Command line: /usr/common/jgi/assemblers/spades/3.0.0_1/bin/spades.py -o /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZH/spades --phred-offset 33 -t 16 -m 120 --sc --careful --12 /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZH/ZHZH.15M.bbqc.fq.gz.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/ZHZH/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/ZHZH/ZHZH.15M.bbqc.fq.gz.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/ZHZH/spades/tmp Threads: 16 Memory limit (in Gb): 120 ======= SPAdes pipeline started. Log can be found here: /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZH/spades/spades.log == Splitting /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZH/ZHZH.15M.bbqc.fq.gz.fastq into left and right reads (in /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZH/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/ZHZH/spades/corrected/configs/config.info 0:00:00.002 4M / 4M INFO General (main.cpp : 82) Loading config from /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZH/spades/corrected/configs/config.info 0:00:00.005 4M / 4M INFO General (memory_limit.hpp : 29) Memory limit set to 120 Gb 0:00:00.006 4M / 4M INFO General (hammer_tools.cpp : 49) Hamming graph threshold tau=1, k=21, subkmer positions = [ 0 10 ] === ITERATION 0 begins === 0:00:00.006 4M / 4M INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:00:00.006 4M / 4M INFO K-mer Splitting (kmer_data.cpp : 127) Splitting kmer instances into 256 buckets. This might take a while. 0:00:00.007 4M / 4M INFO General (file_limit.hpp : 29) Open file limit set to 2048 0:00:00.007 4M / 4M INFO K-mer Splitting (kmer_data.cpp : 150) Memory available for splitting buffers: 2.49992 Gb 0:00:00.007 4M / 4M INFO K-mer Splitting (kmer_data.cpp : 159) Using cell size of 262144 0:00:00.458 8G / 8G INFO K-mer Splitting (kmer_data.cpp : 181) Processed 50156 reads 0:00:00.714 8G / 8G INFO K-mer Splitting (kmer_data.cpp : 181) Processed 100312 reads 0:00:00.714 8G / 8G INFO K-mer Splitting (kmer_data.cpp : 186) Processed 100312 reads 0:00:00.781 64M / 8G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:00:00.883 64M / 8G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 752730 kmers in total. 0:00:00.883 64M / 8G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:00:00.958 64M / 8G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:00:00.991 64M / 8G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:00:01.030 64M / 8G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 260443 bytes occupied (2.76798 bits per kmer). 0:00:01.030 64M / 8G INFO K-mer Counting (kmer_data.cpp : 267) Arranging kmers in hash map order 0:00:01.207 64M / 8G INFO K-mer Counting (kmer_data.cpp : 280) Done. Total swaps: 752539 0:00:01.211 72M / 8G INFO General (main.cpp : 151) Clustering Hamming graph. 0:00:01.211 72M / 8G INFO Hamming Clustering (hamcluster.cpp : 115) Serializing sub-kmers. 0:00:01.211 72M / 8G INFO Hamming Clustering (hamcluster.cpp : 120) Serializing: [0, 10) 0:00:01.329 72M / 8G INFO Hamming Clustering (hamcluster.cpp : 120) Serializing: [10, 21) 0:00:01.447 72M / 8G INFO Hamming Clustering (hamcluster.cpp : 129) Splitting sub-kmers, pass 1. 0:00:01.728 72M / 8G INFO Hamming Clustering (hamcluster.cpp : 134) Splitting done. Processed 2 blocks. Produced 842789 blocks. 0:00:01.728 72M / 8G INFO Hamming Clustering (hamcluster.cpp : 145) Merge sub-kmers, pass 1 0:00:02.026 72M / 8G INFO Hamming Clustering (hamcluster.cpp : 170) Merge done, total 633 new blocks generated. 0:00:02.030 72M / 8G INFO Hamming Clustering (hamcluster.cpp : 175) Spliting sub-kmers, pass 2. 0:00:02.054 72M / 8G INFO Hamming Clustering (hamcluster.cpp : 180) Splitting done. Processed 1266 blocks. Produced 51372 blocks. 0:00:02.054 72M / 8G INFO Hamming Clustering (hamcluster.cpp : 187) Merge sub-kmers, pass 2 0:00:02.103 72M / 8G INFO Hamming Clustering (hamcluster.cpp : 205) Merge done, saw 20 big blocks out of 51372 processed. 0:00:02.306 72M / 8G INFO General (main.cpp : 165) Clustering done. Total clusters: 509157 0:00:02.306 72M / 8G INFO K-mer Counting (kmer_data.cpp : 285) Collecting K-mer information, this takes a while. 0:00:02.876 108M / 8G INFO K-mer Counting (kmer_data.cpp : 297) Collection done, postprocessing. 0:00:02.889 108M / 8G INFO K-mer Counting (kmer_data.cpp : 310) There are 752730 kmers in total. Among them 418174 (55.5543%) are singletons. 0:00:02.889 108M / 8G INFO General (main.cpp : 203) Subclustering Hamming graph 0:00:03.099 108M / 8G INFO Hamming Subclustering (kmer_cluster.cpp : 654) Subclustering done. Total 0 non-read kmers were generated. 0:00:03.099 108M / 8G INFO Hamming Subclustering (kmer_cluster.cpp : 655) Subclustering statistics: 0:00:03.099 108M / 8G INFO Hamming Subclustering (kmer_cluster.cpp : 656) Total singleton hamming clusters: 427432. Among them 296990 (69.4824%) are good 0:00:03.099 108M / 8G INFO Hamming Subclustering (kmer_cluster.cpp : 657) Total singleton subclusters: 2519. Among them 2519 (100%) are good 0:00:03.099 108M / 8G INFO Hamming Subclustering (kmer_cluster.cpp : 658) Total non-singleton subcluster centers: 81568. Among them 57232 (70.1648%) are good 0:00:03.099 108M / 8G INFO Hamming Subclustering (kmer_cluster.cpp : 659) Average size of non-trivial subcluster: 3.98806 kmers 0:00:03.099 108M / 8G INFO Hamming Subclustering (kmer_cluster.cpp : 660) Average number of sub-clusters per non-singleton cluster: 1.0289 0:00:03.099 108M / 8G INFO Hamming Subclustering (kmer_cluster.cpp : 661) Total solid k-mers: 356741 0:00:03.099 108M / 8G INFO Hamming Subclustering (kmer_cluster.cpp : 662) Substitution probabilities: [4,4]((0.931305,0.0210993,0.0260921,0.0215039),(0.0198416,0.946305,0.0126896,0.0211639),(0.0208095,0.0125724,0.946466,0.0201523),(0.0213557,0.0258779,0.0208998,0.931867)) 0:00:03.100 108M / 8G INFO General (main.cpp : 208) Finished clustering. 0:00:03.100 108M / 8G INFO General (main.cpp : 228) Starting solid k-mers expansion in 16 threads. 0:00:03.399 108M / 8G INFO General (main.cpp : 249) Solid k-mers iteration 0 produced 26971 new k-mers. 0:00:03.691 108M / 8G INFO General (main.cpp : 249) Solid k-mers iteration 1 produced 973 new k-mers. 0:00:03.983 108M / 8G INFO General (main.cpp : 249) Solid k-mers iteration 2 produced 81 new k-mers. 0:00:04.275 108M / 8G INFO General (main.cpp : 249) Solid k-mers iteration 3 produced 0 new k-mers. 0:00:04.275 108M / 8G INFO General (main.cpp : 253) Solid k-mers finalized 0:00:04.276 108M / 8G INFO General (hammer_tools.cpp : 223) Starting read correction in 16 threads. 0:00:04.276 108M / 8G INFO General (hammer_tools.cpp : 235) Correcting pair of reads: /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZH/spades/split_input/ZHZH.15M.bbqc.fq.gz_1.fastq and /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZH/spades/split_input/ZHZH.15M.bbqc.fq.gz_2.fastq 0:00:04.616 280M / 8G INFO General (hammer_tools.cpp : 179) Prepared batch 0 of 50156 reads. 0:00:04.836 280M / 8G INFO General (hammer_tools.cpp : 188) Processed batch 0 0:00:05.154 280M / 8G INFO General (hammer_tools.cpp : 198) Written batch 0 0:00:05.213 108M / 8G INFO General (hammer_tools.cpp : 282) Correction done. Changed 10009 bases in 9578 reads. 0:00:05.213 108M / 8G INFO General (hammer_tools.cpp : 283) Failed to correct 707075 bases out of 15000031. 