Command line: /usr/common/jgi/assemblers/spades/3.0.0_1/bin/spades.py -o /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/spades --phred-offset 33 -t 8 -m 40 --sc --careful --12 /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/ZHYY.8454.1.101266.CGTAC.anqdp.bbqc.norm.fastq System information: SPAdes version: 3.0.0 Python version: 2.7.4 OS: Linux-2.6.32-431.46.2.el6.nersc.x86_64-x86_64-with-debian-6.0.6 Output dir: /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/spades Mode: read error correction and assembling Debug mode is turned OFF Dataset parameters: Single-cell mode Reads: Library number: 1, library type: paired-end orientation: fr left reads: not specified right reads: not specified interlaced reads: ['/global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/ZHYY.8454.1.101266.CGTAC.anqdp.bbqc.norm.fastq'] single reads: not specified Read error correction parameters: Iterations: 1 PHRED offset: 33 Corrected reads will be compressed (with gzip) Assembly parameters: k: [21, 33, 55] MismatchCorrector will be used Repeat resolution is enabled Other parameters: Dir for temp files: /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/spades/tmp Threads: 8 Memory limit (in Gb): 40 ======= SPAdes pipeline started. Log can be found here: /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/spades/spades.log == Splitting /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/ZHYY.8454.1.101266.CGTAC.anqdp.bbqc.norm.fastq into left and right reads (in /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/spades/split_input directory) ===== Read error correction started. == Running read error correction tool: /global/common/genepool/jgi/assemblers/spades/3.0.0_1/bin/hammer /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/spades/corrected/configs/config.info 0:00:00.006 4M / 4M INFO General (main.cpp : 82) Loading config from /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/spades/corrected/configs/config.info 0:00:00.009 4M / 4M INFO General (memory_limit.hpp : 29) Memory limit set to 40 Gb 0:00:00.010 4M / 4M INFO General (hammer_tools.cpp : 49) Hamming graph threshold tau=1, k=21, subkmer positions = [ 0 10 ] === ITERATION 0 begins === 0:00:00.010 4M / 4M INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:00:00.010 4M / 4M INFO K-mer Splitting (kmer_data.cpp : 127) Splitting kmer instances into 128 buckets. This might take a while. 0:00:00.010 4M / 4M INFO General (file_limit.hpp : 29) Open file limit set to 2048 0:00:00.010 4M / 4M INFO K-mer Splitting (kmer_data.cpp : 150) Memory available for splitting buffers: 1.6665 Gb 0:00:00.010 4M / 4M INFO K-mer Splitting (kmer_data.cpp : 159) Using cell size of 524288 0:00:00.444 8G / 8G INFO K-mer Splitting (kmer_data.cpp : 181) Processed 41218 reads 0:00:00.444 8G / 8G INFO K-mer Splitting (kmer_data.cpp : 186) Processed 41218 reads 0:00:00.453 32M / 8G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:00:00.663 32M / 8G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 2411496 kmers in total. 0:00:00.663 32M / 8G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:00:01.165 32M / 8G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:00:01.304 32M / 8G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:00:01.326 32M / 8G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 834269 bytes occupied (2.76764 bits per kmer). 0:00:01.327 32M / 8G INFO K-mer Counting (kmer_data.cpp : 267) Arranging kmers in hash map order 0:00:01.909 32M / 8G INFO K-mer Counting (kmer_data.cpp : 280) Done. Total swaps: 2411282 0:00:01.923 52M / 8G INFO General (main.cpp : 151) Clustering Hamming graph. 0:00:01.923 52M / 8G INFO Hamming Clustering (hamcluster.cpp : 115) Serializing sub-kmers. 0:00:01.923 52M / 8G INFO Hamming Clustering (hamcluster.cpp : 120) Serializing: [0, 10) 0:00:02.299 52M / 8G INFO Hamming Clustering (hamcluster.cpp : 120) Serializing: [10, 21) 0:00:02.678 52M / 8G INFO Hamming Clustering (hamcluster.cpp : 129) Splitting sub-kmers, pass 1. 0:00:03.444 52M / 8G INFO Hamming Clustering (hamcluster.cpp : 134) Splitting done. Processed 2 blocks. Produced 1469098 blocks. 0:00:03.444 52M / 8G INFO Hamming Clustering (hamcluster.cpp : 145) Merge sub-kmers, pass 1 0:00:05.726 52M / 8G INFO Hamming Clustering (hamcluster.cpp : 170) Merge done, total 7166 new blocks generated. 0:00:05.735 52M / 8G INFO Hamming Clustering (hamcluster.cpp : 175) Spliting sub-kmers, pass 2. 0:00:06.047 52M / 8G INFO Hamming Clustering (hamcluster.cpp : 180) Splitting done. Processed 14332 blocks. Produced 801919 blocks. 0:00:06.047 52M / 8G INFO Hamming Clustering (hamcluster.cpp : 187) Merge sub-kmers, pass 2 0:00:06.448 52M / 8G INFO Hamming Clustering (hamcluster.cpp : 205) Merge done, saw 6 big blocks out of 801919 processed. 0:00:07.086 52M / 8G INFO General (main.cpp : 165) Clustering done. Total clusters: 891972 0:00:07.086 52M / 8G INFO K-mer Counting (kmer_data.cpp : 285) Collecting K-mer information, this takes a while. 0:00:07.636 164M / 8G INFO K-mer Counting (kmer_data.cpp : 297) Collection done, postprocessing. 0:00:07.677 164M / 8G INFO K-mer Counting (kmer_data.cpp : 310) There are 2411496 kmers in total. Among them 1954098 (81.0326%) are singletons. 0:00:07.677 164M / 8G INFO General (main.cpp : 203) Subclustering Hamming graph 0:18:02.919 164M / 8G INFO Hamming Subclustering (kmer_cluster.cpp : 654) Subclustering done. Total 209 non-read kmers were generated. 0:18:02.919 164M / 8G INFO Hamming Subclustering (kmer_cluster.cpp : 655) Subclustering statistics: 0:18:02.919 164M / 8G INFO Hamming Subclustering (kmer_cluster.cpp : 656) Total singleton hamming clusters: 809769. Among them 115028 (14.205%) are good 0:18:02.919 164M / 8G INFO Hamming Subclustering (kmer_cluster.cpp : 657) Total singleton subclusters: 481. Among them 481 (100%) are good 0:18:02.919 164M / 8G INFO Hamming Subclustering (kmer_cluster.cpp : 658) Total non-singleton subcluster centers: 106604. Among them 84302 (79.0796%) are good 0:18:02.919 164M / 8G INFO Hamming Subclustering (kmer_cluster.cpp : 659) Average size of non-trivial subcluster: 15.0271 kmers 0:18:02.919 164M / 8G INFO Hamming Subclustering (kmer_cluster.cpp : 660) Average number of sub-clusters per non-singleton cluster: 1.30269 0:18:02.919 164M / 8G INFO Hamming Subclustering (kmer_cluster.cpp : 661) Total solid k-mers: 199811 0:18:02.919 164M / 8G INFO Hamming Subclustering (kmer_cluster.cpp : 662) Substitution probabilities: [4,4]((0.925532,0.0252711,0.0287537,0.0204431),(0.0332514,0.923758,0.00997411,0.0330165),(0.0356075,0.00991567,0.920025,0.0344522),(0.0202221,0.0270009,0.0243067,0.92847)) 0:18:02.921 164M / 8G INFO General (main.cpp : 208) Finished clustering. 0:18:02.921 164M / 8G INFO General (main.cpp : 228) Starting solid k-mers expansion in 8 threads. 0:18:03.081 164M / 8G INFO General (main.cpp : 249) Solid k-mers iteration 0 produced 31872 new k-mers. 0:18:03.233 164M / 8G INFO General (main.cpp : 249) Solid k-mers iteration 1 produced 3638 new k-mers. 0:18:03.386 164M / 8G INFO General (main.cpp : 249) Solid k-mers iteration 2 produced 264 new k-mers. 0:18:03.538 164M / 8G INFO General (main.cpp : 249) Solid k-mers iteration 3 produced 0 new k-mers. 0:18:03.538 164M / 8G INFO General (main.cpp : 253) Solid k-mers finalized 0:18:03.538 164M / 8G INFO General (hammer_tools.cpp : 223) Starting read correction in 8 threads. 0:18:03.538 164M / 8G INFO General (hammer_tools.cpp : 235) Correcting pair of reads: /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/spades/split_input/ZHYY.8454.1.101266.CGTAC.anqdp.bbqc.norm_1.fastq and /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/spades/split_input/ZHYY.8454.1.101266.CGTAC.anqdp.bbqc.norm_2.fastq 0:18:03.690 244M / 8G INFO General (hammer_tools.cpp : 179) Prepared batch 0 of 20609 reads. 0:18:03.826 244M / 8G INFO General (hammer_tools.cpp : 188) Processed batch 0 0:18:04.204 244M / 8G INFO General (hammer_tools.cpp : 198) Written batch 0 0:18:04.230 164M / 8G INFO General (hammer_tools.cpp : 282) Correction done. Changed 26600 bases in 20490 reads. 0:18:04.230 164M / 8G INFO General (hammer_tools.cpp : 283) Failed to correct 2289804 bases out of 6078510. 