Command line: --diploid --pe1-1 /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_129/reads.end1.paired.fastq.gz --pe1-2 /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_129/reads.end2.paired.fastq.gz -t 16 -o /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_129-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_129-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_129/reads.end1.paired.fastq.gz'] right reads: ['/N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_129/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_129-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_129-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_129-dipSPAdes-3.5.0-trimmed/spades/corrected/configs/config.info 0:00:00.020 4M / 4M INFO General (main.cpp : 82) Loading config from /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_129-dipSPAdes-3.5.0-trimmed/spades/corrected/configs/config.info 0:00:00.181 4M / 4M INFO General (memory_limit.hpp : 42) Memory limit set to 100 Gb 0:00:00.182 4M / 4M INFO General (main.cpp : 91) Trying to determine PHRED offset 0:00:00.219 4M / 4M INFO General (main.cpp : 97) Determined value is 33 0:00:00.244 4M / 4M INFO General (hammer_tools.cpp : 36) Hamming graph threshold tau=1, k=21, subkmer positions = [ 0 10 ] === ITERATION 0 begins === 0:00:00.245 4M / 4M INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:00:00.245 4M / 4M INFO K-mer Splitting (kmer_data.cpp : 127) Splitting kmer instances into 256 buckets. This might take a while. 0:00:00.246 4M / 4M INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:00:00.246 4M / 4M INFO K-mer Splitting (kmer_data.cpp : 145) Memory available for splitting buffers: 2.08325 Gb 0:00:00.246 4M / 4M INFO K-mer Splitting (kmer_data.cpp : 153) Using cell size of 262144 0:00:03.056 8G / 8G INFO K-mer Splitting (kmer_data.cpp : 167) Processing /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_129/reads.end1.paired.fastq.gz 0:03:32.375 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 176) Processed 3257391 reads 0:04:47.200 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 176) Processed 6456775 reads 0:05:41.487 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 176) Processed 9633447 reads 0:06:27.317 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 176) Processed 12331381 reads 0:06:27.323 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 167) Processing /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_129/reads.end2.paired.fastq.gz 0:07:26.741 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 176) Processed 15814299 reads 0:08:26.376 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 176) Processed 19292585 reads 0:11:54.050 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 176) Processed 22809563 reads 0:13:35.397 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 176) Processed 24662762 reads 0:13:35.399 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 181) Processed 24662762 reads 0:13:36.509 64M / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:14:11.568 64M / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 294010606 kmers in total. 0:14:11.570 64M / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:14:24.955 64M / 9G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:15:03.838 192M / 9G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:15:15.715 192M / 9G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 101709328 bytes occupied (2.7675 bits per kmer). 0:15:15.717 192M / 9G INFO K-mer Counting (kmer_data.cpp : 266) Arranging kmers in hash map order 0:18:10.135 192M / 9G INFO K-mer Counting (kmer_data.cpp : 279) Done. Total swaps: 294010302 0:18:12.166 2G / 9G INFO General (main.cpp : 151) Clustering Hamming graph. 0:18:12.168 2G / 9G INFO Hamming Clustering (hamcluster.cpp : 115) Serializing sub-kmers. 0:18:12.168 2G / 9G INFO Hamming Clustering (hamcluster.cpp : 120) Serializing: [0, 10) 0:21:28.229 2G / 9G INFO Hamming Clustering (hamcluster.cpp : 120) Serializing: [10, 21) 0:24:44.245 2G / 9G INFO Hamming Clustering (hamcluster.cpp : 129) Splitting sub-kmers, pass 1. 0:29:05.640 2G / 9G INFO Hamming Clustering (hamcluster.cpp : 134) Splitting done. Processed 2 blocks. Produced 5020334 blocks. 0:29:05.640 2G / 9G INFO Hamming Clustering (hamcluster.cpp : 145) Merge sub-kmers, pass 1 0:44:20.487 2G / 9G INFO Hamming Clustering (hamcluster.cpp : 170) Merge done, total 1592651 new blocks generated. 0:44:22.131 2G / 9G INFO Hamming Clustering (hamcluster.cpp : 175) Spliting sub-kmers, pass 2. 1:06:20.182 2G / 9G INFO Hamming Clustering (hamcluster.cpp : 180) Splitting done. Processed 3185302 blocks. Produced 556110660 blocks. 1:06:20.182 2G / 9G INFO Hamming Clustering (hamcluster.cpp : 187) Merge sub-kmers, pass 2 1:19:01.846 2G / 9G INFO Hamming Clustering (hamcluster.cpp : 205) Merge done, saw 277178 big blocks out of 556110660 processed. 1:23:14.474 2G / 10G INFO General (main.cpp : 165) Clustering done. Total clusters: 135974093 1:23:14.474 2G / 10G INFO K-mer Counting (kmer_data.cpp : 284) Collecting K-mer information, this takes a while. 1:23:20.434 15G / 15G INFO K-mer Counting (kmer_data.cpp : 290) Processing /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_129/reads.end1.paired.fastq.gz 1:26:25.523 15G / 15G INFO K-mer Counting (kmer_data.cpp : 290) Processing /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_129/reads.end2.paired.fastq.gz 1:29:23.865 15G / 15G INFO K-mer Counting (kmer_data.cpp : 297) Collection done, postprocessing. 1:29:31.213 15G / 15G INFO K-mer Counting (kmer_data.cpp : 310) There are 294010606 kmers in total. Among them 147847934 (50.2866%) are singletons. 1:29:31.213 15G / 15G INFO General (main.cpp : 203) Subclustering Hamming graph 1:33:17.844 15G / 15G INFO Hamming Subclustering (kmer_cluster.cpp : 626) Subclustering done. Total 96467 non-read kmers were generated. 1:33:17.844 15G / 15G INFO Hamming Subclustering (kmer_cluster.cpp : 627) Subclustering statistics: 1:33:17.844 15G / 15G INFO Hamming Subclustering (kmer_cluster.cpp : 628) Total singleton hamming clusters: 77792815. Among them 57847046 (74.3604%) are good 1:33:17.844 15G / 15G INFO Hamming Subclustering (kmer_cluster.cpp : 629) Total singleton subclusters: 7353532. Among them 7353466 (99.9991%) are good 1:33:17.844 15G / 15G INFO Hamming Subclustering (kmer_cluster.cpp : 630) Total non-singleton subcluster centers: 63638937. Among them 43195950 (67.8766%) are good 1:33:17.845 15G / 15G INFO Hamming Subclustering (kmer_cluster.cpp : 631) Average size of non-trivial subcluster: 3.37463 kmers 1:33:17.845 15G / 15G INFO Hamming Subclustering (kmer_cluster.cpp : 632) Average number of sub-clusters per non-singleton cluster: 1.22019 1:33:17.845 15G / 15G INFO Hamming Subclustering (kmer_cluster.cpp : 633) Total solid k-mers: 108396462 1:33:17.845 15G / 15G INFO Hamming Subclustering (kmer_cluster.cpp : 634) Substitution probabilities: [4,4]((0.897645,0.0234307,0.0265132,0.0524108),(0.0362059,0.927895,0.01301,0.0228894),(0.0218941,0.0126578,0.929049,0.0363989),(0.0516839,0.0267764,0.0238344,0.897705)) 1:33:18.323 15G / 15G INFO General (main.cpp : 208) Finished clustering. 1:33:18.323 15G / 15G INFO General (main.cpp : 228) Starting solid k-mers expansion in 16 threads. 1:37:24.911 15G / 15G INFO General (main.cpp : 249) Solid k-mers iteration 0 produced 47212982 new k-mers. 1:41:29.596 15G / 15G INFO General (main.cpp : 249) Solid k-mers iteration 1 produced 1231374 new k-mers. 1:45:34.788 15G / 15G INFO General (main.cpp : 249) Solid k-mers iteration 2 produced 34791 new k-mers. 1:49:39.779 15G / 15G INFO General (main.cpp : 249) Solid k-mers iteration 3 produced 2107 new k-mers. 1:53:47.411 15G / 15G INFO General (main.cpp : 249) Solid k-mers iteration 4 produced 140 new k-mers. 1:57:55.805 15G / 15G INFO General (main.cpp : 249) Solid k-mers iteration 5 produced 22 new k-mers. 2:02:02.863 15G / 15G INFO General (main.cpp : 249) Solid k-mers iteration 6 produced 0 new k-mers. 2:02:02.863 15G / 15G INFO General (main.cpp : 253) Solid k-mers finalized 2:02:02.864 15G / 15G INFO General (hammer_tools.cpp : 210) Starting read correction in 16 threads. 2:02:02.864 15G / 15G INFO General (hammer_tools.cpp : 222) Correcting pair of reads: /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_129/reads.end1.paired.fastq.gz and /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_129/reads.end2.paired.fastq.gz 2:02:28.279 17G / 17G INFO General (hammer_tools.cpp : 166) Prepared batch 0 of 1600000 reads. 2:02:51.212 17G / 17G INFO General (hammer_tools.cpp : 175) Processed batch 0 2:03:27.261 17G / 17G INFO General (hammer_tools.cpp : 185) Written batch 0 2:03:51.519 17G / 17G INFO General (hammer_tools.cpp : 166) Prepared batch 1 of 1600000 reads. 2:04:15.236 17G / 17G INFO General (hammer_tools.cpp : 175) Processed batch 1 2:04:50.932 17G / 17G INFO General (hammer_tools.cpp : 185) Written batch 1 2:05:14.843 17G / 17G INFO General (hammer_tools.cpp : 166) Prepared batch 2 of 1600000 reads. 2:05:35.268 17G / 17G INFO General (hammer_tools.cpp : 175) Processed batch 2 2:05:50.797 17G / 17G INFO General (hammer_tools.cpp : 185) Written batch 2 2:06:14.233 17G / 17G INFO General (hammer_tools.cpp : 166) Prepared batch 3 of 1600000 reads. 2:06:34.693 17G / 17G INFO General (hammer_tools.cpp : 175) Processed batch 3 2:06:50.223 17G / 17G INFO General (hammer_tools.cpp : 185) Written batch 3 2:07:13.519 17G / 17G INFO General (hammer_tools.cpp : 166) Prepared batch 4 of 1600000 reads. 2:07:33.964 17G / 17G INFO General (hammer_tools.cpp : 175) Processed batch 4 2:07:49.476 17G / 17G INFO General (hammer_tools.cpp : 185) Written batch 4 2:08:12.818 17G / 17G INFO General (hammer_tools.cpp : 166) Prepared batch 5 of 1600000 reads. 2:08:33.144 17G / 17G INFO General (hammer_tools.cpp : 175) Processed batch 5 2:08:48.843 17G / 17G INFO General (hammer_tools.cpp : 185) Written batch 5 2:09:11.997 17G / 17G INFO General (hammer_tools.cpp : 166) Prepared batch 6 of 1600000 reads. 