Command line: /N/dc2/projects/marinovg/programs/SPAdes-3.5.0-Linux/bin/spades.py --pe1-1 /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_Indo1-7I/reads.end1.paired.fastq.gz --pe1-2 /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_Indo1-7I/reads.end2.paired.fastq.gz -t 16 -o /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_Indo1-7I-SPAdes-3.5.0-trimmed 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_Indo1-7I-SPAdes-3.5.0-trimmed Mode: read error correction and assembling Debug mode is turned OFF Dataset parameters: Multi-cell mode (you should set '--sc' flag if input data was obtained with MDA (single-cell) technology Reads: Library number: 1, library type: paired-end orientation: fr left reads: ['/N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_Indo1-7I/reads.end1.paired.fastq.gz'] right reads: ['/N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_Indo1-7I/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_Indo1-7I-SPAdes-3.5.0-trimmed/tmp Threads: 16 Memory limit (in Gb): 250 ======= SPAdes pipeline started. Log can be found here: /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_Indo1-7I-SPAdes-3.5.0-trimmed/spades.log ===== Read error correction started. == Running read error correction tool: /N/dc2/projects/marinovg/programs/SPAdes-3.5.0-Linux/bin/hammer /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_Indo1-7I-SPAdes-3.5.0-trimmed/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_Indo1-7I-SPAdes-3.5.0-trimmed/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 0:00:00.058 4M / 4M INFO General (main.cpp : 97) Determined value is 33 0:00:00.058 4M / 4M INFO General (hammer_tools.cpp : 36) Hamming graph threshold tau=1, k=21, subkmer positions = [ 0 10 ] === ITERATION 0 begins === 0:00:00.060 4M / 4M INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:00:00.060 4M / 4M INFO K-mer Splitting (kmer_data.cpp : 127) Splitting kmer instances into 256 buckets. This might take a while. 0:00:00.061 4M / 4M INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:00:00.061 4M / 4M INFO K-mer Splitting (kmer_data.cpp : 145) Memory available for splitting buffers: 2.08325 Gb 0:00:00.061 4M / 4M INFO K-mer Splitting (kmer_data.cpp : 153) Using cell size of 262144 0:00:02.906 8G / 8G INFO K-mer Splitting (kmer_data.cpp : 167) Processing /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_Indo1-7I/reads.end1.paired.fastq.gz 0:03:20.263 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 176) Processed 3512496 reads 0:04:17.847 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 176) Processed 6863416 reads 0:05:14.778 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 176) Processed 10181611 reads 0:07:00.523 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 176) Processed 13531355 reads 0:07:03.406 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 176) Processed 13686306 reads 0:07:03.409 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 167) Processing /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_Indo1-7I/reads.end2.paired.fastq.gz 0:08:01.228 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 176) Processed 17091848 reads 0:09:00.093 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 176) Processed 20522938 reads 0:11:17.014 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 176) Processed 23918023 reads 0:13:38.915 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 176) Processed 27372612 reads 0:13:38.915 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 181) Processed 27372612 reads 0:13:40.133 64M / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:14:35.253 64M / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 314291596 kmers in total. 0:14:35.253 64M / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:14:49.882 64M / 9G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:15:33.614 192M / 10G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:15:48.509 192M / 10G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 108725290 bytes occupied (2.7675 bits per kmer). 0:15:48.511 192M / 10G INFO K-mer Counting (kmer_data.cpp : 266) Arranging kmers in hash map order 0:18:56.804 192M / 10G INFO K-mer Counting (kmer_data.cpp : 279) Done. Total swaps: 314291326 0:18:58.923 2G / 10G INFO General (main.cpp : 151) Clustering Hamming graph. 0:18:58.924 2G / 10G INFO Hamming Clustering (hamcluster.cpp : 115) Serializing sub-kmers. 0:18:58.924 2G / 10G INFO Hamming Clustering (hamcluster.cpp : 120) Serializing: [0, 10) 0:22:50.765 2G / 10G INFO Hamming Clustering (hamcluster.cpp : 120) Serializing: [10, 21) 0:26:47.207 2G / 10G INFO Hamming Clustering (hamcluster.cpp : 129) Splitting sub-kmers, pass 1. 0:31:07.790 2G / 10G INFO Hamming Clustering (hamcluster.cpp : 134) Splitting done. Processed 2 blocks. Produced 4893324 blocks. 0:31:07.791 2G / 10G INFO Hamming Clustering (hamcluster.cpp : 145) Merge sub-kmers, pass 1 0:48:25.938 2G / 10G INFO Hamming Clustering (hamcluster.cpp : 170) Merge done, total 1639251 new blocks generated. 0:48:27.595 2G / 10G INFO Hamming Clustering (hamcluster.cpp : 175) Spliting sub-kmers, pass 2. 1:09:33.458 2G / 10G INFO Hamming Clustering (hamcluster.cpp : 180) Splitting done. Processed 3278502 blocks. Produced 582182284 blocks. 1:09:33.458 2G / 10G INFO Hamming Clustering (hamcluster.cpp : 187) Merge sub-kmers, pass 2 1:23:48.227 2G / 10G INFO Hamming Clustering (hamcluster.cpp : 205) Merge done, saw 347039 big blocks out of 582182284 processed. 1:28:43.417 2G / 10G INFO General (main.cpp : 165) Clustering done. Total clusters: 133044502 1:28:43.417 2G / 10G INFO K-mer Counting (kmer_data.cpp : 284) Collecting K-mer information, this takes a while. 1:28:49.736 16G / 16G INFO K-mer Counting (kmer_data.cpp : 290) Processing /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_Indo1-7I/reads.end1.paired.fastq.gz 1:32:12.343 16G / 16G INFO K-mer Counting (kmer_data.cpp : 290) Processing /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_Indo1-7I/reads.end2.paired.fastq.gz 1:35:23.543 16G / 16G INFO K-mer Counting (kmer_data.cpp : 297) Collection done, postprocessing. 1:35:31.254 16G / 16G INFO K-mer Counting (kmer_data.cpp : 310) There are 314291596 kmers in total. Among them 166558762 (52.995%) are singletons. 1:35:31.254 16G / 16G INFO General (main.cpp : 203) Subclustering Hamming graph 1:39:20.714 16G / 16G INFO Hamming Subclustering (kmer_cluster.cpp : 626) Subclustering done. Total 118440 non-read kmers were generated. 1:39:20.714 16G / 16G INFO Hamming Subclustering (kmer_cluster.cpp : 627) Subclustering statistics: 1:39:20.714 16G / 16G INFO Hamming Subclustering (kmer_cluster.cpp : 628) Total singleton hamming clusters: 70876639. Among them 49525863 (69.8761%) are good 1:39:20.714 16G / 16G INFO Hamming Subclustering (kmer_cluster.cpp : 629) Total singleton subclusters: 6455982. Among them 6455894 (99.9986%) are good 1:39:20.714 16G / 16G INFO Hamming Subclustering (kmer_cluster.cpp : 630) Total non-singleton subcluster centers: 69112512. Among them 45828760 (66.3104%) are good 1:39:20.714 16G / 16G INFO Hamming Subclustering (kmer_cluster.cpp : 631) Average size of non-trivial subcluster: 3.50546 kmers 1:39:20.714 16G / 16G INFO Hamming Subclustering (kmer_cluster.cpp : 632) Average number of sub-clusters per non-singleton cluster: 1.21556 1:39:20.714 16G / 16G INFO Hamming Subclustering (kmer_cluster.cpp : 633) Total solid k-mers: 101810517 1:39:20.714 16G / 16G INFO Hamming Subclustering (kmer_cluster.cpp : 634) Substitution probabilities: [4,4]((0.896519,0.0238797,0.0263847,0.0532166),(0.0360321,0.926617,0.0135384,0.0238121),(0.0227879,0.0131292,0.928043,0.0360397),(0.0527092,0.0267719,0.0242702,0.896249)) 1:39:21.125 16G / 16G INFO General (main.cpp : 208) Finished clustering. 1:39:21.125 16G / 16G INFO General (main.cpp : 228) Starting solid k-mers expansion in 16 threads. 1:44:04.394 16G / 16G INFO General (main.cpp : 249) Solid k-mers iteration 0 produced 49214494 new k-mers. 1:48:36.515 16G / 16G INFO General (main.cpp : 249) Solid k-mers iteration 1 produced 1388709 new k-mers. 1:53:08.694 16G / 16G INFO General (main.cpp : 249) Solid k-mers iteration 2 produced 56694 new k-mers. 1:57:40.983 16G / 16G INFO General (main.cpp : 249) Solid k-mers iteration 3 produced 6122 new k-mers. 2:02:21.151 16G / 16G INFO General (main.cpp : 249) Solid k-mers iteration 4 produced 1168 new k-mers. 2:06:53.148 16G / 16G INFO General (main.cpp : 249) Solid k-mers iteration 5 produced 62 new k-mers. 2:11:25.123 16G / 16G INFO General (main.cpp : 249) Solid k-mers iteration 6 produced 121 new k-mers. 2:16:04.503 16G / 16G INFO General (main.cpp : 249) Solid k-mers iteration 7 produced 0 new k-mers. 2:16:04.503 16G / 16G INFO General (main.cpp : 253) Solid k-mers finalized 2:16:04.507 16G / 16G INFO General (hammer_tools.cpp : 210) Starting read correction in 16 threads. 2:16:04.507 16G / 16G INFO General (hammer_tools.cpp : 222) Correcting pair of reads: /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_Indo1-7I/reads.end1.paired.fastq.gz and /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_Indo1-7I/reads.end2.paired.fastq.gz 2:16:30.448 18G / 18G INFO General (hammer_tools.cpp : 166) Prepared batch 0 of 1600000 reads. 2:16:50.479 18G / 18G INFO General (hammer_tools.cpp : 175) Processed batch 0 2:17:19.429 18G / 18G INFO General (hammer_tools.cpp : 185) Written batch 0 2:17:43.078 18G / 18G INFO General (hammer_tools.cpp : 166) Prepared batch 1 of 1600000 reads. 2:18:02.997 18G / 18G INFO General (hammer_tools.cpp : 175) Processed batch 1 2:18:18.297 18G / 18G INFO General (hammer_tools.cpp : 185) Written batch 1 2:18:41.746 18G / 18G INFO General (hammer_tools.cpp : 166) Prepared batch 2 of 1600000 reads. 2:19:01.726 18G / 18G INFO General (hammer_tools.cpp : 175) Processed batch 2 2:19:17.059 18G / 18G INFO General (hammer_tools.cpp : 185) Written batch 2 2:19:40.405 18G / 18G INFO General (hammer_tools.cpp : 166) Prepared batch 3 of 1600000 reads. 2:20:00.381 18G / 18G INFO General (hammer_tools.cpp : 175) Processed batch 3 2:20:15.654 18G / 18G INFO General (hammer_tools.cpp : 185) Written batch 3 2:20:38.855 18G / 18G INFO General (hammer_tools.cpp : 166) Prepared batch 4 of 1600000 reads. 2:20:58.932 18G / 18G INFO General (hammer_tools.cpp : 175) Processed batch 4 2:21:14.250 18G / 18G INFO General (hammer_tools.cpp : 185) Written batch 4 2:21:37.484 18G / 18G INFO General (hammer_tools.cpp : 166) Prepared batch 5 of 1600000 reads. 