Command line: /N/dc2/projects/marinovg/programs/SPAdes-3.5.0-Linux/bin/spades.py --pe1-1 /N/dc2/projects/marinovg/2015-01-29-P-assem/pentaurelia-strain_870-TS-130302_M00532_0028_LynchDoak527-TS22.R1.trimmed.paired.fastq.gz --pe1-2 /N/dc2/projects/marinovg/2015-01-29-P-assem/pentaurelia-strain_870-TS-130302_M00532_0028_LynchDoak527-TS22.R2.trimmed.paired.fastq.gz --pe2-1 /N/dc2/projects/marinovg/2015-01-29-P-assem/pentaurelia-strain_870-TS-130302_M00532_0028_LynchDoak527-TS27.R1.trimmed.paired.fastq.gz --pe2-2 /N/dc2/projects/marinovg/2015-01-29-P-assem/pentaurelia-strain_870-TS-130302_M00532_0028_LynchDoak527-TS27.R2.trimmed.paired.fastq.gz --pe3-1 /N/dc2/projects/marinovg/2015-01-29-P-assem/pentaurelia-strain_870-TS-130302_M00532_0028_LynchDoak527-TS3.R1.trimmed.paired.fastq.gz --pe3-2 /N/dc2/projects/marinovg/2015-01-29-P-assem/pentaurelia-strain_870-TS-130302_M00532_0028_LynchDoak527-TS3.R2.trimmed.paired.fastq.gz --pe4-1 /N/dc2/projects/marinovg/2015-01-29-P-assem/pentaurelia-strain_870-TS-130302_M00532_0028_LynchDoak527-TS9.R1.trimmed.paired.fastq.gz --pe4-2 /N/dc2/projects/marinovg/2015-01-29-P-assem/pentaurelia-strain_870-TS-130302_M00532_0028_LynchDoak527-TS9.R2.trimmed.paired.fastq.gz --mp1-1 /N/dc2/projects/marinovg/2015-01-29-P-assem/pentaurelia-strain_870-MP-MP.R1.trimmed.paired.fastq.gz --mp1-2 /N/dc2/projects/marinovg/2015-01-29-P-assem/pentaurelia-strain_870-MP-MP.R2.trimmed.paired.fastq.gz -t 16 -o /N/dc2/projects/marinovg/2015-01-29-P-assem/Paramecium_pentaurelia_strain_870-SPAdes-3.5.0-trimmed System information: SPAdes version: 3.5.0 Python version: 2.6.6 OS: Linux-2.6.32-504.8.1.el6.x86_64-x86_64-with-redhat-6.6-Santiago Output dir: /N/dc2/projects/marinovg/2015-01-29-P-assem/Paramecium_pentaurelia_strain_870-SPAdes-3.5.0-trimmed 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: mate-pairs orientation: rf left reads: ['/N/dc2/projects/marinovg/2015-01-29-P-assem/pentaurelia-strain_870-MP-MP.R1.trimmed.paired.fastq.gz'] right reads: ['/N/dc2/projects/marinovg/2015-01-29-P-assem/pentaurelia-strain_870-MP-MP.R2.trimmed.paired.fastq.gz'] interlaced reads: not specified single reads: not specified Library number: 2, library type: paired-end orientation: fr left reads: ['/N/dc2/projects/marinovg/2015-01-29-P-assem/pentaurelia-strain_870-TS-130302_M00532_0028_LynchDoak527-TS22.R1.trimmed.paired.fastq.gz'] right reads: ['/N/dc2/projects/marinovg/2015-01-29-P-assem/pentaurelia-strain_870-TS-130302_M00532_0028_LynchDoak527-TS22.R2.trimmed.paired.fastq.gz'] interlaced reads: not specified single reads: not specified Library number: 3, library type: paired-end orientation: fr left reads: ['/N/dc2/projects/marinovg/2015-01-29-P-assem/pentaurelia-strain_870-TS-130302_M00532_0028_LynchDoak527-TS27.R1.trimmed.paired.fastq.gz'] right reads: ['/N/dc2/projects/marinovg/2015-01-29-P-assem/pentaurelia-strain_870-TS-130302_M00532_0028_LynchDoak527-TS27.R2.trimmed.paired.fastq.gz'] interlaced reads: not specified single reads: not specified Library number: 4, library type: paired-end orientation: fr left reads: ['/N/dc2/projects/marinovg/2015-01-29-P-assem/pentaurelia-strain_870-TS-130302_M00532_0028_LynchDoak527-TS3.R1.trimmed.paired.fastq.gz'] right reads: ['/N/dc2/projects/marinovg/2015-01-29-P-assem/pentaurelia-strain_870-TS-130302_M00532_0028_LynchDoak527-TS3.R2.trimmed.paired.fastq.gz'] interlaced reads: not specified single reads: not specified Library number: 5, library type: paired-end orientation: fr left reads: ['/N/dc2/projects/marinovg/2015-01-29-P-assem/pentaurelia-strain_870-TS-130302_M00532_0028_LynchDoak527-TS9.R1.trimmed.paired.fastq.gz'] right reads: ['/N/dc2/projects/marinovg/2015-01-29-P-assem/pentaurelia-strain_870-TS-130302_M00532_0028_LynchDoak527-TS9.R2.trimmed.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/2015-01-29-P-assem/Paramecium_pentaurelia_strain_870-SPAdes-3.5.0-trimmed/tmp Threads: 16 Memory limit (in Gb): 250 ======= SPAdes pipeline started. Log can be found here: /N/dc2/projects/marinovg/2015-01-29-P-assem/Paramecium_pentaurelia_strain_870-SPAdes-3.5.0-trimmed/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/2015-01-29-P-assem/Paramecium_pentaurelia_strain_870-SPAdes-3.5.0-trimmed/corrected/configs/config.info 0:00:00.004 4M / 4M INFO General (main.cpp : 82) Loading config from /N/dc2/projects/marinovg/2015-01-29-P-assem/Paramecium_pentaurelia_strain_870-SPAdes-3.5.0-trimmed/corrected/configs/config.info 0:00:00.042 4M / 4M INFO General (memory_limit.hpp : 42) Memory limit set to 100 Gb 0:00:00.042 4M / 4M INFO General (main.cpp : 91) Trying to determine PHRED offset 0:00:00.112 4M / 4M INFO General (main.cpp : 97) Determined value is 33 0:00:00.118 4M / 4M INFO General (hammer_tools.cpp : 36) Hamming graph threshold tau=1, k=21, subkmer positions = [ 0 10 ] === ITERATION 0 begins === 0:00:00.119 4M / 4M INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:00:00.119 4M / 4M INFO K-mer Splitting (kmer_data.cpp : 127) Splitting kmer instances into 256 buckets. This might take a while. 0:00:00.120 4M / 4M INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:00:00.120 4M / 4M INFO K-mer Splitting (kmer_data.cpp : 145) Memory available for splitting buffers: 2.08325 Gb 0:00:00.120 4M / 4M INFO K-mer Splitting (kmer_data.cpp : 153) Using cell size of 262144 0:00:02.772 8G / 8G INFO K-mer Splitting (kmer_data.cpp : 167) Processing /N/dc2/projects/marinovg/2015-01-29-P-assem/pentaurelia-strain_870-MP-MP.R1.trimmed.paired.fastq.gz 0:00:31.512 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 176) Processed 1633916 reads 0:00:31.514 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 167) Processing /N/dc2/projects/marinovg/2015-01-29-P-assem/pentaurelia-strain_870-MP-MP.R2.trimmed.paired.fastq.gz 0:00:55.264 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 176) Processed 3267832 reads 0:00:55.266 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 167) Processing /N/dc2/projects/marinovg/2015-01-29-P-assem/pentaurelia-strain_870-TS-130302_M00532_0028_LynchDoak527-TS22.R1.trimmed.paired.fastq.gz 0:01:36.067 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 176) Processed 4473386 reads 0:01:36.070 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 167) Processing /N/dc2/projects/marinovg/2015-01-29-P-assem/pentaurelia-strain_870-TS-130302_M00532_0028_LynchDoak527-TS22.R2.trimmed.paired.fastq.gz 0:02:02.494 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 176) Processed 5678940 reads 0:02:02.495 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 167) Processing /N/dc2/projects/marinovg/2015-01-29-P-assem/pentaurelia-strain_870-TS-130302_M00532_0028_LynchDoak527-TS27.R1.trimmed.paired.fastq.gz 0:02:37.995 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 176) Processed 6709606 reads 0:02:37.998 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 167) Processing /N/dc2/projects/marinovg/2015-01-29-P-assem/pentaurelia-strain_870-TS-130302_M00532_0028_LynchDoak527-TS27.R2.trimmed.paired.fastq.gz 0:03:00.505 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 176) Processed 7740272 reads 0:03:00.506 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 167) Processing /N/dc2/projects/marinovg/2015-01-29-P-assem/pentaurelia-strain_870-TS-130302_M00532_0028_LynchDoak527-TS3.R1.trimmed.paired.fastq.gz 0:03:38.059 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 176) Processed 8858820 reads 0:03:38.061 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 167) Processing /N/dc2/projects/marinovg/2015-01-29-P-assem/pentaurelia-strain_870-TS-130302_M00532_0028_LynchDoak527-TS3.R2.trimmed.paired.fastq.gz 0:04:02.842 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 176) Processed 9977368 reads 0:04:02.843 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 167) Processing /N/dc2/projects/marinovg/2015-01-29-P-assem/pentaurelia-strain_870-TS-130302_M00532_0028_LynchDoak527-TS9.R1.trimmed.paired.fastq.gz 0:04:44.636 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 176) Processed 11215670 reads 0:05:03.828 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 167) Processing /N/dc2/projects/marinovg/2015-01-29-P-assem/pentaurelia-strain_870-TS-130302_M00532_0028_LynchDoak527-TS9.R2.trimmed.paired.fastq.gz 0:05:44.137 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 181) Processed 13604012 reads 0:05:44.995 64M / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:06:30.001 64M / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 510459802 kmers in total. 0:06:30.002 64M / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:06:57.182 64M / 9G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:08:10.599 256M / 16G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:08:27.063 256M / 16G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 176587239 bytes occupied (2.7675 bits per kmer). 0:08:27.064 256M / 16G INFO K-mer Counting (kmer_data.cpp : 266) Arranging kmers in hash map order 0:12:43.627 256M / 16G INFO K-mer Counting (kmer_data.cpp : 279) Done. Total swaps: 510459533 0:12:46.446 4G / 16G INFO General (main.cpp : 151) Clustering Hamming graph. 0:12:46.447 4G / 16G INFO Hamming Clustering (hamcluster.cpp : 115) Serializing sub-kmers. 0:12:46.447 4G / 16G INFO Hamming Clustering (hamcluster.cpp : 120) Serializing: [0, 10) 0:17:02.427 4G / 16G INFO Hamming Clustering (hamcluster.cpp : 120) Serializing: [10, 21) 0:21:15.616 4G / 16G INFO Hamming Clustering (hamcluster.cpp : 129) Splitting sub-kmers, pass 1. 0:27:03.967 4G / 16G INFO Hamming Clustering (hamcluster.cpp : 134) Splitting done. Processed 2 blocks. Produced 5242337 blocks. 0:27:03.967 4G / 16G INFO Hamming Clustering (hamcluster.cpp : 145) Merge sub-kmers, pass 1 0:48:01.872 4G / 16G INFO Hamming Clustering (hamcluster.cpp : 170) Merge done, total 2511447 new blocks generated. 0:48:04.223 4G / 16G INFO Hamming Clustering (hamcluster.cpp : 175) Spliting sub-kmers, pass 2. 1:06:08.871 4G / 16G INFO Hamming Clustering (hamcluster.cpp : 180) Splitting done. Processed 5022894 blocks. Produced 916135836 blocks. 1:06:08.871 4G / 16G INFO Hamming Clustering (hamcluster.cpp : 187) Merge sub-kmers, pass 2 1:26:02.177 4G / 16G INFO Hamming Clustering (hamcluster.cpp : 205) Merge done, saw 825247 big blocks out of 916135836 processed. 1:32:20.550 4G / 17G INFO General (main.cpp : 165) Clustering done. Total clusters: 227428627 1:32:20.550 4G / 17G INFO K-mer Counting (kmer_data.cpp : 284) Collecting K-mer information, this takes a while. 1:32:29.928 26G / 26G INFO K-mer Counting (kmer_data.cpp : 290) Processing /N/dc2/projects/marinovg/2015-01-29-P-assem/pentaurelia-strain_870-MP-MP.R1.trimmed.paired.fastq.gz 1:32:54.851 26G / 26G INFO K-mer Counting (kmer_data.cpp : 290) Processing /N/dc2/projects/marinovg/2015-01-29-P-assem/pentaurelia-strain_870-MP-MP.R2.trimmed.paired.fastq.gz 1:33:14.204 26G / 26G INFO K-mer Counting (kmer_data.cpp : 290) Processing /N/dc2/projects/marinovg/2015-01-29-P-assem/pentaurelia-strain_870-TS-130302_M00532_0028_LynchDoak527-TS22.R1.trimmed.paired.fastq.gz 1:33:54.866 26G / 26G INFO K-mer Counting (kmer_data.cpp : 290) Processing /N/dc2/projects/marinovg/2015-01-29-P-assem/pentaurelia-strain_870-TS-130302_M00532_0028_LynchDoak527-TS22.R2.trimmed.paired.fastq.gz 1:34:19.544 26G / 26G INFO K-mer Counting (kmer_data.cpp : 290) Processing /N/dc2/projects/marinovg/2015-01-29-P-assem/pentaurelia-strain_870-TS-130302_M00532_0028_LynchDoak527-TS27.R1.trimmed.paired.fastq.gz 1:34:54.675 26G / 26G INFO K-mer Counting (kmer_data.cpp : 290) Processing /N/dc2/projects/marinovg/2015-01-29-P-assem/pentaurelia-strain_870-TS-130302_M00532_0028_LynchDoak527-TS27.R2.trimmed.paired.fastq.gz 1:35:16.151 26G / 26G INFO K-mer Counting (kmer_data.cpp : 290) Processing /N/dc2/projects/marinovg/2015-01-29-P-assem/pentaurelia-strain_870-TS-130302_M00532_0028_LynchDoak527-TS3.R1.trimmed.paired.fastq.gz 1:35:54.947 26G / 26G INFO K-mer Counting (kmer_data.cpp : 290) Processing /N/dc2/projects/marinovg/2015-01-29-P-assem/pentaurelia-strain_870-TS-130302_M00532_0028_LynchDoak527-TS3.R2.trimmed.paired.fastq.gz 1:36:18.313 26G / 26G INFO K-mer Counting (kmer_data.cpp : 290) Processing /N/dc2/projects/marinovg/2015-01-29-P-assem/pentaurelia-strain_870-TS-130302_M00532_0028_LynchDoak527-TS9.R1.trimmed.paired.fastq.gz 1:37:20.284 26G / 26G INFO K-mer Counting (kmer_data.cpp : 290) Processing /N/dc2/projects/marinovg/2015-01-29-P-assem/pentaurelia-strain_870-TS-130302_M00532_0028_LynchDoak527-TS9.R2.trimmed.paired.fastq.gz 1:37:57.353 26G / 26G INFO K-mer Counting (kmer_data.cpp : 297) Collection done, postprocessing. 1:38:09.290 26G / 26G INFO K-mer Counting (kmer_data.cpp : 310) There are 510459802 kmers in total. Among them 338127478 (66.2398%) are singletons. 1:38:09.290 26G / 26G INFO General (main.cpp : 203) Subclustering Hamming graph 1:45:16.014 26G / 26G INFO Hamming Subclustering (kmer_cluster.cpp : 626) Subclustering done. Total 229867 non-read kmers were generated. 1:45:16.014 26G / 26G INFO Hamming Subclustering (kmer_cluster.cpp : 627) Subclustering statistics: 1:45:16.014 26G / 26G INFO Hamming Subclustering (kmer_cluster.cpp : 628) Total singleton hamming clusters: 161212216. Among them 38058154 (23.6075%) are good 1:45:16.014 26G / 26G INFO Hamming Subclustering (kmer_cluster.cpp : 629) Total singleton subclusters: 5536742. Among them 5536401 (99.9938%) are good 1:45:16.014 26G / 26G INFO Hamming Subclustering (kmer_cluster.cpp : 630) Total non-singleton subcluster centers: 77250933. Among them 54168888 (70.1207%) are good 1:45:16.014 26G / 26G INFO Hamming Subclustering (kmer_cluster.cpp : 631) Average size of non-trivial subcluster: 4.51268 kmers 1:45:16.014 26G / 26G INFO Hamming Subclustering (kmer_cluster.cpp : 632) Average number of sub-clusters per non-singleton cluster: 1.25026 1:45:16.014 26G / 26G INFO Hamming Subclustering (kmer_cluster.cpp : 633) Total solid k-mers: 97763443 1:45:16.014 26G / 26G INFO Hamming Subclustering (kmer_cluster.cpp : 634) Substitution probabilities: [4,4]((0.879934,0.0306197,0.0251313,0.0643153),(0.0534128,0.903828,0.0133604,0.0293986),(0.0278239,0.0127734,0.905347,0.0540561),(0.0633681,0.0254515,0.0311039,0.880077)) 1:45:16.631 26G / 26G INFO General (main.cpp : 208) Finished clustering. 1:45:16.631 26G / 26G INFO General (main.cpp : 228) Starting solid k-mers expansion in 16 threads. 1:48:25.530 26G / 26G INFO General (main.cpp : 249) Solid k-mers iteration 0 produced 51967518 new k-mers. 1:51:30.876 26G / 26G INFO General (main.cpp : 249) Solid k-mers iteration 1 produced 3230688 new k-mers. 1:54:36.204 26G / 26G INFO General (main.cpp : 249) Solid k-mers iteration 2 produced 288102 new k-mers. 1:57:41.691 26G / 26G INFO General (main.cpp : 249) Solid k-mers iteration 3 produced 29639 new k-mers. 2:00:46.751 26G / 26G INFO General (main.cpp : 249) Solid k-mers iteration 4 produced 4372 new k-mers. 2:03:50.698 26G / 26G INFO General (main.cpp : 249) Solid k-mers iteration 5 produced 637 new k-mers. 2:06:55.862 26G / 26G INFO General (main.cpp : 249) Solid k-mers iteration 6 produced 20 new k-mers. 2:10:00.053 26G / 26G INFO General (main.cpp : 249) Solid k-mers iteration 7 produced 0 new k-mers. 2:10:00.054 26G / 26G INFO General (main.cpp : 253) Solid k-mers finalized 2:10:00.054 26G / 26G INFO General (hammer_tools.cpp : 210) Starting read correction in 16 threads. 2:10:00.055 26G / 26G INFO General (hammer_tools.cpp : 222) Correcting pair of reads: /N/dc2/projects/marinovg/2015-01-29-P-assem/pentaurelia-strain_870-MP-MP.R1.trimmed.paired.fastq.gz and /N/dc2/projects/marinovg/2015-01-29-P-assem/pentaurelia-strain_870-MP-MP.R2.trimmed.paired.fastq.gz 2:10:20.087 28G / 28G INFO General (hammer_tools.cpp : 166) Prepared batch 0 of 1600000 reads. 2:10:37.951 28G / 28G INFO General (hammer_tools.cpp : 175) Processed batch 0 2:10:50.336 28G / 28G INFO General (hammer_tools.cpp : 185) Written batch 0 2:10:50.776 28G / 28G INFO General (hammer_tools.cpp : 166) Prepared batch 1 of 33916 reads. 2:10:51.172 28G / 28G INFO General (hammer_tools.cpp : 175) Processed batch 1 2:10:51.448 28G / 28G INFO General (hammer_tools.cpp : 185) Written batch 1 2:10:53.512 26G / 28G INFO General (hammer_tools.cpp : 222) Correcting pair of reads: /N/dc2/projects/marinovg/2015-01-29-P-assem/pentaurelia-strain_870-TS-130302_M00532_0028_LynchDoak527-TS22.R1.trimmed.paired.fastq.gz and /N/dc2/projects/marinovg/2015-01-29-P-assem/pentaurelia-strain_870-TS-130302_M00532_0028_LynchDoak527-TS22.R2.trimmed.paired.fastq.gz 2:11:16.859 28G / 28G INFO General (hammer_tools.cpp : 166) Prepared batch 0 of 1205554 reads. 2:11:44.155 28G / 28G INFO General (hammer_tools.cpp : 175) Processed batch 0 2:11:57.855 28G / 28G INFO General (hammer_tools.cpp : 185) Written batch 0 2:11:59.627 26G / 28G INFO General (hammer_tools.cpp : 222) Correcting pair of reads: /N/dc2/projects/marinovg/2015-01-29-P-assem/pentaurelia-strain_870-TS-130302_M00532_0028_LynchDoak527-TS27.R1.trimmed.paired.fastq.gz and /N/dc2/projects/marinovg/2015-01-29-P-assem/pentaurelia-strain_870-TS-130302_M00532_0028_LynchDoak527-TS27.R2.trimmed.paired.fastq.gz 2:12:19.584 28G / 28G INFO General (hammer_tools.cpp : 166) Prepared batch 0 of 1030666 reads. 2:12:43.020 28G / 28G INFO General (hammer_tools.cpp : 175) Processed batch 0 2:12:52.988 28G / 28G INFO General (hammer_tools.cpp : 185) Written batch 0 2:12:54.868 26G / 28G INFO General (hammer_tools.cpp : 222) Correcting pair of reads: /N/dc2/projects/marinovg/2015-01-29-P-assem/pentaurelia-strain_870-TS-130302_M00532_0028_LynchDoak527-TS3.R1.trimmed.paired.fastq.gz and /N/dc2/projects/marinovg/2015-01-29-P-assem/pentaurelia-strain_870-TS-130302_M00532_0028_LynchDoak527-TS3.R2.trimmed.paired.fastq.gz 2:13:16.817 28G / 28G INFO General (hammer_tools.cpp : 166) Prepared batch 0 of 1118548 reads. 2:13:45.011 28G / 28G INFO General (hammer_tools.cpp : 175) Processed batch 0 2:13:55.399 28G / 28G INFO General (hammer_tools.cpp : 185) Written batch 0 2:13:56.998 26G / 28G INFO General (hammer_tools.cpp : 222) Correcting pair of reads: /N/dc2/projects/marinovg/2015-01-29-P-assem/pentaurelia-strain_870-TS-130302_M00532_0028_LynchDoak527-TS9.R1.trimmed.paired.fastq.gz and /N/dc2/projects/marinovg/2015-01-29-P-assem/pentaurelia-strain_870-TS-130302_M00532_0028_LynchDoak527-TS9.R2.trimmed.paired.fastq.gz 2:14:28.739 29G / 29G INFO General (hammer_tools.cpp : 166) Prepared batch 0 of 1600000 reads. 2:15:04.808 29G / 29G INFO General (hammer_tools.cpp : 175) Processed batch 0 2:15:19.649 29G / 29G INFO General (hammer_tools.cpp : 185) Written batch 0 2:15:23.642 29G / 29G INFO General (hammer_tools.cpp : 166) Prepared batch 1 of 213322 reads. 2:15:29.619 29G / 29G INFO General (hammer_tools.cpp : 175) Processed batch 1 2:15:31.640 29G / 29G INFO General (hammer_tools.cpp : 185) Written batch 1 2:15:33.926 26G / 29G INFO General (hammer_tools.cpp : 269) Correction done. Changed 5858774 bases in 4167902 reads. 2:15:33.926 26G / 29G INFO General (hammer_tools.cpp : 270) Failed to correct 752783395 bases out of 3162977381. 