.042 1G / 9G INFO General (graph_simplification.hpp : 796) PROCEDURE == Post simplification 1:33:02.042 1G / 9G INFO General (graph_simplification.hpp : 644) Using permanent iterators 1:33:02.042 1G / 9G INFO General (graph_simplification.hpp : 806) Iteration 0 1:33:02.042 1G / 9G INFO General (graph_simplification.hpp : 247) Removal of relatively low covered connections disabled 1:33:02.541 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 1:33:03.647 1G / 9G INFO General (graph_simplification.hpp : 806) Iteration 1 1:33:03.647 1G / 9G INFO General (graph_simplification.hpp : 247) Removal of relatively low covered connections disabled 1:33:03.647 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 1:33:04.089 1G / 9G INFO StageManager (stage.cpp : 125) STAGE == Simplification Cleanup 1:33:04.090 1G / 9G INFO General (graph_simplification.hpp : 403) Removing isolated edges 1:33:04.090 1G / 9G INFO General (graph_simplification.hpp : 404) All edges shorter than 151 will be removed 1:33:04.090 1G / 9G INFO General (graph_simplification.hpp : 405) Also edges shorter than 0 and coverage smaller than 2 will be removed 1:33:04.172 1G / 9G INFO General (simplification.cpp : 56) Removing all the edges having coverage 0 and less 1:33:05.080 1G / 9G INFO General (simplification.cpp : 68) Counting average coverage 1:33:05.244 1G / 9G INFO General (simplification.cpp : 71) Average coverage = 39.5619 1:33:05.244 1G / 9G INFO StageManager (stage.cpp : 125) STAGE == Contig Output 1:33:05.244 1G / 9G INFO General (contig_output.hpp : 283) Outputting contigs to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_131-dipSPAdes-3.5.0-trimmed/spades//K33/simplified_contigs.fasta 1:33:38.547 1G / 9G INFO General (contig_output.hpp : 283) Outputting contigs to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_131-dipSPAdes-3.5.0-trimmed/spades//K33/before_rr.fasta 1:34:37.831 1G / 9G INFO General (contig_output.hpp : 283) Outputting contigs to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_131-dipSPAdes-3.5.0-trimmed/spades//K33/final_contigs.fasta 1:35:37.278 1G / 9G INFO General (launch.hpp : 82) SPAdes finished 1:35:40.405 64M / 9G INFO General (main.cpp : 166) Assembling time: 1 hours 35 minutes 40 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_131-dipSPAdes-3.5.0-trimmed/spades/dataset.info) with K=55 0:00:00.001 4M / 4M INFO General (launch.hpp : 28) SPAdes started 0:00:00.001 4M / 4M INFO General (launch.hpp : 29) Starting from stage: construction 0:00:00.002 4M / 4M INFO General (launch.hpp : 44) Will need read mapping, kmer mapper will be attached 0:00:00.002 4M / 4M INFO StageManager (stage.cpp : 125) STAGE == Construction 0:00:00.002 4M / 4M INFO General (construction.cpp : 44) Contigs from previous K will be used 0:00:00.006 4M / 4M INFO General (read_converter.hpp : 49) Binary reads detected 0:00:00.026 4M / 4M INFO General (graph_construction.hpp : 129) Constructing DeBruijn graph for k=55 0:00:00.029 4M / 4M INFO General (kmer_splitters.hpp : 172) Splitting kmer instances into 256 buckets. This might take a while. 0:00:00.029 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 0:00:00.030 4M / 4M INFO General (kmer_splitters.hpp : 199) Using cell size of 131072 0:08:53.618 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 11308260 reads 0:10:30.516 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 22635524 reads 0:13:44.196 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 33951571 reads 0:14:00.882 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 45271783 reads 0:18:44.218 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 53279044 reads 0:18:44.218 8G / 9G INFO General (kmer_splitters.hpp : 234) Adding contigs from previous K 0:21:22.880 8G / 9G INFO General (kmer_splitters.hpp : 245) Used 53279044 reads. Maximum read length 151 0:21:22.880 8G / 9G INFO General (kmer_splitters.hpp : 246) Average read length 149.776 0:21:25.147 64M / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:26:49.067 64M / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 168078740 kmers in total. 0:26:49.067 64M / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:27:19.267 64M / 9G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:27:19.268 64M / 9G INFO General (kmer_splitters.hpp : 379) Splitting kmer instances into 256 buckets. This might take a while. 0:27:19.268 64M / 9G INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:27:19.268 64M / 9G INFO General (kmer_splitters.hpp : 397) Memory available for splitting buffers: 2.08203 Gb 0:27:19.268 64M / 9G INFO General (kmer_splitters.hpp : 405) Using cell size of 131072 0:28:10.239 8G / 9G INFO General (kmer_splitters.hpp : 428) Processed 168078740 kmers 0:28:10.239 8G / 9G INFO General (kmer_splitters.hpp : 437) Used 168078740 kmers. 0:28:11.152 64M / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:29:31.100 64M / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 167582729 kmers in total. 0:29:31.101 64M / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:30:07.525 64M / 9G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:30:31.611 68M / 9G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:30:49.212 68M / 9G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 57973197 bytes occupied (2.7675 bits per kmer). 0:30:49.476 228M / 9G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 382) Building k-mer extensions from k+1-mers 0:31:14.588 228M / 9G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 386) Building k-mer extensions from k+1-mers finished. 