2:21:57.482 18G / 18G INFO General (hammer_tools.cpp : 175) Processed batch 5 2:22:12.817 18G / 18G INFO General (hammer_tools.cpp : 185) Written batch 5 2:22:35.933 18G / 18G INFO General (hammer_tools.cpp : 166) Prepared batch 6 of 1600000 reads. 2:22:56.060 18G / 18G INFO General (hammer_tools.cpp : 175) Processed batch 6 2:23:11.412 18G / 18G INFO General (hammer_tools.cpp : 185) Written batch 6 2:23:34.230 18G / 18G INFO General (hammer_tools.cpp : 166) Prepared batch 7 of 1600000 reads. 2:23:54.398 18G / 18G INFO General (hammer_tools.cpp : 175) Processed batch 7 2:24:14.637 18G / 18G INFO General (hammer_tools.cpp : 185) Written batch 7 2:24:27.276 18G / 18G INFO General (hammer_tools.cpp : 166) Prepared batch 8 of 886306 reads. 2:24:39.419 18G / 18G INFO General (hammer_tools.cpp : 175) Processed batch 8 2:24:47.944 18G / 18G INFO General (hammer_tools.cpp : 185) Written batch 8 2:24:50.507 16G / 18G INFO General (hammer_tools.cpp : 269) Correction done. Changed 5680242 bases in 4284894 reads. 2:24:50.507 16G / 18G INFO General (hammer_tools.cpp : 270) Failed to correct 529149502 bases out of 4061663438. 2:24:50.583 2G / 18G INFO General (main.cpp : 286) Saving corrected dataset description to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_Indo1-7I-SPAdes-3.5.0-trimmed/corrected/corrected.yaml 2:24:50.596 2G / 18G 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_Indo1-7I-SPAdes-3.5.0-trimmed/corrected/corrected.yaml ===== Read error correction finished. ===== Assembling started. == Running assembler: K21 0:00:00.000 4M / 4M INFO General (memory_limit.hpp : 42) Memory limit set to 100 Gb 0:00:00.001 4M / 4M INFO General (main.cpp : 146) Assembling dataset (/N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_Indo1-7I-SPAdes-3.5.0-trimmed/dataset.info) with K=21 0:00:00.001 4M / 4M INFO General (launch.hpp : 28) SPAdes started 0:00:00.001 4M / 4M INFO General (launch.hpp : 29) Starting from stage: construction 0:00:00.002 4M / 4M INFO StageManager (stage.cpp : 125) STAGE == Construction 0:00:00.006 4M / 4M INFO General (read_converter.hpp : 79) Converting reads to binary format (takes a while) 0:00:00.006 4M / 4M INFO General (read_converter.hpp : 81) Paired reads for library #0 0:00:01.147 80M / 80M INFO General (binary_converter.hpp : 138) 16384 reads processed 0:00:01.553 96M / 96M INFO General (binary_converter.hpp : 138) 32768 reads processed 0:00:02.365 124M / 124M INFO General (binary_converter.hpp : 138) 65536 reads processed 0:00:03.986 184M / 184M INFO General (binary_converter.hpp : 138) 131072 reads processed 0:00:07.290 300M / 300M INFO General (binary_converter.hpp : 138) 262144 reads processed 0:00:13.825 536M / 536M INFO General (binary_converter.hpp : 138) 524288 reads processed 0:00:45.351 900M / 900M INFO General (binary_converter.hpp : 138) 1048576 reads processed 0:01:13.814 900M / 900M INFO General (binary_converter.hpp : 138) 2097152 reads processed 0:02:10.894 904M / 904M INFO General (binary_converter.hpp : 138) 4194304 reads processed 0:04:07.702 904M / 904M INFO General (binary_converter.hpp : 138) 8388608 reads processed 0:06:29.181 556M / 908M INFO General (binary_converter.hpp : 158) 13489445 reads written 0:06:30.047 4M / 908M INFO General (read_converter.hpp : 91) Single reads for library #0 0:06:31.944 140M / 908M INFO General (binary_converter.hpp : 138) 16384 reads processed 0:06:32.182 144M / 908M INFO General (binary_converter.hpp : 138) 32768 reads processed 0:06:32.599 160M / 908M INFO General (binary_converter.hpp : 138) 65536 reads processed 0:06:33.393 188M / 908M INFO General (binary_converter.hpp : 138) 131072 reads processed 0:06:34.470 216M / 908M INFO General (binary_converter.hpp : 158) 196774 reads written 0:06:34.702 4M / 908M INFO General (graph_construction.hpp : 129) Constructing DeBruijn graph for k=21 0:06:34.706 4M / 908M INFO General (kmer_splitters.hpp : 172) Splitting kmer instances into 256 buckets. This might take a while. 0:06:34.707 4M / 908M INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:06:34.707 4M / 908M INFO General (kmer_splitters.hpp : 190) Memory available for splitting buffers: 2.08325 Gb 0:06:34.707 4M / 908M INFO General (kmer_splitters.hpp : 199) Using cell size of 262144 0:10:34.654 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 16726759 reads 0:14:03.781 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 33446211 reads 0:18:00.651 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 50158715 reads 0:18:32.250 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 54351328 reads 0:18:32.251 8G / 9G INFO General (kmer_splitters.hpp : 234) Adding contigs from previous K 0:18:32.251 8G / 9G INFO General (kmer_splitters.hpp : 245) Used 54351328 reads. Maximum read length 151 0:18:32.251 8G / 9G INFO General (kmer_splitters.hpp : 246) Average read length 149.417 0:18:34.541 64M / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:18:43.462 64M / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 127124399 kmers in total. 0:18:43.462 64M / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:18:49.229 64M / 9G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:18:49.229 64M / 9G INFO General (kmer_splitters.hpp : 379) Splitting kmer instances into 256 buckets. This might take a while. 0:18:49.229 64M / 9G INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:18:49.230 64M / 9G INFO General (kmer_splitters.hpp : 397) Memory available for splitting buffers: 2.08203 Gb 0:18:49.230 64M / 9G INFO General (kmer_splitters.hpp : 405) Using cell size of 262144 0:19:04.738 8G / 9G INFO General (kmer_splitters.hpp : 428) Processed 127124399 kmers 0:19:04.738 8G / 9G INFO General (kmer_splitters.hpp : 437) Used 127124399 kmers. 0:19:05.313 64M / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:19:09.149 64M / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 123322718 kmers in total. 0:19:09.149 64M / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:19:15.023 64M / 9G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:19:32.663 68M / 9G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:20:16.582 68M / 9G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 42661990 bytes occupied (2.7675 bits per kmer). 0:20:16.799 188M / 9G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 382) Building k-mer extensions from k+1-mers 0:20:31.624 188M / 9G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 386) Building k-mer extensions from k+1-mers finished. 0:20:31.630 188M / 9G INFO Early tip clipping (early_simplification.hpp : 236) Early tip clipping 0:27:14.960 188M / 9G INFO Early tip clipping (early_simplification.hpp : 239) 7058847 22-mers were removed by early tip clipper 0:27:14.960 188M / 9G INFO General (graph_construction.hpp : 145) Condensing graph 0:27:14.960 188M / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 337) Extracting unbranching paths 0:28:43.019 1G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 351) Extracting unbranching paths finished. 19965241 sequences extracted 0:28:53.289 1G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 311) Collecting perfect loops 0:29:31.198 1G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 326) Collecting perfect loops finished. 14 loops collected 0:29:44.928 3G / 9G INFO General (graph_construction.hpp : 150) Building index with from graph 0:29:44.929 3G / 9G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:29:44.929 3G / 9G INFO General (kmer_splitters.hpp : 289) Splitting kmer instances into 16 buckets. This might take a while. 0:29:44.929 3G / 9G INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:29:44.929 3G / 9G INFO General (kmer_splitters.hpp : 307) Memory available for splitting buffers: 32.0352 Gb 0:29:44.930 3G / 9G INFO General (kmer_splitters.hpp : 312) Using cell size of 4194304 0:34:16.913 4G / 9G INFO General (kmer_splitters.hpp : 325) Processed 11155314 edges 0:36:11.990 4G / 9G INFO General (kmer_splitters.hpp : 325) Processed 19965255 edges 0:36:11.990 4G / 9G INFO General (kmer_splitters.hpp : 330) Used 19965255 sequences. 0:36:12.038 3G / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:37:18.812 3G / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 120065552 kmers in total. 0:37:18.812 3G / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:37:23.914 3G / 9G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:39:57.569 3G / 9G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:40:22.170 3G / 9G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 41535229 bytes occupied (2.7675 bits per kmer). 0:40:24.257 6G / 9G INFO General (edge_index_builders.hpp : 21) Collecting k-mer coverage information from graph, this takes a while. 0:43:56.447 6G / 9G INFO General (graph_construction.hpp : 182) Filling coverage index 0:43:56.447 6G / 9G INFO General (edge_index_builders.hpp : 99) Collecting k-mer coverage information from reads, this takes a while. 0:47:53.958 6G / 9G INFO General (graph_construction.hpp : 184) Filling coverage and flanking coverage from index 0:48:25.286 6G / 9G INFO General (construction.cpp : 33) Figured out: read length = 151 0:48:25.305 6G / 9G INFO StageManager (stage.cpp : 125) STAGE == EC Threshold Finding 0:48:34.706 6G / 9G INFO General (kmer_coverage_model.cpp : 178) Kmer coverage valley at: 17 0:48:34.707 6G / 9G INFO General (kmer_coverage_model.cpp : 198) K-mer histogram maximum: 50 0:48:34.707 6G / 9G INFO General (kmer_coverage_model.cpp : 234) Estimated median coverage: 50. Coverage mad: 11.8608 0:48:34.707 6G / 9G INFO General (kmer_coverage_model.cpp : 261) Fitting coverage model 0:48:34.897 6G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 2 0:48:35.376 6G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 4 0:48:36.932 6G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 8 0:48:40.572 6G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 16 0:48:46.676 6G / 9G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 49.4842. Fitted coverage std. dev: 11.1075 0:48:46.680 6G / 9G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 0.459347 0:48:46.681 6G / 9G INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 31 0:48:46.681 6G / 9G INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 31 0:48:46.681 6G / 9G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 61006318 0:48:46.681 6G / 9G INFO General (genomic_info_filler.cpp : 103) Mean coverage was calculated as 49.4842 0:48:46.682 6G / 9G INFO General (genomic_info_filler.cpp : 117) EC coverage threshold value was calculated