2:15:34.050 3G / 29G INFO General (main.cpp : 286) Saving corrected dataset description to /N/dc2/projects/marinovg/2015-01-29-P-assem/Paramecium_pentaurelia_strain_870-SPAdes-3.5.0-trimmed/corrected/corrected.yaml 2:15:34.055 3G / 29G INFO General (main.cpp : 293) All done. Exiting. == Compressing corrected reads (with gzip) == Dataset description file was created: /N/dc2/projects/marinovg/2015-01-29-P-assem/Paramecium_pentaurelia_strain_870-SPAdes-3.5.0-trimmed/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/2015-01-29-P-assem/Paramecium_pentaurelia_strain_870-SPAdes-3.5.0-trimmed/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 0:00:00.879 84M / 84M INFO General (binary_converter.hpp : 138) 16384 reads processed 0:00:01.206 96M / 96M INFO General (binary_converter.hpp : 138) 32768 reads processed 0:00:01.857 128M / 128M INFO General (binary_converter.hpp : 138) 65536 reads processed 0:00:03.165 192M / 192M INFO General (binary_converter.hpp : 138) 131072 reads processed 0:00:05.799 316M / 316M INFO General (binary_converter.hpp : 138) 262144 reads processed 0:00:10.998 560M / 560M INFO General (binary_converter.hpp : 138) 524288 reads processed 0:00:23.491 948M / 948M INFO General (binary_converter.hpp : 138) 1048576 reads processed 0:00:30.033 404M / 952M INFO General (binary_converter.hpp : 158) 1285607 reads written 0:00:30.563 4M / 952M INFO General (read_converter.hpp : 91) Single reads for library #0 0:00:31.930 140M / 952M INFO General (binary_converter.hpp : 138) 16384 reads processed 0:00:32.105 148M / 952M INFO General (binary_converter.hpp : 138) 32768 reads processed 0:00:32.454 168M / 952M INFO General (binary_converter.hpp : 138) 65536 reads processed 0:00:33.154 204M / 952M INFO General (binary_converter.hpp : 138) 131072 reads processed 0:00:34.546 280M / 952M INFO General (binary_converter.hpp : 138) 262144 reads processed 0:00:35.918 328M / 952M INFO General (binary_converter.hpp : 158) 345550 reads written 0:00:36.201 4M / 952M INFO General (read_converter.hpp : 81) Paired reads for library #1 0:00:37.193 88M / 952M INFO General (binary_converter.hpp : 138) 16384 reads processed 0:00:37.632 112M / 952M INFO General (binary_converter.hpp : 138) 32768 reads processed 0:00:38.521 160M / 952M INFO General (binary_converter.hpp : 138) 65536 reads processed 0:00:40.290 248M / 952M INFO General (binary_converter.hpp : 138) 131072 reads processed 0:00:43.874 432M / 952M INFO General (binary_converter.hpp : 138) 262144 reads processed 0:00:50.891 800M / 952M INFO General (binary_converter.hpp : 138) 524288 reads processed 0:01:07.820 1G / 1G INFO General (binary_converter.hpp : 138) 1048576 reads processed 0:01:13.736 452M / 1G INFO General (binary_converter.hpp : 158) 1205236 reads written 0:01:14.127 4M / 1G INFO General (read_converter.hpp : 91) Single reads for library #1 0:01:15.395 132M / 1G INFO General (binary_converter.hpp : 158) 317 reads written 0:01:15.420 4M / 1G INFO General (read_converter.hpp : 81) Paired reads for library #2 0:01:16.421 88M / 1G INFO General (binary_converter.hpp : 138) 16384 reads processed 0:01:16.863 112M / 1G INFO General (binary_converter.hpp : 138) 32768 reads processed 0:01:17.762 160M / 1G INFO General (binary_converter.hpp : 138) 65536 reads processed 0:01:19.510 248M / 1G INFO General (binary_converter.hpp : 138) 131072 reads processed 0:01:23.047 432M / 1G INFO General (binary_converter.hpp : 138) 262144 reads processed 0:01:30.056 800M / 1G INFO General (binary_converter.hpp : 138) 524288 reads processed 0:01:48.117 204M / 1G INFO General (binary_converter.hpp : 158) 1030477 reads written 0:01:48.262 4M / 1G INFO General (read_converter.hpp : 91) Single reads for library #2 0:01:49.538 132M / 1G INFO General (binary_converter.hpp : 158) 187 reads written 0:01:49.562 4M / 1G INFO General (read_converter.hpp : 81) Paired reads for library #3 0:01:50.561 88M / 1G INFO General (binary_converter.hpp : 138) 16384 reads processed 0:01:51.001 112M / 1G INFO General (binary_converter.hpp : 138) 32768 reads processed 0:01:51.897 160M / 1G INFO General (binary_converter.hpp : 138) 65536 reads processed 0:01:53.679 248M / 1G INFO General (binary_converter.hpp : 138) 131072 reads processed 0:01:57.205 432M / 1G INFO General (binary_converter.hpp : 138) 262144 reads processed 0:02:04.208 800M / 1G INFO General (binary_converter.hpp : 138) 524288 reads processed 0:02:21.149 1G / 1G INFO General (binary_converter.hpp : 138) 1048576 reads processed 0:02:24.706 332M / 1G INFO General (binary_converter.hpp : 158) 1118336 reads written 0:02:24.974 4M / 1G INFO General (read_converter.hpp : 91) Single reads for library #3 0:02:26.249 132M / 1G INFO General (binary_converter.hpp : 158) 208 reads written 0:02:26.274 4M / 1G INFO General (read_converter.hpp : 81) Paired reads for library #4 0:02:27.283 88M / 1G INFO General (binary_converter.hpp : 138) 16384 reads processed 0:02:27.724 112M / 1G INFO General (binary_converter.hpp : 138) 32768 reads processed 0:02:28.610 160M / 1G INFO General (binary_converter.hpp : 138) 65536 reads processed 0:02:30.397 248M / 1G INFO General (binary_converter.hpp : 138) 131072 reads processed 0:02:33.934 432M / 1G INFO General (binary_converter.hpp : 138) 262144 reads processed 0:02:40.976 800M / 1G INFO General (binary_converter.hpp : 138) 524288 reads processed 0:02:57.693 1G / 1G INFO General (binary_converter.hpp : 138) 1048576 reads processed 0:03:21.040 1G / 1G INFO General (binary_converter.hpp : 158) 1812786 reads written 0:03:22.437 4M / 1G INFO General (read_converter.hpp : 91) Single reads for library #4 0:03:23.710 132M / 1G INFO General (binary_converter.hpp : 158) 531 reads written 0:03:23.801 4M / 1G INFO General (graph_construction.hpp : 129) Constructing DeBruijn graph for k=21 0:03:23.803 4M / 1G INFO General (kmer_splitters.hpp : 172) Splitting kmer instances into 256 buckets. This might take a while. 0:03:23.804 4M / 1G INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:03:23.804 4M / 1G INFO General (kmer_splitters.hpp : 190) Memory available for splitting buffers: 2.08325 Gb 0:03:23.804 4M / 1G INFO General (kmer_splitters.hpp : 199) Using cell size of 262144 0:03:50.479 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 8995165 reads 0:04:14.442 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 17986920 reads 0:04:30.811 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 20669826 reads 0:04:30.811 8G / 9G INFO General (kmer_splitters.hpp : 234) Adding contigs from previous K 0:04:30.811 8G / 9G INFO General (kmer_splitters.hpp : 245) Used 20669826 reads. Maximum read length 320 0:04:30.811 8G / 9G INFO General (kmer_splitters.hpp : 246) Average read length 259.734 0:04:32.461 64M / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:04:41.739 64M / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 191827879 kmers in total. 0:04:41.739 64M / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:04:48.401 64M / 9G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:04:48.401 64M / 9G INFO General (kmer_splitters.hpp : 379) Splitting kmer instances into 256 buckets. This might take a while. 0:04:48.402 64M / 9G INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:04:48.402 64M / 9G INFO General (kmer_splitters.hpp : 397) Memory available for splitting buffers: 2.08203 Gb 0:04:48.402 64M / 9G INFO General (kmer_splitters.hpp : 405) Using cell size of 262144 0:05:10.825 8G / 9G INFO General (kmer_splitters.hpp : 428) Processed 191827879 kmers 0:05:10.825 8G / 9G INFO General (kmer_splitters.hpp : 437) Used 191827879 kmers. 0:05:11.316 64M / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:05:16.717 64M / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 186085494 kmers in total. 0:05:16.717 64M / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:05:23.505 64M / 9G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:05:46.600 68M / 9G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:05:51.987 68M / 9G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 64373978 bytes occupied (2.7675 bits per kmer). 0:05:52.236 248M / 9G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 382) Building k-mer extensions from k+1-mers 0:06:12.325 248M / 9G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 386) Building k-mer extensions from k+1-mers finished. 0:06:12.330 248M / 9G INFO Early tip clipping (early_simplification.hpp : 236) Early tip clipping 0:15:39.272 248M / 9G INFO Early tip clipping (early_simplification.hpp : 239) 25734809 22-mers were removed by early tip clipper 0:15:39.272 248M / 9G INFO General (graph_construction.hpp : 145) Condensing graph 0:15:39.272 248M / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 337) Extracting unbranching paths 0:17:50.039 3G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 351) Extracting unbranching paths finished. 29249295 sequences extracted 0:18:05.636 3G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 311) Collecting perfect loops 0:18:52.476 3G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 326) Collecting perfect loops finished. 14 loops collected 0:19:09.157 5G / 9G INFO General (graph_construction.hpp : 150) Building index with from graph 0:19:09.158 5G / 9G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:19:09.158 5G / 9G INFO General (kmer_splitters.hpp : 289) Splitting kmer instances into 16 buckets. This might take a while. 0:19:09.158 5G / 9G INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:19:09.158 5G / 9G INFO General (kmer_splitters.hpp : 307) Memory available for splitting buffers: 31.4427 Gb 0:19:09.158 5G / 9G INFO General (kmer_splitters.hpp : 312) Using cell size of 4194304 0:19:24.721 6G / 9G INFO General (kmer_splitters.hpp : 325) Processed 11815360 edges 0:19:40.606 6G / 9G INFO General (kmer_splitters.hpp : 325) Processed 23637669 edges 0:19:48.101 6G / 9G INFO General (kmer_splitters.hpp : 325) Processed 29249309 edges 0:19:48.101 6G / 9G INFO General (kmer_splitters.hpp : 330) Used 29249309 sequences. 0:19:48.162 5G / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:20:16.345 5G / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 166093070 kmers in total. 0:20:16.345 5G / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:20:21.368 5G / 9G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:24:12.020 5G / 9G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:24:16.906 5G / 9G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 57457856 bytes occupied (2.7675 bits per kmer). 0:24:19.282 9G / 9G INFO General (edge_index_builders.hpp : 21) Collecting k-mer coverage information from graph, this takes a while. 0:29:06.436 9G / 9G INFO General (graph_construction.hpp : 182) Filling coverage index 0:29:06.436 9G / 9G INFO General (edge_index_builders.hpp : 99) Collecting k-mer coverage information from reads, this takes a while. 0:32:01.240 9G / 9G INFO General (graph_construction.hpp : 184) Filling coverage and flanking coverage from index 0:32:45.600 9G / 9G INFO General (construction.cpp : 33) Figured out: read length = 320 0:32:45.650 9G / 9G INFO StageManager (stage.cpp : 125) STAGE == EC Threshold Finding 0:32:52.064 9G / 9G INFO General (kmer_coverage_model.cpp : 178) Kmer coverage valley at: 11 0:32:52.064 9G / 9G INFO General (kmer_coverage_model.cpp : 198) K-mer histogram maximum: 31 0:32:52.064 9G / 9G INFO General (kmer_coverage_model.cpp : 234) Estimated median coverage: 32. Coverage mad: 8.8956 0:32:52.065 9G / 9G INFO General (kmer_coverage_model.cpp : 261) Fitting coverage model 0:32:52.147 9G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 2 0:32:52.370 9G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 4 0:32:53.102 9G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 8 0:32:54.108 9G / 9G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 31.7526. Fitted coverage std. dev: 7.12823 0:32:54.110 9G / 9G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 0.695916 0:32:54.110 9G / 9G INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 21 0:32:54.110 9G / 9G INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 21 0:32:54.110 9G / 9G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 63557477 0:32:54.110 9G / 9G INFO General (genomic_info_filler.cpp : 103) Mean coverage was calculated as 31.7526 0:32:54.111 9G / 9G INFO General (genomic_info_filler.cpp : 117) EC coverage threshold value was calculated as 21 0:32:54.111 9G / 9G INFO General (genomic_info_filler.cpp : 118) Trusted kmer low bound: 0 0:32:54.111 9G / 9G INFO StageManager (stage.cpp : 125) STAGE == Simplification 0:32:54.360 5G / 9G INFO General (graph_simplification.hpp : 911) Graph simplification started 0:32:54.361 5G / 9G INFO General (graph_simplification.hpp : 924) Fast simplification mode enabled 0:32:54.361 5G / 9G INFO General (graph_simplification.hpp : 771) PROCEDURE == Presimplification 0:32:54.361 5G / 9G INFO General (graph_simplification.hpp : 211) Removing short low covered self-conjugate connections 0:32:55.973 5G / 9G INFO General (graph_simplification.hpp : 403) Removing isolated edges 0:32:55.973 5G / 9G INFO General (graph_simplification.hpp : 404) All edges shorter than 320 will be removed 0:32:55.974 5G / 9G INFO General (graph_simplification.hpp : 405) Also edges shorter than 0 and coverage smaller than 0 will be removed 0:32:58.027 5G / 9G INFO General (graph_simplification.hpp : 687) Non parallel mode 0:34:29.768 6G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:37:55.183 6G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:43:05.666 5G / 9G INFO General (graph_simplification.hpp : 644) Using permanent iterators 0:43:05.666 5G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 1 0:43:27.592 5G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:44:17.046 5G / 9G INFO General (graph_simplification.hpp : 147) Removing bulges 1:25:30.809 5G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 1:26:04.607 5G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 2 1:26:04.607 5G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 1:26:06.380 5G / 9G INFO General (graph_simplification.hpp : 147) Removing bulges 1:33:29.357 5G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 1:33:45.768 5G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 3 1:33:45.768 5G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 1:33:46.292 5G / 9G INFO General (graph_simplification.hpp : 147) Removing bulges 1:36:23.460 5G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 1:36:27.961 5G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 4 1:36:27.961 5G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 1:36:28.133 5G / 9G INFO General (graph_simplification.hpp : 147) Removing bulges 1:37:07.483 5G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 1:37:10.054 5G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 5 1:37:10.055 5G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 1:37:10.142 5G / 9G INFO General (graph_simplification.hpp : 147) Removing bulges 1:37:28.525 5G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 1:37:30.131 5G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 6 1:37:30.131 5G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 1:37:30.193 5G / 9G INFO General (graph_simplification.hpp : 147) Removing bulges 1:37:44.224 5G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 1:37:45.647 5G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 7 1:37:45.647 5G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 1:37:45.699 5G / 9G INFO General (graph_simplification.hpp : 147) Removing bulges 1:37:57.921 5G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 1:37:59.189 5G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 8 1:37:59.189 5G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 1:37:59.235 5G / 9G INFO General (graph_simplification.hpp : 147) Removing bulges 1:38:09.641 5G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 1:38:10.759 5G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 9 1:38:10.759 5G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 1:38:10.800 5G / 9G INFO General (graph_simplification.hpp : 147) Removing bulges 1:38:18.892 5G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 1:38:20.064 5G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 10 1:38:20.064 5G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 1:38:20.106 5G / 9G INFO General (graph_simplification.hpp : 147) Removing bulges 1:38:26.814 5G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 1:38:28.592 5G / 9G INFO General (graph_simplification.hpp : 796) PROCEDURE == Post simplification 1:38:28.592 5G / 9G INFO General (graph_simplification.hpp : 644) Using permanent iterators 1:38:28.592 5G / 9G INFO General (graph_simplification.hpp : 806) Iteration 0 1:38:28.596 5G / 9G INFO General (graph_simplification.hpp : 247) Removal of relatively low covered connections disabled 1:38:33.155 5G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 1:38:43.251 5G / 9G INFO General (graph_simplification.hpp : 147) Removing bulges 1:43:43.555 5G / 9G INFO General (graph_simplification.hpp : 806) Iteration 1 1:43:43.555 5G / 9G INFO General (graph_simplification.hpp : 247) Removal of relatively low covered connections disabled 1:43:43.555 5G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 1:43:43.563 5G / 9G INFO General (graph_simplification.hpp : 147) Removing bulges 1:43:45.437 4G / 9G INFO StageManager (stage.cpp : 125) STAGE == Simplification Cleanup 1:43:45.438 4G / 9G INFO General (graph_simplification.hpp : 403) Removing isolated edges 1:43:45.438 4G / 9G INFO General (graph_simplification.hpp : 404) All edges shorter than 320 will be removed 1:43:45.438 4G / 9G INFO General (graph_simplification.hpp : 405) Also edges shorter than 0 and coverage smaller than 2 will be removed 1:43:45.705 4G / 9G INFO General (simplification.cpp : 56) Removing all the edges having coverage 0 and less 1:43:53.655 4G / 9G INFO General (simplification.cpp : 68) Counting average coverage 1:43:54.647 4G / 9G INFO General (simplification.cpp : 71) Average coverage = 36.6355 1:43:54.647 4G / 9G INFO StageManager (stage.cpp : 125) STAGE == Contig Output 1:43:54.682 4G / 9G INFO General (contig_output.hpp : 283) Outputting contigs to /N/dc2/projects/marinovg/2015-01-29-P-assem/Paramecium_pentaurelia_strain_870-SPAdes-3.5.0-trimmed//K21/simplified_contigs.fasta 1:44:36.548 4G / 9G INFO General (contig_output.hpp : 283) Outputting contigs to /N/dc2/projects/marinovg/2015-01-29-P-assem/Paramecium_pentaurelia_strain_870-SPAdes-3.5.0-trimmed//K21/before_rr.fasta 1:46:34.065 4G / 9G INFO General (contig_output.hpp : 283) Outputting contigs to /N/dc2/projects/marinovg/2015-01-29-P-assem/Paramecium_pentaurelia_strain_870-SPAdes-3.5.0-trimmed//K21/final_contigs.fasta 1:48:30.756 4G / 9G INFO General (launch.hpp : 82) SPAdes finished 1:48:43.898 64M / 9G INFO General (main.cpp : 166) Assembling time: 1 hours 48 minutes 43 seconds == Warning == Default k-mer sizes were set to [21, 33, 55, 77, 99, 127] because estimated read length (320) is equal to or greater than 250 == 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/2015-01-29-P-assem/Paramecium_pentaurelia_strain_870-SPAdes-3.5.0-trimmed/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 0:00:00.001 4M / 4M INFO StageManager (stage.cpp : 125) STAGE == Construction 0:00:00.001 4M / 4M INFO General (construction.cpp : 44) Contigs from previous K will be used 0:00:00.005 4M / 4M INFO General (read_converter.hpp : 49) Binary reads detected 0:00:00.070 4M / 4M INFO General (graph_construction.hpp : 129) Constructing DeBruijn graph for k=33 0:00:00.072 4M / 4M INFO General (kmer_splitters.hpp : 172) Splitting kmer instances into 256 buckets. This might take a while. 0:00:00.073 4M / 4M INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:00:00.073 4M / 4M INFO General (kmer_splitters.hpp : 190) Memory available for splitting buffers: 2.08325 Gb 0:00:00.073 4M / 4M INFO General (kmer_splitters.hpp : 199) Using cell size of 131072 0:00:17.556 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 4735761 reads 0:00:31.601 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 9471028 reads 0:00:45.829 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 14206544 reads 0:01:01.916 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 18938479 reads 0:01:08.079 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 20669826 reads 0:01:08.081 8G / 9G INFO General (kmer_splitters.hpp : 234) Adding contigs from previous K 0:01:24.913 8G / 9G INFO General (kmer_splitters.hpp : 245) Used 20669826 reads. Maximum read length 320 0:01:24.913 8G / 9G INFO General (kmer_splitters.hpp : 246) Average read length 259.734 0:01:26.597 64M / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:01:51.011 64M / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 220905879 kmers in total. 0:01:51.012 64M / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:02:05.450 64M / 9G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:02:05.450 64M / 9G INFO General (kmer_splitters.hpp : 379) Splitting kmer instances into 256 buckets. This might take a while. 0:02:05.450 64M / 9G INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:02:05.450 64M / 9G INFO General (kmer_splitters.hpp : 397) Memory available for splitting buffers: 2.08203 Gb 0:02:05.450 64M / 9G INFO General (kmer_splitters.hpp : 405) Using cell size of 131072 0:02:36.731 8G / 9G INFO General (kmer_splitters.hpp : 428) Processed 220905879 kmers 0:02:36.731 8G / 9G INFO General (kmer_splitters.hpp : 437) Used 220905879 kmers. 0:02:37.636 64M / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:02:49.541 64M / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 219225012 kmers in total. 0:02:49.541 64M / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:03:12.340 64M / 9G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:03:41.332 192M / 9G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:03:55.286 192M / 9G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 75838193 bytes occupied (2.7675 bits per kmer). 0:03:55.558 404M / 9G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 382) Building k-mer extensions from k+1-mers 0:04:22.184 404M / 9G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 386) Building k-mer extensions from k+1-mers finished. 0:04:22.188 404M / 9G INFO Early tip clipping (early_simplification.hpp : 236) Early tip clipping 0:14:18.955 404M / 9G INFO Early tip clipping (early_simplification.hpp : 239) 54381800 34-mers were removed by early tip clipper 0:14:18.955 404M / 9G INFO General (graph_construction.hpp : 145) Condensing graph 0:14:18.955 404M / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 337) Extracting unbranching paths 0:16:31.929 1G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 351) Extracting unbranching paths finished. 