Command line: --diploid --pe1-1 /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_137/reads.end1.paired.fastq.gz --pe1-2 /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_137/reads.end2.paired.fastq.gz -t 16 -o /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_137-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_137-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_137/reads.end1.paired.fastq.gz'] right reads: ['/N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_137/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_137-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_137-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_137-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_137-dipSPAdes-3.5.0-trimmed/spades/corrected/configs/config.info 0:00:00.005 4M / 4M INFO General (memory_limit.hpp : 42) Memory limit set to 100 Gb 0:00:00.005 4M / 4M INFO General (main.cpp : 91) Trying to determine PHRED offset 0:00:00.038 4M / 4M INFO General (main.cpp : 97) Determined value is 33 0:00:00.038 4M / 4M INFO General (hammer_tools.cpp : 36) Hamming graph threshold tau=1, k=21, subkmer positions = [ 0 10 ] === ITERATION 0 begins === 0:00:00.039 4M / 4M INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:00:00.039 4M / 4M INFO K-mer Splitting (kmer_data.cpp : 127) Splitting kmer instances into 256 buckets. This might take a while. 0:00:00.040 4M / 4M INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:00:00.040 4M / 4M INFO K-mer Splitting (kmer_data.cpp : 145) Memory available for splitting buffers: 2.08325 Gb 0:00:00.040 4M / 4M INFO K-mer Splitting (kmer_data.cpp : 153) Using cell size of 262144 0:00:02.823 8G / 8G INFO K-mer Splitting (kmer_data.cpp : 167) Processing /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_137/reads.end1.paired.fastq.gz 0:05:26.319 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 176) Processed 3467833 reads 0:12:28.902 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 176) Processed 6943719 reads 0:16:13.306 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 176) Processed 10005163 reads 0:16:35.056 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 176) Processed 11265090 reads 0:16:35.059 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 167) Processing /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_137/reads.end2.paired.fastq.gz 0:17:35.170 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 176) Processed 14722403 reads 0:20:28.936 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 176) Processed 18165186 reads 0:22:40.482 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 176) Processed 21638302 reads 0:22:55.614 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 176) Processed 22530180 reads 0:22:55.617 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 181) Processed 22530180 reads 0:22:56.707 64M / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:23:30.715 64M / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 281884764 kmers in total. 0:23:30.717 64M / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:23:59.634 64M / 9G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:24:39.745 192M / 9G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:25:12.954 192M / 9G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 97514554 bytes occupied (2.7675 bits per kmer). 0:25:12.956 192M / 9G INFO K-mer Counting (kmer_data.cpp : 266) Arranging kmers in hash map order 0:28:01.752 192M / 9G INFO K-mer Counting (kmer_data.cpp : 279) Done. Total swaps: 281884487 0:28:03.642 2G / 9G INFO General (main.cpp : 151) Clustering Hamming graph. 0:28:03.643 2G / 9G INFO Hamming Clustering (hamcluster.cpp : 115) Serializing sub-kmers. 0:28:03.644 2G / 9G INFO Hamming Clustering (hamcluster.cpp : 120) Serializing: [0, 10) 0:31:10.494 2G / 9G INFO Hamming Clustering (hamcluster.cpp : 120) Serializing: [10, 21) 0:34:18.973 2G / 9G INFO Hamming Clustering (hamcluster.cpp : 129) Splitting sub-kmers, pass 1. 0:38:08.237 2G / 9G INFO Hamming Clustering (hamcluster.cpp : 134) Splitting done. Processed 2 blocks. Produced 4896755 blocks. 0:38:08.237 2G / 9G INFO Hamming Clustering (hamcluster.cpp : 145) Merge sub-kmers, pass 1 0:53:54.182 2G / 9G INFO Hamming Clustering (hamcluster.cpp : 170) Merge done, total 1535029 new blocks generated. 0:53:55.833 2G / 9G INFO Hamming Clustering (hamcluster.cpp : 175) Spliting sub-kmers, pass 2. 1:23:28.135 2G / 9G INFO Hamming Clustering (hamcluster.cpp : 180) Splitting done. Processed 3070058 blocks. Produced 532000654 blocks. 1:23:28.136 2G / 9G INFO Hamming Clustering (hamcluster.cpp : 187) Merge sub-kmers, pass 2 1:36:30.865 2G / 9G INFO Hamming Clustering (hamcluster.cpp : 205) Merge done, saw 273335 big blocks out of 532000654 processed. 1:42:01.573 2G / 9G INFO General (main.cpp : 165) Clustering done. Total clusters: 130827970 1:42:01.573 2G / 9G INFO K-mer Counting (kmer_data.cpp : 284) Collecting K-mer information, this takes a while. 1:42:08.711 14G / 14G INFO K-mer Counting (kmer_data.cpp : 290) Processing /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_137/reads.end1.paired.fastq.gz 1:45:01.943 14G / 14G INFO K-mer Counting (kmer_data.cpp : 290) Processing /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_137/reads.end2.paired.fastq.gz 1:47:49.744 14G / 14G INFO K-mer Counting (kmer_data.cpp : 297) Collection done, postprocessing. 1:47:56.778 14G / 14G INFO K-mer Counting (kmer_data.cpp : 310) There are 281884764 kmers in total. Among them 136342832 (48.3683%) are singletons. 1:47:56.778 14G / 14G INFO General (main.cpp : 203) Subclustering Hamming graph 1:51:16.277 14G / 14G INFO Hamming Subclustering (kmer_cluster.cpp : 626) Subclustering done. Total 92713 non-read kmers were generated. 1:51:16.277 14G / 14G INFO Hamming Subclustering (kmer_cluster.cpp : 627) Subclustering statistics: 1:51:16.277 14G / 14G INFO Hamming Subclustering (kmer_cluster.cpp : 628) Total singleton hamming clusters: 73682522. Among them 55605522 (75.4664%) are good 1:51:16.277 14G / 14G INFO Hamming Subclustering (kmer_cluster.cpp : 629) Total singleton subclusters: 7654074. Among them 7654017 (99.9993%) are good 1:51:16.277 14G / 14G INFO Hamming Subclustering (kmer_cluster.cpp : 630) Total non-singleton subcluster centers: 62218335. Among them 39934176 (64.1839%) are good 1:51:16.277 14G / 14G INFO Hamming Subclustering (kmer_cluster.cpp : 631) Average size of non-trivial subcluster: 3.32023 kmers 1:51:16.277 14G / 14G INFO Hamming Subclustering (kmer_cluster.cpp : 632) Average number of sub-clusters per non-singleton cluster: 1.22271 1:51:16.278 14G / 14G INFO Hamming Subclustering (kmer_cluster.cpp : 633) Total solid k-mers: 103193715 1:51:16.278 14G / 14G INFO Hamming Subclustering (kmer_cluster.cpp : 634) Substitution probabilities: [4,4]((0.898257,0.0232969,0.0256514,0.0527948),(0.0356054,0.928752,0.013048,0.0225951),(0.0215744,0.0126707,0.930117,0.0356378),(0.0522739,0.0259663,0.0236882,0.898072)) 1:51:17.124 14G / 14G INFO General (main.cpp : 208) Finished clustering. 1:51:17.124 14G / 14G INFO General (main.cpp : 228) Starting solid k-mers expansion in 16 threads. 1:55:05.940 14G / 14G INFO General (main.cpp : 249) Solid k-mers iteration 0 produced 44176869 new k-mers. 1:58:51.778 14G / 14G INFO General (main.cpp : 249) Solid k-mers iteration 1 produced 1131041 new k-mers. 2:02:37.553 14G / 14G INFO General (main.cpp : 249) Solid k-mers iteration 2 produced 43822 new k-mers. 2:06:23.326 14G / 14G INFO General (main.cpp : 249) Solid k-mers iteration 3 produced 3831 new k-mers. 2:10:13.435 14G / 14G INFO General (main.cpp : 249) Solid k-mers iteration 4 produced 377 new k-mers. 2:14:05.833 14G / 14G INFO General (main.cpp : 249) Solid k-mers iteration 5 produced 41 new k-mers. 2:17:57.701 14G / 14G INFO General (main.cpp : 249) Solid k-mers iteration 6 produced 0 new k-mers. 2:17:57.702 14G / 14G INFO General (main.cpp : 253) Solid k-mers finalized 2:17:57.702 14G / 14G INFO General (hammer_tools.cpp : 210) Starting read correction in 16 threads. 2:17:57.703 14G / 14G INFO General (hammer_tools.cpp : 222) Correcting pair of reads: /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_137/reads.end1.paired.fastq.gz and /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_137/reads.end2.paired.fastq.gz 2:18:23.584 16G / 16G INFO General (hammer_tools.cpp : 166) Prepared batch 0 of 1600000 reads. 2:18:45.313 16G / 16G INFO General (hammer_tools.cpp : 175) Processed batch 0 2:19:41.352 16G / 16G INFO General (hammer_tools.cpp : 185) Written batch 0 2:20:05.150 16G / 16G INFO General (hammer_tools.cpp : 166) Prepared batch 1 of 1600000 reads. 2:20:26.516 16G / 16G INFO General (hammer_tools.cpp : 175) Processed batch 1 2:20:41.800 16G / 16G INFO General (hammer_tools.cpp : 185) Written batch 1 2:21:05.319 16G / 16G INFO General (hammer_tools.cpp : 166) Prepared batch 2 of 1600000 reads. 2:21:26.526 16G / 16G INFO General (hammer_tools.cpp : 175) Processed batch 2 2:21:41.829 16G / 16G INFO General (hammer_tools.cpp : 185) Written batch 2 2:22:05.196 16G / 16G INFO General (hammer_tools.cpp : 166) Prepared batch 3 of 1600000 reads. 2:22:26.775 16G / 16G INFO General (hammer_tools.cpp : 175) Processed batch 3 2:22:42.113 16G / 16G INFO General (hammer_tools.cpp : 185) Written batch 3 2:23:05.429 16G / 16G INFO General (hammer_tools.cpp : 166) Prepared batch 4 of 1600000 reads. 2:23:26.517 16G / 16G INFO General (hammer_tools.cpp : 175) Processed batch 4 2:23:41.947 16G / 16G INFO General (hammer_tools.cpp : 185) Written batch 4 2:24:05.065 16G / 16G INFO General (hammer_tools.cpp : 166) Prepared batch 5 of 1600000 reads. 2:24:26.744 16G / 16G INFO General (hammer_tools.cpp : 175) Processed batch 5 2:24:42.111 16G / 16G INFO General (hammer_tools.cpp : 185) Written batch 5 2:25:05.020 16G / 16G INFO General (hammer_tools.cpp : 166) Prepared batch 6 of 1600000 reads. 