as 31 0:48:46.682 6G / 9G INFO General (genomic_info_filler.cpp : 118) Trusted kmer low bound: 0 0:48:46.682 6G / 9G INFO StageManager (stage.cpp : 125) STAGE == Simplification 0:48:46.917 3G / 9G INFO General (graph_simplification.hpp : 911) Graph simplification started 0:48:46.917 3G / 9G INFO General (graph_simplification.hpp : 924) Fast simplification mode enabled 0:48:46.918 3G / 9G INFO General (graph_simplification.hpp : 771) PROCEDURE == Presimplification 0:48:46.918 3G / 9G INFO General (graph_simplification.hpp : 211) Removing short low covered self-conjugate connections 0:48:48.130 3G / 9G INFO General (graph_simplification.hpp : 403) Removing isolated edges 0:48:48.130 3G / 9G INFO General (graph_simplification.hpp : 404) All edges shorter than 151 will be removed 0:48:48.130 3G / 9G INFO General (graph_simplification.hpp : 405) Also edges shorter than 0 and coverage smaller than 0 will be removed 0:48:49.792 3G / 9G INFO General (graph_simplification.hpp : 687) Non parallel mode 0:49:48.810 4G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:52:15.742 4G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:56:24.407 4G / 9G INFO General (graph_simplification.hpp : 644) Using permanent iterators 0:56:24.408 4G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 1 0:56:35.776 4G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:57:02.365 4G / 9G INFO General (graph_simplification.hpp : 147) Removing bulges 1:10:30.927 3G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 1:10:49.560 3G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 2 1:10:49.560 3G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 1:10:50.400 3G / 9G INFO General (graph_simplification.hpp : 147) Removing bulges 1:12:34.715 3G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 1:12:43.550 3G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 3 1:12:43.550 3G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 1:12:43.775 3G / 9G INFO General (graph_simplification.hpp : 147) Removing bulges 1:13:18.142 3G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 1:13:21.353 3G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 4 1:13:21.353 3G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 1:13:21.450 3G / 9G INFO General (graph_simplification.hpp : 147) Removing bulges 1:13:32.922 3G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 1:13:35.099 3G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 5 1:13:35.099 3G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 1:13:35.157 3G / 9G INFO General (graph_simplification.hpp : 147) Removing bulges 1:13:41.579 3G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 1:13:43.368 3G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 6 1:13:43.368 3G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 1:13:43.414 3G / 9G INFO General (graph_simplification.hpp : 147) Removing bulges 1:13:48.470 3G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 1:13:50.155 3G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 7 1:13:50.155 3G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 1:13:50.199 3G / 9G INFO General (graph_simplification.hpp : 147) Removing bulges 1:13:54.174 3G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 1:13:55.954 3G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 8 1:13:55.954 3G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 1:13:55.994 3G / 9G INFO General (graph_simplification.hpp : 147) Removing bulges 1:13:59.182 3G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 1:14:00.460 3G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 9 1:14:00.460 3G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 1:14:00.495 3G / 9G INFO General (graph_simplification.hpp : 147) Removing bulges 1:14:02.908 3G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 1:14:04.079 3G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 10 1:14:04.079 3G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 1:14:04.110 3G / 9G INFO General (graph_simplification.hpp : 147) Removing bulges 1:14:05.710 3G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 1:14:07.082 3G / 9G INFO General (graph_simplification.hpp : 796) PROCEDURE == Post simplification 1:14:07.082 3G / 9G INFO General (graph_simplification.hpp : 644) Using permanent iterators 1:14:07.082 3G / 9G INFO General (graph_simplification.hpp : 806) Iteration 0 1:14:07.082 3G / 9G INFO General (graph_simplification.hpp : 247) Removal of relatively low covered connections disabled 1:14:10.541 3G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 1:14:18.044 3G / 9G INFO General (graph_simplification.hpp : 147) Removing bulges 1:15:14.511 3G / 9G INFO General (graph_simplification.hpp : 806) Iteration 1 1:15:14.512 3G / 9G INFO General (graph_simplification.hpp : 247) Removal of relatively low covered connections disabled 1:15:14.512 3G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 1:15:14.515 3G / 9G INFO General (graph_simplification.hpp : 147) Removing bulges 1:15:15.908 3G / 9G INFO StageManager (stage.cpp : 125) STAGE == Simplification Cleanup 1:15:15.909 3G / 9G INFO General (graph_simplification.hpp : 403) Removing isolated edges 1:15:15.909 3G / 9G INFO General (graph_simplification.hpp : 404) All edges shorter than 151 will be removed 1:15:15.909 3G / 9G INFO General (graph_simplification.hpp : 405) Also edges shorter than 0 and coverage smaller than 2 will be removed 1:15:16.112 3G / 9G INFO General (simplification.cpp : 56) Removing all the edges having coverage 0 and less 1:15:22.168 3G / 9G INFO General (simplification.cpp : 68) Counting average coverage 1:15:22.897 3G / 9G INFO General (simplification.cpp : 71) Average coverage = 54.1379 1:15:22.897 3G / 9G INFO StageManager (stage.cpp : 125) STAGE == Contig Output 1:15:22.897 3G / 9G INFO General (contig_output.hpp : 283) Outputting contigs to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_Indo1-7I-SPAdes-3.5.0-trimmed//K21/simplified_contigs.fasta 1:16:12.814 3G / 9G INFO General (contig_output.hpp : 283) Outputting contigs to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_Indo1-7I-SPAdes-3.5.0-trimmed//K21/before_rr.fasta 1:18:20.846 3G / 9G INFO General (contig_output.hpp : 283) Outputting contigs to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_Indo1-7I-SPAdes-3.5.0-trimmed//K21/final_contigs.fasta 1:20:15.130 3G / 9G INFO General (launch.hpp : 82) SPAdes finished 1:20:25.008 64M / 9G INFO General (main.cpp : 166) Assembling time: 1 hours 20 minutes 25 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_Indo1-7I-SPAdes-3.5.0-trimmed/dataset.info) with K=33 0:00:00.001 4M / 4M INFO General (launch.hpp : 28) SPAdes started 0:00:00.001 4M / 4M INFO General (launch.hpp : 29) Starting from stage: construction 0:00:00.002 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 0:00:00.028 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 0:05:03.795 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 9216648 reads 0:05:20.710 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 18450493 reads 0:10:10.185 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 27673554 reads 0:17:29.998 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 36890996 reads 0:22:22.424 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 46114626 reads 0:25:54.214 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 54351328 reads 0:25:54.215 8G / 9G INFO General (kmer_splitters.hpp : 234) Adding contigs from previous K 0:26:12.681 8G / 9G INFO General (kmer_splitters.hpp : 245) Used 54351328 reads. Maximum read length 151 0:26:12.681 8G / 9G INFO General (kmer_splitters.hpp : 246) Average read length 149.417 0:26:14.951 64M / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:26:37.897 64M / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 151716190 kmers in total. 0:26:37.897 64M / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:26:51.234 64M / 9G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:26:51.234 64M / 9G INFO General (kmer_splitters.hpp : 379) Splitting kmer instances into 256 buckets. This might take a while. 0:26:51.235 64M / 9G INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:26:51.235 64M / 9G INFO General (kmer_splitters.hpp : 397) Memory available for splitting buffers: 2.08203 Gb 0:26:51.235 64M / 9G INFO General (kmer_splitters.hpp : 405) Using cell size of 131072 0:53:57.343 8G / 9G INFO General (kmer_splitters.hpp : 428) Processed 151716190 kmers 0:53:57.346 8G / 9G INFO General (kmer_splitters.hpp : 437) Used 151716190 kmers. 0:53:58.287 64M / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:55:05.209 64M / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 150160576 kmers in total. 0:55:05.210 64M / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:55:18.230 64M / 9G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:55:40.065 68M / 9G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:55:52.124 68M / 9G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 51946211 bytes occupied (2.7675 bits per kmer). 0:55:52.364 212M / 9G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 382) Building k-mer extensions from k+1-mers 0:56:13.020 212M / 9G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 386) Building k-mer extensions from k+1-mers finished. 0:56:13.025 212M / 9G INFO Early tip clipping (early_simplification.hpp : 236) Early tip clipping 1:03:59.251 212M / 9G INFO Early tip clipping (early_simplification.hpp : 239) 28234250 34-mers were removed by early tip clipper 1:03:59.251 212M / 9G INFO General (graph_construction.hpp : 145) Condensing graph 1:03:59.251 212M / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 337) Extracting unbranching paths 1:05:45.064 1G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 351) Extracting unbranching paths finished. 9436745 sequences extracted 1:05:56.266 1G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 311) Collecting perfect loops 1:06:45.930 1G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 326) Collecting perfect loops finished. 24 loops collected 1:06:52.755 2G / 9G INFO General (graph_construction.hpp : 150) Building index with from graph 1:06:52.757 2G / 9G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 1:06:52.757 2G / 9G INFO General (kmer_splitters.hpp : 289) Splitting kmer instances into 16 buckets. This might take a while. 