0:18:04.240 52M / 8G INFO General (main.cpp : 286) Saving corrected dataset description to /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/spades/corrected/corrected.yaml 0:18:04.241 52M / 8G INFO General (main.cpp : 293) All done. Exiting. == Compressing corrected reads (with gzip) == Dataset description file was created: /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/spades/corrected/corrected.yaml ===== Read error correction finished. ===== Assembling started. == Running assembler: K21 0:00:00.000 4M / 4M INFO General (memory_limit.hpp : 29) Memory limit set to 40 Gb 0:00:00.001 4M / 4M INFO General (main.cpp : 146) Assembling dataset (/global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/spades/dataset.info) with K=21 0:00:00.001 4M / 4M INFO General (launch.hpp : 28) SPAdes started 0:00:00.001 4M / 4M INFO General (launch.hpp : 29) Starting from stage: construction 0:00:00.003 4M / 4M INFO StageManager (stage.cpp : 125) STAGE == Construction 0:00:00.034 4M / 4M INFO General (read_converter.hpp : 79) Converting reads to binary format (takes a while) 0:00:00.034 4M / 4M INFO General (read_converter.hpp : 81) Paired reads for library #0 0:00:00.292 80M / 80M INFO General (binary_converter.hpp : 138) 16384 reads processed 0:00:00.371 84M / 84M INFO General (binary_converter.hpp : 158) 20603 reads written 0:00:00.392 4M / 84M INFO General (read_converter.hpp : 91) Single reads for library #0 0:00:00.532 132M / 148M INFO General (binary_converter.hpp : 158) 6 reads written 0:00:00.547 4M / 148M INFO General (graph_construction.hpp : 127) Constructing DeBruijn graph for k=21 0:00:00.547 4M / 148M INFO General (kmer_splitters.hpp : 164) Splitting kmer instances into 64 buckets. This might take a while. 0:00:00.547 4M / 148M INFO General (file_limit.hpp : 29) Open file limit set to 2048 0:00:00.547 4M / 148M INFO General (kmer_splitters.hpp : 187) Memory available for splitting buffers: 1.6665 Gb 0:00:00.547 4M / 148M INFO General (kmer_splitters.hpp : 197) Using cell size of 1048576 0:00:00.676 6G / 6G INFO General (kmer_splitters.hpp : 225) Processed 82424 reads 0:00:00.676 6G / 6G INFO General (kmer_splitters.hpp : 231) Adding contigs from previous K 0:00:00.676 6G / 6G INFO General (kmer_splitters.hpp : 242) Used 82424 reads. Maximum read length 150 0:00:00.682 32M / 6G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:00:00.783 32M / 6G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 1127960 kmers in total. 0:00:00.783 32M / 6G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:00:01.300 32M / 6G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:00:01.300 32M / 6G INFO General (kmer_splitters.hpp : 381) Splitting kmer instances into 128 buckets. This might take a while. 0:00:01.300 32M / 6G INFO General (file_limit.hpp : 29) Open file limit set to 2048 0:00:01.300 32M / 6G INFO General (kmer_splitters.hpp : 404) Memory available for splitting buffers: 1.66536 Gb 0:00:01.300 32M / 6G INFO General (kmer_splitters.hpp : 413) Using cell size of 524288 0:00:01.565 8G / 8G INFO General (kmer_splitters.hpp : 436) Processed 1127960 kmers 0:00:01.565 8G / 8G INFO General (kmer_splitters.hpp : 445) Used 1127960 kmers. 0:00:01.570 32M / 8G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:00:01.665 32M / 8G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 1090748 kmers in total. 0:00:01.665 32M / 8G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:00:01.711 32M / 8G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:00:01.763 32M / 8G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:00:01.805 32M / 8G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 377372 bytes occupied (2.7678 bits per kmer). 0:00:01.807 32M / 8G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 382) Building k-mer extensions from k+1-mers 0:00:01.903 32M / 8G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 386) Building k-mer extensions from k+1-mers finished. 0:00:01.903 32M / 8G INFO Early tip clipping (early_simplification.hpp : 236) Early tip clipping 0:00:03.127 32M / 8G INFO Early tip clipping (early_simplification.hpp : 239) 190228 22-mers were removed by early tip clipper 0:00:03.127 32M / 8G INFO General (graph_construction.hpp : 143) Condensing graph 0:00:03.127 32M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 346) Extracting unbranching paths 0:00:03.525 52M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 360) Extracting unbranching paths finished. 181104 sequences extracted 0:00:03.593 52M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 320) Collecting perfect loops 0:00:03.754 52M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 335) Collecting perfect loops finished. 0 loops collected 0:00:03.822 48M / 8G INFO General (graph_construction.hpp : 151) Building index with coverage from graph 0:00:03.823 48M / 8G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:00:03.823 48M / 8G INFO General (kmer_splitters.hpp : 285) Splitting kmer instances into 16 buckets. This might take a while. 0:00:03.823 48M / 8G INFO General (file_limit.hpp : 29) Open file limit set to 2048 0:00:03.823 48M / 8G INFO General (kmer_splitters.hpp : 308) Memory available for splitting buffers: 13.3177 Gb 0:00:03.823 48M / 8G INFO General (kmer_splitters.hpp : 314) Using cell size of 4194304 0:00:04.008 624M / 8G INFO General (kmer_splitters.hpp : 327) Processed 181104 edges 0:00:04.008 624M / 8G INFO General (kmer_splitters.hpp : 332) Used 181104 sequences. 0:00:04.009 48M / 8G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:00:04.071 48M / 8G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 937732 kmers in total. 0:00:04.071 48M / 8G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:00:04.087 48M / 8G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:00:04.275 48M / 8G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:00:04.344 48M / 8G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 324442 bytes occupied (2.76789 bits per kmer). 0:00:04.356 72M / 8G INFO General (edge_index_builders.hpp : 21) Collecting k-mer coverage information from graph, this takes a while. 0:00:05.022 72M / 8G INFO General (edge_index_builders.hpp : 99) Collecting k-mer coverage information from reads, this takes a while. 0:00:05.298 68M / 8G INFO General (graph_construction.hpp : 179) Filling coverage and flanking coverage from index 0:00:05.356 68M / 8G INFO General (construction.cpp : 32) Figured out: read length = 150 0:00:05.356 68M / 8G INFO StageManager (stage.cpp : 125) STAGE == EC Threshold Finding 0:00:05.467 68M / 8G INFO ThresholdFinder (omni_tools.hpp : 466) Bucket size: 6 0:00:05.467 68M / 8G INFO General (genomic_info_filler.cpp : 72) Average edge coverage: 5.35447 0:00:05.467 68M / 8G INFO General (genomic_info_filler.cpp : 73) Graph threshold: 14 0:00:05.474 68M / 8G INFO General (genomic_info_filler.cpp : 101) EC coverage threshold value was calculated as 14 0:00:05.474 68M / 8G INFO StageManager (stage.cpp : 125) STAGE == Simplification 0:00:05.514 68M / 8G INFO General (graph_simplification.hpp : 633) PROCEDURE == Presimplification 0:00:05.514 68M / 8G INFO General (graph_simplification.hpp : 416) Removing short low covered self-conjugate connections 0:00:05.813 68M / 8G INFO General (graph_simplification.hpp : 713) PROCEDURE == Simplification cycle, iteration 1 0:00:05.823 68M / 8G INFO General (graph_simplification.hpp : 309) Clipping tips 0:00:06.078 68M / 8G INFO General (graph_simplification.hpp : 370) Removing bulges 0:00:18.391 76M / 8G INFO General (graph_simplification.hpp : 397) Removing low covered connections 0:00:19.778 76M / 8G INFO General (graph_simplification.hpp : 713) PROCEDURE == Simplification cycle, iteration 2 0:00:19.778 76M / 8G INFO General (graph_simplification.hpp : 309) Clipping tips 0:00:19.832 76M / 8G INFO General (graph_simplification.hpp : 370) Removing bulges 0:00:22.108 76M / 8G INFO General (graph_simplification.hpp : 397) Removing low covered connections 0:00:22.289 76M / 8G INFO General (graph_simplification.hpp : 713) PROCEDURE == Simplification cycle, iteration 3 0:00:22.290 76M / 8G