10753190 sequences extracted 0:16:47.395 1G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 311) Collecting perfect loops 0:17:46.975 1G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 326) Collecting perfect loops finished. 42 loops collected 0:17:54.017 2G / 9G INFO General (graph_construction.hpp : 150) Building index with from graph 0:17:54.018 2G / 9G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:17:54.018 2G / 9G INFO General (kmer_splitters.hpp : 289) Splitting kmer instances into 16 buckets. This might take a while. 0:17:54.018 2G / 9G INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:17:54.018 2G / 9G INFO General (kmer_splitters.hpp : 307) Memory available for splitting buffers: 32.5052 Gb 0:17:54.018 2G / 9G INFO General (kmer_splitters.hpp : 312) Using cell size of 2097152 0:18:00.498 3G / 9G INFO General (kmer_splitters.hpp : 325) Processed 2169396 edges 0:18:07.454 3G / 9G INFO General (kmer_splitters.hpp : 325) Processed 4337230 edges 0:18:14.102 3G / 9G INFO General (kmer_splitters.hpp : 325) Processed 6504131 edges 0:18:20.784 3G / 9G INFO General (kmer_splitters.hpp : 325) Processed 8667955 edges 0:18:26.870 3G / 9G INFO General (kmer_splitters.hpp : 325) Processed 10753232 edges 0:18:26.871 3G / 9G INFO General (kmer_splitters.hpp : 330) Used 10753232 sequences. 0:18:26.934 2G / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:19:05.812 2G / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 166524079 kmers in total. 0:19:05.812 2G / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:19:19.611 2G / 9G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:23:13.105 2G / 9G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:23:23.100 2G / 9G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 57606960 bytes occupied (2.7675 bits per kmer). 0:23:25.483 6G / 9G INFO General (edge_index_builders.hpp : 21) Collecting k-mer coverage information from graph, this takes a while. 0:28:04.541 5G / 9G INFO General (graph_construction.hpp : 182) Filling coverage index 0:28:04.541 5G / 9G INFO General (edge_index_builders.hpp : 99) Collecting k-mer coverage information from reads, this takes a while. 0:30:53.129 5G / 9G INFO General (graph_construction.hpp : 184) Filling coverage and flanking coverage from index 0:31:32.562 5G / 9G INFO General (construction.cpp : 33) Figured out: read length = 320 0:31:32.612 5G / 9G INFO StageManager (stage.cpp : 125) STAGE == EC Threshold Finding 0:31:39.532 5G / 9G INFO General (kmer_coverage_model.cpp : 178) Kmer coverage valley at: 10 0:31:39.533 5G / 9G INFO General (kmer_coverage_model.cpp : 198) K-mer histogram maximum: 29 0:31:39.533 5G / 9G INFO General (kmer_coverage_model.cpp : 234) Estimated median coverage: 30. Coverage mad: 8.8956 0:31:39.533 5G / 9G INFO General (kmer_coverage_model.cpp : 261) Fitting coverage model 0:31:39.608 5G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 2 0:31:39.816 5G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 4 0:31:40.474 5G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 8 0:31:41.902 5G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 16 0:31:42.255 5G / 9G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 29.5772. Fitted coverage std. dev: 6.97467 0:31:42.257 5G / 9G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 0.617604 0:31:42.257 5G / 9G INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 19 0:31:42.257 5G / 9G INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 19 0:31:42.257 5G / 9G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 65455765 0:31:42.257 5G / 9G INFO General (genomic_info_filler.cpp : 103) Mean coverage was calculated as 29.5772 0:31:42.257 5G / 9G INFO General (genomic_info_filler.cpp : 117) EC coverage threshold value was calculated as 19 0:31:42.257 5G / 9G INFO General (genomic_info_filler.cpp : 118) Trusted kmer low bound: 0 0:31:42.257 5G / 9G INFO StageManager (stage.cpp : 125) STAGE == Simplification 0:31:42.501 2G / 9G INFO General (graph_simplification.hpp : 911) Graph simplification started 0:31:42.502 2G / 9G INFO General (graph_simplification.hpp : 924) Fast simplification mode enabled 0:31:42.502 2G / 9G INFO General (graph_simplification.hpp : 771) PROCEDURE == Presimplification 0:31:42.502 2G / 9G INFO General (graph_simplification.hpp : 211) Removing short low covered self-conjugate connections 0:31:43.165 2G / 9G INFO General (graph_simplification.hpp : 403) Removing isolated edges 0:31:43.165 2G / 9G INFO General (graph_simplification.hpp : 404) All edges shorter than 320 will be removed 0:31:43.165 2G / 9G INFO General (graph_simplification.hpp : 405) Also edges shorter than 0 and coverage smaller than 0 will be removed 0:31:45.056 2G / 9G INFO General (graph_simplification.hpp : 687) Non parallel mode 0:32:12.890 2G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:33:19.172 2G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:35:04.839 2G / 9G INFO General (graph_simplification.hpp : 644) Using permanent iterators 0:35:04.839 2G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 1 0:35:11.542 2G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:35:26.941 2G / 9G INFO General (graph_simplification.hpp : 147) Removing bulges 0:36:59.644 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:37:02.482 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 2 0:37:02.483 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:37:02.730 1G / 9G INFO General (graph_simplification.hpp : 147) Removing bulges 0:37:04.470 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:37:05.621 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 3 0:37:05.622 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:37:05.647 1G / 9G INFO General (graph_simplification.hpp : 147) Removing bulges 0:37:06.417 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:37:06.864 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 4 0:37:06.864 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:37:06.877 1G / 9G INFO General (graph_simplification.hpp : 147) Removing bulges 0:37:07.201 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:37:07.419 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 5 0:37:07.419 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:37:07.427 1G / 9G INFO General (graph_simplification.hpp : 147) Removing bulges 0:37:07.554 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:37:07.693 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 6 0:37:07.693 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:37:07.698 1G / 9G INFO General (graph_simplification.hpp : 147) Removing bulges 0:37:07.795 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:37:07.897 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 7 0:37:07.897 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:37:07.900 1G / 9G INFO General (graph_simplification.hpp : 147) Removing bulges 0:37:07.991 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:37:08.076 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 8 0:37:08.076 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:37:08.079 1G / 9G INFO General (graph_simplification.hpp : 147) Removing bulges 0:37:08.141 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:37:08.301 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 9 0:37:08.301 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:37:08.304 1G / 9G INFO General (graph_simplification.hpp : 147) Removing bulges 0:37:08.332 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:37:08.415 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 10 0:37:08.415 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:37:08.418 1G / 9G INFO General (graph_simplification.hpp : 147) Removing bulges 0:37:08.453 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:37:08.594 1G / 9G INFO General (graph_simplification.hpp : 796) PROCEDURE == Post simplification 0:37:08.594 1G / 9G INFO General (graph_simplification.hpp : 644) Using permanent iterators 0:37:08.594 1G / 9G INFO General (graph_simplification.hpp : 806) Iteration 0 0:37:08.594 1G / 9G INFO General (graph_simplification.hpp : 247) Removal of relatively low covered connections disabled 0:37:09.045 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:37:09.987 1G / 9G INFO General (graph_simplification.hpp : 147) Removing bulges 0:37:11.173 1G / 9G INFO General (graph_simplification.hpp : 806) Iteration 1 0:37:11.173 1G / 9G INFO General (graph_simplification.hpp : 247) Removal of relatively low covered connections disabled 0:37:11.173 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:37:11.174 1G / 9G INFO General (graph_simplification.hpp : 147) Removing bulges 0:37:11.463 1G / 9G INFO StageManager (stage.cpp : 125) STAGE == Simplification Cleanup 0:37:11.464 1G / 9G INFO General (graph_simplification.hpp : 403) Removing isolated edges 0:37:11.464 1G / 9G INFO General (graph_simplification.hpp : 404) All edges shorter than 320 will be removed 0:37:11.464 1G / 9G INFO General (graph_simplification.hpp : 405) Also edges shorter than 0 and coverage smaller than 2 will be removed 0:37:11.543 1G / 9G INFO General (simplification.cpp : 56) Removing all the edges having coverage 0 and less 0:37:12.300 1G / 9G INFO General (simplification.cpp : 68) Counting average coverage 0:37:12.445 1G / 9G INFO General (simplification.cpp : 71) Average coverage = 29.2029 0:37:12.445 1G / 9G INFO StageManager (stage.cpp : 125) STAGE == Contig Output 0:37:12.445 1G / 9G INFO General (contig_output.hpp : 283) Outputting contigs to /N/dc2/projects/marinovg/2015-01-29-P-assem/Paramecium_pentaurelia_strain_870-SPAdes-3.5.0-trimmed//K33/simplified_contigs.fasta 0:37:27.726 1G / 9G INFO General (contig_output.hpp : 283) Outputting contigs to /N/dc2/projects/marinovg/2015-01-29-P-assem/Paramecium_pentaurelia_strain_870-SPAdes-3.5.0-trimmed//K33/before_rr.fasta 0:38:12.360 1G / 9G INFO General (contig_output.hpp : 283) Outputting contigs to /N/dc2/projects/marinovg/2015-01-29-P-assem/Paramecium_pentaurelia_strain_870-SPAdes-3.5.0-trimmed//K33/final_contigs.fasta 0:38:57.087 1G / 9G INFO General (launch.hpp : 82) SPAdes finished 0:39:00.373 64M / 9G INFO General (main.cpp : 166) Assembling time: 0 hours 39 minutes 0 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/2015-01-29-P-assem/Paramecium_pentaurelia_strain_870-SPAdes-3.5.0-trimmed/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 0:00:00.001 4M / 4M INFO General (launch.hpp : 44) Will need read mapping, kmer mapper will be attached 0:00:00.001 4M / 4M INFO StageManager (stage.cpp : 125) STAGE == Construction 0:00:00.001 4M / 4M INFO General (construction.cpp : 44) Contigs from previous K will be used 0:00:00.005 4M / 4M INFO General (read_converter.hpp : 49) Binary reads detected 0:00:00.067 4M / 4M INFO General (graph_construction.hpp : 129) Constructing DeBruijn graph for k=55 0:00:00.070 4M / 4M INFO General (kmer_splitters.hpp : 172) Splitting kmer instances into 256 buckets. This might take a while. 0:00:00.070 4M / 4M INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:00:00.071 4M / 4M INFO General (kmer_splitters.hpp : 190) Memory available for splitting buffers: 2.08325 Gb 0:00:00.071 4M / 4M INFO General (kmer_splitters.hpp : 199) Using cell size of 131072 0:00:18.144 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 5244222 reads 0:00:34.099 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 10487796 reads 0:00:48.703 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 15731553 reads 0:01:02.440 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 20669826 reads 0:01:02.441 8G / 9G INFO General (kmer_splitters.hpp : 234) Adding contigs from previous K 0:01:18.514 8G / 9G INFO General (kmer_splitters.hpp : 245) Used 20669826 reads. Maximum read length 320 0:01:18.515 8G / 9G INFO General (kmer_splitters.hpp : 246) Average read length 259.734 0:01:20.225 64M / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:01:45.065 64M / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 244868663 kmers in total. 0:01:45.065 64M / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:02:02.489 64M / 9G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:02:02.489 64M / 9G INFO General (kmer_splitters.hpp : 379) Splitting kmer instances into 256 buckets. This might take a while. 0:02:02.489 64M / 9G INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:02:02.489 64M / 9G INFO General (kmer_splitters.hpp : 397) Memory available for splitting buffers: 2.08203 Gb 0:02:02.489 64M / 9G INFO General (kmer_splitters.hpp : 405) Using cell size of 131072 0:02:40.994 8G / 9G INFO General (kmer_splitters.hpp : 428) Processed 244868663 kmers 0:02:40.994 8G / 9G INFO General (kmer_splitters.hpp : 437) Used 244868663 kmers. 0:02:42.015 64M / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:02:54.884 64M / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 244184362 kmers in total. 0:02:54.885 64M / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:03:10.639 64M / 9G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:03:43.448 192M / 9G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:03:58.424 192M / 9G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 84472567 bytes occupied (2.7675 bits per kmer). 0:03:58.754 428M / 9G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 382) Building k-mer extensions from k+1-mers 0:04:30.567 428M / 9G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 386) Building k-mer extensions from k+1-mers finished. 0:04:30.572 428M / 9G INFO General (graph_construction.hpp : 145) Condensing graph 0:04:30.572 428M / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 337) Extracting unbranching paths 0:07:00.923 2G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 351) Extracting unbranching paths finished. 14225898 sequences extracted 0:07:24.931 2G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 311) Collecting perfect loops 0:08:37.046 2G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 326) Collecting perfect loops finished. 0 loops collected 0:08:47.879 3G / 9G INFO General (graph_construction.hpp : 150) Building index with from graph 0:08:47.880 3G / 9G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:08:47.880 3G / 9G INFO General (kmer_splitters.hpp : 289) Splitting kmer instances into 16 buckets. This might take a while. 0:08:47.880 3G / 9G INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:08:47.880 3G / 9G INFO General (kmer_splitters.hpp : 307) Memory available for splitting buffers: 32.1589 Gb 0:08:47.880 3G / 9G INFO General (kmer_splitters.hpp : 312) Using cell size of 2097152 0:08:54.560 4G / 9G INFO General (kmer_splitters.hpp : 325) Processed 1948600 edges 0:09:01.339 4G / 9G INFO General (kmer_splitters.hpp : 325) Processed 3900415 edges 0:09:08.009 4G / 9G INFO General (kmer_splitters.hpp : 325) Processed 5853246 edges 0:09:14.854 4G / 9G INFO General (kmer_splitters.hpp : 325) Processed 7801806 edges 0:09:22.492 4G / 9G INFO General (kmer_splitters.hpp : 325) Processed 9748735 edges 0:09:29.022 4G / 9G INFO General (kmer_splitters.hpp : 325) Processed 11699712 edges 0:09:36.292 4G / 9G INFO General (kmer_splitters.hpp : 325) Processed 13645983 edges 0:09:38.291 4G / 9G INFO General (kmer_splitters.hpp : 325) Processed 14225898 edges 0:09:38.291 4G / 9G INFO General (kmer_splitters.hpp : 330) Used 14225898 sequences. 0:09:38.334 3G / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:10:36.862 3G / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 244868663 kmers in total. 0:10:36.862 3G / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:10:52.448 3G / 9G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:16:11.307 3G / 9G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:16:25.843 3G / 9G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 84709293 bytes occupied (2.7675 bits per kmer). 0:16:29.339 9G / 9G INFO General (edge_index_builders.hpp : 21) Collecting k-mer coverage information from graph, this takes a while. 0:24:02.664 8G / 9G INFO General (graph_construction.hpp : 182) Filling coverage index 0:24:02.664 8G / 9G INFO General (edge_index_builders.hpp : 99) Collecting k-mer coverage information from reads, this takes a while. 0:26:54.759 8G / 9G INFO General (graph_construction.hpp : 184) Filling coverage and flanking coverage from index 0:27:56.684 8G / 9G INFO General (construction.cpp : 33) Figured out: read length = 320 0:27:56.740 8G / 9G INFO StageManager (stage.cpp : 125) STAGE == EC Threshold Finding 0:28:04.388 8G / 9G INFO General (kmer_coverage_model.cpp : 178) Kmer coverage valley at: 7 0:28:04.389 8G / 9G INFO General (kmer_coverage_model.cpp : 198) K-mer histogram maximum: 25 0:28:04.389 8G / 9G INFO General (kmer_coverage_model.cpp : 234) Estimated median coverage: 26. Coverage mad: 7.413 0:28:04.389 8G / 9G INFO General (kmer_coverage_model.cpp : 261) Fitting coverage model 0:28:04.452 8G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 2 0:28:04.619 8G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 4 0:28:05.208 8G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 8 0:28:06.601 8G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 16 0:28:07.717 8G / 9G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 26.0109. Fitted coverage std. dev: 6.63795 0:28:07.719 8G / 9G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 0.744583 0:28:07.719 8G / 9G INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 17 0:28:07.719 8G / 9G INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 16 0:28:07.719 8G / 9G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 66658128 0:28:07.719 8G / 9G INFO General (genomic_info_filler.cpp : 103) Mean coverage was calculated as 26.0109 0:28:07.719 8G / 9G INFO General (genomic_info_filler.cpp : 117) EC coverage threshold value was calculated as 16 0:28:07.719 8G / 9G INFO General (genomic_info_filler.cpp : 118) Trusted kmer low bound: 0 0:28:07.719 8G / 9G INFO StageManager (stage.cpp : 125) STAGE == Gap Closer 0:28:07.754 8G / 9G INFO General (gap_closer.cpp : 157) Preparing shift maps 0:28:21.368 9G / 9G INFO General (gap_closer.cpp : 117) Processing paired reads (takes a while) 0:28:30.411 9G / 9G INFO General (gap_closer.cpp : 136) Used 2410472 paired reads 0:28:30.412 9G / 9G INFO General (gap_closer.cpp : 138) Merging paired indices 0:28:32.279 8G / 9G INFO GapCloser (gap_closer.cpp : 395) Closing short gaps 0:29:03.605 8G / 9G INFO GapCloser (gap_closer.cpp : 424) Closing short gaps complete: filled 45 gaps after checking 2182 candidates 0:29:05.888 8G / 9G INFO General (gap_closer.cpp : 157) Preparing shift maps 0:29:19.757 9G / 9G INFO General (gap_closer.cpp : 117) Processing paired reads (takes a while) 0:29:26.819 9G / 9G INFO General (gap_closer.cpp : 136) Used 2060954 paired reads 0:29:26.820 9G / 9G INFO General (gap_closer.cpp : 138) Merging paired indices 0:29:28.503 8G / 9G INFO GapCloser (gap_closer.cpp : 395) Closing short gaps 0:29:59.764 8G / 9G INFO GapCloser (gap_closer.cpp : 424) Closing short gaps complete: filled 49 gaps after checking 1691 candidates 0:30:01.917 8G / 9G INFO General (gap_closer.cpp : 157) Preparing shift maps 0:30:15.775 9G / 9G INFO General (gap_closer.cpp : 117) Processing paired reads (takes a while) 0:30:23.584 9G / 9G INFO General (gap_closer.cpp : 136) Used 2236672 paired reads 0:30:23.584 9G / 9G INFO General (gap_closer.cpp : 138) Merging paired indices 0:30:25.481 8G / 9G INFO GapCloser (gap_closer.cpp : 395) Closing short gaps 0:30:56.839 8G / 9G INFO GapCloser (gap_closer.cpp : 424) Closing short gaps complete: filled 37 gaps after checking 1616 candidates 0:30:59.031 8G / 9G INFO General (gap_closer.cpp : 157) Preparing shift maps 0:31:12.920 9G / 9G INFO General (gap_closer.cpp : 117) Processing paired reads (takes a while) 0:31:24.728 9G / 9G INFO General (gap_closer.cpp : 136) Used 3625572 paired reads 0:31:24.728 9G / 9G INFO General (gap_closer.cpp : 138) Merging paired indices 0:31:27.107 8G / 9G INFO GapCloser (gap_closer.cpp : 395) Closing short gaps 0:31:58.749 8G / 9G INFO GapCloser (gap_closer.cpp : 424) Closing short gaps complete: filled 50 gaps after checking 3063 candidates 0:32:01.168 8G / 9G INFO StageManager (stage.cpp : 125) STAGE == Simplification 0:32:01.520 3G / 9G INFO General (graph_simplification.hpp : 911) Graph simplification started 0:32:01.520 3G / 9G INFO General (graph_simplification.hpp : 924) Fast simplification mode enabled 0:32:01.520 3G / 9G INFO General (graph_simplification.hpp : 771) PROCEDURE == Presimplification 0:32:01.520 3G / 9G INFO General (graph_simplification.hpp : 211) Removing short low covered self-conjugate connections 