Command line: --diploid --pe1-1 /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_Moz13BIII/reads.end1.paired.fastq.gz --pe1-2 /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_Moz13BIII/reads.end2.paired.fastq.gz -t 16 -o /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_Moz13BIII-dipSPAdes-3.5.0-trimmed/spades System information: SPAdes version: 3.5.0 Python version: 2.6.6 OS: Linux-2.6.32-573.3.1.el6.x86_64-x86_64-with-redhat-6.7-Santiago Output dir: /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_Moz13BIII-dipSPAdes-3.5.0-trimmed/spades Mode: read error correction and assembling Debug mode is turned OFF Dataset parameters: Multi-cell mode (you should set '--sc' flag if input data was obtained with MDA (single-cell) technology Reads: Library number: 1, library type: paired-end orientation: fr left reads: ['/N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_Moz13BIII/reads.end1.paired.fastq.gz'] right reads: ['/N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_Moz13BIII/reads.end2.paired.fastq.gz'] interlaced reads: not specified single reads: not specified Read error correction parameters: Iterations: 1 PHRED offset will be auto-detected Corrected reads will be compressed (with gzip) Assembly parameters: k: automatic selection based on read length Mismatch careful mode is turned OFF Repeat resolution is enabled MismatchCorrector will be SKIPPED Coverage cutoff is turned OFF Other parameters: Dir for temp files: /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_Moz13BIII-dipSPAdes-3.5.0-trimmed/spades/tmp Threads: 16 Memory limit (in Gb): 250 ======= SPAdes pipeline started. Log can be found here: /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_Moz13BIII-dipSPAdes-3.5.0-trimmed/spades/spades.log ===== Read error correction started. == Running read error correction tool: /N/dc2/projects/marinovg/programs/SPAdes-3.5.0-Linux/bin/hammer /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_Moz13BIII-dipSPAdes-3.5.0-trimmed/spades/corrected/configs/config.info 0:00:00.000 4M / 4M INFO General (main.cpp : 82) Loading config from /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_Moz13BIII-dipSPAdes-3.5.0-trimmed/spades/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 0:00:00.084 4M / 4M INFO General (main.cpp : 97) Determined value is 33 0:00:00.085 4M / 4M INFO General (hammer_tools.cpp : 36) Hamming graph threshold tau=1, k=21, subkmer positions = [ 0 10 ] === ITERATION 0 begins === 0:00:00.090 4M / 4M INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:00:00.105 4M / 4M INFO K-mer Splitting (kmer_data.cpp : 127) Splitting kmer instances into 256 buckets. This might take a while. 0:00:00.109 4M / 4M INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:00:00.109 4M / 4M INFO K-mer Splitting (kmer_data.cpp : 145) Memory available for splitting buffers: 2.08325 Gb 0:00:00.109 4M / 4M INFO K-mer Splitting (kmer_data.cpp : 153) Using cell size of 262144 0:00:02.893 8G / 8G INFO K-mer Splitting (kmer_data.cpp : 167) Processing /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_Moz13BIII/reads.end1.paired.fastq.gz 0:00:59.113 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 176) Processed 3239049 reads 0:02:02.384 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 176) Processed 6517183 reads 0:06:10.716 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 176) Processed 9634852 reads 0:06:10.717 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 167) Processing /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_Moz13BIII/reads.end2.paired.fastq.gz 0:09:58.041 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 176) Processed 13253244 reads 0:12:50.312 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 176) Processed 16692965 reads 0:13:34.116 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 176) Processed 19269704 reads 0:13:34.119 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 181) Processed 19269704 reads 0:13:35.277 64M / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:14:17.203 64M / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 261010840 kmers in total. 0:14:17.204 64M / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:14:56.108 64M / 9G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:15:30.274 192M / 9G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:15:45.115 192M / 9G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 90293469 bytes occupied (2.7675 bits per kmer). 0:15:45.120 192M / 9G INFO K-mer Counting (kmer_data.cpp : 266) Arranging kmers in hash map order 0:18:47.469 192M / 9G INFO K-mer Counting (kmer_data.cpp : 279) Done. Total swaps: 261010541 0:18:49.256 2G / 9G INFO General (main.cpp : 151) Clustering Hamming graph. 0:18:49.258 2G / 9G INFO Hamming Clustering (hamcluster.cpp : 115) Serializing sub-kmers. 0:18:49.258 2G / 9G INFO Hamming Clustering (hamcluster.cpp : 120) Serializing: [0, 10) 0:21:42.908 2G / 9G INFO Hamming Clustering (hamcluster.cpp : 120) Serializing: [10, 21) 0:24:36.848 2G / 9G INFO Hamming Clustering (hamcluster.cpp : 129) Splitting sub-kmers, pass 1. 0:28:10.197 2G / 9G INFO Hamming Clustering (hamcluster.cpp : 134) Splitting done. Processed 2 blocks. Produced 4856982 blocks. 0:28:10.198 2G / 9G INFO Hamming Clustering (hamcluster.cpp : 145) Merge sub-kmers, pass 1 0:42:31.641 2G / 9G INFO Hamming Clustering (hamcluster.cpp : 170) Merge done, total 1474543 new blocks generated. 0:42:33.296 2G / 9G INFO Hamming Clustering (hamcluster.cpp : 175) Spliting sub-kmers, pass 2. 0:58:16.489 2G / 9G INFO Hamming Clustering (hamcluster.cpp : 180) Splitting done. Processed 2949086 blocks. Produced 501371601 blocks. 0:58:16.490 2G / 9G INFO Hamming Clustering (hamcluster.cpp : 187) Merge sub-kmers, pass 2 1:08:28.251 2G / 9G INFO Hamming Clustering (hamcluster.cpp : 205) Merge done, saw 200655 big blocks out of 501371601 processed. 1:12:03.967 2G / 9G INFO General (main.cpp : 165) Clustering done. Total clusters: 127258808 1:12:03.967 2G / 9G INFO K-mer Counting (kmer_data.cpp : 284) Collecting K-mer information, this takes a while. 1:12:09.192 13G / 13G INFO K-mer Counting (kmer_data.cpp : 290) Processing /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_Moz13BIII/reads.end1.paired.fastq.gz 1:14:35.322 13G / 13G INFO K-mer Counting (kmer_data.cpp : 290) Processing /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_Moz13BIII/reads.end2.paired.fastq.gz 1:16:56.082 13G / 13G INFO K-mer Counting (kmer_data.cpp : 297) Collection done, postprocessing. 1:17:02.521 13G / 13G INFO K-mer Counting (kmer_data.cpp : 310) There are 261010840 kmers in total. Among them 116612250 (44.6772%) are singletons. 1:17:02.521 13G / 13G INFO General (main.cpp : 203) Subclustering Hamming graph 1:20:02.652 13G / 13G INFO Hamming Subclustering (kmer_cluster.cpp : 626) Subclustering done. Total 78547 non-read kmers were generated. 1:20:02.652 13G / 13G INFO Hamming Subclustering (kmer_cluster.cpp : 627) Subclustering statistics: 1:20:02.652 13G / 13G INFO Hamming Subclustering (kmer_cluster.cpp : 628) Total singleton hamming clusters: 73530524. Among them 58111897 (79.031%) are good 1:20:02.652 13G / 13G INFO Hamming Subclustering (kmer_cluster.cpp : 629) Total singleton subclusters: 8444074. Among them 8444043 (99.9996%) are good 1:20:02.652 13G / 13G INFO Hamming Subclustering (kmer_cluster.cpp : 630) Total non-singleton subcluster centers: 57555702. Among them 35850581 (62.2885%) are good 1:20:02.652 13G / 13G INFO Hamming Subclustering (kmer_cluster.cpp : 631) Average size of non-trivial subcluster: 3.2217 kmers 1:20:02.652 13G / 13G INFO Hamming Subclustering (kmer_cluster.cpp : 632) Average number of sub-clusters per non-singleton cluster: 1.2284 1:20:02.653 13G / 13G INFO Hamming Subclustering (kmer_cluster.cpp : 633) Total solid k-mers: 102406521 1:20:02.653 13G / 13G INFO Hamming Subclustering (kmer_cluster.cpp : 634) Substitution probabilities: [4,4]((0.900761,0.0223659,0.0248855,0.0519877),(0.0351612,0.929443,0.0126716,0.0227239),(0.0219115,0.0123543,0.930492,0.0352422),(0.0513928,0.0252167,0.0226932,0.900697)) 1:20:03.232 13G / 13G INFO General (main.cpp : 208) Finished clustering. 1:20:03.232 13G / 13G INFO General (main.cpp : 228) Starting solid k-mers expansion in 16 threads. 1:23:20.684 13G / 13G INFO General (main.cpp : 249) Solid k-mers iteration 0 produced 38962951 new k-mers. 1:26:35.108 13G / 13G INFO General (main.cpp : 249) Solid k-mers iteration 1 produced 1044839 new k-mers. 1:29:49.556 13G / 13G INFO General (main.cpp : 249) Solid k-mers iteration 2 produced 42183 new k-mers. 1:33:04.509 13G / 13G INFO General (main.cpp : 249) Solid k-mers iteration 3 produced 2545 new k-mers. 1:36:19.416 13G / 13G INFO General (main.cpp : 249) Solid k-mers iteration 4 produced 106 new k-mers. 1:39:35.475 13G / 13G INFO General (main.cpp : 249) Solid k-mers iteration 5 produced 2 new k-mers. 1:39:35.476 13G / 13G INFO General (main.cpp : 253) Solid k-mers finalized 1:39:35.476 13G / 13G INFO General (hammer_tools.cpp : 210) Starting read correction in 16 threads. 1:39:35.477 13G / 13G INFO General (hammer_tools.cpp : 222) Correcting pair of reads: /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_Moz13BIII/reads.end1.paired.fastq.gz and /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_Moz13BIII/reads.end2.paired.fastq.gz 1:40:00.987 15G / 15G INFO General (hammer_tools.cpp : 166) Prepared batch 0 of 1600000 reads. 1:40:24.153 15G / 15G INFO General (hammer_tools.cpp : 175) Processed batch 0 1:41:01.615 15G / 15G INFO General (hammer_tools.cpp : 185) Written batch 0 1:41:25.536 15G / 15G INFO General (hammer_tools.cpp : 166) Prepared batch 1 of 1600000 reads. 1:41:48.618 15G / 15G INFO General (hammer_tools.cpp : 175) Processed batch 1 1:42:04.514 15G / 15G INFO General (hammer_tools.cpp : 185) Written batch 1 1:42:28.115 15G / 15G INFO General (hammer_tools.cpp : 166) Prepared batch 2 of 1600000 reads. 1:42:51.425 15G / 15G INFO General (hammer_tools.cpp : 175) Processed batch 2 1:43:07.463 15G / 15G INFO General (hammer_tools.cpp : 185) Written batch 2 1:43:31.148 15G / 15G INFO General (hammer_tools.cpp : 166) Prepared batch 3 of 1600000 reads. 