0:31:14.592 228M / 9G INFO General (graph_construction.hpp : 145) Condensing graph 0:31:14.592 228M / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 337) Extracting unbranching paths 0:33:11.258 1G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 351) Extracting unbranching paths finished. 11093597 sequences extracted 0:33:29.619 1G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 311) Collecting perfect loops 0:34:26.487 1G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 326) Collecting perfect loops finished. 8 loops collected 0:34:36.893 2G / 9G INFO General (graph_construction.hpp : 150) Building index with from graph 0:34:36.894 2G / 9G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:34:36.894 2G / 9G INFO General (kmer_splitters.hpp : 289) Splitting kmer instances into 16 buckets. This might take a while. 0:34:36.894 2G / 9G INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:34:36.895 2G / 9G INFO General (kmer_splitters.hpp : 307) Memory available for splitting buffers: 32.4349 Gb 0:34:36.895 2G / 9G INFO General (kmer_splitters.hpp : 312) Using cell size of 2097152 0:37:50.984 3G / 9G INFO General (kmer_splitters.hpp : 325) Processed 2214043 edges 0:40:40.564 3G / 9G INFO General (kmer_splitters.hpp : 325) Processed 4429616 edges 0:43:09.965 3G / 9G INFO General (kmer_splitters.hpp : 325) Processed 6644092 edges 0:45:55.448 3G / 9G INFO General (kmer_splitters.hpp : 325) Processed 8858276 edges 0:49:46.204 3G / 9G INFO General (kmer_splitters.hpp : 325) Processed 11073661 edges 0:49:48.392 3G / 9G INFO General (kmer_splitters.hpp : 325) Processed 11093605 edges 0:49:48.393 3G / 9G INFO General (kmer_splitters.hpp : 330) Used 11093605 sequences. 0:49:48.456 2G / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:51:18.533 2G / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 168078740 kmers in total. 0:51:18.533 2G / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:51:35.693 2G / 9G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:55:51.821 2G / 9G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:56:31.001 2G / 9G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 58144785 bytes occupied (2.7675 bits per kmer). 0:56:33.908 6G / 9G INFO General (edge_index_builders.hpp : 21) Collecting k-mer coverage information from graph, this takes a while. 1:02:15.017 6G / 9G INFO General (graph_construction.hpp : 182) Filling coverage index 1:02:15.017 6G / 9G INFO General (edge_index_builders.hpp : 99) Collecting k-mer coverage information from reads, this takes a while. 1:05:49.479 6G / 9G INFO General (graph_construction.hpp : 184) Filling coverage and flanking coverage from index 1:06:32.953 6G / 9G INFO General (construction.cpp : 33) Figured out: read length = 151 1:06:32.971 6G / 9G INFO StageManager (stage.cpp : 125) STAGE == EC Threshold Finding 1:06:46.681 6G / 9G INFO General (kmer_coverage_model.cpp : 178) Kmer coverage valley at: 9 1:06:46.681 6G / 9G INFO General (kmer_coverage_model.cpp : 198) K-mer histogram maximum: 36 1:06:46.681 6G / 9G INFO General (kmer_coverage_model.cpp : 234) Estimated median coverage: 36. Coverage mad: 10.3782 1:06:46.682 6G / 9G INFO General (kmer_coverage_model.cpp : 261) Fitting coverage model 1:06:46.811 6G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 2 1:06:47.155 6G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 4 1:06:48.315 6G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 8 1:06:49.944 6G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 16 1:06:52.200 6G / 9G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 35.1321. Fitted coverage std. dev: 9.96657 1:06:52.202 6G / 9G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 0.691472 1:06:52.202 6G / 9G INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 23 1:06:52.202 6G / 9G INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 22 1:06:52.202 6G / 9G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 59123108 1:06:52.203 6G / 9G INFO General (genomic_info_filler.cpp : 103) Mean coverage was calculated as 35.1321 1:06:52.203 6G / 9G INFO General (genomic_info_filler.cpp : 117) EC coverage threshold value was calculated as 22 1:06:52.203 6G / 9G INFO General (genomic_info_filler.cpp : 118) Trusted kmer low bound: 0 1:06:52.203 6G / 9G INFO StageManager (stage.cpp : 125) STAGE == Gap Closer 1:06:52.213 6G / 9G INFO General (gap_closer.cpp : 157) Preparing shift maps 1:07:02.914 6G / 9G INFO General (gap_closer.cpp : 117) Processing paired reads (takes a while) 1:07:47.425 7G / 9G INFO General (gap_closer.cpp : 136) Used 26497326 paired reads 1:07:47.426 7G / 9G INFO General (gap_closer.cpp : 138) Merging paired indices 1:07:52.540 6G / 9G INFO GapCloser (gap_closer.cpp : 395) Closing short gaps 1:08:21.988 6G / 9G INFO GapCloser (gap_closer.cpp : 424) Closing short gaps complete: filled 1362 gaps after checking 24018 candidates 1:08:26.048 6G / 9G INFO StageManager (stage.cpp : 125) STAGE == Simplification 1:08:26.296 2G / 9G INFO General (graph_simplification.hpp : 911) Graph simplification started 1:08:26.296 2G / 9G INFO General (graph_simplification.hpp : 924) Fast simplification mode enabled 1:08:26.296 2G / 9G INFO General (graph_simplification.hpp : 771) PROCEDURE == Presimplification 1:08:26.296 2G / 9G INFO General (graph_simplification.hpp : 211) Removing short low covered self-conjugate connections 1:08:27.381 