2:09:32.518 17G / 17G INFO General (hammer_tools.cpp : 175) Processed batch 6 2:09:47.973 17G / 17G INFO General (hammer_tools.cpp : 185) Written batch 6 2:10:04.177 17G / 17G INFO General (hammer_tools.cpp : 166) Prepared batch 7 of 1131381 reads. 2:10:20.173 17G / 17G INFO General (hammer_tools.cpp : 175) Processed batch 7 2:10:51.417 17G / 17G INFO General (hammer_tools.cpp : 185) Written batch 7 2:10:54.459 15G / 17G INFO General (hammer_tools.cpp : 269) Correction done. Changed 4255828 bases in 3401344 reads. 2:10:54.460 15G / 17G INFO General (hammer_tools.cpp : 270) Failed to correct 397255414 bases out of 3674208704. 2:10:54.530 2G / 17G INFO General (main.cpp : 286) Saving corrected dataset description to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_129-dipSPAdes-3.5.0-trimmed/spades/corrected/corrected.yaml 2:10:54.533 2G / 17G INFO General (main.cpp : 293) All done. Exiting. == Compressing corrected reads (with gzip) == Dataset description file was created: /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_129-dipSPAdes-3.5.0-trimmed/spades/corrected/corrected.yaml ===== Read error correction finished. ===== Assembling started. == Running assembler: K21 0:00:00.031 4M / 4M INFO General (memory_limit.hpp : 42) Memory limit set to 100 Gb 0:00:00.080 4M / 4M INFO General (main.cpp : 146) Assembling dataset (/N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_129-dipSPAdes-3.5.0-trimmed/spades/dataset.info) with K=21 0:00:00.087 4M / 4M INFO General (launch.hpp : 28) SPAdes started 0:00:00.088 4M / 4M INFO General (launch.hpp : 29) Starting from stage: construction 0:00:00.133 4M / 4M INFO StageManager (stage.cpp : 125) STAGE == Construction 0:00:00.140 4M / 4M INFO General (read_converter.hpp : 79) Converting reads to binary format (takes a while) 0:00:00.140 4M / 4M INFO General (read_converter.hpp : 81) Paired reads for library #0 0:00:01.280 80M / 80M INFO General (binary_converter.hpp : 138) 16384 reads processed 0:00:01.683 96M / 96M INFO General (binary_converter.hpp : 138) 32768 reads processed 0:00:02.482 124M / 124M INFO General (binary_converter.hpp : 138) 65536 reads processed 0:00:04.084 184M / 184M INFO General (binary_converter.hpp : 138) 131072 reads processed 0:00:07.295 300M / 300M INFO General (binary_converter.hpp : 138) 262144 reads processed 0:00:13.734 536M / 536M INFO General (binary_converter.hpp : 138) 524288 reads processed 0:00:29.353 900M / 900M INFO General (binary_converter.hpp : 138) 1048576 reads processed 0:00:58.312 904M / 904M INFO General (binary_converter.hpp : 138) 2097152 reads processed 0:01:56.601 904M / 904M INFO General (binary_converter.hpp : 138) 4194304 reads processed 0:03:54.439 904M / 904M INFO General (binary_converter.hpp : 138) 8388608 reads processed 0:05:42.126 232M / 908M INFO General (binary_converter.hpp : 158) 12210813 reads written 0:05:42.344 4M / 908M INFO General (read_converter.hpp : 91) Single reads for library #0 0:05:44.216 140M / 908M INFO General (binary_converter.hpp : 138) 16384 reads processed 0:05:44.433 144M / 908M INFO General (binary_converter.hpp : 138) 32768 reads processed 0:05:44.820 160M / 908M INFO General (binary_converter.hpp : 138) 65536 reads processed 0:05:45.667 184M / 908M INFO General (binary_converter.hpp : 158) 120366 reads written 0:05:45.836 4M / 908M INFO General (graph_construction.hpp : 129) Constructing DeBruijn graph for k=21 0:05:45.840 4M / 908M INFO General (kmer_splitters.hpp : 172) Splitting kmer instances into 256 buckets. This might take a while. 0:05:45.841 4M / 908M INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:05:45.841 4M / 908M INFO General (kmer_splitters.hpp : 190) Memory available for splitting buffers: 2.08325 Gb 0:05:45.841 4M / 908M INFO General (kmer_splitters.hpp : 199) Using cell size of 262144 0:08:43.164 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 16688980 reads 0:09:08.346 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 33374347 reads 0:09:32.179 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 49083984 reads 0:09:32.180 8G / 9G INFO General (kmer_splitters.hpp : 234) Adding contigs from previous K 0:09:32.180 8G / 9G INFO General (kmer_splitters.hpp : 245) Used 49083984 reads. Maximum read length 151 0:09:32.181 8G / 9G INFO General (kmer_splitters.hpp : 246) Average read length 149.668 0:09:34.286 64M / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:09:57.239 64M / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 119854941 kmers in total. 0:09:57.239 64M / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:10:02.702 64M / 9G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:10:02.703 64M / 9G INFO General (kmer_splitters.hpp : 379) Splitting kmer instances into 256 buckets. This might take a while. 0:10:02.704 64M / 9G INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:10:02.704 64M / 9G INFO General (kmer_splitters.hpp : 397) Memory available for splitting buffers: 2.08203 Gb 0:10:02.704 64M / 9G INFO General (kmer_splitters.hpp : 405) Using cell size of 262144 0:13:15.817 8G / 9G INFO General (kmer_splitters.hpp : 428) Processed 119854941 kmers 0:13:15.818 8G / 9G INFO General (kmer_splitters.hpp : 437) Used 119854941 kmers. 0:13:16.344 64M / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:13:20.413 64M / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 116395096 kmers in total. 0:13:20.413 64M / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:13:25.862 64M / 9G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:13:39.063 64M / 9G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:14:03.830 64M / 9G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 40265462 bytes occupied (2.7675 bits per kmer). 0:14:04.031 176M / 9G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 382) Building k-mer extensions from k+1-mers 0:14:15.614 176M / 9G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 386) Building k-mer extensions from k+1-mers finished. 0:14:15.618 176M / 9G INFO Early tip clipping (early_simplification.hpp : 236) Early tip clipping 0:20:14.403 176M / 9G INFO Early tip clipping (early_simplification.hpp : 239) 5637027 22-mers were removed by early tip clipper 0:20:14.404 176M / 9G INFO General (graph_construction.hpp : 145) Condensing graph 0:20:14.424 176M / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 337) Extracting unbranching paths 0:21:36.245 1G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 351) Extracting unbranching paths finished. 18350608 sequences extracted 0:21:45.902 1G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 311) Collecting perfect loops 0:22:21.465 1G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 326) Collecting perfect loops finished. 24 loops collected 0:22:34.269 3G / 9G INFO General (graph_construction.hpp : 150) Building index with from graph 0:22:34.271 3G / 9G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:22:34.271 3G / 9G INFO General (kmer_splitters.hpp : 289) Splitting kmer instances into 16 buckets. This might take a while. 0:22:34.271 3G / 9G INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:22:34.271 3G / 9G INFO General (kmer_splitters.hpp : 307) Memory available for splitting buffers: 32.138 Gb 0:22:34.271 3G / 9G INFO General (kmer_splitters.hpp : 312) Using cell size of 4194304 0:25:10.495 4G / 9G INFO General (kmer_splitters.hpp : 325) Processed 10785374 edges 0:27:30.508 4G / 9G INFO General (kmer_splitters.hpp : 325) Processed 18350632 edges 0:27:30.509 4G / 9G INFO General (kmer_splitters.hpp : 330) Used 18350632 sequences. 0:27:30.569 3G / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:27:56.105 3G / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 114217914 kmers in total. 0:27:56.106 3G / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:28:00.623 3G / 9G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:30:40.804 3G / 9G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:31:11.956 3G / 9G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 39512297 bytes occupied (2.7675 bits per kmer). 0:31:13.944 6G / 9G INFO General (edge_index_builders.hpp : 21) Collecting k-mer coverage information from graph, this takes a while. 0:34:39.114 6G / 9G INFO General (graph_construction.hpp : 182) Filling coverage index 0:34:39.114 6G / 9G INFO General (edge_index_builders.hpp : 99) Collecting k-mer coverage information from reads, this takes a while. 0:38:12.877 6G / 9G INFO General (graph_construction.hpp : 184) Filling coverage and flanking coverage from index 0:38:40.900 6G / 9G INFO General (construction.cpp : 33) Figured out: read length = 151 0:38:40.917 6G / 9G INFO StageManager (stage.cpp : 125) STAGE == EC Threshold Finding 0:38:53.148 6G / 9G INFO General (kmer_coverage_model.cpp : 178) Kmer coverage valley at: 11 0:38:53.210 6G / 9G INFO General (kmer_coverage_model.cpp : 198) K-mer histogram maximum: 47 0:38:53.210 6G / 9G INFO General (kmer_coverage_model.cpp : 234) Estimated median coverage: 47. Coverage mad: 13.3434 0:38:53.211 6G / 9G INFO General (kmer_coverage_model.cpp : 261) Fitting coverage model 0:38:53.446 6G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 2 0:38:53.890 6G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 4 0:38:55.434 6G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 8 0:38:58.437 6G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 16 0:39:03.675 6G / 9G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 43.8617. Fitted coverage std. dev: 13.2036 0:39:03.679 6G / 9G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 0.337534 0:39:03.679 6G / 9G INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 23 0:39:03.679 6G / 9G INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 23 0:39:03.679 6G / 9G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 61244943 0:39:03.702 6G / 9G INFO General (genomic_info_filler.cpp : 103) Mean coverage was calculated as 43.8617 