1:43:54.299 15G / 15G INFO General (hammer_tools.cpp : 175) Processed batch 3 1:44:09.691 15G / 15G INFO General (hammer_tools.cpp : 185) Written batch 3 1:44:33.466 15G / 15G INFO General (hammer_tools.cpp : 166) Prepared batch 4 of 1600000 reads. 1:44:56.176 15G / 15G INFO General (hammer_tools.cpp : 175) Processed batch 4 1:45:31.930 15G / 15G INFO General (hammer_tools.cpp : 185) Written batch 4 1:45:54.947 15G / 15G INFO General (hammer_tools.cpp : 166) Prepared batch 5 of 1600000 reads. 1:46:18.164 15G / 15G INFO General (hammer_tools.cpp : 175) Processed batch 5 1:46:33.582 15G / 15G INFO General (hammer_tools.cpp : 185) Written batch 5 1:46:34.086 15G / 15G INFO General (hammer_tools.cpp : 166) Prepared batch 6 of 34852 reads. 1:46:34.601 15G / 15G INFO General (hammer_tools.cpp : 175) Processed batch 6 1:46:34.942 15G / 15G INFO General (hammer_tools.cpp : 185) Written batch 6 1:46:37.495 13G / 15G INFO General (hammer_tools.cpp : 269) Correction done. Changed 3877161 bases in 3002396 reads. 1:46:37.495 13G / 15G INFO General (hammer_tools.cpp : 270) Failed to correct 392719898 bases out of 2858475801. 1:46:37.589 2G / 15G INFO General (main.cpp : 286) Saving corrected dataset description to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_Moz13BIII-dipSPAdes-3.5.0-trimmed/spades/corrected/corrected.yaml 1:46:37.603 2G / 15G INFO General (main.cpp : 293) All done. Exiting. == Compressing corrected reads (with gzip) == Dataset description file was created: /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_Moz13BIII-dipSPAdes-3.5.0-trimmed/spades/corrected/corrected.yaml ===== Read error correction finished. ===== Assembling started. == Running assembler: K21 0:00:00.000 4M / 4M INFO General (memory_limit.hpp : 42) Memory limit set to 100 Gb 0:00:00.005 4M / 4M INFO General (main.cpp : 146) Assembling dataset (/N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_Moz13BIII-dipSPAdes-3.5.0-trimmed/spades/dataset.info) with K=21 0:00:00.005 4M / 4M INFO General (launch.hpp : 28) SPAdes started 0:00:00.005 4M / 4M INFO General (launch.hpp : 29) Starting from stage: construction 0:00:00.010 4M / 4M INFO StageManager (stage.cpp : 125) STAGE == Construction 0:00:00.013 4M / 4M INFO General (read_converter.hpp : 79) Converting reads to binary format (takes a while) 0:00:00.013 4M / 4M INFO General (read_converter.hpp : 81) Paired reads for library #0 0:00:01.137 80M / 80M INFO General (binary_converter.hpp : 138) 16384 reads processed 0:00:01.539 96M / 96M INFO General (binary_converter.hpp : 138) 32768 reads processed 0:00:02.338 124M / 124M INFO General (binary_converter.hpp : 138) 65536 reads processed 0:00:03.943 184M / 184M INFO General (binary_converter.hpp : 138) 131072 reads processed 0:00:07.159 300M / 300M INFO General (binary_converter.hpp : 138) 262144 reads processed 0:00:13.604 536M / 536M INFO General (binary_converter.hpp : 138) 524288 reads processed 0:00:29.159 900M / 900M INFO General (binary_converter.hpp : 138) 1048576 reads processed 0:00:57.744 900M / 900M INFO General (binary_converter.hpp : 138) 2097152 reads processed 0:01:55.177 904M / 904M INFO General (binary_converter.hpp : 138) 4194304 reads processed 0:03:52.963 908M / 908M INFO General (binary_converter.hpp : 138) 8388608 reads processed 0:04:24.978 300M / 908M INFO General (binary_converter.hpp : 158) 9491029 reads written 0:04:25.317 4M / 908M INFO General (read_converter.hpp : 91) Single reads for library #0 0:04:27.164 140M / 908M INFO General (binary_converter.hpp : 138) 16384 reads processed 0:04:27.382 144M / 908M INFO General (binary_converter.hpp : 138) 32768 reads processed 0:04:27.770 160M / 908M INFO General (binary_converter.hpp : 138) 65536 reads processed 0:04:28.544 188M / 908M INFO General (binary_converter.hpp : 138) 131072 reads processed 0:04:28.919 192M / 908M INFO General (binary_converter.hpp : 158) 143735 reads written 0:04:29.101 4M / 908M INFO General (graph_construction.hpp : 129) Constructing DeBruijn graph for k=21 0:04:29.105 4M / 908M INFO General (kmer_splitters.hpp : 172) Splitting kmer instances into 256 buckets. This might take a while. 0:04:29.106 4M / 908M INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:04:29.106 4M / 908M INFO General (kmer_splitters.hpp : 190) Memory available for splitting buffers: 2.08325 Gb 0:04:29.106 4M / 908M INFO General (kmer_splitters.hpp : 199) Using cell size of 262144 0:05:28.330 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 16725516 reads 0:05:59.307 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 33439877 reads 0:08:14.198 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 38251586 reads 0:08:14.199 8G / 9G INFO General (kmer_splitters.hpp : 234) Adding contigs from previous K 0:08:14.200 8G / 9G INFO General (kmer_splitters.hpp : 245) Used 38251586 reads. Maximum read length 151 0:08:14.200 8G / 9G INFO General (kmer_splitters.hpp : 246) Average read length 149.412 0:08:16.452 64M / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:08:23.569 64M / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 109527873 kmers in total. 0:08:23.570 64M / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:08:29.431 64M / 9G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:08:29.431 64M / 9G INFO General (kmer_splitters.hpp : 379) Splitting kmer instances into 256 buckets. This might take a while. 0:08:29.432 64M / 9G INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:08:29.432 64M / 9G INFO General (kmer_splitters.hpp : 397) Memory available for splitting buffers: 2.08203 Gb 0:08:29.432 64M / 9G INFO General (kmer_splitters.hpp : 405) Using cell size of 262144 0:08:45.306 8G / 9G INFO General (kmer_splitters.hpp : 428) Processed 109527873 kmers 0:08:45.306 8G / 9G INFO General (kmer_splitters.hpp : 437) Used 109527873 kmers. 0:08:45.852 64M / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:08:49.549 64M / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 106964111 kmers in total. 0:08:49.549 64M / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:08:54.534 64M / 9G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:09:06.616 64M / 9G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:09:31.880 64M / 9G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 37002929 bytes occupied (2.7675 bits per kmer). 0:09:32.067 168M / 9G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 382) Building k-mer extensions from k+1-mers 0:09:45.482 168M / 9G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 386) Building k-mer extensions from k+1-mers finished. 0:09:45.494 168M / 9G INFO Early tip clipping (early_simplification.hpp : 236) Early tip clipping 0:15:08.210 168M / 9G INFO Early tip clipping (early_simplification.hpp : 239) 5411355 22-mers were removed by early tip clipper 0:15:08.210 168M / 9G INFO General (graph_construction.hpp : 145) Condensing graph 0:15:08.211 168M / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 337) Extracting unbranching paths 0:16:22.112 1G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 351) Extracting unbranching paths finished. 13614887 sequences extracted 0:16:31.142 1G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 311) Collecting perfect loops 0:17:03.818 1G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 326) Collecting perfect loops finished. 14 loops collected 0:17:13.190 2G / 9G INFO General (graph_construction.hpp : 150) Building index with from graph 0:17:13.196 2G / 9G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:17:13.196 2G / 9G INFO General (kmer_splitters.hpp : 289) Splitting kmer instances into 16 buckets. This might take a while. 0:17:13.196 2G / 9G INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:17:13.196 2G / 9G INFO General (kmer_splitters.hpp : 307) Memory available for splitting buffers: 32.4323 Gb 0:17:13.197 2G / 9G INFO General (kmer_splitters.hpp : 312) Using cell size of 4194304 0:18:40.966 3G / 9G INFO General (kmer_splitters.hpp : 325) Processed 8778389 edges 0:19:43.532 3G / 9G INFO General (kmer_splitters.hpp : 325) Processed 13614901 edges 0:19:43.532 3G / 9G INFO General (kmer_splitters.hpp : 330) Used 13614901 sequences. 0:19:43.595 2G / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:20:06.382 2G / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 104116518 kmers in total. 0:20:06.383 2G / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:20:10.417 2G / 9G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:22:33.529 2G / 9G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:22:37.784 2G / 9G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 36017849 bytes occupied (2.7675 bits per kmer). 0:22:39.633 5G / 9G INFO General (edge_index_builders.hpp : 21) Collecting k-mer coverage information from graph, this takes a while. 0:25:42.329 4G / 9G INFO General (graph_construction.hpp : 182) Filling coverage index 0:25:42.329 4G / 9G INFO General (edge_index_builders.hpp : 99) Collecting k-mer coverage information from reads, this takes a while. 