0:00:05.216 72M / 8G INFO General (main.cpp : 286) Saving corrected dataset description to /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZH/spades/corrected/corrected.yaml 0:00:05.227 72M / 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/ZHZH/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 120 Gb 0:00:00.001 4M / 4M INFO General (main.cpp : 146) Assembling dataset (/global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZH/spades/dataset.info) with K=21 0:00:00.001 4M / 4M INFO General (launch.hpp : 28) SPAdes started 0:00:00.001 4M / 4M INFO General (launch.hpp : 29) Starting from stage: construction 0:00:00.002 4M / 4M INFO StageManager (stage.cpp : 125) STAGE == Construction 0:00:00.005 4M / 4M INFO General (read_converter.hpp : 79) Converting reads to binary format (takes a while) 0:00:00.005 4M / 4M INFO General (read_converter.hpp : 81) Paired reads for library #0 0:00:00.330 80M / 80M INFO General (binary_converter.hpp : 138) 16384 reads processed 0:00:00.501 96M / 96M INFO General (binary_converter.hpp : 138) 32768 reads processed 0:00:00.748 112M / 112M INFO General (binary_converter.hpp : 158) 50100 reads written 0:00:00.794 4M / 112M INFO General (read_converter.hpp : 91) Single reads for library #0 0:00:00.919 132M / 140M INFO General (binary_converter.hpp : 158) 56 reads written 0:00:00.935 4M / 140M INFO General (graph_construction.hpp : 127) Constructing DeBruijn graph for k=21 0:00:00.959 4M / 140M INFO General (kmer_splitters.hpp : 164) Splitting kmer instances into 256 buckets. This might take a while. 0:00:00.959 4M / 140M INFO General (file_limit.hpp : 29) Open file limit set to 2048 0:00:00.959 4M / 140M INFO General (kmer_splitters.hpp : 187) Memory available for splitting buffers: 2.49992 Gb 0:00:00.959 4M / 140M INFO General (kmer_splitters.hpp : 197) Using cell size of 262144 0:00:01.373 8G / 8G INFO General (kmer_splitters.hpp : 225) Processed 200512 reads 0:00:01.373 8G / 8G INFO General (kmer_splitters.hpp : 231) Adding contigs from previous K 0:00:01.373 8G / 8G INFO General (kmer_splitters.hpp : 242) Used 200512 reads. Maximum read length 150 0:00:01.439 64M / 8G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:00:01.491 64M / 8G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 313431 kmers in total. 0:00:01.492 64M / 8G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:00:01.593 64M / 8G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:00:01.593 64M / 8G INFO General (kmer_splitters.hpp : 381) Splitting kmer instances into 256 buckets. This might take a while. 0:00:01.593 64M / 8G INFO General (file_limit.hpp : 29) Open file limit set to 2048 0:00:01.593 64M / 8G INFO General (kmer_splitters.hpp : 404) Memory available for splitting buffers: 2.4987 Gb 0:00:01.593 64M / 8G INFO General (kmer_splitters.hpp : 413) Using cell size of 262144 0:00:01.735 8G / 8G INFO General (kmer_splitters.hpp : 436) Processed 313431 kmers 0:00:01.735 8G / 8G INFO General (kmer_splitters.hpp : 445) Used 313431 kmers. 0:00:01.777 64M / 8G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:00:01.829 64M / 8G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 309378 kmers in total. 0:00:01.829 64M / 8G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:00:01.893 64M / 8G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:00:01.911 64M / 8G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:00:02.132 64M / 8G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 107066 bytes occupied (2.76855 bits per kmer). 0:00:02.132 64M / 8G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 382) Building k-mer extensions from k+1-mers 0:00:02.158 64M / 8G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 386) Building k-mer extensions from k+1-mers finished. 0:00:02.159 64M / 8G INFO Early tip clipping (early_simplification.hpp : 236) Early tip clipping 0:00:02.447 64M / 8G INFO Early tip clipping (early_simplification.hpp : 239) 40783 22-mers were removed by early tip clipper 0:00:02.447 64M / 8G INFO General (graph_construction.hpp : 143) Condensing graph 0:00:02.447 64M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 346) Extracting unbranching paths 0:00:02.540 68M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 360) Extracting unbranching paths finished. 23538 sequences extracted 0:00:02.550 64M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 320) Collecting perfect loops 0:00:02.596 64M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 335) Collecting perfect loops finished. 0 loops collected 0:00:02.620 64M / 8G INFO General (graph_construction.hpp : 151) Building index with coverage from graph 0:00:02.620 64M / 8G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:00:02.621 64M / 8G INFO General (kmer_splitters.hpp : 285) Splitting kmer instances into 16 buckets. This might take a while. 0:00:02.621 64M / 8G INFO General (file_limit.hpp : 29) Open file limit set to 2048 0:00:02.621 64M / 8G INFO General (kmer_splitters.hpp : 308) Memory available for splitting buffers: 39.9792 Gb 0:00:02.621 64M / 8G INFO General (kmer_splitters.hpp : 314) Using cell size of 4194304 0:00:02.714 640M / 8G INFO General (kmer_splitters.hpp : 327) Processed 23538 edges 0:00:02.714 640M / 8G INFO General (kmer_splitters.hpp : 332) Used 23538 sequences. 0:00:02.715 64M / 8G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:00:02.741 64M / 8G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 272648 kmers in total. 0:00:02.741 64M / 8G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:00:02.750 64M / 8G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:00:02.802 64M / 8G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:00:02.856 64M / 8G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 94358 bytes occupied (2.76864 bits per kmer). 0:00:02.859 72M / 8G INFO General (edge_index_builders.hpp : 21) Collecting k-mer coverage information from graph, this takes a while. 0:00:03.011 72M / 8G INFO General (edge_index_builders.hpp : 99) Collecting k-mer coverage information from reads, this takes a while. 0:00:03.398 72M / 8G INFO General (graph_construction.hpp : 179) Filling coverage and flanking coverage from index 0:00:03.408 72M / 8G INFO General (construction.cpp : 32) Figured out: read length = 150 0:00:03.409 72M / 8G INFO StageManager (stage.cpp : 125) STAGE == EC Threshold Finding 0:00:03.418 72M / 8G INFO ThresholdFinder (omni_tools.hpp : 466) Bucket size: 19 0:00:03.418 72M / 8G INFO General (genomic_info_filler.cpp : 72) Average edge coverage: 47.448 0:00:03.418 72M / 8G INFO General (genomic_info_filler.cpp : 73) Graph threshold: 50 0:00:03.508 76M / 8G INFO General (genomic_info_filler.cpp : 101) EC coverage threshold value was calculated as 50 0:00:03.508 76M / 8G INFO StageManager (stage.cpp : 125) STAGE == Simplification 0:00:03.513 76M / 8G INFO General (graph_simplification.hpp : 633) PROCEDURE == Presimplification 0:00:03.514 76M / 8G INFO General (graph_simplification.hpp : 416) Removing short low covered self-conjugate connections 0:00:03.547 76M / 8G INFO General (graph_simplification.hpp : 713) PROCEDURE == Simplification cycle, iteration 1 0:00:03.548 76M / 8G INFO General (graph_simplification.hpp : 309) Clipping tips 0:00:03.572 76M / 8G INFO General (graph_simplification.hpp : 370) Removing bulges 0:00:04.574 76M / 8G INFO General (graph_simplification.hpp : 397) Removing low covered connections 0:00:05.246 76M / 8G INFO General (graph_simplification.hpp : 713) PROCEDURE == Simplification cycle, iteration 2 0:00:05.246 76M / 8G INFO General (graph_simplification.hpp : 309) Clipping tips 0:00:05.272 76M / 8G INFO General (graph_simplification.hpp : 370) Removing bulges 0:00:05.370 76M / 8G INFO General (graph_simplification.hpp : 397) Removing low covered connections 0:00:05.416 76M / 8G INFO General (graph_simplification.hpp : 713) PROCEDURE == Simplification cycle, iteration 3 0:00:05.416 76M / 8G INFO General (graph_simplification.hpp : 309) Clipping tips 0:00:05.417 76M / 8G INFO General (graph_simplification.hpp : 370) Removing bulges 0:00:05.442 76M / 8G INFO General (graph_simplification.hpp : 397) Removing low covered connections 0:00:05.450 76M / 8G INFO General (graph_simplification.hpp : 713) PROCEDURE == Simplification cycle, iteration 4 0:00:05.450 76M / 8G INFO General (graph_simplification.hpp : 309) Clipping tips 0:00:05.451 76M / 8G INFO General (graph_simplification.hpp : 370) Removing bulges 0:00:05.465 76M / 8G INFO General (graph_simplification.hpp : 397) Removing low covered connections 0:00:05.478 76M / 8G INFO General (graph_simplification.hpp : 713) PROCEDURE == Simplification cycle, iteration 5 0:00:05.478 76M / 8G INFO General (graph_simplification.hpp : 