Command line: /usr/common/jgi/assemblers/spades/3.0.0_1/bin/spades.py -o /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZG/spades --phred-offset 33 -t 8 -m 40 --sc --careful --12 /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZG/ZHZG.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/ZHZG/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/ZHZG/ZHZG.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/ZHZG/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/ZHZG/spades/spades.log == Splitting /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZG/ZHZG.bbqc.fq.gz.fastq into left and right reads (in /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZG/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/ZHZG/spades/corrected/configs/config.info 0:00:00.001 4M / 4M INFO General (main.cpp : 82) Loading config from /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZG/spades/corrected/configs/config.info 0:00:00.004 4M / 4M INFO General (memory_limit.hpp : 29) Memory limit set to 40 Gb 0:00:00.004 4M / 4M INFO General (hammer_tools.cpp : 49) Hamming graph threshold tau=1, k=21, subkmer positions = [ 0 10 ] === ITERATION 0 begins === 0:00:00.005 4M / 4M INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:00:00.005 4M / 4M INFO K-mer Splitting (kmer_data.cpp : 127) Splitting kmer instances into 128 buckets. This might take a while. 0:00:00.005 4M / 4M INFO General (file_limit.hpp : 29) Open file limit set to 2048 0:00:00.005 4M / 4M INFO K-mer Splitting (kmer_data.cpp : 150) Memory available for splitting buffers: 1.6665 Gb 0:00:00.005 4M / 4M INFO K-mer Splitting (kmer_data.cpp : 159) Using cell size of 524288 0:00:11.590 8G / 8G INFO K-mer Splitting (kmer_data.cpp : 181) Processed 1482259 reads 0:00:23.207 8G / 8G INFO K-mer Splitting (kmer_data.cpp : 181) Processed 2966906 reads 0:00:34.773 8G / 8G INFO K-mer Splitting (kmer_data.cpp : 181) Processed 4446461 reads 0:00:47.381 8G / 8G INFO K-mer Splitting (kmer_data.cpp : 181) Processed 5945953 reads 0:00:59.033 8G / 8G INFO K-mer Splitting (kmer_data.cpp : 181) Processed 7438671 reads 0:01:10.535 8G / 8G INFO K-mer Splitting (kmer_data.cpp : 181) Processed 8897712 reads 0:01:22.716 8G / 8G INFO K-mer Splitting (kmer_data.cpp : 181) Processed 10356916 reads 0:01:34.299 8G / 8G INFO K-mer Splitting (kmer_data.cpp : 181) Processed 11819924 reads 0:01:45.921 8G / 8G INFO K-mer Splitting (kmer_data.cpp : 181) Processed 13289678 reads 0:02:25.508 8G / 8G INFO K-mer Splitting (kmer_data.cpp : 181) Processed 18075831 reads 0:04:09.331 8G / 8G INFO K-mer Splitting (kmer_data.cpp : 186) Processed 30227690 reads 0:04:09.601 32M / 8G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:04:22.215 32M / 8G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 86729022 kmers in total. 0:04:22.215 32M / 8G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:04:22.993 32M / 8G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:04:35.929 36M / 8G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:04:36.573 36M / 8G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 30002860 bytes occupied (2.7675 bits per kmer). 0:04:36.573 36M / 8G INFO K-mer Counting (kmer_data.cpp : 267) Arranging kmers in hash map order 0:05:04.706 36M / 8G INFO K-mer Counting (kmer_data.cpp : 280) Done. Total swaps: 86728762 0:05:05.176 700M / 8G INFO General (main.cpp : 151) Clustering Hamming graph. 0:05:05.177 700M / 8G INFO Hamming Clustering (hamcluster.cpp : 115) Serializing sub-kmers. 0:05:05.177 700M / 8G INFO Hamming Clustering (hamcluster.cpp : 120) Serializing: [0, 10) 0:05:18.316 696M / 8G INFO Hamming Clustering (hamcluster.cpp : 120) Serializing: [10, 21) 0:05:31.780 696M / 8G INFO Hamming Clustering (hamcluster.cpp : 129) Splitting sub-kmers, pass 1. 0:05:52.688 700M / 8G INFO Hamming Clustering (hamcluster.cpp : 134) Splitting done. Processed 2 blocks. Produced 5208701 blocks. 0:05:52.688 700M / 8G INFO Hamming Clustering (hamcluster.cpp : 145) Merge sub-kmers, pass 1 0:07:29.963 696M / 8G INFO Hamming Clustering (hamcluster.cpp : 170) Merge done, total 883538 new blocks generated. 0:07:30.081 700M / 8G INFO Hamming Clustering (hamcluster.cpp : 175) Spliting sub-kmers, pass 2. 0:08:14.200 728M / 8G INFO Hamming Clustering (hamcluster.cpp : 180) Splitting done. Processed 1767076 blocks. Produced 133230749 blocks. 0:08:14.200 728M / 8G INFO Hamming Clustering (hamcluster.cpp : 187) Merge sub-kmers, pass 2 0:09:14.725 728M / 8G INFO Hamming Clustering (hamcluster.cpp : 205) Merge done, saw 13751 big blocks out of 133230749 processed. 0:09:52.336 724M / 8G INFO General (main.cpp : 165) Clustering done. Total clusters: 31296727 0:09:52.336 728M / 8G INFO K-mer Counting (kmer_data.cpp : 285) Collecting K-mer information, this takes a while. 0:18:55.324 4G / 8G INFO K-mer Counting (kmer_data.cpp : 297) Collection done, postprocessing. 0:18:56.601 4G / 8G INFO K-mer Counting (kmer_data.cpp : 310) There are 86729022 kmers in total. Among them 66346900 (76.4991%) are singletons. 0:18:56.601 4G / 8G INFO General (main.cpp : 203) Subclustering Hamming graph 0:21:17.278 4G / 8G INFO Hamming Subclustering (kmer_cluster.cpp : 654) Subclustering done. Total 371 non-read kmers were generated. 0:21:17.278 4G / 8G INFO Hamming Subclustering (kmer_cluster.cpp : 655) Subclustering statistics: 0:21:17.278 4G / 8G INFO Hamming Subclustering (kmer_cluster.cpp : 656) Total singleton hamming clusters: 30066646. Among them 2714010 (9.02665%) are good 0:21:17.278 4G / 8G INFO Hamming Subclustering (kmer_cluster.cpp : 657) Total singleton subclusters: 14220. Among them 14211 (99.9367%) are good 0:21:17.278 4G / 8G INFO Hamming Subclustering (kmer_cluster.cpp : 658) Total non-singleton subcluster centers: 1423399. Among them 915173 (64.2949%) are good 0:21:17.278 4G / 8G INFO Hamming Subclustering (kmer_cluster.cpp : 659) Average size of non-trivial subcluster: 39.8108 kmers 0:21:17.278 4G / 8G INFO Hamming Subclustering (kmer_cluster.cpp : 660) Average number of sub-clusters per non-singleton cluster: 1.16872 0:21:17.278 4G / 8G INFO Hamming Subclustering (kmer_cluster.cpp : 661) Total solid k-mers: 3643394 0:21:17.278 4G / 8G INFO Hamming Subclustering (kmer_cluster.cpp : 662) Substitution probabilities: [4,4]((0.907086,0.033794,0.0244224,0.0346974),(0.0391083,0.918392,0.0147872,0.0277127),(0.027308,0.0146937,0.918428,0.0395706),(0.0342306,0.0242065,0.0336191,0.907944)) 0:21:17.309 4G / 8G INFO General (main.cpp : 208) Finished clustering. 0:21:17.309 4G / 8G INFO General (main.cpp : 228) Starting solid k-mers expansion in 8 threads. 0:24:46.211 4G / 8G INFO General (main.cpp : 249) Solid k-mers iteration 0 produced 5305372 new k-mers. 0:28:11.544 4G / 8G INFO General (main.cpp : 249) Solid k-mers iteration 1 produced 1226708 new k-mers. 0:31:35.308 4G / 8G INFO General (main.cpp : 249) Solid k-mers iteration 2 produced 56138 new k-mers. 0:34:58.716 4G / 8G INFO General (main.cpp : 249) Solid k-mers iteration 3 produced 4546 new k-mers. 0:38:21.651 4G / 8G INFO General (main.cpp : 249) Solid k-mers iteration 4 produced 887 new k-mers. 0:41:45.516 4G / 8G INFO General (main.cpp : 249) Solid k-mers iteration 5 produced 22 new k-mers. 0:45:09.095 4G / 8G INFO General (main.cpp : 249) Solid k-mers iteration 6 produced 0 new k-mers. 0:45:09.095 4G / 8G INFO General (main.cpp : 253) Solid k-mers finalized 0:45:09.095 4G / 8G INFO General (hammer_tools.cpp : 223) Starting read correction in 8 threads. 0:45:09.095 4G / 8G INFO General (hammer_tools.cpp : 235) Correcting pair of reads: /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZG/spades/split_input/ZHZG.bbqc.fq.gz_1.fastq and /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZG/spades/split_input/ZHZG.bbqc.fq.gz_2.fastq 0:45:14.012 5G / 8G INFO General (hammer_tools.cpp : 179) Prepared batch 0 of 800000 reads. 0:45:24.300 5G / 8G INFO General (hammer_tools.cpp : 188) Processed batch 0 0:45:27.586 5G / 8G INFO General (hammer_tools.cpp : 198) Written batch 0 0:45:31.753 5G / 8G INFO General (hammer_tools.cpp : 179) Prepared batch 1 of 800000 reads. 0:45:42.046 5G / 8G INFO General (hammer_tools.cpp : 188) Processed batch 1 0:45:43.805 5G / 8G INFO General (hammer_tools.cpp : 198) Written batch 1 0:45:47.882 5G / 8G INFO General (hammer_tools.cpp : 179) Prepared batch 2 of 800000 reads. 0:45:58.207 5G / 8G INFO General (hammer_tools.cpp : 188) Processed batch 2 0:45:59.965 5G / 8G INFO General (hammer_tools.cpp : 198) Written batch 2 0:46:04.036 5G / 8G INFO General (hammer_tools.cpp : 179) Prepared batch 3 of 800000 reads. 0:46:14.310 5G / 8G INFO General (hammer_tools.cpp : 188) Processed batch 3 0:46:17.126 5G / 8G INFO General (hammer_tools.cpp : 198) Written batch 3 0:46:21.165 5G / 8G INFO General (hammer_tools.cpp : 179) Prepared batch 4 of 800000 reads. 0:46:31.469 5G / 8G INFO General (hammer_tools.cpp : 188) Processed batch 4 0:46:34.282 5G / 8G INFO General (hammer_tools.cpp : 198) Written batch 4 0:46:38.417 5G / 8G INFO General (hammer_tools.cpp : 179) Prepared batch 5 of 800000 reads. 0:46:48.737 5G / 8G INFO General (hammer_tools.cpp : 188) Processed batch 5 0:46:51.302 5G / 8G INFO General (hammer_tools.cpp : 198) Written batch 5 0:46:55.418 5G / 8G INFO General (hammer_tools.cpp : 179) Prepared batch 6 of 800000 reads. 0:47:05.838 5G / 8G INFO General (hammer_tools.cpp : 188) Processed batch 6 0:47:07.612 5G / 8G INFO General (hammer_tools.cpp : 198) Written batch 6 0:47:11.734 5G / 8G INFO General (hammer_tools.cpp : 179) Prepared batch 7 of 800000 reads. 0:47:22.049 5G / 8G INFO General (hammer_tools.cpp : 188) Processed batch 7 0:47:25.021 5G / 8G INFO General (hammer_tools.cpp : 198) Written batch 7 0:47:29.137 5G / 8G INFO General (hammer_tools.cpp : 179) Prepared batch 8 of 800000 reads. 0:47:39.464 5G / 8G INFO General (hammer_tools.cpp : 188) Processed batch 8 0:47:41.238 5G / 8G INFO General (hammer_tools.cpp : 198) Written batch 8 0:47:45.302 5G / 8G INFO General (hammer_tools.cpp : 179) Prepared batch 9 of 800000 reads. 0:47:55.578 5G / 8G INFO General (hammer_tools.cpp : 188) Processed batch 9 0:47:57.549 5G / 8G INFO General (hammer_tools.cpp : 198) Written batch 9 0:48:01.690 5G / 8G INFO General (hammer_tools.cpp : 179) Prepared batch 10 of 800000 reads. 0:48:12.004 5G / 8G INFO General (hammer_tools.cpp : 188) Processed batch 10 0:48:13.786 5G / 8G INFO General (hammer_tools.cpp : 198) Written batch 10 0:48:17.937 5G / 8G INFO General (hammer_tools.cpp : 179) Prepared batch 11 of 800000 reads. 0:48:28.235 5G / 8G INFO General (hammer_tools.cpp : 188) Processed batch 11 0:48:30.020 5G / 8G INFO General (hammer_tools.cpp : 198) Written batch 11 0:48:34.084 5G / 8G INFO General (hammer_tools.cpp : 179) Prepared batch 12 of 800000 reads. 0:48:44.339 5G / 8G INFO General (hammer_tools.cpp : 188) Processed batch 12 0:48:46.046 5G / 8G INFO General (hammer_tools.cpp : 198) Written batch 12 0:48:50.074 5G / 8G INFO General (hammer_tools.cpp : 179) Prepared batch 13 of 800000 reads. 0:49:00.396 5G / 8G INFO General (hammer_tools.cpp : 188) Processed batch 13 0:49:02.080 5G / 8G INFO General (hammer_tools.cpp : 198) Written batch 13 0:49:06.100 5G / 8G INFO General (hammer_tools.cpp : 179) Prepared batch 14 of 800000 reads. 0:49:16.353 5G / 8G INFO General (hammer_tools.cpp : 188) Processed batch 14 0:49:18.037 5G / 8G INFO General (hammer_tools.cpp : 198) Written batch 14 0:49:22.054 5G / 8G INFO General (hammer_tools.cpp : 179) Prepared batch 15 of 800000 reads. 0:49:32.366 5G / 8G INFO General (hammer_tools.cpp : 188) Processed batch 15 0:49:34.049 5G / 8G INFO General (hammer_tools.cpp : 198) Written batch 15 0:49:38.071 5G / 8G INFO General (hammer_tools.cpp : 179) Prepared batch 16 of 800000 reads. 0:49:48.362 5G / 8G INFO General (hammer_tools.cpp : 188) Processed batch 16 0:49:50.037 5G / 8G INFO General (hammer_tools.cpp : 198) Written batch 16 0:49:54.058 5G / 8G INFO General (hammer_tools.cpp : 179) Prepared batch 17 of 800000 reads. 0:50:04.352 5G / 8G INFO General (hammer_tools.cpp : 188) Processed batch 17 0:50:06.059 5G / 8G INFO General (hammer_tools.cpp : 198) Written batch 17 0:50:09.650 5G / 8G INFO General (hammer_tools.cpp : 179) Prepared batch 18 of 713845 reads. 0:50:18.839 5G / 8G INFO General (hammer_tools.cpp : 188) Processed batch 18 0:50:20.795 5G / 8G INFO General (hammer_tools.cpp : 198) Written batch 18 0:50:21.770 4G / 8G INFO General (hammer_tools.cpp : 282) Correction done. Changed 2843021 bases in 2404473 reads. 0:50:21.770 4G / 8G INFO General (hammer_tools.cpp : 283) Failed to correct 212944603 bases out of 4520525199. 