1:06:52.757 2G / 9G INFO General (file_limit.hpp : 29) Open file limit set to 32768 1:06:52.757 2G / 9G INFO General (kmer_splitters.hpp : 307) Memory available for splitting buffers: 32.6523 Gb 1:06:52.757 2G / 9G INFO General (kmer_splitters.hpp : 312) Using cell size of 2097152 1:11:40.708 2G / 9G INFO General (kmer_splitters.hpp : 325) Processed 2565958 edges 1:14:30.523 2G / 9G INFO General (kmer_splitters.hpp : 325) Processed 5129792 edges 1:17:29.554 2G / 9G INFO General (kmer_splitters.hpp : 325) Processed 7691303 edges 1:19:54.403 2G / 9G INFO General (kmer_splitters.hpp : 325) Processed 9436769 edges 1:19:54.403 2G / 9G INFO General (kmer_splitters.hpp : 330) Used 9436769 sequences. 1:19:54.465 2G / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 1:21:45.934 2G / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 123481940 kmers in total. 1:21:45.934 2G / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 1:22:54.949 2G / 9G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 1:25:55.046 2G / 9G INFO General (kmer_index.hpp : 371) Merging final buckets. 1:27:38.590 2G / 9G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 42717066 bytes occupied (2.7675 bits per kmer). 1:27:40.772 4G / 9G INFO General (edge_index_builders.hpp : 21) Collecting k-mer coverage information from graph, this takes a while. 1:31:52.471 4G / 9G INFO General (graph_construction.hpp : 182) Filling coverage index 1:31:52.472 4G / 9G INFO General (edge_index_builders.hpp : 99) Collecting k-mer coverage information from reads, this takes a while. 1:35:37.521 4G / 9G INFO General (graph_construction.hpp : 184) Filling coverage and flanking coverage from index 1:36:09.069 4G / 9G INFO General (construction.cpp : 33) Figured out: read length = 151 1:36:09.089 4G / 9G INFO StageManager (stage.cpp : 125) STAGE == EC Threshold Finding 1:36:22.762 4G / 9G INFO General (kmer_coverage_model.cpp : 178) Kmer coverage valley at: 13 1:36:22.762 4G / 9G INFO General (kmer_coverage_model.cpp : 198) K-mer histogram maximum: 45 1:36:22.762 4G / 9G INFO General (kmer_coverage_model.cpp : 234) Estimated median coverage: 45. Coverage mad: 11.8608 1:36:22.762 4G / 9G INFO General (kmer_coverage_model.cpp : 261) Fitting coverage model 1:36:22.934 4G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 2 1:36:23.378 4G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 4 1:36:24.827 4G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 8 1:36:28.279 4G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 16 1:36:34.754 4G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 32 1:36:34.754 4G / 9G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 44.0569. Fitted coverage std. dev: 10.9522 1:36:34.758 4G / 9G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 0.473094 1:36:34.758 4G / 9G INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 27 1:36:34.758 4G / 9G INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 27 1:36:34.758 4G / 9G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 61714132 1:36:34.758 4G / 9G INFO General (genomic_info_filler.cpp : 103) Mean coverage was calculated as 44.0569 1:36:34.759 4G / 9G INFO General (genomic_info_filler.cpp : 117) EC coverage threshold value was calculated as 27 1:36:34.759 4G / 9G INFO General (genomic_info_filler.cpp : 118) Trusted kmer low bound: 0 1:36:34.759 4G / 9G INFO StageManager (stage.cpp : 125) STAGE == Simplification 1:36:35.021 1G / 9G INFO General (graph_simplification.hpp : 911) Graph simplification started 1:36:35.021 1G / 9G INFO General (graph_simplification.hpp : 924) Fast simplification mode enabled 1:36:35.021 1G / 9G INFO General (graph_simplification.hpp : 771) PROCEDURE == Presimplification 1:36:35.021 1G / 9G INFO General (graph_simplification.hpp : 211) Removing short low covered self-conjugate connections 1:36:35.591 1G / 9G INFO General (graph_simplification.hpp : 403) Removing isolated edges 1:36:35.592 1G / 9G INFO General (graph_simplification.hpp : 404) All edges shorter than 151 will be removed 1:36:35.592 1G / 9G INFO General (graph_simplification.hpp : 405) Also edges shorter than 0 and coverage smaller than 0 will be removed 1:36:37.174 1G / 9G INFO General (graph_simplification.hpp : 687) Non parallel mode 1:37:05.541 2G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 1:38:11.894 2G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 1:40:17.762 1G / 9G INFO General (graph_simplification.hpp : 644) Using permanent iterators 1:40:17.762 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 1 1:40:21.088 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 1:40:29.243 1G / 9G INFO General (graph_simplification.hpp : 147) Removing bulges 1:41:30.383 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 1:41:34.365 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 2 1:41:34.365 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 1:41:34.531 1G / 9G INFO General (graph_simplification.hpp : 147) Removing bulges 1:41:37.124 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 1:41:39.716 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 3 1:41:39.716 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 1:41:39.757 1G / 9G INFO General (graph_simplification.hpp : 147) Removing bulges 1:41:41.467 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 1:41:42.394 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 4 1:41:42.394 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 1:41:42.414 1G / 9G INFO General (graph_simplification.hpp : 147) Removing bulges 1:41:43.072 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 1:41:43.488 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 5 1:41:43.488 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 1:41:43.500 1G / 9G INFO General (graph_simplification.hpp : 147) Removing bulges 1:41:43.865 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 1:41:44.136 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 6 1:41:44.136 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 1:41:44.143 1G / 9G INFO General (graph_simplification.hpp : 147) Removing bulges 1:41:44.379 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 1:41:44.644 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 7 1:41:44.644 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 1:41:44.651 1G / 9G INFO General (graph_simplification.hpp : 147) Removing bulges 1:41:44.802 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 1:41:44.936 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 8 1:41:44.936 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 1:41:44.946 1G / 9G INFO General (graph_simplification.hpp : 147) Removing bulges 1:41:45.084 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 1:41:45.178 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 9 1:41:45.178 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 1:41:45.181 1G / 9G INFO General (graph_simplification.hpp : 147) Removing bulges 1:41:45.276 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 1:41:45.348 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 10 1:41:45.348 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 1:41:45.352 1G / 9G INFO General (graph_simplification.hpp : 147) Removing bulges 1:41:45.405 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 1:41:45.474 1G / 9G INFO General (graph_simplification.hpp : 796) PROCEDURE == Post simplification 1:41:45.474 1G / 9G INFO General (graph_simplification.hpp : 644) Using permanent iterators 1:41:45.474 1G / 9G INFO General (graph_simplification.hpp : 806) Iteration 0 1:41:45.474 1G / 9G INFO General (graph_simplification.hpp : 247) Removal of relatively low covered connections disabled 1:41:45.739 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 1:41:46.309 1G / 9G INFO General (graph_simplification.hpp : 147) Removing bulges 1:41:46.942 1G / 9G INFO General (graph_simplification.hpp : 806) Iteration 1 1:41:46.942 1G / 9G INFO General (graph_simplification.hpp : 247) Removal of relatively low covered connections disabled 1:41:46.942 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 1:41:46.943 1G / 9G INFO General (graph_simplification.hpp : 147) Removing bulges 1:41:47.183 1008M / 9G INFO StageManager (stage.cpp : 125) STAGE == Simplification Cleanup 1:41:47.184 1008M / 9G INFO General (graph_simplification.hpp : 403) Removing isolated edges 1:41:47.184 1008M / 9G INFO General (graph_simplification.hpp : 404) All edges shorter than 151 will be removed 1:41:47.184 1008M / 9G INFO General (graph_simplification.hpp : 405) Also edges shorter than 0 and coverage smaller than 2 will be removed 1:41:47.207 1008M / 9G INFO General (simplification.cpp : 56) Removing all the edges having coverage 0 and less 1:41:47.668 1008M / 9G INFO General (simplification.cpp : 68) Counting average coverage 1:41:47.752 1008M / 9G INFO General (simplification.cpp : 71) Average coverage = 44.3492 1:41:47.752 1008M / 9G INFO StageManager (stage.cpp : 125) STAGE == Contig Output 1:41:47.752 1008M / 9G INFO General (contig_output.hpp : 283) Outputting contigs to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_Indo1-7I-SPAdes-3.5.0-trimmed//K33/simplified_contigs.fasta 1:42:48.739 1008M / 9G INFO General (contig_output.hpp : 283) Outputting contigs to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_Indo1-7I-SPAdes-3.5.0-trimmed//K33/before_rr.fasta 1:43:36.696 1008M / 9G INFO General (contig_output.hpp : 283) Outputting contigs to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_Indo1-7I-SPAdes-3.5.0-trimmed//K33/final_contigs.fasta 1:44:41.235 1008M / 9G INFO General (launch.hpp : 82) SPAdes finished 1:44:43.743 64M / 9G INFO General (main.cpp : 166) Assembling time: 1 hours 44 minutes 43 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_Indo1-7I-SPAdes-3.5.0-trimmed/dataset.info) with K=55 0:00:00.001 4M / 4M INFO General (launch.hpp : 28) SPAdes started 0:00:00.001 4M / 4M INFO General (launch.hpp : 29) Starting from stage: construction 0:00:00.002 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 0:00:00.027 4M / 4M INFO General (graph_construction.hpp : 129) Constructing DeBruijn graph for k=55 0:00:00.029 4M / 4M INFO General (kmer_splitters.hpp : 172) Splitting kmer instances into 256 buckets. This might take a while. 