0:32:02.790 3G / 9G INFO General (graph_simplification.hpp : 403) Removing isolated edges 0:32:02.791 3G / 9G INFO General (graph_simplification.hpp : 404) All edges shorter than 320 will be removed 0:32:02.792 3G / 9G INFO General (graph_simplification.hpp : 405) Also edges shorter than 0 and coverage smaller than 0 will be removed 0:32:07.045 3G / 9G INFO General (graph_simplification.hpp : 687) Non parallel mode 0:32:51.617 3G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:34:49.753 3G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:35:51.036 3G / 9G INFO General (graph_simplification.hpp : 644) Using permanent iterators 0:35:51.036 3G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 1 0:35:54.050 3G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:36:00.799 3G / 9G INFO General (graph_simplification.hpp : 147) Removing bulges 0:37:33.365 4G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:37:34.979 4G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 2 0:37:34.979 4G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:37:35.105 4G / 9G INFO General (graph_simplification.hpp : 147) Removing bulges 0:37:35.601 4G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:37:36.233 4G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 3 0:37:36.233 4G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:37:36.246 4G / 9G INFO General (graph_simplification.hpp : 147) Removing bulges 0:37:36.599 4G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:37:36.864 4G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 4 0:37:36.864 4G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:37:36.871 4G / 9G INFO General (graph_simplification.hpp : 147) Removing bulges 0:37:37.068 4G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:37:37.225 4G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 5 0:37:37.225 4G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:37:37.229 4G / 9G INFO General (graph_simplification.hpp : 147) Removing bulges 0:37:37.343 4G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:37:37.444 4G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 6 0:37:37.444 4G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:37:37.447 4G / 9G INFO General (graph_simplification.hpp : 147) Removing bulges 0:37:37.520 4G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:37:37.593 4G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 7 0:37:37.593 4G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:37:37.596 4G / 9G INFO General (graph_simplification.hpp : 147) Removing bulges 0:37:37.645 4G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:37:37.718 4G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 8 0:37:37.719 4G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:37:37.721 4G / 9G INFO General (graph_simplification.hpp : 147) Removing bulges 0:37:37.767 4G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:37:37.802 4G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 9 0:37:37.802 4G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:37:37.804 4G / 9G INFO General (graph_simplification.hpp : 147) Removing bulges 0:37:37.840 4G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:37:37.872 4G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 10 0:37:37.872 4G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:37:37.874 4G / 9G INFO General (graph_simplification.hpp : 147) Removing bulges 0:37:37.896 4G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:37:37.933 4G / 9G INFO General (graph_simplification.hpp : 796) PROCEDURE == Post simplification 0:37:37.933 4G / 9G INFO General (graph_simplification.hpp : 644) Using permanent iterators 0:37:37.933 4G / 9G INFO General (graph_simplification.hpp : 806) Iteration 0 0:37:37.933 4G / 9G INFO General (graph_simplification.hpp : 247) Removal of relatively low covered connections disabled 0:37:38.125 4G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:37:38.492 4G / 9G INFO General (graph_simplification.hpp : 147) Removing bulges 0:37:38.749 4G / 9G INFO General (graph_simplification.hpp : 806) Iteration 1 0:37:38.749 4G / 9G INFO General (graph_simplification.hpp : 247) Removal of relatively low covered connections disabled 0:37:38.749 4G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:37:38.749 4G / 9G INFO General (graph_simplification.hpp : 147) Removing bulges 0:37:38.903 4G / 9G INFO StageManager (stage.cpp : 125) STAGE == Gap Closer 0:37:38.904 4G / 9G INFO General (graph_pack.hpp : 84) Index refill 0:37:38.904 4G / 9G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:37:38.905 4G / 9G INFO General (kmer_splitters.hpp : 289) Splitting kmer instances into 16 buckets. This might take a while. 0:37:38.905 4G / 9G INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:37:38.905 4G / 9G INFO General (kmer_splitters.hpp : 307) Memory available for splitting buffers: 31.9284 Gb 0:37:38.905 4G / 9G INFO General (kmer_splitters.hpp : 312) Using cell size of 2097152 0:37:44.011 4G / 9G INFO General (kmer_splitters.hpp : 325) Processed 46758 edges 0:37:49.139 4G / 9G INFO General (kmer_splitters.hpp : 325) Processed 93745 edges 0:37:51.003 4G / 9G INFO General (kmer_splitters.hpp : 325) Processed 110850 edges 0:37:51.004 4G / 9G INFO General (kmer_splitters.hpp : 330) Used 110850 sequences. 0:37:51.058 4G / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:38:09.033 4G / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 79819387 kmers in total. 0:38:09.033 4G / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:38:14.425 4G / 9G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:39:51.070 4G / 9G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:39:59.009 4G / 9G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 27612558 bytes occupied (2.7675 bits per kmer). 0:40:00.220 6G / 9G INFO General (edge_index_builders.hpp : 21) Collecting k-mer coverage information from graph, this takes a while. 0:41:54.353 6G / 9G INFO General (gap_closer.cpp : 157) Preparing shift maps 0:41:54.466 6G / 9G INFO General (gap_closer.cpp : 117) Processing paired reads (takes a while) 0:42:15.012 6G / 9G INFO General (gap_closer.cpp : 136) Used 2410472 paired reads 0:42:15.013 6G / 9G INFO General (gap_closer.cpp : 138) Merging paired indices 0:42:15.061 6G / 9G INFO GapCloser (gap_closer.cpp : 395) Closing short gaps 0:42:15.217 6G / 9G INFO GapCloser (gap_closer.cpp : 424) Closing short gaps complete: filled 6 gaps after checking 732 candidates 0:42:15.374 6G / 9G INFO General (gap_closer.cpp : 157) Preparing shift maps 0:42:15.482 6G / 9G INFO General (gap_closer.cpp : 117) Processing paired reads (takes a while) 0:42:31.781 6G / 9G INFO General (gap_closer.cpp : 136) Used 2060954 paired reads 0:42:31.782 6G / 9G INFO General (gap_closer.cpp : 138) Merging paired indices 0:42:31.825 6G / 9G INFO GapCloser (gap_closer.cpp : 395) Closing short gaps 0:42:31.978 6G / 9G INFO GapCloser (gap_closer.cpp : 424) Closing short gaps complete: filled 1 gaps after checking 735 candidates 0:42:32.106 6G / 9G INFO General (gap_closer.cpp : 157) Preparing shift maps 0:42:32.214 6G / 9G INFO General (gap_closer.cpp : 117) Processing paired reads (takes a while) 0:42:48.019 6G / 9G INFO General (gap_closer.cpp : 136) Used 2236672 paired reads 0:42:48.019 6G / 9G INFO General (gap_closer.cpp : 138) Merging paired indices 0:42:48.053 6G / 9G INFO GapCloser (gap_closer.cpp : 395) Closing short gaps 0:42:48.208 6G / 9G INFO GapCloser (gap_closer.cpp : 424) Closing short gaps complete: filled 11 gaps after checking 763 candidates 0:42:48.503 6G / 9G INFO General (gap_closer.cpp : 157) Preparing shift maps 0:42:48.611 6G / 9G INFO General (gap_closer.cpp : 117) Processing paired reads (takes a while) 0:43:16.214 6G / 9G INFO General (gap_closer.cpp : 136) Used 3625572 paired reads 0:43:16.214 6G / 9G INFO General (gap_closer.cpp : 138) Merging paired indices 0:43:16.262 6G / 9G INFO GapCloser (gap_closer.cpp : 395) Closing short gaps 0:43:16.424 6G / 9G INFO GapCloser (gap_closer.cpp : 424) Closing short gaps complete: filled 4 gaps after checking 1118 candidates 0:43:16.691 6G / 9G INFO StageManager (stage.cpp : 125) STAGE == Simplification Cleanup 0:43:16.692 6G / 9G INFO General (graph_simplification.hpp : 403) Removing isolated edges 0:43:16.692 6G / 9G INFO General (graph_simplification.hpp : 404) All edges shorter than 320 will be removed 0:43:16.692 6G / 9G INFO General (graph_simplification.hpp : 405) Also edges shorter than 0 and coverage smaller than 2 will be removed 0:43:17.311 5G / 9G INFO General (simplification.cpp : 56) Removing all the edges having coverage 0 and less 0:43:17.609 5G / 9G INFO General (simplification.cpp : 68) Counting average coverage 0:43:17.679 5G / 9G INFO General (simplification.cpp : 71) Average coverage = 24.6572 0:43:17.680 5G / 9G INFO StageManager (stage.cpp : 125) STAGE == Contig Output 0:43:17.680 5G / 9G INFO General (contig_output.hpp : 283) Outputting contigs to /N/dc2/projects/marinovg/2015-01-29-P-assem/Paramecium_pentaurelia_strain_870-SPAdes-3.5.0-trimmed//K55/simplified_contigs.fasta 0:43:31.049 5G / 9G INFO General (contig_output.hpp : 283) Outputting contigs to /N/dc2/projects/marinovg/2015-01-29-P-assem/Paramecium_pentaurelia_strain_870-SPAdes-3.5.0-trimmed//K55/before_rr.fasta 0:44:09.778 5G / 9G INFO General (contig_output.hpp : 283) Outputting contigs to /N/dc2/projects/marinovg/2015-01-29-P-assem/Paramecium_pentaurelia_strain_870-SPAdes-3.5.0-trimmed//K55/final_contigs.fasta 0:44:48.188 5G / 9G INFO General (launch.hpp : 82) SPAdes finished 0:45:09.633 68M / 9G INFO General (main.cpp : 166) Assembling time: 0 hours 45 minutes 9 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/2015-01-29-P-assem/Paramecium_pentaurelia_strain_870-SPAdes-3.5.0-trimmed/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 0:00:00.001 4M / 4M INFO General (launch.hpp : 44) Will need read mapping, kmer mapper will be attached 0:00:00.001 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 0:00:00.005 4M / 4M INFO General (read_converter.hpp : 49) Binary reads detected 0:00:00.073 4M / 4M INFO General (graph_construction.hpp : 129) Constructing DeBruijn graph for k=77 0:00:00.075 4M / 4M INFO General (kmer_splitters.hpp : 172) Splitting kmer instances into 256 buckets. This might take a while. 0:00:00.076 4M / 4M INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:00:00.076 4M / 4M INFO General (kmer_splitters.hpp : 190) Memory available for splitting buffers: 2.08325 Gb 0:00:00.076 4M / 4M INFO General (kmer_splitters.hpp : 199) Using cell size of 87381 0:00:15.917 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 3913727 reads 0:00:27.921 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 7831447 reads 0:00:40.051 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 11748923 reads 0:00:52.335 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 15666673 reads 0:01:05.453 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 19585769 reads 0:01:10.814 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 20669826 reads 0:01:10.814 8G / 9G INFO General (kmer_splitters.hpp : 234) Adding contigs from previous K 0:01:29.364 8G / 9G INFO General (kmer_splitters.hpp : 245) Used 20669826 reads. Maximum read length 320 0:01:29.364 8G / 9G INFO General (kmer_splitters.hpp : 246) Average read length 259.734 0:01:31.039 64M / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:02:11.807 64M / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 252963413 kmers in total. 0:02:11.807 64M / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:02:38.904 64M / 9G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:02:38.904 64M / 9G INFO General (kmer_splitters.hpp : 379) Splitting kmer instances into 256 buckets. This might take a while. 0:02:38.904 64M / 9G INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:02:38.904 64M / 9G INFO General (kmer_splitters.hpp : 397) Memory available for splitting buffers: 2.08203 Gb 0:02:38.904 64M / 9G INFO General (kmer_splitters.hpp : 405) Using cell size of 87381 0:03:16.027 8G / 9G INFO General (kmer_splitters.hpp : 428) Processed 178956288 kmers 0:03:33.889 8G / 9G INFO General (kmer_splitters.hpp : 428) Processed 252963413 kmers 0:03:33.890 8G / 9G INFO General (kmer_splitters.hpp : 437) Used 252963413 kmers. 0:03:35.032 64M / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:04:02.585 64M / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 252826494 kmers in total. 0:04:02.585 64M / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:04:31.896 64M / 9G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:05:07.329 192M / 9G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:05:32.310 192M / 9G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 87462202 bytes occupied (2.7675 bits per kmer). 0:05:32.661 436M / 9G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 382) Building k-mer extensions from k+1-mers 0:06:09.274 436M / 9G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 386) Building k-mer extensions from k+1-mers finished. 0:06:09.280 436M / 9G INFO General (graph_construction.hpp : 145) Condensing graph 0:06:09.280 436M / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 337) Extracting unbranching paths 0:08:34.662 1G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 351) Extracting unbranching paths finished. 12249650 sequences extracted 0:09:00.307 1G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 311) Collecting perfect loops 0:10:22.187 1G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 326) Collecting perfect loops finished. 0 loops collected 0:10:31.536 3G / 9G INFO General (graph_construction.hpp : 150) Building index with from graph 0:10:31.537 3G / 9G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:10:31.537 3G / 9G INFO General (kmer_splitters.hpp : 289) Splitting kmer instances into 16 buckets. This might take a while. 0:10:31.537 3G / 9G INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:10:31.537 3G / 9G INFO General (kmer_splitters.hpp : 307) Memory available for splitting buffers: 32.2448 Gb 0:10:31.537 3G / 9G INFO General (kmer_splitters.hpp : 312) Using cell size of 1398101 0:10:36.575 3G / 9G INFO General (kmer_splitters.hpp : 325) Processed 1085100 edges 0:10:41.678 3G / 9G INFO General (kmer_splitters.hpp : 325) Processed 2167002 edges 0:10:47.869 3G / 9G INFO General (kmer_splitters.hpp : 325) Processed 3250287 edges 0:10:52.831 3G / 9G INFO General (kmer_splitters.hpp : 325) Processed 4332544 edges 0:10:58.014 3G / 9G INFO General (kmer_splitters.hpp : 325) Processed 5417616 edges 0:11:03.210 3G / 9G INFO General (kmer_splitters.hpp : 325) Processed 6502073 edges 0:11:09.401 3G / 9G INFO General (kmer_splitters.hpp : 325) Processed 7584706 edges 0:11:14.511 3G / 9G INFO General (kmer_splitters.hpp : 325) Processed 8668936 edges 0:11:19.634 3G / 9G INFO General (kmer_splitters.hpp : 325) Processed 9751464 edges 0:11:24.897 3G / 9G INFO General (kmer_splitters.hpp : 325) Processed 10834321 edges 0:11:30.348 3G / 9G INFO General (kmer_splitters.hpp : 325) Processed 11917031 edges 0:11:31.924 3G / 9G INFO General (kmer_splitters.hpp : 325) Processed 12249650 edges 0:11:31.925 3G / 9G INFO General (kmer_splitters.hpp : 330) Used 12249650 sequences. 0:11:31.977 3G / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:12:49.660 3G / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 252963413 kmers in total. 0:12:49.660 3G / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:13:15.049 3G / 9G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:19:31.366 3G / 9G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:19:57.451 3G / 9G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 87509572 bytes occupied (2.7675 bits per kmer). 0:20:01.114 9G / 9G INFO General (edge_index_builders.hpp : 21) Collecting k-mer coverage information from graph, this takes a while. 0:29:17.812 8G / 9G INFO General (graph_construction.hpp : 182) Filling coverage index 0:29:17.812 8G / 9G INFO General (edge_index_builders.hpp : 99) Collecting k-mer coverage information from reads, this takes a while. 0:32:19.769 8G / 9G INFO General (graph_construction.hpp : 184) Filling coverage and flanking coverage from index 0:33:17.360 8G / 9G INFO General (construction.cpp : 33) Figured out: read length = 320 0:33:17.414 8G / 9G INFO StageManager (stage.cpp : 125) STAGE == EC Threshold Finding 0:33:24.088 8G / 9G INFO General (kmer_coverage_model.cpp : 178) Kmer coverage valley at: 6 0:33:24.089 8G / 9G INFO General (kmer_coverage_model.cpp : 198) K-mer histogram maximum: 22 0:33:24.089 8G / 9G INFO General (kmer_coverage_model.cpp : 234) Estimated median coverage: 23. Coverage mad: 7.413 0:33:24.089 8G / 9G INFO General (kmer_coverage_model.cpp : 261) Fitting coverage model 0:33:24.146 8G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 2 0:33:24.294 8G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 4 0:33:24.800 8G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 8 0:33:26.004 8G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 16 0:33:27.497 8G / 9G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 22.6843. Fitted coverage std. dev: 6.26388 0:33:27.499 8G / 9G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 0.645233 0:33:27.499 8G / 9G INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 14 0:33:27.499 8G / 9G INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 14 0:33:27.499 8G / 9G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 66543933 0:33:27.499 8G / 9G INFO General (genomic_info_filler.cpp : 103) Mean coverage was calculated as 22.6843 0:33:27.499 8G / 9G INFO General (genomic_info_filler.cpp : 117) EC coverage threshold value was calculated as 14 0:33:27.499 8G / 9G INFO General (genomic_info_filler.cpp : 118) Trusted kmer low bound: 0 0:33:27.499 8G / 9G INFO StageManager (stage.cpp : 125) STAGE == Gap Closer 0:33:27.509 8G / 9G INFO General (gap_closer.cpp : 157) Preparing shift maps 0:33:39.764 9G / 9G INFO General (gap_closer.cpp : 117) Processing paired reads (takes a while) 0:33:47.482 9G / 9G INFO General (gap_closer.cpp : 136) Used 2410472 paired reads 0:33:47.483 9G / 9G INFO General (gap_closer.cpp : 138) Merging paired indices 0:33:49.678 8G / 9G INFO GapCloser (gap_closer.cpp : 395) Closing short gaps 0:34:16.810 8G / 9G INFO GapCloser (gap_closer.cpp : 424) Closing short gaps complete: filled 27 gaps after checking 2165 candidates 0:34:18.936 8G / 9G INFO General (gap_closer.cpp : 157) Preparing shift maps 0:34:31.350 9G / 9G INFO General (gap_closer.cpp : 117) Processing paired reads (takes a while) 0:34:36.064 9G / 9G INFO General (gap_closer.cpp : 136) Used 2060954 paired reads 0:34:36.064 9G / 9G INFO General (gap_closer.cpp : 138) Merging paired indices 0:34:38.138 8G / 9G INFO GapCloser (gap_closer.cpp : 395) Closing short gaps 0:35:05.298 8G / 9G INFO GapCloser (gap_closer.cpp : 424) Closing short gaps complete: filled 26 gaps after checking 1742 candidates 0:35:07.414 8G / 9G INFO General (gap_closer.cpp : 157) Preparing shift maps 0:35:19.621 9G / 9G INFO General (gap_closer.cpp : 117) Processing paired reads (takes a while) 0:35:24.683 9G / 9G INFO General (gap_closer.cpp : 136) Used 2236672 paired reads 0:35:24.686 9G / 9G INFO General (gap_closer.cpp : 138) Merging paired indices 0:35:26.827 8G / 9G INFO GapCloser (gap_closer.cpp : 395) Closing short gaps 0:35:54.026 8G / 9G INFO GapCloser (gap_closer.cpp : 424) Closing short gaps complete: filled 25 gaps after checking 1625 candidates 0:35:56.194 8G / 9G INFO General (gap_closer.cpp : 157) Preparing shift maps 0:36:08.440 9G / 9G INFO General (gap_closer.cpp : 117) Processing paired reads (takes a while) 0:36:16.707 9G / 9G INFO General (gap_closer.cpp : 136) Used 3625572 paired reads 0:36:16.709 9G / 9G INFO General (gap_closer.cpp : 138) Merging paired indices 0:36:19.470 8G / 9G INFO GapCloser (gap_closer.cpp : 395) Closing short gaps 0:36:46.853 8G / 9G INFO GapCloser (gap_closer.cpp : 424) Closing short gaps complete: filled 36 gaps after checking 3050 candidates 0:36:49.157 8G / 9G INFO StageManager (stage.cpp : 125) STAGE == Simplification 0:36:49.581 2G / 9G INFO General (graph_simplification.hpp : 911) Graph simplification started 0:36:49.581 2G / 9G INFO General (graph_simplification.hpp : 924) Fast simplification mode enabled 0:36:49.581 2G / 9G INFO General (graph_simplification.hpp : 771) PROCEDURE == Presimplification 0:36:49.581 2G / 9G INFO General (graph_simplification.hpp : 211) Removing short low covered self-conjugate connections 0:36:50.632 2G / 9G INFO General (graph_simplification.hpp : 403) Removing isolated edges 0:36:50.635 2G / 9G INFO General (graph_simplification.hpp : 404) All edges shorter than 320 will be removed 0:36:50.635 2G / 9G INFO General (graph_simplification.hpp : 405) Also edges