0:50:21.975 696M / 8G INFO General (main.cpp : 286) Saving corrected dataset description to /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZG/spades/corrected/corrected.yaml 0:50:22.003 696M / 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/ZHZG/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/ZHZG/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 0:00:00.022 4M / 4M INFO General (read_converter.hpp : 79) Converting reads to binary format (takes a while) 0:00:00.022 4M / 4M INFO General (read_converter.hpp : 81) Paired reads for library #0 0:00:00.293 80M / 80M INFO General (binary_converter.hpp : 138) 16384 reads processed 0:00:00.474 96M / 96M INFO General (binary_converter.hpp : 138) 32768 reads processed 0:00:00.834 124M / 124M INFO General (binary_converter.hpp : 138) 65536 reads processed 0:00:01.549 184M / 184M INFO General (binary_converter.hpp : 138) 131072 reads processed 0:00:02.975 304M / 304M INFO General (binary_converter.hpp : 138) 262144 reads processed 0:00:05.839 536M / 536M INFO General (binary_converter.hpp : 138) 524288 reads processed 0:00:12.947 904M / 904M INFO General (binary_converter.hpp : 138) 1048576 reads processed 0:00:25.216 904M / 904M INFO General (binary_converter.hpp : 138) 2097152 reads processed 0:00:49.913 904M / 904M INFO General (binary_converter.hpp : 138) 4194304 reads processed 0:01:41.362 904M / 904M INFO General (binary_converter.hpp : 138) 8388608 reads processed 0:03:03.929 292M / 904M INFO General (binary_converter.hpp : 158) 15103812 reads written 0:03:04.254 4M / 904M INFO General (read_converter.hpp : 91) Single reads for library #0 0:03:04.451 136M / 904M INFO General (binary_converter.hpp : 158) 10002 reads written 0:03:04.468 4M / 904M INFO General (graph_construction.hpp : 127) Constructing DeBruijn graph for k=21 0:03:04.469 4M / 904M INFO General (kmer_splitters.hpp : 164) Splitting kmer instances into 64 buckets. This might take a while. 0:03:04.469 4M / 904M INFO General (file_limit.hpp : 29) Open file limit set to 2048 0:03:04.469 4M / 904M INFO General (kmer_splitters.hpp : 187) Memory available for splitting buffers: 1.6665 Gb 0:03:04.469 4M / 904M INFO General (kmer_splitters.hpp : 197) Using cell size of 1048576 0:03:15.791 6G / 6G INFO General (kmer_splitters.hpp : 225) Processed 8346457 reads 0:03:27.252 6G / 6G INFO General (kmer_splitters.hpp : 225) Processed 16693306 reads 0:03:38.682 6G / 6G INFO General (kmer_splitters.hpp : 225) Processed 25040140 reads 0:03:50.163 6G / 6G INFO General (kmer_splitters.hpp : 225) Processed 33387388 reads 0:04:01.659 6G / 6G INFO General (kmer_splitters.hpp : 225) Processed 41736158 reads 0:04:13.141 6G / 6G INFO General (kmer_splitters.hpp : 225) Processed 50086376 reads 0:04:24.691 6G / 6G INFO General (kmer_splitters.hpp : 225) Processed 58434450 reads 0:04:27.593 6G / 6G INFO General (kmer_splitters.hpp : 225) Processed 60435252 reads 0:04:27.593 6G / 6G INFO General (kmer_splitters.hpp : 231) Adding contigs from previous K 0:04:27.593 6G / 6G INFO General (kmer_splitters.hpp : 242) Used 60435252 reads. Maximum read length 150 0:04:27.972 32M / 6G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:04:33.208 32M / 6G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 36438373 kmers in total. 0:04:33.208 32M / 6G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:04:33.521 32M / 6G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:04:33.522 32M / 6G INFO General (kmer_splitters.hpp : 381) Splitting kmer instances into 128 buckets. This might take a while. 0:04:33.522 32M / 6G INFO General (file_limit.hpp : 29) Open file limit set to 2048 0:04:33.522 32M / 6G INFO General (kmer_splitters.hpp : 404) Memory available for splitting buffers: 1.66536 Gb 0:04:33.522 32M / 6G INFO General (kmer_splitters.hpp : 413) Using cell size of 524288 0:04:38.709 8G / 8G INFO General (kmer_splitters.hpp : 436) Processed 36438373 kmers 0:04:38.709 8G / 8G INFO General (kmer_splitters.hpp : 445) Used 36438373 kmers. 0:04:38.787 32M / 8G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:04:42.587 32M / 8G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 34865269 kmers in total. 0:04:42.587 32M / 8G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:04:42.917 32M / 8G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:04:47.015 32M / 8G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:04:47.318 32M / 8G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 12061242 bytes occupied (2.76751 bits per kmer). 0:04:47.358 68M / 8G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 382) Building k-mer extensions from k+1-mers 0:04:50.901 68M / 8G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 386) Building k-mer extensions from k+1-mers finished. 0:04:50.902 68M / 8G INFO Early tip clipping (early_simplification.hpp : 236) Early tip clipping 0:05:44.074 68M / 8G INFO Early tip clipping (early_simplification.hpp : 239) 8218723 22-mers were removed by early tip clipper 0:05:44.074 68M / 8G INFO General (graph_construction.hpp : 143) Condensing graph 0:05:44.074 68M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 346) Extracting unbranching paths 0:06:00.586 868M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 360) Extracting unbranching paths finished. 7393379 sequences extracted 0:06:03.050 864M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 320) Collecting perfect loops 0:06:09.122 864M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 335) Collecting perfect loops finished. 17 loops collected 0:06:11.780 1G / 8G INFO General (graph_construction.hpp : 151) Building index with coverage from graph 0:06:11.782 1G / 8G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:06:11.782 1G / 8G INFO General (kmer_splitters.hpp : 285) Splitting kmer instances into 16 buckets. This might take a while. 0:06:11.782 1G / 8G INFO General (file_limit.hpp : 29) Open file limit set to 2048 0:06:11.782 1G / 8G INFO General (kmer_splitters.hpp : 308) Memory available for splitting buffers: 12.8646 Gb 0:06:11.782 1G / 8G INFO General (kmer_splitters.hpp : 314) Using cell size of 4194304 0:06:16.868 1G / 8G INFO General (kmer_splitters.hpp : 327) Processed 7393396 edges 0:06:16.868 1G / 8G INFO General (kmer_splitters.hpp : 332) Used 7393396 sequences. 0:06:16.888 1G / 8G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:06:19.606 1G / 8G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 28219649 kmers in total. 0:06:19.606 1G / 8G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:06:19.800 1G / 8G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:06:35.036 1G / 8G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:06:35.222 1G / 8G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 9762270 bytes occupied (2.76751 bits per kmer). 0:06:35.572 2G / 8G INFO General (edge_index_builders.hpp : 21) Collecting k-mer coverage information from graph, this takes a while. 0:07:01.446 2G / 8G INFO General (edge_index_builders.hpp : 99) Collecting k-mer coverage information from reads, this takes a while. 0:12:07.713 1G / 8G INFO General (graph_construction.hpp : 179) Filling coverage and flanking coverage from index 0:12:18.290 1G / 8G INFO General (construction.cpp : 32) Figured out: read length = 150 0:12:18.290 1G / 8G INFO StageManager (stage.cpp : 125) STAGE == EC Threshold Finding 0:12:25.582 1G / 8G INFO ThresholdFinder (omni_tools.hpp : 466) Bucket size: 46 0:12:25.584 1G / 8G INFO General (genomic_info_filler.cpp : 72) Average edge coverage: 137.443 0:12:25.584 1G / 8G INFO General (genomic_info_filler.cpp : 73) Graph threshold: 441 0:12:28.108 2G / 8G INFO General (genomic_info_filler.cpp : 101) EC coverage threshold value was calculated as 441 0:12:28.109 2G / 8G INFO StageManager (stage.cpp : 125) STAGE == Simplification 0:12:28.151 2G / 8G INFO General (graph_simplification.hpp : 633) PROCEDURE == Presimplification 0:12:28.151 2G / 8G INFO General (graph_simplification.hpp : 416) Removing short low covered self-conjugate connections 0:12:51.453 2G / 8G INFO General (graph_simplification.hpp : 713) PROCEDURE == Simplification cycle, iteration 1 0:12:51.463 2G / 8G INFO General (graph_simplification.hpp : 309) Clipping tips 0:13:13.666 2G / 8G INFO General (graph_simplification.hpp : 370) Removing bulges 0:30:42.360 2G / 8G INFO General (graph_simplification.hpp : 397) Removing low covered connections 0:32:56.769 1G / 8G INFO General (graph_simplification.hpp : 713) PROCEDURE == Simplification cycle, iteration 2 0:32:56.769 1G / 8G INFO General (graph_simplification.hpp : 309) Clipping tips 0:32:57.883 1G / 8G INFO General (graph_simplification.hpp : 370) Removing bulges 0:33:27.284 1G / 8G INFO General (graph_simplification.hpp : 397) Removing low covered connections 0:33:27.888 1G / 8G INFO General (graph_simplification.hpp : 713) PROCEDURE == Simplification cycle, iteration 3 0:33:27.888 1G / 8G INFO General (graph_simplification.hpp : 309) Clipping tips 0:33:27.983 1G / 8G INFO General (graph_simplification.hpp : 370) Removing bulges 0:33:29.252 1G / 8G INFO General (graph_simplification.hpp : 397) Removing low covered connections 0:33:29.525 1G / 8G INFO General (graph_simplification.hpp : 713) PROCEDURE == Simplification cycle, iteration 4 0:33:29.525 1G / 8G INFO General (graph_simplification.hpp : 309) Clipping tips 0:33:29.605 1G / 8G INFO General (graph_simplification.hpp : 370) Removing bulges 0:33:30.379 1G / 8G INFO General (graph_simplification.hpp : 397) Removing low covered connections 0:33:30.562 1G / 8G INFO General (graph_simplification.hpp : 713) PROCEDURE == Simplification cycle, iteration 5 0:33:30.562 1G / 8G INFO General (graph_simplification.hpp : 309) Clipping tips 0:33:30.637 1G / 8G INFO General (graph_simplification.hpp : 370) Removing bulges 0:33:31.329 1G / 8G INFO General (graph_simplification.hpp : 397) Removing low covered connections 0:33:31.534 1G / 8G INFO General (graph_simplification.hpp : 713) PROCEDURE == Simplification cycle, iteration 6 0:33:31.535 1G / 8G INFO General (graph_simplification.hpp : 309) Clipping tips 0:33:31.609 1G / 8G INFO General (graph_simplification.hpp : 370) Removing bulges 0:33:32.231 1G / 8G INFO General (graph_simplification.hpp : 397) Removing low covered connections 0:33:32.374 1G / 8G INFO General (graph_simplification.hpp : 713) PROCEDURE == Simplification cycle, iteration 7 0:33:32.374 1G / 8G INFO General (graph_simplification.hpp : 309) Clipping tips 0:33:32.441 1G / 8G INFO General (graph_simplification.hpp : 370) Removing bulges 0:33:33.036 1G / 8G INFO General (graph_simplification.hpp : 397) Removing low covered connections 0:33:33.173 1G / 8G INFO General (graph_simplification.hpp : 713) PROCEDURE == Simplification cycle, iteration 8 0:33:33.173 1G / 8G INFO General (graph_simplification.hpp : 309) Clipping tips 0:33:33.237 1G / 8G INFO General (graph_simplification.hpp : 370) Removing bulges 0:33:33.801 1G / 8G INFO General (graph_simplification.hpp : 397) Removing low covered connections 0:33:33.920 1G / 8G INFO General (graph_simplification.hpp : 713) PROCEDURE == Simplification cycle, iteration 9 0:33:33.920 1G / 8G INFO General (graph_simplification.hpp : 309) Clipping tips 0:33:33.980 1G / 8G INFO General (graph_simplification.hpp : 370) Removing bulges 0:33:34.543 1G / 8G INFO General (graph_simplification.hpp : 397) Removing low covered connections 0:33:34.664 1G / 8G INFO General (graph_simplification.hpp : 713) PROCEDURE == Simplification cycle, iteration 10 0:33:34.664 1G / 8G INFO General (graph_simplification.hpp : 309) Clipping tips 0:33:34.725 1G / 8G INFO General (graph_simplification.hpp : 370) Removing bulges 0:33:35.266 1G / 8G INFO General (graph_simplification.hpp : 397) Removing low covered connections 0:33:35.379 1G / 8G INFO General (graph_simplification.hpp : 659) PROCEDURE == Post simplification 0:33:35.379 1G / 8G INFO General (graph_simplification.hpp : 665) Iteration 0 0:33:35.379 1G / 8G INFO General (graph_simplification.hpp : 471) Clipping tips based on topology 0:33:35.446 1G / 8G INFO General (graph_simplification.hpp : 447) Removal of relatively low covered connections disabled 0:33:35.446 1G / 8G INFO General (graph_simplification.hpp : 309) Clipping tips 0:33:35.502 1G / 8G INFO General (graph_simplification.hpp : 370) Removing bulges 0:33:36.038 1G / 8G INFO General (graph_simplification.hpp : 565) Removing hidden erroneous connections 0:33:36.289 1G / 8G INFO StageManager (stage.cpp : 125) STAGE == Simplification Cleanup 0:33:36.289 1G / 8G INFO General (simplification.cpp : 71) Final isolated edges removal: 0:33:36.289 1G / 8G INFO General (simplification.cpp : 73) All edges of length smaller than 150 will be removed 0:33:36.522 1G / 8G INFO General (simplification.cpp : 77) Removed 1646 edges 0:33:36.522 1G / 8G INFO General (simplification.cpp : 106) Counting average coverage 0:33:36.532 1G / 8G INFO General (simplification.cpp : 109) Average coverage = 2992.25 0:33:36.532 1G / 8G INFO StageManager (stage.cpp : 125) STAGE == Contig Output 0:33:36.543 1G / 8G INFO General (contig_output.hpp : 295) Outputting contigs to /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZG/spades//K21/simplified_contigs.fasta 0:33:37.132 1G / 8G INFO General (contig_output.hpp : 295) Outputting contigs to /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZG/spades//K21/before_rr.fasta 0:33:38.245 1G / 8G INFO General (contig_output.hpp : 295) Outputting contigs to /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZG/spades//K21/final_contigs.fasta 0:33:39.238 1G / 8G INFO General (launch.hpp : 84) SPAdes finished 0:33:39.865 32M / 8G INFO General (main.cpp : 166) Assembling time: 0 hours 33 minutes 39 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/ZHZG/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 0:00:00.001 4M / 4M INFO General (read_converter.hpp : 49) Binary reads detected 0:00:00.050 4M / 4M INFO General (graph_construction.hpp : 127) Constructing DeBruijn graph for k=33 0:00:00.050 4M / 4M INFO General (kmer_splitters.hpp : 164) Splitting kmer instances into 64 buckets. This might take a while. 