INFO General (graph_simplification.hpp : 309) Clipping tips 0:00:22.300 76M / 8G INFO General (graph_simplification.hpp : 370) Removing bulges 0:00:22.461 76M / 8G INFO General (graph_simplification.hpp : 397) Removing low covered connections 0:00:22.529 72M / 8G INFO General (graph_simplification.hpp : 713) PROCEDURE == Simplification cycle, iteration 4 0:00:22.529 72M / 8G INFO General (graph_simplification.hpp : 309) Clipping tips 0:00:22.534 72M / 8G INFO General (graph_simplification.hpp : 370) Removing bulges 0:00:22.580 72M / 8G INFO General (graph_simplification.hpp : 397) Removing low covered connections 0:00:22.603 72M / 8G INFO General (graph_simplification.hpp : 713) PROCEDURE == Simplification cycle, iteration 5 0:00:22.603 72M / 8G INFO General (graph_simplification.hpp : 309) Clipping tips 0:00:22.608 72M / 8G INFO General (graph_simplification.hpp : 370) Removing bulges 0:00:22.634 72M / 8G INFO General (graph_simplification.hpp : 397) Removing low covered connections 0:00:22.658 72M / 8G INFO General (graph_simplification.hpp : 713) PROCEDURE == Simplification cycle, iteration 6 0:00:22.658 72M / 8G INFO General (graph_simplification.hpp : 309) Clipping tips 0:00:22.661 72M / 8G INFO General (graph_simplification.hpp : 370) Removing bulges 0:00:22.683 72M / 8G INFO General (graph_simplification.hpp : 397) Removing low covered connections 0:00:22.695 72M / 8G INFO General (graph_simplification.hpp : 713) PROCEDURE == Simplification cycle, iteration 7 0:00:22.695 72M / 8G INFO General (graph_simplification.hpp : 309) Clipping tips 0:00:22.698 72M / 8G INFO General (graph_simplification.hpp : 370) Removing bulges 0:00:22.718 72M / 8G INFO General (graph_simplification.hpp : 397) Removing low covered connections 0:00:22.726 72M / 8G INFO General (graph_simplification.hpp : 713) PROCEDURE == Simplification cycle, iteration 8 0:00:22.726 72M / 8G INFO General (graph_simplification.hpp : 309) Clipping tips 0:00:22.729 72M / 8G INFO General (graph_simplification.hpp : 370) Removing bulges 0:00:22.749 72M / 8G INFO General (graph_simplification.hpp : 397) Removing low covered connections 0:00:22.756 72M / 8G INFO General (graph_simplification.hpp : 713) PROCEDURE == Simplification cycle, iteration 9 0:00:22.756 72M / 8G INFO General (graph_simplification.hpp : 309) Clipping tips 0:00:22.759 72M / 8G INFO General (graph_simplification.hpp : 370) Removing bulges 0:00:22.777 72M / 8G INFO General (graph_simplification.hpp : 397) Removing low covered connections 0:00:22.785 72M / 8G INFO General (graph_simplification.hpp : 713) PROCEDURE == Simplification cycle, iteration 10 0:00:22.785 72M / 8G INFO General (graph_simplification.hpp : 309) Clipping tips 0:00:22.788 72M / 8G INFO General (graph_simplification.hpp : 370) Removing bulges 0:00:22.804 72M / 8G INFO General (graph_simplification.hpp : 397) Removing low covered connections 0:00:22.812 72M / 8G INFO General (graph_simplification.hpp : 659) PROCEDURE == Post simplification 0:00:22.812 72M / 8G INFO General (graph_simplification.hpp : 665) Iteration 0 0:00:22.812 72M / 8G INFO General (graph_simplification.hpp : 471) Clipping tips based on topology 0:00:22.815 72M / 8G INFO General (graph_simplification.hpp : 447) Removal of relatively low covered connections disabled 0:00:22.815 72M / 8G INFO General (graph_simplification.hpp : 309) Clipping tips 0:00:22.818 72M / 8G INFO General (graph_simplification.hpp : 370) Removing bulges 0:00:22.832 72M / 8G INFO General (graph_simplification.hpp : 565) Removing hidden erroneous connections 0:00:22.850 72M / 8G INFO StageManager (stage.cpp : 125) STAGE == Simplification Cleanup 0:00:22.850 72M / 8G INFO General (simplification.cpp : 71) Final isolated edges removal: 0:00:22.850 72M / 8G INFO General (simplification.cpp : 73) All edges of length smaller than 150 will be removed 0:00:22.853 72M / 8G INFO General (simplification.cpp : 77) Removed 8 edges 0:00:22.853 72M / 8G INFO General (simplification.cpp : 106) Counting average coverage 0:00:22.853 72M / 8G INFO General (simplification.cpp : 109) Average coverage = 50.5751 0:00:22.853 72M / 8G INFO StageManager (stage.cpp : 125) STAGE == Contig Output 0:00:22.863 72M / 8G INFO General (contig_output.hpp : 295) Outputting contigs to /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/spades//K21/simplified_contigs.fasta 0:00:22.935 72M / 8G INFO General (contig_output.hpp : 295) Outputting contigs to /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/spades//K21/before_rr.fasta 0:00:23.018 72M / 8G INFO General (contig_output.hpp : 295) Outputting contigs to /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/spades//K21/final_contigs.fasta 0:00:23.089 72M / 8G INFO General (launch.hpp : 84) SPAdes finished 0:00:23.109 32M / 8G INFO General (main.cpp : 166) Assembling time: 0 hours 0 minutes 23 seconds == Running assembler: K33 0:00:00.000 4M / 4M INFO General (memory_limit.hpp : 29) Memory limit set to 40 Gb 0:00:00.000 4M / 4M INFO General (main.cpp : 146) Assembling dataset (/global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/spades/dataset.info) with K=33 0:00:00.000 4M / 4M INFO General (launch.hpp : 28) SPAdes started 0:00:00.000 4M / 4M INFO General (launch.hpp : 29) Starting from stage: construction 0:00:00.000 4M / 4M INFO StageManager (stage.cpp : 125) STAGE == Construction 0:00:00.000 4M / 4M INFO General (construction.cpp : 42) Contigs from previous K will be used 0:00:00.000 4M / 4M INFO General (read_converter.hpp : 49) Binary reads detected 0:00:00.001 4M / 4M INFO General (graph_construction.hpp : 127) Constructing DeBruijn graph for k=33 0:00:00.001 4M / 4M INFO General (kmer_splitters.hpp : 164) Splitting kmer instances into 64 buckets. This might take a while. 0:00:00.001 4M / 4M INFO General (file_limit.hpp : 29) Open file limit set to 2048 0:00:00.001 4M / 4M INFO General (kmer_splitters.hpp : 187) Memory available for splitting buffers: 1.6665 Gb 0:00:00.001 4M / 4M INFO General (kmer_splitters.hpp : 197) Using cell size of 524288 0:00:00.141 6G / 6G INFO General (kmer_splitters.hpp : 225) Processed 82424 reads 0:00:00.141 6G / 6G INFO General (kmer_splitters.hpp : 231) Adding contigs from previous K 0:00:00.177 6G / 6G INFO General (kmer_splitters.hpp : 242) Used 82424 reads. Maximum read length 150 0:00:00.188 32M / 6G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:00:00.467 32M / 6G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 1428029 kmers in total. 0:00:00.467 32M / 6G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:00:00.897 32M / 6G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:00:00.897 32M / 6G INFO General (kmer_splitters.hpp : 381) Splitting kmer instances into 128 buckets. This might take a while. 0:00:00.897 32M / 6G INFO General (file_limit.hpp : 29) Open file limit set to 2048 0:00:00.897 32M / 6G INFO General (kmer_splitters.hpp : 404) Memory available for splitting buffers: 1.66536 Gb 0:00:00.897 32M / 6G INFO General (kmer_splitters.hpp : 413) Using cell size of 262144 0:00:01.139 8G / 8G INFO General (kmer_splitters.hpp : 436) Processed 1428029 kmers 0:00:01.139 8G / 8G INFO General (kmer_splitters.hpp : 445) Used 1428029 kmers. 0:00:01.150 32M / 8G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:00:01.423 32M / 8G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 1411225 kmers in total. 0:00:01.423 32M / 8G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:00:01.922 32M / 8G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:00:02.045 32M / 8G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:00:02.066 32M / 8G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 488235 bytes occupied (2.76772 bits per kmer). 0:00:02.067 32M / 8G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 382) Building k-mer extensions from k+1-mers 0:00:02.212 32M / 8G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 386) Building k-mer extensions from k+1-mers finished. 