2:25:26.853 16G / 16G INFO General (hammer_tools.cpp : 175) Processed batch 6 2:25:42.172 16G / 16G INFO General (hammer_tools.cpp : 185) Written batch 6 2:25:43.109 16G / 16G INFO General (hammer_tools.cpp : 166) Prepared batch 7 of 65090 reads. 2:25:44.019 16G / 16G INFO General (hammer_tools.cpp : 175) Processed batch 7 2:25:44.652 16G / 16G INFO General (hammer_tools.cpp : 185) Written batch 7 2:25:47.397 14G / 16G INFO General (hammer_tools.cpp : 269) Correction done. Changed 4473128 bases in 3446112 reads. 2:25:47.397 14G / 16G INFO General (hammer_tools.cpp : 270) Failed to correct 438985752 bases out of 3352424823. 2:25:47.468 2G / 16G INFO General (main.cpp : 286) Saving corrected dataset description to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_137-dipSPAdes-3.5.0-trimmed/spades/corrected/corrected.yaml 2:25:47.475 2G / 16G 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_137-dipSPAdes-3.5.0-trimmed/spades/corrected/corrected.yaml ===== Read error correction finished. ===== Assembling started. == Running assembler: K21 0:00:00.000 4M / 4M INFO General (memory_limit.hpp : 42) Memory limit set to 100 Gb 0:00:00.001 4M / 4M INFO General (main.cpp : 146) Assembling dataset (/N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_137-dipSPAdes-3.5.0-trimmed/spades/dataset.info) with K=21 0:00:00.001 4M / 4M INFO General (launch.hpp : 28) SPAdes started 0:00:00.001 4M / 4M INFO General (launch.hpp : 29) Starting from stage: construction 0:00:00.002 4M / 4M INFO StageManager (stage.cpp : 125) STAGE == Construction 0:00:00.014 4M / 4M INFO General (read_converter.hpp : 79) Converting reads to binary format (takes a while) 0:00:00.014 4M / 4M INFO General (read_converter.hpp : 81) Paired reads for library #0 0:00:01.135 80M / 80M INFO General (binary_converter.hpp : 138) 16384 reads processed 0:00:01.537 96M / 96M INFO General (binary_converter.hpp : 138) 32768 reads processed 0:00:02.337 124M / 124M INFO General (binary_converter.hpp : 138) 65536 reads processed 0:00:03.941 184M / 184M INFO General (binary_converter.hpp : 138) 131072 reads processed 0:00:07.152 300M / 300M INFO General (binary_converter.hpp : 138) 262144 reads processed 0:00:13.590 536M / 536M INFO General (binary_converter.hpp : 138) 524288 reads processed 0:00:49.159 900M / 900M INFO General (binary_converter.hpp : 138) 1048576 reads processed 0:01:17.782 904M / 904M INFO General (binary_converter.hpp : 138) 2097152 reads processed 0:02:15.265 904M / 904M INFO General (binary_converter.hpp : 138) 4194304 reads processed 0:04:13.407 904M / 904M INFO General (binary_converter.hpp : 138) 8388608 reads processed 0:05:29.822 888M / 908M INFO General (binary_converter.hpp : 158) 11138247 reads written 0:05:31.509 4M / 908M INFO General (read_converter.hpp : 91) Single reads for library #0 0:05:33.363 140M / 908M INFO General (binary_converter.hpp : 138) 16384 reads processed 0:05:33.583 144M / 908M INFO General (binary_converter.hpp : 138) 32768 reads processed 0:05:33.970 160M / 908M INFO General (binary_converter.hpp : 138) 65536 reads processed 0:05:34.906 188M / 908M INFO General (binary_converter.hpp : 158) 126716 reads written 0:05:35.067 4M / 908M INFO General (graph_construction.hpp : 129) Constructing DeBruijn graph for k=21 0:05:35.070 4M / 908M INFO General (kmer_splitters.hpp : 172) Splitting kmer instances into 256 buckets. This might take a while. 0:05:35.071 4M / 908M INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:05:35.071 4M / 908M INFO General (kmer_splitters.hpp : 190) Memory available for splitting buffers: 2.08325 Gb 0:05:35.071 4M / 908M INFO General (kmer_splitters.hpp : 199) Using cell size of 262144 0:10:43.590 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 16703024 reads 0:15:15.555 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 33404266 reads 0:19:24.507 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 44806420 reads 0:19:24.507 8G / 9G INFO General (kmer_splitters.hpp : 234) Adding contigs from previous K 0:19:24.507 8G / 9G INFO General (kmer_splitters.hpp : 245) Used 44806420 reads. Maximum read length 151 0:19:24.507 8G / 9G INFO General (kmer_splitters.hpp : 246) Average read length 149.598 0:19:26.638 64M / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:21:43.871 64M / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 116871012 kmers in total. 0:21:43.871 64M / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:22:16.235 64M / 9G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:22:16.235 64M / 9G INFO General (kmer_splitters.hpp : 379) Splitting kmer instances into 256 buckets. This might take a while. 0:22:16.235 64M / 9G INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:22:16.236 64M / 9G INFO General (kmer_splitters.hpp : 397) Memory available for splitting buffers: 2.08203 Gb 0:22:16.236 64M / 9G INFO General (kmer_splitters.hpp : 405) Using cell size of 262144 0:28:05.335 8G / 9G INFO General (kmer_splitters.hpp : 428) Processed 116871012 kmers 0:28:05.335 8G / 9G INFO General (kmer_splitters.hpp : 437) Used 116871012 kmers. 0:28:05.978 64M / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:28:18.354 64M / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 113740207 kmers in total. 0:28:18.355 64M / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:28:23.761 64M / 9G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:28:36.466 64M / 9G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:28:40.779 64M / 9G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 39347042 bytes occupied (2.7675 bits per kmer). 0:28:40.975 176M / 9G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 382) Building k-mer extensions from k+1-mers 0:28:53.944 176M / 9G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 386) Building k-mer extensions from k+1-mers finished. 0:28:53.950 176M / 9G INFO Early tip clipping (early_simplification.hpp : 236) Early tip clipping 0:35:52.244 176M / 9G INFO Early tip clipping (early_simplification.hpp : 239) 5974160 22-mers were removed by early tip clipper 0:35:52.244 176M / 9G INFO General (graph_construction.hpp : 145) Condensing graph 0:35:52.244 176M / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 337) Extracting unbranching paths 0:37:26.761 1G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 351) Extracting unbranching paths finished. 16523135 sequences extracted 0:37:37.439 1G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 311) Collecting perfect loops 0:38:27.209 1G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 326) Collecting perfect loops finished. 14 loops collected 0:38:39.244 3G / 9G INFO General (graph_construction.hpp : 150) Building index with from graph 0:38:39.245 3G / 9G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:38:39.245 3G / 9G INFO General (kmer_splitters.hpp : 289) Splitting kmer instances into 16 buckets. This might take a while. 0:38:39.246 3G / 9G INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:38:39.246 3G / 9G INFO General (kmer_splitters.hpp : 307) Memory available for splitting buffers: 32.2487 Gb 0:38:39.246 3G / 9G INFO General (kmer_splitters.hpp : 312) Using cell size of 4194304 0:38:57.928 3G / 9G INFO General (kmer_splitters.hpp : 325) Processed 9991931 edges 0:39:10.043 3G / 9G INFO General (kmer_splitters.hpp : 325) Processed 16523149 edges 0:39:10.044 3G / 9G INFO General (kmer_splitters.hpp : 330) Used 16523149 sequences. 0:39:10.110 3G / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:39:34.930 3G / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 110896852 kmers in total. 0:39:34.930 3G / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:39:59.792 3G / 9G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:42:24.091 3G / 9G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:42:28.437 3G / 9G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 38363420 bytes occupied (2.7675 bits per kmer). 0:42:30.373 5G / 9G INFO General (edge_index_builders.hpp : 21) Collecting k-mer coverage information from graph, this takes a while. 0:45:54.172 5G / 9G INFO General (graph_construction.hpp : 182) Filling coverage index 0:45:54.172 5G / 9G INFO General (edge_index_builders.hpp : 99) Collecting k-mer coverage information from reads, this takes a while. 0:49:29.214 5G / 9G INFO General (graph_construction.hpp : 184) Filling coverage and flanking coverage from index 0:49:59.220 5G / 9G INFO General (construction.cpp : 33) Figured out: read length = 151 0:49:59.238 5G / 9G INFO StageManager (stage.cpp : 125) STAGE == EC Threshold Finding 0:50:07.706 5G / 9G INFO General (kmer_coverage_model.cpp : 178) Kmer coverage valley at: 14 0:50:07.706 5G / 9G INFO General (kmer_coverage_model.cpp : 198) K-mer histogram maximum: 40 0:50:07.706 5G / 9G INFO General (kmer_coverage_model.cpp : 234) Estimated median coverage: 41. Coverage mad: 10.3782 0:50:07.707 5G / 9G INFO General (kmer_coverage_model.cpp : 261) Fitting coverage model 0:50:07.862 5G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 2 0:50:08.250 5G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 4 0:50:09.537 5G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 8 0:50:12.654 5G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 16 0:50:18.285 5G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 32 0:50:18.285 5G / 9G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 40.5138. Fitted coverage std. dev: 9.18379 0:50:18.288 5G / 9G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 0.409078 0:50:18.288 5G / 9G INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 25 0:50:18.288 5G / 9G INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 25 0:50:18.289 5G / 9G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 62240177 0:50:18.289 5G / 9G INFO General (genomic_info_filler.cpp : 103) Mean coverage was calculated as 40.5138 0:50:18.289 5G / 9G INFO General (genomic_info_filler.cpp : 117) EC coverage threshold value was calculated as 25 0:50:18.290 5G / 9G INFO General (genomic_info_filler.cpp : 118) Trusted kmer low