shorter than 0 and coverage smaller than 0 will be removed 0:36:55.760 2G / 9G INFO General (graph_simplification.hpp : 687) Non parallel mode 0:37:26.434 3G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:39:01.543 3G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:39:32.427 2G / 9G INFO General (graph_simplification.hpp : 644) Using permanent iterators 0:39:32.427 2G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 1 0:39:33.753 2G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:39:36.940 2G / 9G INFO General (graph_simplification.hpp : 147) Removing bulges 0:40:31.879 3G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:40:32.312 3G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 2 0:40:32.312 3G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:40:32.359 3G / 9G INFO General (graph_simplification.hpp : 147) Removing bulges 0:40:32.491 3G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:40:32.916 2G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 3 0:40:32.917 2G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:40:32.922 2G / 9G INFO General (graph_simplification.hpp : 147) Removing bulges 0:40:33.162 2G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:40:33.450 2G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 4 0:40:33.451 2G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:40:33.458 2G / 9G INFO General (graph_simplification.hpp : 147) Removing bulges 0:40:33.673 2G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:40:33.813 2G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 5 0:40:33.813 2G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:40:33.817 2G / 9G INFO General (graph_simplification.hpp : 147) Removing bulges 0:40:33.910 2G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:40:34.004 2G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 6 0:40:34.004 2G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:40:34.007 2G / 9G INFO General (graph_simplification.hpp : 147) Removing bulges 0:40:34.069 2G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:40:34.149 2G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 7 0:40:34.149 2G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:40:34.151 2G / 9G INFO General (graph_simplification.hpp : 147) Removing bulges 0:40:34.199 2G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:40:34.237 2G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 8 0:40:34.237 2G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:40:34.238 2G / 9G INFO General (graph_simplification.hpp : 147) Removing bulges 0:40:34.267 2G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:40:34.296 2G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 9 0:40:34.296 2G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:40:34.297 2G / 9G INFO General (graph_simplification.hpp : 147) Removing bulges 0:40:34.327 2G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:40:34.361 2G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 10 0:40:34.361 2G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:40:34.363 2G / 9G INFO General (graph_simplification.hpp : 147) Removing bulges 0:40:34.376 2G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:40:34.396 2G / 9G INFO General (graph_simplification.hpp : 796) PROCEDURE == Post simplification 0:40:34.396 2G / 9G INFO General (graph_simplification.hpp : 644) Using permanent iterators 0:40:34.396 2G / 9G INFO General (graph_simplification.hpp : 806) Iteration 0 0:40:34.396 2G / 9G INFO General (graph_simplification.hpp : 247) Removal of relatively low covered connections disabled 0:40:34.505 2G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:40:34.699 2G / 9G INFO General (graph_simplification.hpp : 147) Removing bulges 0:40:34.835 2G / 9G INFO General (graph_simplification.hpp : 806) Iteration 1 0:40:34.835 2G / 9G INFO General (graph_simplification.hpp : 247) Removal of relatively low covered connections disabled 0:40:34.835 2G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:40:34.835 2G / 9G INFO General (graph_simplification.hpp : 147) Removing bulges 0:40:34.927 2G / 9G INFO StageManager (stage.cpp : 125) STAGE == Gap Closer 0:40:34.927 2G / 9G INFO General (graph_pack.hpp : 84) Index refill 0:40:34.928 2G / 9G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:40:34.928 2G / 9G INFO General (kmer_splitters.hpp : 289) Splitting kmer instances into 16 buckets. This might take a while. 0:40:34.928 2G / 9G INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:40:34.928 2G / 9G INFO General (kmer_splitters.hpp : 307) Memory available for splitting buffers: 32.3958 Gb 0:40:34.928 2G / 9G INFO General (kmer_splitters.hpp : 312) Using cell size of 1398101 0:40:38.991 3G / 9G INFO General (kmer_splitters.hpp : 325) Processed 17812 edges 0:40:42.895 3G / 9G INFO General (kmer_splitters.hpp : 325) Processed 35498 edges 0:40:46.754 3G / 9G INFO General (kmer_splitters.hpp : 325) Processed 52870 edges 0:40:49.146 3G / 9G INFO General (kmer_splitters.hpp : 325) Processed 63586 edges 0:40:49.146 3G / 9G INFO General (kmer_splitters.hpp : 330) Used 63586 sequences. 0:40:49.213 2G / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:41:12.772 2G / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 80768122 kmers in total. 0:41:12.772 2G / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:41:20.094 2G / 9G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:43:00.040 2G / 9G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:43:07.168 2G / 9G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 27940766 bytes occupied (2.7675 bits per kmer). 0:43:08.454 4G / 9G INFO General (edge_index_builders.hpp : 21) Collecting k-mer coverage information from graph, this takes a while. 0:45:26.534 4G / 9G INFO General (gap_closer.cpp : 157) Preparing shift maps 0:45:26.610 4G / 9G INFO General (gap_closer.cpp : 117) Processing paired reads (takes a while) 0:45:50.519 4G / 9G INFO General (gap_closer.cpp : 136) Used 2410472 paired reads 0:45:50.519 4G / 9G INFO General (gap_closer.cpp : 138) Merging paired indices 0:45:50.564 4G / 9G INFO GapCloser (gap_closer.cpp : 395) Closing short gaps 0:45:50.670 4G / 9G INFO GapCloser (gap_closer.cpp : 424) Closing short gaps complete: filled 2 gaps after checking 702 candidates 0:45:50.770 4G / 9G INFO General (gap_closer.cpp : 157) Preparing shift maps 0:45:50.837 4G / 9G INFO General (gap_closer.cpp : 117) Processing paired reads (takes a while) 0:46:04.360 4G / 9G INFO General (gap_closer.cpp : 136) Used 2060954 paired reads 0:46:04.360 4G / 9G INFO General (gap_closer.cpp : 138) Merging paired indices 0:46:04.398 4G / 9G INFO GapCloser (gap_closer.cpp : 395) Closing short gaps 0:46:04.504 4G / 9G INFO GapCloser (gap_closer.cpp : 424) Closing short gaps complete: filled 0 gaps after checking 700 candidates 0:46:04.596 4G / 9G INFO General (gap_closer.cpp : 157) Preparing shift maps 0:46:04.666 4G / 9G INFO General (gap_closer.cpp : 117) Processing paired reads (takes a while) 0:46:21.153 4G / 9G INFO General (gap_closer.cpp : 136) Used 2236672 paired reads 0:46:21.155 4G / 9G INFO General (gap_closer.cpp : 138) Merging paired indices 0:46:21.197 4G / 9G INFO GapCloser (gap_closer.cpp : 395) Closing short gaps 0:46:21.299 4G / 9G INFO GapCloser (gap_closer.cpp : 424) Closing short gaps complete: filled 0 gaps after checking 561 candidates 0:46:21.387 4G / 9G INFO General (gap_closer.cpp : 157) Preparing shift maps 0:46:21.453 4G / 9G INFO General (gap_closer.cpp : 117) Processing paired reads (takes a while) 0:46:49.950 4G / 9G INFO General (gap_closer.cpp : 136) Used 3625572 paired reads 0:46:49.951 4G / 9G INFO General (gap_closer.cpp : 138) Merging paired indices 0:46:50.003 4G / 9G INFO GapCloser (gap_closer.cpp : 395) Closing short gaps 0:46:50.120 4G / 9G INFO GapCloser (gap_closer.cpp : 424) Closing short gaps complete: filled 1 gaps after checking 950 candidates 0:46:50.253 4G / 9G INFO StageManager (stage.cpp : 125) STAGE == Simplification Cleanup 0:46:50.254 4G / 9G INFO General (graph_simplification.hpp : 403) Removing isolated edges 0:46:50.254 4G / 9G INFO General (graph_simplification.hpp : 404) All edges shorter than 320 will be removed 0:46:50.254 4G / 9G INFO General (graph_simplification.hpp : 405) Also edges shorter than 0 and coverage smaller than 2 will be removed 0:46:51.081 4G / 9G INFO General (simplification.cpp : 56) Removing all the edges having coverage 0 and less 0:46:51.239 4G / 9G INFO General (simplification.cpp : 68) Counting average coverage 0:46:51.271 4G / 9G INFO General (simplification.cpp : 71) Average coverage = 21.4247 0:46:51.271 4G / 9G INFO StageManager (stage.cpp : 125) STAGE == Contig Output 0:46:51.271 4G / 9G INFO General (contig_output.hpp : 283) Outputting contigs to /N/dc2/projects/marinovg/2015-01-29-P-assem/Paramecium_pentaurelia_strain_870-SPAdes-3.5.0-trimmed//K77/simplified_contigs.fasta 0:47:03.638 4G / 9G INFO General (contig_output.hpp : 283) Outputting contigs to /N/dc2/projects/marinovg/2015-01-29-P-assem/Paramecium_pentaurelia_strain_870-SPAdes-3.5.0-trimmed//K77/before_rr.fasta 0:47:41.104 4G / 9G INFO General (contig_output.hpp : 283) Outputting contigs to /N/dc2/projects/marinovg/2015-01-29-P-assem/Paramecium_pentaurelia_strain_870-SPAdes-3.5.0-trimmed//K77/final_contigs.fasta 0:48:17.351 4G / 9G INFO General (launch.hpp : 82) SPAdes finished 0:48:31.236 68M / 9G INFO General (main.cpp : 166) Assembling time: 0 hours 48 minutes 31 seconds == Running assembler: K99 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/2015-01-29-P-assem/Paramecium_pentaurelia_strain_870-SPAdes-3.5.0-trimmed/dataset.info) with K=99 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 0:00:00.001 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 0:00:00.005 4M / 4M INFO General (read_converter.hpp : 49) Binary reads detected 0:00:00.068 4M / 4M INFO General (graph_construction.hpp : 129) Constructing DeBruijn graph for k=99 0:00:00.070 4M / 4M INFO General (kmer_splitters.hpp : 172) Splitting kmer instances into 256 buckets. This might take a while. 0:00:00.070 4M / 4M INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:00:00.070 4M / 4M INFO General (kmer_splitters.hpp : 190) Memory available for splitting buffers: 2.08325 Gb 0:00:00.070 4M / 4M INFO General (kmer_splitters.hpp : 199) Using cell size of 65536 0:00:15.693 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 3336217 reads 0:00:27.772 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 6677761 reads 0:00:39.698 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 10018616 reads 0:00:52.022 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 13359760 reads 0:01:04.191 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 16695980 reads 0:01:16.220 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 20040327 reads 0:01:20.303 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 20669826 reads 0:01:20.304 8G / 9G INFO General (kmer_splitters.hpp : 234) Adding contigs from previous K 0:01:43.946 8G / 9G INFO General (kmer_splitters.hpp : 245) Used 20669826 reads. Maximum read length 320 0:01:43.947 8G / 9G INFO General (kmer_splitters.hpp : 246) Average read length 259.734 0:01:45.659 64M / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:02:40.737 64M / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 251474966 kmers in total. 0:02:40.737 64M / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:03:17.883 64M / 9G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:03:17.884 64M / 9G INFO General (kmer_splitters.hpp : 379) Splitting kmer instances into 256 buckets. This might take a while. 0:03:17.884 64M / 9G INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:03:17.884 64M / 9G INFO General (kmer_splitters.hpp : 397) Memory available for splitting buffers: 2.08203 Gb 0:03:17.884 64M / 9G INFO General (kmer_splitters.hpp : 405) Using cell size of 65536 0:03:53.492 8G / 9G INFO General (kmer_splitters.hpp : 428) Processed 134217728 kmers 0:04:25.601 8G / 9G INFO General (kmer_splitters.hpp : 428) Processed 251474966 kmers 0:04:25.601 8G / 9G INFO General (kmer_splitters.hpp : 437) Used 251474966 kmers. 0:04:26.776 64M / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:05:05.908 64M / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 251698517 kmers in total. 0:05:05.908 64M / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:05:42.608 64M / 9G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:06:29.366 192M / 9G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:07:02.938 192M / 9G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 87071989 bytes occupied (2.7675 bits per kmer). 0:07:03.287 436M / 9G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 382) Building k-mer extensions from k+1-mers 0:07:43.920 436M / 9G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 386) Building k-mer extensions from k+1-mers finished. 0:07:43.925 436M / 9G INFO General (graph_construction.hpp : 145) Condensing graph 0:07:43.925 436M / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 337) Extracting unbranching paths 0:10:10.111 1G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 351) Extracting unbranching paths finished. 11023458 sequences extracted 0:10:36.591 1G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 311) Collecting perfect loops 0:12:01.921 1G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 326) Collecting perfect loops finished. 0 loops collected 0:12:11.434 3G / 9G INFO General (graph_construction.hpp : 150) Building index with from graph 0:12:11.436 3G / 9G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:12:11.436 3G / 9G INFO General (kmer_splitters.hpp : 289) Splitting kmer instances into 16 buckets. This might take a while. 0:12:11.436 3G / 9G INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:12:11.436 3G / 9G INFO General (kmer_splitters.hpp : 307) Memory available for splitting buffers: 32.3112 Gb 0:12:11.436 3G / 9G INFO General (kmer_splitters.hpp : 312) Using cell size of 1048576 0:12:16.097 3G / 9G INFO General (kmer_splitters.hpp : 325) Processed 735619 edges 0:12:20.836 3G / 9G INFO General (kmer_splitters.hpp : 325) Processed 1472612 edges 0:12:25.380 3G / 9G INFO General (kmer_splitters.hpp : 325) Processed 2206826 edges 0:12:29.602 3G / 9G INFO General (kmer_splitters.hpp : 325) Processed 2941736 edges 0:12:34.056 3G / 9G INFO General (kmer_splitters.hpp : 325) Processed 3678613 edges 0:12:38.389 3G / 9G INFO General (kmer_splitters.hpp : 325) Processed 4414193 edges 0:12:42.726 3G / 9G INFO General (kmer_splitters.hpp : 325) Processed 5148171 edges 0:12:46.998 3G / 9G INFO General (kmer_splitters.hpp : 325) Processed 5884019 edges 0:12:51.269 3G / 9G INFO General (kmer_splitters.hpp : 325) Processed 6619653 edges 0:12:55.646 3G / 9G INFO General (kmer_splitters.hpp : 325) Processed 7354269 edges 0:12:59.867 3G / 9G INFO General (kmer_splitters.hpp : 325) Processed 8089738 edges 0:13:04.089 3G / 9G INFO General (kmer_splitters.hpp : 325) Processed 8825493 edges 0:13:08.493 3G / 9G INFO General (kmer_splitters.hpp : 325) Processed 9561973 edges 0:13:13.018 3G / 9G INFO General (kmer_splitters.hpp : 325) Processed 10297321 edges 0:13:17.239 3G / 9G INFO General (kmer_splitters.hpp : 330) Used 11023458 sequences. 0:13:17.286 3G / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:14:54.811 3G / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 251474966 kmers in total. 0:14:54.812 3G / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:15:29.033 3G / 9G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:21:44.382 3G / 9G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:22:14.589 3G / 9G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 86994664 bytes occupied (2.7675 bits per kmer). 0:22:18.253 8G / 9G INFO General (edge_index_builders.hpp : 21) Collecting k-mer coverage information from graph, this takes a while. 0:30:53.587 8G / 9G INFO General (graph_construction.hpp : 182) Filling coverage index 0:30:53.587 8G / 9G INFO General (edge_index_builders.hpp : 99) Collecting k-mer coverage information from reads, this takes a while. 0:33:40.694 8G / 9G INFO General (graph_construction.hpp : 184) Filling coverage and flanking coverage from index 0:34:47.727 8G / 9G INFO General (construction.cpp : 33) Figured out: read length = 320 0:34:47.789 8G / 9G INFO StageManager (stage.cpp : 125) STAGE == EC Threshold Finding 0:34:54.584 8G / 9G INFO General (kmer_coverage_model.cpp : 178) Kmer coverage valley at: 5 0:34:54.584 8G / 9G INFO General (kmer_coverage_model.cpp : 198) K-mer histogram maximum: 19 0:34:54.584 8G / 9G INFO General (kmer_coverage_model.cpp : 234) Estimated median coverage: 20. Coverage mad: 7.413 0:34:54.584 8G / 9G INFO General (kmer_coverage_model.cpp : 261) Fitting coverage model 0:34:54.636 8G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 2 0:34:54.778 8G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 4 0:34:55.300 8G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 8 0:34:56.288 8G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 16 0:34:57.613 8G / 9G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 19.5259. Fitted coverage std. dev: 5.82742 0:34:57.615 8G / 9G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 0.561969 0:34:57.615 8G / 9G INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 12 0:34:57.615 8G / 9G INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 12 0:34:57.615 8G / 9G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 66440832 0:34:57.615 8G / 9G INFO General (genomic_info_filler.cpp : 103) Mean coverage was calculated as 19.5259 0:34:57.615 8G / 9G INFO General (genomic_info_filler.cpp : 117) EC coverage threshold value was calculated as 12 0:34:57.615 8G / 9G INFO General (genomic_info_filler.cpp : 118) Trusted kmer low bound: 0 0:34:57.615 8G / 9G INFO StageManager (stage.cpp : 125) STAGE == Gap Closer 0:34:57.627 8G / 9G INFO General (gap_closer.cpp : 157) Preparing shift maps 0:35:09.973 8G / 9G INFO General (gap_closer.cpp : 117) Processing paired reads (takes a while) 0:35:14.914 9G / 9G INFO General (gap_closer.cpp : 136) Used 2410472 paired reads 0:35:14.916 9G / 9G INFO General (gap_closer.cpp : 138) Merging paired indices 0:35:17.403 8G / 9G INFO GapCloser (gap_closer.cpp : 395) Closing short gaps 0:35:41.327 8G / 9G INFO GapCloser (gap_closer.cpp : 424) Closing short gaps complete: filled 54 gaps after checking 2328 candidates 0:35:43.464 8G / 9G INFO General (gap_closer.cpp : 157) Preparing shift maps 0:35:56.033 8G / 9G INFO General (gap_closer.cpp : 117) Processing paired reads (takes a while) 0:36:00.248 9G / 9G INFO General (gap_closer.cpp : 136) Used 2060954 paired reads 0:36:00.249 9G / 9G INFO General (gap_closer.cpp : 138) Merging paired indices 0:36:02.520 8G / 9G INFO GapCloser (gap_closer.cpp : 395) Closing short gaps 0:36:26.632 8G / 9G INFO GapCloser (gap_closer.cpp : 424) Closing short gaps complete: filled 54 gaps after checking 1846 candidates 0:36:28.666 8G / 9G INFO General (gap_closer.cpp : 157) Preparing shift maps 0:36:41.280 8G / 9G INFO General (gap_closer.cpp : 117) Processing paired reads (takes a while) 0:36:47.641 9G / 9G INFO General (gap_closer.cpp : 136) Used 2236672 paired reads 0:36:47.641 9G / 9G INFO General (gap_closer.cpp : 138) Merging paired indices 0:36:50.144 8G / 9G INFO GapCloser (gap_closer.cpp : 395) Closing short gaps 0:37:14.413 8G / 9G INFO GapCloser (gap_closer.cpp : 424) Closing short gaps complete: filled 34 gaps after checking 1818 candidates 0:37:16.516 8G / 9G INFO General (gap_closer.cpp : 157) Preparing shift maps 0:37:29.146 8G / 9G INFO General (gap_closer.cpp : 117) Processing paired reads (takes a while) 0:37:39.002 9G / 9G INFO General (gap_closer.cpp : 136) Used 3625572 paired reads 0:37:39.003 9G / 9G INFO General (gap_closer.cpp : 138) Merging paired indices 0:37:42.171 8G / 9G INFO GapCloser (gap_closer.cpp : 395) Closing short gaps 0:38:06.633 8G / 9G INFO GapCloser (gap_closer.cpp : 424) Closing short gaps complete: filled 63 gaps after checking 3351 candidates 0:38:09.009 8G / 9G INFO StageManager (stage.cpp : 125) STAGE == Simplification 0:38:09.383 2G / 9G INFO General (graph_simplification.hpp : 911) Graph simplification started 0:38:09.383 2G / 9G INFO General (graph_simplification.hpp : 924) Fast simplification mode enabled 0:38:09.383 2G / 9G INFO General (graph_simplification.hpp : 771) PROCEDURE == Presimplification 0:38:09.383 2G / 9G INFO General (graph_simplification.hpp : 211) Removing short low covered self-conjugate connections 0:38:10.475 2G / 9G INFO General (graph_simplification.hpp : 403) Removing isolated edges 0:38:10.477 2G / 9G INFO General (graph_simplification.hpp : 404) All edges shorter than 320 will be removed 0:38:10.478 2G / 9G INFO General (graph_simplification.hpp : 405) Also edges shorter