0:00:02.213 32M / 8G INFO Early tip clipping (early_simplification.hpp : 236) Early tip clipping 0:00:03.630 32M / 8G INFO Early tip clipping (early_simplification.hpp : 239) 555352 34-mers were removed by early tip clipper 0:00:03.630 32M / 8G INFO General (graph_construction.hpp : 143) Condensing graph 0:00:03.630 32M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 346) Extracting unbranching paths 0:00:04.293 44M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 360) Extracting unbranching paths finished. 99381 sequences extracted 0:00:04.354 44M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 320) Collecting perfect loops 0:00:04.572 44M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 335) Collecting perfect loops finished. 0 loops collected 0:00:04.610 40M / 8G INFO General (graph_construction.hpp : 151) Building index with coverage from graph 0:00:04.610 40M / 8G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:00:04.610 40M / 8G INFO General (kmer_splitters.hpp : 285) Splitting kmer instances into 16 buckets. This might take a while. 0:00:04.610 40M / 8G INFO General (file_limit.hpp : 29) Open file limit set to 2048 0:00:04.610 40M / 8G INFO General (kmer_splitters.hpp : 308) Memory available for splitting buffers: 13.3203 Gb 0:00:04.611 40M / 8G INFO General (kmer_splitters.hpp : 314) Using cell size of 2097152 0:00:04.733 616M / 8G INFO General (kmer_splitters.hpp : 327) Processed 99381 edges 0:00:04.733 616M / 8G INFO General (kmer_splitters.hpp : 332) Used 99381 sequences. 0:00:04.735 40M / 8G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:00:04.825 40M / 8G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 872677 kmers in total. 0:00:04.825 40M / 8G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:00:04.853 40M / 8G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:00:05.043 40M / 8G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:00:05.113 40M / 8G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 301932 bytes occupied (2.76787 bits per kmer). 0:00:05.124 60M / 8G INFO General (edge_index_builders.hpp : 21) Collecting k-mer coverage information from graph, this takes a while. 0:00:05.789 60M / 8G INFO General (edge_index_builders.hpp : 99) Collecting k-mer coverage information from reads, this takes a while. 0:00:06.080 60M / 8G INFO General (graph_construction.hpp : 179) Filling coverage and flanking coverage from index 0:00:06.117 60M / 8G INFO General (construction.cpp : 32) Figured out: read length = 150 0:00:06.117 60M / 8G INFO StageManager (stage.cpp : 125) STAGE == EC Threshold Finding 0:00:06.152 60M / 8G INFO ThresholdFinder (omni_tools.hpp : 466) Bucket size: 6 0:00:06.152 60M / 8G INFO General (genomic_info_filler.cpp : 72) Average edge coverage: 4.76766 0:00:06.152 60M / 8G INFO General (genomic_info_filler.cpp : 73) Graph threshold: 32 0:00:06.153 60M / 8G INFO General (genomic_info_filler.cpp : 101) EC coverage threshold value was calculated as 32 0:00:06.153 60M / 8G INFO StageManager (stage.cpp : 125) STAGE == Simplification 0:00:06.154 60M / 8G INFO General (graph_simplification.hpp : 633) PROCEDURE == Presimplification 0:00:06.154 60M / 8G INFO General (graph_simplification.hpp : 416) Removing short low covered self-conjugate connections 0:00:06.296 60M / 8G INFO General (graph_simplification.hpp : 713) PROCEDURE == Simplification cycle, iteration 1 0:00:06.296 60M / 8G INFO General (graph_simplification.hpp : 309) Clipping tips 0:00:06.453 60M / 8G INFO General (graph_simplification.hpp : 370) Removing bulges 0:00:13.288 64M / 8G INFO General (graph_simplification.hpp : 397) Removing low covered connections 0:00:14.509 64M / 8G INFO General (graph_simplification.hpp : 713) PROCEDURE == Simplification cycle, iteration 2 0:00:14.509 64M / 8G INFO General (graph_simplification.hpp : 309) Clipping tips 0:00:14.601 64M / 8G INFO General (graph_simplification.hpp : 370) Removing bulges 0:00:15.534 60M / 8G INFO General (graph_simplification.hpp : 397) Removing low covered connections 0:00:15.603 60M / 8G INFO General (graph_simplification.hpp : 713) PROCEDURE == Simplification cycle, iteration 3 0:00:15.603 60M / 8G INFO General (graph_simplification.hpp : 309) Clipping tips 0:00:15.611 60M / 8G INFO General (graph_simplification.hpp : 370) Removing bulges 0:00:15.656 60M / 8G INFO General (graph_simplification.hpp : 397) Removing low covered connections 0:00:15.681 60M / 8G INFO General (graph_simplification.hpp : 713) PROCEDURE == Simplification cycle, iteration 4 0:00:15.681 60M / 8G INFO General (graph_simplification.hpp : 309) Clipping tips 0:00:15.686 60M / 8G INFO General (graph_simplification.hpp : 370) Removing bulges 0:00:15.703 60M / 8G INFO General (graph_simplification.hpp : 397) Removing low covered connections 0:00:15.716 60M / 8G INFO General (graph_simplification.hpp : 713) PROCEDURE == Simplification cycle, iteration 5 0:00:15.716 60M / 8G INFO General (graph_simplification.hpp : 309) Clipping tips 0:00:15.720 60M / 8G INFO General (graph_simplification.hpp : 370) Removing bulges 0:00:15.736 60M / 8G INFO General (graph_simplification.hpp : 397) Removing low covered connections 0:00:15.747 60M / 8G INFO General (graph_simplification.hpp : 713) PROCEDURE == Simplification cycle, iteration 6 0:00:15.747 60M / 8G INFO General (graph_simplification.hpp : 309) Clipping tips 0:00:15.751 60M / 8G INFO General (graph_simplification.hpp : 370) Removing bulges 0:00:15.764 60M / 8G INFO General (graph_simplification.hpp : 397) Removing low covered connections 0:00:15.773 60M / 8G INFO General (graph_simplification.hpp : 713) PROCEDURE == Simplification cycle, iteration 7 0:00:15.773 60M / 8G INFO General (graph_simplification.hpp : 309) Clipping tips 0:00:15.776 60M / 8G INFO General (graph_simplification.hpp : 370) Removing bulges 0:00:15.789 60M / 8G INFO General (graph_simplification.hpp : 397) Removing low covered connections 0:00:15.798 60M / 8G INFO General (graph_simplification.hpp : 713) PROCEDURE == Simplification cycle, iteration 8 0:00:15.798 60M / 8G INFO General (graph_simplification.hpp : 309) Clipping tips 0:00:15.801 60M / 8G INFO General (graph_simplification.hpp : 370) Removing bulges 0:00:15.812 60M / 8G INFO General (graph_simplification.hpp : 397) Removing low covered connections 0:00:15.821 60M / 8G INFO General (graph_simplification.hpp : 713) PROCEDURE == Simplification cycle, iteration 9 0:00:15.821 60M / 8G INFO General (graph_simplification.hpp : 309) Clipping tips 0:00:15.825 60M / 8G INFO General (graph_simplification.hpp : 370) Removing bulges 0:00:15.837 60M / 8G INFO General (graph_simplification.hpp : 397) Removing low covered connections 0:00:15.846 60M / 8G INFO General (graph_simplification.hpp : 713) PROCEDURE == Simplification cycle, iteration 10 0:00:15.846 60M / 8G INFO General (graph_simplification.hpp : 309) Clipping tips 0:00:15.849 60M / 8G INFO General (graph_simplification.hpp : 370) Removing bulges 0:00:15.861 60M / 8G INFO General (graph_simplification.hpp : 397) Removing low covered connections 0:00:15.875 60M / 8G INFO General (graph_simplification.hpp : 659) PROCEDURE == Post simplification 0:00:15.875 60M / 8G INFO General (graph_simplification.hpp : 665) Iteration 0 0:00:15.875 60M / 8G INFO General (graph_simplification.hpp : 471) Clipping tips based on topology 0:00:15.879 60M / 8G INFO General (graph_simplification.hpp : 447) Removal of relatively low covered connections disabled 0:00:15.879 60M / 8G INFO General (graph_simplification.hpp : 309) Clipping tips 0:00:15.882 60M / 8G INFO General (graph_simplification.hpp : 370) Removing bulges 0:00:15.893 60M / 8G INFO General (graph_simplification.hpp : 565) Removing hidden erroneous connections 0:00:15.915 60M / 8G INFO StageManager (stage.cpp : 125) STAGE == Simplification Cleanup 0:00:15.915 60M / 8G INFO General (simplification.cpp : 71) Final isolated edges removal: 0:00:15.915 60M / 8G INFO General (simplification.cpp : 73) All edges of length smaller than 150 will be removed 0:00:15.972 60M / 8G INFO General (simplification.cpp : 77) Removed 675 edges 0:00:15.972 60M / 8G INFO General (simplification.cpp : 106) Counting average coverage 0:00:15.973 60M / 8G INFO General (simplification.cpp : 109) Average coverage = 29.3515 0:00:15.973 60M / 8G INFO StageManager (stage.cpp : 125) STAGE == Contig Output 0:00:15.973 60M / 