bound: 0 0:50:18.290 5G / 9G INFO StageManager (stage.cpp : 125) STAGE == Simplification 0:50:18.518 3G / 9G INFO General (graph_simplification.hpp : 911) Graph simplification started 0:50:18.518 3G / 9G INFO General (graph_simplification.hpp : 924) Fast simplification mode enabled 0:50:18.518 3G / 9G INFO General (graph_simplification.hpp : 771) PROCEDURE == Presimplification 0:50:18.518 3G / 9G INFO General (graph_simplification.hpp : 211) Removing short low covered self-conjugate connections 0:50:19.688 3G / 9G INFO General (graph_simplification.hpp : 403) Removing isolated edges 0:50:19.688 3G / 9G INFO General (graph_simplification.hpp : 404) All edges shorter than 151 will be removed 0:50:19.688 3G / 9G INFO General (graph_simplification.hpp : 405) Also edges shorter than 0 and coverage smaller than 0 will be removed 0:50:21.261 3G / 9G INFO General (graph_simplification.hpp : 687) Non parallel mode 0:51:15.570 3G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:53:22.591 3G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:57:04.404 3G / 9G INFO General (graph_simplification.hpp : 644) Using permanent iterators 0:57:04.405 3G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 1 0:57:15.029 3G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:57:59.374 3G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:58:22.529 3G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 2 0:58:22.529 3G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:58:22.956 3G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:58:37.038 3G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 3 0:58:37.038 3G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:58:37.323 3G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:58:42.307 3G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 4 0:58:42.307 3G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:58:42.410 3G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:58:46.269 3G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 5 0:58:46.269 3G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:58:46.349 3G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:58:49.368 3G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 6 0:58:49.368 3G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:58:49.432 3G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:58:52.759 3G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 7 0:58:52.759 3G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:58:52.823 3G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:58:55.775 3G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 8 0:58:55.775 3G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:58:55.830 3G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:58:58.533 3G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 9 0:58:58.534 3G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:58:58.585 3G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:59:00.523 3G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 10 0:59:00.523 3G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:59:00.563 3G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:59:02.404 3G / 9G INFO General (graph_simplification.hpp : 796) PROCEDURE == Post simplification 0:59:02.404 3G / 9G INFO General (graph_simplification.hpp : 644) Using permanent iterators 0:59:02.404 3G / 9G INFO General (graph_simplification.hpp : 806) Iteration 0 0:59:02.404 3G / 9G INFO General (graph_simplification.hpp : 247) Removal of relatively low covered connections disabled 0:59:06.644 3G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:59:16.189 3G / 9G INFO General (graph_simplification.hpp : 806) Iteration 1 0:59:16.189 3G / 9G INFO General (graph_simplification.hpp : 247) Removal of relatively low covered connections disabled 0:59:16.189 3G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:59:19.095 3G / 9G INFO StageManager (stage.cpp : 125) STAGE == Simplification Cleanup 0:59:19.096 3G / 9G INFO General (graph_simplification.hpp : 403) Removing isolated edges 0:59:19.096 3G / 9G INFO General (graph_simplification.hpp : 404) All edges shorter than 151 will be removed 0:59:19.096 3G / 9G INFO General (graph_simplification.hpp : 405) Also edges shorter than 0 and coverage smaller than 2 will be removed 0:59:19.389 3G / 9G INFO General (simplification.cpp : 56) Removing all the edges having coverage 0 and less 0:59:27.101 3G / 9G INFO General (simplification.cpp : 68) Counting average coverage 0:59:27.973 3G / 9G INFO General (simplification.cpp : 71) Average coverage = 42.2791 0:59:27.973 3G / 9G INFO StageManager (stage.cpp : 125) STAGE == Contig Output 0:59:27.973 3G / 9G INFO General (contig_output.hpp : 283) Outputting contigs to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_137-dipSPAdes-3.5.0-trimmed/spades//K21/simplified_contigs.fasta 1:00:16.629 3G / 9G INFO General (contig_output.hpp : 283) Outputting contigs to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_137-dipSPAdes-3.5.0-trimmed/spades//K21/before_rr.fasta 1:02:52.767 3G / 9G INFO General (contig_output.hpp : 283) Outputting contigs to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_137-dipSPAdes-3.5.0-trimmed/spades//K21/final_contigs.fasta 1:05:25.695 3G / 9G INFO General (launch.hpp : 82) SPAdes finished 1:05:35.103 64M / 9G INFO General (main.cpp : 166) Assembling time: 1 hours 5 minutes 35 seconds == Warning == Default k-mer sizes were set to [21, 33, 55, 77] because estimated read length (151) is equal to or greater than 150 == Running assembler: K33 0:00:00.000 4M / 4M INFO General (memory_limit.hpp : 42) Memory limit set to 100 Gb 0:00:00.001 4M / 4M INFO General (main.cpp : 146) Assembling dataset (/N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_137-dipSPAdes-3.5.0-trimmed/spades/dataset.info) with K=33 0:00:00.001 4M / 4M INFO General (launch.hpp : 28) SPAdes started 0:00:00.001 4M / 4M INFO General (launch.hpp : 29) Starting from stage: construction 0:00:00.002 4M / 4M INFO StageManager (stage.cpp : 125) STAGE == Construction 0:00:00.002 4M / 4M INFO General (construction.cpp : 44) Contigs from previous K will be used 0:00:00.006 4M / 4M INFO General (read_converter.hpp : 49) Binary reads detected 0:00:00.025 4M / 4M INFO General (graph_construction.hpp : 129) Constructing DeBruijn graph for k=33 0:00:00.027 4M / 4M INFO General (kmer_splitters.hpp : 172) Splitting kmer instances into 256 buckets. This might take a while. 0:00:00.028 4M / 4M INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:00:00.028 4M / 4M INFO General (kmer_splitters.hpp : 190) Memory available for splitting buffers: 2.08325 Gb 0:00:00.028 4M / 4M INFO General (kmer_splitters.hpp : 199) Using cell size of 131072 0:06:50.104 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 9206352 reads 0:14:43.659 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 18421980 reads 0:20:45.242 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 27627305 reads 0:28:24.266 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 36838842 reads 0:33:45.009 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 44806420 reads 0:33:45.009 8G / 9G INFO General (kmer_splitters.hpp : 234) Adding contigs from previous K 0:34:06.391 8G / 9G INFO General (kmer_splitters.hpp : 245) Used 44806420 reads. Maximum read length 151 0:34:06.392 8G / 9G INFO General (kmer_splitters.hpp : 246) Average read length 149.598 0:34:08.571 64M / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:34:29.511 64M / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 137148798 kmers in total. 0:34:29.512 64M / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:35:17.696 64M / 9G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:35:17.696 64M / 9G INFO General (kmer_splitters.hpp : 379) Splitting kmer instances into 256 buckets. This might take a while. 0:35:17.697 64M / 9G INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:35:17.697 64M / 9G INFO General (kmer_splitters.hpp : 397) Memory available for splitting buffers: 2.08203 Gb 0:35:17.697 64M / 9G INFO General (kmer_splitters.hpp : 405) Using cell size of 131072 1:06:56.368 8G / 9G INFO General (kmer_splitters.hpp : 428) Processed 137148798 kmers 1:06:56.368 8G / 9G INFO General (kmer_splitters.hpp : 437) Used 137148798 kmers. 1:06:57.428 64M / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 1:14:25.618 64M / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 135867342 kmers in total. 1:14:25.618 64M / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 1:14:57.649 64M / 9G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 1:15:16.136 68M / 9G INFO General (kmer_index.hpp : 371) Merging final buckets. 1:15:36.959 68M / 9G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 47001645 bytes occupied (2.7675 bits per kmer). 1:15:37.180 200M / 9G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 382) Building k-mer extensions from k+1-mers 1:15:54.181 200M / 9G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 386) Building k-mer extensions from k+1-mers finished. 1:15:54.190 200M / 9G INFO Early tip clipping (early_simplification.hpp : 236) Early tip clipping 1:23:25.142 200M / 9G INFO Early tip clipping (early_simplification.hpp : 239) 22656850 34-mers were removed by early tip clipper 1:23:25.142 200M / 9G INFO General (graph_construction.hpp : 145) Condensing graph 1:23:25.142 200M / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 337) Extracting unbranching paths 1:25:02.985 1G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 351) Extracting unbranching paths finished. 7757318 sequences extracted 1:25:14.117 1G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 311) Collecting perfect loops 1:25:59.327 1G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 326) Collecting perfect loops finished. 