than 0 and coverage smaller than 0 will be removed 0:38:17.143 2G / 9G INFO General (graph_simplification.hpp : 687) Non parallel mode 0:38:45.725 3G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:40:16.854 2G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:40:34.452 2G / 9G INFO General (graph_simplification.hpp : 644) Using permanent iterators 0:40:34.452 2G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 1 0:40:35.257 2G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:40:37.148 1G / 9G INFO General (graph_simplification.hpp : 147) Removing bulges 0:41:16.397 2G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:41:16.791 2G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 2 0:41:16.791 2G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:41:16.818 2G / 9G INFO General (graph_simplification.hpp : 147) Removing bulges 0:41:16.871 2G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:41:17.177 2G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 3 0:41:17.177 2G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:41:17.183 2G / 9G INFO General (graph_simplification.hpp : 147) Removing bulges 0:41:17.332 2G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:41:17.588 2G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 4 0:41:17.588 2G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:41:17.592 2G / 9G INFO General (graph_simplification.hpp : 147) Removing bulges 0:41:17.822 2G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:41:17.958 2G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 5 0:41:17.958 2G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:41:17.961 2G / 9G INFO General (graph_simplification.hpp : 147) Removing bulges 0:41:18.054 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:41:18.145 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 6 0:41:18.145 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:41:18.147 1G / 9G INFO General (graph_simplification.hpp : 147) Removing bulges 0:41:18.191 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:41:18.268 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 7 0:41:18.268 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:41:18.269 1G / 9G INFO General (graph_simplification.hpp : 147) Removing bulges 0:41:18.326 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:41:18.366 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 8 0:41:18.366 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:41:18.368 1G / 9G INFO General (graph_simplification.hpp : 147) Removing bulges 0:41:18.391 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:41:18.419 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 9 0:41:18.419 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:41:18.420 1G / 9G INFO General (graph_simplification.hpp : 147) Removing bulges 0:41:18.449 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:41:18.476 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 10 0:41:18.476 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:41:18.477 1G / 9G INFO General (graph_simplification.hpp : 147) Removing bulges 0:41:18.484 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:41:18.501 1G / 9G INFO General (graph_simplification.hpp : 796) PROCEDURE == Post simplification 0:41:18.501 1G / 9G INFO General (graph_simplification.hpp : 644) Using permanent iterators 0:41:18.501 1G / 9G INFO General (graph_simplification.hpp : 806) Iteration 0 0:41:18.501 1G / 9G INFO General (graph_simplification.hpp : 247) Removal of relatively low covered connections disabled 0:41:18.585 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:41:18.717 1G / 9G INFO General (graph_simplification.hpp : 147) Removing bulges 0:41:18.802 1G / 9G INFO General (graph_simplification.hpp : 806) Iteration 1 0:41:18.802 1G / 9G INFO General (graph_simplification.hpp : 247) Removal of relatively low covered connections disabled 0:41:18.802 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:41:18.803 1G / 9G INFO General (graph_simplification.hpp : 147) Removing bulges 0:41:18.855 1G / 9G INFO StageManager (stage.cpp : 125) STAGE == Gap Closer 0:41:18.855 1G / 9G INFO General (graph_pack.hpp : 84) Index refill 0:41:18.856 1G / 9G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:41:18.857 1G / 9G INFO General (kmer_splitters.hpp : 289) Splitting kmer instances into 16 buckets. This might take a while. 0:41:18.857 1G / 9G INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:41:18.857 1G / 9G INFO General (kmer_splitters.hpp : 307) Memory available for splitting buffers: 32.6875 Gb 0:41:18.857 1G / 9G INFO General (kmer_splitters.hpp : 312) Using cell size of 1048576 0:41:22.258 2G / 9G INFO General (kmer_splitters.hpp : 325) Processed 9490 edges 0:41:25.538 2G / 9G INFO General (kmer_splitters.hpp : 325) Processed 18997 edges 0:41:28.867 2G / 9G INFO General (kmer_splitters.hpp : 325) Processed 28486 edges 0:41:32.131 2G / 9G INFO General (kmer_splitters.hpp : 325) Processed 38129 edges 0:41:34.803 2G / 9G INFO General (kmer_splitters.hpp : 325) Processed 45903 edges 0:41:34.804 2G / 9G INFO General (kmer_splitters.hpp : 330) Used 45903 sequences. 0:41:34.858 1G / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:42:04.181 1G / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 81285545 kmers in total. 0:42:04.181 1G / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:42:16.333 1G / 9G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:43:57.825 1G / 9G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:44:08.539 1G / 9G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 28119756 bytes occupied (2.7675 bits per kmer). 0:44:09.770 3G / 9G INFO General (edge_index_builders.hpp : 21) Collecting k-mer coverage information from graph, this takes a while. 0:46:24.013 3G / 9G INFO General (gap_closer.cpp : 157) Preparing shift maps 0:46:24.077 3G / 9G INFO General (gap_closer.cpp : 117) Processing paired reads (takes a while) 0:46:46.863 3G / 9G INFO General (gap_closer.cpp : 136) Used 2410472 paired reads 0:46:46.863 3G / 9G INFO General (gap_closer.cpp : 138) Merging paired indices 0:46:46.913 3G / 9G INFO GapCloser (gap_closer.cpp : 395) Closing short gaps 0:46:46.995 3G / 9G INFO GapCloser (gap_closer.cpp : 424) Closing short gaps complete: filled 1 gaps after checking 288 candidates 0:46:47.201 3G / 9G INFO General (gap_closer.cpp : 157) Preparing shift maps 0:46:47.267 3G / 9G INFO General (gap_closer.cpp : 117) Processing paired reads (takes a while) 0:47:04.129 3G / 9G INFO General (gap_closer.cpp : 136) Used 2060954 paired reads 0:47:04.129 3G / 9G INFO General (gap_closer.cpp : 138) Merging paired indices 0:47:04.172 3G / 9G INFO GapCloser (gap_closer.cpp : 395) Closing short gaps 0:47:04.256 3G / 9G INFO GapCloser (gap_closer.cpp : 424) Closing short gaps complete: filled 1 gaps after checking 367 candidates 0:47:04.350 3G / 9G INFO General (gap_closer.cpp : 157) Preparing shift maps 0:47:04.409 3G / 9G INFO General (gap_closer.cpp : 117) Processing paired reads (takes a while) 0:47:24.313 3G / 9G INFO General (gap_closer.cpp : 136) Used 2236672 paired reads 0:47:24.313 3G / 9G INFO General (gap_closer.cpp : 138) Merging paired indices 0:47:24.354 3G / 9G INFO GapCloser (gap_closer.cpp : 395) Closing short gaps 0:47:24.434 3G / 9G INFO GapCloser (gap_closer.cpp : 424) Closing short gaps complete: filled 0 gaps after checking 273 candidates 0:47:24.526 3G / 9G INFO General (gap_closer.cpp : 157) Preparing shift maps 0:47:24.584 3G / 9G INFO General (gap_closer.cpp : 117) Processing paired reads (takes a while) 0:47:50.745 3G / 9G INFO General (gap_closer.cpp : 136) Used 3625572 paired reads 0:47:50.746 3G / 9G INFO General (gap_closer.cpp : 138) Merging paired indices 0:47:50.805 3G / 9G INFO GapCloser (gap_closer.cpp : 395) Closing short gaps 0:47:50.893 3G / 9G INFO GapCloser (gap_closer.cpp : 424) Closing short gaps complete: filled 0 gaps after checking 468 candidates 0:47:50.986 3G / 9G INFO StageManager (stage.cpp : 125) STAGE == Simplification Cleanup 0:47:50.987 3G / 9G INFO General (graph_simplification.hpp : 403) Removing isolated edges 0:47:50.987 3G / 9G INFO General (graph_simplification.hpp : 404) All edges shorter than 320 will be removed 0:47:50.987 3G / 9G INFO General (graph_simplification.hpp : 405) Also edges shorter than 0 and coverage smaller than 2 will be removed 0:47:52.118 3G / 9G INFO General (simplification.cpp : 56) Removing all the edges having coverage 0 and less 0:47:52.227 3G / 9G INFO General (simplification.cpp : 68) Counting average coverage 0:47:52.243 3G / 9G INFO General (simplification.cpp : 71) Average coverage = 18.4921 0:47:52.244 3G / 9G INFO StageManager (stage.cpp : 125) STAGE == Contig Output 0:47:52.244 3G / 9G INFO General (contig_output.hpp : 283) Outputting contigs to /N/dc2/projects/marinovg/2015-01-29-P-assem/Paramecium_pentaurelia_strain_870-SPAdes-3.5.0-trimmed//K99/simplified_contigs.fasta 0:48:04.489 3G / 9G INFO General (contig_output.hpp : 283) Outputting contigs to /N/dc2/projects/marinovg/2015-01-29-P-assem/Paramecium_pentaurelia_strain_870-SPAdes-3.5.0-trimmed//K99/before_rr.fasta 0:48:40.735 3G / 9G INFO General (contig_output.hpp : 283) Outputting contigs to /N/dc2/projects/marinovg/2015-01-29-P-assem/Paramecium_pentaurelia_strain_870-SPAdes-3.5.0-trimmed//K99/final_contigs.fasta 0:49:17.047 3G / 9G INFO General (launch.hpp : 82) SPAdes finished 0:49:26.329 68M / 9G INFO General (main.cpp : 166) Assembling time: 0 hours 49 minutes 26 seconds == Running assembler: K127 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/2015-01-29-P-assem/Paramecium_pentaurelia_strain_870-SPAdes-3.5.0-trimmed/dataset.info) with K=127 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 0:00:00.005 4M / 4M INFO General (read_converter.hpp : 49) Binary reads detected 0:00:00.064 4M / 4M INFO General (graph_construction.hpp : 129) Constructing DeBruijn graph for k=127 0:00:00.066 4M / 4M INFO General (kmer_splitters.hpp : 172) Splitting kmer instances into 256 buckets. This might take a while. 0:00:00.066 4M / 4M INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:00:00.066 4M / 4M INFO General (kmer_splitters.hpp : 190) Memory available for splitting buffers: 2.08325 Gb 0:00:00.066 4M / 4M INFO General (kmer_splitters.hpp : 199) Using cell size of 65536 0:00:16.061 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 4041725 reads 0:00:28.272 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 8084343 reads 0:00:40.610 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 12128343 reads 0:00:53.912 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 16173217 reads 0:01:06.041 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 20221476 reads 0:01:09.013 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 20669826 reads 0:01:09.014 8G / 9G INFO General (kmer_splitters.hpp : 234) Adding contigs from previous K 0:01:33.370 8G / 9G INFO General (kmer_splitters.hpp : 245) Used 20669826 reads. Maximum read length 320 0:01:33.371 8G / 9G INFO General (kmer_splitters.hpp : 246) Average read length 259.734 0:01:35.068 64M / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:02:24.287 64M / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 240186869 kmers in total. 0:02:24.287 64M / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:02:58.321 64M / 9G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:02:58.322 64M / 9G INFO General (kmer_splitters.hpp : 379) Splitting kmer instances into 256 buckets. This might take a while. 0:02:58.322 64M / 9G INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:02:58.322 64M / 9G INFO General (kmer_splitters.hpp : 397) Memory available for splitting buffers: 2.08203 Gb 0:02:58.322 64M / 9G INFO General (kmer_splitters.hpp : 405) Using cell size of 65536 0:03:35.786 8G / 9G INFO General (kmer_splitters.hpp : 428) Processed 134217728 kmers 0:04:06.522 8G / 9G INFO General (kmer_splitters.hpp : 428) Processed 240186869 kmers 0:04:06.522 8G / 9G INFO General (kmer_splitters.hpp : 437) Used 240186869 kmers. 0:04:07.631 64M / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:04:44.178 64M / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 240744929 kmers in total. 0:04:44.178 64M / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:05:26.503 64M / 9G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:06:00.929 192M / 9G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:06:36.627 192M / 9G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 83282726 bytes occupied (2.7675 bits per kmer). 0:06:36.944 424M / 9G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 382) Building k-mer extensions from k+1-mers 0:07:18.067 424M / 9G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 386) Building k-mer extensions from k+1-mers finished. 0:07:18.071 424M / 9G INFO General (graph_construction.hpp : 145) Condensing graph 0:07:18.071 424M / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 337) Extracting unbranching paths 0:09:35.016 1G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 351) Extracting unbranching paths finished. 10014897 sequences extracted 0:09:59.335 1G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 311) Collecting perfect loops 0:11:19.025 1G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 326) Collecting perfect loops finished. 0 loops collected 0:11:27.089 2G / 9G INFO General (graph_construction.hpp : 150) Building index with from graph 0:11:27.090 2G / 9G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:11:27.090 2G / 9G INFO General (kmer_splitters.hpp : 289) Splitting kmer instances into 16 buckets. This might take a while. 0:11:27.090 2G / 9G INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:11:27.091 2G / 9G INFO General (kmer_splitters.hpp : 307) Memory available for splitting buffers: 32.3503 Gb 0:11:27.091 2G / 9G INFO General (kmer_splitters.hpp : 312) Using cell size of 1048576 0:11:31.363 3G / 9G INFO General (kmer_splitters.hpp : 325) Processed 699485 edges 0:11:35.611 3G / 9G INFO General (kmer_splitters.hpp : 325) Processed 1398726 edges 0:11:39.841 3G / 9G INFO General (kmer_splitters.hpp : 325) Processed 2099310 edges 0:11:44.184 3G / 9G INFO General (kmer_splitters.hpp : 325) Processed 2798874 edges 0:11:48.492 3G / 9G INFO General (kmer_splitters.hpp : 325) Processed 3498865 edges 0:11:53.439 3G / 9G INFO General (kmer_splitters.hpp : 325) Processed 4197950 edges 0:11:58.809 3G / 9G INFO General (kmer_splitters.hpp : 325) Processed 4896477 edges 0:12:03.547 3G / 9G INFO General (kmer_splitters.hpp : 325) Processed 5595175 edges 0:12:08.608 3G / 9G INFO General (kmer_splitters.hpp : 325) Processed 6295583 edges 0:12:13.417 3G / 9G INFO General (kmer_splitters.hpp : 325) Processed 6994551 edges 0:12:18.153 3G / 9G INFO General (kmer_splitters.hpp : 325) Processed 7694148 edges 0:12:23.012 3G / 9G INFO General (kmer_splitters.hpp : 325) Processed 8393740 edges 0:12:27.899 3G / 9G INFO General (kmer_splitters.hpp : 325) Processed 9094893 edges 0:12:32.666 3G / 9G INFO General (kmer_splitters.hpp : 325) Processed 9792916 edges 0:12:34.214 3G / 9G INFO General (kmer_splitters.hpp : 330) Used 10014897 sequences. 0:12:34.272 2G / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:14:02.096 2G / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 240186869 kmers in total. 0:14:02.097 2G / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:14:38.115 2G / 9G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:20:26.592 3G / 9G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:20:56.186 3G / 9G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 83089690 bytes occupied (2.7675 bits per kmer). 0:20:59.673 8G / 9G INFO General (edge_index_builders.hpp : 21) Collecting k-mer coverage information from graph, this takes a while. 0:29:34.587 8G / 9G INFO General (graph_construction.hpp : 182) Filling coverage index 0:29:34.587 8G / 9G INFO General (edge_index_builders.hpp : 99) Collecting k-mer coverage information from reads, this takes a while. 0:31:56.826 8G / 9G INFO General (graph_construction.hpp : 184) Filling coverage and flanking coverage from index 0:32:57.439 8G / 9G INFO General (construction.cpp : 33) Figured out: read length = 320 0:32:57.492 8G / 9G INFO StageManager (stage.cpp : 125) STAGE == EC Threshold Finding 0:33:03.759 8G / 9G INFO General (kmer_coverage_model.cpp : 178) Kmer coverage valley at: 4 0:33:03.759 8G / 9G INFO General (kmer_coverage_model.cpp : 198) K-mer histogram maximum: 15 0:33:03.759 8G / 9G INFO General (kmer_coverage_model.cpp : 234) Estimated median coverage: 16. Coverage mad: 5.9304 0:33:03.759 8G / 9G INFO General (kmer_coverage_model.cpp : 261) Fitting coverage model 0:33:03.801 8G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 2 0:33:03.914 8G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 4 0:33:04.332 8G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 8 0:33:05.192 8G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 16 0:33:06.515 8G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 32 0:33:06.595 8G / 9G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 15.7099. Fitted coverage std. dev: 5.16331 0:33:06.596 8G / 9G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 0.439579 0:33:06.596 8G / 9G INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 10 0:33:06.596 8G / 9G INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 9 0:33:06.596 8G / 9G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 67593166 0:33:06.596 8G / 9G INFO General (genomic_info_filler.cpp : 103) Mean coverage was calculated as 15.7099 0:33:06.597 8G / 9G INFO General (genomic_info_filler.cpp : 117) EC coverage threshold value was calculated as 9 0:33:06.597 8G / 9G INFO General (genomic_info_filler.cpp : 118) Trusted kmer low bound: 0 0:33:06.597 8G / 9G INFO StageManager (stage.cpp : 125) STAGE == Gap Closer 0:33:06.608 8G / 9G INFO General (gap_closer.cpp : 157) Preparing shift maps 0:33:18.750 8G / 9G INFO General (gap_closer.cpp : 117) Processing paired reads (takes a while) 0:33:24.464 8G / 9G INFO General (gap_closer.cpp : 136) Used 2410472 paired reads 0:33:24.465 8G / 9G INFO General (gap_closer.cpp : 138) Merging paired indices 0:33:27.016 8G / 9G INFO GapCloser (gap_closer.cpp : 395) Closing short gaps 0:33:49.078 8G / 9G INFO GapCloser (gap_closer.cpp : 424) Closing short gaps complete: filled 76 gaps after checking 2306 candidates 0:33:51.174 8G / 9G INFO General (gap_closer.cpp : 157) Preparing shift maps 0:34:03.635 8G / 9G INFO General (gap_closer.cpp : 117) Processing paired reads (takes a while) 0:34:08.306 8G / 9G INFO General (gap_closer.cpp : 136) Used 2060954 paired reads 0:34:08.307 8G / 9G INFO General (gap_closer.cpp : 138) Merging paired indices 0:34:10.603 8G / 9G INFO GapCloser (gap_closer.cpp : 395) Closing short gaps 0:34:32.623 8G / 9G INFO GapCloser (gap_closer.cpp : 424) Closing short gaps complete: filled 88 gaps after checking 1835 candidates 0:34:34.658 8G / 9G INFO General (gap_closer.cpp : 157) Preparing shift maps 0:34:47.082 8G / 9G INFO General (gap_closer.cpp : 117) Processing paired reads (takes a while) 0:34:51.858 8G / 9G INFO General (gap_closer.cpp : 136) Used 2236672 paired reads 0:34:51.859 8G / 9G INFO General (gap_closer.cpp : 138) Merging paired indices 0:34:54.366 8G / 9G INFO GapCloser (gap_closer.cpp : 395) Closing short gaps 0:35:16.521 8G / 9G INFO GapCloser (gap_closer.cpp : 424) Closing short gaps complete: filled 52 gaps after checking 1908 candidates 0:35:18.585 8G / 9G INFO General (gap_closer.cpp : 157) Preparing shift maps 0:35:31.024 8G / 9G INFO General (gap_closer.cpp : 117) Processing paired reads (takes a while) 0:35:38.668 8G / 9G INFO General (gap_closer.cpp : 136) Used 3625572 paired reads 0:35:38.668 8G / 9G INFO General (gap_closer.cpp : 138) Merging paired indices 0:35:41.949 8G / 9G INFO GapCloser (gap_closer.cpp : 395) Closing short gaps 0:36:04.569 8G / 9G INFO GapCloser (gap_closer.cpp : 424) Closing short gaps complete: filled 108 gaps after checking 3398 candidates 0:36:06.869 8G / 9G INFO StageManager (stage.cpp : 125) STAGE == Simplification 0:36:07.223 2G / 9G INFO General (graph_simplification.hpp : 911) Graph simplification started 0:36:07.223 2G / 9G INFO General (graph_simplification.hpp : 924) Fast simplification mode enabled 0:36:07.223 2G / 9G INFO General (graph_simplification.hpp : 771) PROCEDURE == Presimplification 0:36:07.223 2G / 9G INFO General (graph_simplification.hpp : 211) Removing short low covered self-conjugate connections 0:36:08.212 2G / 9G INFO General (graph_simplification.hpp : 403) Removing isolated edges 0:36:08.215 2G / 9G INFO General (graph_simplification.hpp : 404) All edges shorter than 320 will be removed 0:36:08.215 2G / 9G INFO General (graph_simplification.hpp : 405) Also edges shorter than 0 and coverage smaller than 