Command line: /oak/stanford/groups/akundaje/marinovg/programs/SPAdes-3.13.0-Linux/bin/spades.py -m 256 --pe1-1 /oak/stanford/groups/akundaje/marinovg/Yeast-TFs/2019-02-03-datasets-Genomes/Run1-BY4742_Rep1_PE1_pf_val_1.fq.gz --pe1-2 /oak/stanford/groups/akundaje/marinovg/Yeast-TFs/2019-02-03-datasets-Genomes/Run1-BY4742_Rep1_PE2_pf_val_2.fq.gz --pe2-1 /oak/stanford/groups/akundaje/marinovg/Yeast-TFs/2019-02-03-datasets-Genomes/Run1-BY4742_Rep2_PE1_pf_val_1.fq.gz --pe2-2 /oak/stanford/groups/akundaje/marinovg/Yeast-TFs/2019-02-03-datasets-Genomes/Run1-BY4742_Rep2_PE2_pf_val_2.fq.gz --pe3-1 /oak/stanford/groups/akundaje/marinovg/Yeast-TFs/2019-02-03-datasets-Genomes/Run2-BY4742_Rep1_PE1_pf_val_1.fq.gz --pe3-2 /oak/stanford/groups/akundaje/marinovg/Yeast-TFs/2019-02-03-datasets-Genomes/Run2-BY4742_Rep1_PE2_pf_val_2.fq.gz --pe4-1 /oak/stanford/groups/akundaje/marinovg/Yeast-TFs/2019-02-03-datasets-Genomes/Run2-BY4742_Rep2_PE1_pf_val_1.fq.gz --pe4-2 /oak/stanford/groups/akundaje/marinovg/Yeast-TFs/2019-02-03-datasets-Genomes/Run2-BY4742_Rep2_PE2_pf_val_2.fq.gz -t 20 -o /oak/stanford/groups/akundaje/marinovg/Yeast-TFs/2019-02-03-datasets-Genomes/SPAdes-3.13-BY4742 System information: SPAdes version: 3.13.0 Python version: 2.7.14 OS: Linux-3.10.0-957.1.3.el7.x86_64-x86_64-with-centos-7.6.1810-Core Output dir: /oak/stanford/groups/akundaje/marinovg/Yeast-TFs/2019-02-03-datasets-Genomes/SPAdes-3.13-BY4742 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 or --meta flag if processing metagenomic dataset) Reads: Library number: 1, library type: paired-end orientation: fr left reads: ['/oak/stanford/groups/akundaje/marinovg/Yeast-TFs/2019-02-03-datasets-Genomes/Run1-BY4742_Rep1_PE1_pf_val_1.fq.gz'] right reads: ['/oak/stanford/groups/akundaje/marinovg/Yeast-TFs/2019-02-03-datasets-Genomes/Run1-BY4742_Rep1_PE2_pf_val_2.fq.gz'] interlaced reads: not specified single reads: not specified merged reads: not specified Library number: 2, library type: paired-end orientation: fr left reads: ['/oak/stanford/groups/akundaje/marinovg/Yeast-TFs/2019-02-03-datasets-Genomes/Run1-BY4742_Rep2_PE1_pf_val_1.fq.gz'] right reads: ['/oak/stanford/groups/akundaje/marinovg/Yeast-TFs/2019-02-03-datasets-Genomes/Run1-BY4742_Rep2_PE2_pf_val_2.fq.gz'] interlaced reads: not specified single reads: not specified merged reads: not specified Library number: 3, library type: paired-end orientation: fr left reads: ['/oak/stanford/groups/akundaje/marinovg/Yeast-TFs/2019-02-03-datasets-Genomes/Run2-BY4742_Rep1_PE1_pf_val_1.fq.gz'] right reads: ['/oak/stanford/groups/akundaje/marinovg/Yeast-TFs/2019-02-03-datasets-Genomes/Run2-BY4742_Rep1_PE2_pf_val_2.fq.gz'] interlaced reads: not specified single reads: not specified merged reads: not specified Library number: 4, library type: paired-end orientation: fr left reads: ['/oak/stanford/groups/akundaje/marinovg/Yeast-TFs/2019-02-03-datasets-Genomes/Run2-BY4742_Rep2_PE1_pf_val_1.fq.gz'] right reads: ['/oak/stanford/groups/akundaje/marinovg/Yeast-TFs/2019-02-03-datasets-Genomes/Run2-BY4742_Rep2_PE2_pf_val_2.fq.gz'] interlaced reads: not specified single reads: not specified merged reads: not specified Read error correction parameters: Iterations: 1 PHRED offset will be auto-detected Corrected reads will be compressed Assembly parameters: k: automatic selection based on read length Repeat resolution is enabled Mismatch careful mode is turned OFF MismatchCorrector will be SKIPPED Coverage cutoff is turned OFF Other parameters: Dir for temp files: /oak/stanford/groups/akundaje/marinovg/Yeast-TFs/2019-02-03-datasets-Genomes/SPAdes-3.13-BY4742/tmp Threads: 20 Memory limit (in Gb): 256 ======= SPAdes pipeline started. Log can be found here: /oak/stanford/groups/akundaje/marinovg/Yeast-TFs/2019-02-03-datasets-Genomes/SPAdes-3.13-BY4742/spades.log ===== Read error correction started. == Running read error correction tool: /oak/stanford/groups/akundaje/marinovg/programs/SPAdes-3.13.0-Linux/bin/spades-hammer /oak/stanford/groups/akundaje/marinovg/Yeast-TFs/2019-02-03-datasets-Genomes/SPAdes-3.13-BY4742/corrected/configs/config.info 0:00:00.011 4M / 4M INFO General (main.cpp : 75) Starting BayesHammer, built from refs/heads/spades_3.13.0, git revision 8ea46659e9b2aca35444a808db550ac333006f8b 0:00:00.029 4M / 4M INFO General (main.cpp : 76) Loading config from /oak/stanford/groups/akundaje/marinovg/Yeast-TFs/2019-02-03-datasets-Genomes/SPAdes-3.13-BY4742/corrected/configs/config.info 0:00:00.079 4M / 4M INFO General (main.cpp : 78) Maximum # of threads to use (adjusted due to OMP capabilities): 1 0:00:00.079 4M / 4M INFO General (memory_limit.cpp : 49) Memory limit set to 256 Gb 0:00:00.079 4M / 4M INFO General (main.cpp : 86) Trying to determine PHRED offset 0:00:00.179 4M / 4M INFO General (main.cpp : 92) Determined value is 33 0:00:00.179 4M / 4M INFO General (hammer_tools.cpp : 36) Hamming graph threshold tau=1, k=21, subkmer positions = [ 0 10 ] 0:00:00.179 4M / 4M INFO General (main.cpp : 113) Size of aux. kmer data 24 bytes === ITERATION 0 begins === 0:00:00.180 4M / 4M INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:00:00.180 4M / 4M INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 16 files using 1 threads. This might take a while. 0:00:00.181 4M / 4M INFO General (file_limit.hpp : 32) Open file limit set to 131072 0:00:00.181 4M / 4M INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 85.332 Gb 0:00:00.181 4M / 4M INFO General (kmer_splitters.hpp : 97) Using cell size of 4194304 0:00:00.181 580M / 616M INFO K-mer Splitting (kmer_data.cpp : 97) Processing /oak/stanford/groups/akundaje/marinovg/Yeast-TFs/2019-02-03-datasets-Genomes/Run1-BY4742_Rep1_PE1_pf_val_1.fq.gz 0:00:16.401 580M / 616M INFO K-mer Splitting (kmer_data.cpp : 107) Processed 492211 reads 0:00:32.263 580M / 616M INFO K-mer Splitting (kmer_data.cpp : 107) Processed 990966 reads 0:00:48.141 580M / 616M INFO K-mer Splitting (kmer_data.cpp : 107) Processed 1488050 reads 0:01:03.926 580M / 616M INFO K-mer Splitting (kmer_data.cpp : 107) Processed 1937631 reads 0:01:21.781 580M / 616M INFO K-mer Splitting (kmer_data.cpp : 107) Processed 2389890 reads 0:01:29.841 580M / 616M INFO K-mer Splitting (kmer_data.cpp : 107) Processed 2611145 reads 0:01:29.842 580M / 616M INFO K-mer Splitting (kmer_data.cpp : 97) Processing /oak/stanford/groups/akundaje/marinovg/Yeast-TFs/2019-02-03-datasets-Genomes/Run1-BY4742_Rep1_PE2_pf_val_2.fq.gz 0:01:45.525 580M / 616M INFO K-mer Splitting (kmer_data.cpp : 107) Processed 3102654 reads 0:02:33.609 580M / 616M INFO K-mer Splitting (kmer_data.cpp : 107) Processed 4548061 reads 0:02:57.367 580M / 616M INFO K-mer Splitting (kmer_data.cpp : 97) Processing /oak/stanford/groups/akundaje/marinovg/Yeast-TFs/2019-02-03-datasets-Genomes/Run1-BY4742_Rep2_PE1_pf_val_1.fq.gz 0:05:10.368 580M / 616M INFO K-mer Splitting (kmer_data.cpp : 107) Processed 8649029 reads 0:05:17.123 580M / 616M INFO K-mer Splitting (kmer_data.cpp : 97) Processing /oak/stanford/groups/akundaje/marinovg/Yeast-TFs/2019-02-03-datasets-Genomes/Run1-BY4742_Rep2_PE2_pf_val_2.fq.gz 0:07:29.731 580M / 616M INFO K-mer Splitting (kmer_data.cpp : 97) Processing /oak/stanford/groups/akundaje/marinovg/Yeast-TFs/2019-02-03-datasets-Genomes/Run2-BY4742_Rep1_PE1_pf_val_1.fq.gz 0:10:10.059 580M / 616M INFO K-mer Splitting (kmer_data.cpp : 107) Processed 16856185 reads 0:12:52.609 580M / 616M INFO K-mer Splitting (kmer_data.cpp : 97) Processing /oak/stanford/groups/akundaje/marinovg/Yeast-TFs/2019-02-03-datasets-Genomes/Run2-BY4742_Rep1_PE2_pf_val_2.fq.gz 0:18:11.428 580M / 616M INFO K-mer Splitting (kmer_data.cpp : 97) Processing /oak/stanford/groups/akundaje/marinovg/Yeast-TFs/2019-02-03-datasets-Genomes/Run2-BY4742_Rep2_PE1_pf_val_1.fq.gz 0:20:36.364 580M / 616M INFO K-mer Splitting (kmer_data.cpp : 107) Processed 33924101 reads 0:20:47.840 580M / 616M INFO K-mer Splitting (kmer_data.cpp : 97) Processing /oak/stanford/groups/akundaje/marinovg/Yeast-TFs/2019-02-03-datasets-Genomes/Run2-BY4742_Rep2_PE2_pf_val_2.fq.gz 0:23:19.497 580M / 616M INFO K-mer Splitting (kmer_data.cpp : 112) Total 38565744 reads processed 0:23:19.548 4M / 616M INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:26:50.466 4M / 616M INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 132880476 kmers in total. 0:26:50.466 4M / 616M INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:26:56.659 4M / 616M INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:27:25.245 60M / 616M INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 0:27:27.818 60M / 616M INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 61625192 bytes occupied (3.71011 bits per kmer). 0:27:27.821 60M / 616M INFO K-mer Counting (kmer_data.cpp : 356) Arranging kmers in hash map order 0:27:50.614 2G / 2G INFO General (main.cpp : 148) Clustering Hamming graph. 0:54:43.024 2G / 2G INFO General (main.cpp : 155) Extracting clusters 0:56:14.822 2G / 4G INFO General (main.cpp : 167) Clustering done. Total clusters: 37383852 0:56:14.934 1G / 4G INFO K-mer Counting (kmer_data.cpp : 376) Collecting K-mer information, this takes a while. 0:56:16.790 4G / 4G INFO K-mer Counting (kmer_data.cpp : 382) Processing /oak/stanford/groups/akundaje/marinovg/Yeast-TFs/2019-02-03-datasets-Genomes/Run1-BY4742_Rep1_PE1_pf_val_1.fq.gz 1:01:14.410 4G / 4G INFO K-mer Counting (kmer_data.cpp : 382) Processing /oak/stanford/groups/akundaje/marinovg/Yeast-TFs/2019-02-03-datasets-Genomes/Run1-BY4742_Rep1_PE2_pf_val_2.fq.gz 1:05:40.666 4G / 4G INFO K-mer Counting (kmer_data.cpp : 382) Processing /oak/stanford/groups/akundaje/marinovg/Yeast-TFs/2019-02-03-datasets-Genomes/Run1-BY4742_Rep2_PE1_pf_val_1.fq.gz 1:12:23.753 4G / 4G INFO K-mer Counting (kmer_data.cpp : 382) Processing /oak/stanford/groups/akundaje/marinovg/Yeast-TFs/2019-02-03-datasets-Genomes/Run1-BY4742_Rep2_PE2_pf_val_2.fq.gz 1:19:06.052 4G / 4G INFO K-mer Counting (kmer_data.cpp : 382) Processing /oak/stanford/groups/akundaje/marinovg/Yeast-TFs/2019-02-03-datasets-Genomes/Run2-BY4742_Rep1_PE1_pf_val_1.fq.gz 1:34:56.404 4G / 4G INFO K-mer Counting (kmer_data.cpp : 382) Processing /oak/stanford/groups/akundaje/marinovg/Yeast-TFs/2019-02-03-datasets-Genomes/Run2-BY4742_Rep1_PE2_pf_val_2.fq.gz 1:50:39.230 4G / 4G INFO K-mer Counting (kmer_data.cpp : 382) Processing /oak/stanford/groups/akundaje/marinovg/Yeast-TFs/2019-02-03-datasets-Genomes/Run2-BY4742_Rep2_PE1_pf_val_1.fq.gz 1:58:27.916 4G / 4G INFO K-mer Counting (kmer_data.cpp : 382) Processing /oak/stanford/groups/akundaje/marinovg/Yeast-TFs/2019-02-03-datasets-Genomes/Run2-BY4742_Rep2_PE2_pf_val_2.fq.gz 2:06:18.321 4G / 4G INFO K-mer Counting (kmer_data.cpp : 389) Collection done, postprocessing. 2:06:18.761 4G / 4G INFO K-mer Counting (kmer_data.cpp : 403) There are 132880476 kmers in total. Among them 98156860 (73.8685%) are singletons. 2:06:18.798 4G / 4G INFO General (main.cpp : 173) Subclustering Hamming graph 2:20:58.931 4G / 4G INFO Hamming Subclustering (kmer_cluster.cpp : 649) Subclustering done. Total 2434 non-read kmers were generated. 2:20:58.931 4G / 4G INFO Hamming Subclustering (kmer_cluster.cpp : 650) Subclustering statistics: 2:20:58.931 4G / 4G INFO Hamming Subclustering (kmer_cluster.cpp : 651) Total singleton hamming clusters: 15789230. Among them 2589316 (16.3993%) are good 2:20:58.931 4G / 4G INFO Hamming Subclustering (kmer_cluster.cpp : 652) Total singleton subclusters: 37780. Among them 36524 (96.6755%) are good 2:20:58.931 4G / 4G INFO Hamming Subclustering (kmer_cluster.cpp : 653) Total non-singleton subcluster centers: 22398435. Among them 20023034 (89.3948%) are good 2:20:58.931 4G / 4G INFO Hamming Subclustering (kmer_cluster.cpp : 654) Average size of non-trivial subcluster: 5.22789 kmers 2:20:58.931 4G / 4G INFO Hamming Subclustering (kmer_cluster.cpp : 655) Average number of sub-clusters per non-singleton cluster: 1.03897 2:20:58.931 4G / 4G INFO Hamming Subclustering (kmer_cluster.cpp : 656) Total solid k-mers: 22648874 2:20:58.931 4G / 4G INFO Hamming Subclustering (kmer_cluster.cpp : 657) Substitution probabilities: [4,4]((0.949873,0.0155129,0.0164902,0.0181235),(0.0279279,0.943585,0.0103587,0.0181283),(0.0180097,0.0103,0.943682,0.0280087),(0.0180404,0.0164722,0.0154752,0.950012)) 2:20:59.028 4G / 4G INFO General (main.cpp : 178) Finished clustering. 2:20:59.039 4G / 4G INFO General (main.cpp : 197) Starting solid k-mers expansion in 1 threads. 2:46:06.926 4G / 4G INFO General (main.cpp : 218) Solid k-mers iteration 0 produced 1613814 new k-mers. 3:09:55.942 4G / 4G INFO General (main.cpp : 218) Solid k-mers iteration 1 produced 145999 new k-mers. 3:33:44.477 4G / 4G INFO General (main.cpp : 218) Solid k-mers iteration 2 produced 7705 new k-mers. 3:57:41.481 4G / 4G INFO General (main.cpp : 218) Solid k-mers iteration 3 produced 1086 new k-mers. 4:21:38.269 4G / 4G INFO General (main.cpp : 218) Solid k-mers iteration 4 produced 294 new k-mers. 4:45:38.397 4G / 4G INFO General (main.cpp : 218) Solid k-mers iteration 5 produced 129 new k-mers. 5:10:00.076 4G / 4G INFO General (main.cpp : 218) Solid k-mers iteration 6 produced 101 new k-mers. 5:34:17.912 4G / 4G INFO General (main.cpp : 218) Solid k-mers iteration 7 produced 0 new k-mers. 5:34:17.923 4G / 4G INFO General (main.cpp : 222) Solid k-mers finalized 5:34:17.955 4G / 4G INFO General (hammer_tools.cpp : 220) Starting read correction in 1 threads. 5:34:18.005 4G / 4G INFO General (hammer_tools.cpp : 233) Correcting pair of reads: /oak/stanford/groups/akundaje/marinovg/Yeast-TFs/2019-02-03-datasets-Genomes/Run1-BY4742_Rep1_PE1_pf_val_1.fq.gz and /oak/stanford/groups/akundaje/marinovg/Yeast-TFs/2019-02-03-datasets-Genomes/Run1-BY4742_Rep1_PE2_pf_val_2.fq.gz 5:34:18.715 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 0 of 100000 reads. 5:34:25.663 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 0 5:34:25.980 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 0 5:34:26.516 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 1 of 100000 reads. 5:34:32.262 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 1 5:34:32.567 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 1 5:34:33.190 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 2 of 100000 reads. 5:34:40.068 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 2 5:34:40.379 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 2 5:34:40.957 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 3 of 100000 reads. 5:34:47.085 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 3 5:34:47.394 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 3 5:34:47.926 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 4 of 100000 reads. 5:34:54.081 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 4 5:34:54.390 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 4 5:34:54.975 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 5 of 100000 reads. 5:35:01.288 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 5 5:35:01.604 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 5 5:35:02.164 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 6 of 100000 reads. 5:35:08.284 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 6 5:35:08.601 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 6 5:35:09.178 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 7 of 100000 reads. 5:35:15.566 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 7 5:35:15.886 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 7 5:35:16.425 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 8 of 100000 reads. 5:35:22.591 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 8 5:35:22.908 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 8 5:35:23.495 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 9 of 100000 reads. 5:35:30.104 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 9 5:35:30.419 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 9 5:35:30.961 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 10 of 100000 reads. 5:35:36.529 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 10 5:35:36.832 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 10 5:35:37.400 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 11 of 100000 reads. 5:35:44.284 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 11 5:35:44.608 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 11 5:35:45.172 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 12 of 100000 reads. 5:35:51.413 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 12 5:35:51.740 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 12 5:35:52.305 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 13 of 100000 reads. 5:35:58.637 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 13 5:35:58.959 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 13 5:35:59.546 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 14 of 100000 reads. 5:36:06.446 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 14 5:36:06.779 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 14 5:36:07.353 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 15 of 100000 reads. 5:36:14.138 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 15 5:36:14.456 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 15 5:36:15.073 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 16 of 100000 reads. 5:36:21.903 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 16 5:36:22.231 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 16 5:36:22.807 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 17 of 100000 reads. 5:36:29.461 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 17 5:36:29.785 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 17 5:36:30.370 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 18 of 100000 reads. 5:36:37.285 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 18 5:36:37.611 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 18 5:36:38.205 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 19 of 100000 reads. 5:36:44.885 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 19 5:36:45.206 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 19 5:36:45.824 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 20 of 100000 reads. 5:36:52.830 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 20 5:36:53.166 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 20 5:36:53.755 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 21 of 100000 reads. 5:37:00.686 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 21 5:37:01.007 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 21 5:37:01.611 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 22 of 100000 reads. 5:37:08.804 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 22 5:37:09.132 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 22 5:37:09.728 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 23 of 100000 reads. 5:37:16.732 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 23 5:37:17.059 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 23 5:37:17.654 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 24 of 100000 reads. 5:37:24.823 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 24 5:37:25.144 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 24 5:37:25.699 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 25 of 100000 reads. 5:37:32.858 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 25 5:37:33.174 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 25 5:37:33.242 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 26 of 11145 reads. 5:37:34.002 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 26 5:37:34.036 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 26 5:37:34.124 4G / 4G INFO General (hammer_tools.cpp : 233) Correcting pair of reads: /oak/stanford/groups/akundaje/marinovg/Yeast-TFs/2019-02-03-datasets-Genomes/Run1-BY4742_Rep2_PE1_pf_val_1.fq.gz and /oak/stanford/groups/akundaje/marinovg/Yeast-TFs/2019-02-03-datasets-Genomes/Run1-BY4742_Rep2_PE2_pf_val_2.fq.gz 5:37:34.788 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 0 of 100000 reads. 