0:28:53.932 4G / 9G INFO General (graph_construction.hpp : 184) Filling coverage and flanking coverage from index 0:29:20.121 4G / 9G INFO General (construction.cpp : 33) Figured out: read length = 151 0:29:20.138 4G / 9G INFO StageManager (stage.cpp : 125) STAGE == EC Threshold Finding 0:29:29.968 4G / 9G INFO General (kmer_coverage_model.cpp : 178) Kmer coverage valley at: 9 0:29:29.969 4G / 9G INFO General (kmer_coverage_model.cpp : 198) K-mer histogram maximum: 36 0:29:29.969 4G / 9G INFO General (kmer_coverage_model.cpp : 234) Estimated median coverage: 36. Coverage mad: 11.8608 0:29:29.969 4G / 9G INFO General (kmer_coverage_model.cpp : 261) Fitting coverage model 0:29:30.100 4G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 2 0:29:30.433 4G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 4 0:29:31.445 4G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 8 0:29:33.948 4G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 16 0:29:39.090 4G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 32 0:29:39.090 4G / 9G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 33.9906. Fitted coverage std. dev: 10.5467 0:29:39.093 4G / 9G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 0.309781 0:29:39.093 4G / 9G INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 18 0:29:39.093 4G / 9G INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 18 0:29:39.093 4G / 9G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 61869890 0:29:39.093 4G / 9G INFO General (genomic_info_filler.cpp : 103) Mean coverage was calculated as 33.9906 0:29:39.094 4G / 9G INFO General (genomic_info_filler.cpp : 117) EC coverage threshold value was calculated as 18 0:29:39.094 4G / 9G INFO General (genomic_info_filler.cpp : 118) Trusted kmer low bound: 0 0:29:39.094 4G / 9G INFO StageManager (stage.cpp : 125) STAGE == Simplification 0:29:39.337 2G / 9G INFO General (graph_simplification.hpp : 911) Graph simplification started 0:29:39.337 2G / 9G INFO General (graph_simplification.hpp : 924) Fast simplification mode enabled 0:29:39.337 2G / 9G INFO General (graph_simplification.hpp : 771) PROCEDURE == Presimplification 0:29:39.337 2G / 9G INFO General (graph_simplification.hpp : 211) Removing short low covered self-conjugate connections 0:29:40.144 2G / 9G INFO General (graph_simplification.hpp : 403) Removing isolated edges 0:29:40.148 2G / 9G INFO General (graph_simplification.hpp : 404) All edges shorter than 151 will be removed 0:29:40.148 2G / 9G INFO General (graph_simplification.hpp : 405) Also edges shorter than 0 and coverage smaller than 0 will be removed 0:29:41.211 2G / 9G INFO General (graph_simplification.hpp : 687) Non parallel mode 0:30:23.414 3G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:32:01.640 3G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:34:44.532 2G / 9G INFO General (graph_simplification.hpp : 644) Using permanent iterators 0:34:44.532 2G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 1 0:34:54.223 2G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:35:33.448 2G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:35:48.426 2G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 2 0:35:48.426 2G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:35:48.700 2G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:35:59.949 2G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 3 0:35:59.949 2G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:36:00.199 2G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:36:06.724 2G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 4 0:36:06.724 2G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:36:06.867 2G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:36:11.071 2G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 5 0:36:11.071 2G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:36:11.167 2G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:36:14.488 2G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 6 0:36:14.489 2G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:36:14.565 2G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:36:17.158 2G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 7 0:36:17.158 2G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:36:17.217 2G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:36:20.040 2G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 8 0:36:20.040 2G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:36:20.102 2G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:36:22.791 2G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 9 0:36:22.791 2G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:36:22.849 2G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:36:25.375 2G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 10 0:36:25.375 2G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:36:25.427 2G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:36:27.790 2G / 9G INFO General (graph_simplification.hpp : 796) PROCEDURE == Post simplification 0:36:27.791 2G / 9G INFO General (graph_simplification.hpp : 644) Using permanent iterators 0:36:27.791 2G / 9G INFO General (graph_simplification.hpp : 806) Iteration 0 0:36:27.791 2G / 9G INFO General (graph_simplification.hpp : 247) Removal of relatively low covered connections disabled 0:36:31.514 2G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:36:39.989 2G / 9G INFO General (graph_simplification.hpp : 806) Iteration 1 0:36:39.989 2G / 9G INFO General (graph_simplification.hpp : 247) Removal of relatively low covered connections disabled 0:36:39.989 2G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:36:42.318 2G / 9G INFO StageManager (stage.cpp : 125) STAGE == Simplification Cleanup 0:36:42.322 2G / 9G INFO General (graph_simplification.hpp : 403) Removing isolated edges 0:36:42.322 2G / 9G INFO General (graph_simplification.hpp : 404) All edges shorter than 151 will be removed 0:36:42.322 2G / 9G INFO General (graph_simplification.hpp : 405) Also edges shorter than 0 and coverage smaller than 2 will be removed 0:36:42.529 2G / 9G INFO General (simplification.cpp : 56) Removing all the edges having coverage 0 and less 0:36:49.400 2G / 9G INFO General (simplification.cpp : 68) Counting average coverage 0:36:50.159 2G / 9G INFO General (simplification.cpp : 71) Average coverage = 36.3761 0:36:50.160 2G / 9G INFO StageManager (stage.cpp : 125) STAGE == Contig Output 0:36:50.160 2G / 9G INFO General (contig_output.hpp : 283) Outputting contigs to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_Moz13BIII-dipSPAdes-3.5.0-trimmed/spades//K21/simplified_contigs.fasta 0:37:37.805 2G / 9G INFO General (contig_output.hpp : 283) Outputting contigs to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_Moz13BIII-dipSPAdes-3.5.0-trimmed/spades//K21/before_rr.fasta 0:39:48.015 2G / 9G INFO General (contig_output.hpp : 283) Outputting contigs to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_Moz13BIII-dipSPAdes-3.5.0-trimmed/spades//K21/final_contigs.fasta 0:41:58.535 2G / 9G INFO General (launch.hpp : 82) SPAdes finished 0:42:06.263 64M / 9G INFO General (main.cpp : 166) Assembling time: 0 hours 42 minutes 6 seconds == Warning == Default k-mer sizes were set to [21, 33, 55, 77] because estimated read length (151) is equal to or greater than 150 == Running assembler: K33 0:00:00.000 4M / 4M INFO General (memory_limit.hpp : 42) Memory limit set to 100 Gb 0:00:00.001 4M / 4M INFO General (main.cpp : 146) Assembling dataset (/N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_Moz13BIII-dipSPAdes-3.5.0-trimmed/spades/dataset.info) with K=33 0:00:00.001 4M / 4M INFO General (launch.hpp : 28) SPAdes started 0:00:00.001 4M / 4M INFO General (launch.hpp : 29) Starting from stage: construction 0:00:00.003 4M / 4M INFO StageManager (stage.cpp : 125) STAGE == Construction 0:00:00.003 4M / 4M INFO General (construction.cpp : 44) Contigs from previous K will be used 0:00:00.008 4M / 4M INFO General (read_converter.hpp : 49) Binary reads detected 0:00:00.029 4M / 4M INFO General (graph_construction.hpp : 129) Constructing DeBruijn graph for k=33 0:00:00.031 4M / 4M INFO General (kmer_splitters.hpp : 172) Splitting kmer instances into 256 buckets. This might take a while. 0:00:00.032 4M / 4M INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:00:00.032 4M / 4M INFO General (kmer_splitters.hpp : 190) Memory available for splitting buffers: 2.08325 Gb 0:00:00.032 4M / 4M INFO General (kmer_splitters.hpp : 199) Using cell size of 131072 0:00:53.378 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 9222361 reads 0:01:47.793 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 18448296 reads 0:04:35.265 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 27670900 reads 0:05:07.121 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 36877154 reads 0:05:11.076 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 38251586 reads 0:05:11.076 8G / 9G INFO General (kmer_splitters.hpp : 234) Adding contigs from previous K 0:05:31.469 8G / 9G INFO General (kmer_splitters.hpp : 245) Used 38251586 reads. Maximum read length 151 0:05:31.469 8G / 9G INFO General (kmer_splitters.hpp : 246) Average read length 149.412 0:05:33.726 64M / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:05:53.672 64M / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 125444684 kmers in total. 0:05:53.672 64M / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:06:06.448 64M / 9G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:06:06.449 64M / 9G INFO General (kmer_splitters.hpp : 379) Splitting kmer instances into 256 buckets. This might take a while. 0:06:06.449 64M / 9G INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:06:06.449 64M / 9G INFO General (kmer_splitters.hpp : 397) Memory available for splitting buffers: 2.08203 Gb 0:06:06.449 64M / 9G INFO General (kmer_splitters.hpp : 405) Using cell size of 131072 0:06:28.080 8G / 9G INFO General (kmer_splitters.hpp : 428) Processed 125444684 kmers 0:06:28.080 8G / 9G INFO General (kmer_splitters.hpp : 437) Used 125444684 kmers. 0:06:28.911 64M / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:06:37.105 64M / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 124456598 kmers in total. 0:06:37.106 64M / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:06:47.820 64M / 9G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:07:02.562 68M / 9G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:07:16.656 68M / 9G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 43054247 bytes occupied (2.7675 bits per kmer). 0:07:16.851 188M / 9G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 382) Building k-mer extensions from k+1-mers 0:07:33.058 188M / 9G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 386) Building k-mer extensions from k+1-mers finished. 0:07:33.069 188M / 9G INFO Early tip clipping (early_simplification.hpp : 236) Early tip clipping 0:14:46.034 184M / 9G INFO Early tip clipping (early_simplification.hpp : 239) 19210047 34-mers were removed by early tip clipper 0:14:46.034 184M / 9G INFO General (graph_construction.hpp : 145) Condensing graph 0:14:46.034 184M / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 337) Extracting unbranching paths 0:16:18.209 784M / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 351) Extracting unbranching paths finished. 