0:00:00.030 4M / 4M INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:00:00.030 4M / 4M INFO General (kmer_splitters.hpp : 190) Memory available for splitting buffers: 2.08325 Gb 0:00:00.030 4M / 4M INFO General (kmer_splitters.hpp : 199) Using cell size of 131072 0:03:01.085 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 11360316 reads 0:03:36.033 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 22736020 reads 0:03:52.309 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 34098492 reads 0:04:07.952 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 45465804 reads 0:04:20.292 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 54351328 reads 0:04:20.293 8G / 9G INFO General (kmer_splitters.hpp : 234) Adding contigs from previous K 0:04:38.309 8G / 9G INFO General (kmer_splitters.hpp : 245) Used 54351328 reads. Maximum read length 151 0:04:38.309 8G / 9G INFO General (kmer_splitters.hpp : 246) Average read length 149.417 0:04:40.623 64M / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:05:03.146 64M / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 173980877 kmers in total. 0:05:03.146 64M / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:05:18.866 64M / 9G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:05:18.866 64M / 9G INFO General (kmer_splitters.hpp : 379) Splitting kmer instances into 256 buckets. This might take a while. 0:05:18.867 64M / 9G INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:05:18.867 64M / 9G INFO General (kmer_splitters.hpp : 397) Memory available for splitting buffers: 2.08203 Gb 0:05:18.867 64M / 9G INFO General (kmer_splitters.hpp : 405) Using cell size of 131072 0:05:49.130 8G / 9G INFO General (kmer_splitters.hpp : 428) Processed 173980877 kmers 0:05:49.130 8G / 9G INFO General (kmer_splitters.hpp : 437) Used 173980877 kmers. 0:05:50.104 64M / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:06:00.234 64M / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 173397631 kmers in total. 0:06:00.234 64M / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:06:54.850 64M / 9G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:07:20.035 68M / 9G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:07:34.749 68M / 9G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 59984779 bytes occupied (2.7675 bits per kmer). 0:07:35.022 236M / 9G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 382) Building k-mer extensions from k+1-mers 0:08:01.296 236M / 9G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 386) Building k-mer extensions from k+1-mers finished. 0:08:01.303 236M / 9G INFO General (graph_construction.hpp : 145) Condensing graph 0:08:01.303 236M / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 337) Extracting unbranching paths 0:09:53.966 1G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 351) Extracting unbranching paths finished. 12555799 sequences extracted 0:10:10.413 1G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 311) Collecting perfect loops 0:11:09.202 1G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 326) Collecting perfect loops finished. 4 loops collected 0:11:20.589 3G / 9G INFO General (graph_construction.hpp : 150) Building index with from graph 0:11:20.590 3G / 9G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:11:20.590 3G / 9G INFO General (kmer_splitters.hpp : 289) Splitting kmer instances into 16 buckets. This might take a while. 0:11:20.590 3G / 9G INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:11:20.590 3G / 9G INFO General (kmer_splitters.hpp : 307) Memory available for splitting buffers: 32.3255 Gb 0:11:20.590 3G / 9G INFO General (kmer_splitters.hpp : 312) Using cell size of 2097152 0:13:40.801 3G / 9G INFO General (kmer_splitters.hpp : 325) Processed 2419246 edges 0:16:56.474 3G / 9G INFO General (kmer_splitters.hpp : 325) Processed 4840919 edges 0:19:10.929 3G / 9G INFO General (kmer_splitters.hpp : 325) Processed 7263750 edges 0:21:04.010 3G / 9G INFO General (kmer_splitters.hpp : 325) Processed 9686370 edges 0:22:29.122 3G / 9G INFO General (kmer_splitters.hpp : 325) Processed 12107752 edges 0:23:51.794 3G / 9G INFO General (kmer_splitters.hpp : 325) Processed 12555803 edges 0:23:51.794 3G / 9G INFO General (kmer_splitters.hpp : 330) Used 12555803 sequences. 0:23:51.873 3G / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:25:26.542 3G / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 173980877 kmers in total. 0:25:26.542 3G / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:25:41.553 3G / 9G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:30:12.106 3G / 9G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:30:26.948 3G / 9G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 60186538 bytes occupied (2.7675 bits per kmer). 0:30:30.080 6G / 9G INFO General (edge_index_builders.hpp : 21) Collecting k-mer coverage information from graph, this takes a while. 0:37:10.718 6G / 9G INFO General (graph_construction.hpp : 182) Filling coverage index 0:37:10.718 6G / 9G INFO General (edge_index_builders.hpp : 99) Collecting k-mer coverage information from reads, this takes a while. 0:40:49.830 6G / 9G INFO General (graph_construction.hpp : 184) Filling coverage and flanking coverage from index 0:41:37.417 6G / 9G INFO General (construction.cpp : 33) Figured out: read length = 151 0:41:37.436 6G / 9G INFO StageManager (stage.cpp : 125) STAGE == EC Threshold Finding 0:41:51.148 6G / 9G INFO General (kmer_coverage_model.cpp : 178) Kmer coverage valley at: 10 0:41:51.148 6G / 9G INFO General (kmer_coverage_model.cpp : 198) K-mer histogram maximum: 35 0:41:51.148 6G / 9G INFO General (kmer_coverage_model.cpp : 234) Estimated median coverage: 36. Coverage mad: 10.3782 0:41:51.148 6G / 9G INFO General (kmer_coverage_model.cpp : 261) Fitting coverage model 0:41:51.272 6G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 2 0:41:51.607 6G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 4 0:41:52.751 6G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 8 0:41:55.706 6G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 16 0:42:00.515 6G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 32 0:42:01.131 6G / 9G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 34.8972. Fitted coverage std. dev: 9.96979 0:42:01.134 6G / 9G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 0.396703 0:42:01.134 6G / 9G INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 21 0:42:01.134 6G / 9G INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 21 0:42:01.134 6G / 9G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 61642000 0:42:01.134 6G / 9G INFO General (genomic_info_filler.cpp : 103) Mean coverage was calculated as 34.8972 0:42:01.135 6G / 9G INFO General (genomic_info_filler.cpp : 117) EC coverage threshold value was calculated as 21 0:42:01.135 6G / 9G INFO General (genomic_info_filler.cpp : 118) Trusted kmer low bound: 0 0:42:01.135 6G / 9G INFO StageManager (stage.cpp : 125) STAGE == Gap Closer 0:42:01.149 6G / 9G INFO General (gap_closer.cpp : 157) Preparing shift maps 0:42:13.771 7G / 9G INFO General (gap_closer.cpp : 117) Processing paired reads (takes a while) 0:42:58.252 7G / 9G INFO General (gap_closer.cpp : 136) Used 26978890 paired reads 0:42:58.252 7G / 9G INFO General (gap_closer.cpp : 138) Merging paired indices 0:43:02.846 6G / 9G INFO GapCloser (gap_closer.cpp : 395) Closing short gaps 0:43:37.052 6G / 9G INFO GapCloser (gap_closer.cpp : 424) Closing short gaps complete: filled 726 gaps after checking 10212 candidates 0:43:40.600 6G / 9G INFO StageManager (stage.cpp : 125) STAGE == Simplification 0:43:40.944 2G / 9G INFO General (graph_simplification.hpp : 911) Graph simplification started 0:43:40.944 2G / 9G INFO General (graph_simplification.hpp : 924) Fast simplification mode enabled 0:43:40.945 2G / 9G INFO General (graph_simplification.hpp : 771) PROCEDURE == Presimplification 0:43:40.945 2G / 9G INFO General (graph_simplification.hpp : 211) Removing short low covered self-conjugate connections 0:43:42.173 2G / 9G INFO General (graph_simplification.hpp : 403) Removing isolated edges 0:43:42.175 2G / 9G INFO General (graph_simplification.hpp : 404) All edges shorter than 151 will be removed 0:43:42.175 2G / 9G INFO General (graph_simplification.hpp : 405) Also edges shorter than 0 and coverage smaller than 0 will be removed 0:43:45.999 2G / 9G INFO General (graph_simplification.hpp : 687) Non parallel mode 0:44:31.707 3G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:46:39.138 3G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:47:47.071 2G / 9G INFO General (graph_simplification.hpp : 644) Using permanent iterators 0:47:47.071 2G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 1 0:47:48.458 2G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:47:52.177 2G / 9G INFO General (graph_simplification.hpp : 147) Removing bulges 0:48:30.517 2G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:48:32.044 2G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 2 0:48:32.044 2G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:48:32.132 2G / 9G INFO General (graph_simplification.hpp : 147) Removing bulges 0:48:32.824 2G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:48:35.206 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 3 0:48:35.206 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:48:35.236 1G / 9G INFO General (graph_simplification.hpp : 147) Removing bulges 0:48:36.684 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:48:37.462 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 4 0:48:37.462 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:48:37.475 1G / 9G INFO General (graph_simplification.hpp : 147) Removing bulges 0:48:37.983 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:48:38.477 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 5 0:48:38.477 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:48:38.486 1G / 9G INFO General (graph_simplification.hpp : 147) Removing bulges 0:48:38.721 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:48:38.961 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 6 0:48:38.961 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:48:38.969 1G / 9G INFO General (graph_simplification.hpp : 147) Removing bulges 0:48:39.150 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:48:39.356 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 7 0:48:39.356 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:48:39.361 1G / 9G INFO General (graph_simplification.hpp : 147) Removing bulges 0:48:39.464 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:48:39.584 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 8 0:48:39.584 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:48:39.587 1G / 9G INFO General (graph_simplification.hpp : 147) Removing bulges 0:48:39.676 