0:39:03.703 6G / 9G INFO General (genomic_info_filler.cpp : 117) EC coverage threshold value was calculated as 23 0:39:03.703 6G / 9G INFO General (genomic_info_filler.cpp : 118) Trusted kmer low bound: 0 0:39:03.703 6G / 9G INFO StageManager (stage.cpp : 125) STAGE == Simplification 0:39:03.986 3G / 9G INFO General (graph_simplification.hpp : 911) Graph simplification started 0:39:04.007 3G / 9G INFO General (graph_simplification.hpp : 924) Fast simplification mode enabled 0:39:04.011 3G / 9G INFO General (graph_simplification.hpp : 771) PROCEDURE == Presimplification 0:39:04.015 3G / 9G INFO General (graph_simplification.hpp : 211) Removing short low covered self-conjugate connections 0:39:05.125 3G / 9G INFO General (graph_simplification.hpp : 403) Removing isolated edges 0:39:05.125 3G / 9G INFO General (graph_simplification.hpp : 404) All edges shorter than 151 will be removed 0:39:05.125 3G / 9G INFO General (graph_simplification.hpp : 405) Also edges shorter than 0 and coverage smaller than 0 will be removed 0:39:06.924 3G / 9G INFO General (graph_simplification.hpp : 687) Non parallel mode 0:40:03.914 4G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:42:16.889 4G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:46:12.580 3G / 9G INFO General (graph_simplification.hpp : 644) Using permanent iterators 0:46:12.592 3G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 1 0:46:21.941 3G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:47:02.110 3G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:47:21.265 3G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 2 0:47:21.265 3G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:47:21.609 3G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:47:35.792 3G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 3 0:47:35.792 3G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:47:36.079 3G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:47:41.279 3G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 4 0:47:41.280 3G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:47:41.393 3G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:47:45.389 3G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 5 0:47:45.389 3G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:47:45.474 3G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:47:48.326 3G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 6 0:47:48.326 3G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:47:48.388 3G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:47:50.853 3G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 7 0:47:50.853 3G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:47:50.904 3G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:47:53.492 3G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 8 0:47:53.492 3G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:47:53.544 3G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:47:55.867 3G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 9 0:47:55.867 3G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:47:55.914 3G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:47:58.186 3G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 10 0:47:58.187 3G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:47:58.229 3G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:48:00.477 3G / 9G INFO General (graph_simplification.hpp : 796) PROCEDURE == Post simplification 0:48:00.478 3G / 9G INFO General (graph_simplification.hpp : 644) Using permanent iterators 0:48:00.478 3G / 9G INFO General (graph_simplification.hpp : 806) Iteration 0 0:48:00.482 3G / 9G INFO General (graph_simplification.hpp : 247) Removal of relatively low covered connections disabled 0:48:03.887 3G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:48:11.874 3G / 9G INFO General (graph_simplification.hpp : 806) Iteration 1 0:48:11.874 3G / 9G INFO General (graph_simplification.hpp : 247) Removal of relatively low covered connections disabled 0:48:11.874 3G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:48:14.576 3G / 9G INFO StageManager (stage.cpp : 125) STAGE == Simplification Cleanup 0:48:14.577 3G / 9G INFO General (graph_simplification.hpp : 403) Removing isolated edges 0:48:14.577 3G / 9G INFO General (graph_simplification.hpp : 404) All edges shorter than 151 will be removed 0:48:14.577 3G / 9G INFO General (graph_simplification.hpp : 405) Also edges shorter than 0 and coverage smaller than 2 will be removed 0:48:14.834 3G / 9G INFO General (simplification.cpp : 56) Removing all the edges having coverage 0 and less 0:48:21.391 3G / 9G INFO General (simplification.cpp : 68) Counting average coverage 0:48:22.136 3G / 9G INFO General (simplification.cpp : 71) Average coverage = 47.085 0:48:22.137 3G / 9G INFO StageManager (stage.cpp : 125) STAGE == Contig Output 0:48:22.157 3G / 9G INFO General (contig_output.hpp : 283) Outputting contigs to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_129-dipSPAdes-3.5.0-trimmed/spades//K21/simplified_contigs.fasta 0:49:09.112 3G / 9G INFO General (contig_output.hpp : 283) Outputting contigs to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_129-dipSPAdes-3.5.0-trimmed/spades//K21/before_rr.fasta 0:51:30.422 3G / 9G INFO General (contig_output.hpp : 283) Outputting contigs to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_129-dipSPAdes-3.5.0-trimmed/spades//K21/final_contigs.fasta 0:53:37.284 3G / 9G INFO General (launch.hpp : 82) SPAdes finished 0:53:47.192 64M / 9G INFO General (main.cpp : 166) Assembling time: 0 hours 53 minutes 47 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_129-dipSPAdes-3.5.0-trimmed/spades/dataset.info) with K=33 0:00:00.001 4M / 4M INFO General (launch.hpp : 28) SPAdes started 0:00:00.001 4M / 4M INFO General (launch.hpp : 29) Starting from stage: construction 0:00:00.002 4M / 4M INFO StageManager (stage.cpp : 125) STAGE == Construction 0:00:00.002 4M / 4M INFO General (construction.cpp : 44) Contigs from previous K will be used 0:00:00.007 4M / 4M INFO General (read_converter.hpp : 49) Binary reads detected 0:00:00.027 4M / 4M INFO General (graph_construction.hpp : 129) Constructing DeBruijn graph for k=33 0:00:00.030 4M / 4M INFO General (kmer_splitters.hpp : 172) Splitting kmer instances into 256 buckets. This might take a while. 0:00:00.031 4M / 4M INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:00:00.031 4M / 4M INFO General (kmer_splitters.hpp : 190) Memory available for splitting buffers: 2.08325 Gb 0:00:00.031 4M / 4M INFO General (kmer_splitters.hpp : 199) Using cell size of 131072 0:02:58.704 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 9195353 reads 0:04:08.061 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 18404605 reads 0:04:22.856 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 27604571 reads 0:07:51.238 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 36812935 reads 0:09:52.266 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 46004573 reads 0:09:58.898 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 49083984 reads 0:09:58.899 8G / 9G INFO General (kmer_splitters.hpp : 234) Adding contigs from previous K 0:10:18.362 8G / 9G INFO General (kmer_splitters.hpp : 245) Used 49083984 reads. Maximum read length 151 0:10:18.362 8G / 9G INFO General (kmer_splitters.hpp : 246) Average read length 149.668 0:10:20.557 64M / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:11:04.568 64M / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 146045430 kmers in total. 0:11:04.568 64M / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:12:12.772 64M / 9G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:12:12.772 64M / 9G INFO General (kmer_splitters.hpp : 379) Splitting kmer instances into 256 buckets. This might take a while. 0:12:12.773 64M / 9G INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:12:12.773 64M / 9G INFO General (kmer_splitters.hpp : 397) Memory available for splitting buffers: 2.08203 Gb 0:12:12.773 64M / 9G INFO General (kmer_splitters.hpp : 405) Using cell size of 131072 0:39:28.625 8G / 9G INFO General (kmer_splitters.hpp : 428) Processed 146045430 kmers 0:39:28.625 8G / 9G INFO General (kmer_splitters.hpp : 437) Used 146045430 kmers. 0:39:29.506 64M / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:40:51.947 64M / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 144299693 kmers in total. 0:40:51.947 64M / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:41:04.721 64M / 9G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:41:26.026 68M / 9G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:41:38.886 68M / 9G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 49918717 bytes occupied (2.7675 bits per kmer). 0:41:39.113 208M / 9G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 382) Building k-mer extensions from k+1-mers 0:41:56.635 208M / 9G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 386) Building k-mer extensions from k+1-mers finished. 0:41:56.639 208M / 9G INFO Early tip clipping (early_simplification.hpp : 236) Early tip clipping 0:49:32.150 208M / 9G INFO Early tip clipping (early_simplification.hpp : 239) 22311324 34-mers were removed by early tip clipper 0:49:32.150 208M / 9G INFO General (graph_construction.hpp : 145) Condensing graph 0:49:32.150 208M / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 337) Extracting unbranching paths 0:51:18.588 1G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 351) Extracting unbranching paths finished. 10147181 sequences extracted 0:51:30.324 1G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 311) Collecting perfect loops 0:52:18.202 1G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 326) Collecting perfect loops finished. 56 loops collected 0:52:25.710 2G / 9G INFO General (graph_construction.hpp : 150) Building index with from graph 0:52:25.712 2G / 9G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:52:25.712 2G / 9G INFO General (kmer_splitters.hpp : 289) Splitting kmer instances into 16 buckets. This might take a while. 