6133900 sequences extracted 0:16:28.563 780M / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 311) Collecting perfect loops 0:17:21.074 780M / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 326) Collecting perfect loops finished. 69 loops collected 0:17:25.592 1G / 9G INFO General (graph_construction.hpp : 150) Building index with from graph 0:17:25.599 1G / 9G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:17:25.599 1G / 9G INFO General (kmer_splitters.hpp : 289) Splitting kmer instances into 16 buckets. This might take a while. 0:17:25.599 1G / 9G INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:17:25.599 1G / 9G INFO General (kmer_splitters.hpp : 307) Memory available for splitting buffers: 32.8672 Gb 0:17:25.599 1G / 9G INFO General (kmer_splitters.hpp : 312) Using cell size of 2097152 0:17:33.787 1G / 9G INFO General (kmer_splitters.hpp : 325) Processed 1938232 edges 0:17:41.717 1G / 9G INFO General (kmer_splitters.hpp : 325) Processed 3875891 edges 0:17:49.529 1G / 9G INFO General (kmer_splitters.hpp : 325) Processed 5811433 edges 0:17:50.904 1G / 9G INFO General (kmer_splitters.hpp : 325) Processed 6133969 edges 0:17:50.905 1G / 9G INFO General (kmer_splitters.hpp : 330) Used 6133969 sequences. 0:17:50.957 1G / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:18:23.486 1G / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 106234636 kmers in total. 0:18:23.486 1G / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:18:32.929 1G / 9G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:20:52.323 1G / 9G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:21:04.605 1G / 9G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 36750591 bytes occupied (2.7675 bits per kmer). 0:21:06.554 3G / 9G INFO General (edge_index_builders.hpp : 21) Collecting k-mer coverage information from graph, this takes a while. 0:24:37.801 3G / 9G INFO General (graph_construction.hpp : 182) Filling coverage index 0:24:37.802 3G / 9G INFO General (edge_index_builders.hpp : 99) Collecting k-mer coverage information from reads, this takes a while. 0:27:32.691 3G / 9G INFO General (graph_construction.hpp : 184) Filling coverage and flanking coverage from index 0:28:01.125 3G / 9G INFO General (construction.cpp : 33) Figured out: read length = 151 0:28:01.147 3G / 9G INFO StageManager (stage.cpp : 125) STAGE == EC Threshold Finding 0:28:09.710 3G / 9G INFO General (kmer_coverage_model.cpp : 178) Kmer coverage valley at: 8 0:28:09.710 3G / 9G INFO General (kmer_coverage_model.cpp : 198) K-mer histogram maximum: 32 0:28:09.711 3G / 9G INFO General (kmer_coverage_model.cpp : 234) Estimated median coverage: 32. Coverage mad: 10.3782 0:28:09.711 3G / 9G INFO General (kmer_coverage_model.cpp : 261) Fitting coverage model 0:28:09.833 3G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 2 0:28:10.137 3G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 4 0:28:11.063 3G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 8 0:28:13.331 3G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 16 0:28:17.852 3G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 32 0:28:17.852 3G / 9G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 30.4065. Fitted coverage std. dev: 9.93414 0:28:17.855 3G / 9G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 0.287261 0:28:17.855 3G / 9G INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 16 0:28:17.855 3G / 9G INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 16 0:28:17.855 3G / 9G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 62565197 0:28:17.855 3G / 9G INFO General (genomic_info_filler.cpp : 103) Mean coverage was calculated as 30.4065 0:28:17.856 3G / 9G INFO General (genomic_info_filler.cpp : 117) EC coverage threshold value was calculated as 16 0:28:17.856 3G / 9G INFO General (genomic_info_filler.cpp : 118) Trusted kmer low bound: 0 0:28:17.856 3G / 9G INFO StageManager (stage.cpp : 125) STAGE == Simplification 0:28:18.082 1G / 9G INFO General (graph_simplification.hpp : 911) Graph simplification started 0:28:18.082 1G / 9G INFO General (graph_simplification.hpp : 924) Fast simplification mode enabled 0:28:18.082 1G / 9G INFO General (graph_simplification.hpp : 771) PROCEDURE == Presimplification 0:28:18.082 1G / 9G INFO General (graph_simplification.hpp : 211) Removing short low covered self-conjugate connections 0:28:18.500 1G / 9G INFO General (graph_simplification.hpp : 403) Removing isolated edges 0:28:18.501 1G / 9G INFO General (graph_simplification.hpp : 404) All edges shorter than 151 will be removed 0:28:18.501 1G / 9G INFO General (graph_simplification.hpp : 405) Also edges shorter than 0 and coverage smaller than 0 will be removed 0:28:19.766 1G / 9G INFO General (graph_simplification.hpp : 687) Non parallel mode 0:28:39.014 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:29:27.405 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:30:53.331 1G / 9G INFO General (graph_simplification.hpp : 644) Using permanent iterators 0:30:53.332 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 1 0:30:55.909 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:31:07.856 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:31:18.338 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 2 0:31:18.338 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:31:18.430 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:31:22.448 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 3 0:31:22.448 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:31:22.508 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:31:25.372 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 4 0:31:25.372 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:31:25.410 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:31:27.545 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 5 0:31:27.546 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:31:27.571 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:31:29.203 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 6 0:31:29.203 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:31:29.221 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:31:30.580 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 7 0:31:30.580 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:31:30.592 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:31:32.006 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 8 0:31:32.006 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:31:32.016 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:31:33.361 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 9 0:31:33.361 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:31:33.370 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:31:34.586 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 10 0:31:34.586 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:31:34.593 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:31:35.661 1G / 9G INFO General (graph_simplification.hpp : 796) PROCEDURE == Post simplification 0:31:35.661 1G / 9G INFO General (graph_simplification.hpp : 644) Using permanent iterators 0:31:35.662 1G / 9G INFO General (graph_simplification.hpp : 806) Iteration 0 0:31:35.662 1G / 9G INFO General (graph_simplification.hpp : 247) Removal of relatively low covered connections disabled 0:31:36.150 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:31:37.451 1G / 9G INFO General (graph_simplification.hpp : 806) Iteration 1 0:31:37.451 1G / 9G INFO General (graph_simplification.hpp : 247) Removal of relatively low covered connections disabled 0:31:37.451 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:31:37.852 1G / 9G INFO StageManager (stage.cpp : 125) STAGE == Simplification Cleanup 0:31:37.855 1G / 9G INFO General (graph_simplification.hpp : 403) Removing isolated edges 0:31:37.855 1G / 9G INFO General (graph_simplification.hpp : 404) All edges shorter than 151 will be removed 0:31:37.855 1G / 9G INFO General (graph_simplification.hpp : 405) Also edges shorter than 0 and coverage smaller than 2 will be removed 0:31:37.902 1G / 9G INFO General (simplification.cpp : 56) Removing all the edges having coverage 0 and less 0:31:39.008 1G / 9G INFO General (simplification.cpp : 68) Counting average coverage 0:31:39.160 1G / 9G INFO General (simplification.cpp : 71) Average coverage = 30.5617 0:31:39.161 1G / 9G INFO StageManager (stage.cpp : 125) STAGE == Contig Output 0:31:39.161 1G / 9G INFO General (contig_output.hpp : 283) Outputting contigs to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_Moz13BIII-dipSPAdes-3.5.0-trimmed/spades//K33/simplified_contigs.fasta 0:32:00.393 1G / 9G INFO General (contig_output.hpp : 283) Outputting contigs to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_Moz13BIII-dipSPAdes-3.5.0-trimmed/spades//K33/before_rr.fasta 0:33:00.055 1G / 9G INFO General (contig_output.hpp : 283) Outputting contigs to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_Moz13BIII-dipSPAdes-3.5.0-trimmed/spades//K33/final_contigs.fasta 0:33:58.855 1G / 9G INFO General (launch.hpp : 82) SPAdes finished 0:34:01.888 64M / 9G INFO General (main.cpp : 166) Assembling time: 0 hours 34 minutes 1 seconds == Running assembler: K55 0:00:00.000 4M / 4M INFO General (memory_limit.hpp : 42) Memory limit set to 100 Gb 0:00:00.001 4M / 4M INFO General (main.cpp : 146) Assembling dataset (/N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_Moz13BIII-dipSPAdes-3.5.0-trimmed/spades/dataset.info) with K=55 0:00:00.001 4M / 4M INFO General (launch.hpp : 28) SPAdes started 0:00:00.001 4M / 4M INFO General (launch.hpp : 29) Starting from stage: construction 0:00:00.003 4M / 4M INFO General (launch.hpp : 44) Will need read mapping, kmer mapper will be attached 0:00:00.003 4M / 4M INFO StageManager (stage.cpp : 125) STAGE == Construction 0:00:00.003 4M / 4M INFO General (construction.cpp : 44) Contigs from previous K will be used 0:00:00.008 4M / 4M INFO General (read_converter.hpp : 49) Binary reads detected 0:00:00.037 4M / 4M INFO General (graph_construction.hpp : 129) Constructing DeBruijn graph for k=55 0:00:00.040 4M / 4M INFO General (kmer_splitters.hpp : 172) Splitting kmer instances into 256 buckets. This might take a while. 