8G INFO General (contig_output.hpp : 295) Outputting contigs to /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/spades//K33/simplified_contigs.fasta 0:00:16.008 60M / 8G INFO General (contig_output.hpp : 295) Outputting contigs to /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/spades//K33/before_rr.fasta 0:00:16.071 60M / 8G INFO General (contig_output.hpp : 295) Outputting contigs to /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/spades//K33/final_contigs.fasta 0:00:16.135 60M / 8G INFO General (launch.hpp : 84) SPAdes finished 0:00:16.149 32M / 8G INFO General (main.cpp : 166) Assembling time: 0 hours 0 minutes 16 seconds == Running assembler: K55 0:00:00.000 4M / 4M INFO General (memory_limit.hpp : 29) Memory limit set to 40 Gb 0:00:00.000 4M / 4M INFO General (main.cpp : 146) Assembling dataset (/global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/spades/dataset.info) with K=55 0:00:00.000 4M / 4M INFO General (launch.hpp : 28) SPAdes started 0:00:00.000 4M / 4M INFO General (launch.hpp : 29) Starting from stage: construction 0:00:00.000 4M / 4M INFO StageManager (stage.cpp : 125) STAGE == Construction 0:00:00.000 4M / 4M INFO General (construction.cpp : 42) Contigs from previous K will be used 0:00:00.001 4M / 4M INFO General (read_converter.hpp : 49) Binary reads detected 0:00:00.002 4M / 4M INFO General (graph_construction.hpp : 127) Constructing DeBruijn graph for k=55 0:00:00.002 4M / 4M INFO General (kmer_splitters.hpp : 164) Splitting kmer instances into 64 buckets. This might take a while. 0:00:00.002 4M / 4M INFO General (file_limit.hpp : 29) Open file limit set to 2048 0:00:00.002 4M / 4M INFO General (kmer_splitters.hpp : 187) Memory available for splitting buffers: 1.6665 Gb 0:00:00.002 4M / 4M INFO General (kmer_splitters.hpp : 197) Using cell size of 524288 0:00:00.116 6G / 6G INFO General (kmer_splitters.hpp : 225) Processed 82424 reads 0:00:00.116 6G / 6G INFO General (kmer_splitters.hpp : 231) Adding contigs from previous K 0:00:00.153 6G / 6G INFO General (kmer_splitters.hpp : 242) Used 82424 reads. Maximum read length 150 0:00:00.162 32M / 6G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:00:00.444 32M / 6G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 1503748 kmers in total. 0:00:00.444 32M / 6G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:00:00.706 32M / 6G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:00:00.706 32M / 6G INFO General (kmer_splitters.hpp : 381) Splitting kmer instances into 128 buckets. This might take a while. 0:00:00.706 32M / 6G INFO General (file_limit.hpp : 29) Open file limit set to 2048 0:00:00.706 32M / 6G INFO General (kmer_splitters.hpp : 404) Memory available for splitting buffers: 1.66536 Gb 0:00:00.706 32M / 6G INFO General (kmer_splitters.hpp : 413) Using cell size of 262144 0:00:01.085 8G / 8G INFO General (kmer_splitters.hpp : 436) Processed 1503748 kmers 0:00:01.085 8G / 8G INFO General (kmer_splitters.hpp : 445) Used 1503748 kmers. 0:00:01.097 32M / 8G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:00:01.369 32M / 8G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 1509738 kmers in total. 0:00:01.369 32M / 8G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:00:02.072 32M / 8G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:00:02.188 32M / 8G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:00:02.211 32M / 8G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 522315 bytes occupied (2.76771 bits per kmer). 0:00:02.212 32M / 8G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 382) Building k-mer extensions from k+1-mers 0:00:02.440 32M / 8G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 386) Building k-mer extensions from k+1-mers finished. 0:00:02.440 32M / 8G INFO General (graph_construction.hpp : 143) Condensing graph 0:00:02.440 32M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 346) Extracting unbranching paths 0:00:02.901 44M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 360) Extracting unbranching paths finished. 76760 sequences extracted 0:00:03.021 44M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 320) Collecting perfect loops 0:00:03.255 44M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 335) Collecting perfect loops finished. 0 loops collected 0:00:03.293 40M / 8G INFO General (graph_construction.hpp : 151) Building index with coverage from graph 0:00:03.293 40M / 8G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:00:03.293 40M / 8G INFO General (kmer_splitters.hpp : 285) Splitting kmer instances into 16 buckets. This might take a while. 0:00:03.293 40M / 8G INFO General (file_limit.hpp : 29) Open file limit set to 2048 0:00:03.293 40M / 8G INFO General (kmer_splitters.hpp : 308) Memory available for splitting buffers: 13.3203 Gb 0:00:03.293 40M / 8G INFO General (kmer_splitters.hpp : 314) Using cell size of 2097152 0:00:03.499 616M / 8G INFO General (kmer_splitters.hpp : 327) Processed 76760 edges 0:00:03.499 616M / 8G INFO General (kmer_splitters.hpp : 332) Used 76760 sequences. 0:00:03.502 40M / 8G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:00:03.808 40M / 8G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 1503748 kmers in total. 0:00:03.808 40M / 8G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:00:03.840 40M / 8G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:00:04.189 40M / 8G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:00:04.212 40M / 8G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 520238 bytes occupied (2.76769 bits per kmer). 0:00:04.231 76M / 8G INFO General (edge_index_builders.hpp : 21) Collecting k-mer coverage information from graph, this takes a while. 0:00:05.622 76M / 8G INFO General (edge_index_builders.hpp : 99) Collecting k-mer coverage information from reads, this takes a while. 0:00:05.886 76M / 8G INFO General (graph_construction.hpp : 179) Filling coverage and flanking coverage from index 0:00:05.933 76M / 8G INFO General (construction.cpp : 32) Figured out: read length = 150 0:00:05.933 76M / 8G INFO StageManager (stage.cpp : 125) STAGE == EC Threshold Finding 0:00:05.956 76M / 8G INFO ThresholdFinder (omni_tools.hpp : 466) Bucket size: 5 0:00:05.956 76M / 8G INFO General (genomic_info_filler.cpp : 72) Average edge coverage: 2.53436 0:00:05.956 76M / 8G INFO General (genomic_info_filler.cpp : 73) Graph threshold: 8 0:00:05.958 76M / 8G INFO General (genomic_info_filler.cpp : 101) EC coverage threshold value was calculated as 8 0:00:05.958 76M / 8G INFO StageManager (stage.cpp : 125) STAGE == Gap Closer 0:00:05.958 76M / 8G INFO General (gap_closer.cpp : 178) Preparing shift maps 0:00:05.989 80M / 8G INFO General (gap_closer.cpp : 132) Processing paired reads (takes a while) 0:00:06.084 80M / 8G INFO General (gap_closer.cpp : 158) Used 41206 paired reads 0:00:06.084 80M / 8G INFO General (gap_closer.cpp : 160) Merging paired indices 0:00:06.089 80M / 8G INFO GapCloser (gap_closer.cpp : 409) Closing short gaps 0:00:06.130 84M / 8G INFO GapCloser (gap_closer.cpp : 438) Closing short gaps complete: filled 3 gaps after checking 181 candidates 0:00:06.163 76M / 8G INFO General (gap_closer.cpp : 506) Detaching and clearing index 0:00:06.166 40M / 8G INFO General (gap_closer.cpp : 509) Index clearing finished 0:00:06.167 40M / 8G INFO StageManager (stage.cpp : 125) STAGE == Simplification 0:00:06.167 40M / 8G INFO General (graph_simplification.hpp : 633) PROCEDURE == Presimplification 0:00:06.167 40M / 8G INFO General (graph_simplification.hpp : 416) Removing short low covered self-conjugate connections 0:00:06.293 40M / 8G INFO General (graph_simplification.hpp : 713) PROCEDURE == Simplification cycle, iteration 1 0:00:06.293 40M / 8G INFO General (graph_simplification.hpp : 309) Clipping tips 0:00:06.531 40M / 8G INFO General (graph_simplification.hpp : 370) Removing bulges 0:00:06.754 48M / 8G INFO General (graph_simplification.hpp : 397) Removing low covered connections 0:00:06.780 48M / 8G INFO General (graph_simplification.hpp : 713) PROCEDURE == Simplification cycle, iteration 2 0:00:06.780 48M / 8G INFO General (graph_simplification.hpp : 309) Clipping