2G / 9G INFO General (graph_simplification.hpp : 403) Removing isolated edges 1:08:27.383 2G / 9G INFO General (graph_simplification.hpp : 404) All edges shorter than 151 will be removed 1:08:27.384 2G / 9G INFO General (graph_simplification.hpp : 405) Also edges shorter than 0 and coverage smaller than 0 will be removed 1:08:30.350 2G / 9G INFO General (graph_simplification.hpp : 687) Non parallel mode 1:09:07.691 2G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 1:10:55.849 2G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 1:11:48.664 2G / 9G INFO General (graph_simplification.hpp : 644) Using permanent iterators 1:11:48.664 2G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 1 1:11:49.943 2G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 1:11:55.588 2G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 1:11:58.637 2G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 2 1:11:58.637 2G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 1:11:58.679 2G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 1:12:01.885 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 3 1:12:01.885 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 1:12:01.942 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 1:12:03.628 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 4 1:12:03.628 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 1:12:03.647 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 1:12:04.921 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 5 1:12:04.921 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 1:12:04.933 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 1:12:06.267 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 6 1:12:06.267 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 1:12:06.274 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 1:12:07.670 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 7 1:12:07.670 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 1:12:07.676 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 1:12:09.353 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 8 1:12:09.354 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 1:12:09.358 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 1:12:10.933 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 9 1:12:10.934 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 1:12:10.937 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 1:12:12.101 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 10 1:12:12.101 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 1:12:12.104 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 1:12:12.700 1G / 9G INFO General (graph_simplification.hpp : 796) PROCEDURE == Post simplification 1:12:12.700 1G / 9G INFO General (graph_simplification.hpp : 644) Using permanent iterators 1:12:12.700 1G / 9G INFO General (graph_simplification.hpp : 806) Iteration 0 1:12:12.700 1G / 9G INFO General (graph_simplification.hpp : 247) Removal of relatively low covered connections disabled 1:12:12.893 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 1:12:13.285 1G / 9G INFO General (graph_simplification.hpp : 806) Iteration 1 1:12:13.285 1G / 9G INFO General (graph_simplification.hpp : 247) Removal of relatively low covered connections disabled 1:12:13.285 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 1:12:13.532 1016M / 9G INFO StageManager (stage.cpp : 125) STAGE == Gap Closer 1:12:13.532 1016M / 9G INFO General (graph_pack.hpp : 84) Index refill 1:12:13.533 1016M / 9G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 1:12:13.533 1016M / 9G INFO General (kmer_splitters.hpp : 289) Splitting kmer instances into 16 buckets. This might take a while. 1:12:13.534 1016M / 9G INFO General (file_limit.hpp : 29) Open file limit set to 32768 1:12:13.534 1016M / 9G INFO General (kmer_splitters.hpp : 307) Memory available for splitting buffers: 33.0026 Gb 1:12:13.534 1016M / 9G INFO General (kmer_splitters.hpp : 312) Using cell size of 2097152 1:16:23.748 1G / 9G INFO General (kmer_splitters.hpp : 325) Processed 41842 edges 1:19:01.376 1G / 9G INFO General (kmer_splitters.hpp : 325) Processed 83850 edges 1:21:30.409 1G / 9G INFO General (kmer_splitters.hpp : 325) Processed 95920 edges 1:21:30.409 1G / 9G INFO General (kmer_splitters.hpp : 330) Used 95920 sequences. 1:21:30.487 1004M / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 1:23:28.941 1004M / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 76666758 kmers in total. 1:23:28.941 1004M / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 1:23:56.633 1004M / 9G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 1:25:36.430 1G / 9G INFO General (kmer_index.hpp : 371) Merging final buckets. 1:25:43.039 1G / 9G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 26521942 bytes occupied (2.7675 bits per kmer). 1:25:44.400 2G / 9G INFO General (edge_index_builders.hpp : 21) Collecting k-mer coverage information from graph, this takes a while. 