0:00:00.041 4M / 4M INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:00:00.041 4M / 4M INFO General (kmer_splitters.hpp : 190) Memory available for splitting buffers: 2.08325 Gb 0:00:00.041 4M / 4M INFO General (kmer_splitters.hpp : 199) Using cell size of 131072 0:01:12.523 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 11368440 reads 0:04:53.082 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 22730984 reads 0:05:11.909 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 34087464 reads 0:06:11.968 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 38251586 reads 0:06:11.969 8G / 9G INFO General (kmer_splitters.hpp : 234) Adding contigs from previous K 0:06:30.059 8G / 9G INFO General (kmer_splitters.hpp : 245) Used 38251586 reads. Maximum read length 151 0:06:30.059 8G / 9G INFO General (kmer_splitters.hpp : 246) Average read length 149.412 0:06:32.331 64M / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:06:52.703 64M / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 139109854 kmers in total. 0:06:52.704 64M / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:07:05.906 64M / 9G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:07:05.906 64M / 9G INFO General (kmer_splitters.hpp : 379) Splitting kmer instances into 256 buckets. This might take a while. 0:07:05.907 64M / 9G INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:07:05.907 64M / 9G INFO General (kmer_splitters.hpp : 397) Memory available for splitting buffers: 2.08203 Gb 0:07:05.907 64M / 9G INFO General (kmer_splitters.hpp : 405) Using cell size of 131072 0:07:31.385 8G / 9G INFO General (kmer_splitters.hpp : 428) Processed 139109854 kmers 0:07:31.386 8G / 9G INFO General (kmer_splitters.hpp : 437) Used 139109854 kmers. 0:07:32.293 64M / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:07:41.689 64M / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 138780726 kmers in total. 0:07:41.689 64M / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:08:54.738 64M / 9G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:09:12.540 68M / 9G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:09:27.902 68M / 9G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 48009488 bytes occupied (2.7675 bits per kmer). 0:09:28.154 204M / 9G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 382) Building k-mer extensions from k+1-mers 0:09:49.321 204M / 9G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 386) Building k-mer extensions from k+1-mers finished. 0:09:49.330 204M / 9G INFO General (graph_construction.hpp : 145) Condensing graph 0:09:49.330 204M / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 337) Extracting unbranching paths 0:11:28.219 1G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 351) Extracting unbranching paths finished. 8154670 sequences extracted 0:11:42.742 1G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 311) Collecting perfect loops 0:12:45.839 1G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 326) Collecting perfect loops finished. 2 loops collected 0:12:53.518 2G / 9G INFO General (graph_construction.hpp : 150) Building index with from graph 0:12:53.522 2G / 9G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:12:53.523 2G / 9G INFO General (kmer_splitters.hpp : 289) Splitting kmer instances into 16 buckets. This might take a while. 0:12:53.523 2G / 9G INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:12:53.523 2G / 9G INFO General (kmer_splitters.hpp : 307) Memory available for splitting buffers: 32.6576 Gb 0:12:53.523 2G / 9G INFO General (kmer_splitters.hpp : 312) Using cell size of 2097152 0:13:22.329 2G / 9G INFO General (kmer_splitters.hpp : 325) Processed 1967610 edges 0:14:31.318 2G / 9G INFO General (kmer_splitters.hpp : 325) Processed 3934943 edges 0:16:23.333 2G / 9G INFO General (kmer_splitters.hpp : 325) Processed 5900801 edges 0:17:36.553 2G / 9G INFO General (kmer_splitters.hpp : 325) Processed 7867785 edges 0:17:37.835 2G / 9G INFO General (kmer_splitters.hpp : 325) Processed 8154672 edges 0:17:37.836 2G / 9G INFO General (kmer_splitters.hpp : 330) Used 8154672 sequences. 0:17:37.886 2G / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:18:21.987 2G / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 139109854 kmers in total. 0:18:21.987 2G / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:18:36.612 2G / 9G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:21:34.694 2G / 9G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:21:52.985 2G / 9G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 48123352 bytes occupied (2.7675 bits per kmer). 0:21:55.473 5G / 9G INFO General (edge_index_builders.hpp : 21) Collecting k-mer coverage information from graph, this takes a while. 0:26:27.950 5G / 9G INFO General (graph_construction.hpp : 182) Filling coverage index 0:26:27.951 5G / 9G INFO General (edge_index_builders.hpp : 99) Collecting k-mer coverage information from reads, this takes a while. 0:29:05.370 5G / 9G INFO General (graph_construction.hpp : 184) Filling coverage and flanking coverage from index 0:29:40.180 5G / 9G INFO General (construction.cpp : 33) Figured out: read length = 151 0:29:40.201 5G / 9G INFO StageManager (stage.cpp : 125) STAGE == EC Threshold Finding 0:29:50.340 5G / 9G INFO General (kmer_coverage_model.cpp : 178) Kmer coverage valley at: 6 0:29:50.341 5G / 9G INFO General (kmer_coverage_model.cpp : 198) K-mer histogram maximum: 25 0:29:50.341 5G / 9G INFO General (kmer_coverage_model.cpp : 234) Estimated median coverage: 25. Coverage mad: 8.8956 0:29:50.341 5G / 9G INFO General (kmer_coverage_model.cpp : 261) Fitting coverage model 0:29:50.428 5G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 2 0:29:50.663 5G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 4 0:29:51.474 5G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 8 0:29:52.843 5G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 16 0:29:54.752 5G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 32 0:29:54.977 5G / 9G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 24.529. Fitted coverage std. dev: 8.31308 0:29:54.979 5G / 9G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 0.42331 0:29:54.979 5G / 9G INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 14 0:29:54.979 5G / 9G INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 14 0:29:54.979 5G / 9G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 61022524 0:29:54.979 5G / 9G INFO General (genomic_info_filler.cpp : 103) Mean coverage was calculated as 24.529 0:29:54.979 5G / 9G INFO General (genomic_info_filler.cpp : 117) EC coverage threshold value was calculated as 14 0:29:54.980 5G / 9G INFO General (genomic_info_filler.cpp : 118) Trusted kmer low bound: 0 0:29:54.980 5G / 9G INFO StageManager (stage.cpp : 125) STAGE == Gap Closer 0:29:54.996 5G / 9G INFO General (gap_closer.cpp : 157) Preparing shift maps 0:30:03.093 5G / 9G INFO General (gap_closer.cpp : 117) Processing paired reads (takes a while) 0:30:33.227 5G / 9G INFO General (gap_closer.cpp : 136) Used 18982058 paired reads 0:30:33.227 5G / 9G INFO General (gap_closer.cpp : 138) Merging paired indices 0:30:35.876 5G / 9G INFO GapCloser (gap_closer.cpp : 395) Closing short gaps 0:30:55.733 5G / 9G INFO GapCloser (gap_closer.cpp : 424) Closing short gaps complete: filled 689 gaps after checking 8129 candidates 0:30:58.072 5G / 9G INFO StageManager (stage.cpp : 125) STAGE == Simplification 0:30:58.748 1G / 9G INFO General (graph_simplification.hpp : 911) Graph simplification started 0:30:58.748 1G / 9G INFO General (graph_simplification.hpp : 924) Fast simplification mode enabled 0:30:58.748 1G / 9G INFO General (graph_simplification.hpp : 771) PROCEDURE == Presimplification 0:30:58.748 1G / 9G INFO General (graph_simplification.hpp : 211) Removing short low covered self-conjugate connections 0:30:59.520 1G / 9G INFO General (graph_simplification.hpp : 403) Removing isolated edges 0:30:59.521 1G / 9G INFO General (graph_simplification.hpp : 404) All edges shorter than 151 will be removed 0:30:59.521 1G / 9G INFO General (graph_simplification.hpp : 405) Also edges shorter than 0 and coverage smaller than 0 will be removed 0:31:01.921 1G / 9G INFO General (graph_simplification.hpp : 687) Non parallel mode 0:31:25.904 2G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:32:41.351 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:33:14.614 1G / 9G INFO General (graph_simplification.hpp : 644) Using permanent iterators 0:33:14.614 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 1 0:33:15.740 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:33:20.441 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:33:22.296 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 2 0:33:22.296 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:33:22.321 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:33:24.065 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 3 0:33:24.066 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:33:24.095 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:33:25.838 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 4 0:33:25.838 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:33:25.864 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:33:27.310 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 5 0:33:27.310 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:33:27.325 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:33:28.761 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 6 0:33:28.762 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:33:28.772 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:33:30.154 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 7 0:33:30.154 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:33:30.162 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:33:31.715 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 8 0:33:31.715 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:33:31.721 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:33:33.241 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 9 0:33:33.241 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:33:33.246 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:33:34.643 924M / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 10 0:33:34.643 924M / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:33:34.647 924M / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:33:35.770 820M / 9G INFO General (graph_simplification.hpp : 796) PROCEDURE == Post simplification 0:33:35.770 820M / 9G INFO General (graph_simplification.hpp : 644) Using permanent iterators 0:33:35.770 820M / 9G INFO General (graph_simplification.hpp : 806) Iteration 0 0:33:35.770 820M / 9G INFO General (graph_simplification.hpp : 247) Removal of relatively low covered connections disabled 0:33:35.925 820M / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:33:36.434 788M / 9G INFO StageManager (stage.cpp : 125) STAGE == Gap Closer 0:33:36.434 788M / 9G INFO General (graph_pack.hpp : 84) Index refill 0:33:36.436 788M / 9G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:33:36.436 788M / 9G INFO General (kmer_splitters.hpp : 289) Splitting kmer instances into 16 buckets. This might take a while. 