5:37:43.250 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 0 5:37:43.688 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 0 5:37:44.228 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 1 of 100000 reads. 5:37:53.480 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 1 5:37:53.839 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 1 5:37:54.491 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 2 of 100000 reads. 5:38:01.941 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 2 5:38:02.263 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 2 5:38:02.873 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 3 of 100000 reads. 5:38:09.943 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 3 5:38:10.281 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 3 5:38:10.890 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 4 of 100000 reads. 5:38:18.038 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 4 5:38:18.932 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 4 5:38:19.623 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 5 of 100000 reads. 5:38:26.860 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 5 5:38:27.513 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 5 5:38:28.116 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 6 of 100000 reads. 5:38:35.345 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 6 5:38:35.670 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 6 5:38:36.264 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 7 of 100000 reads. 5:38:43.745 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 7 5:38:44.055 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 7 5:38:44.663 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 8 of 100000 reads. 5:38:51.761 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 8 5:38:52.080 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 8 5:38:52.689 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 9 of 100000 reads. 5:38:59.786 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 9 5:39:00.231 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 9 5:39:00.822 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 10 of 100000 reads. 5:39:07.899 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 10 5:39:08.200 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 10 5:39:08.793 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 11 of 100000 reads. 5:39:15.857 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 11 5:39:16.184 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 11 5:39:16.778 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 12 of 100000 reads. 5:39:23.982 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 12 5:39:24.315 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 12 5:39:24.945 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 13 of 100000 reads. 5:39:32.282 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 13 5:39:32.617 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 13 5:39:33.237 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 14 of 100000 reads. 5:39:41.592 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 14 5:39:41.933 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 14 5:39:42.476 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 15 of 100000 reads. 5:39:52.231 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 15 5:39:52.557 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 15 5:39:53.101 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 16 of 100000 reads. 5:40:02.876 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 16 5:40:03.198 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 16 5:40:03.751 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 17 of 100000 reads. 5:40:13.614 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 17 5:40:14.063 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 17 5:40:14.638 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 18 of 100000 reads. 5:40:24.663 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 18 5:40:24.994 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 18 5:40:25.543 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 19 of 100000 reads. 5:40:34.985 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 19 5:40:35.298 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 19 5:40:35.830 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 20 of 100000 reads. 5:40:45.534 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 20 5:40:46.189 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 20 5:40:46.706 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 21 of 100000 reads. 5:40:57.331 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 21 5:40:57.836 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 21 5:40:58.370 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 22 of 100000 reads. 5:41:08.940 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 22 5:41:09.251 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 22 5:41:09.814 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 23 of 100000 reads. 5:41:19.302 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 23 5:41:19.788 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 23 5:41:20.318 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 24 of 100000 reads. 5:41:35.313 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 24 5:41:35.719 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 24 5:41:36.329 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 25 of 100000 reads. 5:41:45.913 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 25 5:41:46.253 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 25 5:41:46.844 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 26 of 100000 reads. 5:41:55.168 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 26 5:41:55.508 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 26 5:41:56.095 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 27 of 100000 reads. 5:42:03.942 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 27 5:42:04.274 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 27 5:42:04.887 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 28 of 100000 reads. 5:42:12.705 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 28 5:42:13.039 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 28 5:42:13.650 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 29 of 100000 reads. 5:42:21.291 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 29 5:42:21.623 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 29 5:42:22.230 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 30 of 100000 reads. 5:42:29.547 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 30 5:42:30.472 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 30 5:42:31.060 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 31 of 100000 reads. 5:42:38.278 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 31 5:42:38.599 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 31 5:42:39.197 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 32 of 100000 reads. 5:42:46.483 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 32 5:42:46.815 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 32 5:42:47.432 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 33 of 100000 reads. 5:42:54.720 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 33 5:42:55.059 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 33 5:42:55.696 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 34 of 100000 reads. 5:43:02.989 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 34 5:43:03.317 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 34 5:43:03.908 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 35 of 100000 reads. 5:43:11.338 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 35 5:43:11.656 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 35 5:43:11.717 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 36 of 10226 reads. 5:43:12.483 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 36 5:43:12.516 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 36 5:43:12.600 4G / 4G INFO General (hammer_tools.cpp : 233) Correcting pair of reads: /oak/stanford/groups/akundaje/marinovg/Yeast-TFs/2019-02-03-datasets-Genomes/Run2-BY4742_Rep1_PE1_pf_val_1.fq.gz and /oak/stanford/groups/akundaje/marinovg/Yeast-TFs/2019-02-03-datasets-Genomes/Run2-BY4742_Rep1_PE2_pf_val_2.fq.gz 5:43:13.225 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 0 of 100000 reads. 5:43:20.065 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 0 5:43:20.381 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 0 5:43:20.989 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 1 of 100000 reads. 5:43:28.009 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 1 5:43:28.474 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 1 5:43:29.071 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 2 of 100000 reads. 5:43:36.124 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 2 5:43:36.440 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 2 5:43:37.033 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 3 of 100000 reads. 5:43:44.063 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 3 5:43:44.901 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 3 5:43:45.477 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 4 of 100000 reads. 5:43:52.434 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 4 5:43:53.227 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 4 5:43:53.848 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 5 of 100000 reads. 5:44:01.219 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 5 5:44:01.685 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 5 5:44:02.310 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 6 of 100000 reads. 5:44:09.393 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 6 5:44:09.924 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 6 5:44:10.544 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 7 of 100000 reads. 5:44:17.580 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 7 5:44:17.903 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 7 5:44:18.511 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 8 of 100000 reads. 5:44:25.587 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 8 5:44:26.258 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 8 5:44:26.858 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 9 of 100000 reads. 5:44:33.789 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 9 5:44:34.610 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 9 5:44:35.181 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 10 of 100000 reads. 5:44:42.060 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 10 5:44:42.542 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 10 5:44:43.156 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 11 of 100000 reads. 5:44:49.991 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 11 5:44:51.269 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 11 5:44:51.851 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 12 of 100000 reads. 5:44:58.925 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 12 5:44:59.555 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 12 5:45:00.169 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 13 of 100000 reads. 5:45:07.410 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 13 5:45:08.140 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 13 5:45:08.747 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 14 of 100000 reads. 5:45:15.873 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 14 5:45:16.196 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 14 5:45:16.810 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 15 of 100000 reads. 5:45:23.837 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 15 5:45:24.399 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 15 5:45:24.967 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 16 of 100000 reads. 5:45:32.002 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 16 5:45:32.535 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 16 5:45:33.153 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 17 of 100000 reads. 5:45:40.259 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 17 5:45:40.564 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 17 5:45:41.143 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 18 of 100000 reads. 5:45:48.029 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 18 5:45:48.326 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 18 5:45:48.894 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 19 of 100000 reads. 5:45:55.790 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 19 5:45:56.105 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 19 5:45:56.692 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 20 of 100000 reads. 5:46:03.716 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 20 5:46:04.655 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 20 5:46:05.263 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 21 of 100000 reads. 5:46:12.333 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 21 5:46:12.661 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 21 5:46:13.249 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 22 of 100000 reads. 5:46:20.187 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 22 5:46:20.648 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 22 5:46:21.299 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 23 of 100000 reads. 5:46:28.498 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 23 5:46:29.059 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 23 5:46:29.716 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 24 of 100000 reads. 5:46:36.885 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 24 5:46:37.511 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 24 5:46:38.164 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 25 of 100000 reads. 5:46:45.216 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 25 5:46:45.527 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 25 5:46:46.144 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 26 of 100000 reads. 5:46:53.331 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 26 5:46:54.030 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 26 5:46:54.691 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 27 of 100000 reads. 5:47:01.627 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 27 5:47:02.085 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 27 5:47:02.718 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 28 of 100000 reads. 5:47:09.701 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 28 5:47:11.068 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 28 5:47:11.671 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 29 of 100000 reads. 5:47:18.741 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 29 5:47:19.067 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 29 5:47:19.679 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 30 of 100000 reads. 5:47:26.612 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 30 5:47:26.940 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 30 5:47:27.532 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 31 of 100000 reads. 5:47:34.567 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 31 5:47:34.962 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 31 5:47:35.575 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 32 of 100000 reads. 5:47:42.709 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 32 5:47:43.052 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 32 5:47:43.662 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 33 of 100000 reads. 5:47:50.845 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 33 5:47:51.173 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 33 5:47:51.792 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 34 of 100000 reads. 5:47:58.820 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 34 5:47:59.162 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 34 5:47:59.776 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 35 of 100000 reads. 5:48:06.878 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 35 5:48:07.400 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 35 5:48:08.009 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 36 of 100000 reads. 5:48:15.076 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 36 5:48:15.812 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 36 5:48:16.402 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 37 of 100000 reads. 5:48:23.644 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 37 5:48:23.953 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 37 5:48:24.535 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 38 of 100000 reads. 5:48:31.572 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 38 5:48:31.890 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 38 5:48:32.477 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 39 of 100000 reads. 5:48:39.519 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 39 5:48:39.858 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 39 5:48:40.483 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 40 of 100000 reads. 5:48:47.839 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 40 5:48:48.352 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 40 5:48:48.984 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 41 of 100000 reads. 5:48:56.052 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 41 5:48:56.869 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 41 5:48:57.455 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 42 of 100000 reads. 5:49:04.773 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 42 5:49:05.111 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 42 5:49:05.727 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 43 of 100000 reads. 5:49:13.020 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 43 5:49:13.328 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 43 5:49:13.924 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 44 of 100000 reads. 5:49:22.006 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 44 5:49:22.336 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 44 5:49:22.884 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 45 of 100000 reads. 5:49:32.613 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 45 5:49:32.945 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 45 5:49:33.485 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 46 of 100000 reads. 5:49:43.184 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 46 5:49:43.816 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 46 5:49:44.358 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 47 of 100000 reads. 5:49:51.807 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 47 5:49:52.125 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 47 5:49:52.676 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 48 of 100000 reads. 5:50:00.063 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 48 5:50:01.165 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 48 5:50:01.749 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 49 of 100000 reads. 5:50:09.663 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 49 5:50:10.162 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 49 5:50:10.809 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 50 of 100000 reads. 5:50:18.514 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 50 5:50:18.982 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 50 5:50:19.602 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 51 of 100000 reads. 5:50:27.564 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 51 5:50:27.884 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 51 5:50:28.486 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 52 of 100000 reads. 