1:27:53.353 2G / 9G INFO General (gap_closer.cpp : 157) Preparing shift maps 1:27:53.497 2G / 9G INFO General (gap_closer.cpp : 117) Processing paired reads (takes a while) 1:28:40.026 2G / 9G INFO General (gap_closer.cpp : 136) Used 26497326 paired reads 1:28:40.027 2G / 9G INFO General (gap_closer.cpp : 138) Merging paired indices 1:28:40.287 2G / 9G INFO GapCloser (gap_closer.cpp : 395) Closing short gaps 1:28:40.684 2G / 9G INFO GapCloser (gap_closer.cpp : 424) Closing short gaps complete: filled 140 gaps after checking 11002 candidates 1:28:41.688 2G / 9G INFO StageManager (stage.cpp : 125) STAGE == Simplification Cleanup 1:28:41.689 2G / 9G INFO General (graph_simplification.hpp : 403) Removing isolated edges 1:28:41.689 2G / 9G INFO General (graph_simplification.hpp : 404) All edges shorter than 151 will be removed 1:28:41.689 2G / 9G INFO General (graph_simplification.hpp : 405) Also edges shorter than 0 and coverage smaller than 2 will be removed 1:28:42.251 2G / 9G INFO General (simplification.cpp : 56) Removing all the edges having coverage 0 and less 1:28:42.579 2G / 9G INFO General (simplification.cpp : 68) Counting average coverage 1:28:42.659 2G / 9G INFO General (simplification.cpp : 71) Average coverage = 31.3773 1:28:42.660 2G / 9G INFO StageManager (stage.cpp : 125) STAGE == Contig Output 1:28:42.660 2G / 9G INFO General (contig_output.hpp : 283) Outputting contigs to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_131-dipSPAdes-3.5.0-trimmed/spades//K55/simplified_contigs.fasta 1:28:59.701 2G / 9G INFO General (contig_output.hpp : 283) Outputting contigs to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_131-dipSPAdes-3.5.0-trimmed/spades//K55/before_rr.fasta 1:30:02.698 2G / 9G INFO General (contig_output.hpp : 283) Outputting contigs to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_131-dipSPAdes-3.5.0-trimmed/spades//K55/final_contigs.fasta 1:31:04.188 2G / 9G INFO General (launch.hpp : 82) SPAdes finished 1:31:07.380 64M / 9G INFO General (main.cpp : 166) Assembling time: 1 hours 31 minutes 7 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_131-dipSPAdes-3.5.0-trimmed/spades/dataset.info) with K=77 0:00:00.001 4M / 4M INFO General (launch.hpp : 28) SPAdes started 0:00:00.001 4M / 4M INFO General (launch.hpp : 29) Starting from stage: construction 0:00:00.002 4M / 4M INFO General (launch.hpp : 44) Will need read mapping, kmer mapper will be attached 0:00:00.002 4M / 4M INFO StageManager (stage.cpp : 125) STAGE == Construction 0:00:00.002 4M / 4M INFO General (construction.cpp : 44) Contigs from previous K will be used 0:00:00.006 4M / 4M INFO General (read_converter.hpp : 49) Binary reads detected 0:00:00.026 4M / 4M INFO General (graph_construction.hpp : 129) Constructing DeBruijn graph for k=77 0:00:00.028 4M / 4M INFO General (kmer_splitters.hpp : 172) Splitting kmer instances into 256 buckets. This might take a while. 0:00:00.029 4M / 4M INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:00:00.029 4M / 4M INFO General (kmer_splitters.hpp : 190) Memory available for splitting buffers: 2.08325 Gb 0:00:00.029 4M / 4M INFO General (kmer_splitters.hpp : 199) Using cell size of 87381 0:10:17.713 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 9801052 reads 0:19:16.975 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 19623700 reads 0:52:47.981 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 29432017 reads 1:01:28.040 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 39251598 reads 1:05:35.327 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 49053104 reads 1:05:43.072 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 53279044 reads 1:05:43.072 8G / 9G INFO General (kmer_splitters.hpp : 234) Adding contigs from previous K 1:06:07.087 8G / 9G INFO General (kmer_splitters.hpp : 245) Used 53279044 reads. Maximum read length 151 1:06:07.087 8G / 9G INFO General (kmer_splitters.hpp : 246) Average read length 149.776 1:06:09.364 64M / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 1:09:58.675 64M / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 170846847 kmers in total. 1:09:58.676 64M / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 1:10:45.073 64M / 9G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 1:10:45.073 64M / 9G INFO General (kmer_splitters.hpp : 379) Splitting kmer instances into 256 buckets. This might take a while. 1:10:45.074 64M / 9G INFO General (file_limit.hpp : 29) Open file limit set to 32768 1:10:45.074 64M / 9G INFO General (kmer_splitters.hpp : 397) Memory available for splitting buffers: 2.08203 Gb 1:10:45.074 64M / 9G INFO General (kmer_splitters.hpp : 405) Using cell size of 87381 1:46:02.364 8G / 9G INFO General (kmer_splitters.hpp : 428) Processed 170846847 kmers 1:46:02.364 8G / 9G INFO General (kmer_splitters.hpp : 437) Used 170846847 kmers. 1:46:03.770 64M / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 1:48:46.889 64M / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 171017292 kmers in total. 1:48:46.890 64M / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 1:49:11.186 64M / 9G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 1:49:33.410 68M / 9G INFO General (kmer_index.hpp : 371) Merging final buckets. 1:49:55.602 68M / 9G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 59161333 bytes occupied (2.7675 bits per kmer). 1:49:55.875 232M / 9G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 382) Building k-mer extensions from k+1-mers 1:50:23.292 232M / 9G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 386) Building k-mer extensions from k+1-mers finished. 1:50:23.297 232M / 9G INFO General (graph_construction.hpp : 145) Condensing graph 1:50:23.297 232M / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 337) Extracting unbranching paths 1:52:15.125 1G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 351) Extracting unbranching paths finished. 