tips 0:00:06.800 48M / 8G INFO General (graph_simplification.hpp : 370) Removing bulges 0:00:06.851 48M / 8G INFO General (graph_simplification.hpp : 397) Removing low covered connections 0:00:06.909 48M / 8G INFO General (graph_simplification.hpp : 713) PROCEDURE == Simplification cycle, iteration 3 0:00:06.909 48M / 8G INFO General (graph_simplification.hpp : 309) Clipping tips 0:00:06.926 48M / 8G INFO General (graph_simplification.hpp : 370) Removing bulges 0:00:06.955 48M / 8G INFO General (graph_simplification.hpp : 397) Removing low covered connections 0:00:06.983 48M / 8G INFO General (graph_simplification.hpp : 713) PROCEDURE == Simplification cycle, iteration 4 0:00:06.983 48M / 8G INFO General (graph_simplification.hpp : 309) Clipping tips 0:00:06.997 48M / 8G INFO General (graph_simplification.hpp : 370) Removing bulges 0:00:07.023 48M / 8G INFO General (graph_simplification.hpp : 397) Removing low covered connections 0:00:07.048 48M / 8G INFO General (graph_simplification.hpp : 713) PROCEDURE == Simplification cycle, iteration 5 0:00:07.048 48M / 8G INFO General (graph_simplification.hpp : 309) Clipping tips 0:00:07.061 48M / 8G INFO General (graph_simplification.hpp : 370) Removing bulges 0:00:07.085 48M / 8G INFO General (graph_simplification.hpp : 397) Removing low covered connections 0:00:07.111 48M / 8G INFO General (graph_simplification.hpp : 713) PROCEDURE == Simplification cycle, iteration 6 0:00:07.111 48M / 8G INFO General (graph_simplification.hpp : 309) Clipping tips 0:00:07.123 48M / 8G INFO General (graph_simplification.hpp : 370) Removing bulges 0:00:07.148 48M / 8G INFO General (graph_simplification.hpp : 397) Removing low covered connections 0:00:07.171 48M / 8G INFO General (graph_simplification.hpp : 713) PROCEDURE == Simplification cycle, iteration 7 0:00:07.171 48M / 8G INFO General (graph_simplification.hpp : 309) Clipping tips 0:00:07.184 48M / 8G INFO General (graph_simplification.hpp : 370) Removing bulges 0:00:07.208 48M / 8G INFO General (graph_simplification.hpp : 397) Removing low covered connections 0:00:07.232 48M / 8G INFO General (graph_simplification.hpp : 713) PROCEDURE == Simplification cycle, iteration 8 0:00:07.232 48M / 8G INFO General (graph_simplification.hpp : 309) Clipping tips 0:00:07.245 48M / 8G INFO General (graph_simplification.hpp : 370) Removing bulges 0:00:07.268 48M / 8G INFO General (graph_simplification.hpp : 397) Removing low covered connections 0:00:07.291 48M / 8G INFO General (graph_simplification.hpp : 713) PROCEDURE == Simplification cycle, iteration 9 0:00:07.291 48M / 8G INFO General (graph_simplification.hpp : 309) Clipping tips 0:00:07.304 48M / 8G INFO General (graph_simplification.hpp : 370) Removing bulges 0:00:07.328 48M / 8G INFO General (graph_simplification.hpp : 397) Removing low covered connections 0:00:07.351 48M / 8G INFO General (graph_simplification.hpp : 713) PROCEDURE == Simplification cycle, iteration 10 0:00:07.351 48M / 8G INFO General (graph_simplification.hpp : 309) Clipping tips 0:00:07.363 48M / 8G INFO General (graph_simplification.hpp : 370) Removing bulges 0:00:07.387 48M / 8G INFO General (graph_simplification.hpp : 397) Removing low covered connections 0:00:07.410 48M / 8G INFO General (graph_simplification.hpp : 659) PROCEDURE == Post simplification 0:00:07.410 48M / 8G INFO General (graph_simplification.hpp : 665) Iteration 0 0:00:07.410 48M / 8G INFO General (graph_simplification.hpp : 471) Clipping tips based on topology 0:00:07.423 48M / 8G INFO General (graph_simplification.hpp : 447) Removal of relatively low covered connections disabled 0:00:07.423 48M / 8G INFO General (graph_simplification.hpp : 457) Removing connections based on topology 0:00:07.436 48M / 8G INFO General (graph_simplification.hpp : 513) Removing connections based on topology and reliable coverage 0:00:07.448 48M / 8G INFO General (graph_simplification.hpp : 500) Removing interstrand connections 0:00:07.475 48M / 8G INFO General (graph_simplification.hpp : 487) Removing connections based on topological multiplicity counting 0:00:07.487 48M / 8G INFO General (graph_simplification.hpp : 309) Clipping tips 0:00:07.500 48M / 8G INFO General (graph_simplification.hpp : 370) Removing bulges 0:00:07.523 48M / 8G INFO General (graph_simplification.hpp : 665) Iteration 1 0:00:07.523 48M / 8G INFO General (graph_simplification.hpp : 471) Clipping tips based on topology 0:00:07.536 48M / 8G INFO General (graph_simplification.hpp : 447) Removal of relatively low covered connections disabled 0:00:07.536 48M / 8G INFO General (graph_simplification.hpp : 457) Removing connections based on topology 0:00:07.548 48M / 8G INFO General (graph_simplification.hpp : 513) Removing connections based on topology and reliable coverage 0:00:07.561 48M / 8G INFO General (graph_simplification.hpp : 500) Removing interstrand connections 0:00:07.583 48M / 8G INFO General (graph_simplification.hpp : 487) Removing connections based on topological multiplicity counting 0:00:07.596 48M / 8G INFO General (graph_simplification.hpp : 309) Clipping tips 0:00:07.608 48M / 8G INFO General (graph_simplification.hpp : 370) Removing bulges 0:00:07.631 48M / 8G INFO General (graph_simplification.hpp : 665) Iteration 2 0:00:07.631 48M / 8G INFO General (graph_simplification.hpp : 471) Clipping tips based on topology 0:00:07.644 48M / 8G INFO General (graph_simplification.hpp : 447) Removal of relatively low covered connections disabled 0:00:07.644 48M / 8G INFO General (graph_simplification.hpp : 457) Removing connections based on topology 0:00:07.656 48M / 8G INFO General (graph_simplification.hpp : 513) Removing connections based on topology and reliable coverage 0:00:07.668 48M / 8G INFO General (graph_simplification.hpp : 500) Removing interstrand connections 0:00:07.691 48M / 8G INFO General (graph_simplification.hpp : 487) Removing connections based on topological multiplicity counting 0:00:07.703 48M / 8G INFO General (graph_simplification.hpp : 309) Clipping tips 0:00:07.716 48M / 8G INFO General (graph_simplification.hpp : 370) Removing bulges 0:00:07.739 48M / 8G INFO General (graph_simplification.hpp : 565) Removing hidden erroneous connections 0:00:07.747 48M / 8G INFO StageManager (stage.cpp : 125) STAGE == Gap Closer 0:00:07.747 48M / 8G INFO General (gap_closer.cpp : 489) Refilling index 0:00:07.747 48M / 8G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:00:07.747 48M / 8G INFO General (kmer_splitters.hpp : 285) Splitting kmer instances into 16 buckets. This might take a while. 0:00:07.747 48M / 8G INFO General (file_limit.hpp : 29) Open file limit set to 2048 0:00:07.747 48M / 8G INFO General (kmer_splitters.hpp : 308) Memory available for splitting buffers: 13.3177 Gb 0:00:07.747 48M / 8G INFO General (kmer_splitters.hpp : 314) Using cell size of 2097152 0:00:07.840 624M / 8G INFO General (kmer_splitters.hpp : 327) Processed 15882 edges 0:00:07.840 624M / 8G INFO General (kmer_splitters.hpp : 332) Used 15882 sequences. 0:00:07.842 48M / 8G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:00:07.926 48M / 8G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 801461 kmers in total. 0:00:07.926 48M / 8G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:00:07.953 48M / 8G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:00:08.125 48M / 8G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:00:08.176 48M / 8G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 277287 bytes occupied (2.76782 bits per kmer). 0:00:08.187 68M / 8G INFO General (edge_index_builders.hpp : 21) Collecting k-mer coverage information from graph, this takes a while. 