309) Clipping tips 0:00:05.479 76M / 8G INFO General (graph_simplification.hpp : 370) Removing bulges 0:00:05.490 76M / 8G INFO General (graph_simplification.hpp : 397) Removing low covered connections 0:00:05.498 76M / 8G INFO General (graph_simplification.hpp : 713) PROCEDURE == Simplification cycle, iteration 6 0:00:05.498 76M / 8G INFO General (graph_simplification.hpp : 309) Clipping tips 0:00:05.499 76M / 8G INFO General (graph_simplification.hpp : 370) Removing bulges 0:00:05.508 76M / 8G INFO General (graph_simplification.hpp : 397) Removing low covered connections 0:00:05.510 76M / 8G INFO General (graph_simplification.hpp : 713) PROCEDURE == Simplification cycle, iteration 7 0:00:05.510 76M / 8G INFO General (graph_simplification.hpp : 309) Clipping tips 0:00:05.510 76M / 8G INFO General (graph_simplification.hpp : 370) Removing bulges 0:00:05.517 76M / 8G INFO General (graph_simplification.hpp : 397) Removing low covered connections 0:00:05.533 76M / 8G INFO General (graph_simplification.hpp : 713) PROCEDURE == Simplification cycle, iteration 8 0:00:05.533 76M / 8G INFO General (graph_simplification.hpp : 309) Clipping tips 0:00:05.534 76M / 8G INFO General (graph_simplification.hpp : 370) Removing bulges 0:00:05.540 76M / 8G INFO General (graph_simplification.hpp : 397) Removing low covered connections 0:00:05.550 76M / 8G INFO General (graph_simplification.hpp : 713) PROCEDURE == Simplification cycle, iteration 9 0:00:05.550 76M / 8G INFO General (graph_simplification.hpp : 309) Clipping tips 0:00:05.551 76M / 8G INFO General (graph_simplification.hpp : 370) Removing bulges 0:00:05.556 76M / 8G INFO General (graph_simplification.hpp : 397) Removing low covered connections 0:00:05.558 76M / 8G INFO General (graph_simplification.hpp : 713) PROCEDURE == Simplification cycle, iteration 10 0:00:05.558 76M / 8G INFO General (graph_simplification.hpp : 309) Clipping tips 0:00:05.559 76M / 8G INFO General (graph_simplification.hpp : 370) Removing bulges 0:00:05.564 76M / 8G INFO General (graph_simplification.hpp : 397) Removing low covered connections 0:00:05.565 76M / 8G INFO General (graph_simplification.hpp : 659) PROCEDURE == Post simplification 0:00:05.565 76M / 8G INFO General (graph_simplification.hpp : 665) Iteration 0 0:00:05.565 76M / 8G INFO General (graph_simplification.hpp : 471) Clipping tips based on topology 0:00:05.566 76M / 8G INFO General (graph_simplification.hpp : 447) Removal of relatively low covered connections disabled 0:00:05.567 76M / 8G INFO General (graph_simplification.hpp : 309) Clipping tips 0:00:05.567 76M / 8G INFO General (graph_simplification.hpp : 370) Removing bulges 0:00:05.572 76M / 8G INFO General (graph_simplification.hpp : 565) Removing hidden erroneous connections 0:00:05.619 76M / 8G INFO StageManager (stage.cpp : 125) STAGE == Simplification Cleanup 0:00:05.619 76M / 8G INFO General (simplification.cpp : 71) Final isolated edges removal: 0:00:05.619 76M / 8G INFO General (simplification.cpp : 73) All edges of length smaller than 150 will be removed 0:00:05.630 76M / 8G INFO General (simplification.cpp : 77) Removed 147 edges 0:00:05.630 76M / 8G INFO General (simplification.cpp : 106) Counting average coverage 0:00:05.630 76M / 8G INFO General (simplification.cpp : 109) Average coverage = 77.2694 0:00:05.630 76M / 8G INFO StageManager (stage.cpp : 125) STAGE == Contig Output 0:00:05.631 76M / 8G INFO General (contig_output.hpp : 295) Outputting contigs to /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZH/spades//K21/simplified_contigs.fasta 0:00:05.654 76M / 8G INFO General (contig_output.hpp : 295) Outputting contigs to /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZH/spades//K21/before_rr.fasta 0:00:05.689 76M / 8G INFO General (contig_output.hpp : 295) Outputting contigs to /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZH/spades//K21/final_contigs.fasta 0:00:05.724 76M / 8G INFO General (launch.hpp : 84) SPAdes finished 0:00:05.727 64M / 8G INFO General (main.cpp : 166) Assembling time: 0 hours 0 minutes 5 seconds == Running assembler: K33 0:00:00.000 4M / 4M INFO General (memory_limit.hpp : 29) Memory limit set to 120 Gb 0:00:00.000 4M / 4M INFO General (main.cpp : 146) Assembling dataset (/global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZH/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 0:00:00.002 4M / 4M INFO General (kmer_splitters.hpp : 164) Splitting kmer instances into 256 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: 2.49992 Gb 0:00:00.002 4M / 4M INFO General (kmer_splitters.hpp : 197) Using cell size of 131072 0:00:00.302 8G / 8G INFO General (kmer_splitters.hpp : 225) Processed 200512 reads 0:00:00.302 8G / 8G INFO General (kmer_splitters.hpp : 231) Adding contigs from previous K 0:00:00.350 8G / 8G INFO General (kmer_splitters.hpp : 242) Used 200512 reads. Maximum read length 150 0:00:00.426 64M / 8G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:00:00.519 64M / 8G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 350778 kmers in total. 0:00:00.519 64M / 8G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:00:00.594 64M / 8G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:00:00.594 64M / 8G INFO General (kmer_splitters.hpp : 381) Splitting kmer instances into 256 buckets. This might take a while. 0:00:00.594 64M / 8G INFO General (file_limit.hpp : 29) Open file limit set to 2048 0:00:00.594 64M / 8G INFO General (kmer_splitters.hpp : 404) Memory available for splitting buffers: 2.4987 Gb 0:00:00.594 64M / 8G INFO General (kmer_splitters.hpp : 413) Using cell size of 131072 0:00:00.736 8G / 8G INFO General (kmer_splitters.hpp : 436) Processed 350778 kmers 0:00:00.736 8G / 8G INFO General (kmer_splitters.hpp : 445) Used 350778 kmers. 0:00:00.777 64M / 8G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:00:00.861 64M / 8G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 348337 kmers in total. 0:00:00.861 64M / 8G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:00:00.915 64M / 8G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:00:00.946 64M / 8G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:00:01.059 64M / 8G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 120537 bytes occupied (2.76828 bits per kmer). 0:00:01.059 64M / 8G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 382) Building k-mer extensions from k+1-mers 0:00:01.080 64M / 8G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 386) Building k-mer extensions from k+1-mers finished. 0:00:01.080 64M / 8G INFO Early tip clipping (early_simplification.hpp : 236) Early tip clipping 0:00:01.416 64M / 8G INFO Early tip clipping (early_simplification.hpp : 239) 67290 34-mers were removed by early tip clipper 0:00:01.416 64M / 8G INFO General (graph_construction.hpp : 143) Condensing graph 0:00:01.416 64M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 346) Extracting unbranching paths 0:00:01.535 64M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 360) Extracting unbranching paths finished. 16150 sequences extracted 0:00:01.547 64M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 320) Collecting perfect loops 0:00:01.600 64M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 335) Collecting perfect loops finished. 0 loops collected 0:00:01.609 64M / 8G INFO General (graph_construction.hpp : 151) Building index with coverage from graph 0:00:01.610 64M / 8G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:00:01.610 64M / 8G INFO General (kmer_splitters.hpp : 285) Splitting kmer instances into 16 buckets. This might take a while. 0:00:01.610 64M / 8G INFO General (file_limit.hpp : 29) Open file limit set to 2048 0:00:01.610 64M / 8G INFO General (kmer_splitters.hpp : 308) Memory available for splitting buffers: 39.9792 Gb 0:00:01.610 64M / 8G INFO General (kmer_splitters.hpp : 314) Using cell size of 2097152 0:00:01.844 640M / 8G INFO General (kmer_splitters.hpp : 327) Processed 16150 edges 0:00:01.844 640M / 8G INFO General (kmer_splitters.hpp : 332) Used 16150 sequences. 