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:48:39.742 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 9 0:48:39.742 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:48:39.744 1G / 9G INFO General (graph_simplification.hpp : 147) Removing bulges 0:48:39.799 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:48:39.854 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 10 0:48:39.855 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:48:39.856 1G / 9G INFO General (graph_simplification.hpp : 147) Removing bulges 0:48:39.899 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:48:39.935 1G / 9G INFO General (graph_simplification.hpp : 796) PROCEDURE == Post simplification 0:48:39.935 1G / 9G INFO General (graph_simplification.hpp : 644) Using permanent iterators 0:48:39.935 1G / 9G INFO General (graph_simplification.hpp : 806) Iteration 0 0:48:39.935 1G / 9G INFO General (graph_simplification.hpp : 247) Removal of relatively low covered connections disabled 0:48:40.026 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:48:40.191 1G / 9G INFO General (graph_simplification.hpp : 147) Removing bulges 0:48:40.387 1G / 9G INFO General (graph_simplification.hpp : 806) Iteration 1 0:48:40.387 1G / 9G INFO General (graph_simplification.hpp : 247) Removal of relatively low covered connections disabled 0:48:40.388 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:48:40.388 1G / 9G INFO General (graph_simplification.hpp : 147) Removing bulges 0:48:40.457 1G / 9G INFO StageManager (stage.cpp : 125) STAGE == Gap Closer 0:48:40.457 1G / 9G INFO General (graph_pack.hpp : 84) Index refill 0:48:40.458 1G / 9G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:48:40.459 1G / 9G INFO General (kmer_splitters.hpp : 289) Splitting kmer instances into 16 buckets. This might take a while. 0:48:40.459 1G / 9G INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:48:40.459 1G / 9G INFO General (kmer_splitters.hpp : 307) Memory available for splitting buffers: 32.7799 Gb 0:48:40.459 1G / 9G INFO General (kmer_splitters.hpp : 312) Using cell size of 2097152 0:51:27.587 2G / 9G INFO General (kmer_splitters.hpp : 325) Processed 22865 edges 0:52:28.280 2G / 9G INFO General (kmer_splitters.hpp : 325) Processed 45518 edges 0:52:45.921 2G / 9G INFO General (kmer_splitters.hpp : 325) Processed 47876 edges 0:52:45.922 2G / 9G INFO General (kmer_splitters.hpp : 330) Used 47876 sequences. 0:52:46.003 1G / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:54:01.494 1G / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 70819945 kmers in total. 0:54:01.494 1G / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:54:07.446 1G / 9G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:55:41.815 1G / 9G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:56:40.922 1G / 9G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 24499321 bytes occupied (2.76751 bits per kmer). 0:56:42.183 3G / 9G INFO General (edge_index_builders.hpp : 21) Collecting k-mer coverage information from graph, this takes a while. 0:58:51.101 3G / 9G INFO General (gap_closer.cpp : 157) Preparing shift maps 0:58:51.156 3G / 9G INFO General (gap_closer.cpp : 117) Processing paired reads (takes a while) 0:59:59.981 3G / 9G INFO General (gap_closer.cpp : 136) Used 26978890 paired reads 0:59:59.981 3G / 9G INFO General (gap_closer.cpp : 138) Merging paired indices 1:00:00.056 3G / 9G INFO GapCloser (gap_closer.cpp : 395) Closing short gaps 1:00:00.195 3G / 9G INFO GapCloser (gap_closer.cpp : 424) Closing short gaps complete: filled 65 gaps after checking 3057 candidates 1:00:00.936 3G / 9G INFO StageManager (stage.cpp : 125) STAGE == Simplification Cleanup 1:00:00.937 3G / 9G INFO General (graph_simplification.hpp : 403) Removing isolated edges 1:00:00.937 3G / 9G INFO General (graph_simplification.hpp : 404) All edges shorter than 151 will be removed 1:00:00.937 3G / 9G INFO General (graph_simplification.hpp : 405) Also edges shorter than 0 and coverage smaller than 2 will be removed 1:00:01.214 3G / 9G INFO General (simplification.cpp : 56) Removing all the edges having coverage 0 and less 1:00:01.360 3G / 9G INFO General (simplification.cpp : 68) Counting average coverage 1:00:01.377 3G / 9G INFO General (simplification.cpp : 71) Average coverage = 34.7386 1:00:01.378 3G / 9G INFO StageManager (stage.cpp : 125) STAGE == Contig Output 1:00:01.378 3G / 9G INFO General (contig_output.hpp : 283) Outputting contigs to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_Indo1-7I-SPAdes-3.5.0-trimmed//K55/simplified_contigs.fasta 1:00:54.963 3G / 9G INFO General (contig_output.hpp : 283) Outputting contigs to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_Indo1-7I-SPAdes-3.5.0-trimmed//K55/before_rr.fasta 1:02:05.030 3G / 9G INFO General (contig_output.hpp : 283) Outputting contigs to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_Indo1-7I-SPAdes-3.5.0-trimmed//K55/final_contigs.fasta 1:03:00.227 3G / 9G INFO General (launch.hpp : 82) SPAdes finished 1:03:07.871 68M / 9G INFO General (main.cpp : 166) Assembling time: 1 hours 3 minutes 7 seconds == Running assembler: K77 0:00:00.000 4M / 4M INFO General (memory_limit.hpp : 42) Memory limit set to 100 Gb 0:00:00.001 4M / 4M INFO General (main.cpp : 146) Assembling dataset (/N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_Indo1-7I-SPAdes-3.5.0-trimmed/dataset.info) with K=77 0:00:00.001 4M / 4M INFO General (launch.hpp : 28) SPAdes started 0:00:00.001 4M / 4M INFO General (launch.hpp : 29) Starting from stage: construction 0:00:00.002 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 0:00:00.008 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=77 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 87381 0:06:31.710 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 9852837 reads 0:06:44.498 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 19724502 reads 0:20:52.435 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 29581753 reads 0:38:09.983 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 39447094 reads 0:42:00.324 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 49285856 reads 0:42:08.774 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 54351328 reads 0:42:08.774 8G / 9G INFO General (kmer_splitters.hpp : 234) Adding contigs from previous K 0:43:27.349 8G / 9G INFO General (kmer_splitters.hpp : 245) Used 54351328 reads. Maximum read length 151 0:43:27.350 8G / 9G INFO General (kmer_splitters.hpp : 246) Average read length 149.417 0:43:29.652 64M / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:46:55.000 64M / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 177571749 kmers in total. 0:46:55.000 64M / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:47:20.637 64M / 9G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:47:20.637 64M / 9G INFO General (kmer_splitters.hpp : 379) Splitting kmer instances into 256 buckets. This might take a while. 0:47:20.638 64M / 9G INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:47:20.638 64M / 9G INFO General (kmer_splitters.hpp : 397) Memory available for splitting buffers: 2.08203 Gb 0:47:20.638 64M / 9G INFO General (kmer_splitters.hpp : 405) Using cell size of 87381 1:03:40.289 8G / 9G INFO General (kmer_splitters.hpp : 428) Processed 177571749 kmers 1:03:40.289 8G / 9G INFO General (kmer_splitters.hpp : 437) Used 177571749 kmers. 1:03:41.869 64M / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 1:06:38.851 64M / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 177756693 kmers in total. 1:06:38.851 64M / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 1:07:03.213 64M / 9G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 1:07:26.617 68M / 9G INFO General (kmer_index.hpp : 371) Merging final buckets. 1:07:54.286 68M / 9G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 61492747 bytes occupied (2.7675 bits per kmer). 1:07:54.598 240M / 9G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 382) Building k-mer extensions from k+1-mers 1:08:20.666 240M / 9G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 386) Building k-mer extensions from k+1-mers finished. 1:08:20.673 240M / 9G INFO General (graph_construction.hpp : 145) Condensing graph 1:08:20.673 240M / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 337) Extracting unbranching paths 1:10:29.098 1G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 351) Extracting unbranching paths finished. 10771129 sequences extracted 1:10:47.480 1G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 311) Collecting perfect loops 1:11:57.902 1G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 326) Collecting perfect loops finished. 12 loops collected 1:12:08.341 2G / 9G INFO General (graph_construction.hpp : 150) Building index with from graph 1:12:08.342 2G / 9G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 1:12:08.342 2G / 9G INFO General (kmer_splitters.hpp : 289) Splitting kmer instances into 16 buckets. This might take a while. 1:12:08.342 2G / 9G INFO General (file_limit.hpp : 29) Open file limit set to 32768 1:12:08.342 2G / 9G INFO General (kmer_splitters.hpp : 307) Memory available for splitting buffers: 32.3971 Gb 1:12:08.343 2G / 9G INFO General (kmer_splitters.hpp : 312) Using cell size of 1398101 1:13:44.810 3G / 9G INFO General (kmer_splitters.hpp : 325) Processed 1356678 edges 1:16:45.381 3G / 9G INFO General (kmer_splitters.hpp : 325) Processed 2713233 edges 1:18:31.015 3G / 9G INFO General (kmer_splitters.hpp : 325) Processed 4068654 edges 1:19:03.968 3G / 9G INFO General (kmer_splitters.hpp : 325) Processed 5425193 edges 1:21:21.039 3G / 9G INFO General (kmer_splitters.hpp : 325) Processed 6783755 edges 1:24:04.989 3G / 9G INFO General (kmer_splitters.hpp : 325) Processed 8141497 edges 1:26:17.595 3G / 9G INFO General (kmer_splitters.hpp : 325) Processed 9498100 edges 1:29:05.799 3G / 9G INFO General (kmer_splitters.hpp : 325) Processed 10771141 edges 1:29:05.799 3G / 9G INFO General (kmer_splitters.hpp : 330) Used 10771141 sequences. 1:29:05.874 2G / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 1:32:00.950 2G / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 177571749 kmers in total. 1:32:00.950 2G / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 1:33:08.344 2G / 9G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 1:37:47.848 2G / 9G INFO General (kmer_index.hpp : 371) Merging final buckets. 1:38:48.948 2G / 9G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 61428766 bytes occupied (2.7675 bits per kmer). 