5:50:36.823 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 52 5:50:37.478 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 52 5:50:38.076 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 53 of 100000 reads. 5:50:46.814 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 53 5:50:47.134 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 53 5:50:47.732 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 54 of 100000 reads. 5:50:55.465 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 54 5:50:55.788 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 54 5:50:56.394 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 55 of 100000 reads. 5:51:04.191 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 55 5:51:04.513 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 55 5:51:05.095 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 56 of 100000 reads. 5:51:12.266 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 56 5:51:12.646 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 56 5:51:13.276 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 57 of 100000 reads. 5:51:20.497 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 57 5:51:20.811 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 57 5:51:21.389 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 58 of 100000 reads. 5:51:28.900 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 58 5:51:29.226 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 58 5:51:29.818 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 59 of 100000 reads. 5:51:37.060 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 59 5:51:37.378 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 59 5:51:37.965 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 60 of 100000 reads. 5:51:45.176 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 60 5:51:46.501 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 60 5:51:47.079 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 61 of 100000 reads. 5:51:54.466 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 61 5:51:54.809 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 61 5:51:55.382 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 62 of 100000 reads. 5:52:02.763 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 62 5:52:03.075 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 62 5:52:03.669 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 63 of 100000 reads. 5:52:10.926 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 63 5:52:11.262 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 63 5:52:11.860 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 64 of 100000 reads. 5:52:19.104 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 64 5:52:19.925 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 64 5:52:20.548 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 65 of 100000 reads. 5:52:27.888 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 65 5:52:28.211 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 65 5:52:28.821 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 66 of 100000 reads. 5:52:36.082 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 66 5:52:36.406 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 66 5:52:36.993 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 67 of 100000 reads. 5:52:44.357 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 67 5:52:44.674 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 67 5:52:45.276 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 68 of 100000 reads. 5:52:52.568 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 68 5:52:53.305 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 68 5:52:53.875 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 69 of 100000 reads. 5:53:01.584 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 69 5:53:01.913 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 69 5:53:02.533 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 70 of 100000 reads. 5:53:10.177 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 70 5:53:10.728 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 70 5:53:11.317 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 71 of 100000 reads. 5:53:18.710 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 71 5:53:19.310 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 71 5:53:19.927 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 72 of 100000 reads. 5:53:27.323 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 72 5:53:29.256 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 72 5:53:29.857 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 73 of 100000 reads. 5:53:37.343 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 73 5:53:37.673 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 73 5:53:38.248 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 74 of 100000 reads. 5:53:45.584 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 74 5:53:45.904 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 74 5:53:46.493 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 75 of 100000 reads. 5:53:54.011 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 75 5:53:54.337 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 75 5:53:54.934 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 76 of 100000 reads. 5:54:02.674 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 76 5:54:03.622 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 76 5:54:04.220 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 77 of 100000 reads. 5:54:11.929 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 77 5:54:12.255 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 77 5:54:12.857 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 78 of 100000 reads. 5:54:20.780 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 78 5:54:21.098 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 78 5:54:21.679 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 79 of 100000 reads. 5:54:29.993 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 79 5:54:30.589 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 79 5:54:31.225 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 80 of 100000 reads. 5:54:40.515 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 80 5:54:40.844 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 80 5:54:41.458 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 81 of 100000 reads. 5:54:50.503 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 81 5:54:51.302 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 81 5:54:51.940 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 82 of 100000 reads. 5:55:01.003 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 82 5:55:01.547 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 82 5:55:02.197 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 83 of 100000 reads. 5:55:10.549 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 83 5:55:12.190 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 83 5:55:12.843 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 84 of 100000 reads. 5:55:20.982 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 84 5:55:21.332 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 84 5:55:21.934 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 85 of 100000 reads. 5:55:29.748 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 85 5:55:30.079 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 85 5:55:30.709 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 86 of 100000 reads. 5:55:38.703 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 86 5:55:39.023 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 86 5:55:39.324 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 87 of 49140 reads. 5:55:43.588 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 87 5:55:43.745 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 87 5:55:43.836 4G / 4G INFO General (hammer_tools.cpp : 233) Correcting pair of reads: /oak/stanford/groups/akundaje/marinovg/Yeast-TFs/2019-02-03-datasets-Genomes/Run2-BY4742_Rep2_PE1_pf_val_1.fq.gz and /oak/stanford/groups/akundaje/marinovg/Yeast-TFs/2019-02-03-datasets-Genomes/Run2-BY4742_Rep2_PE2_pf_val_2.fq.gz 5:55:44.500 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 0 of 100000 reads. 5:55:51.796 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 0 5:55:52.113 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 0 5:55:52.848 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 1 of 100000 reads. 5:56:00.104 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 1 5:56:00.424 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 1 5:56:01.056 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 2 of 100000 reads. 5:56:08.307 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 2 5:56:08.638 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 2 5:56:09.249 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 3 of 100000 reads. 5:56:16.397 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 3 5:56:16.772 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 3 5:56:17.413 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 4 of 100000 reads. 5:56:24.571 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 4 5:56:24.904 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 4 5:56:25.515 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 5 of 100000 reads. 5:56:33.195 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 5 5:56:33.516 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 5 5:56:34.128 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 6 of 100000 reads. 5:56:41.496 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 6 5:56:41.826 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 6 5:56:42.450 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 7 of 100000 reads. 5:56:49.693 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 7 5:56:50.018 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 7 5:56:50.610 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 8 of 100000 reads. 5:56:58.023 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 8 5:56:58.357 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 8 5:56:58.975 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 9 of 100000 reads. 5:57:06.332 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 9 5:57:07.192 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 9 5:57:07.829 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 10 of 100000 reads. 5:57:15.159 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 10 5:57:15.692 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 10 5:57:16.332 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 11 of 100000 reads. 5:57:23.661 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 11 5:57:24.004 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 11 5:57:24.632 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 12 of 100000 reads. 5:57:31.839 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 12 5:57:32.159 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 12 5:57:32.778 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 13 of 100000 reads. 5:57:40.037 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 13 5:57:40.361 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 13 5:57:40.970 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 14 of 100000 reads. 5:57:48.043 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 14 5:57:48.494 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 14 5:57:49.087 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 15 of 100000 reads. 5:57:56.228 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 15 5:57:56.748 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 15 5:57:57.381 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 16 of 100000 reads. 5:58:04.695 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 16 5:58:05.027 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 16 5:58:05.630 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 17 of 100000 reads. 5:58:12.888 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 17 5:58:13.223 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 17 5:58:13.845 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 18 of 100000 reads. 5:58:21.322 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 18 5:58:21.658 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 18 5:58:22.252 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 19 of 100000 reads. 5:58:29.597 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 19 5:58:29.933 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 19 5:58:30.534 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 20 of 100000 reads. 5:58:37.873 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 20 5:58:38.204 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 20 5:58:38.809 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 21 of 100000 reads. 5:58:46.174 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 21 5:58:46.493 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 21 5:58:47.098 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 22 of 100000 reads. 5:58:54.570 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 22 5:58:54.890 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 22 5:58:55.501 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 23 of 100000 reads. 5:59:02.921 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 23 5:59:03.242 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 23 5:59:03.830 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 24 of 100000 reads. 5:59:11.405 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 24 5:59:11.733 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 24 5:59:12.333 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 25 of 100000 reads. 5:59:20.652 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 25 5:59:21.081 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 25 5:59:21.693 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 26 of 100000 reads. 5:59:29.947 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 26 5:59:30.276 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 26 5:59:30.902 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 27 of 100000 reads. 5:59:38.657 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 27 5:59:38.986 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 27 5:59:39.573 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 28 of 100000 reads. 5:59:47.001 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 28 5:59:47.330 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 28 5:59:47.906 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 29 of 100000 reads. 5:59:55.168 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 29 5:59:55.498 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 29 5:59:56.098 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 30 of 100000 reads. 6:00:03.371 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 30 6:00:03.702 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 30 6:00:04.301 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 31 of 100000 reads. 6:00:11.701 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 31 6:00:12.231 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 31 6:00:12.836 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 32 of 100000 reads. 6:00:20.278 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 32 6:00:20.601 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 32 6:00:21.204 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 33 of 100000 reads. 6:00:28.532 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 33 6:00:28.862 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 33 6:00:29.473 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 34 of 100000 reads. 6:00:36.903 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 34 6:00:37.240 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 34 6:00:37.834 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 35 of 100000 reads. 6:00:45.198 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 35 6:00:45.520 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 35 6:00:46.123 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 36 of 100000 reads. 6:00:53.626 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 36 6:00:53.949 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 36 6:00:54.555 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 37 of 100000 reads. 6:01:02.096 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 37 6:01:02.731 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 37 6:01:03.340 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 38 of 100000 reads. 6:01:11.071 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 38 6:01:11.398 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 38 6:01:12.007 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 39 of 100000 reads. 6:01:20.789 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 39 6:01:21.317 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 39 6:01:21.943 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 40 of 100000 reads. 6:01:30.836 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 40 6:01:31.169 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 40 6:01:31.776 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 41 of 100000 reads. 6:01:40.033 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 41 6:01:40.362 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 41 6:01:40.944 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 42 of 100000 reads. 6:01:48.923 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 42 6:01:49.255 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 42 6:01:49.335 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 43 of 12361 reads. 6:01:50.586 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 43 6:01:50.626 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 43 6:01:50.718 4G / 4G INFO General (hammer_tools.cpp : 274) Correction done. Changed 4164231 bases in 2857285 reads. 6:01:50.718 4G / 4G INFO General (hammer_tools.cpp : 275) Failed to correct 1331444 bases out of 3673082438. 