0:00:01.844 64M / 8G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:00:01.882 64M / 8G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 283488 kmers in total. 0:00:01.882 64M / 8G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:00:01.894 64M / 8G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:00:01.949 64M / 8G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:00:02.034 64M / 8G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 98109 bytes occupied (2.76863 bits per kmer). 0:00:02.037 72M / 8G INFO General (edge_index_builders.hpp : 21) Collecting k-mer coverage information from graph, this takes a while. 0:00:02.222 72M / 8G INFO General (edge_index_builders.hpp : 99) Collecting k-mer coverage information from reads, this takes a while. 0:00:02.539 72M / 8G INFO General (graph_construction.hpp : 179) Filling coverage and flanking coverage from index 0:00:02.547 72M / 8G INFO General (construction.cpp : 32) Figured out: read length = 150 0:00:02.548 72M / 8G INFO StageManager (stage.cpp : 125) STAGE == EC Threshold Finding 0:00:02.553 72M / 8G INFO ThresholdFinder (omni_tools.hpp : 466) Bucket size: 17 0:00:02.553 72M / 8G INFO General (genomic_info_filler.cpp : 72) Average edge coverage: 40.9773 0:00:02.553 72M / 8G INFO General (genomic_info_filler.cpp : 73) Graph threshold: 45 0:00:02.565 72M / 8G INFO General (genomic_info_filler.cpp : 101) EC coverage threshold value was calculated as 45 0:00:02.565 72M / 8G INFO StageManager (stage.cpp : 125) STAGE == Simplification 0:00:02.565 72M / 8G INFO General (graph_simplification.hpp : 633) PROCEDURE == Presimplification 0:00:02.565 72M / 8G INFO General (graph_simplification.hpp : 416) Removing short low covered self-conjugate connections 0:00:02.584 72M / 8G INFO General (graph_simplification.hpp : 713) PROCEDURE == Simplification cycle, iteration 1 0:00:02.584 72M / 8G INFO General (graph_simplification.hpp : 309) Clipping tips 0:00:02.603 72M / 8G INFO General (graph_simplification.hpp : 370) Removing bulges 0:00:03.370 72M / 8G INFO General (graph_simplification.hpp : 397) Removing low covered connections 0:00:04.138 72M / 8G INFO General (graph_simplification.hpp : 713) PROCEDURE == Simplification cycle, iteration 2 0:00:04.138 72M / 8G INFO General (graph_simplification.hpp : 309) Clipping tips 0:00:04.173 72M / 8G INFO General (graph_simplification.hpp : 370) Removing bulges 0:00:04.272 72M / 8G INFO General (graph_simplification.hpp : 397) Removing low covered connections 0:00:04.334 72M / 8G INFO General (graph_simplification.hpp : 713) PROCEDURE == Simplification cycle, iteration 3 0:00:04.334 72M / 8G INFO General (graph_simplification.hpp : 309) Clipping tips 0:00:04.335 72M / 8G INFO General (graph_simplification.hpp : 370) Removing bulges 0:00:04.386 72M / 8G INFO General (graph_simplification.hpp : 397) Removing low covered connections 0:00:04.402 72M / 8G INFO General (graph_simplification.hpp : 713) PROCEDURE == Simplification cycle, iteration 4 0:00:04.402 72M / 8G INFO General (graph_simplification.hpp : 309) Clipping tips 0:00:04.403 72M / 8G INFO General (graph_simplification.hpp : 370) Removing bulges 0:00:04.407 72M / 8G INFO General (graph_simplification.hpp : 397) Removing low covered connections 0:00:04.423 72M / 8G INFO General (graph_simplification.hpp : 713) PROCEDURE == Simplification cycle, iteration 5 0:00:04.423 72M / 8G INFO General (graph_simplification.hpp : 309) Clipping tips 0:00:04.424 72M / 8G INFO General (graph_simplification.hpp : 370) Removing bulges 0:00:04.428 72M / 8G INFO General (graph_simplification.hpp : 397) Removing low covered connections 0:00:04.446 72M / 8G INFO General (graph_simplification.hpp : 713) PROCEDURE == Simplification cycle, iteration 6 0:00:04.446 72M / 8G INFO General (graph_simplification.hpp : 309) Clipping tips 0:00:04.447 72M / 8G INFO General (graph_simplification.hpp : 370) Removing bulges 0:00:04.449 72M / 8G INFO General (graph_simplification.hpp : 397) Removing low covered connections 0:00:04.451 72M / 8G INFO General (graph_simplification.hpp : 713) PROCEDURE == Simplification cycle, iteration 7 0:00:04.451 72M / 8G INFO General (graph_simplification.hpp : 309) Clipping tips 0:00:04.451 72M / 8G INFO General (graph_simplification.hpp : 370) Removing bulges 0:00:04.453 72M / 8G INFO General (graph_simplification.hpp : 397) Removing low covered connections 0:00:04.475 72M / 8G INFO General (graph_simplification.hpp : 713) PROCEDURE == Simplification cycle, iteration 8 0:00:04.475 72M / 8G INFO General (graph_simplification.hpp : 309) Clipping tips 0:00:04.475 72M / 8G INFO General (graph_simplification.hpp : 370) Removing bulges 0:00:04.477 72M / 8G INFO General (graph_simplification.hpp : 397) Removing low covered connections 0:00:04.497 72M / 8G INFO General (graph_simplification.hpp : 713) PROCEDURE == Simplification cycle, iteration 9 0:00:04.497 72M / 8G INFO General (graph_simplification.hpp : 309) Clipping tips 0:00:04.497 72M / 8G INFO General (graph_simplification.hpp : 370) Removing bulges 0:00:04.499 72M / 8G INFO General (graph_simplification.hpp : 397) Removing low covered connections 0:00:04.500 72M / 8G INFO General (graph_simplification.hpp : 713) PROCEDURE == Simplification cycle, iteration 10 0:00:04.500 72M / 8G INFO General (graph_simplification.hpp : 309) Clipping tips 0:00:04.501 72M / 8G INFO General (graph_simplification.hpp : 370) Removing bulges 0:00:04.502 72M / 8G INFO General (graph_simplification.hpp : 397) Removing low covered connections 0:00:04.503 72M / 8G INFO General (graph_simplification.hpp : 659) PROCEDURE == Post simplification 0:00:04.503 72M / 8G INFO General (graph_simplification.hpp : 665) Iteration 0 0:00:04.503 72M / 8G INFO General (graph_simplification.hpp : 471) Clipping tips based on topology 0:00:04.504 72M / 8G INFO General (graph_simplification.hpp : 447) Removal of relatively low covered connections disabled 0:00:04.504 72M / 8G INFO General (graph_simplification.hpp : 309) Clipping tips 0:00:04.505 72M / 8G INFO General (graph_simplification.hpp : 370) Removing bulges 0:00:04.506 72M / 8G INFO General (graph_simplification.hpp : 565) Removing hidden erroneous connections 0:00:04.583 72M / 8G INFO StageManager (stage.cpp : 125) STAGE == Simplification Cleanup 0:00:04.583 72M / 8G INFO General (simplification.cpp : 71) Final isolated edges removal: 0:00:04.583 72M / 8G INFO General (simplification.cpp : 73) All edges of length smaller than 150 will be removed 0:00:04.604 72M / 8G INFO General (simplification.cpp : 77) Removed 275 edges 0:00:04.604 72M / 8G INFO General (simplification.cpp : 106) Counting average coverage 0:00:04.604 72M / 8G INFO General (simplification.cpp : 109) Average coverage = 70.5891 0:00:04.604 72M / 8G INFO StageManager (stage.cpp : 125) STAGE == Contig Output 0:00:04.604 72M / 8G INFO General (contig_output.hpp : 295) Outputting contigs to /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZH/spades//K33/simplified_contigs.fasta 0:00:04.619 72M / 8G INFO General (contig_output.hpp : 295) Outputting contigs to /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZH/spades//K33/before_rr.fasta 0:00:04.648 72M / 8G INFO General (contig_output.hpp : 295) Outputting contigs to /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZH/spades//K33/final_contigs.fasta 0:00:04.679 72M / 8G INFO General (launch.hpp : 84) SPAdes finished 0:00:04.681 64M / 8G INFO General (main.cpp : 166) Assembling time: 0 hours 0 minutes 4 seconds == Running assembler: K55 0:00:00.000 4M / 4M INFO General (memory_limit.hpp : 29) Memory limit set to 120 Gb 0:00:00.000 4M / 4M INFO General (main.cpp : 146) Assembling dataset (/global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZH/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 0:00:00.000 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=55 0:00:00.002 4M / 4M INFO General (kmer_splitters.hpp : 164) Splitting kmer instances into 256 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: 2.49992 Gb 0:00:00.002 4M / 4M INFO General (kmer_splitters.hpp : 197) Using cell size of 131072 0:00:00.264 8G / 8G INFO General (kmer_splitters.hpp : 225) Processed 200512 reads 0:00:00.264 8G / 8G INFO General (kmer_splitters.hpp : 231) Adding contigs from previous K 0:00:00.571 8G / 8G INFO General (kmer_splitters.hpp : 242) Used 200512 reads. Maximum read length 150 0:00:00.644 64M / 8G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:00:00.740 64M / 8G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 379691 kmers in total. 