0:52:25.712 2G / 9G INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:52:25.712 2G / 9G INFO General (kmer_splitters.hpp : 307) Memory available for splitting buffers: 32.6107 Gb 0:52:25.712 2G / 9G INFO General (kmer_splitters.hpp : 312) Using cell size of 2097152 0:56:56.620 2G / 9G INFO General (kmer_splitters.hpp : 325) Processed 2751240 edges 0:59:06.503 2G / 9G INFO General (kmer_splitters.hpp : 325) Processed 5503638 edges 1:01:04.266 2G / 9G INFO General (kmer_splitters.hpp : 325) Processed 8252588 edges 1:04:11.976 2G / 9G INFO General (kmer_splitters.hpp : 325) Processed 10147237 edges 1:04:11.976 2G / 9G INFO General (kmer_splitters.hpp : 330) Used 10147237 sequences. 1:04:12.060 2G / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 1:04:49.485 2G / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 123734106 kmers in total. 1:04:49.485 2G / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 1:05:01.241 2G / 9G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 1:07:59.505 2G / 9G INFO General (kmer_index.hpp : 371) Merging final buckets. 1:08:08.820 2G / 9G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 42804307 bytes occupied (2.7675 bits per kmer). 1:08:10.992 4G / 9G INFO General (edge_index_builders.hpp : 21) Collecting k-mer coverage information from graph, this takes a while. 1:12:01.034 4G / 9G INFO General (graph_construction.hpp : 182) Filling coverage index 1:12:01.034 4G / 9G INFO General (edge_index_builders.hpp : 99) Collecting k-mer coverage information from reads, this takes a while. 1:15:28.394 4G / 9G INFO General (graph_construction.hpp : 184) Filling coverage and flanking coverage from index 1:15:57.780 4G / 9G INFO General (construction.cpp : 33) Figured out: read length = 151 1:15:57.797 4G / 9G INFO StageManager (stage.cpp : 125) STAGE == EC Threshold Finding 1:16:07.850 4G / 9G INFO General (kmer_coverage_model.cpp : 178) Kmer coverage valley at: 10 1:16:07.850 4G / 9G INFO General (kmer_coverage_model.cpp : 198) K-mer histogram maximum: 42 1:16:07.850 4G / 9G INFO General (kmer_coverage_model.cpp : 234) Estimated median coverage: 42. Coverage mad: 11.8608 1:16:07.851 4G / 9G INFO General (kmer_coverage_model.cpp : 261) Fitting coverage model 1:16:08.001 4G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 2 1:16:08.401 4G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 4 1:16:09.569 4G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 8 1:16:12.585 4G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 16 1:16:18.318 4G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 32 1:16:18.318 4G / 9G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 39.3381. Fitted coverage std. dev: 12.424 1:16:18.321 4G / 9G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 0.300848 1:16:18.321 4G / 9G INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 21 1:16:18.322 4G / 9G INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 21 1:16:18.322 4G / 9G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 61585809 1:16:18.322 4G / 9G INFO General (genomic_info_filler.cpp : 103) Mean coverage was calculated as 39.3381 1:16:18.323 4G / 9G INFO General (genomic_info_filler.cpp : 117) EC coverage threshold value was calculated as 21 1:16:18.323 4G / 9G INFO General (genomic_info_filler.cpp : 118) Trusted kmer low bound: 0 1:16:18.323 4G / 9G INFO StageManager (stage.cpp : 125) STAGE == Simplification 1:16:18.590 1G / 9G INFO General (graph_simplification.hpp : 911) Graph simplification started 1:16:18.590 1G / 9G INFO General (graph_simplification.hpp : 924) Fast simplification mode enabled 1:16:18.590 1G / 9G INFO General (graph_simplification.hpp : 771) PROCEDURE == Presimplification 1:16:18.590 1G / 9G INFO General (graph_simplification.hpp : 211) Removing short low covered self-conjugate connections 1:16:19.273 1G / 9G INFO General (graph_simplification.hpp : 403) Removing isolated edges 1:16:19.273 1G / 9G INFO General (graph_simplification.hpp : 404) All edges shorter than 151 will be removed 1:16:19.273 1G / 9G INFO General (graph_simplification.hpp : 405) Also edges shorter than 0 and coverage smaller than 0 will be removed 1:16:20.758 1G / 9G INFO General (graph_simplification.hpp : 687) Non parallel mode 1:16:50.296 2G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 1:18:00.647 2G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 1:20:21.605 2G / 9G INFO General (graph_simplification.hpp : 644) Using permanent iterators 1:20:21.605 2G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 1 1:20:24.233 2G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 1:20:35.219 2G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 1:20:46.750 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 2 1:20:46.751 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 1:20:46.839 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 1:20:52.335 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 3 1:20:52.335 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 1:20:52.404 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 1:20:54.511 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 4 1:20:54.511 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 1:20:54.538 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 1:20:56.054 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 5 1:20:56.054 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 1:20:56.069 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 1:20:57.166 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 6 1:20:57.166 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 1:20:57.176 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 1:20:58.120 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 7 1:20:58.121 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 1:20:58.128 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 1:20:59.076 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 8 1:20:59.076 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 1:20:59.082 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 1:21:00.097 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 9 1:21:00.098 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 1:21:00.103 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 1:21:01.079 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 10 1:21:01.079 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 1:21:01.084 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 1:21:01.868 1G / 9G INFO General (graph_simplification.hpp : 796) PROCEDURE == Post simplification 1:21:01.868 1G / 9G INFO General (graph_simplification.hpp : 644) Using permanent iterators 1:21:01.868 1G / 9G INFO General (graph_simplification.hpp : 806) Iteration 0 1:21:01.868 1G / 9G INFO General (graph_simplification.hpp : 247) Removal of relatively low covered connections disabled 1:21:02.292 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 1:21:03.256 1G / 9G INFO General (graph_simplification.hpp : 806) Iteration 1 1:21:03.257 1G / 9G INFO General (graph_simplification.hpp : 247) Removal of relatively low covered connections disabled 1:21:03.257 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 1:21:03.689 1G / 9G INFO StageManager (stage.cpp : 125) STAGE == Simplification Cleanup 1:21:03.689 1G / 9G INFO General (graph_simplification.hpp : 403) Removing isolated edges 1:21:03.690 1G / 9G INFO General (graph_simplification.hpp : 404) All edges shorter than 151 will be removed 1:21:03.690 1G / 9G INFO General (graph_simplification.hpp : 405) Also edges shorter than 0 and coverage smaller than 2 will be removed 1:21:03.733 1G / 9G INFO General (simplification.cpp : 56) Removing all the edges having coverage 0 and less 1:21:04.506 1G / 9G INFO General (simplification.cpp : 68) Counting average coverage 1:21:04.638 1G / 9G INFO General (simplification.cpp : 71) Average coverage = 39.592 1:21:04.638 1G / 9G INFO StageManager (stage.cpp : 125) STAGE == Contig Output 1:21:04.638 1G / 9G INFO General (contig_output.hpp : 283) Outputting contigs to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_129-dipSPAdes-3.5.0-trimmed/spades//K33/simplified_contigs.fasta 1:21:23.607 1G / 9G INFO General (contig_output.hpp : 283) Outputting contigs to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_129-dipSPAdes-3.5.0-trimmed/spades//K33/before_rr.fasta 1:22:17.757 1G / 9G INFO General (contig_output.hpp : 283) Outputting contigs to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_129-dipSPAdes-3.5.0-trimmed/spades//K33/final_contigs.fasta 1:23:12.067 1G / 9G INFO General (launch.hpp : 82) SPAdes finished 1:23:15.222 64M / 9G INFO General (main.cpp : 166) Assembling time: 1 hours 23 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_129-dipSPAdes-3.5.0-trimmed/spades/dataset.info) with K=55 0:00:00.001 4M / 4M INFO General (launch.hpp : 28) SPAdes started 0:00:00.001 4M / 4M INFO General (launch.hpp : 29) Starting from stage: construction 0:00:00.002 4M / 4M INFO General (launch.hpp : 44) Will need read mapping, kmer mapper will be attached 0:00:00.002 4M / 4M INFO StageManager (stage.cpp : 125) STAGE == Construction 0:00:00.002 4M / 4M INFO General (construction.cpp : 44) Contigs from previous K will be used 0:00:00.006 4M / 4M INFO General (read_converter.hpp : 49) Binary reads detected 0:00:00.025 4M / 4M INFO General (graph_construction.hpp : 129) Constructing DeBruijn graph for k=55 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 0:03:13.967 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 11328339 reads 0:05:47.379 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 22676750 reads 0:06:19.483 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 34006766 reads 0:06:34.623 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 45337645 reads 0:06:40.933 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 49083984 reads 0:06:40.934 8G / 9G INFO General (kmer_splitters.hpp : 234) Adding contigs from previous K 0:08:28.349 8G / 9G INFO General (kmer_splitters.hpp : 245) Used 49083984 reads. Maximum read length 151 0:08:28.350 8G / 9G INFO General (kmer_splitters.hpp : 246) Average read length 149.668 0:08:30.572 64M / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:08:53.349 64M / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 172672937 kmers in total. 