0:00:00.050 4M / 4M INFO General (file_limit.hpp : 29) Open file limit set to 2048 0:00:00.050 4M / 4M INFO General (kmer_splitters.hpp : 187) Memory available for splitting buffers: 1.6665 Gb 0:00:00.050 4M / 4M INFO General (kmer_splitters.hpp : 197) Using cell size of 524288 0:00:06.572 6G / 6G INFO General (kmer_splitters.hpp : 225) Processed 4605511 reads 0:00:14.292 6G / 6G INFO General (kmer_splitters.hpp : 225) Processed 9210858 reads 0:00:23.217 6G / 6G INFO General (kmer_splitters.hpp : 225) Processed 13815891 reads 0:00:31.913 6G / 6G INFO General (kmer_splitters.hpp : 225) Processed 18422056 reads 0:00:39.632 6G / 6G INFO General (kmer_splitters.hpp : 225) Processed 23027667 reads 0:00:47.142 6G / 6G INFO General (kmer_splitters.hpp : 225) Processed 27632541 reads 0:00:55.432 6G / 6G INFO General (kmer_splitters.hpp : 225) Processed 32238522 reads 0:01:03.766 6G / 6G INFO General (kmer_splitters.hpp : 225) Processed 36845092 reads 0:01:11.208 6G / 6G INFO General (kmer_splitters.hpp : 225) Processed 41452133 reads 0:01:19.424 6G / 6G INFO General (kmer_splitters.hpp : 225) Processed 46059634 reads 0:01:27.779 6G / 6G INFO General (kmer_splitters.hpp : 225) Processed 50667060 reads 0:01:45.295 6G / 6G INFO General (kmer_splitters.hpp : 231) Adding contigs from previous K 0:01:45.500 6G / 6G INFO General (kmer_splitters.hpp : 242) Used 60435252 reads. Maximum read length 150 0:01:45.884 32M / 6G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:01:58.263 32M / 6G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 52521698 kmers in total. 0:01:58.263 32M / 6G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:01:59.134 32M / 6G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:01:59.134 32M / 6G INFO General (kmer_splitters.hpp : 381) Splitting kmer instances into 128 buckets. This might take a while. 0:01:59.134 32M / 6G INFO General (file_limit.hpp : 29) Open file limit set to 2048 0:01:59.134 32M / 6G INFO General (kmer_splitters.hpp : 404) Memory available for splitting buffers: 1.66536 Gb 0:01:59.134 32M / 6G INFO General (kmer_splitters.hpp : 413) Using cell size of 262144 0:02:07.274 8G / 8G INFO General (kmer_splitters.hpp : 436) Processed 52521698 kmers 0:02:07.274 8G / 8G INFO General (kmer_splitters.hpp : 445) Used 52521698 kmers. 0:02:07.439 32M / 8G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:02:19.690 32M / 8G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 51372161 kmers in total. 0:02:19.690 32M / 8G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:02:20.621 32M / 8G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:02:28.859 32M / 8G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:02:29.726 32M / 8G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 17771595 bytes occupied (2.76751 bits per kmer). 0:02:29.786 84M / 8G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 382) Building k-mer extensions from k+1-mers 0:02:35.872 84M / 8G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 386) Building k-mer extensions from k+1-mers finished. 0:02:35.872 84M / 8G INFO Early tip clipping (early_simplification.hpp : 236) Early tip clipping 0:03:57.102 84M / 8G INFO Early tip clipping (early_simplification.hpp : 239) 14771890 34-mers were removed by early tip clipper 0:03:57.102 84M / 8G INFO General (graph_construction.hpp : 143) Condensing graph 0:03:57.102 84M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 346) Extracting unbranching paths 0:04:22.950 616M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 360) Extracting unbranching paths finished. 5967432 sequences extracted 0:04:26.831 616M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 320) Collecting perfect loops 0:04:36.168 616M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 335) Collecting perfect loops finished. 27 loops collected 0:04:38.456 1G / 8G INFO General (graph_construction.hpp : 151) Building index with coverage from graph 0:04:38.458 1G / 8G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:04:38.458 1G / 8G INFO General (kmer_splitters.hpp : 285) Splitting kmer instances into 16 buckets. This might take a while. 0:04:38.458 1G / 8G INFO General (file_limit.hpp : 29) Open file limit set to 2048 0:04:38.458 1G / 8G INFO General (kmer_splitters.hpp : 308) Memory available for splitting buffers: 12.931 Gb 0:04:38.458 1G / 8G INFO General (kmer_splitters.hpp : 314) Using cell size of 2097152 0:04:44.371 1G / 8G INFO General (kmer_splitters.hpp : 327) Processed 5304662 edges 0:04:46.361 1G / 8G INFO General (kmer_splitters.hpp : 327) Processed 5967459 edges 0:04:46.361 1G / 8G INFO General (kmer_splitters.hpp : 332) Used 5967459 sequences. 0:04:46.399 1G / 8G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:04:54.719 1G / 8G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 37749807 kmers in total. 0:04:54.719 1G / 8G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:04:55.181 1G / 8G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:05:19.281 1G / 8G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:05:19.771 1G / 8G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 13059106 bytes occupied (2.76751 bits per kmer). 0:05:20.236 2G / 8G INFO General (edge_index_builders.hpp : 21) Collecting k-mer coverage information from graph, this takes a while. 0:05:59.463 2G / 8G INFO General (edge_index_builders.hpp : 99) Collecting k-mer coverage information from reads, this takes a while. 0:11:05.211 2G / 8G INFO General (graph_construction.hpp : 179) Filling coverage and flanking coverage from index 0:11:16.556 2G / 8G INFO General (construction.cpp : 32) Figured out: read length = 150 0:11:16.556 2G / 8G INFO StageManager (stage.cpp : 125) STAGE == EC Threshold Finding 0:11:22.437 2G / 8G INFO ThresholdFinder (omni_tools.hpp : 466) Bucket size: 32 0:11:22.438 2G / 8G INFO General (genomic_info_filler.cpp : 72) Average edge coverage: 92.9067 0:11:22.438 2G / 8G INFO General (genomic_info_filler.cpp : 73) Graph threshold: 345 0:11:22.945 2G / 8G INFO General (genomic_info_filler.cpp : 101) EC coverage threshold value was calculated as 345 0:11:22.945 2G / 8G INFO StageManager (stage.cpp : 125) STAGE == Simplification 0:11:22.946 2G / 8G INFO General (graph_simplification.hpp : 633) PROCEDURE == Presimplification 0:11:22.946 2G / 8G INFO General (graph_simplification.hpp : 416) Removing short low covered self-conjugate connections 0:11:41.614 2G / 8G INFO General (graph_simplification.hpp : 713) PROCEDURE == Simplification cycle, iteration 1 0:11:41.614 2G / 8G INFO General (graph_simplification.hpp : 309) Clipping tips 0:12:00.802 2G / 8G INFO General (graph_simplification.hpp : 370) Removing bulges 0:23:14.174 2G / 8G INFO General (graph_simplification.hpp : 397) Removing low covered connections 0:25:43.512 2G / 8G INFO General (graph_simplification.hpp : 713) PROCEDURE == Simplification cycle, iteration 2 0:25:43.512 2G / 8G INFO General (graph_simplification.hpp : 309) Clipping tips 0:25:45.925 1G / 8G INFO General (graph_simplification.hpp : 370) Removing bulges 0:26:12.176 1G / 8G INFO General (graph_simplification.hpp : 397) Removing low covered connections 0:26:13.037 1G / 8G INFO General (graph_simplification.hpp : 713) PROCEDURE == Simplification cycle, iteration 3 0:26:13.037 1G / 8G INFO General (graph_simplification.hpp : 309) Clipping tips 0:26:13.362 1G / 8G INFO General (graph_simplification.hpp : 370) Removing bulges 0:26:14.171 1G / 8G INFO General (graph_simplification.hpp : 397) Removing low covered connections 0:26:14.672 1G / 8G INFO General (graph_simplification.hpp : 713) PROCEDURE == Simplification cycle, iteration 4 0:26:14.672 1G / 8G INFO General (graph_simplification.hpp : 309) Clipping tips 0:26:14.926 1G / 8G INFO General (graph_simplification.hpp : 370) Removing bulges 0:26:15.472 1G / 8G INFO General (graph_simplification.hpp : 397) Removing low covered connections 0:26:15.912 1G / 8G INFO General (graph_simplification.hpp : 713) PROCEDURE == Simplification cycle, iteration 5 0:26:15.912 1G / 8G INFO General (graph_simplification.hpp : 309) Clipping tips 0:26:16.157 1G / 8G INFO General (graph_simplification.hpp : 370) Removing bulges 0:26:16.623 1G / 8G INFO General (graph_simplification.hpp : 397) Removing low covered connections 0:26:17.010 1G / 8G INFO General (graph_simplification.hpp : 713) PROCEDURE == Simplification cycle, iteration 6 0:26:17.010 1G / 8G INFO General (graph_simplification.hpp : 309) Clipping tips 0:26:17.252 1G / 8G INFO General (graph_simplification.hpp : 370) Removing bulges 0:26:17.687 1G / 8G INFO General (graph_simplification.hpp : 397) Removing low covered connections 0:26:18.051 1G / 8G INFO General (graph_simplification.hpp : 713) PROCEDURE == Simplification cycle, iteration 7 0:26:18.051 1G / 8G INFO General (graph_simplification.hpp : 309) Clipping tips 0:26:18.290 1G / 8G INFO General (graph_simplification.hpp : 370) Removing bulges 0:26:18.699 1G / 8G INFO General (graph_simplification.hpp : 397) Removing low covered connections 0:26:19.049 1G / 8G INFO General (graph_simplification.hpp : 713) PROCEDURE == Simplification cycle, iteration 8 0:26:19.049 1G / 8G INFO General (graph_simplification.hpp : 309) Clipping tips 0:26:19.286 1G / 8G INFO General (graph_simplification.hpp : 370) Removing bulges 0:26:19.690 1G / 8G INFO General (graph_simplification.hpp : 397) Removing low covered connections 0:26:20.023 1G / 8G INFO General (graph_simplification.hpp : 713) PROCEDURE == Simplification cycle, iteration 9 0:26:20.023 1G / 8G INFO General (graph_simplification.hpp : 309) Clipping tips 0:26:20.260 1G / 8G INFO General (graph_simplification.hpp : 370) Removing bulges 0:26:20.651 1G / 8G INFO General (graph_simplification.hpp : 397) Removing low covered connections 0:26:20.988 1G / 8G INFO General (graph_simplification.hpp : 713) PROCEDURE == Simplification cycle, iteration 10 0:26:20.988 1G / 8G INFO General (graph_simplification.hpp : 309) Clipping tips 0:26:21.224 1G / 8G INFO General (graph_simplification.hpp : 370) Removing bulges 0:26:21.616 1G / 8G INFO General (graph_simplification.hpp : 397) Removing low covered connections 0:26:21.958 1G / 8G INFO General (graph_simplification.hpp : 659) PROCEDURE == Post simplification 0:26:21.958 1G / 8G INFO General (graph_simplification.hpp : 665) Iteration 0 0:26:21.958 1G / 8G INFO General (graph_simplification.hpp : 471) Clipping tips based on topology 0:26:22.193 1G / 8G INFO General (graph_simplification.hpp : 447) Removal of relatively low covered connections disabled 0:26:22.194 1G / 8G INFO General (graph_simplification.hpp : 309) Clipping tips 0:26:22.426 1G / 8G INFO General (graph_simplification.hpp : 370) Removing bulges 0:26:22.814 1G / 8G INFO General (graph_simplification.hpp : 565) Removing hidden erroneous connections 0:26:23.588 1G / 8G INFO StageManager (stage.cpp : 125) STAGE == Simplification Cleanup 0:26:23.589 1G / 8G INFO General (simplification.cpp : 71) Final isolated edges removal: 0:26:23.589 1G / 8G INFO General (simplification.cpp : 73) All edges of length smaller than 150 will be removed 0:26:28.479 1G / 8G INFO General (simplification.cpp : 77) Removed 46316 edges 0:26:28.479 1G / 8G INFO General (simplification.cpp : 106) Counting average coverage 0:26:28.488 1G / 8G INFO General (simplification.cpp : 109) Average coverage = 3512.53 0:26:28.488 1G / 8G INFO StageManager (stage.cpp : 125) STAGE == Contig Output 0:26:28.488 1G / 8G INFO General (contig_output.hpp : 295) Outputting contigs to /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZG/spades//K33/simplified_contigs.fasta 0:26:28.923 1G / 8G INFO General (contig_output.hpp : 295) Outputting contigs to /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZG/spades//K33/before_rr.fasta 0:26:29.593 1G / 8G INFO General (contig_output.hpp : 295) Outputting contigs to /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZG/spades//K33/final_contigs.fasta 0:26:30.215 1G / 8G INFO General (launch.hpp : 84) SPAdes finished 0:26:30.588 32M / 8G INFO General (main.cpp : 166) Assembling time: 0 hours 26 minutes 30 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/ZHZG/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 0:00:06.647 6G / 6G INFO General (kmer_splitters.hpp : 225) Processed 5676697 reads 0:00:15.195 6G / 6G INFO General (kmer_splitters.hpp : 225) Processed 11353294 reads 0:00:22.976 6G / 6G INFO General (kmer_splitters.hpp : 225) Processed 17030582 reads 0:00:33.731 6G / 6G INFO General (kmer_splitters.hpp : 225) Processed 22707811 reads 0:00:41.947 6G / 6G INFO General (kmer_splitters.hpp : 225) Processed 28383971 reads 0:00:49.673 6G / 6G INFO General (kmer_splitters.hpp : 225) Processed 34061681 reads 0:00:57.806 6G / 6G INFO General (kmer_splitters.hpp : 225) Processed 39740349 reads 0:01:07.016 6G / 6G INFO General (kmer_splitters.hpp : 225) Processed 45420421 reads 0:01:14.544 6G / 6G INFO General (kmer_splitters.hpp : 225) Processed 51099818 reads 0:01:22.582 6G / 6G INFO General (kmer_splitters.hpp : 225) Processed 56778530 reads 0:01:27.851 6G / 6G INFO General (kmer_splitters.hpp : 225) Processed 60435252 reads 0:01:27.851 6G / 6G INFO General (kmer_splitters.hpp : 231) Adding contigs from previous K 0:01:28.046 6G / 6G INFO General (kmer_splitters.hpp : 242) Used 60435252 reads. Maximum read length 150 0:01:28.425 32M / 6G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:01:43.331 32M / 6G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 70008225 kmers in total. 