9624423 sequences extracted 1:52:31.593 1G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 311) Collecting perfect loops 1:53:35.171 1G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 326) Collecting perfect loops finished. 6 loops collected 1:53:44.875 2G / 9G INFO General (graph_construction.hpp : 150) Building index with from graph 1:53:44.878 2G / 9G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 1:53:44.878 2G / 9G INFO General (kmer_splitters.hpp : 289) Splitting kmer instances into 16 buckets. This might take a while. 1:53:44.878 2G / 9G INFO General (file_limit.hpp : 29) Open file limit set to 32768 1:53:44.878 2G / 9G INFO General (kmer_splitters.hpp : 307) Memory available for splitting buffers: 32.4883 Gb 1:53:44.878 2G / 9G INFO General (kmer_splitters.hpp : 312) Using cell size of 1398101 1:54:31.204 3G / 9G INFO General (kmer_splitters.hpp : 325) Processed 1260289 edges 1:57:45.808 3G / 9G INFO General (kmer_splitters.hpp : 325) Processed 2521475 edges 2:00:41.704 3G / 9G INFO General (kmer_splitters.hpp : 325) Processed 3779024 edges 2:04:03.592 3G / 9G INFO General (kmer_splitters.hpp : 325) Processed 5040218 edges 2:08:20.906 3G / 9G INFO General (kmer_splitters.hpp : 325) Processed 6300584 edges 2:11:08.018 3G / 9G INFO General (kmer_splitters.hpp : 325) Processed 7561083 edges 2:14:02.098 3G / 9G INFO General (kmer_splitters.hpp : 325) Processed 8820463 edges 2:16:06.920 3G / 9G INFO General (kmer_splitters.hpp : 325) Processed 9624429 edges 2:16:06.920 3G / 9G INFO General (kmer_splitters.hpp : 330) Used 9624429 sequences. 2:16:06.988 2G / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 2:18:18.921 2G / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 170846847 kmers in total. 2:18:18.922 2G / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 2:18:41.997 2G / 9G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 2:23:05.772 2G / 9G INFO General (kmer_index.hpp : 371) Merging final buckets. 2:23:27.634 2G / 9G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 59102362 bytes occupied (2.7675 bits per kmer). 2:23:30.604 6G / 9G INFO General (edge_index_builders.hpp : 21) Collecting k-mer coverage information from graph, this takes a while. 2:29:52.900 6G / 9G INFO General (graph_construction.hpp : 182) Filling coverage index 2:29:52.900 6G / 9G INFO General (edge_index_builders.hpp : 99) Collecting k-mer coverage information from reads, this takes a while. 2:33:28.545 6G / 9G INFO General (graph_construction.hpp : 184) Filling coverage and flanking coverage from index 2:34:11.032 6G / 9G INFO General (construction.cpp : 33) Figured out: read length = 151 2:34:11.049 6G / 9G INFO StageManager (stage.cpp : 125) STAGE == EC Threshold Finding 2:34:23.739 6G / 9G INFO General (kmer_coverage_model.cpp : 178) Kmer coverage valley at: 7 2:34:23.739 6G / 9G INFO General (kmer_coverage_model.cpp : 198) K-mer histogram maximum: 27 2:34:23.739 6G / 9G INFO General (kmer_coverage_model.cpp : 234) Estimated median coverage: 27. Coverage mad: 8.8956 2:34:23.740 6G / 9G INFO General (kmer_coverage_model.cpp : 261) Fitting coverage model 2:34:23.831 6G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 2 2:34:24.065 6G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 4 2:34:24.681 6G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 8 2:34:25.647 6G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 16 2:34:26.379 6G / 9G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 26.3801. Fitted coverage std. dev: 8.44156 2:34:26.381 6G / 9G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 0.500085 2:34:26.381 6G / 9G INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 16 2:34:26.381 6G / 9G INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 16 2:34:26.381 6G / 9G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 59407557 2:34:26.381 6G / 9G INFO General (genomic_info_filler.cpp : 103) Mean coverage was calculated as 26.3801 2:34:26.381 6G / 9G INFO General (genomic_info_filler.cpp : 117) EC coverage threshold value was calculated as 16 2:34:26.381 6G / 9G INFO General (genomic_info_filler.cpp : 118) Trusted kmer low bound: 0 2:34:26.381 6G / 9G INFO StageManager (stage.cpp : 125) STAGE == Gap Closer 2:34:26.391 6G / 9G INFO General (gap_closer.cpp : 157) Preparing shift maps 2:34:37.849 6G / 9G INFO General (gap_closer.cpp : 117) Processing paired reads (takes a while) 2:35:13.294 7G / 9G INFO General (gap_closer.cpp : 136) Used 26497326 paired reads 2:35:13.294 7G / 9G INFO General (gap_closer.cpp : 138) Merging paired indices 2:35:20.297 6G / 9G INFO GapCloser (gap_closer.cpp : 395) Closing short gaps 2:35:46.195 6G / 9G INFO GapCloser (gap_closer.cpp : 424) Closing short gaps complete: filled 1080 gaps after checking 25671 candidates 2:35:50.021 6G / 9G INFO StageManager (stage.cpp : 125) STAGE == Simplification 2:35:50.409 2G / 9G INFO General (graph_simplification.hpp : 911) Graph simplification started 2:35:50.409 2G / 9G INFO General (graph_simplification.hpp : 924) Fast simplification mode enabled 2:35:50.409 2G / 9G INFO General (graph_simplification.hpp : 771) PROCEDURE == Presimplification 2:35:50.409 2G / 9G INFO General (graph_simplification.hpp : 211) Removing short low covered self-conjugate connections 2:35:51.305 2G / 9G INFO General (graph_simplification.hpp : 403) Removing isolated edges 2:35:51.307 2G / 9G INFO General (graph_simplification.hpp : 404) All edges shorter than 151 will be removed 2:35:51.307 2G / 9G INFO General (graph_simplification.hpp : 405) Also edges shorter than 0 and coverage smaller than 0 will be removed 2:35:55.699 2G / 9G INFO General (graph_simplification.hpp : 687) Non parallel mode 2:36:26.308 2G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 2:38:08.373 2G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 2:38:13.308 1G / 9G INFO General (graph_simplification.hpp : 644) Using permanent iterators 2:38:13.308 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 1 2:38:13.999 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 2:38:16.804 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 2:38:16.972 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 2 2:38:16.972 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 2:38:16.975 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 2:38:18.371 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 3 2:38:18.371 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 2:38:18.398 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 2:38:19.431 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 4 2:38:19.431 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 2:38:19.444 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 2:38:20.456 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 5 2:38:20.456 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 2:38:20.464 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 2:38:21.331 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 6 2:38:21.331 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 2:38:21.336 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 2:38:22.591 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 7 2:38:22.592 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 2:38:22.595 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 2:38:23.966 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 8 2:38:23.967 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 2:38:23.970 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 2:38:25.558 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 9 2:38:25.558 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 2:38:25.562 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 2:38:26.975 984M / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 10 2:38:26.975 984M / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 2:38:26.978 984M / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 2:38:27.981 912M / 9G INFO General (graph_simplification.hpp : 796) PROCEDURE == Post simplification 2:38:27.981 912M / 9G INFO General (graph_simplification.hpp : 644) Using permanent iterators 2:38:27.981 912M / 9G INFO General (graph_simplification.hpp : 806) Iteration 0 2:38:27.981 912M / 9G INFO General (graph_simplification.hpp : 247) Removal of relatively low covered connections disabled 2:38:28.137 912M / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 2:38:28.453 912M / 9G INFO General (graph_simplification.hpp : 806) Iteration 1 2:38:28.454 912M / 9G INFO General (graph_simplification.hpp : 247) Removal of relatively low covered connections disabled 2:38:28.454 912M / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 2:38:28.573 892M / 9G INFO StageManager (stage.cpp : 125) STAGE == Gap Closer 2:38:28.573 892M / 9G INFO General (graph_pack.hpp : 84) Index refill 2:38:28.574 892M / 9G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 2:38:28.574 892M / 9G INFO General (kmer_splitters.hpp : 289) Splitting kmer instances into 16 buckets. This might take a while. 2:38:28.574 892M / 9G INFO General (file_limit.hpp : 29) Open file limit set to 32768 2:38:28.574 892M / 9G INFO General (kmer_splitters.hpp : 307) Memory available for splitting buffers: 33.043 Gb 2:38:28.574 892M / 9G INFO General (kmer_splitters.hpp : 312) Using cell size of 1398101 2:41:57.774 1G / 9G INFO General (kmer_splitters.hpp : 325) Processed 21193 edges 2:44:05.861 1G / 9G INFO General (kmer_splitters.hpp : 325) Processed 42923 edges 2:46:11.926 1G / 9G INFO General (kmer_splitters.hpp : 325) Processed 64756 edges 2:49:02.769 1G / 9G INFO General (kmer_splitters.hpp : 325) Processed 74044 edges 2:49:02.769 1G / 9G INFO General (kmer_splitters.hpp : 330) Used 74044 sequences. 2:49:02.854 876M / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 2:50:33.426 876M / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 76850102 kmers in total. 2:50:33.426 876M / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 2:50:43.917 876M / 9G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 2:52:25.495 904M / 9G INFO General (kmer_index.hpp : 371) Merging final buckets. 2:52:57.520 904M / 9G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 26585369 bytes occupied (2.7675 bits per kmer). 2:52:58.894 2G / 9G INFO General (edge_index_builders.hpp : 21) Collecting k-mer coverage information from graph, this takes a while. 