6:01:51.295 4M / 4G INFO General (main.cpp : 255) Saving corrected dataset description to /oak/stanford/groups/akundaje/marinovg/Yeast-TFs/2019-02-03-datasets-Genomes/SPAdes-3.13-BY4742/corrected/corrected.yaml 6:01:51.298 4M / 4G INFO General (main.cpp : 262) All done. Exiting. == Compressing corrected reads (with pigz) == Dataset description file was created: /oak/stanford/groups/akundaje/marinovg/Yeast-TFs/2019-02-03-datasets-Genomes/SPAdes-3.13-BY4742/corrected/corrected.yaml ===== Read error correction finished. ===== Assembling started. == Running assembler: K21 0:00:00.002 4M / 4M INFO General (main.cpp : 74) Loaded config from /oak/stanford/groups/akundaje/marinovg/Yeast-TFs/2019-02-03-datasets-Genomes/SPAdes-3.13-BY4742/K21/configs/config.info 0:00:00.047 4M / 4M INFO General (memory_limit.cpp : 49) Memory limit set to 256 Gb 0:00:00.047 4M / 4M INFO General (main.cpp : 87) Starting SPAdes, built from refs/heads/spades_3.13.0, git revision 8ea46659e9b2aca35444a808db550ac333006f8b 0:00:00.047 4M / 4M INFO General (main.cpp : 88) Maximum k-mer length: 128 0:00:00.047 4M / 4M INFO General (main.cpp : 89) Assembling dataset (/oak/stanford/groups/akundaje/marinovg/Yeast-TFs/2019-02-03-datasets-Genomes/SPAdes-3.13-BY4742/dataset.info) with K=21 0:00:00.047 4M / 4M INFO General (main.cpp : 90) Maximum # of threads to use (adjusted due to OMP capabilities): 1 0:00:00.047 4M / 4M INFO General (launch.hpp : 51) SPAdes started 0:00:00.047 4M / 4M INFO General (launch.hpp : 58) Starting from stage: construction 0:00:00.047 4M / 4M INFO General (launch.hpp : 65) Two-step RR enabled: 0 0:00:00.086 4M / 4M INFO StageManager (stage.cpp : 132) STAGE == de Bruijn graph construction 0:00:00.091 4M / 4M INFO General (read_converter.hpp : 77) Converting reads to binary format for library #0 (takes a while) 0:00:00.091 4M / 4M INFO General (read_converter.hpp : 78) Converting paired reads 0:00:00.474 76M / 132M INFO General (binary_converter.hpp : 93) 16384 reads processed 0:00:00.618 88M / 132M INFO General (binary_converter.hpp : 93) 32768 reads processed 0:00:00.945 112M / 132M INFO General (binary_converter.hpp : 93) 65536 reads processed 0:00:01.509 152M / 152M INFO General (binary_converter.hpp : 93) 131072 reads processed 0:00:02.645 236M / 236M INFO General (binary_converter.hpp : 93) 262144 reads processed 0:00:04.950 404M / 404M INFO General (binary_converter.hpp : 93) 524288 reads processed 0:00:11.286 672M / 672M INFO General (binary_converter.hpp : 93) 1048576 reads processed 0:00:22.266 764M / 764M INFO General (binary_converter.hpp : 93) 2097152 reads processed 0:00:28.775 656M / 800M INFO General (binary_converter.hpp : 117) 2607082 reads written 0:00:29.410 4M / 800M INFO General (read_converter.hpp : 87) Converting single reads 0:00:29.724 132M / 800M INFO General (binary_converter.hpp : 117) 4020 reads written 0:00:29.739 4M / 800M INFO General (read_converter.hpp : 95) Converting merged reads 0:00:30.031 132M / 800M INFO General (binary_converter.hpp : 117) 0 reads written 0:00:30.049 4M / 800M INFO General (read_converter.hpp : 77) Converting reads to binary format for library #1 (takes a while) 0:00:30.049 4M / 800M INFO General (read_converter.hpp : 78) Converting paired reads 0:00:30.342 76M / 800M INFO General (binary_converter.hpp : 93) 16384 reads processed 0:00:30.488 88M / 800M INFO General (binary_converter.hpp : 93) 32768 reads processed 0:00:30.780 112M / 800M INFO General (binary_converter.hpp : 93) 65536 reads processed 0:00:31.369 156M / 800M INFO General (binary_converter.hpp : 93) 131072 reads processed 0:00:32.581 244M / 800M INFO General (binary_converter.hpp : 93) 262144 reads processed 0:00:35.075 420M / 800M INFO General (binary_converter.hpp : 93) 524288 reads processed 0:00:42.025 700M / 800M INFO General (binary_converter.hpp : 93) 1048576 reads processed 0:00:53.494 704M / 800M INFO General (binary_converter.hpp : 93) 2097152 reads processed 0:01:11.484 636M / 800M INFO General (binary_converter.hpp : 117) 3604658 reads written 0:01:12.069 4M / 800M INFO General (read_converter.hpp : 87) Converting single reads 0:01:12.392 132M / 800M INFO General (binary_converter.hpp : 117) 5536 reads written 0:01:12.406 4M / 800M INFO General (read_converter.hpp : 95) Converting merged reads 0:01:12.690 132M / 800M INFO General (binary_converter.hpp : 117) 0 reads written 0:01:12.710 4M / 800M INFO General (read_converter.hpp : 77) Converting reads to binary format for library #2 (takes a while) 0:01:12.710 4M / 800M INFO General (read_converter.hpp : 78) Converting paired reads 0:01:13.108 76M / 800M INFO General (binary_converter.hpp : 93) 16384 reads processed 0:01:13.253 88M / 800M INFO General (binary_converter.hpp : 93) 32768 reads processed 0:01:13.679 112M / 800M INFO General (binary_converter.hpp : 93) 65536 reads processed 0:01:14.255 156M / 800M INFO General (binary_converter.hpp : 93) 131072 reads processed 0:01:15.492 244M / 800M INFO General (binary_converter.hpp : 93) 262144 reads processed 0:01:18.170 420M / 800M INFO General (binary_converter.hpp : 93) 524288 reads processed 0:01:25.086 692M / 800M INFO General (binary_converter.hpp : 93) 1048576 reads processed 0:01:36.597 692M / 800M INFO General (binary_converter.hpp : 93) 2097152 reads processed 0:01:58.654 696M / 800M INFO General (binary_converter.hpp : 93) 4194304 reads processed 0:02:47.048 724M / 800M INFO General (binary_converter.hpp : 93) 8388608 reads processed 0:02:51.745 436M / 800M INFO General (binary_converter.hpp : 117) 8734990 reads written 0:02:52.162 4M / 800M INFO General (read_converter.hpp : 87) Converting single reads 0:02:52.579 136M / 800M INFO General (binary_converter.hpp : 117) 14038 reads written 0:02:52.595 4M / 800M INFO General (read_converter.hpp : 95) Converting merged reads 0:02:52.881 132M / 800M INFO General (binary_converter.hpp : 117) 0 reads written 0:02:52.926 4M / 800M INFO General (read_converter.hpp : 77) Converting reads to binary format for library #3 (takes a while) 0:02:52.926 4M / 800M INFO General (read_converter.hpp : 78) Converting paired reads 0:02:53.345 76M / 800M INFO General (binary_converter.hpp : 93) 16384 reads processed 0:02:53.493 88M / 800M INFO General (binary_converter.hpp : 93) 32768 reads processed 0:02:53.861 112M / 800M INFO General (binary_converter.hpp : 93) 65536 reads processed 0:02:54.455 156M / 800M INFO General (binary_converter.hpp : 93) 131072 reads processed 0:02:55.710 244M / 800M INFO General (binary_converter.hpp : 93) 262144 reads processed 0:02:58.279 416M / 800M INFO General (binary_converter.hpp : 93) 524288 reads processed 0:03:04.919 692M / 800M INFO General (binary_converter.hpp : 93) 1048576 reads processed 0:03:16.147 692M / 800M INFO General (binary_converter.hpp : 93) 2097152 reads processed 0:03:39.210 708M / 800M INFO General (binary_converter.hpp : 93) 4194304 reads processed 0:03:41.929 524M / 800M INFO General (binary_converter.hpp : 117) 4303904 reads written 0:03:42.473 4M / 800M INFO General (read_converter.hpp : 87) Converting single reads 0:03:42.810 132M / 800M INFO General (binary_converter.hpp : 117) 8393 reads written 0:03:42.824 4M / 800M INFO General (read_converter.hpp : 95) Converting merged reads 0:03:43.126 132M / 800M INFO General (binary_converter.hpp : 117) 0 reads written 0:03:43.144 4M / 800M INFO General (construction.cpp : 111) Max read length 101 0:03:43.144 4M / 800M INFO General (construction.cpp : 117) Average read length 95.2496 0:03:43.145 4M / 800M INFO General (stage.cpp : 101) PROCEDURE == k+1-mer counting 0:03:43.146 4M / 800M INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 1 files using 1 threads. This might take a while. 0:03:43.146 4M / 800M INFO General (file_limit.hpp : 32) Open file limit set to 131072 0:03:43.146 4M / 800M INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 85.332 Gb 0:03:43.146 4M / 800M INFO General (kmer_splitters.hpp : 97) Using cell size of 67108864 0:03:57.865 568M / 1G INFO General (kmer_splitters.hpp : 289) Processed 2001245 reads 0:04:12.148 568M / 1G INFO General (kmer_splitters.hpp : 289) Processed 4034568 reads 0:04:26.617 568M / 1G INFO General (kmer_splitters.hpp : 289) Processed 6046800 reads 0:04:39.910 568M / 1G INFO General (kmer_splitters.hpp : 289) Processed 7878076 reads 0:04:54.017 568M / 1G INFO General (kmer_splitters.hpp : 289) Processed 9707108 reads 0:05:08.685 568M / 1G INFO General (kmer_splitters.hpp : 289) Processed 11478672 reads 0:05:23.276 568M / 1G INFO General (kmer_splitters.hpp : 289) Processed 13219570 reads 0:05:37.837 568M / 1G INFO General (kmer_splitters.hpp : 289) Processed 14957441 reads 0:05:52.363 568M / 1G INFO General (kmer_splitters.hpp : 289) Processed 16695899 reads 0:06:06.313 568M / 1G INFO General (kmer_splitters.hpp : 289) Processed 18440554 reads 0:08:17.703 568M / 1G INFO General (kmer_splitters.hpp : 289) Processed 34429482 reads 0:12:52.377 568M / 1G INFO General (kmer_splitters.hpp : 289) Processed 68681005 reads 0:13:59.108 568M / 1G INFO General (kmer_splitters.hpp : 295) Adding contigs from previous K 0:13:59.163 4M / 1G INFO General (kmer_splitters.hpp : 308) Used 77066510 reads 0:13:59.163 4M / 1G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:20:19.227 4M / 1G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 17496683 kmers in total. 0:20:19.227 4M / 1G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:20:19.987 4M / 1G INFO General (stage.cpp : 101) PROCEDURE == Extension index construction 0:20:19.987 4M / 1G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:20:19.987 4M / 1G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 16 files using 1 threads. This might take a while. 0:20:19.988 4M / 1G INFO General (file_limit.hpp : 32) Open file limit set to 131072 0:20:19.988 4M / 1G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 85.332 Gb 0:20:19.988 4M / 1G INFO General (kmer_splitters.hpp : 97) Using cell size of 4194304 0:20:27.408 580M / 1G INFO General (kmer_splitters.hpp : 380) Processed 17496683 kmers 0:20:27.408 580M / 1G INFO General (kmer_splitters.hpp : 385) Used 17496683 kmers. 0:20:27.437 4M / 1G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:20:36.110 4M / 1G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 17257414 kmers in total. 0:20:36.110 4M / 1G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:20:38.954 4M / 1G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:20:42.792 12M / 1G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 0:20:47.931 12M / 1G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 8010560 bytes occupied (3.71345 bits per kmer). 0:20:47.954 32M / 1G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 99) Building k-mer extensions from k+1-mers 0:20:54.667 32M / 1G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 103) Building k-mer extensions from k+1-mers finished. 0:20:54.669 32M / 1G INFO General (stage.cpp : 101) PROCEDURE == Early tip clipping 0:20:54.669 32M / 1G INFO General (construction.cpp : 253) Early tip clipper length bound set as (RL - K) 0:20:54.669 32M / 1G INFO Early tip clipping (early_simplification.hpp : 181) Early tip clipping 0:21:10.509 32M / 1G INFO Early tip clipping (early_simplification.hpp : 184) 2179857 22-mers were removed by early tip clipper 0:21:10.509 32M / 1G INFO General (stage.cpp : 101) PROCEDURE == Condensing graph 0:21:10.510 32M / 1G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 355) Extracting unbranching paths 0:21:20.097 68M / 1G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 374) Extracting unbranching paths finished. 638279 sequences extracted 0:21:25.046 68M / 1G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 310) Collecting perfect loops 0:21:27.141 68M / 1G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 343) Collecting perfect loops finished. 3 loops collected 0:21:28.072 204M / 1G INFO General (stage.cpp : 101) PROCEDURE == Filling coverage indices (PHM) 0:21:28.072 204M / 1G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:21:28.072 204M / 1G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:21:31.762 216M / 1G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 8113760 bytes occupied (3.70985 bits per kmer). 0:21:31.811 284M / 1G INFO General (construction.cpp : 388) Collecting k-mer coverage information from reads, this takes a while. 0:31:28.981 284M / 1G INFO General (construction.cpp : 508) Filling coverage and flanking coverage from PHM 0:31:34.397 284M / 1G INFO General (construction.cpp : 464) Processed 1000000 edges 0:31:35.822 284M / 1G INFO General (construction.cpp : 464) Processed 1276063 edges 0:31:35.908 184M / 1G INFO StageManager (stage.cpp : 132) STAGE == EC Threshold Finding 0:31:35.930 192M / 1G INFO General (kmer_coverage_model.cpp : 181) Kmer coverage valley at: 48 0:31:35.930 184M / 1G INFO General (kmer_coverage_model.cpp : 201) K-mer histogram maximum: 197 0:31:35.930 184M / 1G INFO General (kmer_coverage_model.cpp : 237) Estimated median coverage: 206. Coverage mad: 45.9606 0:31:35.931 184M / 1G INFO General (kmer_coverage_model.cpp : 259) Fitting coverage model 0:31:36.318 192M / 1G INFO General (kmer_coverage_model.cpp : 295) ... iteration 2 0:31:37.027 192M / 1G INFO General (kmer_coverage_model.cpp : 295) ... iteration 4 0:31:39.298 192M / 1G INFO General (kmer_coverage_model.cpp : 295) ... iteration 8 0:31:43.209 192M / 1G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 209.903. Fitted coverage std. dev: 45.0943 0:31:43.217 192M / 1G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 0.993717 0:31:43.217 192M / 1G INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 115 0:31:43.217 192M / 1G INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 115 0:31:43.217 192M / 1G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 11310199 0:31:43.217 184M / 1G INFO General (genomic_info_filler.cpp : 112) Mean coverage was calculated as 209.903 0:31:43.217 184M / 1G INFO General (genomic_info_filler.cpp : 127) EC coverage threshold value was calculated as 115 0:31:43.217 184M / 1G INFO General (genomic_info_filler.cpp : 128) Trusted kmer low bound: 0 0:31:43.217 184M / 1G INFO StageManager (stage.cpp : 132) STAGE == Raw Simplification 0:31:43.217 184M / 1G INFO General (simplification.cpp : 128) PROCEDURE == InitialCleaning 0:31:43.240 184M / 1G INFO General (graph_simplification.hpp : 662) Flanking coverage based disconnection disabled 0:31:43.240 184M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Self conjugate edge remover 0:31:43.380 184M / 1G INFO Simplification (parallel_processing.hpp : 167) Self conjugate edge remover triggered 0 times 0:31:43.380 184M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Initial tip clipper 0:31:43.712 184M / 1G INFO Simplification (parallel_processing.hpp : 167) Initial tip clipper triggered 3660 times 0:31:43.712 184M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Initial ec remover 0:31:47.478 200M / 1G INFO Simplification (parallel_processing.hpp : 167) Initial ec remover triggered 168624 times 0:31:47.478 200M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Initial isolated edge remover 0:31:47.569 200M / 1G INFO Simplification (parallel_processing.hpp : 167) Initial isolated edge remover triggered 2267 times 0:31:47.591 200M / 1G INFO StageManager (stage.cpp : 132) STAGE == Simplification 0:31:47.591 200M / 1G INFO General (simplification.cpp : 357) Graph simplification started 0:31:47.591 200M / 1G INFO General (graph_simplification.hpp : 634) Creating parallel br instance 0:31:47.591 200M / 1G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 1 0:31:47.591 200M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:31:47.704 200M / 1G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 1543 times 0:31:47.704 200M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:32:10.286 196M / 1G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 24464 times 0:32:10.286 196M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:32:11.075 176M / 1G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 32883 times 0:32:11.075 176M / 1G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 2 0:32:11.075 176M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:32:11.085 172M / 1G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 138 times 0:32:11.086 172M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:32:12.488 164M / 1G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 2690 times 0:32:12.488 164M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:32:12.586 148M / 1G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 4242 times 0:32:12.586 148M / 1G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 3 0:32:12.586 148M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:32:12.588 148M / 1G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 1 times 0:32:12.588 148M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:32:12.886 148M / 1G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 290 times 0:32:12.886 148M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:32:12.926 140M / 1G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 1380 times 0:32:12.926 140M / 1G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 4 0:32:12.926 140M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:32:12.926 140M / 1G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:32:12.926 140M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:32:13.030 140M / 1G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 102 times 0:32:13.030 140M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:32:13.043 136M / 1G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 614 times 0:32:13.043 136M / 1G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 5 0:32:13.043 136M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:32:13.043 136M / 1G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:32:13.043 136M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:32:13.106 136M / 1G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 59 times 0:32:13.106 136M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:32:13.114 132M / 1G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 349 times 0:32:13.114 132M / 1G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 6 0:32:13.114 132M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:32:13.114 132M / 1G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 1 times 0:32:13.114 132M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:32:13.137 132M / 1G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 37 times 0:32:13.137 132M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:32:13.142 132M / 1G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 218 times 0:32:13.142 132M / 1G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 7 0:32:13.142 132M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:32:13.142 132M / 1G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:32:13.142 132M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:32:13.156 132M / 1G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 18 times 0:32:13.156 132M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:32:13.159 132M / 1G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 177 times 0:32:13.159 132M / 1G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 8 0:32:13.159 132M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:32:13.159 132M / 1G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:32:13.159 132M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:32:13.171 128M / 1G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 25 times 0:32:13.172 128M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:32:13.174 128M / 1G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 141 times 0:32:13.174 128M / 1G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 9 0:32:13.174 128M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:32:13.174 128M / 1G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:32:13.174 128M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:32:13.181 128M / 1G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 14 times 0:32:13.181 128M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:32:13.183 128M / 1G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 109 times 0:32:13.183 128M / 1G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 10 0:32:13.183 128M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:32:13.183 128M / 1G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:32:13.183 128M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:32:13.188 128M / 1G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 7 times 0:32:13.188 128M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:32:13.202 128M / 1G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 114 times 0:32:13.202 128M / 1G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 11 0:32:13.202 128M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:32:13.208 128M / 1G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:32:13.208 128M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:32:13.322 128M / 1G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 16 times 0:32:13.322 128M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:32:13.327 124M / 1G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:32:13.327 124M / 1G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 12 0:32:13.327 124M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:32:13.327 124M / 1G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:32:13.327 124M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:32:13.327 124M / 1G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:32:13.327 124M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:32:13.327 124M / 1G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:32:13.327 124M / 1G INFO StageManager (stage.cpp : 132) STAGE == Simplification Cleanup 0:32:13.327 