0 will be removed 0:36:17.427 2G / 9G INFO General (graph_simplification.hpp : 687) Non parallel mode 0:36:42.156 2G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:38:04.414 2G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:38:13.697 1G / 9G INFO General (graph_simplification.hpp : 644) Using permanent iterators 0:38:13.697 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 1 0:38:14.197 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:38:15.361 1G / 9G INFO General (graph_simplification.hpp : 147) Removing bulges 0:38:43.204 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:38:43.212 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 2 0:38:43.212 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:38:43.225 1G / 9G INFO General (graph_simplification.hpp : 147) Removing bulges 0:38:43.226 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:38:43.416 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 3 0:38:43.417 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:38:43.418 1G / 9G INFO General (graph_simplification.hpp : 147) Removing bulges 0:38:43.452 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:38:43.640 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 4 0:38:43.641 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:38:43.643 1G / 9G INFO General (graph_simplification.hpp : 147) Removing bulges 0:38:43.872 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:38:44.020 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 5 0:38:44.020 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:38:44.022 1G / 9G INFO General (graph_simplification.hpp : 147) Removing bulges 0:38:44.169 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:38:44.266 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 6 0:38:44.266 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:38:44.267 1G / 9G INFO General (graph_simplification.hpp : 147) Removing bulges 0:38:44.319 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:38:44.389 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 7 0:38:44.389 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:38:44.391 1G / 9G INFO General (graph_simplification.hpp : 147) Removing bulges 0:38:44.436 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:38:44.492 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 8 0:38:44.492 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:38:44.493 1G / 9G INFO General (graph_simplification.hpp : 147) Removing bulges 0:38:44.519 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:38:44.562 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 9 0:38:44.562 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:38:44.563 1G / 9G INFO General (graph_simplification.hpp : 147) Removing bulges 0:38:44.575 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:38:44.604 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 10 0:38:44.604 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:38:44.604 1G / 9G INFO General (graph_simplification.hpp : 147) Removing bulges 0:38:44.627 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:38:44.638 1G / 9G INFO General (graph_simplification.hpp : 796) PROCEDURE == Post simplification 0:38:44.638 1G / 9G INFO General (graph_simplification.hpp : 644) Using permanent iterators 0:38:44.638 1G / 9G INFO General (graph_simplification.hpp : 806) Iteration 0 0:38:44.638 1G / 9G INFO General (graph_simplification.hpp : 247) Removal of relatively low covered connections disabled 0:38:44.705 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:38:44.804 1G / 9G INFO General (graph_simplification.hpp : 147) Removing bulges 0:38:44.873 1G / 9G INFO General (graph_simplification.hpp : 806) Iteration 1 0:38:44.873 1G / 9G INFO General (graph_simplification.hpp : 247) Removal of relatively low covered connections disabled 0:38:44.873 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:38:44.873 1G / 9G INFO General (graph_simplification.hpp : 147) Removing bulges 0:38:44.907 1G / 9G INFO StageManager (stage.cpp : 125) STAGE == Gap Closer 0:38:44.907 1G / 9G INFO General (graph_pack.hpp : 84) Index refill 0:38:44.908 1G / 9G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:38:44.908 1G / 9G INFO General (kmer_splitters.hpp : 289) Splitting kmer instances into 16 buckets. This might take a while. 0:38:44.908 1G / 9G INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:38:44.908 1G / 9G INFO General (kmer_splitters.hpp : 307) Memory available for splitting buffers: 32.8464 Gb 0:38:44.908 1G / 9G INFO General (kmer_splitters.hpp : 312) Using cell size of 1048576 0:38:48.339 2G / 9G INFO General (kmer_splitters.hpp : 325) Processed 7556 edges 0:38:51.890 2G / 9G INFO General (kmer_splitters.hpp : 325) Processed 15053 edges 0:38:55.111 2G / 9G INFO General (kmer_splitters.hpp : 325) Processed 22548 edges 0:38:58.849 2G / 9G INFO General (kmer_splitters.hpp : 325) Processed 30018 edges 0:39:01.498 2G / 9G INFO General (kmer_splitters.hpp : 325) Processed 36422 edges 0:39:01.498 2G / 9G INFO General (kmer_splitters.hpp : 330) Used 36422 sequences. 0:39:01.564 1G / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:39:30.654 1G / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 81320154 kmers in total. 0:39:30.654 1G / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:39:40.971 1G / 9G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:41:19.761 1G / 9G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:41:29.952 1G / 9G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 28131733 bytes occupied (2.7675 bits per kmer). 0:41:31.203 3G / 9G INFO General (edge_index_builders.hpp : 21) Collecting k-mer coverage information from graph, this takes a while. 0:44:04.999 3G / 9G INFO General (gap_closer.cpp : 157) Preparing shift maps 0:44:05.057 3G / 9G INFO General (gap_closer.cpp : 117) Processing paired reads (takes a while) 0:44:27.616 3G / 9G INFO General (gap_closer.cpp : 136) Used 2410472 paired reads 0:44:27.616 3G / 9G INFO General (gap_closer.cpp : 138) Merging paired indices 0:44:27.664 3G / 9G INFO GapCloser (gap_closer.cpp : 395) Closing short gaps 0:44:27.730 3G / 9G INFO GapCloser (gap_closer.cpp : 424) Closing short gaps complete: filled 0 gaps after checking 197 candidates 0:44:27.796 3G / 9G INFO General (gap_closer.cpp : 157) Preparing shift maps 0:44:27.842 3G / 9G INFO General (gap_closer.cpp : 117) Processing paired reads (takes a while) 0:44:43.457 3G / 9G INFO General (gap_closer.cpp : 136) Used 2060954 paired reads 0:44:43.458 3G / 9G INFO General (gap_closer.cpp : 138) Merging paired indices 0:44:43.496 3G / 9G INFO GapCloser (gap_closer.cpp : 395) Closing short gaps 0:44:43.563 3G / 9G INFO GapCloser (gap_closer.cpp : 424) Closing short gaps complete: filled 0 gaps after checking 250 candidates 0:44:43.626 3G / 9G INFO General (gap_closer.cpp : 157) Preparing shift maps 0:44:43.670 3G / 9G INFO General (gap_closer.cpp : 117) Processing paired reads (takes a while) 0:44:59.418 3G / 9G INFO General (gap_closer.cpp : 136) Used 2236672 paired reads 0:44:59.419 3G / 9G INFO General (gap_closer.cpp : 138) Merging paired indices 0:44:59.462 3G / 9G INFO GapCloser (gap_closer.cpp : 395) Closing short gaps 0:44:59.525 3G / 9G INFO GapCloser (gap_closer.cpp : 424) Closing short gaps complete: filled 0 gaps after checking 176 candidates 0:44:59.593 3G / 9G INFO General (gap_closer.cpp : 157) Preparing shift maps 0:44:59.638 3G / 9G INFO General (gap_closer.cpp : 117) Processing paired reads (takes a while) 0:45:26.147 3G / 9G INFO General (gap_closer.cpp : 136) Used 3625572 paired reads 0:45:26.147 3G / 9G INFO General (gap_closer.cpp : 138) Merging paired indices 0:45:26.207 3G / 9G INFO GapCloser (gap_closer.cpp : 395) Closing short gaps 0:45:26.281 3G / 9G INFO GapCloser (gap_closer.cpp : 424) Closing short gaps complete: filled 0 gaps after checking 323 candidates 0:45:26.337 3G / 9G INFO StageManager (stage.cpp : 125) STAGE == Simplification Cleanup 0:45:26.337 3G / 9G INFO General (graph_simplification.hpp : 403) Removing isolated edges 0:45:26.337 3G / 9G INFO General (graph_simplification.hpp : 404) All edges shorter than 320 will be removed 0:45:26.338 3G / 9G INFO General (graph_simplification.hpp : 405) Also edges shorter than 0 and coverage smaller than 2 will be removed 0:45:27.508 3G / 9G INFO General (simplification.cpp : 56) Removing all the edges having coverage 0 and less 0:45:27.594 3G / 9G INFO General (simplification.cpp : 68) Counting average coverage 0:45:27.603 3G / 9G INFO General (simplification.cpp : 71) Average coverage = 15.033 0:45:27.603 3G / 9G INFO StageManager (stage.cpp : 125) STAGE == Mismatch Correction 0:47:45.815 3G / 9G INFO General (mismatch_shall_not_pass.hp: 188) Finished collecting potential mismatches positions 0:48:16.357 3G / 9G INFO General (mismatch_shall_not_pass.hp: 291) All edges processed 0:48:16.400 3G / 9G INFO General (mismatch_correction.cpp : 18) Corrected 151 nucleotides 0:48:16.470 3G / 9G INFO StageManager (stage.cpp : 125) STAGE == Paired Information Counting 0:48:16.821 3G / 9G INFO General (pair_info_count.cpp : 150) Graph N50: 32920 0:48:16.841 3G / 9G INFO General (pair_info_count.cpp : 152) Estimating insert size for library #0 0:48:16.841 3G / 9G INFO General (pair_info_count.cpp : 31) Estimating insert size (takes a while) 0:48:16.852 3G / 9G INFO General (short_read_mapper.hpp : 81) Mapping mate-pair library, selecting sensitive read mapper with k=19 0:48:16.853 3G / 9G INFO General (edge_multi_index.hpp : 97) DeBruijnEdgeMultiIndex constructing 0:48:16.854 3G / 9G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:48:16.854 3G / 9G INFO General (kmer_splitters.hpp : 289) Splitting kmer instances into 16 buckets. This might take a while. 0:48:16.854 3G / 9G INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:48:16.854 3G / 9G INFO General (kmer_splitters.hpp : 307) Memory available for splitting buffers: 32.2539 Gb 0:48:16.854 3G / 9G INFO General (kmer_splitters.hpp : 312) Using cell size of 4194304 0:48:22.852 3G / 9G INFO General (kmer_splitters.hpp : 325) Processed 12275 edges 0:48:28.714 3G / 9G INFO General (kmer_splitters.hpp : 325) Processed 24525 edges 0:48:31.380 3G / 9G INFO General (kmer_splitters.hpp : 325) Processed 30145 edges 0:48:31.381 3G / 9G INFO General (kmer_splitters.hpp : 330) Used 30145 sequences. 0:48:31.444 3G / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:48:58.549 3G / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 146580848 kmers in total. 0:48:58.550 3G / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:49:03.077 3G / 9G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:52:24.273 3G / 9G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:52:28.812 3G / 9G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 50707839 bytes occupied (2.7675 bits per kmer). 0:52:30.884 6G / 9G INFO General (perfect_hash_map.hpp : 178) Arranging kmers in hash map order 0:53:38.886 6G / 9G INFO General (perfect_hash_map.hpp : 190) Done. Total swaps: 146580579 0:53:38.888 6G / 9G INFO General (edge_index_builders.hpp : 21) Collecting k-mer coverage information from graph, this takes a while. 1:01:06.967 11G / 11G INFO General (sequence_mapper_notifier.h: 81) Processed 80351 reads 1:01:30.015 11G / 11G INFO General (sequence_mapper_notifier.h: 81) Processed 160702 reads 1:01:41.204 11G / 11G INFO General (sequence_mapper_notifier.h: 81) Processed 241052 reads 1:01:42.281 11G / 11G INFO General (sequence_mapper_notifier.h: 81) Processed 321402 reads 1:02:06.471 11G / 11G INFO General (sequence_mapper_notifier.h: 81) Processed 562454 reads 1:02:33.372 11G / 11G INFO General (sequence_mapper_notifier.h: 81) Processed 1124905 reads 1:02:47.053 11G / 11G INFO General (sequence_mapper_notifier.h: 89) Processed 1285607 reads 1:02:47.053 11G / 11G INFO General (pair_info_count.cpp : 41) 271455 paired reads (21.1149% of all) aligned to long edges 1:02:47.070 11G / 11G INFO General (pair_info_count.cpp : 170) Estimated insert size for paired library #0 1:02:47.070 11G / 11G INFO General (pair_info_count.cpp : 175) Insert size = 3598.52, deviation = 832.959, left quantile = 2993, right quantile = 4559, read length = 320 1:02:47.070 11G / 11G INFO General (pair_info_count.cpp : 152) Estimating insert size for library #1 1:02:47.070 11G / 11G INFO General (pair_info_count.cpp : 31) Estimating insert size (takes a while) 1:02:47.079 11G / 11G INFO General (short_read_mapper.hpp : 91) Selecting usual mapper 1:02:55.634 11G / 11G INFO General (sequence_mapper_notifier.h: 81) Processed 75327 reads 1:02:55.665 11G / 11G INFO General (sequence_mapper_notifier.h: 81) Processed 150654 reads 1:02:55.688 11G / 11G INFO General (sequence_mapper_notifier.h: 81) Processed 225981 reads 1:02:55.714 11G / 11G INFO General (sequence_mapper_notifier.h: 81) Processed 301308 reads 1:02:56.825 11G / 11G INFO General (sequence_mapper_notifier.h: 81) Processed 527291 reads 1:02:58.758 11G / 11G INFO General (sequence_mapper_notifier.h: 81) Processed 1054582 reads 1:02:59.047 11G / 11G INFO General (sequence_mapper_notifier.h: 89) Processed 1205236 reads 1:02:59.047 11G / 11G INFO General (pair_info_count.cpp : 41) 559610 paired reads (46.4316% of all) aligned to long edges 1:02:59.056 11G / 11G INFO General (pair_info_count.cpp : 170) Estimated insert size for paired library #1 1:02:59.056 11G / 11G INFO General (pair_info_count.cpp : 175) Insert size = 457.419, deviation = 89.6779, left quantile = 349, right quantile = 578, read length = 320 1:02:59.056 11G / 11G INFO General (pair_info_count.cpp : 152) Estimating insert size for library #2 1:02:59.056 11G / 11G INFO General (pair_info_count.cpp : 31) Estimating insert size (takes a while) 1:02:59.064 11G / 11G INFO General (short_read_mapper.hpp : 91) Selecting usual mapper 1:03:05.827 11G / 11G INFO General (sequence_mapper_notifier.h: 81) Processed 64405 reads 1:03:05.838 11G / 11G INFO General (sequence_mapper_notifier.h: 81) Processed 128810 reads 1:03:05.876 11G / 11G INFO General (sequence_mapper_notifier.h: 81) Processed 193215 reads 1:03:05.918 11G / 11G INFO General (sequence_mapper_notifier.h: 81) Processed 322025 reads 1:03:06.360 11G / 11G INFO General (sequence_mapper_notifier.h: 81) Processed 579643 reads 1:03:06.486 11G / 11G INFO General (sequence_mapper_notifier.h: 89) Processed 1030477 reads 1:03:06.488 11G / 11G INFO General (pair_info_count.cpp : 41) 503702 paired reads (48.8805% of all) aligned to long edges 1:03:06.497 11G / 11G INFO General (pair_info_count.cpp : 170) Estimated insert size for paired library #2 1:03:06.497 11G / 11G INFO General (pair_info_count.cpp : 175) Insert size = 459.714, deviation = 91.0944, left quantile = 349, right quantile = 582, read length = 320 1:03:06.497 11G / 11G INFO General (pair_info_count.cpp : 152) Estimating insert size for library #3 1:03:06.497 11G / 11G INFO General (pair_info_count.cpp : 31) Estimating insert size (takes a while) 1:03:06.504 11G / 11G INFO General (short_read_mapper.hpp : 91) Selecting usual mapper 1:03:14.696 11G / 11G INFO General (sequence_mapper_notifier.h: 81) Processed 69896 reads 1:03:14.728 11G / 11G INFO General (sequence_mapper_notifier.h: 81) Processed 139792 reads 1:03:14.741 11G / 11G INFO General (sequence_mapper_notifier.h: 81) Processed 209688 reads 1:03:14.762 11G / 11G INFO General (sequence_mapper_notifier.h: 81) Processed 279584 reads 1:03:14.785 11G / 11G INFO General (sequence_mapper_notifier.h: 81) Processed 559168 reads 1:03:15.416 11G / 11G INFO General (sequence_mapper_notifier.h: 81) Processed 1118336 reads 1:03:15.416 11G / 11G INFO General (sequence_mapper_notifier.h: 89) Processed 1118336 reads 1:03:15.416 11G / 11G INFO General (pair_info_count.cpp : 41) 531703 paired reads (47.5441% of all) aligned to long edges 1:03:15.426 11G / 11G INFO General (pair_info_count.cpp : 170) Estimated insert size for paired library #3 1:03:15.426 11G / 11G INFO General (pair_info_count.cpp : 175) Insert size = 452.421, deviation = 87.3217, left quantile = 347, right quantile = 570, read length = 320 1:03:15.426 11G / 11G INFO General (pair_info_count.cpp : 152) Estimating insert size for library #4 1:03:15.426 11G / 11G INFO General (pair_info_count.cpp : 31) Estimating insert size (takes a while) 1:03:15.436 11G / 11G INFO General (short_read_mapper.hpp : 91) Selecting usual mapper 1:03:29.338 11G / 11G INFO General (sequence_mapper_notifier.h: 81) Processed 113299 reads 1:03:30.328 11G / 11G INFO General (sequence_mapper_notifier.h: 81) Processed 226598 reads 1:03:30.395 11G / 11G INFO General (sequence_mapper_notifier.h: 81) Processed 339897 reads 1:03:30.402 11G / 11G INFO General (sequence_mapper_notifier.h: 81) Processed 453196 reads 1:03:30.424 11G / 11G INFO General (sequence_mapper_notifier.h: 81) Processed 566495 reads 1:03:30.693 11G / 11G INFO General (sequence_mapper_notifier.h: 81) Processed 1132991 reads 1:03:32.294 11G / 11G INFO General (sequence_mapper_notifier.h: 89) Processed 1812786 reads 1:03:32.294 11G / 11G INFO General (pair_info_count.cpp : 41) 824141 paired reads (45.4627% of all) aligned to long edges 1:03:32.304 11G / 11G INFO General (pair_info_count.cpp : 170) Estimated insert size for paired library #4 1:03:32.304 11G / 11G INFO General (pair_info_count.cpp : 175) Insert size = 457.354, deviation = 89.684, left quantile = 349, right quantile = 578, read length = 320 1:03:32.304 11G / 11G INFO General (pair_info_count.cpp : 187) Mapping library #0 1:03:32.304 11G / 11G INFO General (pair_info_count.cpp : 189) Mapping paired reads (takes a while) 1:03:32.304 11G / 11G INFO General (pair_info_count.cpp : 73) Left insert size qauntile 2993, right insert size quantile 4559 1:03:32.313 11G / 11G INFO General (short_read_mapper.hpp : 81) Mapping mate-pair library, selecting sensitive read mapper with k=19 1:12:05.637 11G / 11G INFO General (sequence_mapper_notifier.h: 81) Processed 160702 reads 1:12:18.974 11G / 11G INFO General (sequence_mapper_notifier.h: 81) Processed 321402 reads 1:12:20.383 11G / 11G INFO General (sequence_mapper_notifier.h: 81) Processed 482102 reads 1:12:43.039 11G / 11G INFO General (sequence_mapper_notifier.h: 81) Processed 642804 reads 1:12:45.840 11G / 11G INFO General (sequence_mapper_notifier.h: 81) Processed 803506 reads 1:12:53.187 11G / 11G INFO General (sequence_mapper_notifier.h: 81) Processed 1124908 reads 1:14:03.156 11G / 11G INFO General (sequence_mapper_notifier.h: 81) Processed 2249810 reads 1:14:30.625 11G / 11G INFO General (sequence_mapper_notifier.h: 89) Processed 2571214 reads 1:14:30.637 11G / 11G INFO General (pair_info_count.cpp : 187) Mapping library #1 1:14:30.637 11G / 11G INFO General (pair_info_count.cpp : 189) Mapping paired reads (takes a while) 1:14:30.637 11G / 11G INFO General (pair_info_count.cpp : 73) Left insert size qauntile 349, right insert size quantile 578 1:14:30.647 11G / 11G INFO General (short_read_mapper.hpp : 91) Selecting usual mapper 1:14:48.010 13G / 13G INFO General (sequence_mapper_notifier.h: 81) Processed 150654 reads 1:14:48.660 13G / 13G INFO General (sequence_mapper_notifier.h: 81) Processed 301308 reads 1:14:49.337 13G / 13G INFO General (sequence_mapper_notifier.h: 81) Processed 451962 reads 1:14:50.000 13G / 13G INFO General (sequence_mapper_notifier.h: 81) Processed 602616 reads 1:14:50.695 13G / 13G INFO General (sequence_mapper_notifier.h: 81) Processed 753270 reads 1:14:52.192 13G / 13G INFO General (sequence_mapper_notifier.h: 81) Processed 1054580 reads 1:14:58.058 12G / 13G INFO General (sequence_mapper_notifier.h: 81) Processed 2109164 reads 1:15:00.763 11G / 13G INFO General (sequence_mapper_notifier.h: 89) Processed 2410472 reads 1:16:05.103 11G / 13G INFO General (split_graph_pair_info.hpp : 344) Threshold for paired information 0.0106357 1:16:06.608 11G / 13G INFO General (pair_info_count.cpp : 187) Mapping library #2 1:16:06.608 11G / 13G INFO General (pair_info_count.cpp : 189) Mapping paired reads (takes a while) 1:16:06.609 11G / 13G INFO General (pair_info_count.cpp : 73) Left insert size qauntile 349, right insert size quantile 582 1:16:06.619 11G / 13G INFO General (short_read_mapper.hpp : 91) Selecting usual mapper 1:16:20.334 13G / 13G INFO General (sequence_mapper_notifier.h: 81) Processed 128810 reads 1:16:20.926 13G / 13G INFO General (sequence_mapper_notifier.h: 81) Processed 257620 reads 1:16:21.525 13G / 13G INFO General (sequence_mapper_notifier.h: 81) Processed 386430 reads 1:16:22.107 13G / 13G INFO General (sequence_mapper_notifier.h: 81) Processed 515240 reads 1:16:22.733 13G / 13G INFO General (sequence_mapper_notifier.h: 81) Processed 644050 reads 1:16:25.505 12G / 13G INFO General (sequence_mapper_notifier.h: 81) Processed 1159290 reads 1:16:31.944 11G / 13G INFO General (sequence_mapper_notifier.h: 89) Processed 2060954 reads 1:17:27.284 