2:55:22.234 2G / 9G INFO General (gap_closer.cpp : 157) Preparing shift maps 2:55:22.354 2G / 9G INFO General (gap_closer.cpp : 117) Processing paired reads (takes a while) 2:56:08.716 2G / 9G INFO General (gap_closer.cpp : 136) Used 26497326 paired reads 2:56:08.717 2G / 9G INFO General (gap_closer.cpp : 138) Merging paired indices 2:56:08.994 2G / 9G INFO GapCloser (gap_closer.cpp : 395) Closing short gaps 2:56:09.392 2G / 9G INFO GapCloser (gap_closer.cpp : 424) Closing short gaps complete: filled 66 gaps after checking 8836 candidates 2:56:10.732 2G / 9G INFO StageManager (stage.cpp : 125) STAGE == Simplification Cleanup 2:56:10.733 2G / 9G INFO General (graph_simplification.hpp : 403) Removing isolated edges 2:56:10.733 2G / 9G INFO General (graph_simplification.hpp : 404) All edges shorter than 151 will be removed 2:56:10.733 2G / 9G INFO General (graph_simplification.hpp : 405) Also edges shorter than 0 and coverage smaller than 2 will be removed 2:56:11.793 2G / 9G INFO General (simplification.cpp : 56) Removing all the edges having coverage 0 and less 2:56:12.005 2G / 9G INFO General (simplification.cpp : 68) Counting average coverage 2:56:12.054 2G / 9G INFO General (simplification.cpp : 71) Average coverage = 23.7731 2:56:12.055 2G / 9G INFO StageManager (stage.cpp : 125) STAGE == Mismatch Correction 2:57:02.268 2G / 9G INFO General (mismatch_shall_not_pass.hp: 188) Finished collecting potential mismatches positions 2:57:02.361 2G / 9G INFO General (mismatch_shall_not_pass.hp: 291) All edges processed 2:57:02.365 2G / 9G INFO General (mismatch_correction.cpp : 18) Corrected 0 nucleotides 2:57:02.381 2G / 9G INFO StageManager (stage.cpp : 125) STAGE == Paired Information Counting 2:57:02.630 2G / 9G INFO General (pair_info_count.cpp : 150) Graph N50: 23077 2:57:02.630 2G / 9G INFO General (pair_info_count.cpp : 152) Estimating insert size for library #0 2:57:02.631 2G / 9G INFO General (pair_info_count.cpp : 31) Estimating insert size (takes a while) 2:57:02.641 2G / 9G INFO General (short_read_mapper.hpp : 91) Selecting usual mapper 2:57:08.210 2G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 200000 reads 2:57:08.211 2G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 400000 reads 2:57:08.226 2G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 600000 reads 2:57:08.228 2G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 800000 reads 2:57:08.245 2G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 1000000 reads 2:57:08.279 2G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 1200000 reads 2:57:08.645 2G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 2200000 reads 2:57:14.339 2G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 4200000 reads 2:57:21.483 2G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 8400000 reads 2:57:32.460 2G / 9G INFO General (sequence_mapper_notifier.h: 89) Processed 13248663 reads 2:57:32.461 2G / 9G INFO General (pair_info_count.cpp : 41) 6889244 paired reads (51.9995% of all) aligned to long edges 2:57:32.472 2G / 9G INFO General (pair_info_count.cpp : 170) Estimated insert size for paired library #0 2:57:32.472 2G / 9G INFO General (pair_info_count.cpp : 175) Insert size = 322.549, deviation = 95.2429, left quantile = 205, right quantile = 447, read length = 151 2:57:32.472 2G / 9G INFO General (pair_info_count.cpp : 187) Mapping library #0 2:57:32.472 2G / 9G INFO General (pair_info_count.cpp : 189) Mapping paired reads (takes a while) 2:57:32.472 2G / 9G INFO General (pair_info_count.cpp : 73) Left insert size qauntile 205, right insert size quantile 447 2:57:32.482 2G / 9G INFO General (short_read_mapper.hpp : 91) Selecting usual mapper 2:57:40.196 4G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 200000 reads 2:57:40.932 4G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 400000 reads 2:57:41.836 4G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 600000 reads 2:57:42.916 4G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 800000 reads 2:57:44.097 4G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 1000000 reads 2:57:45.362 4G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 1200000 reads 2:57:52.501 4G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 2200000 reads 2:58:08.101 5G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 4200000 reads 2:58:42.885 5G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 8400000 reads 2:59:54.776 5G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 16800000 reads 3:01:22.956 3G / 9G INFO General (sequence_mapper_notifier.h: 89) Processed 26497326 reads 3:04:14.923 3G / 9G INFO General (split_graph_pair_info.hpp : 344) Threshold for paired information 0.0600836 3:04:19.215 2G / 9G INFO StageManager (stage.cpp : 125) STAGE == Distance Estimation 3:04:19.215 2G / 9G INFO General (distance_estimation.cpp : 234) Processing library #0 3:04:19.215 2G / 9G INFO General (distance_estimation.cpp : 136) Weight Filter Done 3:04:19.215 2G / 9G INFO DistanceEstimator (distance_estimation.hpp : 187) Using SIMPLE distance estimator 3:04:27.603 2G / 9G INFO DistanceEstimator (distance_estimation.hpp : 208) Merging maps 3:04:28.848 2G / 9G INFO General (distance_estimation.cpp : 38) Filtering info 3:04:30.625 2G / 9G INFO General (pair_info_filters.hpp : 354) Pruning the index 3:04:30.695 2G / 9G INFO General (distance_estimation.cpp : 184) Refining clustered pair information 3:04:30.841 2G / 9G INFO General (distance_estimation.cpp : 186) The refining of clustered pair information has been finished 3:04:30.841 2G / 9G INFO General (distance_estimation.cpp : 188) Filling paired information 3:04:33.516 2G / 9G INFO PairInfoImprover (pair_info_improver.hpp : 61) Paired info stats: missing = 69769; contradictional = 5846 3:04:36.169 2G / 9G INFO PairInfoImprover (pair_info_improver.hpp : 61) Paired info stats: missing = 12466; contradictional = 0 3:04:36.170 2G / 9G INFO General (distance_estimation.cpp : 193) Filling scaffolding index 3:04:36.170 2G / 9G INFO DistanceEstimator (distance_estimation.hpp : 187) Using SMOOTHING