34 loops collected 1:26:05.009 1G / 9G INFO General (graph_construction.hpp : 150) Building index with from graph 1:26:05.015 1G / 9G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 1:26:05.015 1G / 9G INFO General (kmer_splitters.hpp : 289) Splitting kmer instances into 16 buckets. This might take a while. 1:26:05.015 1G / 9G INFO General (file_limit.hpp : 29) Open file limit set to 32768 1:26:05.015 1G / 9G INFO General (kmer_splitters.hpp : 307) Memory available for splitting buffers: 32.7643 Gb 1:26:05.015 1G / 9G INFO General (kmer_splitters.hpp : 312) Using cell size of 2097152 1:30:06.986 2G / 9G INFO General (kmer_splitters.hpp : 325) Processed 2269234 edges 1:32:15.955 2G / 9G INFO General (kmer_splitters.hpp : 325) Processed 4542977 edges 1:35:25.536 2G / 9G INFO General (kmer_splitters.hpp : 325) Processed 6818808 edges 1:38:10.585 2G / 9G INFO General (kmer_splitters.hpp : 325) Processed 7757352 edges 1:38:10.585 2G / 9G INFO General (kmer_splitters.hpp : 330) Used 7757352 sequences. 1:38:10.640 1G / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 1:39:46.306 1G / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 114491948 kmers in total. 1:39:46.306 1G / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 1:39:55.929 1G / 9G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 1:42:27.874 1G / 9G INFO General (kmer_index.hpp : 371) Merging final buckets. 1:42:36.629 1G / 9G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 39607091 bytes occupied (2.7675 bits per kmer). 1:42:38.629 4G / 9G INFO General (edge_index_builders.hpp : 21) Collecting k-mer coverage information from graph, this takes a while. 1:46:01.934 4G / 9G INFO General (graph_construction.hpp : 182) Filling coverage index 1:46:01.934 4G / 9G INFO General (edge_index_builders.hpp : 99) Collecting k-mer coverage information from reads, this takes a while. 1:49:12.941 4G / 9G INFO General (graph_construction.hpp : 184) Filling coverage and flanking coverage from index 1:49:40.480 4G / 9G INFO General (construction.cpp : 33) Figured out: read length = 151 1:49:40.498 4G / 9G INFO StageManager (stage.cpp : 125) STAGE == EC Threshold Finding 1:49:49.758 4G / 9G INFO General (kmer_coverage_model.cpp : 178) Kmer coverage valley at: 12 1:49:49.758 4G / 9G INFO General (kmer_coverage_model.cpp : 198) K-mer histogram maximum: 36 1:49:49.758 4G / 9G INFO General (kmer_coverage_model.cpp : 234) Estimated median coverage: 37. Coverage mad: 8.8956 1:49:49.759 4G / 9G INFO General (kmer_coverage_model.cpp : 261) Fitting coverage model 1:49:49.895 4G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 2 1:49:50.248 4G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 4 1:49:51.360 4G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 8 1:49:54.199 4G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 16 1:49:59.265 4G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 32 1:49:59.581 4G / 9G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 36.0777. Fitted coverage std. dev: 9.02301 1:49:59.584 4G / 9G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 0.319166 1:49:59.584 4G / 9G INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 21 1:49:59.584 4G / 9G INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 21 1:49:59.584 4G / 9G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 63361116 1:49:59.584 4G / 9G INFO General (genomic_info_filler.cpp : 103) Mean coverage was calculated as 36.0777 1:49:59.584 4G / 9G INFO General (genomic_info_filler.cpp : 117) EC coverage threshold value was calculated as 21 1:49:59.585 4G / 9G INFO General (genomic_info_filler.cpp : 118) Trusted kmer low bound: 0 1:49:59.585 4G / 9G INFO StageManager (stage.cpp : 125) STAGE == Simplification 1:49:59.742 1G / 9G INFO General (graph_simplification.hpp : 911) Graph simplification started 1:49:59.742 1G / 9G INFO General (graph_simplification.hpp : 924) Fast simplification mode enabled 1:49:59.742 1G / 9G INFO General (graph_simplification.hpp : 771) PROCEDURE == Presimplification 1:49:59.743 1G / 9G INFO General (graph_simplification.hpp : 211) Removing short low covered self-conjugate connections 1:50:00.267 1G / 9G INFO General (graph_simplification.hpp : 403) Removing isolated edges 1:50:00.268 1G / 9G INFO General (graph_simplification.hpp : 404) All edges shorter than 151 will be removed 1:50:00.268 1G / 9G INFO General (graph_simplification.hpp : 405) Also edges shorter than 0 and coverage smaller than 0 will be removed 1:50:01.618 1G / 9G INFO General (graph_simplification.hpp : 687) Non parallel mode 1:50:23.348 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 1:51:15.626 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 1:52:55.752 1G / 9G INFO General (graph_simplification.hpp : 644) Using permanent iterators 1:52:55.753 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 1 1:52:58.565 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 1:53:10.120 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 1:53:21.910 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 2 1:53:21.910 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 1:53:22.006 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 1:53:26.642 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 3 1:53:26.642 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 1:53:26.705 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 1:53:28.857 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 4 1:53:28.857 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 1:53:28.888 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 1:53:30.318 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 5 1:53:30.318 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 1:53:30.337 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 1:53:31.575 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 6 1:53:31.575 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 1:53:31.589 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 1:53:32.977 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 7 1:53:32.978 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 1:53:32.989 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 1:53:34.534 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 8 1:53:34.534 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 1:53:34.545 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 1:53:36.133 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 9 1:53:36.133 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 1:53:36.143 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 1:53:37.250 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 10 1:53:37.250 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 1:53:37.257 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 1:53:37.945 1G / 9G INFO General (graph_simplification.hpp : 796) PROCEDURE == Post simplification 1:53:37.945 1G / 9G INFO General (graph_simplification.hpp : 644) Using permanent iterators 1:53:37.945 1G / 9G INFO General (graph_simplification.hpp : 806) Iteration 0 1:53:37.945 1G / 9G INFO General (graph_simplification.hpp : 247) Removal of relatively low covered connections disabled 1:53:38.336 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 1:53:39.220 1G / 9G INFO General (graph_simplification.hpp : 806) Iteration 1 1:53:39.220 1G / 9G INFO General (graph_simplification.hpp : 247) Removal of relatively low covered connections disabled 1:53:39.220 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 1:53:39.618 1G / 9G INFO StageManager (stage.cpp : 125) STAGE == Simplification Cleanup 1:53:39.620 1G / 9G INFO General (graph_simplification.hpp : 403) Removing isolated edges 1:53:39.620 1G / 9G INFO General (graph_simplification.hpp : 404) All edges shorter than 151 will be removed 1:53:39.620 1G / 9G INFO General (graph_simplification.hpp : 405) Also edges shorter than 0 and coverage smaller than 2 will be removed 1:53:39.662 1G / 9G INFO General (simplification.cpp : 56) Removing all the edges having coverage 0 and less 1:53:40.374 1G / 9G INFO General (simplification.cpp : 68) Counting average coverage 1:53:40.494 1G / 9G INFO General (simplification.cpp : 71) Average coverage = 35.8386 1:53:40.494 1G / 9G INFO StageManager (stage.cpp : 125) STAGE == Contig Output 1:53:40.494 1G / 9G INFO General (contig_output.hpp : 283) Outputting contigs to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_137-dipSPAdes-3.5.0-trimmed/spades//K33/simplified_contigs.fasta 1:53:58.985 1G / 9G INFO General (contig_output.hpp : 283) Outputting contigs to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_137-dipSPAdes-3.5.0-trimmed/spades//K33/before_rr.fasta 1:54:56.576 1G / 9G INFO General (contig_output.hpp : 283) Outputting contigs to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_137-dipSPAdes-3.5.0-trimmed/spades//K33/final_contigs.fasta 1:56:12.537 1G / 9G INFO General (launch.hpp : 82) SPAdes finished 1:56:15.421 64M / 9G INFO General (main.cpp : 166) Assembling time: 1 hours 56 minutes 15 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_137-dipSPAdes-3.5.0-trimmed/spades/dataset.info) with K=55 0:00:00.001 4M / 4M INFO General (launch.hpp : 28) SPAdes started 0:00:00.001 4M / 4M INFO General (launch.hpp : 29) Starting from stage: construction 0:00:00.002 4M / 4M INFO General (launch.hpp : 44) Will need read mapping, kmer mapper will be attached 0:00:00.002 4M / 4M INFO StageManager (stage.cpp : 125) STAGE == Construction 0:00:00.002 4M / 4M INFO General (construction.cpp : 44) Contigs from previous K will be used 0:00:00.007 4M / 4M INFO General (read_converter.hpp : 49) Binary reads detected 0:00:00.023 4M / 4M INFO General (graph_construction.hpp : 129) Constructing DeBruijn graph for k=55 0:00:00.025 4M / 4M INFO General (kmer_splitters.hpp : 172) Splitting kmer instances into 256 buckets. This might take a while. 