0:33:36.436 788M / 9G INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:33:36.436 788M / 9G INFO General (kmer_splitters.hpp : 307) Memory available for splitting buffers: 33.0768 Gb 0:33:36.436 788M / 9G INFO General (kmer_splitters.hpp : 312) Using cell size of 2097152 0:34:23.377 1G / 9G INFO General (kmer_splitters.hpp : 325) Processed 40599 edges 0:35:11.948 1G / 9G INFO General (kmer_splitters.hpp : 325) Processed 81079 edges 0:35:37.970 1G / 9G INFO General (kmer_splitters.hpp : 325) Processed 86156 edges 0:35:37.970 1G / 9G INFO General (kmer_splitters.hpp : 330) Used 86156 sequences. 0:35:38.029 780M / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:36:09.623 780M / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 71162453 kmers in total. 0:36:09.623 780M / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:36:15.272 780M / 9G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:37:45.456 804M / 9G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:37:53.636 804M / 9G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 24617802 bytes occupied (2.7675 bits per kmer). 0:37:54.749 2G / 9G INFO General (edge_index_builders.hpp : 21) Collecting k-mer coverage information from graph, this takes a while. 0:39:45.737 2G / 9G INFO General (gap_closer.cpp : 157) Preparing shift maps 0:39:45.815 2G / 9G INFO General (gap_closer.cpp : 117) Processing paired reads (takes a while) 0:40:20.552 2G / 9G INFO General (gap_closer.cpp : 136) Used 18982058 paired reads 0:40:20.552 2G / 9G INFO General (gap_closer.cpp : 138) Merging paired indices 0:40:20.630 2G / 9G INFO GapCloser (gap_closer.cpp : 395) Closing short gaps 0:40:20.811 2G / 9G INFO GapCloser (gap_closer.cpp : 424) Closing short gaps complete: filled 57 gaps after checking 2349 candidates 0:40:21.478 2G / 9G INFO StageManager (stage.cpp : 125) STAGE == Simplification Cleanup 0:40:21.482 2G / 9G INFO General (graph_simplification.hpp : 403) Removing isolated edges 0:40:21.482 2G / 9G INFO General (graph_simplification.hpp : 404) All edges shorter than 151 will be removed 0:40:21.482 2G / 9G INFO General (graph_simplification.hpp : 405) Also edges shorter than 0 and coverage smaller than 2 will be removed 0:40:21.702 2G / 9G INFO General (simplification.cpp : 56) Removing all the edges having coverage 0 and less 0:40:22.201 2G / 9G INFO General (simplification.cpp : 68) Counting average coverage 0:40:22.251 2G / 9G INFO General (simplification.cpp : 71) Average coverage = 24.1026 0:40:22.251 2G / 9G INFO StageManager (stage.cpp : 125) STAGE == Contig Output 0:40:22.252 2G / 9G INFO General (contig_output.hpp : 283) Outputting contigs to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_Moz13BIII-dipSPAdes-3.5.0-trimmed/spades//K55/simplified_contigs.fasta 0:40:37.997 2G / 9G INFO General (contig_output.hpp : 283) Outputting contigs to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_Moz13BIII-dipSPAdes-3.5.0-trimmed/spades//K55/before_rr.fasta 0:41:23.870 2G / 9G INFO General (contig_output.hpp : 283) Outputting contigs to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_Moz13BIII-dipSPAdes-3.5.0-trimmed/spades//K55/final_contigs.fasta 0:42:09.804 2G / 9G INFO General (launch.hpp : 82) SPAdes finished 0:42:12.434 64M / 9G INFO General (main.cpp : 166) Assembling time: 0 hours 42 minutes 12 seconds == Running assembler: K77 0:00:00.000 4M / 4M INFO General (memory_limit.hpp : 42) Memory limit set to 100 Gb 0:00:00.001 4M / 4M INFO General (main.cpp : 146) Assembling dataset (/N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_Moz13BIII-dipSPAdes-3.5.0-trimmed/spades/dataset.info) with K=77 0:00:00.001 4M / 4M INFO General (launch.hpp : 28) SPAdes started 0:00:00.001 4M / 4M INFO General (launch.hpp : 29) Starting from stage: construction 0:00:00.003 4M / 4M INFO General (launch.hpp : 44) Will need read mapping, kmer mapper will be attached 0:00:00.003 4M / 4M INFO StageManager (stage.cpp : 125) STAGE == Construction 0:00:00.003 4M / 4M INFO General (construction.cpp : 44) Contigs from previous K will be used 0:00:00.008 4M / 4M INFO General (read_converter.hpp : 49) Binary reads detected 0:00:00.036 4M / 4M INFO General (graph_construction.hpp : 129) Constructing DeBruijn graph for k=77 0:00:00.038 4M / 4M INFO General (kmer_splitters.hpp : 172) Splitting kmer instances into 256 buckets. This might take a while. 0:00:00.039 4M / 4M INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:00:00.039 4M / 4M INFO General (kmer_splitters.hpp : 190) Memory available for splitting buffers: 2.08325 Gb 0:00:00.039 4M / 4M INFO General (kmer_splitters.hpp : 199) Using cell size of 87381 0:01:43.831 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 9863910 reads 0:08:34.498 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 19724769 reads 0:11:11.773 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 29592305 reads 0:11:23.637 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 38251586 reads 0:11:23.638 8G / 9G INFO General (kmer_splitters.hpp : 234) Adding contigs from previous K 0:11:45.147 8G / 9G INFO General (kmer_splitters.hpp : 245) Used 38251586 reads. Maximum read length 151 0:11:45.147 8G / 9G INFO General (kmer_splitters.hpp : 246) Average read length 149.412 0:11:47.411 64M / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:12:15.019 64M / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 140627598 kmers in total. 0:12:15.019 64M / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:12:35.286 64M / 9G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:12:35.286 64M / 9G INFO General (kmer_splitters.hpp : 379) Splitting kmer instances into 256 buckets. This might take a while. 0:12:35.287 64M / 9G INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:12:35.287 64M / 9G INFO General (kmer_splitters.hpp : 397) Memory available for splitting buffers: 2.08203 Gb 0:12:35.287 64M / 9G INFO General (kmer_splitters.hpp : 405) Using cell size of 87381 0:13:11.514 8G / 9G INFO General (kmer_splitters.hpp : 428) Processed 140627598 kmers 0:13:11.514 8G / 9G INFO General (kmer_splitters.hpp : 437) Used 140627598 kmers. 0:13:12.950 64M / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:13:26.734 64M / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 140768009 kmers in total. 0:13:26.735 64M / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:13:50.643 64M / 9G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:14:08.305 68M / 9G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:14:27.830 68M / 9G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 48696975 bytes occupied (2.7675 bits per kmer). 0:14:28.055 204M / 9G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 382) Building k-mer extensions from k+1-mers 0:14:53.356 204M / 9G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 386) Building k-mer extensions from k+1-mers finished. 0:14:53.365 204M / 9G INFO General (graph_construction.hpp : 145) Condensing graph 0:14:53.365 204M / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 337) Extracting unbranching paths 0:16:26.394 1G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 351) Extracting unbranching paths finished. 7011183 sequences extracted 0:16:40.075 1G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 311) Collecting perfect loops 0:17:31.684 1G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 326) Collecting perfect loops finished. 2 loops collected 0:17:39.225 1G / 9G INFO General (graph_construction.hpp : 150) Building index with from graph 0:17:39.748 1G / 9G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:17:39.748 1G / 9G INFO General (kmer_splitters.hpp : 289) Splitting kmer instances into 16 buckets. This might take a while. 0:17:39.748 1G / 9G INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:17:39.749 1G / 9G INFO General (kmer_splitters.hpp : 307) Memory available for splitting buffers: 32.7031 Gb 0:17:39.749 1G / 9G INFO General (kmer_splitters.hpp : 312) Using cell size of 1398101 0:17:46.048 2G / 9G INFO General (kmer_splitters.hpp : 325) Processed 1115618 edges 0:18:28.083 2G / 9G INFO General (kmer_splitters.hpp : 325) Processed 2230212 edges 0:19:10.884 2G / 9G INFO General (kmer_splitters.hpp : 325) Processed 3344524 edges 0:20:24.895 2G / 9G INFO General (kmer_splitters.hpp : 325) Processed 4460361 edges 0:21:35.543 2G / 9G INFO General (kmer_splitters.hpp : 325) Processed 5576185 edges 0:22:43.229 2G / 9G INFO General (kmer_splitters.hpp : 325) Processed 6691825 edges 0:24:03.772 2G / 9G INFO General (kmer_splitters.hpp : 325) Processed 7011185 edges 0:24:03.773 2G / 9G INFO General (kmer_splitters.hpp : 330) Used 7011185 sequences. 0:24:03.843 1G / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:25:34.012 1G / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 140627598 kmers in total. 0:25:34.012 1G / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:25:57.462 1G / 9G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:29:03.948 1G / 9G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:29:30.185 1G / 9G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 48648402 bytes occupied (2.7675 bits per kmer). 