0:08:53.351 64M / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:09:07.935 64M / 9G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:09:07.935 64M / 9G INFO General (kmer_splitters.hpp : 379) Splitting kmer instances into 256 buckets. This might take a while. 0:09:07.935 64M / 9G INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:09:07.936 64M / 9G INFO General (kmer_splitters.hpp : 397) Memory available for splitting buffers: 2.08203 Gb 0:09:07.936 64M / 9G INFO General (kmer_splitters.hpp : 405) Using cell size of 131072 0:09:37.896 8G / 9G INFO General (kmer_splitters.hpp : 428) Processed 172672937 kmers 0:09:37.896 8G / 9G INFO General (kmer_splitters.hpp : 437) Used 172672937 kmers. 0:09:38.894 64M / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:09:49.898 64M / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 171911233 kmers in total. 0:09:49.899 64M / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:10:05.474 64M / 9G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:10:26.973 68M / 9G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:10:40.846 68M / 9G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 59470584 bytes occupied (2.7675 bits per kmer). 0:10:41.114 232M / 9G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 382) Building k-mer extensions from k+1-mers 0:11:03.128 232M / 9G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 386) Building k-mer extensions from k+1-mers finished. 0:11:03.134 232M / 9G INFO General (graph_construction.hpp : 145) Condensing graph 0:11:03.134 232M / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 337) Extracting unbranching paths 0:12:52.927 1G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 351) Extracting unbranching paths finished. 12636861 sequences extracted 0:13:09.146 1G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 311) Collecting perfect loops 0:14:07.101 1G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 326) Collecting perfect loops finished. 6 loops collected 0:14:18.450 2G / 9G INFO General (graph_construction.hpp : 150) Building index with from graph 0:14:18.451 2G / 9G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:14:18.451 2G / 9G INFO General (kmer_splitters.hpp : 289) Splitting kmer instances into 16 buckets. This might take a while. 0:14:18.451 2G / 9G INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:14:18.451 2G / 9G INFO General (kmer_splitters.hpp : 307) Memory available for splitting buffers: 32.3346 Gb 0:14:18.451 2G / 9G INFO General (kmer_splitters.hpp : 312) Using cell size of 2097152 0:17:15.093 3G / 9G INFO General (kmer_splitters.hpp : 325) Processed 2455674 edges 0:20:16.420 3G / 9G INFO General (kmer_splitters.hpp : 325) Processed 4911925 edges 0:23:55.402 3G / 9G INFO General (kmer_splitters.hpp : 325) Processed 7367822 edges 0:26:48.774 3G / 9G INFO General (kmer_splitters.hpp : 325) Processed 9822091 edges 0:30:37.865 3G / 9G INFO General (kmer_splitters.hpp : 325) Processed 12279556 edges 0:31:34.217 3G / 9G INFO General (kmer_splitters.hpp : 325) Processed 12636867 edges 0:31:34.217 3G / 9G INFO General (kmer_splitters.hpp : 330) Used 12636867 sequences. 0:31:34.293 2G / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:32:43.643 2G / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 172672937 kmers in total. 0:32:43.644 2G / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:32:58.262 2G / 9G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:37:06.053 3G / 9G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:37:21.400 3G / 9G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 59734081 bytes occupied (2.7675 bits per kmer). 0:37:24.411 6G / 9G INFO General (edge_index_builders.hpp : 21) Collecting k-mer coverage information from graph, this takes a while. 0:43:15.520 6G / 9G INFO General (graph_construction.hpp : 182) Filling coverage index 0:43:15.520 6G / 9G INFO General (edge_index_builders.hpp : 99) Collecting k-mer coverage information from reads, this takes a while. 0:46:25.850 6G / 9G INFO General (graph_construction.hpp : 184) Filling coverage and flanking coverage from index 0:47:08.292 6G / 9G INFO General (construction.cpp : 33) Figured out: read length = 151 0:47:08.310 6G / 9G INFO StageManager (stage.cpp : 125) STAGE == EC Threshold Finding 0:47:20.496 6G / 9G INFO General (kmer_coverage_model.cpp : 178) Kmer coverage valley at: 7 0:47:20.496 6G / 9G INFO General (kmer_coverage_model.cpp : 198) K-mer histogram maximum: 33 0:47:20.496 6G / 9G INFO General (kmer_coverage_model.cpp : 234) Estimated median coverage: 33. Coverage mad: 11.8608 0:47:20.497 6G / 9G INFO General (kmer_coverage_model.cpp : 261) Fitting coverage model 0:47:20.611 6G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 2 0:47:20.928 6G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 4 0:47:22.106 6G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 8 0:47:24.568 6G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 16 0:47:27.496 6G / 9G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 31.4834. Fitted coverage std. dev: 10.6629 0:47:27.499 6G / 9G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 0.40122 0:47:27.499 6G / 9G INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 17 0:47:27.499 6G / 9G INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 17 0:47:27.499 6G / 9G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 61260844 0:47:27.499 6G / 9G INFO General (genomic_info_filler.cpp : 103) Mean coverage was calculated as 31.4834 0:47:27.500 6G / 9G INFO General (genomic_info_filler.cpp : 117) EC coverage threshold value was calculated as 17 0:47:27.500 6G / 9G INFO General (genomic_info_filler.cpp : 118) Trusted kmer low bound: 0 0:47:27.500 6G / 9G INFO StageManager (stage.cpp : 125) STAGE == Gap Closer 0:47:27.535 6G / 9G INFO General (gap_closer.cpp : 157) Preparing shift maps 0:47:38.707 7G / 9G INFO General (gap_closer.cpp : 117) Processing paired reads (takes a while) 0:48:19.125 7G / 9G INFO General (gap_closer.cpp : 136) Used 24421626 paired reads 0:48:19.125 7G / 9G INFO General (gap_closer.cpp : 138) Merging paired indices 0:48:24.767 6G / 9G INFO GapCloser (gap_closer.cpp : 395) Closing short gaps 0:48:58.421 6G / 9G INFO GapCloser (gap_closer.cpp : 424) Closing short gaps complete: filled 340 gaps after checking 10332 candidates 0:49:01.564 6G / 9G INFO StageManager (stage.cpp : 125) STAGE == Simplification 0:49:01.840 2G / 9G INFO General (graph_simplification.hpp : 911) Graph simplification started 0:49:01.840 2G / 9G INFO General (graph_simplification.hpp : 924) Fast simplification mode enabled 0:49:01.840 2G / 9G INFO General (graph_simplification.hpp : 771) PROCEDURE == Presimplification 0:49:01.840 2G / 9G INFO General (graph_simplification.hpp : 211) Removing short low covered self-conjugate connections 0:49:02.775 2G / 9G INFO General (graph_simplification.hpp : 403) Removing isolated edges 0:49:02.776 2G / 9G INFO General (graph_simplification.hpp : 404) All edges shorter than 151 will be removed 0:49:02.776 2G / 9G INFO General (graph_simplification.hpp : 405) Also edges shorter than 0 and coverage smaller than 0 will be removed 0:49:05.259 2G / 9G INFO General (graph_simplification.hpp : 687) Non parallel mode 0:49:42.563 3G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:51:32.358 3G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:52:42.139 2G / 9G INFO General (graph_simplification.hpp : 644) Using permanent iterators 0:52:42.140 2G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 1 0:52:43.173 2G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:52:47.535 2G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:52:50.051 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 2 0:52:50.051 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:52:50.086 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:52:52.860 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 3 0:52:52.860 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:52:52.893 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:52:54.413 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 4 0:52:54.413 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:52:54.430 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:52:55.446 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 5 0:52:55.446 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:52:55.455 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:52:56.511 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 6 0:52:56.511 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:52:56.517 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:52:57.431 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 7 0:52:57.431 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:52:57.436 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:52:58.547 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 8 0:52:58.547 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:52:58.550 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:52:59.714 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 9 0:52:59.714 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:52:59.717 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:53:00.870 972M / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 10 0:53:00.870 972M / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:53:00.873 972M / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:53:01.859 868M / 9G INFO General (graph_simplification.hpp : 796) PROCEDURE == Post simplification 0:53:01.859 868M / 9G INFO General (graph_simplification.hpp : 644) Using permanent iterators 0:53:01.859 868M / 9G INFO General (graph_simplification.hpp : 806) Iteration 0 0:53:01.859 868M / 9G INFO General (graph_simplification.hpp : 247) Removal of relatively low covered connections disabled 0:53:02.007 868M / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:53:02.317 868M / 9G INFO General (graph_simplification.hpp : 806) Iteration 1 0:53:02.317 868M / 9G INFO General (graph_simplification.hpp : 247) Removal of relatively low covered connections disabled 0:53:02.317 868M / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:53:02.512 836M / 9G INFO StageManager (stage.cpp : 125) STAGE == Gap Closer 0:53:02.512 836M / 9G INFO General (graph_pack.hpp : 84) Index refill 0:53:02.513 836M / 9G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:53:02.513 836M / 9G INFO General (kmer_splitters.hpp : 289) Splitting kmer instances into 16 buckets. This might take a while. 