1:38:52.023 6G / 9G INFO General (edge_index_builders.hpp : 21) Collecting k-mer coverage information from graph, this takes a while. 1:45:30.864 6G / 9G INFO General (graph_construction.hpp : 182) Filling coverage index 1:45:30.864 6G / 9G INFO General (edge_index_builders.hpp : 99) Collecting k-mer coverage information from reads, this takes a while. 1:48:53.283 6G / 9G INFO General (graph_construction.hpp : 184) Filling coverage and flanking coverage from index 1:49:38.383 6G / 9G INFO General (construction.cpp : 33) Figured out: read length = 151 1:49:38.402 6G / 9G INFO StageManager (stage.cpp : 125) STAGE == EC Threshold Finding 1:49:49.564 6G / 9G INFO General (kmer_coverage_model.cpp : 178) Kmer coverage valley at: 7 1:49:49.564 6G / 9G INFO General (kmer_coverage_model.cpp : 198) K-mer histogram maximum: 26 1:49:49.564 6G / 9G INFO General (kmer_coverage_model.cpp : 234) Estimated median coverage: 27. Coverage mad: 8.8956 1:49:49.565 6G / 9G INFO General (kmer_coverage_model.cpp : 261) Fitting coverage model 1:49:49.657 6G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 2 1:49:49.907 6G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 4 1:49:50.792 6G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 8 1:49:52.932 6G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 16 1:49:56.516 6G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 32 1:49:57.257 6G / 9G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 26.2171. Fitted coverage std. dev: 8.52754 1:49:57.260 6G / 9G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 0.368667 1:49:57.260 6G / 9G INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 15 1:49:57.260 6G / 9G INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 15 1:49:57.260 6G / 9G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 61907169 1:49:57.260 6G / 9G INFO General (genomic_info_filler.cpp : 103) Mean coverage was calculated as 26.2171 1:49:57.260 6G / 9G INFO General (genomic_info_filler.cpp : 117) EC coverage threshold value was calculated as 15 1:49:57.260 6G / 9G INFO General (genomic_info_filler.cpp : 118) Trusted kmer low bound: 0 1:49:57.260 6G / 9G INFO StageManager (stage.cpp : 125) STAGE == Gap Closer 1:49:57.271 6G / 9G INFO General (gap_closer.cpp : 157) Preparing shift maps 1:50:10.378 7G / 9G INFO General (gap_closer.cpp : 117) Processing paired reads (takes a while) 1:50:44.211 7G / 9G INFO General (gap_closer.cpp : 136) Used 26978890 paired reads 1:50:44.212 7G / 9G INFO General (gap_closer.cpp : 138) Merging paired indices 1:50:50.834 6G / 9G INFO GapCloser (gap_closer.cpp : 395) Closing short gaps 1:51:20.005 6G / 9G INFO GapCloser (gap_closer.cpp : 424) Closing short gaps complete: filled 980 gaps after checking 14493 candidates 1:51:24.160 6G / 9G INFO StageManager (stage.cpp : 125) STAGE == Simplification 1:51:24.571 2G / 9G INFO General (graph_simplification.hpp : 911) Graph simplification started 1:51:24.571 2G / 9G INFO General (graph_simplification.hpp : 924) Fast simplification mode enabled 1:51:24.571 2G / 9G INFO General (graph_simplification.hpp : 771) PROCEDURE == Presimplification 1:51:24.571 2G / 9G INFO General (graph_simplification.hpp : 211) Removing short low covered self-conjugate connections 1:51:25.764 2G / 9G INFO General (graph_simplification.hpp : 403) Removing isolated edges 1:51:25.764 2G / 9G INFO General (graph_simplification.hpp : 404) All edges shorter than 151 will be removed 1:51:25.764 2G / 9G INFO General (graph_simplification.hpp : 405) Also edges shorter than 0 and coverage smaller than 0 will be removed 1:51:31.133 2G / 9G INFO General (graph_simplification.hpp : 687) Non parallel mode 1:52:05.872 3G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 1:54:00.220 2G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 1:54:06.721 1G / 9G INFO General (graph_simplification.hpp : 644) Using permanent iterators 1:54:06.722 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 1 1:54:07.395 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 1:54:09.067 1G / 9G INFO General (graph_simplification.hpp : 147) Removing bulges 1:54:34.171 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 1:54:34.264 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 2 1:54:34.265 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 1:54:34.290 1G / 9G INFO General (graph_simplification.hpp : 147) Removing bulges 1:54:34.335 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 1:54:35.113 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 3 1:54:35.113 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 1:54:35.125 1G / 9G INFO General (graph_simplification.hpp : 147) Removing bulges 1:54:35.717 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 1:54:36.209 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 4 1:54:36.209 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 1:54:36.218 1G / 9G INFO General (graph_simplification.hpp : 147) Removing bulges 1:54:36.595 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 1:54:36.899 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 5 1:54:36.899 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 1:54:36.904 1G / 9G INFO General (graph_simplification.hpp : 147) Removing bulges 1:54:37.036 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 1:54:37.311 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 6 1:54:37.311 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 1:54:37.314 1G / 9G INFO General (graph_simplification.hpp : 147) Removing bulges 1:54:37.394 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 1:54:37.535 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 7 1:54:37.535 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 1:54:37.537 1G / 9G INFO General (graph_simplification.hpp : 147) Removing bulges 1:54:37.584 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 1:54:37.680 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 8 1:54:37.681 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 1:54:37.682 1G / 9G INFO General (graph_simplification.hpp : 147) Removing bulges 1:54:37.713 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 1:54:37.798 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 9 1:54:37.799 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 1:54:37.800 1G / 9G INFO General (graph_simplification.hpp : 147) Removing bulges 1:54:37.813 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 1:54:37.850 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 10 1:54:37.850 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 1:54:37.851 1G / 9G INFO General (graph_simplification.hpp : 147) Removing bulges 1:54:37.861 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 1:54:37.890 1G / 9G INFO General (graph_simplification.hpp : 796) PROCEDURE == Post simplification 1:54:37.890 1G / 9G INFO General (graph_simplification.hpp : 644) Using permanent iterators 1:54:37.890 1G / 9G INFO General (graph_simplification.hpp : 806) Iteration 0 1:54:37.890 1G / 9G INFO General (graph_simplification.hpp : 247) Removal of relatively low covered connections disabled 1:54:37.954 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 1:54:38.063 1G / 9G INFO General (graph_simplification.hpp : 147) Removing bulges 1:54:38.162 1G / 9G INFO General (graph_simplification.hpp : 806) Iteration 1 1:54:38.162 1G / 9G INFO General (graph_simplification.hpp : 247) Removal of relatively low covered connections disabled 1:54:38.162 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 1:54:38.162 1G / 9G INFO General (graph_simplification.hpp : 147) Removing bulges 1:54:38.196 1G / 9G INFO StageManager (stage.cpp : 125) STAGE == Gap Closer 1:54:38.196 1G / 9G INFO General (graph_pack.hpp : 84) Index refill 1:54:38.199 1G / 9G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 1:54:38.200 1G / 9G INFO General (kmer_splitters.hpp : 289) Splitting kmer instances into 16 buckets. This might take a while. 1:54:38.200 1G / 9G INFO General (file_limit.hpp : 29) Open file limit set to 32768 1:54:38.200 1G / 9G INFO General (kmer_splitters.hpp : 307) Memory available for splitting buffers: 32.8724 Gb 1:54:38.200 1G / 9G INFO General (kmer_splitters.hpp : 312) Using cell size of 1398101 1:58:49.596 1G / 9G INFO General (kmer_splitters.hpp : 325) Processed 10118 edges 2:02:35.036 1G / 9G INFO General (kmer_splitters.hpp : 325) Processed 20913 edges 2:04:30.672 1G / 9G INFO General (kmer_splitters.hpp : 325) Processed 31521 edges 2:06:17.081 1G / 9G INFO General (kmer_splitters.hpp : 325) Processed 33691 edges 2:06:17.081 1G / 9G INFO General (kmer_splitters.hpp : 330) Used 33691 sequences. 2:06:17.162 1G / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 2:07:40.322 1G / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 71423622 kmers in total. 2:07:40.322 1G / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 2:08:17.470 1G / 9G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 2:09:52.162 1G / 9G INFO General (kmer_index.hpp : 371) Merging final buckets. 2:11:20.089 1G / 9G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 24708152 bytes occupied (2.7675 bits per kmer). 2:11:21.454 2G / 9G INFO General (edge_index_builders.hpp : 21) Collecting k-mer coverage information from graph, this takes a while. 