0:00:00.026 4M / 4M INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:00:00.026 4M / 4M INFO General (kmer_splitters.hpp : 190) Memory available for splitting buffers: 2.08325 Gb 0:00:00.026 4M / 4M INFO General (kmer_splitters.hpp : 199) Using cell size of 131072 0:08:59.471 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 11347639 reads 0:09:29.717 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 22696314 reads 0:09:45.984 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 34045866 reads 0:10:01.387 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 44806420 reads 0:10:01.387 8G / 9G INFO General (kmer_splitters.hpp : 234) Adding contigs from previous K 0:10:20.523 8G / 9G INFO General (kmer_splitters.hpp : 245) Used 44806420 reads. Maximum read length 151 0:10:20.523 8G / 9G INFO General (kmer_splitters.hpp : 246) Average read length 149.598 0:10:22.721 64M / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:10:43.108 64M / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 155342950 kmers in total. 0:10:43.109 64M / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:10:57.475 64M / 9G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:10:57.475 64M / 9G INFO General (kmer_splitters.hpp : 379) Splitting kmer instances into 256 buckets. This might take a while. 0:10:57.476 64M / 9G INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:10:57.476 64M / 9G INFO General (kmer_splitters.hpp : 397) Memory available for splitting buffers: 2.08203 Gb 0:10:57.476 64M / 9G INFO General (kmer_splitters.hpp : 405) Using cell size of 131072 0:11:25.707 8G / 9G INFO General (kmer_splitters.hpp : 428) Processed 155342950 kmers 0:11:25.708 8G / 9G INFO General (kmer_splitters.hpp : 437) Used 155342950 kmers. 0:11:26.740 64M / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:11:37.928 64M / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 154873367 kmers in total. 0:11:37.928 64M / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:11:52.267 64M / 9G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:12:13.439 68M / 9G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:12:44.657 68M / 9G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 53576550 bytes occupied (2.7675 bits per kmer). 0:12:44.905 216M / 9G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 382) Building k-mer extensions from k+1-mers 0:13:05.982 216M / 9G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 386) Building k-mer extensions from k+1-mers finished. 0:13:05.990 216M / 9G INFO General (graph_construction.hpp : 145) Condensing graph 0:13:05.990 216M / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 337) Extracting unbranching paths 0:14:50.939 1G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 351) Extracting unbranching paths finished. 10304517 sequences extracted 0:15:06.284 1G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 311) Collecting perfect loops 0:16:08.094 1G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 326) Collecting perfect loops finished. 4 loops collected 0:16:17.403 2G / 9G INFO General (graph_construction.hpp : 150) Building index with from graph 0:16:17.409 2G / 9G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:16:17.409 2G / 9G INFO General (kmer_splitters.hpp : 289) Splitting kmer instances into 16 buckets. This might take a while. 0:16:17.410 2G / 9G INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:16:17.410 2G / 9G INFO General (kmer_splitters.hpp : 307) Memory available for splitting buffers: 32.4987 Gb 0:16:17.410 2G / 9G INFO General (kmer_splitters.hpp : 312) Using cell size of 2097152 0:20:18.196 3G / 9G INFO General (kmer_splitters.hpp : 325) Processed 2226308 edges 0:24:02.864 3G / 9G INFO General (kmer_splitters.hpp : 325) Processed 4450706 edges 0:25:30.903 3G / 9G INFO General (kmer_splitters.hpp : 325) Processed 6675187 edges 0:28:52.582 3G / 9G INFO General (kmer_splitters.hpp : 325) Processed 8899912 edges 0:32:15.616 3G / 9G INFO General (kmer_splitters.hpp : 325) Processed 10304521 edges 0:32:15.616 3G / 9G INFO General (kmer_splitters.hpp : 330) Used 10304521 sequences. 0:32:15.716 2G / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:34:26.140 2G / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 155342950 kmers in total. 0:34:26.140 2G / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:34:38.962 2G / 9G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:38:30.517 2G / 9G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:39:03.024 2G / 9G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 53738993 bytes occupied (2.7675 bits per kmer). 0:39:05.713 6G / 9G INFO General (edge_index_builders.hpp : 21) Collecting k-mer coverage information from graph, this takes a while. 0:44:10.586 5G / 9G INFO General (graph_construction.hpp : 182) Filling coverage index 0:44:10.586 5G / 9G INFO General (edge_index_builders.hpp : 99) Collecting k-mer coverage information from reads, this takes a while. 0:48:15.308 5G / 9G INFO General (graph_construction.hpp : 184) Filling coverage and flanking coverage from index 0:48:56.112 5G / 9G INFO General (construction.cpp : 33) Figured out: read length = 151 0:48:56.128 5G / 9G INFO StageManager (stage.cpp : 125) STAGE == EC Threshold Finding 0:49:06.663 5G / 9G INFO General (kmer_coverage_model.cpp : 178) Kmer coverage valley at: 8 0:49:06.664 5G / 9G INFO General (kmer_coverage_model.cpp : 198) K-mer histogram maximum: 29 0:49:06.664 5G / 9G INFO General (kmer_coverage_model.cpp : 234) Estimated median coverage: 29. Coverage mad: 8.8956 0:49:06.664 5G / 9G INFO General (kmer_coverage_model.cpp : 261) Fitting coverage model 0:49:06.770 5G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 2 0:49:07.049 5G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 4 0:49:08.028 5G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 8 0:49:10.621 5G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 16 0:49:14.710 5G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 32 0:49:15.472 5G / 9G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 28.5946. Fitted coverage std. dev: 8.12767 0:49:15.475 5G / 9G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 0.37693 0:49:15.475 5G / 9G INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 17 0:49:15.475 5G / 9G INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 17 0:49:15.475 5G / 9G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 62922084 0:49:15.475 5G / 9G INFO General (genomic_info_filler.cpp : 103) Mean coverage was calculated as 28.5946 0:49:15.476 5G / 9G INFO General (genomic_info_filler.cpp : 117) EC coverage threshold value was calculated as 17 0:49:15.476 5G / 9G INFO General (genomic_info_filler.cpp : 118) Trusted kmer low bound: 0 0:49:15.476 5G / 9G INFO StageManager (stage.cpp : 125) STAGE == Gap Closer 0:49:15.489 5G / 9G INFO General (gap_closer.cpp : 157) Preparing shift maps 0:49:25.293 6G / 9G INFO General (gap_closer.cpp : 117) Processing paired reads (takes a while) 0:50:00.328 6G / 9G INFO General (gap_closer.cpp : 136) Used 22276494 paired reads 0:50:00.328 6G / 9G INFO General (gap_closer.cpp : 138) Merging paired indices 0:50:04.305 5G / 9G INFO GapCloser (gap_closer.cpp : 395) Closing short gaps 0:50:30.408 5G / 9G INFO GapCloser (gap_closer.cpp : 424) Closing short gaps complete: filled 477 gaps after checking 8096 candidates 0:50:33.066 5G / 9G INFO StageManager (stage.cpp : 125) STAGE == Simplification 0:50:33.284 2G / 9G INFO General (graph_simplification.hpp : 911) Graph simplification started 0:50:33.284 2G / 9G INFO General (graph_simplification.hpp : 924) Fast simplification mode enabled 0:50:33.284 2G / 9G INFO General (graph_simplification.hpp : 771) PROCEDURE == Presimplification 0:50:33.284 2G / 9G INFO General (graph_simplification.hpp : 211) Removing short low covered self-conjugate connections 0:50:34.178 2G / 9G INFO General (graph_simplification.hpp : 403) Removing isolated edges 0:50:34.179 2G / 9G INFO General (graph_simplification.hpp : 404) All edges shorter than 151 will be removed 0:50:34.180 2G / 9G INFO General (graph_simplification.hpp : 405) Also edges shorter than 0 and coverage smaller than 0 will be removed 0:50:36.748 2G / 9G INFO General (graph_simplification.hpp : 687) Non parallel mode 0:51:08.319 2G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:52:43.487 2G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:53:30.790 1G / 9G INFO General (graph_simplification.hpp : 644) Using permanent iterators 0:53:30.790 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 1 0:53:31.932 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:53:36.626 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:53:38.970 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 2 0:53:38.970 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:53:39.005 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:53:41.168 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 3 0:53:41.168 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:53:41.202 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:53:42.593 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 4 0:53:42.594 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:53:42.611 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:53:43.671 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 5 0:53:43.671 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:53:43.683 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:53:45.020 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 6 0:53:45.020 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:53:45.029 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:53:46.633 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 7 0:53:46.633 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:53:46.641 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:53:48.457 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 8 0:53:48.457 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:53:48.464 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:53:50.382 1008M / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 9 0:53:50.382 1008M / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:53:50.388 1008M / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:53:51.920 852M / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 10 0:53:51.920 852M / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:53:51.926 852M / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:53:52.983 748M / 9G INFO General (graph_simplification.hpp : 796) PROCEDURE == Post simplification 0:53:52.983 748M / 9G INFO General (graph_simplification.hpp : 644) Using permanent iterators 0:53:52.983 748M / 9G INFO General (graph_simplification.hpp : 806) Iteration 0 0:53:52.983 748M / 9G INFO General (graph_simplification.hpp : 247) Removal of relatively low covered connections disabled 0:53:53.105 748M / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:53:53.350 748M / 9G INFO General (graph_simplification.hpp : 806) Iteration 1 0:53:53.350 748M / 9G INFO General (graph_simplification.hpp : 247) Removal of relatively low covered connections disabled 0:53:53.350 748M / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:53:53.542 712M / 9G INFO StageManager (stage.cpp : 125) STAGE == Gap Closer 0:53:53.542 712M / 9G INFO General (graph_pack.hpp : 84) Index refill 0:53:53.547 712M / 9G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:53:53.547 712M / 9G INFO General (kmer_splitters.hpp : 289) Splitting kmer instances into 16 buckets. This might take a while. 