124M / 1G INFO General (simplification.cpp : 196) PROCEDURE == Post simplification 0:32:13.327 124M / 1G INFO General (graph_simplification.hpp : 453) Disconnection of relatively low covered edges disabled 0:32:13.327 124M / 1G INFO General (graph_simplification.hpp : 489) Complex tip clipping disabled 0:32:13.327 124M / 1G INFO General (graph_simplification.hpp : 634) Creating parallel br instance 0:32:13.327 124M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:32:13.331 124M / 1G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:32:13.331 124M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:32:13.440 124M / 1G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:32:13.440 124M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:32:13.444 124M / 1G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:32:13.444 124M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:32:13.552 124M / 1G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:32:13.552 124M / 1G INFO General (simplification.cpp : 330) Disrupting self-conjugate edges 0:32:13.559 124M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Removing isolated edges 0:32:13.563 124M / 1G INFO Simplification (parallel_processing.hpp : 167) Removing isolated edges triggered 322 times 0:32:13.563 124M / 1G INFO General (simplification.cpp : 470) Counting average coverage 0:32:13.565 124M / 1G INFO General (simplification.cpp : 476) Average coverage = 250.21 0:32:13.565 124M / 1G INFO StageManager (stage.cpp : 132) STAGE == Contig Output 0:32:13.565 124M / 1G INFO General (contig_output_stage.cpp : 40) Writing GFA to /oak/stanford/groups/akundaje/marinovg/Yeast-TFs/2019-02-03-datasets-Genomes/SPAdes-3.13-BY4742//K21/assembly_graph_with_scaffolds.gfa 0:32:13.739 120M / 1G INFO General (contig_output.hpp : 22) Outputting contigs to /oak/stanford/groups/akundaje/marinovg/Yeast-TFs/2019-02-03-datasets-Genomes/SPAdes-3.13-BY4742//K21/before_rr.fasta 0:32:14.053 120M / 1G INFO General (contig_output_stage.cpp : 51) Outputting FastG graph to /oak/stanford/groups/akundaje/marinovg/Yeast-TFs/2019-02-03-datasets-Genomes/SPAdes-3.13-BY4742//K21/assembly_graph.fastg 0:32:14.679 124M / 1G INFO General (contig_output.hpp : 22) Outputting contigs to /oak/stanford/groups/akundaje/marinovg/Yeast-TFs/2019-02-03-datasets-Genomes/SPAdes-3.13-BY4742//K21/simplified_contigs.fasta 0:32:14.988 120M / 1G INFO General (contig_output.hpp : 22) Outputting contigs to /oak/stanford/groups/akundaje/marinovg/Yeast-TFs/2019-02-03-datasets-Genomes/SPAdes-3.13-BY4742//K21/final_contigs.fasta 0:32:15.297 120M / 1G INFO StageManager (stage.cpp : 132) STAGE == Contig Output 0:32:15.297 120M / 1G INFO General (contig_output_stage.cpp : 40) Writing GFA to /oak/stanford/groups/akundaje/marinovg/Yeast-TFs/2019-02-03-datasets-Genomes/SPAdes-3.13-BY4742//K21/assembly_graph_with_scaffolds.gfa 0:32:15.471 120M / 1G INFO General (contig_output.hpp : 22) Outputting contigs to /oak/stanford/groups/akundaje/marinovg/Yeast-TFs/2019-02-03-datasets-Genomes/SPAdes-3.13-BY4742//K21/before_rr.fasta 0:32:15.786 120M / 1G INFO General (contig_output_stage.cpp : 51) Outputting FastG graph to /oak/stanford/groups/akundaje/marinovg/Yeast-TFs/2019-02-03-datasets-Genomes/SPAdes-3.13-BY4742//K21/assembly_graph.fastg 0:32:16.401 124M / 1G INFO General (contig_output.hpp : 22) Outputting contigs to /oak/stanford/groups/akundaje/marinovg/Yeast-TFs/2019-02-03-datasets-Genomes/SPAdes-3.13-BY4742//K21/simplified_contigs.fasta 0:32:16.717 120M / 1G INFO General (contig_output.hpp : 22) Outputting contigs to /oak/stanford/groups/akundaje/marinovg/Yeast-TFs/2019-02-03-datasets-Genomes/SPAdes-3.13-BY4742//K21/final_contigs.fasta 0:32:17.039 120M / 1G INFO General (launch.hpp : 149) SPAdes finished 0:32:17.133 8M / 1G INFO General (main.cpp : 109) Assembling time: 0 hours 32 minutes 17 seconds Max read length detected as 101 == Running assembler: K33 0:00:00.000 4M / 4M INFO General (main.cpp : 74) Loaded config from /oak/stanford/groups/akundaje/marinovg/Yeast-TFs/2019-02-03-datasets-Genomes/SPAdes-3.13-BY4742/K33/configs/config.info 0:00:00.000 4M / 4M INFO General (memory_limit.cpp : 49) Memory limit set to 256 Gb 0:00:00.000 4M / 4M INFO General (main.cpp : 87) Starting SPAdes, built from refs/heads/spades_3.13.0, git revision 8ea46659e9b2aca35444a808db550ac333006f8b 0:00:00.000 4M / 4M INFO General (main.cpp : 88) Maximum k-mer length: 128 0:00:00.000 4M / 4M INFO General (main.cpp : 89) Assembling dataset (/oak/stanford/groups/akundaje/marinovg/Yeast-TFs/2019-02-03-datasets-Genomes/SPAdes-3.13-BY4742/dataset.info) with K=33 0:00:00.000 4M / 4M INFO General (main.cpp : 90) Maximum # of threads to use (adjusted due to OMP capabilities): 1 0:00:00.000 4M / 4M INFO General (launch.hpp : 51) SPAdes started 0:00:00.000 4M / 4M INFO General (launch.hpp : 58) Starting from stage: construction 0:00:00.000 4M / 4M INFO General (launch.hpp : 65) Two-step RR enabled: 0 0:00:00.000 4M / 4M INFO StageManager (stage.cpp : 132) STAGE == de Bruijn graph construction 0:00:00.001 4M / 4M INFO General (read_converter.hpp : 59) Binary reads detected 0:00:00.003 4M / 4M INFO General (read_converter.hpp : 59) Binary reads detected 0:00:00.024 4M / 4M INFO General (read_converter.hpp : 59) Binary reads detected 0:00:00.038 4M / 4M INFO General (read_converter.hpp : 59) Binary reads detected 0:00:00.039 4M / 4M INFO General (construction.cpp : 111) Max read length 101 0:00:00.039 4M / 4M INFO General (construction.cpp : 117) Average read length 95.2496 0:00:00.039 4M / 4M INFO General (stage.cpp : 101) PROCEDURE == k+1-mer counting 0:00:00.040 4M / 4M INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 1 files using 1 threads. This might take a while. 0:00:00.040 4M / 4M INFO General (file_limit.hpp : 32) Open file limit set to 131072 0:00:00.040 4M / 4M INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 85.332 Gb 0:00:00.040 4M / 4M INFO General (kmer_splitters.hpp : 97) Using cell size of 33554432 0:00:08.800 568M / 1G INFO General (kmer_splitters.hpp : 289) Processed 1194758 reads 0:00:17.180 568M / 1G INFO General (kmer_splitters.hpp : 289) Processed 2432905 reads 0:00:25.394 568M / 1G INFO General (kmer_splitters.hpp : 289) Processed 3701775 reads 0:00:33.798 568M / 1G INFO General (kmer_splitters.hpp : 289) Processed 4945185 reads 0:00:41.256 568M / 1G INFO General (kmer_splitters.hpp : 289) Processed 6144970 reads 0:00:49.458 568M / 1G INFO General (kmer_splitters.hpp : 289) Processed 7235758 reads 0:00:57.834 568M / 1G INFO General (kmer_splitters.hpp : 289) Processed 8321081 reads 0:01:06.153 568M / 1G INFO General (kmer_splitters.hpp : 289) Processed 9420388 reads 0:01:14.369 568M / 1G INFO General (kmer_splitters.hpp : 289) Processed 10504542 reads 0:02:11.776 568M / 1G INFO General (kmer_splitters.hpp : 289) Processed 17708670 reads 0:04:25.002 568M / 1G INFO General (kmer_splitters.hpp : 289) Processed 34593386 reads 0:08:31.639 568M / 1G INFO General (kmer_splitters.hpp : 289) Processed 67897898 reads 0:09:41.704 568M / 1G INFO General (kmer_splitters.hpp : 295) Adding contigs from previous K 0:09:45.512 4M / 1G INFO General (kmer_splitters.hpp : 308) Used 77066510 reads 0:09:45.512 4M / 1G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 1:05:49.691 4M / 1G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 19720853 kmers in total. 1:05:49.808 4M / 1G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 1:05:51.843 4M / 1G INFO General (stage.cpp : 101) PROCEDURE == Extension index construction 1:05:51.880 4M / 1G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 1:05:51.881 4M / 1G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 16 files using 1 threads. This might take a while. 1:05:51.881 4M / 1G INFO General (file_limit.hpp : 32) Open file limit set to 131072 1:05:51.881 4M / 1G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 85.332 Gb 1:05:51.881 4M / 1G INFO General (kmer_splitters.hpp : 97) Using cell size of 2097152 1:06:00.472 580M / 1G INFO General (kmer_splitters.hpp : 380) Processed 16752034 kmers 1:06:01.938 580M / 1G INFO General (kmer_splitters.hpp : 380) Processed 19720854 kmers 1:06:01.938 580M / 1G INFO General (kmer_splitters.hpp : 385) Used 19720854 kmers. 1:06:01.999 4M / 1G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 1:06:10.767 4M / 1G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 19581777 kmers in total. 1:06:10.767 4M / 1G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 1:06:13.009 4M / 1G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 1:06:17.077 12M / 1G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 1:06:21.912 12M / 1G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 9088144 bytes occupied (3.7129 bits per kmer). 1:06:21.942 32M / 1G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 99) Building k-mer extensions from k+1-mers 1:06:30.288 32M / 1G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 103) Building k-mer extensions from k+1-mers finished. 1:06:30.288 32M / 1G INFO General (stage.cpp : 101) PROCEDURE == Early tip clipping 1:06:30.288 32M / 1G INFO General (construction.cpp : 253) Early tip clipper length bound set as (RL - K) 1:06:30.288 32M / 1G INFO Early tip clipping (early_simplification.hpp : 181) Early tip clipping 1:06:49.715 32M / 1G INFO Early tip clipping (early_simplification.hpp : 184) 3843508 34-mers were removed by early tip clipper 1:06:49.715 32M / 1G INFO General (stage.cpp : 101) PROCEDURE == Condensing graph 1:06:49.715 32M / 1G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 355) Extracting unbranching paths 1:07:01.355 64M / 1G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 374) Extracting unbranching paths finished. 448068 sequences extracted 1:07:06.880 64M / 1G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 310) Collecting perfect loops 1:07:09.587 64M / 1G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 343) Collecting perfect loops finished. 4 loops collected 1:07:10.413 160M / 1G INFO General (stage.cpp : 101) PROCEDURE == Filling coverage indices (PHM) 1:07:10.413 160M / 1G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 1:07:10.413 160M / 1G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 1:07:14.308 172M / 1G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 9145088 bytes occupied (3.70981 bits per kmer). 1:07:14.353 248M / 1G INFO General (construction.cpp : 388) Collecting k-mer coverage information from reads, this takes a while. 1:15:56.243 248M / 1G INFO General (construction.cpp : 508) Filling coverage and flanking coverage from PHM 1:16:03.434 248M / 1G INFO General (construction.cpp : 464) Processed 895819 edges 1:16:03.582 136M / 1G INFO StageManager (stage.cpp : 132) STAGE == EC Threshold Finding 1:16:03.586 136M / 1G INFO General (kmer_coverage_model.cpp : 181) Kmer coverage valley at: 45 1:16:03.586 136M / 1G INFO General (kmer_coverage_model.cpp : 201) K-mer histogram maximum: 165 1:16:03.586 136M / 1G INFO General (kmer_coverage_model.cpp : 237) Estimated median coverage: 172. Coverage mad: 41.5128 1:16:03.586 136M / 1G INFO General (kmer_coverage_model.cpp : 259) Fitting coverage model 1:16:03.816 136M / 1G INFO General (kmer_coverage_model.cpp : 295) ... iteration 2 1:16:04.379 136M / 1G INFO General (kmer_coverage_model.cpp : 295) ... iteration 4 1:16:06.323 136M / 1G INFO General (kmer_coverage_model.cpp : 295) ... iteration 8 1:16:10.638 136M / 1G INFO General (kmer_coverage_model.cpp : 295) ... iteration 16 1:16:12.824 136M / 1G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 175.532. Fitted coverage std. dev: 41.294 1:16:12.831 136M / 1G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 0.958521 1:16:12.831 136M / 1G INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 94 1:16:12.831 136M / 1G INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 94 1:16:12.831 136M / 1G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 11319754 1:16:12.831 132M / 1G INFO General (genomic_info_filler.cpp : 112) Mean coverage was calculated as 175.532 1:16:12.831 132M / 1G INFO General (genomic_info_filler.cpp : 127) EC coverage threshold value was calculated as 94 1:16:12.831 132M / 1G INFO General (genomic_info_filler.cpp : 128) Trusted kmer low bound: 0 1:16:12.831 132M / 1G INFO StageManager (stage.cpp : 132) STAGE == Raw Simplification 1:16:12.848 132M / 1G INFO General (simplification.cpp : 128) PROCEDURE == InitialCleaning 1:16:12.884 132M / 1G INFO General (graph_simplification.hpp : 662) Flanking coverage based disconnection disabled 1:16:12.884 132M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Self conjugate edge remover 1:16:13.125 132M / 1G INFO Simplification (parallel_processing.hpp : 167) Self conjugate edge remover triggered 3 times 1:16:13.125 132M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Initial tip clipper 1:16:13.432 132M / 1G INFO Simplification (parallel_processing.hpp : 167) Initial tip clipper triggered 9078 times 1:16:13.432 132M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Initial ec remover 1:16:15.919 144M / 1G INFO Simplification (parallel_processing.hpp : 167) Initial ec remover triggered 104417 times 1:16:15.919 144M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Initial isolated edge remover 1:16:16.021 144M / 1G INFO Simplification (parallel_processing.hpp : 167) Initial isolated edge remover triggered 11376 times 1:16:16.034 144M / 1G INFO StageManager (stage.cpp : 132) STAGE == Simplification 1:16:16.034 144M / 1G INFO General (simplification.cpp : 357) Graph simplification started 1:16:16.034 144M / 1G INFO General (graph_simplification.hpp : 634) Creating parallel br instance 1:16:16.034 144M / 1G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 1 1:16:16.034 144M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 1:16:16.111 144M / 1G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 2687 times 1:16:16.111 144M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 1:16:22.826 140M / 1G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 23522 times 1:16:22.826 140M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 1:16:23.263 120M / 1G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 15399 times 1:16:23.263 120M / 1G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 2 1:16:23.263 120M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 1:16:23.277 120M / 1G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 314 times 1:16:23.277 120M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 1:16:23.619 104M / 1G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 2696 times 1:16:23.619 104M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 1:16:23.665 96M / 1G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 1307 times 1:16:23.665 96M / 1G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 3 1:16:23.665 96M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 1:16:23.666 92M / 1G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 18 times 1:16:23.666 92M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 1:16:23.709 92M / 1G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 246 times 1:16:23.709 92M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 1:16:23.719 88M / 1G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 311 times 1:16:23.719 88M / 1G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 4 1:16:23.719 88M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 1:16:23.719 88M / 1G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 3 times 1:16:23.719 88M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 1:16:23.726 88M / 1G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 61 times 1:16:23.726 88M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 1:16:23.731 84M / 1G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 131 times 1:16:23.731 84M / 1G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 5 1:16:23.731 84M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 1:16:23.731 84M / 1G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 1:16:23.731 84M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 1:16:23.735 84M / 1G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 32 times 1:16:23.735 84M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 1:16:23.738 84M / 1G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 85 times 1:16:23.738 84M / 1G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 6 1:16:23.738 84M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 1:16:23.738 84M / 1G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 1:16:23.738 84M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 1:16:23.741 84M / 1G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 23 times 1:16:23.741 84M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 1:16:23.743 80M / 1G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 69 times 1:16:23.743 80M / 1G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 7 1:16:23.743 80M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 1:16:23.743 80M / 1G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 1:16:23.743 80M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 1:16:23.753 80M / 1G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 9 times 1:16:23.753 80M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 1:16:23.755 80M / 1G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 61 times 1:16:23.755 80M / 1G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 8 1:16:23.755 80M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 1:16:23.755 80M / 1G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 1 times 1:16:23.755 80M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 1:16:23.758 80M / 1G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 14 times 1:16:23.758 80M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 1:16:23.759 80M / 1G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 46 times 1:16:23.759 80M / 1G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 9 1:16:23.759 80M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 1:16:23.759 80M / 1G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 1:16:23.759 80M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 1:16:23.761 80M / 1G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 9 times 1:16:23.761 80M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 1:16:23.762 80M / 1G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 30 times 1:16:23.762 80M / 1G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 10 1:16:23.762 80M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 1:16:23.762 80M / 1G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 2 times 1:16:23.762 80M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 1:16:23.764 80M / 1G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 5 times 1:16:23.764 80M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 1:16:23.765 80M / 1G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 32 times 1:16:23.765 80M / 1G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 11 1:16:23.765 80M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 1:16:23.767 80M / 1G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 4 times 1:16:23.767 80M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 1:16:23.778 80M / 1G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 9 times 1:16:23.779 80M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 1:16:23.781 76M / 1G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 1:16:23.781 76M / 1G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 12 1:16:23.781 76M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 1:16:23.781 76M / 1G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 1:16:23.781 76M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 1:16:23.781 76M / 1G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 1:16:23.781 76M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 1:16:23.781 76M / 1G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 1:16:23.781 76M / 1G INFO StageManager (stage.cpp : 132) STAGE == Simplification Cleanup 1:16:23.781 76M / 1G INFO General (simplification.cpp : 196) PROCEDURE == Post simplification 1:16:23.781 76M / 1G INFO General (graph_simplification.hpp : 453) Disconnection of relatively low covered edges disabled 1:16:23.781 76M / 1G INFO General (graph_simplification.hpp : 489) Complex tip clipping disabled 1:16:23.781 76M / 1G INFO General (graph_simplification.hpp : 634) Creating parallel br instance 1:16:23.781 76M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 1:16:23.782 76M / 1G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 1:16:23.782 76M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 1:16:23.793 76M / 1G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 1:16:23.793 76M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 1:16:23.794 76M / 1G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 1:16:23.794 76M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 1:16:23.805 76M / 1G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 1:16:23.805 76M / 1G INFO General (simplification.cpp : 330) Disrupting self-conjugate edges 1:16:23.828 76M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Removing isolated edges 1:16:23.830 76M / 1G INFO Simplification (parallel_processing.hpp : 167) Removing isolated edges triggered 208 times 1:16:23.830 76M / 1G INFO General (simplification.cpp : 470) Counting average coverage 1:16:23.831 76M / 1G INFO General (simplification.cpp : 476) Average coverage = 208.009 1:16:23.831 76M / 1G INFO StageManager (stage.cpp : 132) STAGE == Contig Output 1:16:23.833 76M / 1G INFO General (contig_output_stage.cpp : 40) Writing GFA to /oak/stanford/groups/akundaje/marinovg/Yeast-TFs/2019-02-03-datasets-Genomes/SPAdes-3.13-BY4742//K33/assembly_graph_with_scaffolds.gfa 1:16:23.983 76M / 1G INFO General (contig_output.hpp : 22) Outputting contigs to /oak/stanford/groups/akundaje/marinovg/Yeast-TFs/2019-02-03-datasets-Genomes/SPAdes-3.13-BY4742//K33/before_rr.fasta 1:16:24.207 76M / 1G INFO General (contig_output_stage.cpp : 51) Outputting FastG graph to /oak/stanford/groups/akundaje/marinovg/Yeast-TFs/2019-02-03-datasets-Genomes/SPAdes-3.13-BY4742//K33/assembly_graph.fastg 1:16:24.755 76M / 1G INFO General (contig_output.hpp : 22) Outputting contigs to /oak/stanford/groups/akundaje/marinovg/Yeast-TFs/2019-02-03-datasets-Genomes/SPAdes-3.13-BY4742//K33/simplified_contigs.fasta 1:16:24.971 76M / 1G INFO General (contig_output.hpp : 22) Outputting contigs to /oak/stanford/groups/akundaje/marinovg/Yeast-TFs/2019-02-03-datasets-Genomes/SPAdes-3.13-BY4742//K33/final_contigs.fasta 1:16:25.179 76M / 1G INFO StageManager (stage.cpp : 132) STAGE == Contig Output 1:16:25.179 76M / 1G INFO General (contig_output_stage.cpp : 40) Writing GFA to /oak/stanford/groups/akundaje/marinovg/Yeast-TFs/2019-02-03-datasets-Genomes/SPAdes-3.13-BY4742//K33/assembly_graph_with_scaffolds.gfa 1:16:25.318 76M / 1G INFO General (contig_output.hpp : 22) Outputting contigs to /oak/stanford/groups/akundaje/marinovg/Yeast-TFs/2019-02-03-datasets-Genomes/SPAdes-3.13-BY4742//K33/before_rr.fasta 1:16:25.543 76M / 1G INFO General (contig_output_stage.cpp : 51) Outputting FastG graph to /oak/stanford/groups/akundaje/marinovg/Yeast-TFs/2019-02-03-datasets-Genomes/SPAdes-3.13-BY4742//K33/assembly_graph.fastg 1:16:26.087 76M / 1G INFO General (contig_output.hpp : 22) Outputting contigs to /oak/stanford/groups/akundaje/marinovg/Yeast-TFs/2019-02-03-datasets-Genomes/SPAdes-3.13-BY4742//K33/simplified_contigs.fasta 1:16:26.307 76M / 1G INFO General (contig_output.hpp : 22) Outputting contigs to /oak/stanford/groups/akundaje/marinovg/Yeast-TFs/2019-02-03-datasets-Genomes/SPAdes-3.13-BY4742//K33/final_contigs.fasta 1:16:27.015 76M / 1G INFO General (launch.hpp : 149) SPAdes finished 1:16:27.070 8M / 1G INFO General (main.cpp : 109) Assembling time: 1 hours 16 minutes 27 seconds == Running assembler: K55 0:00:00.000 4M / 4M INFO General (main.cpp : 74) Loaded config from /oak/stanford/groups/akundaje/marinovg/Yeast-TFs/2019-02-03-datasets-Genomes/SPAdes-3.13-BY4742/K55/configs/config.info 0:00:00.000 4M / 4M INFO General (memory_limit.cpp : 49) Memory limit set to 256 Gb 0:00:00.000 4M / 4M INFO General (main.cpp : 87) Starting SPAdes, built from refs/heads/spades_3.13.0, git revision 8ea46659e9b2aca35444a808db550ac333006f8b 0:00:00.000 4M / 4M INFO General (main.cpp : 88) Maximum k-mer length: 128 0:00:00.000 4M / 4M INFO General (main.cpp : 89) Assembling dataset (/oak/stanford/groups/akundaje/marinovg/Yeast-TFs/2019-02-03-datasets-Genomes/SPAdes-3.13-BY4742/dataset.info) with K=55 0:00:00.000 4M / 4M INFO General (main.cpp : 90) Maximum # of threads to use (adjusted due to OMP capabilities): 1 0:00:00.000 4M / 4M INFO General (launch.hpp : 51) SPAdes started 0:00:00.000 4M / 4M INFO General (launch.hpp : 58) Starting from stage: construction 0:00:00.000 4M / 4M INFO General (launch.hpp : 65) Two-step RR enabled: 0 0:00:00.000 4M / 4M INFO General (launch.hpp : 76) Will need read mapping, kmer mapper will be attached 0:00:00.000 4M / 4M INFO StageManager (stage.cpp : 132) STAGE == de Bruijn graph construction 0:00:00.022 4M / 4M INFO General (read_converter.hpp : 59) Binary reads detected 0:00:00.049 4M / 4M INFO General (read_converter.hpp : 59) Binary reads detected 0:00:00.093 4M / 4M INFO General (read_converter.hpp : 59) Binary reads detected 0:00:00.153 4M / 4M INFO General (read_converter.hpp : 59) Binary reads detected 0:00:00.156 4M / 4M INFO General (construction.cpp : 111) Max read length 101 0:00:00.156 4M / 4M INFO General (construction.cpp : 117) Average read length 95.2496 0:00:00.156 4M / 4M INFO General (stage.cpp : 101) PROCEDURE == k+1-mer counting 0:00:00.157 4M / 4M INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 1 files using 1 threads. This might take a while. 0:00:00.157 4M / 4M INFO General (file_limit.hpp : 32) Open file limit set to 131072 0:00:00.157 4M / 4M INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 85.332 Gb 0:00:00.157 4M / 4M INFO General (kmer_splitters.hpp : 97) Using cell size of 33554432 0:00:08.917 568M / 1G INFO General (kmer_splitters.hpp : 289) Processed 2005066 reads 0:00:17.450 568M / 1G INFO General (kmer_splitters.hpp : 289) Processed 4080931 reads 0:00:26.601 568M / 1G INFO General (kmer_splitters.hpp : 289) Processed 6096443 reads 0:00:35.843 568M / 1G INFO General (kmer_splitters.hpp : 289) Processed 7778507 reads 0:00:45.235 568M / 1G INFO General (kmer_splitters.hpp : 289) Processed 9476923 reads 0:00:54.465 568M / 1G INFO General (kmer_splitters.hpp : 289) Processed 11094776 reads 0:01:04.085 568M / 1G INFO General (kmer_splitters.hpp : 289) Processed 12648373 reads 0:01:13.226 568M / 1G INFO General (kmer_splitters.hpp : 289) Processed 14196849 reads 0:01:22.097 568M / 1G INFO General (kmer_splitters.hpp : 289) Processed 15741595 reads 0:01:31.745 568M / 1G INFO General (kmer_splitters.hpp : 289) Processed 17296341 reads 0:03:15.565 568M / 1G INFO General (kmer_splitters.hpp : 289) Processed 34955607 reads 0:06:19.777 568M / 1G INFO General (kmer_splitters.hpp : 289) Processed 67880286 reads 0:07:11.121 568M / 1G INFO General (kmer_splitters.hpp : 295) Adding contigs from previous K 0:07:15.415 4M / 1G INFO General (kmer_splitters.hpp : 308) Used 77066510 reads 0:07:15.415 4M / 1G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:33:54.450 4M / 1G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 20908934 kmers in total. 0:33:54.450 4M / 1G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:33:56.021 4M / 1G INFO General (stage.cpp : 101) PROCEDURE == Extension index construction 0:33:56.022 4M / 1G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:33:56.022 4M / 1G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 16 files using 1 threads. This might take a while. 0:33:56.022 4M / 1G INFO General (file_limit.hpp : 32) Open file limit set to 131072 0:33:56.022 4M / 1G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 85.332 Gb 0:33:56.022 4M / 1G INFO General (kmer_splitters.hpp : 97) Using cell size of 2097152 0:34:06.252 580M / 1G INFO General (kmer_splitters.hpp : 380) Processed 16758590 kmers 0:34:08.504 580M / 1G INFO General (kmer_splitters.hpp : 380) Processed 20908935 kmers 0:34:08.504 580M / 1G INFO General (kmer_splitters.hpp : 385) Used 20908935 kmers. 0:34:08.567 4M / 1G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:34:21.333 4M / 1G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 20924842 kmers in total. 0:34:21.333 4M / 1G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:34:29.209 4M / 1G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:34:33.434 12M / 1G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 0:34:42.143 12M / 1G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 9711192 bytes occupied (3.71279 bits per kmer). 0:34:42.174 32M / 1G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 99) Building k-mer extensions from k+1-mers 0:34:51.470 32M / 1G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 103) Building k-mer extensions from k+1-mers finished. 0:34:51.471 32M / 1G INFO General (stage.cpp : 101) PROCEDURE == Condensing graph 0:34:51.472 32M / 1G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 355) Extracting unbranching paths 0:35:07.319 92M / 1G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 374) Extracting unbranching paths finished. 900337 sequences extracted 0:35:16.532 92M / 1G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 310) Collecting perfect loops 0:35:19.976 92M / 1G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 343) Collecting perfect loops finished. 0 loops collected 0:35:21.761 320M / 1G INFO General (stage.cpp : 101) PROCEDURE == Filling coverage indices (PHM) 0:35:21.761 320M / 1G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:35:21.761 320M / 1G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:35:25.721 332M / 1G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 9696016 bytes occupied (3.70981 bits per kmer). 0:35:25.769 412M / 1G INFO General (construction.cpp : 388) Collecting k-mer coverage information from reads, this takes a while. 0:41:30.499 412M / 1G INFO General (construction.cpp : 508) Filling coverage and flanking coverage from PHM 0:41:35.944 412M / 1G INFO General (construction.cpp : 464) Processed 1000000 edges 0:41:40.197 412M / 1G INFO General (construction.cpp : 464) Processed 1800547 edges 0:41:40.350 292M / 1G INFO StageManager (stage.cpp : 132) STAGE == EC Threshold Finding 0:41:40.353 292M / 1G INFO General (kmer_coverage_model.cpp : 181) Kmer coverage valley at: 29 0:41:40.353 292M / 1G INFO General (kmer_coverage_model.cpp : 201) K-mer histogram maximum: 102 0:41:40.353 292M / 1G INFO General (kmer_coverage_model.cpp : 237) Estimated median coverage: 109. Coverage mad: 32.6172 0:41:40.353 292M / 1G INFO General (kmer_coverage_model.cpp : 259) Fitting coverage model 0:41:40.466 292M / 1G INFO General (kmer_coverage_model.cpp : 295) ... iteration 2 0:41:40.769 292M / 1G INFO General (kmer_coverage_model.cpp : 295) ... iteration 4 0:41:41.977 292M / 1G INFO General (kmer_coverage_model.cpp : 295) ... iteration 8 0:41:44.609 292M / 1G INFO General (kmer_coverage_model.cpp : 295) ... iteration 16 0:41:46.631 292M / 1G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 113.368. Fitted coverage std. dev: 31.7664 0:41:46.635 292M / 1G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 0.827647 0:41:46.635 292M / 1G INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 58 0:41:46.635 292M / 1G INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 58 0:41:46.635 292M / 1G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 11261126 0:41:46.636 292M / 1G INFO General (genomic_info_filler.cpp : 112) Mean coverage was calculated as 113.368 0:41:46.636 292M / 1G INFO General (genomic_info_filler.cpp : 127) EC coverage threshold value was calculated as 58 0:41:46.636 292M / 1G INFO General (genomic_info_filler.cpp : 128) Trusted kmer low bound: 0 0:41:46.636 292M / 1G INFO StageManager (stage.cpp : 132) STAGE == Gap Closer 0:41:46.636 292M / 1G INFO General (graph_pack.hpp : 101) Index refill 0:41:46.637 292M / 1G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:41:46.637 292M / 1G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 16 files using 1 threads. This might take a while. 0:41:46.637 292M / 1G INFO General (file_limit.hpp : 32) Open file limit set to 131072 0:41:46.637 292M / 1G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 85.2383 Gb 0:41:46.637 292M / 1G INFO General (kmer_splitters.hpp : 97) Using cell size of 2097152 0:41:53.162 868M / 1G INFO General (edge_index_builders.hpp : 77) Processed 1800547 edges 0:41:53.162 868M / 1G INFO General (edge_index_builders.hpp : 82) Used 1800547 sequences. 0:41:53.213 292M / 1G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:42:01.039 292M / 1G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 20908934 kmers in total. 0:42:01.039 292M / 1G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:42:05.497 292M / 1G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:42:09.081 300M / 1G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 0:42:13.574 300M / 1G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 9703816 bytes occupied (3.71279 bits per kmer). 0:42:13.859 780M / 1G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while. 0:42:19.969 780M / 1G INFO General (edge_index.hpp : 92) Index refilled 0:42:19.969 780M / 1G INFO General (gap_closer.cpp : 159) Preparing shift maps 0:42:21.048 848M / 1G INFO General (gap_closer.cpp : 119) Processing paired reads (takes a while) 0:42:40.829 852M / 1G INFO General (gap_closer.cpp : 138) Used 2607082 paired reads 0:42:40.829 852M / 1G INFO General (gap_closer.cpp : 140) Merging paired indices 0:42:40.986 780M / 1G INFO GapCloser (gap_closer.cpp : 346) Closing short gaps 0:42:42.478 780M / 1G INFO GapCloser (gap_closer.cpp : 380) Closing short gaps complete: filled 10 gaps after checking 214 candidates 0:42:42.521 780M / 1G INFO General (gap_closer.cpp : 159) Preparing shift maps 0:42:43.575 852M / 1G INFO General (gap_closer.cpp : 119) Processing paired reads (takes a while) 0:43:14.927 852M / 1G INFO General (gap_closer.cpp : 138) Used 3604658 paired reads 0:43:14.927 852M / 1G INFO General (gap_closer.cpp : 140) Merging paired indices 0:43:15.065 780M / 1G INFO GapCloser (gap_closer.cpp : 346) Closing short gaps 0:43:16.546 780M / 1G INFO GapCloser (gap_closer.cpp : 380) Closing short gaps complete: filled 15 gaps after checking 232 candidates 0:43:16.587 780M / 1G INFO General (gap_closer.cpp : 159) Preparing shift maps 0:43:17.659 852M / 1G INFO General (gap_closer.cpp : 119) Processing paired reads (takes a while) 0:44:31.334 852M / 1G INFO General (gap_closer.cpp : 138) Used 8734990 paired reads 0:44:31.334 852M / 1G INFO General (gap_closer.cpp : 140) Merging paired indices 0:44:31.491 780M / 1G INFO GapCloser (gap_closer.cpp : 346) Closing short gaps 0:44:33.099 784M / 1G INFO GapCloser (gap_closer.cpp : 380) Closing short gaps complete: filled 39 gaps after checking 588 candidates 0:44:33.145 780M / 1G INFO General (gap_closer.cpp : 159) Preparing shift maps 0:44:33.981 852M / 1G INFO General (gap_closer.cpp : 119) Processing paired reads (takes a while) 0:45:10.229 852M / 1G INFO General (gap_closer.cpp : 138) Used 4303904 paired reads 0:45:10.229 852M / 1G INFO General (gap_closer.cpp : 140) Merging paired indices 0:45:10.377 780M / 1G INFO GapCloser (gap_closer.cpp : 346) Closing short gaps 0:45:11.884 780M / 1G INFO GapCloser (gap_closer.cpp : 380) Closing short gaps complete: filled 14 gaps after checking 340 candidates 0:45:11.922 780M / 1G INFO StageManager (stage.cpp : 132) STAGE == Raw Simplification 0:45:11.966 292M / 1G INFO General (simplification.cpp : 128) PROCEDURE == InitialCleaning 0:45:11.966 292M / 1G INFO General (graph_simplification.hpp : 662) Flanking coverage based disconnection disabled 0:45:11.966 292M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Self conjugate edge remover 0:45:12.195 292M / 1G INFO Simplification (parallel_processing.hpp : 167) Self conjugate edge remover triggered 1 times 0:45:12.195 292M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Initial tip clipper 0:45:17.074 312M / 1G INFO Simplification (parallel_processing.hpp : 167) Initial tip clipper triggered 376025 times 0:45:17.074 312M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Initial ec remover 0:45:17.608 308M / 1G INFO Simplification (parallel_processing.hpp : 167) Initial ec remover triggered 17770 times 0:45:17.608 308M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Initial isolated edge remover 0:45:17.877 288M / 1G INFO Simplification (parallel_processing.hpp : 167) Initial isolated edge remover triggered 54893 times 0:45:17.887 284M / 1G INFO StageManager (stage.cpp : 132) STAGE == Simplification 0:45:17.887 284M / 1G INFO General (simplification.cpp : 357) Graph simplification started 0:45:17.887 284M / 1G INFO General (graph_simplification.hpp : 634) Creating parallel br instance 0:45:17.887 284M / 1G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 1 0:45:17.887 284M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:45:17.941 280M / 1G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 2727 times 0:45:17.941 280M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:45:21.668 276M / 1G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 14600 times 0:45:21.668 276M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:45:21.795 244M / 1G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 3256 times 0:45:21.795 244M / 1G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 2 0:45:21.795 244M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:45:21.814 236M / 1G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 550 times 0:45:21.814 236M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:45:22.130 228M / 1G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 1245 times 0:45:22.130 228M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:45:22.146 216M / 1G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 525 times 0:45:22.146 216M / 1G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 3 0:45:22.146 216M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:45:22.149 216M / 1G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 78 times 0:45:22.149 216M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:45:22.180 212M / 1G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 153 times 0:45:22.180 212M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:45:22.201 212M / 1G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 139 times 0:45:22.201 212M / 1G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 4 0:45:22.201 212M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:45:22.201 212M / 1G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 15 times 0:45:22.201 212M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:45:22.206 212M / 1G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 26 times 0:45:22.206 212M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:45:22.208 208M / 1G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 83 times 0:45:22.208 208M / 1G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 5 0:45:22.208 208M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:45:22.208 208M / 1G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 8 times 0:45:22.208 208M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:45:22.216 208M / 1G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 22 times 0:45:22.216 208M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:45:22.216 208M / 1G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 32 times 0:45:22.216 208M / 1G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 6 0:45:22.216 208M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:45:22.216 208M / 1G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 3 times 0:45:22.216 208M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:45:22.218 208M / 1G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 8 times 0:45:22.218 