0:01:43.331 32M / 6G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:01:44.298 32M / 6G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:01:44.298 32M / 6G INFO General (kmer_splitters.hpp : 381) Splitting kmer instances into 128 buckets. This might take a while. 0:01:44.298 32M / 6G INFO General (file_limit.hpp : 29) Open file limit set to 2048 0:01:44.298 32M / 6G INFO General (kmer_splitters.hpp : 404) Memory available for splitting buffers: 1.66536 Gb 0:01:44.298 32M / 6G INFO General (kmer_splitters.hpp : 413) Using cell size of 262144 0:01:56.983 8G / 8G INFO General (kmer_splitters.hpp : 436) Processed 70008225 kmers 0:01:56.983 8G / 8G INFO General (kmer_splitters.hpp : 445) Used 70008225 kmers. 0:01:57.178 32M / 8G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:02:13.535 32M / 8G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 69515320 kmers in total. 0:02:13.535 32M / 8G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:02:14.756 32M / 8G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:02:25.979 32M / 8G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:02:27.135 32M / 8G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 24047996 bytes occupied (2.7675 bits per kmer). 0:02:27.217 100M / 8G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 382) Building k-mer extensions from k+1-mers 0:02:37.534 100M / 8G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 386) Building k-mer extensions from k+1-mers finished. 0:02:37.535 100M / 8G INFO General (graph_construction.hpp : 143) Condensing graph 0:02:37.535 100M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 346) Extracting unbranching paths 0:03:08.529 964M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 360) Extracting unbranching paths finished. 6671410 sequences extracted 0:03:16.573 960M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 320) Collecting perfect loops 0:03:29.364 960M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 335) Collecting perfect loops finished. 6 loops collected 0:03:32.395 1G / 8G INFO General (graph_construction.hpp : 151) Building index with coverage from graph 0:03:32.397 1G / 8G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:03:32.397 1G / 8G INFO General (kmer_splitters.hpp : 285) Splitting kmer instances into 16 buckets. This might take a while. 0:03:32.397 1G / 8G INFO General (file_limit.hpp : 29) Open file limit set to 2048 0:03:32.397 1G / 8G INFO General (kmer_splitters.hpp : 308) Memory available for splitting buffers: 12.8294 Gb 0:03:32.397 1G / 8G INFO General (kmer_splitters.hpp : 314) Using cell size of 2097152 0:03:37.458 2G / 8G INFO General (kmer_splitters.hpp : 327) Processed 3198647 edges 0:03:43.085 2G / 8G INFO General (kmer_splitters.hpp : 327) Processed 6395528 edges 0:03:44.026 2G / 8G INFO General (kmer_splitters.hpp : 327) Processed 6671416 edges 0:03:44.026 2G / 8G INFO General (kmer_splitters.hpp : 332) Used 6671416 sequences. 0:03:44.064 1G / 8G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:04:03.036 1G / 8G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 70008225 kmers in total. 0:04:03.036 1G / 8G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:04:04.515 1G / 8G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:05:00.912 1G / 8G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:05:01.954 1G / 8G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 24218506 bytes occupied (2.7675 bits per kmer). 0:05:02.782 3G / 8G INFO General (edge_index_builders.hpp : 21) Collecting k-mer coverage information from graph, this takes a while. 0:06:30.214 3G / 8G INFO General (edge_index_builders.hpp : 99) Collecting k-mer coverage information from reads, this takes a while. 0:11:31.835 3G / 8G INFO General (graph_construction.hpp : 179) Filling coverage and flanking coverage from index 0:11:54.102 3G / 8G INFO General (construction.cpp : 32) Figured out: read length = 150 0:11:54.102 3G / 8G INFO StageManager (stage.cpp : 125) STAGE == EC Threshold Finding 0:11:59.849 3G / 8G INFO ThresholdFinder (omni_tools.hpp : 466) Bucket size: 17 0:11:59.849 3G / 8G INFO General (genomic_info_filler.cpp : 72) Average edge coverage: 40.8133 0:11:59.849 3G / 8G INFO General (genomic_info_filler.cpp : 73) Graph threshold: 251 0:12:00.239 3G / 8G INFO General (genomic_info_filler.cpp : 101) EC coverage threshold value was calculated as 251 0:12:00.240 3G / 8G INFO StageManager (stage.cpp : 125) STAGE == Gap Closer 0:12:00.240 3G / 8G INFO General (gap_closer.cpp : 178) Preparing shift maps 0:12:04.354 3G / 8G INFO General (gap_closer.cpp : 132) Processing paired reads (takes a while) 0:23:24.862 3G / 8G INFO General (gap_closer.cpp : 158) Used 30207624 paired reads 0:23:24.863 3G / 8G INFO General (gap_closer.cpp : 160) Merging paired indices 0:23:24.983 3G / 8G INFO GapCloser (gap_closer.cpp : 409) Closing short gaps 0:23:32.436 3G / 8G INFO GapCloser (gap_closer.cpp : 438) Closing short gaps complete: filled 21 gaps after checking 3724 candidates 0:23:34.462 3G / 8G INFO General (gap_closer.cpp : 506) Detaching and clearing index 0:23:34.547 1G / 8G INFO General (gap_closer.cpp : 509) Index clearing finished 0:23:34.547 1G / 8G INFO StageManager (stage.cpp : 125) STAGE == Simplification 0:23:34.548 1G / 8G INFO General (graph_simplification.hpp : 633) PROCEDURE == Presimplification 0:23:34.548 1G / 8G INFO General (graph_simplification.hpp : 416) Removing short low covered self-conjugate connections 0:23:57.190 1G / 8G INFO General (graph_simplification.hpp : 713) PROCEDURE == Simplification cycle, iteration 1 0:23:57.190 1G / 8G INFO General (graph_simplification.hpp : 309) Clipping tips 0:24:33.292 1G / 8G INFO General (graph_simplification.hpp : 370) Removing bulges 0:28:12.595 2G / 8G INFO General (graph_simplification.hpp : 397) Removing low covered connections 0:28:51.188 2G / 8G INFO General (graph_simplification.hpp : 713) PROCEDURE == Simplification cycle, iteration 2 0:28:51.188 2G / 8G INFO General (graph_simplification.hpp : 309) Clipping tips 0:28:53.099 2G / 8G INFO General (graph_simplification.hpp : 370) Removing bulges 0:29:03.153 2G / 8G INFO General (graph_simplification.hpp : 397) Removing low covered connections 0:29:04.352 2G / 8G INFO General (graph_simplification.hpp : 713) PROCEDURE == Simplification cycle, iteration 3 0:29:04.352 2G / 8G INFO General (graph_simplification.hpp : 309) Clipping tips 0:29:05.217 2G / 8G INFO General (graph_simplification.hpp : 370) Removing bulges 0:29:06.517 2G / 8G INFO General (graph_simplification.hpp : 397) Removing low covered connections 0:29:07.651 2G / 8G INFO General (graph_simplification.hpp : 713) PROCEDURE == Simplification cycle, iteration 4 0:29:07.651 2G / 8G INFO General (graph_simplification.hpp : 309) Clipping tips 0:29:08.502 2G / 8G INFO General (graph_simplification.hpp : 370) Removing bulges 0:29:09.697 2G / 8G INFO General (graph_simplification.hpp : 397) Removing low covered connections 0:29:10.810 2G / 8G INFO General (graph_simplification.hpp : 713) PROCEDURE == Simplification cycle, iteration 5 0:29:10.810 2G / 8G INFO General (graph_simplification.hpp : 309) Clipping tips 0:29:11.659 2G / 8G INFO General (graph_simplification.hpp : 370) Removing bulges 0:29:12.825 2G / 8G INFO General (graph_simplification.hpp : 397) Removing low covered connections 0:29:13.928 2G / 8G INFO General (graph_simplification.hpp : 713) PROCEDURE == Simplification cycle, iteration 6 0:29:13.928 2G / 8G INFO General (graph_simplification.hpp : 309) Clipping tips 0:29:14.773 2G / 8G INFO General (graph_simplification.hpp : 370) Removing bulges 0:29:15.925 2G / 8G INFO General (graph_simplification.hpp : 397) Removing low covered connections 0:29:17.020 2G / 8G INFO General (graph_simplification.hpp : 713) PROCEDURE == Simplification cycle, iteration 7 0:29:17.020 2G / 8G INFO General (graph_simplification.hpp : 309) Clipping tips 0:29:17.865 2G / 8G INFO General (graph_simplification.hpp : 370) Removing bulges 0:29:19.009 2G / 8G INFO General (graph_simplification.hpp : 397) Removing low covered connections 0:29:20.103 2G / 8G INFO General (graph_simplification.hpp : 713) PROCEDURE == Simplification cycle, iteration 8 0:29:20.103 2G / 8G INFO General (graph_simplification.hpp : 309) Clipping tips 0:29:20.948 2G / 8G INFO General (graph_simplification.hpp : 370) Removing bulges 0:29:22.084 2G / 8G INFO General (graph_simplification.hpp : 397) Removing low covered connections 0:29:23.173 2G / 8G INFO General (graph_simplification.hpp : 713) PROCEDURE == Simplification cycle, iteration 9 0:29:23.173 2G / 8G INFO General (graph_simplification.hpp : 309) Clipping tips 0:29:24.014 2G / 8G INFO General (graph_simplification.hpp : 370) Removing bulges 0:29:25.147 2G / 8G INFO General (graph_simplification.hpp : 397) Removing low covered connections 0:29:26.234 2G / 8G INFO General (graph_simplification.hpp : 713) PROCEDURE == Simplification cycle, iteration 10 0:29:26.234 2G / 8G INFO General (graph_simplification.hpp : 309) Clipping tips 0:29:27.076 2G / 8G INFO General (graph_simplification.hpp : 370) Removing bulges 0:29:28.206 2G / 8G INFO General (graph_simplification.hpp : 397) Removing low covered connections 0:29:29.295 2G / 8G INFO General (graph_simplification.hpp : 659) PROCEDURE == Post simplification 0:29:29.295 2G / 8G INFO General (graph_simplification.hpp : 665) Iteration 0 0:29:29.295 2G / 8G INFO General (graph_simplification.hpp : 471) Clipping tips based on topology 0:29:30.142 2G / 8G INFO General (graph_simplification.hpp : 447) Removal of relatively low covered connections disabled 0:29:30.142 2G / 8G INFO General (graph_simplification.hpp : 457) Removing connections based on topology 0:29:31.022 2G / 8G INFO General (graph_simplification.hpp : 513) Removing connections based on topology and reliable coverage 0:29:31.899 2G / 8G INFO General (graph_simplification.hpp : 500) Removing interstrand connections 0:29:34.957 2G / 8G INFO General (graph_simplification.hpp : 487) Removing connections based on topological multiplicity counting 0:29:35.827 2G / 8G INFO General (graph_simplification.hpp : 309) Clipping tips 0:29:36.661 2G / 8G INFO General (graph_simplification.hpp : 370) Removing bulges 0:29:37.765 2G / 8G INFO General (graph_simplification.hpp : 665) Iteration 1 0:29:37.765 2G / 8G INFO General (graph_simplification.hpp : 471) Clipping tips based on topology 0:29:38.598 2G / 8G INFO General (graph_simplification.hpp : 447) Removal of relatively low covered connections disabled 0:29:38.598 2G / 8G INFO General (graph_simplification.hpp : 457) Removing connections based on topology 0:29:39.468 2G / 8G INFO General (graph_simplification.hpp : 513) Removing connections based on topology and reliable coverage 0:29:40.339 2G / 8G INFO General (graph_simplification.hpp : 500) Removing interstrand connections 0:29:41.410 2G / 8G INFO General (graph_simplification.hpp : 487) Removing connections based on topological multiplicity counting 0:29:42.280 2G / 8G INFO General (graph_simplification.hpp : 309) Clipping tips 0:29:43.117 2G / 8G INFO General (graph_simplification.hpp : 370) Removing bulges 0:29:44.216 2G / 8G INFO General (graph_simplification.hpp : 665) Iteration 2 0:29:44.216 2G / 8G INFO General (graph_simplification.hpp : 471) Clipping tips based on topology 0:29:45.049 2G / 8G INFO General (graph_simplification.hpp : 447) Removal of relatively low covered connections disabled 0:29:45.049 2G / 8G INFO General (graph_simplification.hpp : 457) Removing connections based on topology 0:29:45.919 2G / 8G INFO General (graph_simplification.hpp : 513) Removing connections based on topology and reliable coverage 0:29:46.788 2G / 8G INFO General (graph_simplification.hpp : 500) Removing interstrand connections 0:29:47.861 2G / 8G INFO General (graph_simplification.hpp : 487) Removing connections based on topological multiplicity counting 0:29:48.730 2G / 8G INFO General (graph_simplification.hpp : 309) Clipping tips 0:29:49.564 2G / 8G INFO General (graph_simplification.hpp : 370) Removing bulges 0:29:50.662 2G / 8G INFO General (graph_simplification.hpp : 565) Removing hidden erroneous connections 0:29:51.374 2G / 8G INFO StageManager (stage.cpp : 125) STAGE == Gap Closer 0:29:51.374 2G / 8G INFO General (gap_closer.cpp : 489) Refilling index 0:29:51.375 2G / 8G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:29:51.375 2G / 8G INFO General (kmer_splitters.hpp : 285) Splitting kmer instances into 16 buckets. This might take a while. 0:29:51.375 2G / 8G INFO General (file_limit.hpp : 29) Open file limit set to 2048 0:29:51.375 2G / 8G INFO General (kmer_splitters.hpp : 308) Memory available for splitting buffers: 12.6107 Gb 0:29:51.375 2G / 8G INFO General (kmer_splitters.hpp : 314) Using cell size of 2097152 0:29:53.223 2G / 8G INFO General (kmer_splitters.hpp : 327) Processed 339378 edges 0:29:53.223 2G / 8G INFO General (kmer_splitters.hpp : 332) Used 339378 sequences. 