0:53:02.514 836M / 9G INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:53:02.514 836M / 9G INFO General (kmer_splitters.hpp : 307) Memory available for splitting buffers: 33.0612 Gb 0:53:02.514 836M / 9G INFO General (kmer_splitters.hpp : 312) Using cell size of 2097152 0:57:39.887 1G / 9G INFO General (kmer_splitters.hpp : 325) Processed 39433 edges 1:01:17.628 1G / 9G INFO General (kmer_splitters.hpp : 325) Processed 78113 edges 1:02:00.454 1G / 9G INFO General (kmer_splitters.hpp : 325) Processed 81946 edges 1:02:00.455 1G / 9G INFO General (kmer_splitters.hpp : 330) Used 81946 sequences. 1:02:00.525 812M / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 1:02:21.455 812M / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 70480411 kmers in total. 1:02:21.455 812M / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 1:02:29.858 812M / 9G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 1:03:58.919 832M / 9G INFO General (kmer_index.hpp : 371) Merging final buckets. 1:04:04.786 832M / 9G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 24381858 bytes occupied (2.7675 bits per kmer). 1:04:05.890 2G / 9G INFO General (edge_index_builders.hpp : 21) Collecting k-mer coverage information from graph, this takes a while. 1:05:57.063 2G / 9G INFO General (gap_closer.cpp : 157) Preparing shift maps 1:05:57.136 2G / 9G INFO General (gap_closer.cpp : 117) Processing paired reads (takes a while) 1:06:38.039 2G / 9G INFO General (gap_closer.cpp : 136) Used 24421626 paired reads 1:06:38.041 2G / 9G INFO General (gap_closer.cpp : 138) Merging paired indices 1:06:38.111 2G / 9G INFO GapCloser (gap_closer.cpp : 395) Closing short gaps 1:06:38.319 2G / 9G INFO GapCloser (gap_closer.cpp : 424) Closing short gaps complete: filled 38 gaps after checking 4979 candidates 1:06:38.835 2G / 9G INFO StageManager (stage.cpp : 125) STAGE == Simplification Cleanup 1:06:38.835 2G / 9G INFO General (graph_simplification.hpp : 403) Removing isolated edges 1:06:38.835 2G / 9G INFO General (graph_simplification.hpp : 404) All edges shorter than 151 will be removed 1:06:38.835 2G / 9G INFO General (graph_simplification.hpp : 405) Also edges shorter than 0 and coverage smaller than 2 will be removed 1:06:39.033 2G / 9G INFO General (simplification.cpp : 56) Removing all the edges having coverage 0 and less 1:06:39.290 2G / 9G INFO General (simplification.cpp : 68) Counting average coverage 1:06:39.336 2G / 9G INFO General (simplification.cpp : 71) Average coverage = 31.2017 1:06:39.336 2G / 9G INFO StageManager (stage.cpp : 125) STAGE == Contig Output 1:06:39.336 2G / 9G INFO General (contig_output.hpp : 283) Outputting contigs to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_129-dipSPAdes-3.5.0-trimmed/spades//K55/simplified_contigs.fasta 1:06:54.657 2G / 9G INFO General (contig_output.hpp : 283) Outputting contigs to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_129-dipSPAdes-3.5.0-trimmed/spades//K55/before_rr.fasta 1:07:39.423 2G / 9G INFO General (contig_output.hpp : 283) Outputting contigs to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_129-dipSPAdes-3.5.0-trimmed/spades//K55/final_contigs.fasta 1:08:24.158 2G / 9G INFO General (launch.hpp : 82) SPAdes finished 1:08:27.249 68M / 9G INFO General (main.cpp : 166) Assembling time: 1 hours 8 minutes 27 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_129-dipSPAdes-3.5.0-trimmed/spades/dataset.info) with K=77 0:00:00.001 4M / 4M INFO General (launch.hpp : 28) SPAdes started 0:00:00.001 4M / 4M INFO General (launch.hpp : 29) Starting from stage: construction 0:00:00.002 4M / 4M INFO General (launch.hpp : 44) Will need read mapping, kmer mapper will be attached 0:00:00.002 4M / 4M INFO StageManager (stage.cpp : 125) STAGE == Construction 0:00:00.002 4M / 4M INFO General (construction.cpp : 44) Contigs from previous K will be used 0:00:00.006 4M / 4M INFO General (read_converter.hpp : 49) Binary reads detected 0:00:00.025 4M / 4M INFO General (graph_construction.hpp : 129) Constructing DeBruijn graph for k=77 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 87381 0:08:27.251 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 9823004 reads 0:37:06.413 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 19665570 reads 0:58:50.001 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 29493767 reads 1:27:48.960 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 39337767 reads 1:31:42.882 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 49083984 reads 1:31:42.882 8G / 9G INFO General (kmer_splitters.hpp : 234) Adding contigs from previous K 1:32:04.679 8G / 9G INFO General (kmer_splitters.hpp : 245) Used 49083984 reads. Maximum read length 151 1:32:04.679 8G / 9G INFO General (kmer_splitters.hpp : 246) Average read length 149.668 1:32:06.873 64M / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 1:32:39.816 64M / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 179003343 kmers in total. 1:32:39.816 64M / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 1:33:05.744 64M / 9G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 1:33:05.744 64M / 9G INFO General (kmer_splitters.hpp : 379) Splitting kmer instances into 256 buckets. This might take a while. 1:33:05.745 64M / 9G INFO General (file_limit.hpp : 29) Open file limit set to 32768 1:33:05.745 64M / 9G INFO General (kmer_splitters.hpp : 397) Memory available for splitting buffers: 2.08203 Gb 1:33:05.746 64M / 9G INFO General (kmer_splitters.hpp : 405) Using cell size of 87381 2:05:12.560 8G / 9G INFO General (kmer_splitters.hpp : 428) Processed 178949045 kmers 2:05:14.250 8G / 9G INFO General (kmer_splitters.hpp : 428) Processed 179003343 kmers 2:05:14.250 8G / 9G INFO General (kmer_splitters.hpp : 437) Used 179003343 kmers. 2:05:15.819 64M / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 2:06:34.741 64M / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 179121963 kmers in total. 2:06:34.741 64M / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 2:07:00.912 64M / 9G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 2:07:24.592 68M / 9G INFO General (kmer_index.hpp : 371) Merging final buckets. 2:07:47.341 68M / 9G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 61965037 bytes occupied (2.7675 bits per kmer). 2:07:47.654 240M / 9G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 382) Building k-mer extensions from k+1-mers 2:08:16.390 240M / 9G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 386) Building k-mer extensions from k+1-mers finished. 2:08:16.395 240M / 9G INFO General (graph_construction.hpp : 145) Condensing graph 2:08:16.395 240M / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 337) Extracting unbranching paths 2:10:16.159 1G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 351) Extracting unbranching paths finished. 10809333 sequences extracted 2:10:34.708 1G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 311) Collecting perfect loops 2:11:46.588 1G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 326) Collecting perfect loops finished. 12 loops collected 2:11:57.344 2G / 9G INFO General (graph_construction.hpp : 150) Building index with from graph 2:11:57.345 2G / 9G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 2:11:57.345 2G / 9G INFO General (kmer_splitters.hpp : 289) Splitting kmer instances into 16 buckets. This might take a while. 2:11:57.345 2G / 9G INFO General (file_limit.hpp : 29) Open file limit set to 32768 2:11:57.346 2G / 9G INFO General (kmer_splitters.hpp : 307) Memory available for splitting buffers: 32.3958 Gb 2:11:57.346 2G / 9G INFO General (kmer_splitters.hpp : 312) Using cell size of 1398101 2:15:42.397 3G / 9G INFO General (kmer_splitters.hpp : 325) Processed 1351801 edges 2:18:05.510 3G / 9G INFO General (kmer_splitters.hpp : 325) Processed 2703137 edges 2:20:52.626 3G / 9G INFO General (kmer_splitters.hpp : 325) Processed 4053857 edges 2:23:20.203 3G / 9G INFO General (kmer_splitters.hpp : 325) Processed 5405173 edges 2:26:48.233 3G / 9G INFO General (kmer_splitters.hpp : 325) Processed 6757143 edges 2:28:58.382 3G / 9G INFO General (kmer_splitters.hpp : 325) Processed 8106785 edges 2:29:06.774 3G / 9G INFO General (kmer_splitters.hpp : 325) Processed 9455902 edges 2:29:15.291 3G / 9G INFO General (kmer_splitters.hpp : 325) Processed 10806532 edges 2:29:17.307 3G / 9G INFO General (kmer_splitters.hpp : 325) Processed 10809345 edges 2:29:17.307 3G / 9G INFO General (kmer_splitters.hpp : 330) Used 10809345 sequences. 2:29:17.384 2G / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 3:00:16.224 2G / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 179003343 kmers in total. 3:00:16.225 2G / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 3:00:59.797 2G / 9G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 3:05:40.792 2G / 9G INFO General (kmer_index.hpp : 371) Merging final buckets. 