208M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:45:22.219 208M / 1G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 27 times 0:45:22.219 208M / 1G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 7 0:45:22.219 208M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:45:22.219 208M / 1G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 1 times 0:45:22.219 208M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:45:22.220 208M / 1G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 7 times 0:45:22.220 208M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:45:22.220 208M / 1G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 18 times 0:45:22.220 208M / 1G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 8 0:45:22.220 208M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:45:22.220 208M / 1G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:45:22.220 208M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:45:22.221 208M / 1G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 5 times 0:45:22.221 208M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:45:22.221 208M / 1G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 10 times 0:45:22.221 208M / 1G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 9 0:45:22.221 208M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:45:22.221 208M / 1G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:45:22.221 208M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:45:22.222 208M / 1G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 3 times 0:45:22.222 208M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:45:22.222 208M / 1G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 6 times 0:45:22.222 208M / 1G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 10 0:45:22.222 208M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:45:22.222 208M / 1G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:45:22.222 208M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:45:22.222 204M / 1G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 1 times 0:45:22.222 204M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:45:22.223 204M / 1G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 13 times 0:45:22.223 204M / 1G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 11 0:45:22.223 204M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:45:22.224 204M / 1G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 2 times 0:45:22.224 204M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:45:22.229 204M / 1G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 5 times 0:45:22.229 204M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:45:22.230 204M / 1G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:45:22.230 204M / 1G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 12 0:45:22.230 204M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:45:22.231 204M / 1G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:45:22.231 204M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:45:22.231 204M / 1G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:45:22.231 204M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:45:22.231 204M / 1G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:45:22.231 204M / 1G INFO StageManager (stage.cpp : 132) STAGE == Gap Closer 0:45:22.231 204M / 1G INFO General (graph_pack.hpp : 101) Index refill 0:45:22.232 204M / 1G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:45:22.232 204M / 1G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 16 files using 1 threads. This might take a while. 0:45:22.232 204M / 1G INFO General (file_limit.hpp : 32) Open file limit set to 131072 0:45:22.232 204M / 1G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 85.2669 Gb 0:45:22.232 204M / 1G INFO General (kmer_splitters.hpp : 97) Using cell size of 2097152 0:45:25.114 780M / 1G INFO General (edge_index_builders.hpp : 77) Processed 7299 edges 0:45:25.114 780M / 1G INFO General (edge_index_builders.hpp : 82) Used 7299 sequences. 0:45:25.135 204M / 1G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:45:49.938 204M / 1G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 11562887 kmers in total. 0:45:49.938 204M / 1G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:45:56.786 204M / 1G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:45:58.967 212M / 1G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 0:46:04.282 212M / 1G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 5369712 bytes occupied (3.71514 bits per kmer). 0:46:04.566 480M / 1G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while. 0:46:07.519 480M / 1G INFO General (edge_index.hpp : 92) Index refilled 0:46:07.520 480M / 1G INFO General (gap_closer.cpp : 159) Preparing shift maps 0:46:07.524 480M / 1G INFO General (gap_closer.cpp : 119) Processing paired reads (takes a while) 0:46:22.542 480M / 1G INFO General (gap_closer.cpp : 138) Used 2607082 paired reads 0:46:22.542 480M / 1G INFO General (gap_closer.cpp : 140) Merging paired indices 0:46:22.542 480M / 1G INFO GapCloser (gap_closer.cpp : 346) Closing short gaps 0:46:22.548 480M / 1G INFO GapCloser (gap_closer.cpp : 380) Closing short gaps complete: filled 1 gaps after checking 150 candidates 0:46:22.573 480M / 1G INFO General (gap_closer.cpp : 159) Preparing shift maps 0:46:22.575 480M / 1G INFO General (gap_closer.cpp : 119) Processing paired reads (takes a while) 0:46:45.466 480M / 1G INFO General (gap_closer.cpp : 138) Used 3604658 paired reads 0:46:45.466 480M / 1G INFO General (gap_closer.cpp : 140) Merging paired indices 0:46:45.467 480M / 1G INFO GapCloser (gap_closer.cpp : 346) Closing short gaps 0:46:45.472 480M / 1G INFO GapCloser (gap_closer.cpp : 380) Closing short gaps complete: filled 1 gaps after checking 180 candidates 0:46:45.576 480M / 1G INFO General (gap_closer.cpp : 159) Preparing shift maps 0:46:45.579 480M / 1G INFO General (gap_closer.cpp : 119) Processing paired reads (takes a while) 0:47:33.726 480M / 1G INFO General (gap_closer.cpp : 138) Used 8734990 paired reads 0:47:33.726 480M / 1G INFO General (gap_closer.cpp : 140) Merging paired indices 0:47:33.726 480M / 1G INFO GapCloser (gap_closer.cpp : 346) Closing short gaps 0:47:33.732 480M / 1G INFO GapCloser (gap_closer.cpp : 380) Closing short gaps complete: filled 1 gaps after checking 204 candidates 0:47:33.764 480M / 1G INFO General (gap_closer.cpp : 159) Preparing shift maps 0:47:33.765 480M / 1G INFO General (gap_closer.cpp : 119) Processing paired reads (takes a while) 0:47:57.284 480M / 1G INFO General (gap_closer.cpp : 138) Used 4303904 paired reads 0:47:57.284 480M / 1G INFO General (gap_closer.cpp : 140) Merging paired indices 0:47:57.284 480M / 1G INFO GapCloser (gap_closer.cpp : 346) Closing short gaps 0:47:57.290 480M / 1G INFO GapCloser (gap_closer.cpp : 380) Closing short gaps complete: filled 0 gaps after checking 184 candidates 0:47:57.291 480M / 1G INFO StageManager (stage.cpp : 132) STAGE == Simplification Cleanup 0:47:57.291 480M / 1G INFO General (simplification.cpp : 196) PROCEDURE == Post simplification 0:47:57.291 480M / 1G INFO General (graph_simplification.hpp : 453) Disconnection of relatively low covered edges disabled 0:47:57.291 480M / 1G INFO General (graph_simplification.hpp : 489) Complex tip clipping disabled 0:47:57.291 480M / 1G INFO General (graph_simplification.hpp : 634) Creating parallel br instance 0:47:57.291 480M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:47:57.292 480M / 1G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:47:57.292 480M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:47:57.297 480M / 1G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:47:57.297 480M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:47:57.298 480M / 1G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:47:57.298 480M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:47:57.302 480M / 1G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:47:57.302 480M / 1G INFO General (simplification.cpp : 330) Disrupting self-conjugate edges 0:47:57.304 480M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Removing isolated edges 0:47:57.305 480M / 1G INFO Simplification (parallel_processing.hpp : 167) Removing isolated edges triggered 14 times 0:47:57.306 480M / 1G INFO General (simplification.cpp : 470) Counting average coverage 0:47:57.306 480M / 1G INFO General (simplification.cpp : 476) Average coverage = 134.137 0:47:57.306 480M / 1G INFO StageManager (stage.cpp : 132) STAGE == Mismatch Correction 0:47:57.306 480M / 1G INFO General (graph_pack.hpp : 109) Normalizing k-mer map. Total 1696708 kmers to process 0:47:58.217 480M / 1G INFO General (graph_pack.hpp : 111) Normalizing done 0:53:43.927 480M / 1G INFO General (mismatch_shall_not_pass.hp: 189) Finished collecting potential mismatches positions 0:53:44.189 480M / 1G INFO General (mismatch_shall_not_pass.hp: 290) All edges processed 0:53:44.207 480M / 1G INFO General (mismatch_correction.cpp : 27) Corrected 4 nucleotides 0:53:44.210 480M / 1G INFO StageManager (stage.cpp : 132) STAGE == Contig Output 0:53:44.210 480M / 1G INFO General (contig_output_stage.cpp : 40) Writing GFA to /oak/stanford/groups/akundaje/marinovg/Yeast-TFs/2019-02-03-datasets-Genomes/SPAdes-3.13-BY4742//K55/assembly_graph_with_scaffolds.gfa 0:53:45.009 480M / 1G INFO General (contig_output.hpp : 22) Outputting contigs to /oak/stanford/groups/akundaje/marinovg/Yeast-TFs/2019-02-03-datasets-Genomes/SPAdes-3.13-BY4742//K55/before_rr.fasta 0:53:45.360 480M / 1G INFO General (contig_output_stage.cpp : 51) Outputting FastG graph to /oak/stanford/groups/akundaje/marinovg/Yeast-TFs/2019-02-03-datasets-Genomes/SPAdes-3.13-BY4742//K55/assembly_graph.fastg 0:53:45.980 480M / 1G INFO General (contig_output.hpp : 22) Outputting contigs to /oak/stanford/groups/akundaje/marinovg/Yeast-TFs/2019-02-03-datasets-Genomes/SPAdes-3.13-BY4742//K55/simplified_contigs.fasta 0:53:46.161 480M / 1G INFO General (contig_output.hpp : 22) Outputting contigs to /oak/stanford/groups/akundaje/marinovg/Yeast-TFs/2019-02-03-datasets-Genomes/SPAdes-3.13-BY4742//K55/intermediate_contigs.fasta 0:53:46.339 480M / 1G INFO StageManager (stage.cpp : 132) STAGE == Paired Information Counting 0:53:46.377 480M / 1G INFO General (graph_pack.hpp : 109) Normalizing k-mer map. Total 1696988 kmers to process 0:53:47.268 480M / 1G INFO General (graph_pack.hpp : 111) Normalizing done 0:53:47.270 480M / 1G INFO General (pair_info_count.cpp : 320) Min edge length for estimation: 32008 0:53:47.270 480M / 1G INFO General (pair_info_count.cpp : 331) Estimating insert size for library #0 0:53:47.270 480M / 1G INFO General (pair_info_count.cpp : 190) Estimating insert size (takes a while) 0:53:47.289 512M / 1G INFO General (pair_info_count.cpp : 39) Selecting usual mapper 0:53:48.276 512M / 1G INFO General (sequence_mapper_notifier.h: 80) Processed 200000 reads 0:53:49.363 512M / 1G INFO General (sequence_mapper_notifier.h: 80) Processed 400000 reads 0:53:50.418 512M / 1G INFO General (sequence_mapper_notifier.h: 80) Processed 600000 reads 0:53:51.452 512M / 1G INFO General (sequence_mapper_notifier.h: 80) Processed 800000 reads 0:53:52.464 512M / 1G INFO General (sequence_mapper_notifier.h: 80) Processed 1000000 reads 0:53:53.466 512M / 1G INFO General (sequence_mapper_notifier.h: 80) Processed 1200000 reads 0:53:59.002 512M / 1G INFO General (sequence_mapper_notifier.h: 80) Processed 2200000 reads 0:54:01.491 512M / 1G INFO General (sequence_mapper_notifier.h: 98) Total 2607082 reads processed 0:54:02.681 512M / 1G INFO General (pair_info_count.cpp : 209) Edge pairs: 67108864 (rough upper limit) 0:54:02.681 512M / 1G INFO General (pair_info_count.cpp : 213) 1029953 paired reads (39.506% of all) aligned to long edges 0:54:02.685 480M / 1G INFO General (pair_info_count.cpp : 354) Insert size = 166.828, deviation = 96.7715, left quantile = 69, right quantile = 302, read length = 101 0:54:02.783 672M / 1G INFO General (pair_info_count.cpp : 371) Filtering data for library #0 0:54:02.784 672M / 1G INFO General (pair_info_count.cpp : 39) Selecting usual mapper 0:54:03.831 672M / 1G INFO General (sequence_mapper_notifier.h: 80) Processed 200000 reads 0:54:04.903 672M / 1G INFO General (sequence_mapper_notifier.h: 80) Processed 400000 reads 0:54:05.946 672M / 1G INFO General (sequence_mapper_notifier.h: 80) Processed 600000 reads 0:54:06.965 672M / 1G INFO General (sequence_mapper_notifier.h: 80) Processed 800000 reads 0:54:07.983 672M / 1G INFO General (sequence_mapper_notifier.h: 80) Processed 1000000 reads 0:54:08.988 672M / 1G INFO General (sequence_mapper_notifier.h: 80) Processed 1200000 reads 0:54:14.803 672M / 1G INFO General (sequence_mapper_notifier.h: 80) Processed 2200000 reads 0:54:17.308 672M / 1G INFO General (sequence_mapper_notifier.h: 98) Total 2607082 reads processed 0:54:17.308 672M / 1G INFO General (pair_info_count.cpp : 383) Mapping library #0 0:54:17.308 672M / 1G INFO General (pair_info_count.cpp : 385) Mapping paired reads (takes a while) 0:54:17.308 672M / 1G INFO General (pair_info_count.cpp : 289) Left insert size quantile 69, right insert size quantile 302, filtering threshold 2, rounding threshold 0 0:54:17.318 684M / 1G INFO General (pair_info_count.cpp : 39) Selecting usual mapper 0:54:18.492 684M / 1G INFO General (sequence_mapper_notifier.h: 80) Processed 200000 reads 0:54:19.750 684M / 1G INFO General (sequence_mapper_notifier.h: 80) Processed 400000 reads 0:54:21.010 688M / 1G INFO General (sequence_mapper_notifier.h: 80) Processed 600000 reads 0:54:22.215 688M / 1G INFO General (sequence_mapper_notifier.h: 80) Processed 800000 reads 0:54:23.422 688M / 1G INFO General (sequence_mapper_notifier.h: 80) Processed 1000000 reads 0:54:24.603 688M / 1G INFO General (sequence_mapper_notifier.h: 80) Processed 1200000 reads 0:54:31.329 692M / 1G INFO General (sequence_mapper_notifier.h: 80) Processed 2200000 reads 0:54:34.169 692M / 1G INFO General (sequence_mapper_notifier.h: 98) Total 2607082 reads processed 0:54:34.194 488M / 1G INFO General (pair_info_count.cpp : 331) Estimating insert size for library #1 0:54:34.194 488M / 1G INFO General (pair_info_count.cpp : 190) Estimating insert size (takes a while) 0:54:34.216 520M / 1G INFO General (pair_info_count.cpp : 39) Selecting usual mapper 0:54:35.498 520M / 1G INFO General (sequence_mapper_notifier.h: 80) Processed 200000 reads 0:54:36.784 520M / 1G INFO General (sequence_mapper_notifier.h: 80) Processed 400000 reads 0:54:38.055 520M / 1G INFO General (sequence_mapper_notifier.h: 80) Processed 600000 reads 0:54:39.321 520M / 1G INFO General (sequence_mapper_notifier.h: 80) Processed 800000 reads 0:54:40.614 520M / 1G INFO General (sequence_mapper_notifier.h: 80) Processed 1000000 reads 0:54:41.899 520M / 1G INFO General (sequence_mapper_notifier.h: 80) Processed 1200000 reads 0:54:48.289 520M / 1G INFO General (sequence_mapper_notifier.h: 80) Processed 2200000 reads 0:54:57.483 520M / 1G INFO General (sequence_mapper_notifier.h: 98) Total 3604658 reads processed 0:54:58.766 520M / 1G INFO General (pair_info_count.cpp : 209) Edge pairs: 67108864 (rough upper limit) 0:54:58.766 520M / 1G INFO General (pair_info_count.cpp : 213) 1513824 paired reads (41.9963% of all) aligned to long edges 0:54:58.770 488M / 1G INFO General (pair_info_count.cpp : 354) Insert size = 215.672, deviation = 116.002, left quantile = 97, right quantile = 379, read length = 101 0:54:58.876 680M / 1G INFO General (pair_info_count.cpp : 371) Filtering data for library #1 0:54:58.878 680M / 1G INFO General (pair_info_count.cpp : 39) Selecting usual mapper 0:55:00.208 680M / 1G INFO General (sequence_mapper_notifier.h: 80) Processed 200000 reads 0:55:01.553 680M / 1G INFO General (sequence_mapper_notifier.h: 80) Processed 400000 reads 0:55:02.833 680M / 1G INFO General (sequence_mapper_notifier.h: 80) Processed 600000 reads 0:55:04.114 680M / 1G INFO General (sequence_mapper_notifier.h: 80) Processed 800000 reads 0:55:05.429 680M / 1G INFO General (sequence_mapper_notifier.h: 80) Processed 1000000 reads 0:55:06.710 680M / 1G INFO General (sequence_mapper_notifier.h: 80) Processed 1200000 reads 0:55:13.182 680M / 1G INFO General (sequence_mapper_notifier.h: 80) Processed 2200000 reads 0:55:22.439 680M / 1G INFO General (sequence_mapper_notifier.h: 98) Total 3604658 reads processed 0:55:22.439 680M / 1G INFO General (pair_info_count.cpp : 383) Mapping library #1 0:55:22.439 680M / 1G INFO General (pair_info_count.cpp : 385) Mapping paired reads (takes a while) 0:55:22.439 680M / 1G INFO General (pair_info_count.cpp : 289) Left insert size quantile 97, right insert size quantile 379, filtering threshold 2, rounding threshold 0 0:55:22.450 692M / 1G INFO General (pair_info_count.cpp : 39) Selecting usual mapper 0:55:23.903 692M / 1G INFO General (sequence_mapper_notifier.h: 80) Processed 200000 reads 0:55:25.385 696M / 1G INFO General (sequence_mapper_notifier.h: 80) Processed 400000 reads 0:55:26.833 696M / 1G INFO General (sequence_mapper_notifier.h: 80) Processed 600000 reads 0:55:28.272 696M / 1G INFO General (sequence_mapper_notifier.h: 80) Processed 800000 reads 0:55:29.713 696M / 1G INFO General (sequence_mapper_notifier.h: 80) Processed 1000000 reads 0:55:31.171 700M / 1G INFO General (sequence_mapper_notifier.h: 80) Processed 1200000 reads 0:55:38.497 700M / 1G INFO General (sequence_mapper_notifier.h: 80) Processed 2200000 reads 0:55:48.996 704M / 1G INFO General (sequence_mapper_notifier.h: 98) Total 3604658 reads processed 0:55:49.021 500M / 1G INFO General (pair_info_count.cpp : 331) Estimating insert size for library #2 0:55:49.021 500M / 1G INFO General (pair_info_count.cpp : 190) Estimating insert size (takes a while) 0:55:49.041 532M / 1G INFO General (pair_info_count.cpp : 39) Selecting usual mapper 0:55:50.264 532M / 1G INFO General (sequence_mapper_notifier.h: 80) Processed 200000 reads 0:55:51.537 532M / 1G INFO General (sequence_mapper_notifier.h: 80) Processed 400000 reads 0:55:52.785 532M / 1G INFO General (sequence_mapper_notifier.h: 80) Processed 600000 reads 0:55:54.041 532M / 1G INFO General (sequence_mapper_notifier.h: 80) Processed 800000 reads 0:55:55.282 532M / 1G INFO General (sequence_mapper_notifier.h: 80) Processed 1000000 reads 0:55:56.519 532M / 1G INFO General (sequence_mapper_notifier.h: 80) Processed 1200000 reads 0:56:02.776 532M / 1G INFO General (sequence_mapper_notifier.h: 80) Processed 2200000 reads 0:56:14.801 532M / 1G INFO General (sequence_mapper_notifier.h: 80) Processed 4200000 reads 0:56:40.405 532M / 1G INFO General (sequence_mapper_notifier.h: 80) Processed 8400000 reads 0:56:42.714 532M / 1G INFO General (sequence_mapper_notifier.h: 98) Total 8734990 reads processed 0:56:43.965 532M / 1G INFO General (pair_info_count.cpp : 209) Edge pairs: 67108864 (rough upper limit) 0:56:43.965 532M / 1G INFO General (pair_info_count.cpp : 213) 3543428 paired reads (40.5659% of all) aligned to long edges 0:56:43.970 500M / 1G INFO General (pair_info_count.cpp : 354) Insert size = 218.182, deviation = 123.548, left quantile = 88, right quantile = 394, read length = 101 0:56:44.075 692M / 1G INFO General (pair_info_count.cpp : 371) Filtering data for library #2 0:56:44.076 692M / 1G INFO General (pair_info_count.cpp : 39) Selecting usual mapper 0:56:45.381 692M / 1G INFO General (sequence_mapper_notifier.h: 80) Processed 200000 reads 0:56:46.636 692M / 1G INFO General (sequence_mapper_notifier.h: 80) Processed 400000 reads 0:56:47.896 692M / 1G INFO General (sequence_mapper_notifier.h: 80) Processed 600000 reads 0:56:49.158 692M / 1G INFO General (sequence_mapper_notifier.h: 80) Processed 800000 reads 0:56:50.431 692M / 1G INFO General (sequence_mapper_notifier.h: 80) Processed 1000000 reads 0:56:51.700 692M / 1G INFO General (sequence_mapper_notifier.h: 80) Processed 1200000 reads 0:56:58.341 692M / 1G INFO General (sequence_mapper_notifier.h: 80) Processed 2200000 reads 0:57:11.106 692M / 1G INFO General (sequence_mapper_notifier.h: 80) Processed 4200000 reads 0:57:38.778 692M / 1G INFO General (sequence_mapper_notifier.h: 80) Processed 