2:13:32.776 2G / 9G INFO General (gap_closer.cpp : 157) Preparing shift maps 2:13:32.828 2G / 9G INFO General (gap_closer.cpp : 117) Processing paired reads (takes a while) 2:14:38.530 3G / 9G INFO General (gap_closer.cpp : 136) Used 26978890 paired reads 2:14:38.531 3G / 9G INFO General (gap_closer.cpp : 138) Merging paired indices 2:14:38.622 2G / 9G INFO GapCloser (gap_closer.cpp : 395) Closing short gaps 2:14:38.800 2G / 9G INFO GapCloser (gap_closer.cpp : 424) Closing short gaps complete: filled 54 gaps after checking 3940 candidates 2:14:39.516 2G / 9G INFO StageManager (stage.cpp : 125) STAGE == Simplification Cleanup 2:14:39.518 2G / 9G INFO General (graph_simplification.hpp : 403) Removing isolated edges 2:14:39.518 2G / 9G INFO General (graph_simplification.hpp : 404) All edges shorter than 151 will be removed 2:14:39.518 2G / 9G INFO General (graph_simplification.hpp : 405) Also edges shorter than 0 and coverage smaller than 2 will be removed 2:14:40.264 2G / 9G INFO General (simplification.cpp : 56) Removing all the edges having coverage 0 and less 2:14:40.350 2G / 9G INFO General (simplification.cpp : 68) Counting average coverage 2:14:40.358 2G / 9G INFO General (simplification.cpp : 71) Average coverage = 26.1575 2:14:40.358 2G / 9G INFO StageManager (stage.cpp : 125) STAGE == Mismatch Correction 2:16:39.235 2G / 9G INFO General (mismatch_shall_not_pass.hp: 188) Finished collecting potential mismatches positions 2:16:47.767 2G / 9G INFO General (mismatch_shall_not_pass.hp: 291) All edges processed 2:16:47.931 2G / 9G INFO General (mismatch_correction.cpp : 18) Corrected 49 nucleotides 2:16:47.950 2G / 9G INFO StageManager (stage.cpp : 125) STAGE == Paired Information Counting 2:16:48.035 2G / 9G INFO General (pair_info_count.cpp : 150) Graph N50: 40851 2:16:48.035 2G / 9G INFO General (pair_info_count.cpp : 152) Estimating insert size for library #0 2:16:48.035 2G / 9G INFO General (pair_info_count.cpp : 31) Estimating insert size (takes a while) 2:16:48.046 2G / 9G INFO General (short_read_mapper.hpp : 91) Selecting usual mapper 2:16:55.995 2G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 200000 reads 2:16:56.283 2G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 400000 reads 2:16:56.528 2G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 600000 reads 2:16:56.633 2G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 800000 reads 2:16:56.674 2G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 1000000 reads 2:16:56.696 2G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 1200000 reads 2:16:56.834 2G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 2200000 reads 2:17:06.329 2G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 4200000 reads 2:17:15.464 2G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 8400000 reads 2:17:28.331 2G / 9G INFO General (sequence_mapper_notifier.h: 89) Processed 13489445 reads 2:17:28.332 2G / 9G INFO General (pair_info_count.cpp : 41) 6604912 paired reads (48.9636% of all) aligned to long edges 2:17:28.344 2G / 9G INFO General (pair_info_count.cpp : 170) Estimated insert size for paired library #0 2:17:28.344 2G / 9G INFO General (pair_info_count.cpp : 175) Insert size = 333.05, deviation = 97.9896, left quantile = 213, right quantile = 460, read length = 151 2:17:28.344 2G / 9G INFO General (pair_info_count.cpp : 187) Mapping library #0 2:17:28.344 2G / 9G INFO General (pair_info_count.cpp : 189) Mapping paired reads (takes a while) 2:17:28.344 2G / 9G INFO General (pair_info_count.cpp : 73) Left insert size qauntile 213, right insert size quantile 460 2:17:28.354 2G / 9G INFO General (short_read_mapper.hpp : 91) Selecting usual mapper 2:17:37.976 4G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 200000 reads 2:17:38.710 4G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 400000 reads 2:17:39.645 4G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 600000 reads 2:17:40.732 4G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 800000 reads 2:17:41.890 4G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 1000000 reads 2:17:43.128 4G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 1200000 reads 2:17:50.168 4G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 2200000 reads 2:18:05.249 5G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 4200000 reads 2:18:38.435 5G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 8400000 reads 2:19:46.200 5G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 16800000 reads 2:21:13.335 3G / 9G INFO General (sequence_mapper_notifier.h: 89) Processed 26978890 reads 2:24:02.805 3G / 9G INFO General (split_graph_pair_info.hpp : 344) Threshold for paired information 0.0542285 2:24:07.133 3G / 9G INFO StageManager (stage.cpp : 125) STAGE == Distance Estimation 2:24:07.133 3G / 9G INFO General (distance_estimation.cpp : 234) Processing library #0 2:24:07.133 3G / 9G INFO General (distance_estimation.cpp : 136) Weight Filter Done 2:24:07.133 3G / 9G INFO DistanceEstimator (distance_estimation.hpp : 187) Using SIMPLE distance estimator 2:24:15.786 3G / 9G INFO DistanceEstimator (distance_estimation.hpp : 208) Merging maps 2:24:16.567 3G / 9G INFO General (distance_estimation.cpp : 38) Filtering info 2:24:17.410 3G / 9G INFO General (pair_info_filters.hpp : 354) Pruning the index 2:24:17.446 3G / 9G INFO General (distance_estimation.cpp : 184) Refining clustered pair information 2:24:17.525 3G / 9G INFO General (distance_estimation.cpp : 186) The refining of clustered pair information has been finished 2:24:17.525 3G / 9G INFO General (distance_estimation.cpp : 188) Filling paired information 2:24:19.538 3G / 9G INFO PairInfoImprover (pair_info_improver.hpp : 61) Paired info stats: missing = 64953; contradictional = 3784 2:24:21.540 3G / 9G INFO PairInfoImprover (pair_info_improver.hpp : 61) Paired info stats: missing = 9104; contradictional = 0 2:24:21.541 3G / 9G INFO General (distance_estimation.cpp : 193) Filling scaffolding index 2:24:21.541 3G / 9G INFO DistanceEstimator (distance_estimation.hpp : 187) Using SMOOTHING distance estimator 2:24:31.386 3G / 9G INFO DistanceEstimator (distance_estimation.hpp : 208) Merging maps 2:24:31.412 3G / 9G INFO General (distance_estimation.cpp : 38) Filtering info 2:24:31.433 3G / 9G INFO General (pair_info_filters.hpp : 354) Pruning the index 2:24:31.864 2G / 9G INFO StageManager (stage.cpp : 125) STAGE == Repeat Resolving 2:24:31.864 2G / 9G INFO General (contig_output.hpp : 283) Outputting contigs to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_Indo1-7I-SPAdes-3.5.0-trimmed//K77/before_rr.fasta 2:25:22.005 2G / 9G INFO General (repeat_resolving.cpp : 59) Using Path-Extend repeat resolving 2:25:22.006 2G / 9G INFO General (path_extend_launch.hpp : 459) Threshold for library #0 is 0.0542285 2:25:22.007 2G / 9G INFO General (path_extend_launch.hpp : 298) Path-Extend repeat resolving tool started 2:25:22.034 2G / 9G INFO General (path_extend_launch.hpp : 316) Using 1 paired-end library 2:25:22.034 2G / 9G INFO General (path_extend_launch.hpp : 317) Using 1 paired-end scaffolding library 2:25:22.034 2G / 9G INFO General (path_extend_launch.hpp : 318) Using 0 mate-pair libraries 2:25:22.034 2G / 9G INFO General (path_extend_launch.hpp : 319) Using 0 single read libraries 2:25:22.034 2G / 9G INFO General (path_extend_launch.hpp : 320) Scaffolder is on 2:25:22.183 2G / 9G INFO General (path_extend_launch.hpp : 332) Growing paths using paired-end and long single reads 2:25:22.183 2G / 9G INFO PathExtender (path_extender.hpp : 611) Processed 0 paths from 12718 (0%) 2:25:23.460 2G / 9G INFO PathExtender (path_extender.hpp : 609) Processed 128 paths from 12718 (1%) 2:25:24.342 2G / 9G INFO PathExtender (path_extender.hpp : 609) Processed 256 paths from 12718 (2%) 2:25:25.240 2G / 9G INFO PathExtender (path_extender.hpp : 609) Processed 512 paths from 12718 (4%) 2:25:26.054 2G / 9G INFO PathExtender (path_extender.hpp : 609) Processed 1024 paths from 12718 (8%) 2:25:26.332 2G / 9G INFO PathExtender (path_extender.hpp : 611) Processed 1272 paths from 12718 (10%) 2:25:26.830 2G / 9G INFO PathExtender (path_extender.hpp : 609) Processed 2048 paths from 12718 (16%) 2:25:26.959 2G / 9G INFO PathExtender (path_extender.hpp : 611) Processed 2544 paths from 12718 (20%) 2:25:27.421 2G / 9G INFO PathExtender (path_extender.hpp : 611) Processed 3816 paths from 12718 (30%) 2:25:27.559 2G / 9G INFO PathExtender (path_extender.hpp : 609) Processed 4096 paths from 12718 (32%) 2:25:27.762 2G / 9G INFO PathExtender (path_extender.hpp : 611) Processed 5088 paths from 12718 (40%) 2:25:28.106 2G / 9G INFO PathExtender (path_extender.hpp : 611) Processed 6360 paths from 12718 (50%) 2:25:28.225 3G / 9G INFO PathExtender (path_extender.hpp : 611) Processed 7632 paths from 12718 (60%) 2:25:28.292 3G / 9G INFO PathExtender (path_extender.hpp : 609) Processed 8192 paths from 12718 (64%) 2:25:28.477 3G / 9G INFO PathExtender (path_extender.hpp : 611) Processed 8904 paths from 12718 (70%) 2:25:30.047 3G / 9G INFO PathExtender (path_extender.hpp : 611) Processed 10176 paths from 12718 (80%) 2:25:30.652 3G / 9G INFO PathExtender (path_extender.hpp : 611) Processed 11448 paths from 12718 (90%) 2:25:31.380 3G / 9G INFO PathExtendIO (pe_io.hpp : 339) Constructing FASTG file from paths 2:25:31.611 3G / 9G INFO PathExtendIO (pe_io.hpp : 342) Writing contigs in FASTG to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_Indo1-7I-SPAdes-3.5.0-trimmed//K77/final_contigs.fastg 2:25:31.611 3G / 9G INFO PathExtendIO (pe_io.hpp : 343) Writing contigs in FASTA to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_Indo1-7I-SPAdes-3.5.0-trimmed//K77/final_contigs.fasta 2:27:16.633 3G / 9G INFO PathExtendIO (pe_io.hpp : 339) Constructing FASTG file from paths 2:27:16.868 3G / 9G INFO PathExtendIO (pe_io.hpp : 342) Writing contigs in FASTG to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_Indo1-7I-SPAdes-3.5.0-trimmed//K77/path_extend/pe_before_traversal.fastg 2:27:16.868 3G / 9G INFO PathExtendIO (pe_io.hpp : 343) Writing contigs in FASTA to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_Indo1-7I-SPAdes-3.5.0-trimmed//K77/path_extend/pe_before_traversal.fasta 2:27:58.413 3G / 9G INFO General (path_extend_launch.hpp : 281) Traversing tandem repeats 2:27:58.634 3G / 9G INFO PathExtendIO (pe_io.hpp : 339) Constructing FASTG file from paths 2:27:58.864 3G / 9G INFO PathExtendIO (pe_io.hpp : 342) Writing contigs in FASTG to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_Indo1-7I-SPAdes-3.5.0-trimmed//K77/scaffolds.fastg 2:27:58.864 3G / 9G INFO PathExtendIO (pe_io.hpp : 343) Writing contigs in FASTA to /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_Indo1-7I-SPAdes-3.5.0-trimmed//K77/scaffolds.fasta 2:29:01.157 3G / 9G INFO General (launch.hpp : 82) SPAdes finished 2:29:07.918 176M / 9G INFO General (main.cpp : 166) Assembling time: 2 hours 29 minutes 7 seconds ===== Assembling finished. * Corrected reads are in /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_Indo1-7I-SPAdes-3.5.0-trimmed/corrected/ * Assembled contigs are in /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_Indo1-7I-SPAdes-3.5.0-trimmed/contigs.fasta (contigs.fastg) * Assembled scaffolds are in /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_Indo1-7I-SPAdes-3.5.0-trimmed/scaffolds.fasta (scaffolds.fastg) ======= SPAdes pipeline finished WITH WARNINGS! === Pipeline warnings: * Default k-mer sizes were set to [21, 33, 55, 77] 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_Indo1-7I-SPAdes-3.5.0-trimmed/warnings.log SPAdes log can be found here: /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_Indo1-7I-SPAdes-3.5.0-trimmed/spades.log Thank you for using SPAdes!