0:29:53.244 2G / 8G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:29:55.366 2G / 8G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 14520989 kmers in total. 0:29:55.366 2G / 8G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:29:55.603 2G / 8G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:30:01.292 2G / 8G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:30:01.515 2G / 8G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 5023395 bytes occupied (2.76752 bits per kmer). 0:30:01.692 2G / 8G INFO General (edge_index_builders.hpp : 21) Collecting k-mer coverage information from graph, this takes a while. 0:30:16.362 2G / 8G INFO General (gap_closer.cpp : 491) Index refilled 0:30:16.362 2G / 8G INFO General (gap_closer.cpp : 492) Attaching index 0:30:16.362 2G / 8G INFO General (gap_closer.cpp : 494) Index attached 0:30:16.363 2G / 8G INFO General (gap_closer.cpp : 178) Preparing shift maps 0:30:17.020 2G / 8G INFO General (gap_closer.cpp : 132) Processing paired reads (takes a while) 0:31:50.820 2G / 8G INFO General (gap_closer.cpp : 158) Used 30207624 paired reads 0:31:50.820 2G / 8G INFO General (gap_closer.cpp : 160) Merging paired indices 0:31:50.844 2G / 8G INFO GapCloser (gap_closer.cpp : 409) Closing short gaps 0:31:51.200 2G / 8G INFO GapCloser (gap_closer.cpp : 438) Closing short gaps complete: filled 1 gaps after checking 580 candidates 0:31:51.572 2G / 8G INFO General (gap_closer.cpp : 506) Detaching and clearing index 0:31:51.591 2G / 8G INFO General (gap_closer.cpp : 509) Index clearing finished 0:31:51.591 2G / 8G INFO StageManager (stage.cpp : 125) STAGE == Simplification Cleanup 0:31:51.591 2G / 8G INFO General (simplification.cpp : 71) Final isolated edges removal: 0:31:51.591 2G / 8G INFO General (simplification.cpp : 73) All edges of length smaller than 150 will be removed 0:31:53.182 1G / 8G INFO General (simplification.cpp : 77) Removed 166841 edges 0:31:53.182 1G / 8G INFO General (simplification.cpp : 97) Final index refill 0:31:53.183 1G / 8G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:31:53.184 1G / 8G INFO General (kmer_splitters.hpp : 285) Splitting kmer instances into 16 buckets. This might take a while. 0:31:53.184 1G / 8G INFO General (file_limit.hpp : 29) Open file limit set to 2048 0:31:53.184 1G / 8G INFO General (kmer_splitters.hpp : 308) Memory available for splitting buffers: 12.9388 Gb 0:31:53.184 1G / 8G INFO General (kmer_splitters.hpp : 314) Using cell size of 2097152 0:31:53.261 1G / 8G INFO General (kmer_splitters.hpp : 327) Processed 5696 edges 0:31:53.261 1G / 8G INFO General (kmer_splitters.hpp : 332) Used 5696 sequences. 0:31:53.262 1G / 8G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:31:53.320 1G / 8G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 661713 kmers in total. 0:31:53.320 1G / 8G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:31:53.341 1G / 8G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:31:53.466 1G / 8G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:31:53.541 1G / 8G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 228944 bytes occupied (2.76789 bits per kmer). 0:31:53.549 1G / 8G INFO General (edge_index_builders.hpp : 21) Collecting k-mer coverage information from graph, this takes a while. 0:31:54.030 1G / 8G INFO General (simplification.cpp : 99) Final index refill finished 0:31:54.030 1G / 8G INFO General (simplification.cpp : 106) Counting average coverage 0:31:54.031 1G / 8G INFO General (simplification.cpp : 109) Average coverage = 4129.07 0:31:54.031 1G / 8G INFO StageManager (stage.cpp : 125) STAGE == Mismatch Correction 0:34:21.274 1G / 8G INFO General (mismatch_shall_not_pass.hp: 188) Finished collecting potential mismatches positions 0:34:21.750 1G / 8G INFO General (mismatch_shall_not_pass.hp: 291) All edges processed 0:34:21.798 1G / 8G INFO General (mismatch_correction.cpp : 17) Corrected 1 nucleotides 0:34:21.798 1G / 8G INFO StageManager (stage.cpp : 125) STAGE == Paired Information Counting 0:34:21.804 1G / 8G INFO General (pair_info_count.cpp : 174) Estimating insert size for library #0 0:34:21.804 1G / 8G INFO General (pair_info_count.cpp : 82) Estimating insert size (takes a while) 0:34:21.804 1G / 8G INFO General (short_read_mapper.hpp : 93) Read length = 150, selecting usual mapper 0:34:27.396 1G / 8G INFO General (pair_info_count.cpp : 86) 2771915 paired reads (18.3524% of all) aligned to long edges 0:34:27.397 1G / 8G INFO General (pair_info_count.cpp : 199) Estimated insert size for paired library #0 0:34:27.397 1G / 8G INFO General (pair_info_count.cpp : 204) Insert size = 390.188, deviation = 91.9193, left quantile = 268, right quantile = 499, read length = 150 0:34:27.397 1G / 8G INFO General (pair_info_count.cpp : 224) Mapping library #0 0:34:27.397 1G / 8G INFO General (pair_info_count.cpp : 226) Mapping paired reads (takes a while) 0:34:27.397 1G / 8G INFO General (pair_info_count.cpp : 127) Left insert size qauntile 268, right insert size quantile 499 0:34:27.404 1G / 8G INFO General (short_read_mapper.hpp : 93) Read length = 150, selecting usual mapper 1:11:51.363 2G / 8G INFO General (split_graph_pair_info.hpp : 345) Threshold for paired information 0.0603822 1:11:51.595 2G / 8G INFO StageManager (stage.cpp : 125) STAGE == Distance Estimation 1:11:51.606 2G / 8G INFO General (distance_estimation.cpp : 242) Processing library #0 1:11:51.616 2G / 8G INFO General (distance_estimation.cpp : 145) Weight Filter Done 1:11:51.616 2G / 8G INFO DistanceEstimator (distance_estimation.hpp : 226) Using SIMPLE distance estimator 1:11:58.281 2G / 8G INFO General (distance_estimation.cpp : 40) Filtering info 1:11:58.387 2G / 8G INFO General (pair_info_filters.hpp : 352) Pruning the index 1:11:58.392 2G / 8G INFO General (distance_estimation.cpp : 193) Refining clustered pair information 1:11:58.398 2G / 8G INFO General (distance_estimation.cpp : 195) The refining of clustered pair information has been finished 1:11:58.398 2G / 8G INFO General (distance_estimation.cpp : 197) Filling paired information 1:12:01.080 2G / 8G INFO PairInfoImprover (pair_info_improver.hpp : 58) Paired info stats: missing = 3670; contradictional = 12 1:12:03.767 2G / 8G INFO PairInfoImprover (pair_info_improver.hpp : 58) Paired info stats: missing = 224; contradictional = 0 1:12:03.768 2G / 8G INFO General (distance_estimation.cpp : 202) Filling scaffolding index 1:12:03.768 2G / 8G INFO DistanceEstimator (distance_estimation.hpp : 226) Using SMOOTHING distance estimator 1:13:07.023 2G / 8G INFO General (distance_estimation.cpp : 40) Filtering info 1:13:07.101 2G / 8G INFO General (pair_info_filters.hpp : 352) Pruning the index 1:13:07.117 2G / 8G INFO StageManager (stage.cpp : 125) STAGE == Repeat Resolving 1:13:07.118 2G / 8G INFO General (contig_output.hpp : 295) Outputting contigs to /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZG/spades//K55/simplified_contigs.fasta 1:13:20.222 2G / 8G INFO General (contig_output.hpp : 295) Outputting contigs to /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZG/spades//K55/before_rr.fasta 1:13:20.422 2G / 8G INFO General (repeat_resolving.cpp : 103) Using Path-Extend repeat resolving 1:13:20.440 2G / 8G INFO General (path_extend_launch.hpp : 413) Threshold for library #0 is 0.0603822 1:13:20.441 2G / 8G INFO General (path_extend_launch.hpp : 222) Path-Extend repeat resolving tool started 1:13:20.441 2G / 8G INFO General (path_extend_launch.hpp : 230) Using 1 paired-end library 1:13:20.441 2G / 8G INFO General (path_extend_launch.hpp : 231) Using 1 paired-end scaffolding library 1:13:20.441 2G / 8G INFO General (path_extend_launch.hpp : 232) Using 0 mate-pair libraries 1:13:20.441 2G / 8G INFO General (path_extend_launch.hpp : 233) Using 1 single read library 1:13:20.441 2G / 8G INFO General (path_extend_launch.hpp : 234) Scaffolder is on 1:13:20.459 2G / 8G INFO General (path_extend_launch.hpp : 258) Growing paths using paired-end and long single reads 1:13:21.235 2G / 8G INFO PathExtendIO (pe_io.hpp : 272) Constructing FASTG file from paths 1:13:21.252 2G / 8G INFO PathExtendIO (pe_io.hpp : 275) Writing contigs in FASTG to /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZG/spades//K55/final_contigs.fastg 1:13:21.252 2G / 8G INFO PathExtendIO (pe_io.hpp : 276) Writing contigs in FASTA to /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZG/spades//K55/final_contigs.fasta 1:13:28.979 2G / 8G INFO General (path_extend_launch.hpp : 278) Traversing tandem repeats 1:13:28.993 2G / 8G INFO PathExtendIO (pe_io.hpp : 272) Constructing FASTG file from paths 1:13:29.009 2G / 8G INFO PathExtendIO (pe_io.hpp : 275) Writing contigs in FASTG to /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZG/spades//K55/scaffolds.fastg 1:13:29.010 2G / 8G INFO PathExtendIO (pe_io.hpp : 276) Writing contigs in FASTA to /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZG/spades//K55/scaffolds.fasta 1:13:36.194 2G / 8G INFO General (launch.hpp : 84) SPAdes finished 1:13:43.582 72M / 8G INFO General (main.cpp : 166) Assembling time: 1 hours 13 minutes 43 seconds ===== Assembling finished. ===== Mismatch correction started. == Processing of contigs Config: {'skip_masked': 1, 'contigs': '/global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZG/spades/misc/assembled_contigs.fasta', 'use_multiple_aligned': 0, 'reads2': ['/global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZG/spades/corrected/ZHZG.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/ZHZG/spades/corrected/ZHZG.bbqc.fq.gz_1.00.0_0.cor.fastq.gz'], 'output_dirpath': '/global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZG/spades/tmp/mis_cor_contigs_gLdtyY', 't': 8, 'debug': 0, 'mate_weight': 1.0, 'work_dir': '/global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZG/spades/tmp/mis_cor_contigs_gLdtyY/mismatch_corrector_tmp', 'insert_size': 390} no sam file, running aligner running bwa [bwa_index] Pack FASTA... 0.02 sec [bwa_index] Construct BWT for the packed sequence... [bwa_index] 0.18 seconds elapse. [bwa_index] Update BWT... 0.00 sec [bwa_index] Pack forward-only FASTA... 0.01 sec [bwa_index] Construct SA from BWT and Occ... 0.10 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/ZHZG/spades/tmp/mis_cor_contigs_gLdtyY/mismatch_corrector_tmp/assembled_contigs.fasta 2 [main] Real time: 0.324 sec; CPU: 0.319 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... 76.96 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 262144 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 76.16 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 524288 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 76.18 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 786432 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 76.20 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 1048576 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 76.59 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 1310720 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 76.74 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 1572864 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 76.88 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 1835008 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 76.82 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 2097152 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 78.19 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 2359296 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 77.84 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 2621440 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 77.89 sec [bwa_aln_core] write to the disk... 0.01 sec [bwa_aln_core] 2883584 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 76.10 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 3145728 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 76.80 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 3407872 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 76.99 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 3670016 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 77.27 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 3932160 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 75.88 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 4194304 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 77.23 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 4456448 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 76.14 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 4718592 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 80.36 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 4980736 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 83.51 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 5242880 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 80.24 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 5505024 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 77.31 sec [bwa_aln_core] write to the disk... 0.01 sec [bwa_aln_core] 5767168 