0:00:08.855 68M / 8G INFO General (gap_closer.cpp : 491) Index refilled 0:00:08.855 68M / 8G INFO General (gap_closer.cpp : 492) Attaching index 0:00:08.855 68M / 8G INFO General (gap_closer.cpp : 494) Index attached 0:00:08.856 68M / 8G INFO General (gap_closer.cpp : 178) Preparing shift maps 0:00:08.870 72M / 8G INFO General (gap_closer.cpp : 132) Processing paired reads (takes a while) 0:00:09.060 72M / 8G INFO General (gap_closer.cpp : 158) Used 41206 paired reads 0:00:09.060 72M / 8G INFO General (gap_closer.cpp : 160) Merging paired indices 0:00:09.064 72M / 8G INFO GapCloser (gap_closer.cpp : 409) Closing short gaps 0:00:09.076 72M / 8G INFO GapCloser (gap_closer.cpp : 438) Closing short gaps complete: filled 0 gaps after checking 233 candidates 0:00:09.088 68M / 8G INFO General (gap_closer.cpp : 506) Detaching and clearing index 0:00:09.090 48M / 8G INFO General (gap_closer.cpp : 509) Index clearing finished 0:00:09.090 48M / 8G INFO StageManager (stage.cpp : 125) STAGE == Simplification Cleanup 0:00:09.090 48M / 8G INFO General (simplification.cpp : 71) Final isolated edges removal: 0:00:09.090 48M / 8G INFO General (simplification.cpp : 73) All edges of length smaller than 150 will be removed 0:00:09.122 44M / 8G INFO General (simplification.cpp : 77) Removed 7648 edges 0:00:09.122 44M / 8G INFO General (simplification.cpp : 97) Final index refill 0:00:09.122 44M / 8G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:00:09.122 44M / 8G INFO General (kmer_splitters.hpp : 285) Splitting kmer instances into 16 buckets. This might take a while. 0:00:09.122 44M / 8G INFO General (file_limit.hpp : 29) Open file limit set to 2048 0:00:09.122 44M / 8G INFO General (kmer_splitters.hpp : 308) Memory available for splitting buffers: 13.319 Gb 0:00:09.122 44M / 8G INFO General (kmer_splitters.hpp : 314) Using cell size of 2097152 0:00:09.136 620M / 8G INFO General (kmer_splitters.hpp : 332) Used 586 sequences. 0:00:09.137 44M / 8G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:00:09.156 44M / 8G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 103691 kmers in total. 0:00:09.156 44M / 8G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:00:09.164 44M / 8G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:00:09.184 44M / 8G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:00:09.246 44M / 8G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 35907 bytes occupied (2.77031 bits per kmer). 0:00:09.247 44M / 8G INFO General (edge_index_builders.hpp : 21) Collecting k-mer coverage information from graph, this takes a while. 0:00:09.325 44M / 8G INFO General (simplification.cpp : 99) Final index refill finished 0:00:09.325 44M / 8G INFO General (simplification.cpp : 106) Counting average coverage 0:00:09.325 44M / 8G INFO General (simplification.cpp : 109) Average coverage = 23.2499 0:00:09.325 44M / 8G INFO StageManager (stage.cpp : 125) STAGE == Mismatch Correction 0:00:09.857 48M / 8G INFO General (mismatch_shall_not_pass.hp: 188) Finished collecting potential mismatches positions 0:00:09.864 44M / 8G INFO General (mismatch_shall_not_pass.hp: 291) All edges processed 0:00:09.864 44M / 8G INFO General (mismatch_correction.cpp : 17) Corrected 1 nucleotides 0:00:09.864 44M / 8G INFO StageManager (stage.cpp : 125) STAGE == Paired Information Counting 0:00:09.865 44M / 8G INFO General (pair_info_count.cpp : 174) Estimating insert size for library #0 0:00:09.865 44M / 8G INFO General (pair_info_count.cpp : 82) Estimating insert size (takes a while) 0:00:09.866 44M / 8G INFO General (short_read_mapper.hpp : 93) Read length = 150, selecting usual mapper 0:00:09.874 44M / 8G INFO General (pair_info_count.cpp : 86) 2315 paired reads (11.2362% of all) aligned to long edges 0:00:09.875 44M / 8G INFO General (pair_info_count.cpp : 199) Estimated insert size for paired library #0 0:00:09.875 44M / 8G INFO General (pair_info_count.cpp : 204) Insert size = 427.554, deviation = 104.989, left quantile = 275, right quantile = 533, read length = 150 0:00:09.875 44M / 8G INFO General (pair_info_count.cpp : 224) Mapping library #0 0:00:09.875 44M / 8G INFO General (pair_info_count.cpp : 226) Mapping paired reads (takes a while) 0:00:09.875 44M / 8G INFO General (pair_info_count.cpp : 127) Left insert size qauntile 275, right insert size quantile 533 0:00:09.876 44M / 8G INFO General (short_read_mapper.hpp : 93) Read length = 150, selecting usual mapper 0:00:10.264 48M / 8G INFO General (split_graph_pair_info.hpp : 345) Threshold for paired information 0.0344887 0:00:10.266 48M / 8G INFO StageManager (stage.cpp : 125) STAGE == Distance Estimation 0:00:10.266 48M / 8G INFO General (distance_estimation.cpp : 242) Processing library #0 0:00:10.267 48M / 8G INFO General (distance_estimation.cpp : 145) Weight Filter Done 0:00:10.267 48M / 8G INFO DistanceEstimator (distance_estimation.hpp : 226) Using SIMPLE distance estimator 0:00:10.278 48M / 8G INFO General (distance_estimation.cpp : 40) Filtering info 0:00:10.280 48M / 8G INFO General (pair_info_filters.hpp : 352) Pruning the index 0:00:10.280 48M / 8G INFO General (distance_estimation.cpp : 193) Refining clustered pair information 0:00:10.280 48M / 8G INFO General (distance_estimation.cpp : 195) The refining of clustered pair information has been finished 0:00:10.280 48M / 8G INFO General (distance_estimation.cpp : 197) Filling paired information 0:00:10.333 48M / 8G INFO PairInfoImprover (pair_info_improver.hpp : 58) Paired info stats: missing = 202; contradictional = 0 0:00:10.389 48M / 8G INFO PairInfoImprover (pair_info_improver.hpp : 58) Paired info stats: missing = 0; contradictional = 0 0:00:10.389 48M / 8G INFO General (distance_estimation.cpp : 202) Filling scaffolding index 0:00:10.389 48M / 8G INFO DistanceEstimator (distance_estimation.hpp : 226) Using SMOOTHING distance estimator 0:00:21.764 48M / 8G INFO General (distance_estimation.cpp : 40) Filtering info 0:00:21.764 48M / 8G INFO General (pair_info_filters.hpp : 352) Pruning the index 0:00:21.764 48M / 8G INFO StageManager (stage.cpp : 125) STAGE == Repeat Resolving 0:00:21.764 48M / 8G INFO General (contig_output.hpp : 295) Outputting contigs to /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/spades//K55/simplified_contigs.fasta 0:00:21.790 48M / 8G INFO General (contig_output.hpp : 295) Outputting contigs to /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/spades//K55/before_rr.fasta 0:00:21.815 48M / 8G INFO General (repeat_resolving.cpp : 103) Using Path-Extend repeat resolving 0:00:21.843 48M / 8G INFO General (path_extend_launch.hpp : 413) Threshold for library #0 is 0.0344887 0:00:21.843 48M / 8G INFO General (path_extend_launch.hpp : 222) Path-Extend repeat resolving tool started 0:00:21.843 48M / 8G INFO General (path_extend_launch.hpp : 230) Using 1 paired-end library 0:00:21.843 48M / 8G INFO General (path_extend_launch.hpp : 231) Using 1 paired-end scaffolding library 0:00:21.843 48M / 8G INFO General (path_extend_launch.hpp : 232) Using 0 mate-pair libraries 0:00:21.843 48M / 8G INFO General (path_extend_launch.hpp : 233) Using 1 single read library 0:00:21.843 48M / 8G INFO General (path_extend_launch.hpp : 234) Scaffolder is on 0:00:21.844 48M / 8G INFO General (path_extend_launch.hpp : 258) Growing paths using paired-end and long single reads 0:00:21.882 48M / 8G INFO PathExtendIO (pe_io.hpp : 272) Constructing FASTG file from paths 0:00:21.883 48M / 8G INFO PathExtendIO (pe_io.hpp : 275) Writing contigs in FASTG to /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/spades//K55/final_contigs.fastg 0:00:21.883 48M / 8G INFO PathExtendIO (pe_io.hpp : 276) Writing contigs in FASTA to /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/spades//K55/final_contigs.fasta 0:00:21.908 48M / 8G INFO General (path_extend_launch.hpp : 278) Traversing tandem repeats 0:00:21.910 48M / 8G INFO PathExtendIO (pe_io.hpp : 272) Constructing FASTG file from paths 0:00:21.911 48M / 8G INFO PathExtendIO (pe_io.hpp : 275) Writing contigs in FASTG to /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/spades//K55/scaffolds.fastg 0:00:21.911 48M / 8G INFO PathExtendIO (pe_io.hpp : 276) Writing contigs in FASTA to /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/spades//K55/scaffolds.fasta 0:00:21.955 48M / 8G INFO General (launch.hpp : 84) SPAdes finished 0:00:21.980 36M / 8G INFO General (main.cpp : 166) Assembling time: 0 hours 0 minutes 21 seconds ===== Assembling finished. ===== Mismatch correction started. == Processing of contigs Config: {'skip_masked': 1, 'contigs': '/global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/spades/misc/assembled_contigs.fasta', 'use_multiple_aligned': 0, 'reads2': ['/global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/spades/corrected/ZHYY.8454.1.101266.CGTAC.anqdp.bbqc.norm_2.00.0_0.cor.fastq.gz'], 'make_latest_symlink': False, 'use_quality': 0, 'bwa': '/global/common/genepool/jgi/assemblers/spades/3.0.0_1/bin/bwa-spades', 'reads1': ['/global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/spades/corrected/ZHYY.8454.1.101266.CGTAC.anqdp.bbqc.norm_1.00.0_0.cor.fastq.gz'], 'output_dirpath': '/global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/spades/tmp/mis_cor_contigs_C_9G46', 't': 8, 'debug': 0, 'mate_weight': 1.0, 'work_dir': '/global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/spades/tmp/mis_cor_contigs_C_9G46/mismatch_corrector_tmp', 'insert_size': 428} no sam file, running aligner running bwa [bwa_index] Pack FASTA... 