3:06:22.018 2G / 9G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 61923989 bytes occupied (2.7675 bits per kmer). 3:06:25.129 6G / 9G INFO General (edge_index_builders.hpp : 21) Collecting k-mer coverage information from graph, this takes a while. 3:13:16.210 6G / 9G INFO General (graph_construction.hpp : 182) Filling coverage index 3:13:16.211 6G / 9G INFO General (edge_index_builders.hpp : 99) Collecting k-mer coverage information from reads, this takes a while. 3:16:21.575 6G / 9G INFO General (graph_construction.hpp : 184) Filling coverage and flanking coverage from index 3:17:06.001 6G / 9G INFO General (construction.cpp : 33) Figured out: read length = 151 3:17:06.017 6G / 9G INFO StageManager (stage.cpp : 125) STAGE == EC Threshold Finding 3:17:14.679 6G / 9G INFO General (kmer_coverage_model.cpp : 178) Kmer coverage valley at: 5 3:17:14.679 6G / 9G INFO General (kmer_coverage_model.cpp : 198) K-mer histogram maximum: 24 3:17:14.679 6G / 9G INFO General (kmer_coverage_model.cpp : 234) Estimated median coverage: 24. Coverage mad: 10.3782 3:17:14.680 6G / 9G INFO General (kmer_coverage_model.cpp : 261) Fitting coverage model 3:17:14.766 6G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 2 3:17:14.993 6G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 4 3:17:15.754 6G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 8 3:17:16.582 6G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 16 3:17:17.558 6G / 9G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 23.9303. Fitted coverage std. dev: 8.72712 3:17:17.560 6G / 9G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 0.453358 3:17:17.560 6G / 9G INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 13 3:17:17.560 6G / 9G INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 13 3:17:17.560 6G / 9G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 60572213 3:17:17.560 6G / 9G INFO General (genomic_info_filler.cpp : 103) Mean coverage was calculated as 23.9303 3:17:17.560 6G / 9G INFO General (genomic_info_filler.cpp : 117) EC coverage threshold value was calculated as 13 3:17:17.560 6G / 9G INFO General (genomic_info_filler.cpp : 118) Trusted kmer low bound: 0 3:17:17.560 6G / 9G INFO StageManager (stage.cpp : 125) STAGE == Gap Closer 3:17:17.570 6G / 9G INFO General (gap_closer.cpp : 157) Preparing shift maps 3:17:29.612 7G / 9G INFO General (gap_closer.cpp : 117) Processing paired reads (takes a while) 3:17:59.515 7G / 9G INFO General (gap_closer.cpp : 136) Used 24421626 paired reads 3:17:59.518 7G / 9G INFO General (gap_closer.cpp : 138) Merging paired indices 3:18:07.479 6G / 9G INFO GapCloser (gap_closer.cpp : 395) Closing short gaps 3:18:36.560 6G / 9G INFO GapCloser (gap_closer.cpp : 424) Closing short gaps complete: filled 491 gaps after checking 14789 candidates 3:18:40.292 6G / 9G INFO StageManager (stage.cpp : 125) STAGE == Simplification 3:18:40.731 2G / 9G INFO General (graph_simplification.hpp : 911) Graph simplification started 3:18:40.731 2G / 9G INFO General (graph_simplification.hpp : 924) Fast simplification mode enabled 3:18:40.731 2G / 9G INFO General (graph_simplification.hpp : 771) PROCEDURE == Presimplification 3:18:40.731 2G / 9G INFO General (graph_simplification.hpp : 211) Removing short low covered self-conjugate connections 3:18:41.635 2G / 9G INFO General (graph_simplification.hpp : 403) Removing isolated edges 3:18:41.638 2G / 9G INFO General (graph_simplification.hpp : 404) All edges shorter than 151 will be removed 3:18:41.638 2G / 9G INFO General (graph_simplification.hpp : 405) Also edges shorter than 0 and coverage smaller than 0 will be removed 3:18:45.998 2G / 9G INFO General (graph_simplification.hpp : 687) Non parallel mode 3:19:18.540 3G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 3:21:06.774 2G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 3:21:16.517 1G / 9G INFO General (graph_simplification.hpp : 644) Using permanent iterators 3:21:16.517 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 1 3:21:17.017 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 3:21:19.141 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 3:21:19.230 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 2 3:21:19.230 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 3:21:19.233 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 3:21:20.011 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 3 3:21:20.011 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 3:21:20.026 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 3:21:20.902 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 4 3:21:20.902 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 3:21:20.918 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 3:21:21.768 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 5 3:21:21.768 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 3:21:21.778 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 3:21:22.519 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 6 3:21:22.519 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 3:21:22.525 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 3:21:23.480 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 7 3:21:23.480 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 3:21:23.485 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 3:21:24.590 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 8 3:21:24.590 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 3:21:24.595 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 3:21:25.772 932M / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 9 3:21:25.772 932M / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 3:21:25.776 932M / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 3:21:26.944 792M / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 10 3:21:26.944 792M / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 3:21:26.948 792M / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 3:21:28.021 684M / 9G INFO General (graph_simplification.hpp : 796) PROCEDURE == Post simplification 3:21:28.021 684M / 9G INFO General (graph_simplification.hpp : 644) Using permanent iterators 3:21:28.021 684M / 9G INFO General (graph_simplification.hpp : 806) Iteration 0 3:21:28.021 684M / 9G INFO General (graph_simplification.hpp : 247) Removal of relatively low covered connections disabled 3:21:28.126 684M / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 3:21:28.327 684M / 9G INFO General (graph_simplification.hpp : 806) Iteration 1 3:21:28.327 684M / 9G INFO General (graph_simplification.hpp : 247) Removal of relatively low covered connections disabled 3:21:28.327 684M / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 3:21:28.411 664M / 9G INFO StageManager (stage.cpp : 125) STAGE == Gap Closer 3:21:28.411 664M / 9G INFO General (graph_pack.hpp : 84) Index refill 3:21:28.412 664M / 9G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 3:21:28.412 664M / 9G INFO General (kmer_splitters.hpp : 289) Splitting kmer instances into 16 buckets. This might take a while. 3:21:28.412 664M / 9G INFO General (file_limit.hpp : 29) Open file limit set to 32768 3:21:28.412 664M / 9G INFO General (kmer_splitters.hpp : 307) Memory available for splitting buffers: 33.1172 Gb 3:21:28.412 664M / 9G INFO General (kmer_splitters.hpp : 312) Using cell size of 1398101 3:21:54.041 1G / 9G INFO General (kmer_splitters.hpp : 325) Processed 17392 edges 3:22:13.481 1G / 9G INFO General (kmer_splitters.hpp : 325) Processed 35640 edges 3:22:32.262 1G / 9G INFO General (kmer_splitters.hpp : 325) Processed 54209 edges 3:22:33.122 1G / 9G INFO General (kmer_splitters.hpp : 325) Processed 57437 edges 3:22:33.123 1G / 9G INFO General (kmer_splitters.hpp : 330) Used 57437 sequences. 3:22:33.200 660M / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 3:23:20.631 660M / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 70868888 kmers in total. 3:23:20.631 660M / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 3:23:29.082 660M / 9G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 3:25:03.226 684M / 9G INFO General (kmer_index.hpp : 371) Merging final buckets. 3:25:12.567 684M / 9G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 24516248 bytes occupied (2.7675 bits per kmer). 3:25:13.804 2G / 9G INFO General (edge_index_builders.hpp : 21) Collecting k-mer coverage information from graph, this takes a while. 3:27:22.117 2G / 9G INFO General (gap_closer.cpp : 157) Preparing shift maps 3:27:22.183 2G / 9G INFO General (gap_closer.cpp : 117) Processing paired reads (takes a while) 3:28:12.523 2G / 9G INFO General (gap_closer.cpp : 136) Used 24421626 paired reads 3:28:12.523 2G / 9G INFO General (gap_closer.cpp : 138) Merging paired indices 3:28:12.675 2G / 9G INFO GapCloser (gap_closer.cpp : 395) Closing short gaps 3:28:12.870 2G / 9G INFO GapCloser (gap_closer.cpp : 424) Closing short gaps complete: filled 34 gaps after checking 3181 candidates 3:28:13.338 2G / 9G INFO StageManager (stage.cpp : 125) STAGE == Simplification Cleanup 3:28:13.339 2G / 9G INFO General (graph_simplification.hpp : 403) Removing isolated edges 3:28:13.339 2G / 9G INFO General (graph_simplification.hpp : 404) All edges shorter than 151 will be removed 3:28:13.339 2G / 9G INFO General (graph_simplification.hpp : 405) Also edges shorter than 0 and coverage smaller than 2 will be removed 3:28:13.968 2G / 9G INFO General (simplification.cpp : 56) Removing all the edges having coverage 0 and less 3:28:14.131 2G / 9G INFO General (simplification.cpp : 68) Counting average coverage 3:28:14.153 2G / 9G INFO General (simplification.cpp : 71) Average coverage = 23.4488 3:28:14.153 2G / 9G INFO StageManager (stage.cpp : 125) STAGE == Mismatch Correction 3:29:04.718 2G / 9G INFO General (mismatch_shall_not_pass.hp: 188) Finished collecting potential mismatches positions 3:29:04.847 2G / 9G INFO General (mismatch_shall_not_pass.hp: 291) All edges processed 3:29:04.850 2G / 9G INFO