0:53:53.547 712M / 9G INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:53:53.547 712M / 9G INFO General (kmer_splitters.hpp : 307) Memory available for splitting buffers: 33.1016 Gb 0:53:53.547 712M / 9G INFO General (kmer_splitters.hpp : 312) Using cell size of 2097152 0:56:08.323 1G / 9G INFO General (kmer_splitters.hpp : 325) Processed 32447 edges 0:57:54.455 1G / 9G INFO General (kmer_splitters.hpp : 325) Processed 64622 edges 0:58:51.011 1G / 9G INFO General (kmer_splitters.hpp : 325) Processed 68403 edges 0:58:51.012 1G / 9G INFO General (kmer_splitters.hpp : 330) Used 68403 sequences. 0:58:51.074 708M / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 1:00:54.925 708M / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 71026500 kmers in total. 1:00:54.925 708M / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 1:01:01.151 708M / 9G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 1:02:31.964 732M / 9G INFO General (kmer_index.hpp : 371) Merging final buckets. 1:02:56.665 732M / 9G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 24570772 bytes occupied (2.7675 bits per kmer). 1:02:57.962 2G / 9G INFO General (edge_index_builders.hpp : 21) Collecting k-mer coverage information from graph, this takes a while. 1:04:53.649 2G / 9G INFO General (gap_closer.cpp : 157) Preparing shift maps 1:04:53.712 2G / 9G INFO General (gap_closer.cpp : 117) Processing paired reads (takes a while) 1:05:32.150 2G / 9G INFO General (gap_closer.cpp : 136) Used 22276494 paired reads 1:05:32.150 2G / 9G INFO General (gap_closer.cpp : 138) Merging paired indices 1:05:32.200 2G / 9G INFO GapCloser (gap_closer.cpp : 395) Closing short gaps 1:05:32.335 2G / 9G INFO GapCloser (gap_closer.cpp : 424) Closing short gaps complete: filled 36 gaps after checking 1419 candidates 1:05:32.922 2G / 9G INFO StageManager (stage.cpp : 125) STAGE == Simplification Cleanup 1:05:32.926 2G / 9G INFO General (graph_simplification.hpp : 403) Removing isolated edges 1:05:32.926 2G / 9G INFO General (graph_simplification.hpp : 404) All edges shorter than 151 will be removed 1:05:32.926 2G / 9G INFO General (graph_simplification.hpp : 405) Also edges shorter than 0 and coverage smaller than 2 will be removed 1:05:33.178 2G / 9G INFO General (simplification.cpp : 56) Removing all the edges having coverage 0 and less 1:05:33.400 2G / 9G INFO General (simplification.cpp : 68) Counting average coverage 1:05:33.434 2G / 9G INFO General (simplification.cpp : 71) Average coverage = 28.2635 1:05:33.434 2G / 9G INFO StageManager (stage.cpp : 125) STAGE == Contig Output 1:05:33.435 2G / 9G INFO General (contig_output.hpp : 283) Outputting contigs to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_137-dipSPAdes-3.5.0-trimmed/spades//K55/simplified_contigs.fasta 1:05:48.339 2G / 9G INFO General (contig_output.hpp : 283) Outputting contigs to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_137-dipSPAdes-3.5.0-trimmed/spades//K55/before_rr.fasta 1:06:32.232 2G / 9G INFO General (contig_output.hpp : 283) Outputting contigs to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_137-dipSPAdes-3.5.0-trimmed/spades//K55/final_contigs.fasta 1:07:34.532 2G / 9G INFO General (launch.hpp : 82) SPAdes finished 1:07:36.400 68M / 9G INFO General (main.cpp : 166) Assembling time: 1 hours 7 minutes 36 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_137-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 0:00:00.066 4M / 4M INFO General (read_converter.hpp : 49) Binary reads detected 0:00:00.106 4M / 4M INFO General (graph_construction.hpp : 129) Constructing DeBruijn graph for k=77 0:00:00.108 4M / 4M INFO General (kmer_splitters.hpp : 172) 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 General (kmer_splitters.hpp : 190) Memory available for splitting buffers: 2.08325 Gb 0:00:00.109 4M / 4M INFO General (kmer_splitters.hpp : 199) Using cell size of 87381 0:08:12.244 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 9835786 reads 0:35:21.238 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 19687177 reads 0:43:05.039 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 29522040 reads 0:50:22.239 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 39353104 reads 0:55:38.476 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 44806420 reads 0:55:38.477 8G / 9G INFO General (kmer_splitters.hpp : 234) Adding contigs from previous K 0:56:01.050 8G / 9G INFO General (kmer_splitters.hpp : 245) Used 44806420 reads. Maximum read length 151 0:56:01.051 8G / 9G INFO General (kmer_splitters.hpp : 246) Average read length 149.598 0:56:03.262 64M / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:56:36.078 64M / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 158211366 kmers in total. 0:56:36.080 64M / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:56:58.099 64M / 9G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:56:58.100 64M / 9G INFO General (kmer_splitters.hpp : 379) Splitting kmer instances into 256 buckets. This might take a while. 0:56:58.100 64M / 9G INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:56:58.100 64M / 9G INFO General (kmer_splitters.hpp : 397) Memory available for splitting buffers: 2.08203 Gb 0:56:58.100 64M / 9G INFO General (kmer_splitters.hpp : 405) Using cell size of 87381 0:57:34.401 8G / 9G INFO General (kmer_splitters.hpp : 428) Processed 158211366 kmers 0:57:34.401 8G / 9G INFO General (kmer_splitters.hpp : 437) Used 158211366 kmers. 0:57:36.478 64M / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 1:00:22.073 64M / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 158359456 kmers in total. 1:00:22.073 64M / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 1:00:42.546 64M / 9G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 1:01:02.791 68M / 9G INFO General (kmer_index.hpp : 371) Merging final buckets. 1:01:21.368 68M / 9G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 54782512 bytes occupied (2.7675 bits per kmer). 1:01:21.616 220M / 9G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 382) Building k-mer extensions from k+1-mers 1:01:45.993 220M / 9G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 386) Building k-mer extensions from k+1-mers finished. 1:01:46.004 220M / 9G INFO General (graph_construction.hpp : 145) Condensing graph 1:01:46.004 220M / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 337) Extracting unbranching paths 1:03:28.908 1G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 351) Extracting unbranching paths finished. 8898972 sequences extracted 1:03:44.212 1G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 311) Collecting perfect loops 1:04:42.413 1G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 326) Collecting perfect loops finished. 8 loops collected 1:04:51.148 2G / 9G INFO General (graph_construction.hpp : 150) Building index with from graph 1:04:51.153 2G / 9G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 1:04:51.153 2G / 9G INFO General (kmer_splitters.hpp : 289) Splitting kmer instances into 16 buckets. This might take a while. 1:04:51.153 2G / 9G INFO General (file_limit.hpp : 29) Open file limit set to 32768 1:04:51.154 2G / 9G INFO General (kmer_splitters.hpp : 307) Memory available for splitting buffers: 32.5495 Gb 1:04:51.154 2G / 9G INFO General (kmer_splitters.hpp : 312) Using cell size of 1398101 1:07:37.065 2G / 9G INFO General (kmer_splitters.hpp : 325) Processed 1256510 edges 1:11:50.641 2G / 9G INFO General (kmer_splitters.hpp : 325) Processed 2512880 edges 1:15:29.244 2G / 9G INFO General (kmer_splitters.hpp : 325) Processed 3771590 edges 1:18:19.134 2G / 9G INFO General (kmer_splitters.hpp : 325) Processed 5029890 edges 1:20:45.127 2G / 9G INFO General (kmer_splitters.hpp : 325) Processed 6289626 edges 1:24:40.925 2G / 9G INFO General (kmer_splitters.hpp : 325) Processed 7550090 edges 1:26:48.881 2G / 9G INFO General (kmer_splitters.hpp : 325) Processed 8806837 edges 1:27:40.547 2G / 9G INFO General (kmer_splitters.hpp : 325) Processed 8898980 edges 1:27:40.548 2G / 9G INFO General (kmer_splitters.hpp : 330) Used 8898980 sequences. 1:27:40.622 2G / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 1:28:49.567 2G / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 158211366 kmers in total. 1:28:49.567 2G / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 1:29:08.497 2G / 9G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 1:33:10.963 2G / 9G INFO General (kmer_index.hpp : 371) Merging final buckets. 1:33:31.529 2G / 9G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 54731277 bytes occupied (2.7675 bits per kmer). 