0:00:00.740 64M / 8G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:00:01.289 64M / 8G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:00:01.289 64M / 8G INFO General (kmer_splitters.hpp : 381) Splitting kmer instances into 256 buckets. This might take a while. 0:00:01.289 64M / 8G INFO General (file_limit.hpp : 29) Open file limit set to 2048 0:00:01.290 64M / 8G INFO General (kmer_splitters.hpp : 404) Memory available for splitting buffers: 2.4987 Gb 0:00:01.290 64M / 8G INFO General (kmer_splitters.hpp : 413) Using cell size of 131072 0:00:01.839 8G / 8G INFO General (kmer_splitters.hpp : 436) Processed 379691 kmers 0:00:01.839 8G / 8G INFO General (kmer_splitters.hpp : 445) Used 379691 kmers. 0:00:01.882 64M / 8G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:00:04.512 64M / 8G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 379208 kmers in total. 0:00:04.512 64M / 8G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:00:06.707 64M / 8G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:00:06.738 64M / 8G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:00:06.815 64M / 8G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 131220 bytes occupied (2.7683 bits per kmer). 0:00:06.816 64M / 8G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 382) Building k-mer extensions from k+1-mers 0:00:06.850 64M / 8G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 386) Building k-mer extensions from k+1-mers finished. 0:00:06.850 64M / 8G INFO General (graph_construction.hpp : 143) Condensing graph 0:00:06.850 64M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 346) Extracting unbranching paths 0:00:06.959 68M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 360) Extracting unbranching paths finished. 21208 sequences extracted 0:00:06.977 64M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 320) Collecting perfect loops 0:00:07.035 64M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 335) Collecting perfect loops finished. 0 loops collected 0:00:07.047 64M / 8G INFO General (graph_construction.hpp : 151) Building index with coverage from graph 0:00:07.047 64M / 8G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:00:07.047 64M / 8G INFO General (kmer_splitters.hpp : 285) Splitting kmer instances into 16 buckets. This might take a while. 0:00:07.047 64M / 8G INFO General (file_limit.hpp : 29) Open file limit set to 2048 0:00:07.047 64M / 8G INFO General (kmer_splitters.hpp : 308) Memory available for splitting buffers: 39.9792 Gb 0:00:07.047 64M / 8G INFO General (kmer_splitters.hpp : 314) Using cell size of 2097152 0:00:07.107 640M / 8G INFO General (kmer_splitters.hpp : 327) Processed 21208 edges 0:00:07.107 640M / 8G INFO General (kmer_splitters.hpp : 332) Used 21208 sequences. 0:00:07.108 64M / 8G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:00:07.155 64M / 8G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 379691 kmers in total. 0:00:07.155 64M / 8G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:00:07.169 64M / 8G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:00:07.246 64M / 8G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:00:07.524 64M / 8G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 131397 bytes occupied (2.7685 bits per kmer). 0:00:07.528 76M / 8G INFO General (edge_index_builders.hpp : 21) Collecting k-mer coverage information from graph, this takes a while. 0:00:07.834 76M / 8G INFO General (edge_index_builders.hpp : 99) Collecting k-mer coverage information from reads, this takes a while. 0:00:08.263 76M / 8G INFO General (graph_construction.hpp : 179) Filling coverage and flanking coverage from index 0:00:08.275 76M / 8G INFO General (construction.cpp : 32) Figured out: read length = 150 0:00:08.276 76M / 8G INFO StageManager (stage.cpp : 125) STAGE == EC Threshold Finding 0:00:08.281 76M / 8G INFO ThresholdFinder (omni_tools.hpp : 466) Bucket size: 12 0:00:08.281 76M / 8G INFO General (genomic_info_filler.cpp : 72) Average edge coverage: 24.9641 0:00:08.281 76M / 8G INFO General (genomic_info_filler.cpp : 73) Graph threshold: 38 0:00:08.291 76M / 8G INFO General (genomic_info_filler.cpp : 101) EC coverage threshold value was calculated as 38 0:00:08.291 76M / 8G INFO StageManager (stage.cpp : 125) STAGE == Gap Closer 0:00:08.291 76M / 8G INFO General (gap_closer.cpp : 178) Preparing shift maps 0:00:08.298 76M / 8G INFO General (gap_closer.cpp : 132) Processing paired reads (takes a while) 0:00:08.483 80M / 8G INFO General (gap_closer.cpp : 158) Used 100200 paired reads 0:00:08.483 80M / 8G INFO General (gap_closer.cpp : 160) Merging paired indices 0:00:08.484 80M / 8G INFO GapCloser (gap_closer.cpp : 409) Closing short gaps 0:00:08.495 80M / 8G INFO GapCloser (gap_closer.cpp : 438) Closing short gaps complete: filled 7 gaps after checking 169 candidates 0:00:08.509 76M / 8G INFO General (gap_closer.cpp : 506) Detaching and clearing index 0:00:08.510 64M / 8G INFO General (gap_closer.cpp : 509) Index clearing finished 0:00:08.510 64M / 8G INFO StageManager (stage.cpp : 125) STAGE == Simplification 0:00:08.510 64M / 8G INFO General (graph_simplification.hpp : 633) PROCEDURE == Presimplification 0:00:08.510 64M / 8G INFO General (graph_simplification.hpp : 416) Removing short low covered self-conjugate connections 0:00:08.538 64M / 8G INFO General (graph_simplification.hpp : 713) PROCEDURE == Simplification cycle, iteration 1 0:00:08.538 64M / 8G INFO General (graph_simplification.hpp : 309) Clipping tips 0:00:08.595 64M / 8G INFO General (graph_simplification.hpp : 370) Removing bulges 0:00:08.761 68M / 8G INFO General (graph_simplification.hpp : 397) Removing low covered connections 0:00:08.784 68M / 8G INFO General (graph_simplification.hpp : 713) PROCEDURE == Simplification cycle, iteration 2 0:00:08.784 68M / 8G INFO General (graph_simplification.hpp : 309) Clipping tips 0:00:08.786 68M / 8G INFO General (graph_simplification.hpp : 370) Removing bulges 0:00:08.814 68M / 8G INFO General (graph_simplification.hpp : 397) Removing low covered connections 0:00:08.817 68M / 8G INFO General (graph_simplification.hpp : 713) PROCEDURE == Simplification cycle, iteration 3 0:00:08.817 68M / 8G INFO General (graph_simplification.hpp : 309) Clipping tips 0:00:08.819 68M / 8G INFO General (graph_simplification.hpp : 370) Removing bulges 0:00:08.826 68M / 8G INFO General (graph_simplification.hpp : 397) Removing low covered connections 0:00:08.828 68M / 8G INFO General (graph_simplification.hpp : 713) PROCEDURE == Simplification cycle, iteration 4 0:00:08.828 68M / 8G INFO General (graph_simplification.hpp : 309) Clipping tips 0:00:08.830 68M / 8G INFO General (graph_simplification.hpp : 370) Removing bulges 0:00:08.833 68M / 8G INFO General (graph_simplification.hpp : 397) Removing low covered connections 0:00:08.836 68M / 8G INFO General (graph_simplification.hpp : 713) PROCEDURE == Simplification cycle, iteration 5 0:00:08.836 68M / 8G INFO General (graph_simplification.hpp : 309) Clipping tips 0:00:08.837 68M / 8G INFO General (graph_simplification.hpp : 370) Removing bulges 0:00:08.840 68M / 8G INFO General (graph_simplification.hpp : 397) Removing low covered connections 0:00:08.842 68M / 8G INFO General (graph_simplification.hpp : 713) PROCEDURE == Simplification cycle, iteration 6 0:00:08.842 68M / 8G INFO General (graph_simplification.hpp : 309) Clipping tips 0:00:08.843 68M / 8G INFO General (graph_simplification.hpp : 370) Removing bulges 0:00:08.845 68M / 8G INFO General (graph_simplification.hpp : 397) Removing low covered connections 0:00:08.848 68M / 8G INFO General (graph_simplification.hpp : 713) PROCEDURE == Simplification cycle, iteration 7 0:00:08.848 68M / 8G INFO General (graph_simplification.hpp : 309) Clipping tips 0:00:08.849 68M / 8G INFO General (graph_simplification.hpp : 370) Removing bulges 0:00:08.851 68M / 8G INFO General (graph_simplification.hpp : 397) Removing low covered connections 0:00:08.853 68M / 8G INFO General (graph_simplification.hpp : 713) PROCEDURE == Simplification cycle, iteration 8 0:00:08.853 68M / 8G INFO General (graph_simplification.hpp : 309) Clipping tips 0:00:08.854 68M / 8G INFO General (graph_simplification.hpp : 370) Removing bulges 0:00:08.856 68M / 8G INFO General (graph_simplification.hpp : 397) Removing low covered connections 0:00:08.859 68M / 8G INFO General (graph_simplification.hpp : 713) PROCEDURE == Simplification cycle, iteration 9 0:00:08.859 68M / 8G INFO General (graph_simplification.hpp : 309) Clipping tips 0:00:08.860 68M / 8G INFO General (graph_simplification.hpp : 370) Removing bulges 0:00:08.862 68M / 8G INFO General (graph_simplification.hpp : 397) Removing low covered connections 0:00:08.864 68M / 8G INFO General (graph_simplification.hpp : 713) PROCEDURE == Simplification cycle, iteration 10 0:00:08.864 68M / 8G INFO General (graph_simplification.hpp : 309) Clipping tips 0:00:08.865 68M / 8G INFO General (graph_simplification.hpp : 370) Removing bulges 0:00:08.867 68M / 8G INFO General (graph_simplification.hpp : 397) Removing low covered connections 0:00:08.869 68M / 8G INFO General (graph_simplification.hpp : 659) PROCEDURE == Post simplification 0:00:08.869 68M / 8G INFO General (graph_simplification.hpp : 665) Iteration 0 0:00:08.869 68M / 8G INFO General (graph_simplification.hpp : 471) Clipping tips based on topology 0:00:08.870 68M / 8G INFO General (graph_simplification.hpp : 447) Removal of relatively low covered connections disabled 0:00:08.870 68M / 8G INFO General (graph_simplification.hpp : 457) Removing connections based on topology 0:00:08.871 68M / 8G INFO General (graph_simplification.hpp : 513) Removing connections based on topology and reliable coverage 0:00:08.872 68M / 8G INFO General (graph_simplification.hpp : 500) Removing interstrand connections 0:00:08.874 68M / 8G INFO General (graph_simplification.hpp : 487) Removing connections based on topological multiplicity counting 0:00:08.875 68M / 8G INFO General (graph_simplification.hpp : 309) Clipping tips 0:00:08.876 68M / 8G INFO General (graph_simplification.hpp : 370) Removing bulges 0:00:08.878 68M / 8G INFO General (graph_simplification.hpp : 665) Iteration 1 0:00:08.878 68M / 8G INFO General (graph_simplification.hpp : 471) Clipping tips based on topology 0:00:08.879 68M / 8G INFO General (graph_simplification.hpp : 447) Removal of relatively low covered connections disabled 0:00:08.879 68M / 8G INFO General (graph_simplification.hpp : 457) Removing connections based on topology 0:00:08.880 68M / 8G INFO General (graph_simplification.hpp : 513) Removing connections based on topology and reliable coverage 0:00:08.881 68M / 8G INFO General (graph_simplification.hpp : 500) Removing interstrand connections 0:00:08.882 68M / 8G INFO General (graph_simplification.hpp : 487) Removing connections based on topological multiplicity counting 0:00:08.883 68M / 8G INFO General (graph_simplification.hpp : 309) Clipping tips 0:00:08.884 68M / 8G INFO General (graph_simplification.hpp : 370) Removing bulges 0:00:08.886 68M / 8G INFO General (graph_simplification.hpp : 565) Removing hidden erroneous connections 0:00:08.887 68M / 8G INFO StageManager (stage.cpp : 125) STAGE == Gap Closer 0:00:08.887 68M / 8G INFO General (gap_closer.cpp : 489) Refilling index 0:00:08.887 68M / 8G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:00:08.887 68M / 8G INFO General (kmer_splitters.hpp : 285) Splitting kmer instances into 16 buckets. This might take a while. 0:00:08.887 68M / 8G INFO General (file_limit.hpp : 29) Open file limit set to 2048 0:00:08.887 68M / 8G INFO General (kmer_splitters.hpp : 308) Memory available for splitting buffers: 39.9779 Gb 0:00:08.887 68M / 8G INFO General (kmer_splitters.hpp : 314) Using cell size of 2097152 0:00:08.913 644M / 8G INFO General (kmer_splitters.hpp : 327) Processed 1474 edges 0:00:08.913 644M / 8G INFO General (kmer_splitters.hpp : 332) Used 1474 sequences. 0:00:08.914 68M / 8G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:00:08.945 68M / 8G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 211205 kmers in total. 0:00:08.945 68M / 8G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:00:08.955 68M / 8G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:00:08.994 68M / 8G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:00:09.123 68M / 8G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 73106 bytes occupied (2.7691 bits per kmer). 0:00:09.125 76M / 8G INFO General (edge_index_builders.hpp : 21) Collecting k-mer coverage information from graph, this takes a while. 0:00:09.286 76M / 8G INFO General (gap_closer.cpp : 491) Index refilled 0:00:09.286 76M / 8G INFO General (gap_closer.cpp : 492) Attaching index 0:00:09.286 76M / 8G INFO General (gap_closer.cpp : 494) Index attached 0:00:09.286 76M / 8G INFO General (gap_closer.cpp : 178) Preparing shift maps 0:00:09.287 76M / 8G INFO General (gap_closer.cpp : 132) Processing paired reads (takes a while) 0:00:09.414 76M / 8G INFO General (gap_closer.cpp : 158) Used 100200 paired reads 0:00:09.414 76M / 8G INFO General (gap_closer.cpp : 160) Merging paired indices 0:00:09.415 76M / 8G INFO GapCloser (gap_closer.cpp : 409) Closing short gaps 0:00:09.418 76M / 8G INFO GapCloser (gap_closer.cpp : 438) Closing short gaps complete: filled 2 gaps after checking 212 candidates 0:00:09.452 76M / 8G INFO General (gap_closer.cpp : 506) Detaching and clearing index 0:00:09.452 68M / 8G INFO General (gap_closer.cpp : 509) Index clearing finished 0:00:09.452 68M / 8G INFO StageManager (stage.cpp : 125) STAGE == Simplification Cleanup 0:00:09.452 68M / 8G INFO General (simplification.cpp : 71) Final isolated edges removal: 0:00:09.452 68M / 8G INFO General (simplification.cpp : 73) All edges of length smaller than 150 will be removed 0:00:09.455 68M / 8G INFO General (simplification.cpp : 77) Removed 583 edges 0:00:09.455 68M / 8G INFO General (simplification.cpp : 97) Final index refill 0:00:09.455 68M / 8G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:00:09.455 68M / 8G INFO General (kmer_splitters.hpp : 285) Splitting kmer instances into 16 buckets. This might take a while. 0:00:09.456 68M / 8G INFO General (file_limit.hpp : 29) Open file limit set to 2048 0:00:09.456 68M / 8G INFO General (kmer_splitters.hpp : 308) Memory available for splitting buffers: 39.9779 Gb 0:00:09.456 68M / 8G INFO General (kmer_splitters.hpp : 314) Using cell size of 2097152 0:00:09.476 644M / 8G INFO General (kmer_splitters.hpp : 332) Used 304 sequences. 0:00:09.476 68M / 8G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:00:09.656 68M / 8G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 158972 kmers in total. 0:00:09.656 68M / 8G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:00:09.664 68M / 8G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:00:09.693 68M / 8G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:00:09.884 68M / 8G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 55028 bytes occupied (2.76919 bits per kmer). 0:00:09.886 72M / 8G INFO General (edge_index_builders.hpp : 21) Collecting k-mer coverage information from graph, this takes a while. 