General (mismatch_correction.cpp : 18) Corrected 0 nucleotides 3:29:04.866 2G / 9G INFO StageManager (stage.cpp : 125) STAGE == Paired Information Counting 3:29:05.047 2G / 9G INFO General (pair_info_count.cpp : 150) Graph N50: 15197 3:29:05.068 2G / 9G INFO General (pair_info_count.cpp : 152) Estimating insert size for library #0 3:29:05.068 2G / 9G INFO General (pair_info_count.cpp : 31) Estimating insert size (takes a while) 3:29:05.077 2G / 9G INFO General (short_read_mapper.hpp : 91) Selecting usual mapper 3:29:11.258 2G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 200000 reads 3:29:11.263 2G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 400000 reads 3:29:11.351 2G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 600000 reads 3:29:11.372 2G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 800000 reads 3:29:11.378 2G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 1000000 reads 3:29:11.390 2G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 1200000 reads 3:29:11.502 2G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 2200000 reads 3:29:17.861 2G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 4200000 reads 3:29:24.291 2G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 8400000 reads 3:29:29.322 2G / 9G INFO General (sequence_mapper_notifier.h: 89) Processed 12210813 reads 3:29:29.323 2G / 9G INFO General (pair_info_count.cpp : 41) 5747263 paired reads (47.067% of all) aligned to long edges 3:29:29.335 2G / 9G INFO General (pair_info_count.cpp : 170) Estimated insert size for paired library #0 3:29:29.335 2G / 9G INFO General (pair_info_count.cpp : 175) Insert size = 315.703, deviation = 97.9388, left quantile = 190, right quantile = 442, read length = 151 3:29:29.335 2G / 9G INFO General (pair_info_count.cpp : 187) Mapping library #0 3:29:29.335 2G / 9G INFO General (pair_info_count.cpp : 189) Mapping paired reads (takes a while) 3:29:29.335 2G / 9G INFO General (pair_info_count.cpp : 73) Left insert size qauntile 190, right insert size quantile 442 3:29:29.345 2G / 9G INFO General (short_read_mapper.hpp : 91) Selecting usual mapper 3:29:37.020 4G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 200000 reads 3:29:37.816 4G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 400000 reads 3:29:38.731 4G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 600000 reads 3:29:39.825 4G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 800000 reads 3:29:41.026 4G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 1000000 reads 3:29:42.362 4G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 1200000 reads 3:29:49.732 4G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 2200000 reads 3:30:06.506 4G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 4200000 reads 3:30:44.063 4G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 8400000 reads 3:32:03.408 5G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 16800000 reads 3:33:19.706 3G / 9G INFO General (sequence_mapper_notifier.h: 89) Processed 24421626 reads 3:36:39.285 3G / 9G INFO General (split_graph_pair_info.hpp : 344) Threshold for paired information 0.0549403 3:36:43.527 2G / 9G INFO StageManager (stage.cpp : 125) STAGE == Distance Estimation 3:36:43.542 2G / 9G INFO General (distance_estimation.cpp : 234) Processing library #0 3:36:43.542 2G / 9G INFO General (distance_estimation.cpp : 136) Weight Filter Done 3:36:43.542 2G / 9G INFO DistanceEstimator (distance_estimation.hpp : 187) Using SIMPLE distance estimator 3:36:51.504 2G / 9G INFO DistanceEstimator (distance_estimation.hpp : 208) Merging maps 3:36:52.333 2G / 9G INFO General (distance_estimation.cpp : 38) Filtering info 3:36:53.588 2G / 9G INFO General (pair_info_filters.hpp : 354) Pruning the index 3:36:53.633 2G / 9G INFO General (distance_estimation.cpp : 184) Refining clustered pair information 3:36:53.738 2G / 9G INFO General (distance_estimation.cpp : 186) The refining of clustered pair information has been finished 3:36:53.739 2G / 9G INFO General (distance_estimation.cpp : 188) Filling paired information 3:36:55.476 2G / 9G INFO PairInfoImprover (pair_info_improver.hpp : 61) Paired info stats: missing = 38994; contradictional = 7576 3:36:57.193 2G / 9G INFO PairInfoImprover (pair_info_improver.hpp : 61) Paired info stats: missing = 5356; contradictional = 0 3:36:57.194 2G / 9G INFO General (distance_estimation.cpp : 193) Filling scaffolding index 3:36:57.194 2G / 9G INFO DistanceEstimator (distance_estimation.hpp : 187) Using SMOOTHING distance estimator 3:37:07.422 2G / 9G INFO DistanceEstimator (distance_estimation.hpp : 208) Merging maps 3:37:07.586 2G / 9G INFO General (distance_estimation.cpp : 38) Filtering info 3:37:07.929 2G / 9G INFO General (pair_info_filters.hpp : 354) Pruning the index 3:37:08.577 2G / 9G INFO StageManager (stage.cpp : 125) STAGE == Repeat Resolving 3:37:08.581 2G / 9G INFO General (contig_output.hpp : 283) Outputting contigs to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_129-dipSPAdes-3.5.0-trimmed/spades//K77/before_rr.fasta 3:38:08.450 2G / 9G INFO General (repeat_resolving.cpp : 59) Using Path-Extend repeat resolving 3:38:08.451 2G / 9G INFO General (path_extend_launch.hpp : 459) Threshold for library #0 is 0.0549403 3:38:08.451 2G / 9G INFO General (path_extend_launch.hpp : 298) Path-Extend repeat resolving tool started 3:38:08.496 2G / 9G INFO General (path_extend_launch.hpp : 316) Using 1 paired-end library 3:38:08.496 2G / 9G INFO General (path_extend_launch.hpp : 317) Using 1 paired-end scaffolding library 3:38:08.496 2G / 9G INFO General (path_extend_launch.hpp : 318) Using 0 mate-pair libraries 3:38:08.496 2G / 9G INFO General (path_extend_launch.hpp : 319) Using 0 single read libraries 3:38:08.496 2G / 9G INFO General (path_extend_launch.hpp : 320) Scaffolder is on 3:38:08.821 2G / 9G INFO General (path_extend_launch.hpp : 332) Growing paths using paired-end and long single reads 3:38:08.821 2G / 9G INFO PathExtender (path_extender.hpp : 611) Processed 0 paths from 25706 (0%) 3:38:08.927 2G / 9G INFO PathExtender (path_extender.hpp : 609) Processed 128 paths from 25706 (0%) 3:38:09.091 2G / 9G INFO PathExtender (path_extender.hpp : 609) Processed 256 paths from 25706 (0%) 3:38:09.326 2G / 9G INFO PathExtender (path_extender.hpp : 609) Processed 512 paths from 25706 (1%) 3:38:09.834 2G / 9G INFO PathExtender (path_extender.hpp : 609) Processed 1024 paths from 25706 (3%) 3:38:10.897 2G / 9G INFO PathExtender (path_extender.hpp : 609) Processed 2048 paths from 25706 (7%) 3:38:11.173 2G / 9G INFO PathExtender (path_extender.hpp : 611) Processed 2571 paths from 25706 (10%) 3:38:12.414 2G / 9G INFO PathExtender (path_extender.hpp : 609) Processed 4096 paths from 25706 (15%) 3:38:13.210 2G / 9G INFO PathExtender (path_extender.hpp : 611) Processed 5142 paths from 25706 (20%) 3:38:14.392 2G / 9G INFO PathExtender (path_extender.hpp : 611) Processed 7713 paths from 25706 (30%) 3:38:14.535 2G / 9G INFO PathExtender (path_extender.hpp : 609) Processed 8192 paths from 25706 (31%) 3:38:15.515 2G / 9G INFO PathExtender (path_extender.hpp : 611) Processed 10284 paths from 25706 (40%) 3:38:16.183 2G / 9G INFO PathExtender (path_extender.hpp : 611) Processed 12855 paths from 25706 (50%) 3:38:18.112 2G / 9G INFO PathExtender (path_extender.hpp : 611) Processed 15426 paths from 25706 (60%) 3:38:19.100 2G / 9G INFO PathExtender (path_extender.hpp : 609) Processed 16384 paths from 25706 (63%) 3:38:20.537 2G / 9G INFO PathExtender (path_extender.hpp : 611) Processed 17997 paths from 25706 (70%) 3:38:22.584 2G / 9G INFO PathExtender (path_extender.hpp : 611) Processed 20568 paths from 25706 (80%) 3:38:24.413 2G / 9G INFO PathExtender (path_extender.hpp : 611) Processed 23139 paths from 25706 (90%) 3:38:27.187 2G / 9G INFO PathExtendIO (pe_io.hpp : 339) Constructing FASTG file from paths 3:38:27.685 2G / 9G INFO PathExtendIO (pe_io.hpp : 342) Writing contigs in FASTG to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_129-dipSPAdes-3.5.0-trimmed/spades//K77/final_contigs.fastg 3:38:27.685 2G / 9G INFO PathExtendIO (pe_io.hpp : 343) Writing contigs in FASTA to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_129-dipSPAdes-3.5.0-trimmed/spades//K77/final_contigs.fasta 3:39:11.796 2G / 9G INFO PathExtendIO (pe_io.hpp : 339) Constructing FASTG file from paths 3:39:12.323 2G / 9G INFO PathExtendIO (pe_io.hpp : 342) Writing contigs in FASTG to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_129-dipSPAdes-3.5.0-trimmed/spades//K77/path_extend/pe_before_traversal.fastg 3:39:12.323 2G / 9G INFO PathExtendIO (pe_io.hpp : 343) Writing contigs in FASTA to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_129-dipSPAdes-3.5.0-trimmed/spades//K77/path_extend/pe_before_traversal.fasta 3:39:54.380 2G / 9G INFO General (path_extend_launch.hpp : 281) Traversing tandem repeats 3:39:55.693 2G / 9G INFO PathExtendIO (pe_io.hpp : 339) Constructing FASTG file from paths 3:39:56.098 2G / 9G INFO PathExtendIO (pe_io.hpp : 342) Writing contigs in FASTG to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_129-dipSPAdes-3.5.0-trimmed/spades//K77/scaffolds.fastg 3:39:56.098 2G / 9G INFO PathExtendIO (pe_io.hpp : 343) Writing contigs in FASTA to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_129-dipSPAdes-3.5.0-trimmed/spades//K77/scaffolds.fasta 3:40:38.360 2G / 9G INFO General (launch.hpp : 82) SPAdes finished 3:40:41.899 320M / 9G INFO General (main.cpp : 166) Assembling time: 3 hours 40 minutes 41 seconds ===== Assembling finished. * Corrected reads are in /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_129-dipSPAdes-3.5.0-trimmed/spades/corrected/ * Assembled contigs are in /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_129-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_129-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_129-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_129-dipSPAdes-3.5.0-trimmed/spades/spades.log Thank you for using SPAdes!