8400000 reads 0:57:41.090 692M / 1G INFO General (sequence_mapper_notifier.h: 98) Total 8734990 reads processed 0:57:41.090 692M / 1G INFO General (pair_info_count.cpp : 383) Mapping library #2 0:57:41.090 692M / 1G INFO General (pair_info_count.cpp : 385) Mapping paired reads (takes a while) 0:57:41.090 692M / 1G INFO General (pair_info_count.cpp : 289) Left insert size quantile 88, right insert size quantile 394, filtering threshold 2, rounding threshold 0 0:57:41.099 704M / 1G INFO General (pair_info_count.cpp : 39) Selecting usual mapper 0:57:42.483 708M / 1G INFO General (sequence_mapper_notifier.h: 80) Processed 200000 reads 0:57:43.882 708M / 1G INFO General (sequence_mapper_notifier.h: 80) Processed 400000 reads 0:57:45.357 712M / 1G INFO General (sequence_mapper_notifier.h: 80) Processed 600000 reads 0:57:46.824 712M / 1G INFO General (sequence_mapper_notifier.h: 80) Processed 800000 reads 0:57:48.245 712M / 1G INFO General (sequence_mapper_notifier.h: 80) Processed 1000000 reads 0:57:49.695 712M / 1G INFO General (sequence_mapper_notifier.h: 80) Processed 1200000 reads 0:57:56.945 716M / 1G INFO General (sequence_mapper_notifier.h: 80) Processed 2200000 reads 0:58:11.612 720M / 1G INFO General (sequence_mapper_notifier.h: 80) Processed 4200000 reads 0:58:42.846 728M / 1G INFO General (sequence_mapper_notifier.h: 80) Processed 8400000 reads 0:58:45.425 728M / 1G INFO General (sequence_mapper_notifier.h: 98) Total 8734990 reads processed 0:58:45.451 524M / 1G INFO General (pair_info_count.cpp : 331) Estimating insert size for library #3 0:58:45.451 524M / 1G INFO General (pair_info_count.cpp : 190) Estimating insert size (takes a while) 0:58:45.472 556M / 1G INFO General (pair_info_count.cpp : 39) Selecting usual mapper 0:58:46.689 556M / 1G INFO General (sequence_mapper_notifier.h: 80) Processed 200000 reads 0:58:47.918 556M / 1G INFO General (sequence_mapper_notifier.h: 80) Processed 400000 reads 0:58:49.140 556M / 1G INFO General (sequence_mapper_notifier.h: 80) Processed 600000 reads 0:58:50.376 556M / 1G INFO General (sequence_mapper_notifier.h: 80) Processed 800000 reads 0:58:51.662 556M / 1G INFO General (sequence_mapper_notifier.h: 80) Processed 1000000 reads 0:58:52.906 556M / 1G INFO General (sequence_mapper_notifier.h: 80) Processed 1200000 reads 0:58:59.165 556M / 1G INFO General (sequence_mapper_notifier.h: 80) Processed 2200000 reads 0:59:12.135 556M / 1G INFO General (sequence_mapper_notifier.h: 80) Processed 4200000 reads 0:59:12.877 556M / 1G INFO General (sequence_mapper_notifier.h: 98) Total 4303904 reads processed 0:59:14.145 556M / 1G INFO General (pair_info_count.cpp : 209) Edge pairs: 67108864 (rough upper limit) 0:59:14.145 556M / 1G INFO General (pair_info_count.cpp : 213) 1757076 paired reads (40.8252% of all) aligned to long edges 0:59:14.150 524M / 1G INFO General (pair_info_count.cpp : 354) Insert size = 210.14, deviation = 118.298, left quantile = 87, right quantile = 376, read length = 101 0:59:14.254 716M / 1G INFO General (pair_info_count.cpp : 371) Filtering data for library #3 0:59:14.257 716M / 1G INFO General (pair_info_count.cpp : 39) Selecting usual mapper 0:59:15.525 716M / 1G INFO General (sequence_mapper_notifier.h: 80) Processed 200000 reads 0:59:16.775 716M / 1G INFO General (sequence_mapper_notifier.h: 80) Processed 400000 reads 0:59:18.021 716M / 1G INFO General (sequence_mapper_notifier.h: 80) Processed 600000 reads 0:59:19.266 716M / 1G INFO General (sequence_mapper_notifier.h: 80) Processed 800000 reads 0:59:20.516 716M / 1G INFO General (sequence_mapper_notifier.h: 80) Processed 1000000 reads 0:59:21.812 716M / 1G INFO General (sequence_mapper_notifier.h: 80) Processed 1200000 reads 0:59:28.158 716M / 1G INFO General (sequence_mapper_notifier.h: 80) Processed 2200000 reads 0:59:41.080 716M / 1G INFO General (sequence_mapper_notifier.h: 80) Processed 4200000 reads 0:59:41.795 716M / 1G INFO General (sequence_mapper_notifier.h: 98) Total 4303904 reads processed 0:59:41.796 716M / 1G INFO General (pair_info_count.cpp : 383) Mapping library #3 0:59:41.796 716M / 1G INFO General (pair_info_count.cpp : 385) Mapping paired reads (takes a while) 0:59:41.796 716M / 1G INFO General (pair_info_count.cpp : 289) Left insert size quantile 87, right insert size quantile 376, filtering threshold 2, rounding threshold 0 0:59:41.805 728M / 1G INFO General (pair_info_count.cpp : 39) Selecting usual mapper 0:59:43.188 732M / 1G INFO General (sequence_mapper_notifier.h: 80) Processed 200000 reads 0:59:44.597 732M / 1G INFO General (sequence_mapper_notifier.h: 80) Processed 400000 reads 0:59:45.988 736M / 1G INFO General (sequence_mapper_notifier.h: 80) Processed 600000 reads 0:59:47.403 736M / 1G INFO General (sequence_mapper_notifier.h: 80) Processed 800000 reads 0:59:48.826 736M / 1G INFO General (sequence_mapper_notifier.h: 80) Processed 1000000 reads 0:59:50.255 736M / 1G INFO General (sequence_mapper_notifier.h: 80) Processed 1200000 reads 0:59:57.365 740M / 1G INFO General (sequence_mapper_notifier.h: 80) Processed 2200000 reads 1:00:12.061 744M / 1G INFO General (sequence_mapper_notifier.h: 80) Processed 4200000 reads 1:00:12.852 744M / 1G INFO General (sequence_mapper_notifier.h: 98) Total 4303904 reads processed 1:00:12.877 540M / 1G INFO StageManager (stage.cpp : 132) STAGE == Distance Estimation 1:00:12.877 540M / 1G INFO General (distance_estimation.cpp : 173) Processing library #0 1:00:12.877 540M / 1G INFO General (distance_estimation.cpp : 149) Weight Filter Done 1:00:12.877 540M / 1G INFO DistanceEstimator (distance_estimation.hpp : 116) Using SIMPLE distance estimator 1:00:13.326 544M / 1G INFO General (distance_estimation.cpp : 34) Filtering info 1:00:13.326 544M / 1G INFO General (pair_info_filters.hpp : 242) Start filtering; index size: 112248 1:00:13.355 548M / 1G INFO General (pair_info_filters.hpp : 263) Done filtering 1:00:13.355 544M / 1G INFO General (distance_estimation.cpp : 156) Refining clustered pair information 1:00:13.371 544M / 1G INFO General (distance_estimation.cpp : 158) The refining of clustered pair information has been finished 1:00:13.371 544M / 1G INFO General (distance_estimation.cpp : 160) Improving paired information 1:00:13.787 544M / 1G INFO PairInfoImprover (pair_info_improver.hpp : 103) Paired info stats: missing = 7286; contradictional = 344 1:00:14.252 544M / 1G INFO PairInfoImprover (pair_info_improver.hpp : 103) Paired info stats: missing = 832; contradictional = 2 1:00:14.252 544M / 1G INFO General (distance_estimation.cpp : 103) Filling scaffolding index 1:00:14.252 544M / 1G INFO DistanceEstimator (distance_estimation.hpp : 116) Using SMOOTHING distance estimator 1:00:15.342 544M / 1G INFO General (distance_estimation.cpp : 34) Filtering info 1:00:15.342 544M / 1G INFO General (pair_info_filters.hpp : 242) Start filtering; index size: 17974 1:00:15.347 548M / 1G INFO General (pair_info_filters.hpp : 263) Done filtering 1:00:15.347 544M / 1G INFO General (distance_estimation.cpp : 182) Clearing raw paired index 1:00:15.355 544M / 1G INFO General (distance_estimation.cpp : 173) Processing library #1 1:00:15.355 544M / 1G INFO General (distance_estimation.cpp : 149) Weight Filter Done 1:00:15.355 544M / 1G INFO DistanceEstimator (distance_estimation.hpp : 116) Using SIMPLE distance estimator 1:00:16.695 540M / 1G INFO General (distance_estimation.cpp : 34) Filtering info 1:00:16.695 540M / 1G INFO General (pair_info_filters.hpp : 242) Start filtering; index size: 174798 1:00:16.738 540M / 1G INFO General (pair_info_filters.hpp : 263) Done filtering 1:00:16.739 536M / 1G INFO General (distance_estimation.cpp : 156) Refining clustered pair information 1:00:16.759 536M / 1G INFO General (distance_estimation.cpp : 158) The refining of clustered pair information has been finished 1:00:16.759 536M / 1G INFO General (distance_estimation.cpp : 160) Improving paired information 1:00:17.552 540M / 1G INFO PairInfoImprover (pair_info_improver.hpp : 103) Paired info stats: missing = 11500; contradictional = 1012 1:00:18.334 540M / 1G INFO PairInfoImprover (pair_info_improver.hpp : 103) Paired info stats: missing = 1104; contradictional = 24 1:00:18.334 540M / 1G INFO General (distance_estimation.cpp : 103) Filling scaffolding index 1:00:18.334 540M / 1G INFO DistanceEstimator (distance_estimation.hpp : 116) Using SMOOTHING distance estimator 1:00:20.500 540M / 1G INFO General (distance_estimation.cpp : 34) Filtering info 1:00:20.500 540M / 1G INFO General (pair_info_filters.hpp : 242) Start filtering; index size: 20366 1:00:20.505 540M / 1G INFO General (pair_info_filters.hpp : 263) Done filtering 1:00:20.505 540M / 1G INFO General (distance_estimation.cpp : 182) Clearing raw paired index 1:00:20.514 532M / 1G INFO General (distance_estimation.cpp : 173) Processing library #2 1:00:20.514 532M / 1G INFO General (distance_estimation.cpp : 149) Weight Filter Done 1:00:20.514 532M / 1G INFO DistanceEstimator (distance_estimation.hpp : 116) Using SIMPLE distance estimator 1:00:22.469 528M / 1G INFO General (distance_estimation.cpp : 34) Filtering info 1:00:22.469 528M / 1G INFO General (pair_info_filters.hpp : 242) Start filtering; index size: 236176 1:00:22.530 532M / 1G INFO General (pair_info_filters.hpp : 263) Done filtering 1:00:22.530 528M / 1G INFO General (distance_estimation.cpp : 156) Refining clustered pair information 1:00:22.557 528M / 1G INFO General (distance_estimation.cpp : 158) The refining of clustered pair information has been finished 1:00:22.557 528M / 1G INFO General (distance_estimation.cpp : 160) Improving paired information 1:00:23.960 532M / 1G INFO PairInfoImprover (pair_info_improver.hpp : 103) Paired info stats: missing = 11009; contradictional = 2180 1:00:25.081 532M / 1G INFO PairInfoImprover (pair_info_improver.hpp : 103) Paired info stats: missing = 1030; contradictional = 36 1:00:25.081 532M / 1G INFO General (distance_estimation.cpp : 103) Filling scaffolding index 1:00:25.081 532M / 1G INFO DistanceEstimator (distance_estimation.hpp : 116) Using SMOOTHING distance estimator 1:00:28.925 532M / 1G INFO General (distance_estimation.cpp : 34) Filtering info 1:00:28.925 532M / 1G INFO General (pair_info_filters.hpp : 242) Start filtering; index size: 30582 1:00:28.932 532M / 1G INFO General (pair_info_filters.hpp : 263) Done filtering 1:00:28.932 532M / 1G INFO General (distance_estimation.cpp : 182) Clearing raw paired index 1:00:28.947 520M / 1G INFO General (distance_estimation.cpp : 173) Processing library #3 1:00:28.947 520M / 1G INFO General (distance_estimation.cpp : 149) Weight Filter Done 1:00:28.947 520M / 1G INFO DistanceEstimator (distance_estimation.hpp : 116) Using SIMPLE distance estimator 1:00:30.196 512M / 1G INFO General (distance_estimation.cpp : 34) Filtering info 1:00:30.196 512M / 1G INFO General (pair_info_filters.hpp : 242) Start filtering; index size: 184060 1:00:30.244 512M / 1G INFO General (pair_info_filters.hpp : 263) Done filtering 1:00:30.244 508M / 1G INFO General (distance_estimation.cpp : 156) Refining clustered pair information 1:00:30.265 508M / 1G INFO General (distance_estimation.cpp : 158) The refining of clustered pair information has been finished 1:00:30.265 508M / 1G INFO General (distance_estimation.cpp : 160) Improving paired information 1:00:30.997 512M / 1G INFO PairInfoImprover (pair_info_improver.hpp : 103) Paired info stats: missing = 11324; contradictional = 918 1:00:31.763 512M / 1G INFO PairInfoImprover (pair_info_improver.hpp : 103) Paired info stats: missing = 1097; contradictional = 20 1:00:31.763 512M / 1G INFO General (distance_estimation.cpp : 103) Filling scaffolding index 1:00:31.763 512M / 1G INFO DistanceEstimator (distance_estimation.hpp : 116) Using SMOOTHING distance estimator 1:00:33.939 512M / 1G INFO General (distance_estimation.cpp : 34) Filtering info 1:00:33.939 512M / 1G INFO General (pair_info_filters.hpp : 242) Start filtering; index size: 21442 1:00:33.944 512M / 1G INFO General (pair_info_filters.hpp : 263) Done filtering 1:00:33.944 512M / 1G INFO General (distance_estimation.cpp : 182) Clearing raw paired index 1:00:33.953 504M / 1G INFO StageManager (stage.cpp : 132) STAGE == Repeat Resolving 1:00:33.953 504M / 1G INFO General (repeat_resolving.cpp : 69) Using Path-Extend repeat resolving 1:00:33.953 504M / 1G INFO General (launcher.cpp : 477) ExSPAnder repeat resolving tool started 1:00:33.966 508M / 1G INFO General (launcher.cpp : 392) Creating main extenders, unique edge length = 2000 1:00:33.966 508M / 1G INFO General (extenders_logic.cpp : 275) Estimated coverage of library #0 is 17.2481 1:00:33.967 508M / 1G INFO General (extenders_logic.cpp : 275) Estimated coverage of library #0 is 17.2481 1:00:33.968 508M / 1G INFO General (extenders_logic.cpp : 275) Estimated coverage of library #1 is 25.8464 1:00:33.969 508M / 1G INFO General (extenders_logic.cpp : 275) Estimated coverage of library #1 is 25.8464 1:00:33.970 508M / 1G INFO General (extenders_logic.cpp : 275) Estimated coverage of library #2 is 61.0347 1:00:33.970 508M / 1G INFO General (extenders_logic.cpp : 275) Estimated coverage of library #2 is 61.0347 1:00:33.972 508M / 1G INFO General (extenders_logic.cpp : 275) Estimated coverage of library #3 is 30.0076 1:00:33.972 508M / 1G INFO General (extenders_logic.cpp : 275) Estimated coverage of library #3 is 30.0076 1:00:33.973 512M / 1G INFO General (extenders_logic.cpp : 472) Using 4 paired-end libraries 1:00:33.973 512M / 1G INFO General (extenders_logic.cpp : 473) Using 4 paired-end scaffolding libraries 1:00:33.973 512M / 1G INFO General (extenders_logic.cpp : 474) Using 0 single read libraries 1:00:33.973 512M / 1G INFO General (launcher.cpp : 420) Total number of extenders is 12 1:00:33.973 512M / 1G INFO General (path_extender.hpp : 885) Processed 0 paths from 3536 (0%) 1:00:35.699 520M / 1G INFO General (path_extender.hpp : 883) Processed 128 paths from 3536 (3%) 1:00:37.230 532M / 1G INFO General (path_extender.hpp : 883) Processed 256 paths from 3536 (7%) 1:00:38.175 540M / 1G INFO General (path_extender.hpp : 885) Processed 354 paths from 3536 (10%) 1:00:38.614 544M / 1G INFO General (path_extender.hpp : 883) Processed 512 paths from 3536 (14%) 1:00:38.927 544M / 1G INFO General (path_extender.hpp : 885) Processed 708 paths from 3536 (20%) 1:00:39.756 552M / 1G INFO General (path_extender.hpp : 883) Processed 1024 paths from 3536 (28%) 1:00:39.824 552M / 1G INFO General (path_extender.hpp : 885) Processed 1062 paths from 3536 (30%) 1:00:40.509 560M / 1G INFO General (path_extender.hpp : 885) Processed 1416 paths from 3536 (40%) 1:00:41.553 564M / 1G INFO General (path_extender.hpp : 885) Processed 1770 paths from 3536 (50%) 1:00:41.851 568M / 1G INFO General (path_extender.hpp : 883) Processed 2048 paths from 3536 (57%) 1:00:41.890 568M / 1G INFO General (path_extender.hpp : 885) Processed 2124 paths from 3536 (60%) 1:00:42.116 568M / 1G INFO General (path_extender.hpp : 885) Processed 2478 paths from 3536 (70%) 1:00:42.257 568M / 1G INFO General (path_extender.hpp : 885) Processed 2832 paths from 3536 (80%) 1:00:42.281 568M / 1G INFO General (path_extender.hpp : 885) Processed 3186 paths from 3536 (90%) 1:00:42.284 568M / 1G INFO General (launcher.cpp : 234) Finalizing paths 1:00:42.284 568M / 1G INFO General (launcher.cpp : 236) Deduplicating paths 1:00:42.767 568M / 1G INFO General (launcher.cpp : 240) Paths deduplicated 1:00:42.767 568M / 1G INFO PEResolver (pe_resolver.hpp : 295) Removing overlaps 1:00:42.767 568M / 1G INFO PEResolver (pe_resolver.hpp : 298) Sorting paths 1:00:42.768 568M / 1G INFO PEResolver (pe_resolver.hpp : 305) Marking overlaps 1:00:42.768 568M / 1G INFO OverlapRemover (pe_resolver.hpp : 130) Marking start/end overlaps 1:00:43.367 568M / 1G INFO OverlapRemover (pe_resolver.hpp : 133) Marking remaining overlaps 1:00:43.971 568M / 1G INFO PEResolver (pe_resolver.hpp : 308) Splitting paths 1:00:43.987 572M / 1G INFO PEResolver (pe_resolver.hpp : 313) Deduplicating paths 1:00:44.020 572M / 1G INFO PEResolver (pe_resolver.hpp : 315) Overlaps removed 1:00:44.026 572M / 1G INFO General (launcher.cpp : 257) Paths finalized 1:00:44.026 572M / 1G INFO General (launcher.cpp : 427) Closing gaps in paths 1:00:44.031 572M / 1G INFO General (launcher.cpp : 455) Gap closing completed 1:00:44.034 572M / 1G INFO General (launcher.cpp : 286) Traversing tandem repeats 1:00:44.049 572M / 1G INFO General (launcher.cpp : 296) Traversed 11 loops 1:00:44.049 572M / 1G INFO General (launcher.cpp : 234) Finalizing paths 1:00:44.049 572M / 1G INFO General (launcher.cpp : 236) Deduplicating paths 1:00:44.052 572M / 1G INFO General (launcher.cpp : 240) Paths deduplicated 1:00:44.052 572M / 1G INFO PEResolver (pe_resolver.hpp : 295) Removing overlaps 1:00:44.052 572M / 1G INFO PEResolver (pe_resolver.hpp : 298) Sorting paths 1:00:44.052 572M / 1G INFO PEResolver (pe_resolver.hpp : 305) Marking overlaps 1:00:44.052 572M / 1G INFO OverlapRemover (pe_resolver.hpp : 130) Marking start/end overlaps 1:00:44.058 572M / 1G INFO OverlapRemover (pe_resolver.hpp : 133) Marking remaining overlaps 1:00:44.065 572M / 1G INFO PEResolver (pe_resolver.hpp : 308) Splitting paths 1:00:44.066 572M / 1G INFO PEResolver (pe_resolver.hpp : 313) Deduplicating paths 1:00:44.068 572M / 1G INFO PEResolver (pe_resolver.hpp : 315) Overlaps removed 1:00:44.069 572M / 1G INFO General (launcher.cpp : 257) Paths finalized 1:00:44.074 572M / 1G INFO General (launcher.cpp : 529) ExSPAnder repeat resolving tool finished 1:00:44.237 508M / 1G INFO StageManager (stage.cpp : 132) STAGE == Contig Output 1:00:44.237 508M / 1G INFO General (contig_output_stage.cpp : 40) Writing GFA to /oak/stanford/groups/akundaje/marinovg/Yeast-TFs/2019-02-03-datasets-Genomes/SPAdes-3.13-BY4742//K55/assembly_graph_with_scaffolds.gfa 1:00:46.004 504M / 1G INFO General (contig_output.hpp : 22) Outputting contigs to /oak/stanford/groups/akundaje/marinovg/Yeast-TFs/2019-02-03-datasets-Genomes/SPAdes-3.13-BY4742//K55/before_rr.fasta 1:00:46.195 504M / 1G INFO General (contig_output_stage.cpp : 51) Outputting FastG graph to /oak/stanford/groups/akundaje/marinovg/Yeast-TFs/2019-02-03-datasets-Genomes/SPAdes-3.13-BY4742//K55/assembly_graph.fastg 1:00:46.768 508M / 1G INFO General (contig_output_stage.cpp : 20) Outputting FastG paths to /oak/stanford/groups/akundaje/marinovg/Yeast-TFs/2019-02-03-datasets-Genomes/SPAdes-3.13-BY4742//K55/final_contigs.paths 1:00:46.993 504M / 1G INFO General (contig_output_stage.cpp : 20) Outputting FastG paths to /oak/stanford/groups/akundaje/marinovg/Yeast-TFs/2019-02-03-datasets-Genomes/SPAdes-3.13-BY4742//K55/scaffolds.paths 1:00:47.221 504M / 1G INFO General (launch.hpp : 149) SPAdes finished 1:00:47.773 12M / 1G INFO General (main.cpp : 109) Assembling time: 1 hours 0 minutes 47 seconds ===== Assembling finished. Used k-mer sizes: 21, 33, 55 * Corrected reads are in /oak/stanford/groups/akundaje/marinovg/Yeast-TFs/2019-02-03-datasets-Genomes/SPAdes-3.13-BY4742/corrected/ * Assembled contigs are in /oak/stanford/groups/akundaje/marinovg/Yeast-TFs/2019-02-03-datasets-Genomes/SPAdes-3.13-BY4742/contigs.fasta * Assembled scaffolds are in /oak/stanford/groups/akundaje/marinovg/Yeast-TFs/2019-02-03-datasets-Genomes/SPAdes-3.13-BY4742/scaffolds.fasta * Assembly graph is in /oak/stanford/groups/akundaje/marinovg/Yeast-TFs/2019-02-03-datasets-Genomes/SPAdes-3.13-BY4742/assembly_graph.fastg * Assembly graph in GFA format is in /oak/stanford/groups/akundaje/marinovg/Yeast-TFs/2019-02-03-datasets-Genomes/SPAdes-3.13-BY4742/assembly_graph_with_scaffolds.gfa * Paths in the assembly graph corresponding to the contigs are in /oak/stanford/groups/akundaje/marinovg/Yeast-TFs/2019-02-03-datasets-Genomes/SPAdes-3.13-BY4742/contigs.paths * Paths in the assembly graph corresponding to the scaffolds are in /oak/stanford/groups/akundaje/marinovg/Yeast-TFs/2019-02-03-datasets-Genomes/SPAdes-3.13-BY4742/scaffolds.paths ======= SPAdes pipeline finished. SPAdes log can be found here: /oak/stanford/groups/akundaje/marinovg/Yeast-TFs/2019-02-03-datasets-Genomes/SPAdes-3.13-BY4742/spades.log Thank you for using SPAdes!