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 76.94 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 6029312 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 77.09 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 6291456 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 77.01 sec [bwa_aln_core] write to the disk... 0.01 sec [bwa_aln_core] 6553600 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 76.22 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 6815744 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 76.83 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 7077888 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 76.80 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 7340032 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 76.54 sec [bwa_aln_core] write to the disk... 0.01 sec [bwa_aln_core] 7602176 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 76.75 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 7864320 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 76.02 sec [bwa_aln_core] write to the disk... 0.01 sec [bwa_aln_core] 8126464 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 77.46 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 8388608 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 76.79 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 8650752 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 76.87 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 8912896 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 76.63 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 9175040 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 76.75 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 9437184 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 76.48 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 9699328 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 76.44 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 9961472 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 76.74 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 10223616 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 76.77 sec [bwa_aln_core] write to the disk... 0.01 sec [bwa_aln_core] 10485760 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 76.70 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 10747904 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 78.15 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 11010048 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 76.08 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 11272192 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 77.34 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 11534336 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 76.90 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 11796480 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 77.26 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 12058624 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 76.48 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 12320768 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 76.62 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 12582912 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 76.59 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 12845056 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 76.92 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 13107200 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 75.85 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 13369344 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 77.35 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 13631488 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 75.64 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 13893632 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 77.75 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 14155776 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 76.79 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 14417920 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 76.78 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 14680064 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 76.13 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 14942208 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 47.17 sec [bwa_aln_core] write to the disk... 0.01 sec [bwa_aln_core] 15103812 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/ZHZG/spades/tmp/mis_cor_contigs_gLdtyY/mismatch_corrector_tmp/assembled_contigs.fasta /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZG/spades/corrected/ZHZG.bbqc.fq.gz_1.00.0_0.cor.fastq.gz [main] Real time: 715.043 sec; CPU: 4509.435 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... 80.41 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 262144 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 80.29 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 524288 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 80.93 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 786432 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 80.02 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 1048576 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 80.23 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 1310720 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 79.97 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 1572864 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 79.74 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 1835008 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 78.62 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 2097152 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 80.42 sec [bwa_aln_core] write to the disk... 0.01 sec [bwa_aln_core] 2359296 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 80.16 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 2621440 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 82.16 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 2883584 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 80.15 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 3145728 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 81.57 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 3407872 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 79.82 sec [bwa_aln_core] write to the disk... 0.01 sec [bwa_aln_core] 3670016 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 82.19 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 3932160 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 79.74 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 4194304 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 82.02 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 4456448 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 80.26 sec [bwa_aln_core] write to the disk... 0.01 sec [bwa_aln_core] 4718592 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 82.74 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 4980736 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 81.07 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 5242880 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 83.69 sec [bwa_aln_core] write to the disk... 0.01 sec [bwa_aln_core] 5505024 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 80.34 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 5767168 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 82.41 sec [bwa_aln_core] write to the disk... 0.01 sec [bwa_aln_core] 6029312 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 80.15 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 6291456 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 81.47 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 6553600 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 80.42 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 6815744 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 82.80 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 7077888 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 80.95 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 7340032 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 82.78 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 7602176 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 78.89 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 7864320 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 80.04 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 8126464 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 79.30 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 8388608 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 80.14 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 8650752 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 78.89 sec [bwa_aln_core] write to the disk... 0.01 sec [bwa_aln_core] 8912896 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 79.37 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 9175040 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 79.23 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 9437184 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 79.00 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 9699328 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 79.03 sec [bwa_aln_core] write to the disk... 0.01 sec [bwa_aln_core] 9961472 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 80.38 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 10223616 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 80.51 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 10485760 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 78.66 sec [bwa_aln_core] write to the disk... 0.01 sec [bwa_aln_core] 10747904 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 80.68 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 11010048 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 79.25 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 11272192 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 81.32 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 11534336 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 79.83 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 11796480 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 82.28 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 12058624 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 82.33 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 12320768 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 81.34 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 12582912 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 79.83 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 12845056 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 81.74 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 13107200 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 78.94 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 13369344 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 81.38 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 13631488 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 78.60 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 13893632 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 81.10 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 14155776 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 79.44 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 14417920 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 82.07 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 14680064 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 79.30 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 14942208 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 50.39 sec [bwa_aln_core] write to the disk... 0.01 sec [bwa_aln_core] 15103812 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/ZHZG/spades/tmp/mis_cor_contigs_gLdtyY/mismatch_corrector_tmp/assembled_contigs.fasta /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZG/spades/corrected/ZHZG.bbqc.fq.gz_2.00.0_0.cor.fastq.gz [main] Real time: 688.603 sec; CPU: 4714.791 sec contigs were split, starting splitting .sam file file /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZG/spades/tmp/mis_cor_contigs_gLdtyY/mismatch_corrector_tmp/tmp.sam opened 1000000 dropping cashed lines... 2000000 dropping cashed lines... 3000000 dropping cashed lines... 4000000 dropping cashed lines... 5000000 dropping cashed lines... 6000000 dropping cashed lines... 7000000 dropping cashed lines... 8000000 dropping cashed lines... 9000000 dropping cashed lines... 10000000 dropping cashed lines... 11000000 dropping cashed lines... 12000000 dropping cashed lines... 13000000 dropping cashed lines... 14000000 dropping cashed lines... 15000000 dropping cashed lines... 16000000 dropping cashed lines... 17000000 dropping cashed lines... 18000000 dropping cashed lines... 19000000 dropping cashed lines... 20000000 dropping cashed lines... 21000000 dropping cashed lines... 22000000 dropping cashed lines... 23000000 dropping cashed lines... 24000000 dropping cashed lines... 25000000 dropping cashed lines... 