1:33:34.338 5G / 9G INFO General (edge_index_builders.hpp : 21) Collecting k-mer coverage information from graph, this takes a while. 1:39:25.884 5G / 9G INFO General (graph_construction.hpp : 182) Filling coverage index 1:39:25.884 5G / 9G INFO General (edge_index_builders.hpp : 99) Collecting k-mer coverage information from reads, this takes a while. 1:42:04.318 5G / 9G INFO General (graph_construction.hpp : 184) Filling coverage and flanking coverage from index 1:42:46.023 5G / 9G INFO General (construction.cpp : 33) Figured out: read length = 151 1:42:46.038 5G / 9G INFO StageManager (stage.cpp : 125) STAGE == EC Threshold Finding 1:42:57.813 5G / 9G INFO General (kmer_coverage_model.cpp : 178) Kmer coverage valley at: 5 1:42:57.813 5G / 9G INFO General (kmer_coverage_model.cpp : 198) K-mer histogram maximum: 21 1:42:57.813 5G / 9G INFO General (kmer_coverage_model.cpp : 234) Estimated median coverage: 22. Coverage mad: 7.413 1:42:57.813 5G / 9G INFO General (kmer_coverage_model.cpp : 261) Fitting coverage model 1:42:57.881 5G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 2 1:42:58.054 5G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 4 1:42:58.727 5G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 8 1:42:59.706 5G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 16 1:43:02.911 5G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 32 1:43:05.900 5G / 9G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 21.5041. Fitted coverage std. dev: 6.89549 1:43:05.902 5G / 9G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 0.435213 1:43:05.902 5G / 9G INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 12 1:43:05.902 5G / 9G INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 12 1:43:05.902 5G / 9G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 63426178 1:43:05.902 5G / 9G INFO General (genomic_info_filler.cpp : 103) Mean coverage was calculated as 21.5041 1:43:05.902 5G / 9G INFO General (genomic_info_filler.cpp : 117) EC coverage threshold value was calculated as 12 1:43:05.902 5G / 9G INFO General (genomic_info_filler.cpp : 118) Trusted kmer low bound: 0 1:43:05.902 5G / 9G INFO StageManager (stage.cpp : 125) STAGE == Gap Closer 1:43:05.916 5G / 9G INFO General (gap_closer.cpp : 157) Preparing shift maps 1:43:16.862 6G / 9G INFO General (gap_closer.cpp : 117) Processing paired reads (takes a while) 1:43:44.907 6G / 9G INFO General (gap_closer.cpp : 136) Used 22276494 paired reads 1:43:44.907 6G / 9G INFO General (gap_closer.cpp : 138) Merging paired indices 1:43:50.694 5G / 9G INFO GapCloser (gap_closer.cpp : 395) Closing short gaps 1:44:14.195 5G / 9G INFO GapCloser (gap_closer.cpp : 424) Closing short gaps complete: filled 756 gaps after checking 10908 candidates 1:44:17.405 5G / 9G INFO StageManager (stage.cpp : 125) STAGE == Simplification 1:44:17.744 2G / 9G INFO General (graph_simplification.hpp : 911) Graph simplification started 1:44:17.744 2G / 9G INFO General (graph_simplification.hpp : 924) Fast simplification mode enabled 1:44:17.744 2G / 9G INFO General (graph_simplification.hpp : 771) PROCEDURE == Presimplification 1:44:17.744 2G / 9G INFO General (graph_simplification.hpp : 211) Removing short low covered self-conjugate connections 1:44:18.602 2G / 9G INFO General (graph_simplification.hpp : 403) Removing isolated edges 1:44:18.604 2G / 9G INFO General (graph_simplification.hpp : 404) All edges shorter than 151 will be removed 1:44:18.604 2G / 9G INFO General (graph_simplification.hpp : 405) Also edges shorter than 0 and coverage smaller than 0 will be removed 1:44:23.741 2G / 9G INFO General (graph_simplification.hpp : 687) Non parallel mode 1:44:55.944 2G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 1:46:43.439 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 1:46:48.804 1G / 9G INFO General (graph_simplification.hpp : 644) Using permanent iterators 1:46:48.804 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 1 1:46:49.501 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 1:46:52.627 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 1:46:52.688 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 2 1:46:52.689 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 1:46:52.691 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 1:46:53.181 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 3 1:46:53.181 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 1:46:53.192 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 1:46:54.003 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 4 1:46:54.003 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 1:46:54.022 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 1:46:54.859 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 5 1:46:54.859 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 1:46:54.868 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 1:46:55.797 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 6 1:46:55.798 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 1:46:55.807 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 1:46:57.229 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 7 1:46:57.229 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 1:46:57.237 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 1:46:58.963 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 8 1:46:58.963 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 1:46:58.970 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 1:47:00.903 984M / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 9 1:47:00.903 984M / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 1:47:00.909 984M / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 1:47:02.831 808M / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 10 1:47:02.831 808M / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 1:47:02.837 808M / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 1:47:04.376 668M / 9G INFO General (graph_simplification.hpp : 796) PROCEDURE == Post simplification 1:47:04.376 668M / 9G INFO General (graph_simplification.hpp : 644) Using permanent iterators 1:47:04.376 668M / 9G INFO General (graph_simplification.hpp : 806) Iteration 0 1:47:04.377 668M / 9G INFO General (graph_simplification.hpp : 247) Removal of relatively low covered connections disabled 1:47:04.492 664M / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 1:47:04.728 664M / 9G INFO General (graph_simplification.hpp : 806) Iteration 1 1:47:04.728 664M / 9G INFO General (graph_simplification.hpp : 247) Removal of relatively low covered connections disabled 1:47:04.728 664M / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 1:47:04.887 648M / 9G INFO StageManager (stage.cpp : 125) STAGE == Gap Closer 1:47:04.887 648M / 9G INFO General (graph_pack.hpp : 84) Index refill 1:47:04.893 648M / 9G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 1:47:04.893 648M / 9G INFO General (kmer_splitters.hpp : 289) Splitting kmer instances into 16 buckets. This might take a while. 1:47:04.893 648M / 9G INFO General (file_limit.hpp : 29) Open file limit set to 32768 1:47:04.893 648M / 9G INFO General (kmer_splitters.hpp : 307) Memory available for splitting buffers: 33.1224 Gb 1:47:04.893 648M / 9G INFO General (kmer_splitters.hpp : 312) Using cell size of 1398101 1:50:13.849 1G / 9G INFO General (kmer_splitters.hpp : 325) Processed 17850 edges 1:52:14.073 1G / 9G INFO General (kmer_splitters.hpp : 325) Processed 35259 edges 1:55:46.502 1G / 9G INFO General (kmer_splitters.hpp : 325) Processed 52955 edges 1:57:27.341 1G / 9G INFO General (kmer_splitters.hpp : 325) Processed 56443 edges 1:57:27.341 1G / 9G INFO General (kmer_splitters.hpp : 330) Used 56443 sequences. 1:57:27.435 648M / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 1:58:44.517 648M / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 71601670 kmers in total. 1:58:44.517 648M / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 1:59:14.212 648M / 9G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 2:00:59.989 668M / 9G INFO General (kmer_index.hpp : 371) Merging final buckets. 2:01:29.093 668M / 9G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 24769740 bytes occupied (2.7675 bits per kmer). 2:01:30.466 2G / 9G INFO General (edge_index_builders.hpp : 21) Collecting k-mer coverage information from graph, this takes a while. 2:03:52.545 2G / 9G INFO General (gap_closer.cpp : 157) Preparing shift maps 2:03:52.607 2G / 9G INFO General (gap_closer.cpp : 117) Processing paired reads (takes a while) 2:04:30.805 2G / 9G INFO General (gap_closer.cpp : 136) Used 22276494 paired reads 2:04:30.805 2G / 9G INFO General (gap_closer.cpp : 138) Merging paired indices 2:04:30.891 2G / 9G INFO GapCloser (gap_closer.cpp : 395) Closing short gaps 2:04:31.052 2G / 9G INFO GapCloser (gap_closer.cpp : 424) Closing short gaps complete: filled 52 gaps after checking 2315 candidates 2:04:31.741 2G / 9G INFO StageManager (stage.cpp : 125) STAGE == Simplification Cleanup 2:04:31.745 2G / 9G INFO General (graph_simplification.hpp : 403) Removing isolated edges 2:04:31.745 2G / 9G INFO General (graph_simplification.hpp : 404) All edges shorter than 151 will be removed 2:04:31.746 2G / 9G INFO General (graph_simplification.hpp : 405) Also edges shorter than 0 and coverage smaller than 2 will be removed 2:04:32.286 2G / 9G INFO General (simplification.cpp : 56) Removing all the edges having coverage 0 and less 2:04:32.502 2G / 9G INFO General (simplification.cpp : 68) Counting average coverage 2:04:32.524 2G / 9G INFO General (simplification.cpp : 71) Average coverage = 21.2517 2:04:32.524 2G / 9G INFO StageManager (stage.cpp : 125) STAGE == Mismatch Correction 2:05:13.281 2G / 9G INFO General (mismatch_shall_not_pass.hp: 188) Finished collecting potential mismatches positions 2:05:13.342 2G / 9G INFO General (mismatch_shall_not_pass.hp: 291) All edges processed 2:05:13.345 2G / 9G INFO