distance estimator 3:04:46.177 2G / 9G INFO DistanceEstimator (distance_estimation.hpp : 208) Merging maps 3:04:46.246 2G / 9G INFO General (distance_estimation.cpp : 38) Filtering info 3:04:46.518 2G / 9G INFO General (pair_info_filters.hpp : 354) Pruning the index 3:04:47.098 2G / 9G INFO StageManager (stage.cpp : 125) STAGE == Repeat Resolving 3:04:47.099 2G / 9G INFO General (contig_output.hpp : 283) Outputting contigs to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_131-dipSPAdes-3.5.0-trimmed/spades//K77/before_rr.fasta 3:06:23.910 2G / 9G INFO General (repeat_resolving.cpp : 59) Using Path-Extend repeat resolving 3:06:23.911 2G / 9G INFO General (path_extend_launch.hpp : 459) Threshold for library #0 is 0.0600836 3:06:23.911 2G / 9G INFO General (path_extend_launch.hpp : 298) Path-Extend repeat resolving tool started 3:06:23.976 2G / 9G INFO General (path_extend_launch.hpp : 316) Using 1 paired-end library 3:06:23.976 2G / 9G INFO General (path_extend_launch.hpp : 317) Using 1 paired-end scaffolding library 3:06:23.976 2G / 9G INFO General (path_extend_launch.hpp : 318) Using 0 mate-pair libraries 3:06:23.976 2G / 9G INFO General (path_extend_launch.hpp : 319) Using 0 single read libraries 3:06:23.976 2G / 9G INFO General (path_extend_launch.hpp : 320) Scaffolder is on 3:06:24.369 2G / 9G INFO General (path_extend_launch.hpp : 332) Growing paths using paired-end and long single reads 3:06:24.370 2G / 9G INFO PathExtender (path_extender.hpp : 611) Processed 0 paths from 31793 (0%) 3:06:24.692 2G / 9G INFO PathExtender (path_extender.hpp : 609) Processed 128 paths from 31793 (0%) 3:06:25.158 2G / 9G INFO PathExtender (path_extender.hpp : 609) Processed 256 paths from 31793 (0%) 3:06:25.731 2G / 9G INFO PathExtender (path_extender.hpp : 609) Processed 512 paths from 31793 (1%) 3:06:26.615 2G / 9G INFO PathExtender (path_extender.hpp : 609) Processed 1024 paths from 31793 (3%) 3:06:28.166 2G / 9G INFO PathExtender (path_extender.hpp : 609) Processed 2048 paths from 31793 (6%) 3:06:28.900 2G / 9G INFO PathExtender (path_extender.hpp : 611) Processed 3180 paths from 31793 (10%) 3:06:30.019 2G / 9G INFO PathExtender (path_extender.hpp : 609) Processed 4096 paths from 31793 (12%) 3:06:30.758 2G / 9G INFO PathExtender (path_extender.hpp : 611) Processed 6360 paths from 31793 (20%) 3:06:31.238 2G / 9G INFO PathExtender (path_extender.hpp : 609) Processed 8192 paths from 31793 (25%) 3:06:31.489 2G / 9G INFO PathExtender (path_extender.hpp : 611) Processed 9540 paths from 31793 (30%) 3:06:32.314 2G / 9G INFO PathExtender (path_extender.hpp : 611) Processed 12720 paths from 31793 (40%) 3:06:32.990 2G / 9G INFO PathExtender (path_extender.hpp : 611) Processed 15900 paths from 31793 (50%) 3:06:33.123 2G / 9G INFO PathExtender (path_extender.hpp : 609) Processed 16384 paths from 31793 (51%) 3:06:33.414 2G / 9G INFO PathExtender (path_extender.hpp : 611) Processed 19080 paths from 31793 (60%) 3:06:34.124 2G / 9G INFO PathExtender (path_extender.hpp : 611) Processed 22260 paths from 31793 (70%) 3:06:38.748 2G / 9G INFO PathExtender (path_extender.hpp : 611) Processed 25440 paths from 31793 (80%) 3:06:42.456 2G / 9G INFO PathExtender (path_extender.hpp : 611) Processed 28620 paths from 31793 (90%) 3:06:44.770 2G / 9G INFO PathExtendIO (pe_io.hpp : 339) Constructing FASTG file from paths 3:06:45.498 2G / 9G INFO PathExtendIO (pe_io.hpp : 342) Writing contigs in FASTG to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_131-dipSPAdes-3.5.0-trimmed/spades//K77/final_contigs.fastg 3:06:45.498 2G / 9G INFO PathExtendIO (pe_io.hpp : 343) Writing contigs in FASTA to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_131-dipSPAdes-3.5.0-trimmed/spades//K77/final_contigs.fasta 3:07:43.756 2G / 9G INFO PathExtendIO (pe_io.hpp : 339) Constructing FASTG file from paths 3:07:44.487 2G / 9G INFO PathExtendIO (pe_io.hpp : 342) Writing contigs in FASTG to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_131-dipSPAdes-3.5.0-trimmed/spades//K77/path_extend/pe_before_traversal.fastg 3:07:44.488 2G / 9G INFO PathExtendIO (pe_io.hpp : 343) Writing contigs in FASTA to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_131-dipSPAdes-3.5.0-trimmed/spades//K77/path_extend/pe_before_traversal.fasta 3:08:30.835 2G / 9G INFO General (path_extend_launch.hpp : 281) Traversing tandem repeats 3:08:31.715 2G / 9G INFO PathExtendIO (pe_io.hpp : 339) Constructing FASTG file from paths 3:08:32.425 2G / 9G INFO PathExtendIO (pe_io.hpp : 342) Writing contigs in FASTG to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_131-dipSPAdes-3.5.0-trimmed/spades//K77/scaffolds.fastg 3:08:32.425 2G / 9G INFO PathExtendIO (pe_io.hpp : 343) Writing contigs in FASTA to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_131-dipSPAdes-3.5.0-trimmed/spades//K77/scaffolds.fasta 3:09:27.927 2G / 9G INFO General (launch.hpp : 82) SPAdes finished 3:09:31.561 344M / 9G INFO General (main.cpp : 166) Assembling time: 3 hours 9 minutes 31 seconds ===== Assembling finished. * Corrected reads are in /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_131-dipSPAdes-3.5.0-trimmed/spades/corrected/ * Assembled contigs are in /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_131-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_131-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_131-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_131-dipSPAdes-3.5.0-trimmed/spades/spades.log Thank you for using SPAdes!