0:29:32.671 5G / 9G INFO General (edge_index_builders.hpp : 21) Collecting k-mer coverage information from graph, this takes a while. 0:34:34.640 4G / 9G INFO General (graph_construction.hpp : 182) Filling coverage index 0:34:34.641 4G / 9G INFO General (edge_index_builders.hpp : 99) Collecting k-mer coverage information from reads, this takes a while. 0:36:50.247 4G / 9G INFO General (graph_construction.hpp : 184) Filling coverage and flanking coverage from index 0:37:25.783 4G / 9G INFO General (construction.cpp : 33) Figured out: read length = 151 0:37:26.346 4G / 9G INFO StageManager (stage.cpp : 125) STAGE == EC Threshold Finding 0:37:34.393 4G / 9G INFO General (kmer_coverage_model.cpp : 178) Kmer coverage valley at: 4 0:37:34.393 4G / 9G INFO General (kmer_coverage_model.cpp : 198) K-mer histogram maximum: 18 0:37:34.393 4G / 9G INFO General (kmer_coverage_model.cpp : 234) Estimated median coverage: 19. Coverage mad: 8.8956 0:37:34.393 4G / 9G INFO General (kmer_coverage_model.cpp : 261) Fitting coverage model 0:37:34.463 4G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 2 0:37:34.646 4G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 4 0:37:35.291 4G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 8 0:37:36.245 4G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 16 0:37:37.061 4G / 9G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 18.4583. Fitted coverage std. dev: 6.8884 0:37:37.062 4G / 9G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 0.43186 0:37:37.063 4G / 9G INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 11 0:37:37.063 4G / 9G INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 11 0:37:37.063 4G / 9G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 59706898 0:37:37.063 4G / 9G INFO General (genomic_info_filler.cpp : 103) Mean coverage was calculated as 18.4583 0:37:37.063 4G / 9G INFO General (genomic_info_filler.cpp : 117) EC coverage threshold value was calculated as 11 0:37:37.063 4G / 9G INFO General (genomic_info_filler.cpp : 118) Trusted kmer low bound: 0 0:37:37.063 4G / 9G INFO StageManager (stage.cpp : 125) STAGE == Gap Closer 0:37:37.081 4G / 9G INFO General (gap_closer.cpp : 157) Preparing shift maps 0:37:45.013 5G / 9G INFO General (gap_closer.cpp : 117) Processing paired reads (takes a while) 0:38:08.978 5G / 9G INFO General (gap_closer.cpp : 136) Used 18982058 paired reads 0:38:08.979 5G / 9G INFO General (gap_closer.cpp : 138) Merging paired indices 0:38:12.702 5G / 9G INFO GapCloser (gap_closer.cpp : 395) Closing short gaps 0:38:30.386 5G / 9G INFO GapCloser (gap_closer.cpp : 424) Closing short gaps complete: filled 1039 gaps after checking 11083 candidates 0:38:33.196 4G / 9G INFO StageManager (stage.cpp : 125) STAGE == Simplification 0:38:33.778 1G / 9G INFO General (graph_simplification.hpp : 911) Graph simplification started 0:38:33.778 1G / 9G INFO General (graph_simplification.hpp : 924) Fast simplification mode enabled 0:38:33.778 1G / 9G INFO General (graph_simplification.hpp : 771) PROCEDURE == Presimplification 0:38:33.778 1G / 9G INFO General (graph_simplification.hpp : 211) Removing short low covered self-conjugate connections 0:38:34.517 1G / 9G INFO General (graph_simplification.hpp : 403) Removing isolated edges 0:38:34.519 1G / 9G INFO General (graph_simplification.hpp : 404) All edges shorter than 151 will be removed 0:38:34.519 1G / 9G INFO General (graph_simplification.hpp : 405) Also edges shorter than 0 and coverage smaller than 0 will be removed 0:38:38.402 1G / 9G INFO General (graph_simplification.hpp : 687) Non parallel mode 0:39:00.067 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:40:14.533 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:40:17.710 1G / 9G INFO General (graph_simplification.hpp : 644) Using permanent iterators 0:40:17.710 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 1 0:40:18.347 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:40:20.948 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:40:20.985 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 2 0:40:20.985 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:40:20.988 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:40:21.323 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 3 0:40:21.324 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:40:21.333 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:40:22.355 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 4 0:40:22.355 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:40:22.374 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:40:23.349 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 5 0:40:23.349 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:40:23.363 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:40:24.589 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 6 0:40:24.589 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:40:24.597 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:40:25.942 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 7 0:40:25.943 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:40:25.949 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:40:27.406 1016M / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 8 0:40:27.406 1016M / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:40:27.412 1016M / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:40:28.988 892M / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 9 0:40:28.988 892M / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:40:28.992 892M / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:40:30.457 760M / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 10 0:40:30.457 760M / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:40:30.460 756M / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:40:31.624 660M / 9G INFO General (graph_simplification.hpp : 796) PROCEDURE == Post simplification 0:40:31.624 660M / 9G INFO General (graph_simplification.hpp : 644) Using permanent iterators 0:40:31.624 660M / 9G INFO General (graph_simplification.hpp : 806) Iteration 0 0:40:31.624 660M / 9G INFO General (graph_simplification.hpp : 247) Removal of relatively low covered connections disabled 0:40:31.728 660M / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:40:31.925 660M / 9G INFO General (graph_simplification.hpp : 806) Iteration 1 0:40:31.925 660M / 9G INFO General (graph_simplification.hpp : 247) Removal of relatively low covered connections disabled 0:40:31.925 660M / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:40:32.066 636M / 9G INFO StageManager (stage.cpp : 125) STAGE == Gap Closer 0:40:32.066 636M / 9G INFO General (graph_pack.hpp : 84) Index refill 0:40:32.069 636M / 9G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:40:32.069 636M / 9G INFO General (kmer_splitters.hpp : 289) Splitting kmer instances into 16 buckets. This might take a while. 0:40:32.069 636M / 9G INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:40:32.069 636M / 9G INFO General (kmer_splitters.hpp : 307) Memory available for splitting buffers: 33.1263 Gb 0:40:32.069 636M / 9G INFO General (kmer_splitters.hpp : 312) Using cell size of 1398101 0:41:05.307 1G / 9G INFO General (kmer_splitters.hpp : 325) Processed 17587 edges 0:41:29.595 1G / 9G INFO General (kmer_splitters.hpp : 325) Processed 35886 edges 0:44:05.056 1G / 9G INFO General (kmer_splitters.hpp : 325) Processed 53343 edges 0:44:46.577 1G / 9G INFO General (kmer_splitters.hpp : 325) Processed 57087 edges 0:44:46.577 1G / 9G INFO General (kmer_splitters.hpp : 330) Used 57087 sequences. 0:44:46.677 632M / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:45:33.136 632M / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 71622908 kmers in total. 0:45:33.136 632M / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:45:43.174 632M / 9G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:47:17.392 656M / 9G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:47:29.054 656M / 9G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 24777086 bytes occupied (2.7675 bits per kmer). 0:47:30.341 2G / 9G INFO General (edge_index_builders.hpp : 21) Collecting k-mer coverage information from graph, this takes a while. 0:49:42.508 2G / 9G INFO General (gap_closer.cpp : 157) Preparing shift maps 0:49:42.573 2G / 9G INFO General (gap_closer.cpp : 117) Processing paired reads (takes a while) 0:50:19.187 2G / 9G INFO General (gap_closer.cpp : 136) Used 18982058 paired reads 0:50:19.187 2G / 9G INFO General (gap_closer.cpp : 138) Merging paired indices 0:50:19.290 2G / 9G INFO GapCloser (gap_closer.cpp : 395) Closing short gaps 0:50:19.483 2G / 9G INFO GapCloser (gap_closer.cpp : 424) Closing short gaps complete: filled 61 gaps after checking 3346 candidates 0:50:20.386 2G / 9G INFO StageManager (stage.cpp : 125) STAGE == Simplification Cleanup 0:50:20.390 2G / 9G INFO General (graph_simplification.hpp : 403) Removing isolated edges 0:50:20.391 2G / 9G INFO General (graph_simplification.hpp : 404) All edges shorter than 151 will be removed 0:50:20.391 2G / 9G INFO General (graph_simplification.hpp : 405) Also edges shorter than 0 and coverage smaller than 2 will be removed 0:50:20.974 2G / 9G INFO General (simplification.cpp : 56) Removing all the edges having coverage 0 and less 0:50:21.148 2G / 9G INFO General (simplification.cpp : 68) Counting average coverage 0:50:21.167 2G / 9G INFO General (simplification.cpp : 71) Average coverage = 18.1521 0:50:21.167 2G / 9G INFO StageManager (stage.cpp : 125) STAGE == Mismatch Correction 0:50:59.113 2G / 9G INFO General (mismatch_shall_not_pass.hp: 188) Finished collecting potential mismatches positions 0:50:59.189 2G / 9G INFO General (mismatch_shall_not_pass.hp: 291) All edges processed 0:50:59.192 2G / 9G INFO General (mismatch_correction.cpp : 18) Corrected 0 nucleotides 0:50:59.403 2G / 9G INFO StageManager (stage.cpp : 125) STAGE == Paired Information Counting 0:50:59.603 2G / 9G INFO General (pair_info_count.cpp : 150) Graph N50: 18911 0:50:59.603 2G / 9G INFO General (pair_info_count.cpp : 