General (mismatch_correction.cpp : 18) Corrected 0 nucleotides 2:05:13.359 2G / 9G INFO StageManager (stage.cpp : 125) STAGE == Paired Information Counting 2:05:13.507 2G / 9G INFO General (pair_info_count.cpp : 150) Graph N50: 17516 2:05:13.507 2G / 9G INFO General (pair_info_count.cpp : 152) Estimating insert size for library #0 2:05:13.507 2G / 9G INFO General (pair_info_count.cpp : 31) Estimating insert size (takes a while) 2:05:13.520 2G / 9G INFO General (short_read_mapper.hpp : 91) Selecting usual mapper 2:05:19.665 2G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 200000 reads 2:05:19.674 2G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 400000 reads 2:05:19.688 2G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 600000 reads 2:05:19.692 2G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 800000 reads 2:05:19.702 2G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 1000000 reads 2:05:19.707 2G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 1200000 reads 2:05:19.969 2G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 2200000 reads 2:05:26.032 2G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 4200000 reads 2:05:32.642 2G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 8400000 reads 2:05:36.167 2G / 9G INFO General (sequence_mapper_notifier.h: 89) Processed 11138247 reads 2:05:36.167 2G / 9G INFO General (pair_info_count.cpp : 41) 5319600 paired reads (47.7598% of all) aligned to long edges 2:05:36.179 2G / 9G INFO General (pair_info_count.cpp : 170) Estimated insert size for paired library #0 2:05:36.179 2G / 9G INFO General (pair_info_count.cpp : 175) Insert size = 309.218, deviation = 88.943, left quantile = 200, right quantile = 426, read length = 151 2:05:36.179 2G / 9G INFO General (pair_info_count.cpp : 187) Mapping library #0 2:05:36.180 2G / 9G INFO General (pair_info_count.cpp : 189) Mapping paired reads (takes a while) 2:05:36.180 2G / 9G INFO General (pair_info_count.cpp : 73) Left insert size qauntile 200, right insert size quantile 426 2:05:36.193 2G / 9G INFO General (short_read_mapper.hpp : 91) Selecting usual mapper 2:05:43.836 4G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 200000 reads 2:05:44.560 4G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 400000 reads 2:05:45.405 4G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 600000 reads 2:05:46.428 4G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 800000 reads 2:05:47.568 4G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 1000000 reads 2:05:48.807 4G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 1200000 reads 2:05:55.945 4G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 2200000 reads 2:06:11.599 4G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 4200000 reads 2:06:46.476 4G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 8400000 reads 2:08:00.402 5G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 16800000 reads 2:08:51.201 3G / 9G INFO General (sequence_mapper_notifier.h: 89) Processed 22276494 reads 2:11:01.555 3G / 9G INFO General (split_graph_pair_info.hpp : 344) Threshold for paired information 0.0604812 2:11:05.379 2G / 9G INFO StageManager (stage.cpp : 125) STAGE == Distance Estimation 2:11:05.379 2G / 9G INFO General (distance_estimation.cpp : 234) Processing library #0 2:11:05.379 2G / 9G INFO General (distance_estimation.cpp : 136) Weight Filter Done 2:11:05.379 2G / 9G INFO DistanceEstimator (distance_estimation.hpp : 187) Using SIMPLE distance estimator 2:11:12.279 2G / 9G INFO DistanceEstimator (distance_estimation.hpp : 208) Merging maps 2:11:13.176 2G / 9G INFO General (distance_estimation.cpp : 38) Filtering info 2:11:14.619 2G / 9G INFO General (pair_info_filters.hpp : 354) Pruning the index 2:11:14.666 2G / 9G INFO General (distance_estimation.cpp : 184) Refining clustered pair information 2:11:14.778 2G / 9G INFO General (distance_estimation.cpp : 186) The refining of clustered pair information has been finished 2:11:14.778 2G / 9G INFO General (distance_estimation.cpp : 188) Filling paired information 2:11:16.321 2G / 9G INFO PairInfoImprover (pair_info_improver.hpp : 61) Paired info stats: missing = 41043; contradictional = 7300 2:11:17.864 2G / 9G INFO PairInfoImprover (pair_info_improver.hpp : 61) Paired info stats: missing = 6014; contradictional = 0 2:11:17.864 2G / 9G INFO General (distance_estimation.cpp : 193) Filling scaffolding index 2:11:17.864 2G / 9G INFO DistanceEstimator (distance_estimation.hpp : 187) Using SMOOTHING distance estimator 2:11:27.956 2G / 9G INFO DistanceEstimator (distance_estimation.hpp : 208) Merging maps 2:11:28.003 2G / 9G INFO General (distance_estimation.cpp : 38) Filtering info 2:11:28.303 2G / 9G INFO General (pair_info_filters.hpp : 354) Pruning the index 2:11:28.816 2G / 9G INFO StageManager (stage.cpp : 125) STAGE == Repeat Resolving 2:11:28.816 2G / 9G INFO General (contig_output.hpp : 283) Outputting contigs to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_137-dipSPAdes-3.5.0-trimmed/spades//K77/before_rr.fasta 2:12:13.283 2G / 9G INFO General (repeat_resolving.cpp : 59) Using Path-Extend repeat resolving 2:12:13.283 2G / 9G INFO General (path_extend_launch.hpp : 459) Threshold for library #0 is 0.0604812 2:12:13.284 2G / 9G INFO General (path_extend_launch.hpp : 298) Path-Extend repeat resolving tool started 2:12:13.336 2G / 9G INFO General (path_extend_launch.hpp : 316) Using 1 paired-end library 2:12:13.336 2G / 9G INFO General (path_extend_launch.hpp : 317) Using 1 paired-end scaffolding library 2:12:13.337 2G / 9G INFO General (path_extend_launch.hpp : 318) Using 0 mate-pair libraries 2:12:13.337 2G / 9G INFO General (path_extend_launch.hpp : 319) Using 0 single read libraries 2:12:13.337 2G / 9G INFO General (path_extend_launch.hpp : 320) Scaffolder is on 2:12:13.685 2G / 9G INFO General (path_extend_launch.hpp : 332) Growing paths using paired-end and long single reads 2:12:13.685 2G / 9G INFO PathExtender (path_extender.hpp : 611) Processed 0 paths from 25225 (0%) 2:12:14.001 2G / 9G INFO PathExtender (path_extender.hpp : 609) Processed 128 paths from 25225 (0%) 2:12:14.193 2G / 9G INFO PathExtender (path_extender.hpp : 609) Processed 256 paths from 25225 (1%) 2:12:14.757 2G / 9G INFO PathExtender (path_extender.hpp : 609) Processed 512 paths from 25225 (2%) 2:12:15.672 2G / 9G INFO PathExtender (path_extender.hpp : 609) Processed 1024 paths from 25225 (4%) 2:12:16.883 2G / 9G INFO PathExtender (path_extender.hpp : 609) Processed 2048 paths from 25225 (8%) 2:12:17.352 2G / 9G INFO PathExtender (path_extender.hpp : 611) Processed 2523 paths from 25225 (10%) 2:12:18.084 2G / 9G INFO PathExtender (path_extender.hpp : 609) Processed 4096 paths from 25225 (16%) 2:12:18.688 2G / 9G INFO PathExtender (path_extender.hpp : 611) Processed 5046 paths from 25225 (20%) 2:12:19.699 2G / 9G INFO PathExtender (path_extender.hpp : 611) Processed 7569 paths from 25225 (30%) 2:12:19.801 2G / 9G INFO PathExtender (path_extender.hpp : 609) Processed 8192 paths from 25225 (32%) 2:12:20.388 2G / 9G INFO PathExtender (path_extender.hpp : 611) Processed 10092 paths from 25225 (40%) 2:12:21.028 2G / 9G INFO PathExtender (path_extender.hpp : 611) Processed 12615 paths from 25225 (50%) 2:12:22.907 2G / 9G INFO PathExtender (path_extender.hpp : 611) Processed 15138 paths from 25225 (60%) 2:12:24.299 2G / 9G INFO PathExtender (path_extender.hpp : 609) Processed 16384 paths from 25225 (64%) 2:12:25.849 2G / 9G INFO PathExtender (path_extender.hpp : 611) Processed 17661 paths from 25225 (70%) 2:12:28.299 2G / 9G INFO PathExtender (path_extender.hpp : 611) Processed 20184 paths from 25225 (80%) 2:12:29.869 2G / 9G INFO PathExtender (path_extender.hpp : 611) Processed 22707 paths from 25225 (90%) 2:12:31.763 2G / 9G INFO PathExtendIO (pe_io.hpp : 339) Constructing FASTG file from paths 2:12:32.303 2G / 9G INFO PathExtendIO (pe_io.hpp : 342) Writing contigs in FASTG to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_137-dipSPAdes-3.5.0-trimmed/spades//K77/final_contigs.fastg 2:12:32.303 2G / 9G INFO PathExtendIO (pe_io.hpp : 343) Writing contigs in FASTA to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_137-dipSPAdes-3.5.0-trimmed/spades//K77/final_contigs.fasta 2:13:15.693 2G / 9G INFO PathExtendIO (pe_io.hpp : 339) Constructing FASTG file from paths 2:13:16.261 2G / 9G INFO PathExtendIO (pe_io.hpp : 342) Writing contigs in FASTG to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_137-dipSPAdes-3.5.0-trimmed/spades//K77/path_extend/pe_before_traversal.fastg 2:13:16.261 2G / 9G INFO PathExtendIO (pe_io.hpp : 343) Writing contigs in FASTA to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_137-dipSPAdes-3.5.0-trimmed/spades//K77/path_extend/pe_before_traversal.fasta 2:14:17.772 2G / 9G INFO General (path_extend_launch.hpp : 281) Traversing tandem repeats 2:14:19.923 2G / 9G INFO PathExtendIO (pe_io.hpp : 339) Constructing FASTG file from paths 2:14:20.355 2G / 9G INFO PathExtendIO (pe_io.hpp : 342) Writing contigs in FASTG to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_137-dipSPAdes-3.5.0-trimmed/spades//K77/scaffolds.fastg 2:14:20.355 2G / 9G INFO PathExtendIO (pe_io.hpp : 343) Writing contigs in FASTA to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_137-dipSPAdes-3.5.0-trimmed/spades//K77/scaffolds.fasta 2:15:03.566 2G / 9G INFO General (launch.hpp : 82) SPAdes finished 2:15:07.752 308M / 9G INFO General (main.cpp : 166) Assembling time: 2 hours 15 minutes 7 seconds ===== Assembling finished. * Corrected reads are in /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_137-dipSPAdes-3.5.0-trimmed/spades/corrected/ * Assembled contigs are in /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_137-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_137-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_137-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_137-dipSPAdes-3.5.0-trimmed/spades/spades.log Thank you for using SPAdes!