0:00:10.005 72M / 8G INFO General (simplification.cpp : 99) Final index refill finished 0:00:10.005 72M / 8G INFO General (simplification.cpp : 106) Counting average coverage 0:00:10.005 72M / 8G INFO General (simplification.cpp : 109) Average coverage = 57.9026 0:00:10.005 72M / 8G INFO StageManager (stage.cpp : 125) STAGE == Mismatch Correction 0:00:10.297 72M / 8G INFO General (mismatch_shall_not_pass.hp: 188) Finished collecting potential mismatches positions 0:00:10.317 72M / 8G INFO General (mismatch_shall_not_pass.hp: 291) All edges processed 0:00:10.318 72M / 8G INFO General (mismatch_correction.cpp : 17) Corrected 0 nucleotides 0:00:10.318 72M / 8G INFO StageManager (stage.cpp : 125) STAGE == Paired Information Counting 0:00:10.318 72M / 8G INFO General (pair_info_count.cpp : 174) Estimating insert size for library #0 0:00:10.319 72M / 8G INFO General (pair_info_count.cpp : 82) Estimating insert size (takes a while) 0:00:10.319 72M / 8G INFO General (short_read_mapper.hpp : 93) Read length = 150, selecting usual mapper 0:00:10.332 72M / 8G INFO General (pair_info_count.cpp : 86) 22093 paired reads (44.0978% of all) aligned to long edges 0:00:10.333 72M / 8G INFO General (pair_info_count.cpp : 199) Estimated insert size for paired library #0 0:00:10.333 72M / 8G INFO General (pair_info_count.cpp : 204) Insert size = 421.222, deviation = 102.558, left quantile = 281, right quantile = 538, read length = 150 0:00:10.333 72M / 8G INFO General (pair_info_count.cpp : 224) Mapping library #0 0:00:10.333 72M / 8G INFO General (pair_info_count.cpp : 226) Mapping paired reads (takes a while) 0:00:10.333 72M / 8G INFO General (pair_info_count.cpp : 127) Left insert size qauntile 281, right insert size quantile 538 0:00:10.334 72M / 8G INFO General (short_read_mapper.hpp : 93) Read length = 150, selecting usual mapper 0:00:10.857 72M / 8G INFO General (split_graph_pair_info.hpp : 345) Threshold for paired information 0.0277695 0:00:10.861 72M / 8G INFO StageManager (stage.cpp : 125) STAGE == Distance Estimation 0:00:10.862 72M / 8G INFO General (distance_estimation.cpp : 242) Processing library #0 0:00:10.862 72M / 8G INFO General (distance_estimation.cpp : 145) Weight Filter Done 0:00:10.864 72M / 8G INFO DistanceEstimator (distance_estimation.hpp : 226) Using SIMPLE distance estimator 0:00:10.897 72M / 8G INFO General (distance_estimation.cpp : 40) Filtering info 0:00:10.898 72M / 8G INFO General (pair_info_filters.hpp : 352) Pruning the index 0:00:10.898 72M / 8G INFO General (distance_estimation.cpp : 193) Refining clustered pair information 0:00:10.898 72M / 8G INFO General (distance_estimation.cpp : 195) The refining of clustered pair information has been finished 0:00:10.898 72M / 8G INFO General (distance_estimation.cpp : 197) Filling paired information 0:00:10.932 72M / 8G INFO PairInfoImprover (pair_info_improver.hpp : 58) Paired info stats: missing = 11; contradictional = 16 0:00:10.963 72M / 8G INFO PairInfoImprover (pair_info_improver.hpp : 58) Paired info stats: missing = 0; contradictional = 0 0:00:10.963 72M / 8G INFO General (distance_estimation.cpp : 202) Filling scaffolding index 0:00:10.963 72M / 8G INFO DistanceEstimator (distance_estimation.hpp : 226) Using SMOOTHING distance estimator 0:00:11.000 72M / 8G INFO General (distance_estimation.cpp : 40) Filtering info 0:00:11.000 72M / 8G INFO General (pair_info_filters.hpp : 352) Pruning the index 0:00:11.000 72M / 8G INFO StageManager (stage.cpp : 125) STAGE == Repeat Resolving 0:00:11.001 72M / 8G INFO General (contig_output.hpp : 295) Outputting contigs to /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZH/spades//K55/simplified_contigs.fasta 0:00:11.029 72M / 8G INFO General (contig_output.hpp : 295) Outputting contigs to /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZH/spades//K55/before_rr.fasta 0:00:11.057 72M / 8G INFO General (repeat_resolving.cpp : 103) Using Path-Extend repeat resolving 0:00:11.059 72M / 8G INFO General (path_extend_launch.hpp : 413) Threshold for library #0 is 0.0277695 0:00:11.059 72M / 8G INFO General (path_extend_launch.hpp : 222) Path-Extend repeat resolving tool started 0:00:11.059 72M / 8G INFO General (path_extend_launch.hpp : 230) Using 1 paired-end library 0:00:11.059 72M / 8G INFO General (path_extend_launch.hpp : 231) Using 1 paired-end scaffolding library 0:00:11.059 72M / 8G INFO General (path_extend_launch.hpp : 232) Using 0 mate-pair libraries 0:00:11.059 72M / 8G INFO General (path_extend_launch.hpp : 233) Using 1 single read library 0:00:11.059 72M / 8G INFO General (path_extend_launch.hpp : 234) Scaffolder is on 0:00:11.060 72M / 8G INFO General (path_extend_launch.hpp : 258) Growing paths using paired-end and long single reads 0:00:11.070 76M / 8G INFO PathExtendIO (pe_io.hpp : 272) Constructing FASTG file from paths 0:00:11.070 76M / 8G INFO PathExtendIO (pe_io.hpp : 275) Writing contigs in FASTG to /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZH/spades//K55/final_contigs.fastg 0:00:11.071 76M / 8G INFO PathExtendIO (pe_io.hpp : 276) Writing contigs in FASTA to /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZH/spades//K55/final_contigs.fasta 0:00:11.099 76M / 8G INFO General (path_extend_launch.hpp : 278) Traversing tandem repeats 0:00:11.100 76M / 8G INFO PathExtendIO (pe_io.hpp : 272) Constructing FASTG file from paths 0:00:11.100 76M / 8G INFO PathExtendIO (pe_io.hpp : 275) Writing contigs in FASTG to /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZH/spades//K55/scaffolds.fastg 0:00:11.100 76M / 8G INFO PathExtendIO (pe_io.hpp : 276) Writing contigs in FASTA to /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZH/spades//K55/scaffolds.fasta 0:00:11.154 76M / 8G INFO General (launch.hpp : 84) SPAdes finished 0:00:11.166 68M / 8G INFO General (main.cpp : 166) Assembling time: 0 hours 0 minutes 11 seconds ===== Assembling finished. ===== Mismatch correction started. == Processing of contigs Config: {'skip_masked': 1, 'contigs': '/global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZH/spades/misc/assembled_contigs.fasta', 'use_multiple_aligned': 0, 'reads2': ['/global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZH/spades/corrected/ZHZH.15M.bbqc.fq.gz_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/ZHZH/spades/corrected/ZHZH.15M.bbqc.fq.gz_1.00.0_0.cor.fastq.gz'], 'output_dirpath': '/global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZH/spades/tmp/mis_cor_contigs_pT1r9L', 't': 16, 'debug': 0, 'mate_weight': 1.0, 'work_dir': '/global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZH/spades/tmp/mis_cor_contigs_pT1r9L/mismatch_corrector_tmp', 'insert_size': 421} no sam file, running aligner running bwa [bwa_index] Pack FASTA... 0.00 sec [bwa_index] Construct BWT for the packed sequence... [bwa_index] 0.03 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... 0.02 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/ZHZH/spades/tmp/mis_cor_contigs_pT1r9L/mismatch_corrector_tmp/assembled_contigs.fasta 2 [main] Real time: 0.112 sec; CPU: 0.061 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... 19.73 sec [bwa_aln_core] write to the disk... 0.01 sec [bwa_aln_core] 50100 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 16 -O 7 -E 2 -k 3 -n 0.08 -q 15 /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZH/spades/tmp/mis_cor_contigs_pT1r9L/mismatch_corrector_tmp/assembled_contigs.fasta /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZH/spades/corrected/ZHZH.15M.bbqc.fq.gz_1.00.0_0.cor.fastq.gz [main] Real time: 1.504 sec; CPU: 19.967 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... 