152) Estimating insert size for library #0 0:50:59.603 2G / 9G INFO General (pair_info_count.cpp : 31) Estimating insert size (takes a while) 0:50:59.619 2G / 9G INFO General (short_read_mapper.hpp : 91) Selecting usual mapper 0:51:05.629 2G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 200000 reads 0:51:05.634 2G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 400000 reads 0:51:05.642 2G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 600000 reads 0:51:05.643 2G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 800000 reads 0:51:05.645 2G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 1000000 reads 0:51:05.657 2G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 1200000 reads 0:51:05.716 2G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 2200000 reads 0:51:11.806 2G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 4200000 reads 0:51:17.336 2G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 8525083 reads 0:51:20.250 2G / 9G INFO General (sequence_mapper_notifier.h: 89) Processed 9491029 reads 0:51:20.250 2G / 9G INFO General (pair_info_count.cpp : 41) 4540436 paired reads (47.8392% of all) aligned to long edges 0:51:20.263 2G / 9G INFO General (pair_info_count.cpp : 170) Estimated insert size for paired library #0 0:51:20.263 2G / 9G INFO General (pair_info_count.cpp : 175) Insert size = 327.234, deviation = 96.8977, left quantile = 212, right quantile = 455, read length = 151 0:51:20.263 2G / 9G INFO General (pair_info_count.cpp : 187) Mapping library #0 0:51:20.263 2G / 9G INFO General (pair_info_count.cpp : 189) Mapping paired reads (takes a while) 0:51:20.263 2G / 9G INFO General (pair_info_count.cpp : 73) Left insert size qauntile 212, right insert size quantile 455 0:51:20.385 2G / 9G INFO General (short_read_mapper.hpp : 91) Selecting usual mapper 0:51:27.866 4G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 200000 reads 0:51:28.534 4G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 400000 reads 0:51:29.365 4G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 600000 reads 0:51:30.347 4G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 800000 reads 0:51:31.482 4G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 1000000 reads 0:51:32.698 4G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 1200000 reads 0:51:39.625 4G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 2200000 reads 0:51:54.904 4G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 4200000 reads 0:52:28.941 4G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 8400000 reads 0:53:42.010 4G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 16931892 reads 0:54:01.156 3G / 9G INFO General (sequence_mapper_notifier.h: 89) Processed 18982058 reads 0:56:21.300 3G / 9G INFO General (split_graph_pair_info.hpp : 344) Threshold for paired information 0.0504662 0:56:24.799 2G / 9G INFO StageManager (stage.cpp : 125) STAGE == Distance Estimation 0:56:24.800 2G / 9G INFO General (distance_estimation.cpp : 234) Processing library #0 0:56:24.800 2G / 9G INFO General (distance_estimation.cpp : 136) Weight Filter Done 0:56:24.800 2G / 9G INFO DistanceEstimator (distance_estimation.hpp : 187) Using SIMPLE distance estimator 0:56:37.334 2G / 9G INFO DistanceEstimator (distance_estimation.hpp : 208) Merging maps 0:56:38.525 2G / 9G INFO General (distance_estimation.cpp : 38) Filtering info 0:56:40.311 2G / 9G INFO General (pair_info_filters.hpp : 354) Pruning the index 0:56:40.384 2G / 9G INFO General (distance_estimation.cpp : 184) Refining clustered pair information 0:56:40.538 2G / 9G INFO General (distance_estimation.cpp : 186) The refining of clustered pair information has been finished 0:56:40.538 2G / 9G INFO General (distance_estimation.cpp : 188) Filling paired information 0:56:42.892 2G / 9G INFO PairInfoImprover (pair_info_improver.hpp : 61) Paired info stats: missing = 88245; contradictional = 7086 0:56:45.351 2G / 9G INFO PairInfoImprover (pair_info_improver.hpp : 61) Paired info stats: missing = 18093; contradictional = 0 0:56:45.351 2G / 9G INFO General (distance_estimation.cpp : 193) Filling scaffolding index 0:56:45.351 2G / 9G INFO DistanceEstimator (distance_estimation.hpp : 187) Using SMOOTHING distance estimator 0:56:56.469 2G / 9G INFO DistanceEstimator (distance_estimation.hpp : 208) Merging maps 0:56:56.510 2G / 9G INFO General (distance_estimation.cpp : 38) Filtering info 0:56:56.768 2G / 9G INFO General (pair_info_filters.hpp : 354) Pruning the index 0:56:57.151 2G / 9G INFO StageManager (stage.cpp : 125) STAGE == Repeat Resolving 0:56:57.151 2G / 9G INFO General (contig_output.hpp : 283) Outputting contigs to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_Moz13BIII-dipSPAdes-3.5.0-trimmed/spades//K77/before_rr.fasta 0:57:41.972 2G / 9G INFO General (repeat_resolving.cpp : 59) Using Path-Extend repeat resolving 0:57:41.972 2G / 9G INFO General (path_extend_launch.hpp : 459) Threshold for library #0 is 0.0504662 0:57:41.973 2G / 9G INFO General (path_extend_launch.hpp : 298) Path-Extend repeat resolving tool started 0:57:42.023 2G / 9G INFO General (path_extend_launch.hpp : 316) Using 1 paired-end library 0:57:42.023 2G / 9G INFO General (path_extend_launch.hpp : 317) Using 1 paired-end scaffolding library 0:57:42.023 2G / 9G INFO General (path_extend_launch.hpp : 318) Using 0 mate-pair libraries 0:57:42.023 2G / 9G INFO General (path_extend_launch.hpp : 319) Using 0 single read libraries 0:57:42.023 2G / 9G INFO General (path_extend_launch.hpp : 320) Scaffolder is on 0:57:42.361 2G / 9G INFO General (path_extend_launch.hpp : 332) Growing paths using paired-end and long single reads 0:57:42.361 2G / 9G INFO PathExtender (path_extender.hpp : 611) Processed 0 paths from 25322 (0%) 0:57:42.578 2G / 9G INFO PathExtender (path_extender.hpp : 609) Processed 128 paths from 25322 (0%) 0:57:42.835 2G / 9G INFO PathExtender (path_extender.hpp : 609) Processed 256 paths from 25322 (1%) 0:57:43.292 2G / 9G INFO PathExtender (path_extender.hpp : 609) Processed 512 paths from 25322 (2%) 0:57:44.059 2G / 9G INFO PathExtender (path_extender.hpp : 609) Processed 1024 paths from 25322 (4%) 0:57:44.993 2G / 9G INFO PathExtender (path_extender.hpp : 609) Processed 2048 paths from 25322 (8%) 0:57:45.680 2G / 9G INFO PathExtender (path_extender.hpp : 611) Processed 2533 paths from 25322 (10%) 0:57:46.699 2G / 9G INFO PathExtender (path_extender.hpp : 609) Processed 4096 paths from 25322 (16%) 0:57:47.089 2G / 9G INFO PathExtender (path_extender.hpp : 611) Processed 5066 paths from 25322 (20%) 0:57:48.291 2G / 9G INFO PathExtender (path_extender.hpp : 611) Processed 7599 paths from 25322 (30%) 0:57:48.557 2G / 9G INFO PathExtender (path_extender.hpp : 609) Processed 8192 paths from 25322 (32%) 0:57:49.342 2G / 9G INFO PathExtender (path_extender.hpp : 611) Processed 10132 paths from 25322 (40%) 0:57:50.176 2G / 9G INFO PathExtender (path_extender.hpp : 611) Processed 12665 paths from 25322 (50%) 0:57:52.674 2G / 9G INFO PathExtender (path_extender.hpp : 611) Processed 15198 paths from 25322 (60%) 0:57:54.081 2G / 9G INFO PathExtender (path_extender.hpp : 609) Processed 16384 paths from 25322 (64%) 0:57:55.648 2G / 9G INFO PathExtender (path_extender.hpp : 611) Processed 17731 paths from 25322 (70%) 0:57:58.783 2G / 9G INFO PathExtender (path_extender.hpp : 611) Processed 20264 paths from 25322 (80%) 0:58:00.474 2G / 9G INFO PathExtender (path_extender.hpp : 611) Processed 22797 paths from 25322 (90%) 0:58:02.482 2G / 9G INFO PathExtendIO (pe_io.hpp : 339) Constructing FASTG file from paths 0:58:02.955 2G / 9G INFO PathExtendIO (pe_io.hpp : 342) Writing contigs in FASTG to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_Moz13BIII-dipSPAdes-3.5.0-trimmed/spades//K77/final_contigs.fastg 0:58:02.955 2G / 9G INFO PathExtendIO (pe_io.hpp : 343) Writing contigs in FASTA to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_Moz13BIII-dipSPAdes-3.5.0-trimmed/spades//K77/final_contigs.fasta 0:58:46.155 2G / 9G INFO PathExtendIO (pe_io.hpp : 339) Constructing FASTG file from paths 0:58:46.635 2G / 9G INFO PathExtendIO (pe_io.hpp : 342) Writing contigs in FASTG to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_Moz13BIII-dipSPAdes-3.5.0-trimmed/spades//K77/path_extend/pe_before_traversal.fastg 0:58:46.635 2G / 9G INFO PathExtendIO (pe_io.hpp : 343) Writing contigs in FASTA to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_Moz13BIII-dipSPAdes-3.5.0-trimmed/spades//K77/path_extend/pe_before_traversal.fasta 0:59:29.487 2G / 9G INFO General (path_extend_launch.hpp : 281) Traversing tandem repeats 0:59:31.263 2G / 9G INFO PathExtendIO (pe_io.hpp : 339) Constructing FASTG file from paths 0:59:31.647 2G / 9G INFO PathExtendIO (pe_io.hpp : 342) Writing contigs in FASTG to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_Moz13BIII-dipSPAdes-3.5.0-trimmed/spades//K77/scaffolds.fastg 0:59:31.647 2G / 9G INFO PathExtendIO (pe_io.hpp : 343) Writing contigs in FASTA to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_Moz13BIII-dipSPAdes-3.5.0-trimmed/spades//K77/scaffolds.fasta 1:00:14.748 2G / 9G INFO General (launch.hpp : 82) SPAdes finished 1:00:18.029 308M / 9G INFO General (main.cpp : 166) Assembling time: 1 hours 0 minutes 18 seconds ===== Assembling finished. * Corrected reads are in /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_Moz13BIII-dipSPAdes-3.5.0-trimmed/spades/corrected/ * Assembled contigs are in /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_Moz13BIII-dipSPAdes-3.5.0-trimmed/spades/contigs.fasta (contigs.fastg) * Assembled scaffolds are in /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_Moz13BIII-dipSPAdes-3.5.0-trimmed/spades/scaffolds.fasta (scaffolds.fastg) ======= SPAdes pipeline finished WITH WARNINGS! === Pipeline warnings: * Default k-mer sizes were set to [21, 33, 55, 77] because estimated read length (151) is equal to or greater than 150 ======= Warnings saved to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_Moz13BIII-dipSPAdes-3.5.0-trimmed/spades/warnings.log SPAdes log can be found here: /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_Moz13BIII-dipSPAdes-3.5.0-trimmed/spades/spades.log Thank you for using SPAdes!