26000000 dropping cashed lines... 27000000 dropping cashed lines... 28000000 dropping cashed lines... 29000000 dropping cashed lines... 30000000 dropping cashed lines... dropping cashed lines... .sam file was split processing long contig /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZG/spades/tmp/mis_cor_contigs_gLdtyY/mismatch_corrector_tmp/NODE_1_length_33292_cov_377.fasta, contig length:33292 processing long contig /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZG/spades/tmp/mis_cor_contigs_gLdtyY/mismatch_corrector_tmp/NODE_2_length_30321_cov_514.fasta, contig length:30321 concatenating /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZG/spades/tmp/mis_cor_contigs_gLdtyY/mismatch_corrector_tmp/*.ref.fasta INTO /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZG/spades/tmp/mis_cor_contigs_gLdtyY/corrected_contigs.fasta TOTAL - replaced: 3134 deleted: 441 inserted: 92 == Warning == Creating /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZG/spades/contigs.fastg: failed to find appropriate name for contig >NODE_127_length_996_cov_39.2655_ID_255 (looking for names in /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZG/spades/misc/assembled_contigs.fastg)! Skipping this contig. == Warning == Creating /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZG/spades/contigs.fastg: failed to find appropriate name for contig >NODE_314_length_373_cov_182.916_ID_627 (looking for names in /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZG/spades/misc/assembled_contigs.fastg)! Skipping this contig. == Warning == Creating /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZG/spades/contigs.fastg: failed to find appropriate name for contig >NODE_44_length_2429_cov_4.38728_ID_89 (looking for names in /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZG/spades/misc/assembled_contigs.fastg)! Skipping this contig. == Warning == Creating /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZG/spades/contigs.fastg: failed to find appropriate name for contig >NODE_46_length_2328_cov_415.003_ID_93 (looking for names in /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZG/spades/misc/assembled_contigs.fastg)! Skipping this contig. == Warning == Creating /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZG/spades/contigs.fastg: failed to find appropriate name for contig >NODE_176_length_792_cov_634.176_ID_351 (looking for names in /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZG/spades/misc/assembled_contigs.fastg)! Skipping this contig. == Warning == Creating /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZG/spades/contigs.fastg: failed to find appropriate name for contig >NODE_304_length_383_cov_2.12329_ID_607 (looking for names in /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZG/spades/misc/assembled_contigs.fastg)! Skipping this contig. == Warning == Creating /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZG/spades/contigs.fastg: failed to find appropriate name for contig >NODE_8_length_6504_cov_45.7336_ID_15 (looking for names in /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZG/spades/misc/assembled_contigs.fastg)! Skipping this contig. == Warning == Creating /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZG/spades/contigs.fastg: failed to find appropriate name for contig >NODE_104_length_1126_cov_240.09_ID_209 (looking for names in /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZG/spades/misc/assembled_contigs.fastg)! Skipping this contig. == Warning == Creating /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZG/spades/contigs.fastg: failed to find appropriate name for contig >NODE_42_length_2500_cov_1307.67_ID_85 (looking for names in /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZG/spades/misc/assembled_contigs.fastg)! Skipping this contig. == Warning == Creating /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZG/spades/contigs.fastg: failed to find appropriate name for contig >NODE_130_length_981_cov_525.935_ID_261 (looking for names in /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZG/spades/misc/assembled_contigs.fastg)! Skipping this contig. == Warning == Creating /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZG/spades/contigs.fastg: failed to find appropriate name for contig >NODE_135_length_958_cov_57.8124_ID_271 (looking for names in /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZG/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/ZHZG/spades/misc/assembled_scaffolds.fasta', 'use_multiple_aligned': 0, 'reads2': ['/global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZG/spades/corrected/ZHZG.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/ZHZG/spades/corrected/ZHZG.bbqc.fq.gz_1.00.0_0.cor.fastq.gz'], 'output_dirpath': '/global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZG/spades/tmp/mis_cor_scaffolds_RagYPN', 't': 8, 'debug': 0, 'mate_weight': 1.0, 'work_dir': '/global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZG/spades/tmp/mis_cor_scaffolds_RagYPN/mismatch_corrector_tmp', 'insert_size': 390} no sam file, running aligner running bwa [bwa_index] Pack FASTA... 0.01 sec [bwa_index] Construct BWT for the packed sequence... [bwa_index] 0.19 seconds elapse. [bwa_index] Update BWT... 0.01 sec [bwa_index] Pack forward-only FASTA... 0.01 sec [bwa_index] Construct SA from BWT and Occ... 0.09 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/ZHZG/spades/tmp/mis_cor_scaffolds_RagYPN/mismatch_corrector_tmp/assembled_scaffolds.fasta 2 [main] Real time: 0.430 sec; CPU: 0.330 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... 77.01 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 262144 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 76.19 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 524288 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 76.19 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 786432 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 76.18 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 1048576 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 76.57 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 1310720 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 76.77 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 1572864 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 76.83 sec [bwa_aln_core] write to the disk... 0.01 sec [bwa_aln_core] 1835008 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 76.84 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 2097152 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 78.18 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 2359296 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 77.87 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 2621440 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 77.92 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 2883584 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 76.09 sec [bwa_aln_core] write to the disk... 0.01 sec [bwa_aln_core] 3145728 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 76.79 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 3407872 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 77.00 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 3670016 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 77.26 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 3932160 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 75.87 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 4194304 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 77.25 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 4456448 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 76.13 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 4718592 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 80.25 sec [bwa_aln_core] write to the disk... 0.01 sec [bwa_aln_core] 4980736 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 83.51 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 5242880 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 80.27 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 5505024 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 77.28 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 5767168 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 76.92 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 6029312 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 77.04 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 6291456 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 76.99 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 6553600 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 76.22 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 6815744 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 76.79 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 7077888 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 76.75 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 7340032 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 76.51 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 7602176 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 76.70 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 7864320 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 76.00 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 8126464 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 77.49 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 8388608 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 76.77 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 8650752 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 76.88 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 8912896 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 76.60 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 9175040 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 76.74 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 9437184 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 76.46 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 9699328 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 76.40 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 9961472 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 76.66 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 10223616 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 76.72 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 10485760 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 76.69 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 10747904 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 78.15 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 11010048 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 76.05 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 11272192 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 77.24 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 11534336 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 76.85 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 11796480 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 77.29 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 12058624 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 76.49 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 12320768 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 76.61 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 12582912 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 76.59 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 12845056 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 76.94 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 13107200 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 75.83 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 13369344 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 77.33 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 13631488 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 75.61 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 13893632 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 77.80 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 14155776 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 76.82 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 14417920 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 76.78 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 14680064 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 76.09 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 14942208 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 47.15 sec [bwa_aln_core] write to the disk... 0.01 sec [bwa_aln_core] 15103812 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/ZHZG/spades/tmp/mis_cor_scaffolds_RagYPN/mismatch_corrector_tmp/assembled_scaffolds.fasta /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZG/spades/corrected/ZHZG.bbqc.fq.gz_1.00.0_0.cor.fastq.gz [main] Real time: 637.705 sec; CPU: 4508.571 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... 