19.11 sec [bwa_aln_core] write to the disk... 0.00 sec [bwa_aln_core] 50100 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 16 -O 7 -E 2 -k 3 -n 0.08 -q 15 /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZH/spades/tmp/mis_cor_contigs_pT1r9L/mismatch_corrector_tmp/assembled_contigs.fasta /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZH/spades/corrected/ZHZH.15M.bbqc.fq.gz_2.00.0_0.cor.fastq.gz [main] Real time: 1.523 sec; CPU: 19.384 sec contigs were split, starting splitting .sam file file /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZH/spades/tmp/mis_cor_contigs_pT1r9L/mismatch_corrector_tmp/tmp.sam opened dropping cashed lines... .sam file was split concatenating /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZH/spades/tmp/mis_cor_contigs_pT1r9L/mismatch_corrector_tmp/*.ref.fasta INTO /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZH/spades/tmp/mis_cor_contigs_pT1r9L/corrected_contigs.fasta TOTAL - replaced: 69 deleted: 12 inserted: 6 == Warning == Creating /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZH/spades/contigs.fastg: failed to find appropriate name for contig >NODE_15_length_1877_cov_83.9172_ID_33 (looking for names in /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZH/spades/misc/assembled_contigs.fastg)! Skipping this contig. == Warning == Creating /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZH/spades/contigs.fastg: failed to find appropriate name for contig >NODE_10_length_4999_cov_18.4072_ID_25 (looking for names in /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZH/spades/misc/assembled_contigs.fastg)! Skipping this contig. == Warning == Creating /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZH/spades/contigs.fastg: failed to find appropriate name for contig >NODE_13_length_2464_cov_9.42795_ID_29 (looking for names in /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZH/spades/misc/assembled_contigs.fastg)! Skipping this contig. == Warning == Creating /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZH/spades/contigs.fastg: failed to find appropriate name for contig >NODE_18_length_1442_cov_9.93921_ID_39 (looking for names in /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZH/spades/misc/assembled_contigs.fastg)! Skipping this contig. == Warning == Creating /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZH/spades/contigs.fastg: failed to find appropriate name for contig >NODE_17_length_1496_cov_17.4674_ID_37 (looking for names in /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZH/spades/misc/assembled_contigs.fastg)! Skipping this contig. == Warning == Creating /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZH/spades/contigs.fastg: failed to find appropriate name for contig >NODE_22_length_1025_cov_21.638_ID_45 (looking for names in /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZH/spades/misc/assembled_contigs.fastg)! Skipping this contig. == Warning == Creating /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZH/spades/contigs.fastg: failed to find appropriate name for contig >NODE_12_length_2567_cov_29.1613_ID_27 (looking for names in /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZH/spades/misc/assembled_contigs.fastg)! Skipping this contig. == Processing of scaffolds Config: {'skip_masked': 1, 'contigs': '/global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZH/spades/misc/assembled_scaffolds.fasta', 'use_multiple_aligned': 0, 'reads2': ['/global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZH/spades/corrected/ZHZH.15M.bbqc.fq.gz_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/ZHZH/spades/corrected/ZHZH.15M.bbqc.fq.gz_1.00.0_0.cor.fastq.gz'], 'output_dirpath': '/global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZH/spades/tmp/mis_cor_scaffolds_rCZ3Qi', 't': 16, 'debug': 0, 'mate_weight': 1.0, 'work_dir': '/global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZH/spades/tmp/mis_cor_scaffolds_rCZ3Qi/mismatch_corrector_tmp', 'insert_size': 421} no sam file, running aligner running bwa [bwa_index] Pack FASTA... 0.00 sec [bwa_index] Construct BWT for the packed sequence... [bwa_index] 0.03 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... 0.02 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/ZHZH/spades/tmp/mis_cor_scaffolds_rCZ3Qi/mismatch_corrector_tmp/assembled_scaffolds.fasta 2 [main] Real time: 0.159 sec; CPU: 0.059 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... 19.70 sec [bwa_aln_core] write to the disk... 0.00 sec [bwa_aln_core] 50100 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 16 -O 7 -E 2 -k 3 -n 0.08 -q 15 /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZH/spades/tmp/mis_cor_scaffolds_rCZ3Qi/mismatch_corrector_tmp/assembled_scaffolds.fasta /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZH/spades/corrected/ZHZH.15M.bbqc.fq.gz_1.00.0_0.cor.fastq.gz [main] Real time: 1.503 sec; CPU: 19.935 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... 19.13 sec [bwa_aln_core] write to the disk... 0.01 sec [bwa_aln_core] 50100 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 16 -O 7 -E 2 -k 3 -n 0.08 -q 15 /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZH/spades/tmp/mis_cor_scaffolds_rCZ3Qi/mismatch_corrector_tmp/assembled_scaffolds.fasta /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZH/spades/corrected/ZHZH.15M.bbqc.fq.gz_2.00.0_0.cor.fastq.gz [main] Real time: 1.524 sec; CPU: 19.408 sec contigs were split, starting splitting .sam file file /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZH/spades/tmp/mis_cor_scaffolds_rCZ3Qi/mismatch_corrector_tmp/tmp.sam opened dropping cashed lines... .sam file was split concatenating /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZH/spades/tmp/mis_cor_scaffolds_rCZ3Qi/mismatch_corrector_tmp/*.ref.fasta INTO /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZH/spades/tmp/mis_cor_scaffolds_rCZ3Qi/corrected_contigs.fasta TOTAL - replaced: 68 deleted: 12 inserted: 6 == Warning == Creating /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZH/spades/scaffolds.fastg: failed to find appropriate name for contig >NODE_11_length_4999_cov_18.4072_ID_289 (looking for names in /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZH/spades/misc/assembled_scaffolds.fastg)! Skipping this contig. == Warning == Creating /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZH/spades/scaffolds.fastg: failed to find appropriate name for contig >NODE_15_length_1877_cov_83.9172_ID_299 (looking for names in /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZH/spades/misc/assembled_scaffolds.fastg)! Skipping this contig. == Warning == Creating /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZH/spades/scaffolds.fastg: failed to find appropriate name for contig >NODE_13_length_2464_cov_9.42795_ID_293 (looking for names in /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZH/spades/misc/assembled_scaffolds.fastg)! Skipping this contig. == Warning == Creating /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZH/spades/scaffolds.fastg: failed to find appropriate name for contig >NODE_18_length_1442_cov_9.93921_ID_285 (looking for names in /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZH/spades/misc/assembled_scaffolds.fastg)! Skipping this contig. == Warning == Creating /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZH/spades/scaffolds.fastg: failed to find appropriate name for contig >NODE_17_length_1496_cov_17.4674_ID_269 (looking for names in /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZH/spades/misc/assembled_scaffolds.fastg)! Skipping this contig. == Warning == Creating /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZH/spades/scaffolds.fastg: failed to find appropriate name for contig >NODE_21_length_1025_cov_21.638_ID_273 (looking for names in /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZH/spades/misc/assembled_scaffolds.fastg)! Skipping this contig. == Warning == Creating /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZH/spades/scaffolds.fastg: failed to find appropriate name for contig >NODE_12_length_2567_cov_29.1613_ID_287 (looking for names in /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZH/spades/misc/assembled_scaffolds.fastg)! Skipping this contig. ===== Mismatch correction finished. * Corrected reads are in /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZH/spades/corrected/ * Assembled contigs are in /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZH/spades/contigs.fasta (contigs.fastg) * Assembled scaffolds are in /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZH/spades/scaffolds.fasta (scaffolds.fastg) ======= SPAdes pipeline finished. SPAdes log can be found here: /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZH/spades/spades.log Thank you for using SPAdes!