11G / 13G INFO General (split_graph_pair_info.hpp : 344) Threshold for paired information 0.0104772 1:17:28.739 11G / 13G INFO General (pair_info_count.cpp : 187) Mapping library #3 1:17:28.739 11G / 13G INFO General (pair_info_count.cpp : 189) Mapping paired reads (takes a while) 1:17:28.739 11G / 13G INFO General (pair_info_count.cpp : 73) Left insert size qauntile 347, right insert size quantile 570 1:17:28.749 11G / 13G INFO General (short_read_mapper.hpp : 91) Selecting usual mapper 1:17:45.011 13G / 13G INFO General (sequence_mapper_notifier.h: 81) Processed 139792 reads 1:17:45.630 13G / 13G INFO General (sequence_mapper_notifier.h: 81) Processed 279584 reads 1:17:46.253 13G / 13G INFO General (sequence_mapper_notifier.h: 81) Processed 419376 reads 1:17:46.861 13G / 13G INFO General (sequence_mapper_notifier.h: 81) Processed 559168 reads 1:17:47.541 13G / 13G INFO General (sequence_mapper_notifier.h: 81) Processed 698960 reads 1:17:49.701 13G / 13G INFO General (sequence_mapper_notifier.h: 81) Processed 1118336 reads 1:17:56.303 12G / 13G INFO General (sequence_mapper_notifier.h: 81) Processed 2236672 reads 1:17:57.163 11G / 13G INFO General (sequence_mapper_notifier.h: 89) Processed 2236672 reads 1:18:57.029 11G / 13G INFO General (split_graph_pair_info.hpp : 344) Threshold for paired information 0.0105445 1:18:58.535 11G / 13G INFO General (pair_info_count.cpp : 187) Mapping library #4 1:18:58.535 11G / 13G INFO General (pair_info_count.cpp : 189) Mapping paired reads (takes a while) 1:18:58.535 11G / 13G INFO General (pair_info_count.cpp : 73) Left insert size qauntile 349, right insert size quantile 578 1:18:58.546 11G / 13G INFO General (short_read_mapper.hpp : 91) Selecting usual mapper 1:19:22.380 13G / 13G INFO General (sequence_mapper_notifier.h: 81) Processed 200000 reads 1:19:23.157 13G / 14G INFO General (sequence_mapper_notifier.h: 81) Processed 400000 reads 1:19:24.071 13G / 14G INFO General (sequence_mapper_notifier.h: 81) Processed 600000 reads 1:19:24.999 13G / 14G INFO General (sequence_mapper_notifier.h: 81) Processed 800000 reads 1:19:25.960 13G / 14G INFO General (sequence_mapper_notifier.h: 81) Processed 1000000 reads 1:19:26.985 13G / 14G INFO General (sequence_mapper_notifier.h: 81) Processed 1200000 reads 1:19:32.442 13G / 14G INFO General (sequence_mapper_notifier.h: 81) Processed 2200000 reads 1:19:43.368 12G / 14G INFO General (sequence_mapper_notifier.h: 89) Processed 3625572 reads 1:20:49.354 12G / 14G INFO General (split_graph_pair_info.hpp : 344) Threshold for paired information 0.0124612 1:22:25.438 3G / 14G INFO StageManager (stage.cpp : 125) STAGE == Distance Estimation 1:22:25.450 3G / 14G INFO General (distance_estimation.cpp : 234) Processing library #1 1:22:25.450 3G / 14G INFO General (distance_estimation.cpp : 136) Weight Filter Done 1:22:25.450 3G / 14G INFO DistanceEstimator (distance_estimation.hpp : 187) Using SIMPLE distance estimator 1:22:25.953 3G / 14G INFO DistanceEstimator (distance_estimation.hpp : 208) Merging maps 1:22:26.108 3G / 14G INFO General (distance_estimation.cpp : 38) Filtering info 1:22:26.284 3G / 14G INFO General (pair_info_filters.hpp : 354) Pruning the index 1:22:26.296 3G / 14G INFO General (distance_estimation.cpp : 184) Refining clustered pair information 1:22:26.306 3G / 14G INFO General (distance_estimation.cpp : 186) The refining of clustered pair information has been finished 1:22:26.306 3G / 14G INFO General (distance_estimation.cpp : 188) Filling paired information 1:22:26.432 3G / 14G INFO PairInfoImprover (pair_info_improver.hpp : 61) Paired info stats: missing = 5981; contradictional = 172 1:22:26.535 3G / 14G INFO PairInfoImprover (pair_info_improver.hpp : 61) Paired info stats: missing = 1317; contradictional = 0 1:22:26.535 3G / 14G INFO General (distance_estimation.cpp : 193) Filling scaffolding index 1:22:26.536 3G / 14G INFO DistanceEstimator (distance_estimation.hpp : 187) Using SMOOTHING distance estimator 1:22:27.393 3G / 14G INFO DistanceEstimator (distance_estimation.hpp : 208) Merging maps 1:22:27.396 3G / 14G INFO General (distance_estimation.cpp : 38) Filtering info 1:22:27.410 3G / 14G INFO General (pair_info_filters.hpp : 354) Pruning the index 1:22:27.451 3G / 14G INFO General (distance_estimation.cpp : 234) Processing library #2 1:22:27.451 3G / 14G INFO General (distance_estimation.cpp : 136) Weight Filter Done 1:22:27.451 3G / 14G INFO DistanceEstimator (distance_estimation.hpp : 187) Using SIMPLE distance estimator 1:22:27.906 3G / 14G INFO DistanceEstimator (distance_estimation.hpp : 208) Merging maps 1:22:28.051 3G / 14G INFO General (distance_estimation.cpp : 38) Filtering info 1:22:28.175 3G / 14G INFO General (pair_info_filters.hpp : 354) Pruning the index 1:22:28.188 3G / 14G INFO General (distance_estimation.cpp : 184) Refining clustered pair information 1:22:28.198 3G / 14G INFO General (distance_estimation.cpp : 186) The refining of clustered pair information has been finished 1:22:28.198 3G / 14G INFO General (distance_estimation.cpp : 188) Filling paired information 1:22:28.305 3G / 14G INFO PairInfoImprover (pair_info_improver.hpp : 61) Paired info stats: missing = 5825; contradictional = 192 1:22:28.404 3G / 14G INFO PairInfoImprover (pair_info_improver.hpp : 61) Paired info stats: missing = 1442; contradictional = 0 1:22:28.404 3G / 14G INFO General (distance_estimation.cpp : 193) Filling scaffolding index 1:22:28.404 3G / 14G INFO DistanceEstimator (distance_estimation.hpp : 187) Using SMOOTHING distance estimator 1:22:29.712 3G / 14G INFO DistanceEstimator (distance_estimation.hpp : 208) Merging maps 1:22:29.714 3G / 14G INFO General (distance_estimation.cpp : 38) Filtering info 1:22:29.729 3G / 14G INFO General (pair_info_filters.hpp : 354) Pruning the index 1:22:29.768 3G / 14G INFO General (distance_estimation.cpp : 234) Processing library #3 1:22:29.768 3G / 14G INFO General (distance_estimation.cpp : 136) Weight Filter Done 1:22:29.768 3G / 14G INFO DistanceEstimator (distance_estimation.hpp : 187) Using SIMPLE distance estimator 1:22:30.211 3G / 14G INFO DistanceEstimator (distance_estimation.hpp : 208) Merging maps 1:22:30.361 3G / 14G INFO General (distance_estimation.cpp : 38) Filtering info 1:22:30.510 3G / 14G INFO General (pair_info_filters.hpp : 354) Pruning the index 1:22:30.522 3G / 14G INFO General (distance_estimation.cpp : 184) Refining clustered pair information 1:22:30.532 3G / 14G INFO General (distance_estimation.cpp : 186) The refining of clustered pair information has been finished 1:22:30.532 3G / 14G INFO General (distance_estimation.cpp : 188) Filling paired information 1:22:30.650 3G / 14G INFO PairInfoImprover (pair_info_improver.hpp : 61) Paired info stats: missing = 7049; contradictional = 164 1:22:30.818 3G / 14G INFO PairInfoImprover (pair_info_improver.hpp : 61) Paired info stats: missing = 1779; contradictional = 0 1:22:30.818 3G / 14G INFO General (distance_estimation.cpp : 193) Filling scaffolding index 1:22:30.819 3G / 14G INFO DistanceEstimator (distance_estimation.hpp : 187) Using SMOOTHING distance estimator 1:22:31.709 3G / 14G INFO DistanceEstimator (distance_estimation.hpp : 208) Merging maps 1:22:31.712 3G / 14G INFO General (distance_estimation.cpp : 38) Filtering info 1:22:31.726 3G / 14G INFO General (pair_info_filters.hpp : 354) Pruning the index 1:22:31.774 3G / 14G INFO General (distance_estimation.cpp : 234) Processing library #4 1:22:31.774 3G / 14G INFO General (distance_estimation.cpp : 136) Weight Filter Done 1:22:31.774 3G / 14G INFO DistanceEstimator (distance_estimation.hpp : 187) Using SIMPLE distance estimator 1:22:32.355 3G / 14G INFO DistanceEstimator (distance_estimation.hpp : 208) Merging maps 1:22:32.525 3G / 14G INFO General (distance_estimation.cpp : 38) Filtering info 1:22:32.709 3G / 14G INFO General (pair_info_filters.hpp : 354) Pruning the index 1:22:32.721 3G / 14G INFO General (distance_estimation.cpp : 184) Refining clustered pair information 1:22:32.732 3G / 14G INFO General (distance_estimation.cpp : 186) The refining of clustered pair information has been finished 1:22:32.733 3G / 14G INFO General (distance_estimation.cpp : 188) Filling paired information 1:22:32.877 3G / 14G INFO PairInfoImprover (pair_info_improver.hpp : 61) Paired info stats: missing = 8254; contradictional = 268 1:22:33.226 3G / 14G INFO PairInfoImprover (pair_info_improver.hpp : 61) Paired info stats: missing = 1658; contradictional = 0 1:22:33.226 3G / 14G INFO General (distance_estimation.cpp : 193) Filling scaffolding index 1:22:33.226 3G / 14G INFO DistanceEstimator (distance_estimation.hpp : 187) Using SMOOTHING distance estimator 1:22:34.763 3G / 14G INFO DistanceEstimator (distance_estimation.hpp : 208) Merging maps 1:22:34.766 3G / 14G INFO General (distance_estimation.cpp : 38) Filtering info 1:22:34.780 3G / 14G INFO General (pair_info_filters.hpp : 354) Pruning the index 1:22:34.844 3G / 14G INFO StageManager (stage.cpp : 125) STAGE == Repeat Resolving 1:22:34.844 3G / 14G INFO General (contig_output.hpp : 283) Outputting contigs to /N/dc2/projects/marinovg/2015-01-29-P-assem/Paramecium_pentaurelia_strain_870-SPAdes-3.5.0-trimmed//K127/before_rr.fasta 1:23:10.900 3G / 14G INFO General (repeat_resolving.cpp : 59) Using Path-Extend repeat resolving 1:23:10.900 3G / 14G INFO General (path_extend_launch.hpp : 459) Threshold for library #1 is 0.0106357 1:23:10.900 3G / 14G INFO General (path_extend_launch.hpp : 459) Threshold for library #2 is 0.0104772 1:23:10.901 3G / 14G INFO General (path_extend_launch.hpp : 459) Threshold for library #3 is 0.0105445 1:23:10.901 3G / 14G INFO General (path_extend_launch.hpp : 459) Threshold for library #4 is 0.0124612 1:23:10.904 3G / 14G INFO General (path_extend_launch.hpp : 298) Path-Extend repeat resolving tool started 1:23:10.966 3G / 14G INFO General (path_extend_launch.hpp : 316) Using 4 paired-end libraries 1:23:10.966 3G / 14G INFO General (path_extend_launch.hpp : 317) Using 4 paired-end scaffolding libraries 1:23:10.966 3G / 14G INFO General (path_extend_launch.hpp : 318) Using 1 mate-pair library 1:23:10.966 3G / 14G INFO General (path_extend_launch.hpp : 319) Using 0 single read libraries 1:23:10.966 3G / 14G INFO General (path_extend_launch.hpp : 320) Scaffolder is on 1:23:11.127 3G / 14G INFO General (path_extend_launch.hpp : 332) Growing paths using paired-end and long single reads 1:23:11.127 3G / 14G INFO PathExtender (path_extender.hpp : 611) Processed 0 paths from 14854 (0%) 1:23:12.572 3G / 14G INFO PathExtender (path_extender.hpp : 609) Processed 128 paths from 14854 (0%) 1:23:13.483 3G / 14G INFO PathExtender (path_extender.hpp : 609) Processed 256 paths from 14854 (1%) 1:23:14.371 3G / 14G INFO PathExtender (path_extender.hpp : 609) Processed 512 paths from 14854 (3%) 1:23:16.294 3G / 14G INFO PathExtender (path_extender.hpp : 609) Processed 1024 paths from 14854 (6%) 1:23:17.117 3G / 14G INFO PathExtender (path_extender.hpp : 611) Processed 1486 paths from 14854 (10%) 1:23:17.636 3G / 14G INFO PathExtender (path_extender.hpp : 609) Processed 2048 paths from 14854 (13%) 1:23:18.356 3G / 14G INFO PathExtender (path_extender.hpp : 611) Processed 2972 paths from 14854 (20%) 1:23:18.749 3G / 14G INFO PathExtender (path_extender.hpp : 609) Processed 4096 paths from 14854 (27%) 1:23:18.828 3G / 14G INFO PathExtender (path_extender.hpp : 611) Processed 4458 paths from 14854 (30%) 1:23:19.101 3G / 14G INFO PathExtender (path_extender.hpp : 611) Processed 5944 paths from 14854 (40%) 1:23:19.364 3G / 14G INFO PathExtender (path_extender.hpp : 611) Processed 7430 paths from 14854 (50%) 1:23:19.455 3G / 14G INFO PathExtender (path_extender.hpp : 609) Processed 8192 paths from 14854 (55%) 1:23:19.522 3G / 14G INFO PathExtender (path_extender.hpp : 611) Processed 8916 paths from 14854 (60%) 1:23:19.697 3G / 14G INFO PathExtender (path_extender.hpp : 611) Processed 10402 paths from 14854 (70%) 1:23:19.880 3G / 14G INFO PathExtender (path_extender.hpp : 611) Processed 11888 paths from 14854 (80%) 1:23:20.625 3G / 14G INFO PathExtender (path_extender.hpp : 611) Processed 13374 paths from 14854 (90%) 1:23:21.587 3G / 14G INFO PathExtendIO (pe_io.hpp : 339) Constructing FASTG file from paths 1:23:21.836 3G / 14G INFO PathExtendIO (pe_io.hpp : 342) Writing contigs in FASTG to /N/dc2/projects/marinovg/2015-01-29-P-assem/Paramecium_pentaurelia_strain_870-SPAdes-3.5.0-trimmed//K127/pe_contigs.fastg 1:23:21.836 3G / 14G INFO PathExtendIO (pe_io.hpp : 343) Writing contigs in FASTA to /N/dc2/projects/marinovg/2015-01-29-P-assem/Paramecium_pentaurelia_strain_870-SPAdes-3.5.0-trimmed//K127/pe_contigs.fasta 1:23:56.951 3G / 14G INFO PathExtendIO (pe_io.hpp : 339) Constructing FASTG file from paths 1:23:57.203 3G / 14G INFO PathExtendIO (pe_io.hpp : 342) Writing contigs in FASTG to /N/dc2/projects/marinovg/2015-01-29-P-assem/Paramecium_pentaurelia_strain_870-SPAdes-3.5.0-trimmed//K127/path_extend/pe_before_traversal.fastg 1:23:57.203 3G / 14G INFO PathExtendIO (pe_io.hpp : 343) Writing contigs in FASTA to /N/dc2/projects/marinovg/2015-01-29-P-assem/Paramecium_pentaurelia_strain_870-SPAdes-3.5.0-trimmed//K127/path_extend/pe_before_traversal.fasta 1:24:32.328 3G / 14G INFO General (path_extend_launch.hpp : 281) Traversing tandem repeats 1:24:32.559 3G / 14G INFO PathExtendIO (pe_io.hpp : 339) Constructing FASTG file from paths 1:24:32.805 3G / 14G INFO PathExtendIO (pe_io.hpp : 342) Writing contigs in FASTG to /N/dc2/projects/marinovg/2015-01-29-P-assem/Paramecium_pentaurelia_strain_870-SPAdes-3.5.0-trimmed//K127/pe_scaffolds.fastg 1:24:32.805 3G / 14G INFO PathExtendIO (pe_io.hpp : 343) Writing contigs in FASTA to /N/dc2/projects/marinovg/2015-01-29-P-assem/Paramecium_pentaurelia_strain_870-SPAdes-3.5.0-trimmed//K127/pe_scaffolds.fasta 1:25:08.212 3G / 14G INFO General (path_extend_launch.hpp : 367) Adding mate-pairs 1:25:08.257 3G / 14G INFO General (path_extend_launch.hpp : 379) Growing paths using mate-pairs 1:25:08.288 3G / 14G INFO PathExtender (path_extender.hpp : 611) Processed 0 paths from 8996 (0%) 2:51:18.976 3G / 14G INFO PathExtender (path_extender.hpp : 609) Processed 128 paths from 8996 (1%) 3:54:01.701 3G / 14G INFO PathExtender (path_extender.hpp : 609) Processed 256 paths from 8996 (2%) 4:13:42.744 3G / 14G INFO PathExtender (path_extender.hpp : 609) Processed 512 paths from 8996 (5%) 5:51:26.169 3G / 14G INFO PathExtender (path_extender.hpp : 611) Processed 900 paths from 8996 (10%) 5:51:28.269 3G / 14G INFO PathExtender (path_extender.hpp : 609) Processed 1024 paths from 8996 (11%) 6:31:34.441 3G / 14G INFO PathExtender (path_extender.hpp : 611) Processed 1800 paths from 8996 (20%) 6:31:34.613 3G / 14G INFO PathExtender (path_extender.hpp : 609) Processed 2048 paths from 8996 (22%) 6:31:34.707 3G / 14G INFO PathExtender (path_extender.hpp : 611) Processed 2700 paths from 8996 (30%) 6:31:34.800 3G / 14G INFO PathExtender (path_extender.hpp : 611) Processed 3600 paths from 8996 (40%) 6:31:34.852 3G / 14G INFO PathExtender (path_extender.hpp : 609) Processed 4096 paths from 8996 (45%) 6:31:34.894 3G / 14G INFO PathExtender (path_extender.hpp : 611) Processed 4500 paths from 8996 (50%) 6:31:34.963 3G / 14G INFO PathExtender (path_extender.hpp : 611) Processed 5400 paths from 8996 (60%) 6:31:35.031 3G / 14G INFO PathExtender (path_extender.hpp : 611) Processed 6300 paths from 8996 (70%) 6:31:35.090 3G / 14G INFO PathExtender (path_extender.hpp : 611) Processed 7200 paths from 8996 (80%) 6:31:35.148 3G / 14G INFO PathExtender (path_extender.hpp : 611) Processed 8100 paths from 8996 (90%) 6:31:35.153 3G / 14G INFO PathExtender (path_extender.hpp : 609) Processed 8192 paths from 8996 (91%) 6:31:35.523 3G / 14G INFO PathExtendIO (pe_io.hpp : 339) Constructing FASTG file from paths 6:31:35.745 3G / 14G INFO PathExtendIO (pe_io.hpp : 342) Writing contigs in FASTG to /N/dc2/projects/marinovg/2015-01-29-P-assem/Paramecium_pentaurelia_strain_870-SPAdes-3.5.0-trimmed//K127/path_extend/mp_prefinal.fastg 6:31:35.745 3G / 14G INFO PathExtendIO (pe_io.hpp : 343) Writing contigs in FASTA to /N/dc2/projects/marinovg/2015-01-29-P-assem/Paramecium_pentaurelia_strain_870-SPAdes-3.5.0-trimmed//K127/path_extend/mp_prefinal.fasta 6:32:09.724 3G / 14G INFO PathExtender (path_extender.hpp : 611) Processed 0 paths from 9342 (0%) 6:32:10.028 3G / 14G INFO PathExtender (path_extender.hpp : 609) Processed 128 paths from 9342 (1%) 6:32:10.264 3G / 14G INFO PathExtender (path_extender.hpp : 609) Processed 256 paths from 9342 (2%) 6:32:10.569 3G / 14G INFO PathExtender (path_extender.hpp : 609) Processed 512 paths from 9342 (5%) 6:32:10.906 3G / 14G INFO PathExtender (path_extender.hpp : 611) Processed 935 paths from 9342 (10%) 6:32:10.936 3G / 14G INFO PathExtender (path_extender.hpp : 609) Processed 1024 paths from 9342 (10%) 6:32:11.082 3G / 14G INFO PathExtender (path_extender.hpp : 611) Processed 1870 paths from 9342 (20%) 6:32:11.098 3G / 14G INFO PathExtender (path_extender.hpp : 609) Processed 2048 paths from 9342 (21%) 6:32:11.186 3G / 14G INFO PathExtender (path_extender.hpp : 611) Processed 2805 paths from 9342 (30%) 6:32:11.264 3G / 14G INFO PathExtender (path_extender.hpp : 611) Processed 3740 paths from 9342 (40%) 6:32:11.295 3G / 14G INFO PathExtender (path_extender.hpp : 609) Processed 4096 paths from 9342 (43%) 6:32:11.348 3G / 14G INFO PathExtender (path_extender.hpp : 611) Processed 4675 paths from 9342 (50%) 6:32:11.430 3G / 14G INFO PathExtender (path_extender.hpp : 611) Processed 5610 paths from 9342 (60%) 6:32:11.508 3G / 14G INFO PathExtender (path_extender.hpp : 611) Processed 6545 paths from 9342 (70%) 6:32:11.571 3G / 14G INFO PathExtender (path_extender.hpp : 611) Processed 7480 paths from 9342 (80%) 6:32:11.632 3G / 14G INFO PathExtender (path_extender.hpp : 609) Processed 8192 paths from 9342 (87%) 6:32:11.642 3G / 14G INFO PathExtender (path_extender.hpp : 611) Processed 8415 paths from 9342 (90%) 6:32:12.110 3G / 14G INFO PathExtendIO (pe_io.hpp : 339) Constructing FASTG file from paths 6:32:12.327 3G / 14G INFO PathExtendIO (pe_io.hpp : 342) Writing contigs in FASTG to /N/dc2/projects/marinovg/2015-01-29-P-assem/Paramecium_pentaurelia_strain_870-SPAdes-3.5.0-trimmed//K127/path_extend/mp_before_traversal.fastg 6:32:12.327 3G / 14G INFO PathExtendIO (pe_io.hpp : 343) Writing contigs in FASTA to /N/dc2/projects/marinovg/2015-01-29-P-assem/Paramecium_pentaurelia_strain_870-SPAdes-3.5.0-trimmed//K127/path_extend/mp_before_traversal.fasta 6:32:47.617 3G / 14G INFO General (path_extend_launch.hpp : 281) Traversing tandem repeats 6:32:47.824 3G / 14G INFO PathExtendIO (pe_io.hpp : 339) Constructing FASTG file from paths 6:32:48.040 3G / 14G INFO PathExtendIO (pe_io.hpp : 342) Writing contigs in FASTG to /N/dc2/projects/marinovg/2015-01-29-P-assem/Paramecium_pentaurelia_strain_870-SPAdes-3.5.0-trimmed//K127/final_contigs.fastg 6:32:48.040 3G / 14G INFO PathExtendIO (pe_io.hpp : 343) Writing contigs in FASTA to /N/dc2/projects/marinovg/2015-01-29-P-assem/Paramecium_pentaurelia_strain_870-SPAdes-3.5.0-trimmed//K127/final_contigs.fasta 6:33:23.344 3G / 14G INFO PathExtendIO (pe_io.hpp : 339) Constructing FASTG file from paths 6:33:23.566 3G / 14G INFO PathExtendIO (pe_io.hpp : 342) Writing contigs in FASTG to /N/dc2/projects/marinovg/2015-01-29-P-assem/Paramecium_pentaurelia_strain_870-SPAdes-3.5.0-trimmed//K127/scaffolds.fastg 6:33:23.566 3G / 14G INFO PathExtendIO (pe_io.hpp : 343) Writing contigs in FASTA to /N/dc2/projects/marinovg/2015-01-29-P-assem/Paramecium_pentaurelia_strain_870-SPAdes-3.5.0-trimmed//K127/scaffolds.fasta 6:33:58.658 3G / 14G INFO General (path_extend_launch.hpp : 418) Path-Extend repeat resolving tool finished 6:34:00.144 3G / 14G INFO General (launch.hpp : 82) SPAdes finished 6:34:07.900 212M / 14G INFO General (main.cpp : 166) Assembling time: 6 hours 34 minutes 7 seconds ===== Assembling finished. * Corrected reads are in /N/dc2/projects/marinovg/2015-01-29-P-assem/Paramecium_pentaurelia_strain_870-SPAdes-3.5.0-trimmed/corrected/ * Assembled contigs are in /N/dc2/projects/marinovg/2015-01-29-P-assem/Paramecium_pentaurelia_strain_870-SPAdes-3.5.0-trimmed/contigs.fasta (contigs.fastg) * Assembled scaffolds are in /N/dc2/projects/marinovg/2015-01-29-P-assem/Paramecium_pentaurelia_strain_870-SPAdes-3.5.0-trimmed/scaffolds.fasta (scaffolds.fastg) ======= SPAdes pipeline finished WITH WARNINGS! === Pipeline warnings: * Default k-mer sizes were set to [21, 33, 55, 77, 99, 127] because estimated read length (320) is equal to or greater than 250 ======= Warnings saved to /N/dc2/projects/marinovg/2015-01-29-P-assem/Paramecium_pentaurelia_strain_870-SPAdes-3.5.0-trimmed/warnings.log SPAdes log can be found here: /N/dc2/projects/marinovg/2015-01-29-P-assem/Paramecium_pentaurelia_strain_870-SPAdes-3.5.0-trimmed/spades.log Thank you for using SPAdes!