80.42 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 262144 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 80.21 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 524288 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 80.83 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 786432 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 79.95 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 1048576 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 80.14 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 1310720 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 79.91 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 1572864 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 79.63 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 1835008 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 78.52 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 2097152 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 80.40 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 2359296 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 80.08 sec [bwa_aln_core] write to the disk... 0.01 sec [bwa_aln_core] 2621440 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 82.11 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 2883584 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 80.07 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 3145728 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 81.52 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 3407872 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 79.69 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 3670016 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 82.08 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 3932160 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 79.66 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 4194304 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 81.96 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 4456448 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 80.17 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 4718592 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 82.66 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 4980736 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 81.05 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 5242880 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 83.62 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 5505024 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 80.25 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 5767168 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 82.34 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 6029312 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 80.05 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 6291456 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 81.40 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 6553600 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 80.28 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 6815744 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 82.75 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 7077888 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 80.92 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 7340032 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 82.72 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 7602176 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 78.82 sec [bwa_aln_core] write to the disk... 0.01 sec [bwa_aln_core] 7864320 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 79.91 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 8126464 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 79.18 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 8388608 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 80.01 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 8650752 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 78.75 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 8912896 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 79.36 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 9175040 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 79.09 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 9437184 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 78.90 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 9699328 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 78.97 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 9961472 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 80.30 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 10223616 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 80.41 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 10485760 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 78.57 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 10747904 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 80.59 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 11010048 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 79.16 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 11272192 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 81.27 sec [bwa_aln_core] write to the disk... 0.01 sec [bwa_aln_core] 11534336 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 79.71 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 11796480 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 82.26 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 12058624 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 82.28 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 12320768 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 81.24 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 12582912 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 79.74 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 12845056 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 81.72 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 13107200 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 78.78 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 13369344 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 81.25 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 13631488 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 78.54 sec [bwa_aln_core] write to the disk... 0.01 sec [bwa_aln_core] 13893632 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 81.02 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 14155776 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 79.34 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 14417920 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 81.92 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 14680064 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 79.11 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 14942208 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 50.35 sec [bwa_aln_core] write to the disk... 0.01 sec [bwa_aln_core] 15103812 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/ZHZG/spades/tmp/mis_cor_scaffolds_RagYPN/mismatch_corrector_tmp/assembled_scaffolds.fasta /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZG/spades/corrected/ZHZG.bbqc.fq.gz_2.00.0_0.cor.fastq.gz [main] Real time: 664.194 sec; CPU: 4709.640 sec contigs were split, starting splitting .sam file file /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZG/spades/tmp/mis_cor_scaffolds_RagYPN/mismatch_corrector_tmp/tmp.sam opened 1000000 dropping cashed lines... 2000000 dropping cashed lines... 3000000 dropping cashed lines... 4000000 dropping cashed lines... 5000000 dropping cashed lines... 6000000 dropping cashed lines... 7000000 dropping cashed lines... 8000000 dropping cashed lines... 9000000 dropping cashed lines... 10000000 dropping cashed lines... 11000000 dropping cashed lines... 12000000 dropping cashed lines... 13000000 dropping cashed lines... 14000000 dropping cashed lines... 15000000 dropping cashed lines... 16000000 dropping cashed lines... 17000000 dropping cashed lines... 18000000 dropping cashed lines... 19000000 dropping cashed lines... 20000000 dropping cashed lines... 21000000 dropping cashed lines... 22000000 dropping cashed lines... 23000000 dropping cashed lines... 24000000 dropping cashed lines... 25000000 dropping cashed lines... 26000000 dropping cashed lines... 27000000 dropping cashed lines... 28000000 dropping cashed lines... 29000000 dropping cashed lines... 30000000 dropping cashed lines... dropping cashed lines... .sam file was split processing long contig /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZG/spades/tmp/mis_cor_scaffolds_RagYPN/mismatch_corrector_tmp/NODE_1_length_33292_cov_377.fasta, contig length:33292 processing long contig /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZG/spades/tmp/mis_cor_scaffolds_RagYPN/mismatch_corrector_tmp/NODE_2_length_30321_cov_514.fasta, contig length:30321 concatenating /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZG/spades/tmp/mis_cor_scaffolds_RagYPN/mismatch_corrector_tmp/*.ref.fasta INTO /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZG/spades/tmp/mis_cor_scaffolds_RagYPN/corrected_contigs.fasta TOTAL - replaced: 3149 deleted: 438 inserted: 92 == Warning == Creating /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZG/spades/scaffolds.fastg: failed to find appropriate name for contig >NODE_310_length_373_cov_182.916_ID_4253 (looking for names in /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZG/spades/misc/assembled_scaffolds.fastg)! Skipping this contig. == Warning == Creating /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZG/spades/scaffolds.fastg: failed to find appropriate name for contig >NODE_43_length_2500_cov_1307.67_ID_4219 (looking for names in /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZG/spades/misc/assembled_scaffolds.fastg)! Skipping this contig. == Warning == Creating /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZG/spades/scaffolds.fastg: failed to find appropriate name for contig >NODE_47_length_2328_cov_415.003_ID_4337 (looking for names in /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZG/spades/misc/assembled_scaffolds.fastg)! Skipping this contig. == Warning == Creating /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZG/spades/scaffolds.fastg: failed to find appropriate name for contig >NODE_132_length_958_cov_57.8124_ID_4217 (looking for names in /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZG/spades/misc/assembled_scaffolds.fastg)! Skipping this contig. == Warning == Creating /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZG/spades/scaffolds.fastg: failed to find appropriate name for contig >NODE_8_length_6504_cov_45.7336_ID_4321 (looking for names in /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZG/spades/misc/assembled_scaffolds.fastg)! Skipping this contig. == Warning == Creating /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZG/spades/scaffolds.fastg: failed to find appropriate name for contig >NODE_45_length_2429_cov_4.38728_ID_4323 (looking for names in /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZG/spades/misc/assembled_scaffolds.fastg)! Skipping this contig. == Warning == Creating /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZG/spades/scaffolds.fastg: failed to find appropriate name for contig >NODE_172_length_792_cov_634.176_ID_4285 (looking for names in /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZG/spades/misc/assembled_scaffolds.fastg)! Skipping this contig. == Warning == Creating /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZG/spades/scaffolds.fastg: failed to find appropriate name for contig >NODE_127_length_981_cov_525.935_ID_4287 (looking for names in /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZG/spades/misc/assembled_scaffolds.fastg)! Skipping this contig. == Warning == Creating /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZG/spades/scaffolds.fastg: failed to find appropriate name for contig >NODE_124_length_996_cov_39.2655_ID_4341 (looking for names in /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZG/spades/misc/assembled_scaffolds.fastg)! Skipping this contig. == Warning == Creating /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZG/spades/scaffolds.fastg: failed to find appropriate name for contig >NODE_101_length_1126_cov_240.09_ID_4303 (looking for names in /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZG/spades/misc/assembled_scaffolds.fastg)! Skipping this contig. == Warning == Creating /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZG/spades/scaffolds.fastg: failed to find appropriate name for contig >NODE_300_length_383_cov_2.12329_ID_4247 (looking for names in /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZG/spades/misc/assembled_scaffolds.fastg)! Skipping this contig. ===== Mismatch correction finished. * Corrected reads are in /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZG/spades/corrected/ * Assembled contigs are in /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZG/spades/contigs.fasta (contigs.fastg) * Assembled scaffolds are in /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZG/spades/scaffolds.fasta (scaffolds.fastg) ======= SPAdes pipeline finished. SPAdes log can be found here: /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZG/spades/spades.log Thank you for using SPAdes!