0.00 sec [bwa_index] Construct BWT for the packed sequence... [bwa_index] 0.02 seconds elapse. [bwa_index] Update BWT... 0.00 sec [bwa_index] Pack forward-only FASTA... 0.00 sec [bwa_index] Construct SA from BWT and Occ... 0.01 sec [main] Version: 0.6.2-r126 [main] CMD: /global/common/genepool/jgi/assemblers/spades/3.0.0_1/bin/bwa-spades index -a is /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/spades/tmp/mis_cor_contigs_C_9G46/mismatch_corrector_tmp/assembled_contigs.fasta 2 [main] Real time: 0.045 sec; CPU: 0.045 sec [bwa_aln] 17bp reads: max_diff = 1 [bwa_aln] 24bp reads: max_diff = 2 [bwa_aln] 50bp reads: max_diff = 3 [bwa_aln] 81bp reads: max_diff = 4 [bwa_aln] 114bp reads: max_diff = 5 [bwa_aln] 149bp reads: max_diff = 6 [bwa_aln] 184bp reads: max_diff = 7 [bwa_aln] 221bp reads: max_diff = 8 [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 3.46 sec [bwa_aln_core] write to the disk... 0.01 sec [bwa_aln_core] 20603 sequences have been processed. [main] Version: 0.6.2-r126 [main] CMD: /global/common/genepool/jgi/assemblers/spades/3.0.0_1/bin/bwa-spades aln -t 8 -O 7 -E 2 -k 3 -n 0.08 -q 15 /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/spades/tmp/mis_cor_contigs_C_9G46/mismatch_corrector_tmp/assembled_contigs.fasta /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/spades/corrected/ZHYY.8454.1.101266.CGTAC.anqdp.bbqc.norm_1.00.0_0.cor.fastq.gz [main] Real time: 0.578 sec; CPU: 3.571 sec [bwa_aln] 17bp reads: max_diff = 1 [bwa_aln] 24bp reads: max_diff = 2 [bwa_aln] 50bp reads: max_diff = 3 [bwa_aln] 81bp reads: max_diff = 4 [bwa_aln] 114bp reads: max_diff = 5 [bwa_aln] 149bp reads: max_diff = 6 [bwa_aln] 184bp reads: max_diff = 7 [bwa_aln] 221bp reads: max_diff = 8 [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 3.34 sec [bwa_aln_core] write to the disk... 0.00 sec [bwa_aln_core] 20603 sequences have been processed. [main] Version: 0.6.2-r126 [main] CMD: /global/common/genepool/jgi/assemblers/spades/3.0.0_1/bin/bwa-spades aln -t 8 -O 7 -E 2 -k 3 -n 0.08 -q 15 /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/spades/tmp/mis_cor_contigs_C_9G46/mismatch_corrector_tmp/assembled_contigs.fasta /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/spades/corrected/ZHYY.8454.1.101266.CGTAC.anqdp.bbqc.norm_2.00.0_0.cor.fastq.gz [main] Real time: 0.610 sec; CPU: 3.442 sec contigs were split, starting splitting .sam file file /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/spades/tmp/mis_cor_contigs_C_9G46/mismatch_corrector_tmp/tmp.sam opened dropping cashed lines... .sam file was split concatenating /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/spades/tmp/mis_cor_contigs_C_9G46/mismatch_corrector_tmp/*.ref.fasta INTO /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/spades/tmp/mis_cor_contigs_C_9G46/corrected_contigs.fasta TOTAL - replaced: 1050 deleted: 36 inserted: 5 == Processing of scaffolds Config: {'skip_masked': 1, 'contigs': '/global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/spades/misc/assembled_scaffolds.fasta', 'use_multiple_aligned': 0, 'reads2': ['/global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/spades/corrected/ZHYY.8454.1.101266.CGTAC.anqdp.bbqc.norm_2.00.0_0.cor.fastq.gz'], 'make_latest_symlink': False, 'use_quality': 0, 'bwa': '/global/common/genepool/jgi/assemblers/spades/3.0.0_1/bin/bwa-spades', 'reads1': ['/global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/spades/corrected/ZHYY.8454.1.101266.CGTAC.anqdp.bbqc.norm_1.00.0_0.cor.fastq.gz'], 'output_dirpath': '/global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/spades/tmp/mis_cor_scaffolds_8xf0Uq', 't': 8, 'debug': 0, 'mate_weight': 1.0, 'work_dir': '/global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/spades/tmp/mis_cor_scaffolds_8xf0Uq/mismatch_corrector_tmp', 'insert_size': 428} no sam file, running aligner running bwa [bwa_index] Pack FASTA... 0.00 sec [bwa_index] Construct BWT for the packed sequence... [bwa_index] 0.02 seconds elapse. [bwa_index] Update BWT... 0.00 sec [bwa_index] Pack forward-only FASTA... 0.00 sec [bwa_index] Construct SA from BWT and Occ... 0.01 sec [main] Version: 0.6.2-r126 [main] CMD: /global/common/genepool/jgi/assemblers/spades/3.0.0_1/bin/bwa-spades index -a is /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/spades/tmp/mis_cor_scaffolds_8xf0Uq/mismatch_corrector_tmp/assembled_scaffolds.fasta 2 [main] Real time: 0.049 sec; CPU: 0.045 sec [bwa_aln] 17bp reads: max_diff = 1 [bwa_aln] 24bp reads: max_diff = 2 [bwa_aln] 50bp reads: max_diff = 3 [bwa_aln] 81bp reads: max_diff = 4 [bwa_aln] 114bp reads: max_diff = 5 [bwa_aln] 149bp reads: max_diff = 6 [bwa_aln] 184bp reads: max_diff = 7 [bwa_aln] 221bp reads: max_diff = 8 [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 3.47 sec [bwa_aln_core] write to the disk... 0.00 sec [bwa_aln_core] 20603 sequences have been processed. [main] Version: 0.6.2-r126 [main] CMD: /global/common/genepool/jgi/assemblers/spades/3.0.0_1/bin/bwa-spades aln -t 8 -O 7 -E 2 -k 3 -n 0.08 -q 15 /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/spades/tmp/mis_cor_scaffolds_8xf0Uq/mismatch_corrector_tmp/assembled_scaffolds.fasta /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/spades/corrected/ZHYY.8454.1.101266.CGTAC.anqdp.bbqc.norm_1.00.0_0.cor.fastq.gz [main] Real time: 0.581 sec; CPU: 3.568 sec [bwa_aln] 17bp reads: max_diff = 1 [bwa_aln] 24bp reads: max_diff = 2 [bwa_aln] 50bp reads: max_diff = 3 [bwa_aln] 81bp reads: max_diff = 4 [bwa_aln] 114bp reads: max_diff = 5 [bwa_aln] 149bp reads: max_diff = 6 [bwa_aln] 184bp reads: max_diff = 7 [bwa_aln] 221bp reads: max_diff = 8 [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 3.34 sec [bwa_aln_core] write to the disk... 0.00 sec [bwa_aln_core] 20603 sequences have been processed. [main] Version: 0.6.2-r126 [main] CMD: /global/common/genepool/jgi/assemblers/spades/3.0.0_1/bin/bwa-spades aln -t 8 -O 7 -E 2 -k 3 -n 0.08 -q 15 /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/spades/tmp/mis_cor_scaffolds_8xf0Uq/mismatch_corrector_tmp/assembled_scaffolds.fasta /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/spades/corrected/ZHYY.8454.1.101266.CGTAC.anqdp.bbqc.norm_2.00.0_0.cor.fastq.gz [main] Real time: 0.578 sec; CPU: 3.442 sec contigs were split, starting splitting .sam file file /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/spades/tmp/mis_cor_scaffolds_8xf0Uq/mismatch_corrector_tmp/tmp.sam opened dropping cashed lines... .sam file was split concatenating /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/spades/tmp/mis_cor_scaffolds_8xf0Uq/mismatch_corrector_tmp/*.ref.fasta INTO /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/spades/tmp/mis_cor_scaffolds_8xf0Uq/corrected_contigs.fasta TOTAL - replaced: 1050 deleted: 36 inserted: 5 ===== Mismatch correction finished. * Corrected reads are in /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/spades/corrected/ * Assembled contigs are in /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/spades/contigs.fasta (contigs.fastg) * Assembled scaffolds are in /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/spades/scaffolds.fasta (scaffolds.fastg) ======= SPAdes pipeline finished. SPAdes log can be found here: /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/spades/spades.log Thank you for using SPAdes!