Command line: /N/dc2/projects/marinovg/programs/SPAdes-3.5.0-Linux/bin/spades.py --pe1-1 /N/dc2/projects/marinovg/2015-01-29-P-assem/biaurelia-100709_IRIS_0005-s_7_1_sequence.trimmed.paired.fastq.gz --pe1-2 /N/dc2/projects/marinovg/2015-01-29-P-assem/biaurelia-100709_IRIS_0005-s_7_2_sequence.trimmed.paired.fastq.gz --pe2-1 /N/dc2/projects/marinovg/2015-01-29-P-assem/biaurelia-100727_IRIS_0006-pbia_1_sequence.paired.fastq.gz --pe2-2 /N/dc2/projects/marinovg/2015-01-29-P-assem/biaurelia-100727_IRIS_0006-pbia_2_sequence.paired.fastq.gz -t 16 -o /N/dc2/projects/marinovg/2015-01-29-P-assem/Paramecium_biaurelia-SPAdes-3.5.0-trimmed System information: SPAdes version: 3.5.0 Python version: 2.6.6 OS: Linux-2.6.32-504.8.1.el6.x86_64-x86_64-with-redhat-6.6-Santiago Output dir: /N/dc2/projects/marinovg/2015-01-29-P-assem/Paramecium_biaurelia-SPAdes-3.5.0-trimmed Mode: read error correction and assembling Debug mode is turned OFF Dataset parameters: Multi-cell mode (you should set '--sc' flag if input data was obtained with MDA (single-cell) technology Reads: Library number: 1, library type: paired-end orientation: fr left reads: ['/N/dc2/projects/marinovg/2015-01-29-P-assem/biaurelia-100709_IRIS_0005-s_7_1_sequence.trimmed.paired.fastq.gz'] right reads: ['/N/dc2/projects/marinovg/2015-01-29-P-assem/biaurelia-100709_IRIS_0005-s_7_2_sequence.trimmed.paired.fastq.gz'] interlaced reads: not specified single reads: not specified Library number: 2, library type: paired-end orientation: fr left reads: ['/N/dc2/projects/marinovg/2015-01-29-P-assem/biaurelia-100727_IRIS_0006-pbia_1_sequence.paired.fastq.gz'] right reads: ['/N/dc2/projects/marinovg/2015-01-29-P-assem/biaurelia-100727_IRIS_0006-pbia_2_sequence.paired.fastq.gz'] interlaced reads: not specified single reads: not specified Read error correction parameters: Iterations: 1 PHRED offset will be auto-detected Corrected reads will be compressed (with gzip) Assembly parameters: k: automatic selection based on read length Mismatch careful mode is turned OFF Repeat resolution is enabled MismatchCorrector will be SKIPPED Coverage cutoff is turned OFF Other parameters: Dir for temp files: /N/dc2/projects/marinovg/2015-01-29-P-assem/Paramecium_biaurelia-SPAdes-3.5.0-trimmed/tmp Threads: 16 Memory limit (in Gb): 250 ======= SPAdes pipeline started. Log can be found here: /N/dc2/projects/marinovg/2015-01-29-P-assem/Paramecium_biaurelia-SPAdes-3.5.0-trimmed/spades.log ===== Read error correction started. == Running read error correction tool: /N/dc2/projects/marinovg/programs/SPAdes-3.5.0-Linux/bin/hammer /N/dc2/projects/marinovg/2015-01-29-P-assem/Paramecium_biaurelia-SPAdes-3.5.0-trimmed/corrected/configs/config.info 0:00:00.020 4M / 4M INFO General (main.cpp : 82) Loading config from /N/dc2/projects/marinovg/2015-01-29-P-assem/Paramecium_biaurelia-SPAdes-3.5.0-trimmed/corrected/configs/config.info 0:00:00.193 4M / 4M INFO General (memory_limit.hpp : 42) Memory limit set to 250 Gb 0:00:00.193 4M / 4M INFO General (main.cpp : 91) Trying to determine PHRED offset 0:00:00.283 4M / 4M INFO General (main.cpp : 97) Determined value is 64 0:00:00.308 4M / 4M INFO General (hammer_tools.cpp : 36) Hamming graph threshold tau=1, k=21, subkmer positions = [ 0 10 ] === ITERATION 0 begins === 0:00:00.309 4M / 4M INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:00:00.309 4M / 4M INFO K-mer Splitting (kmer_data.cpp : 127) Splitting kmer instances into 256 buckets. This might take a while. 0:00:00.310 4M / 4M INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:00:00.310 4M / 4M INFO K-mer Splitting (kmer_data.cpp : 145) Memory available for splitting buffers: 5.20825 Gb 0:00:00.310 4M / 4M INFO K-mer Splitting (kmer_data.cpp : 153) Using cell size of 262144 0:00:04.018 8G / 8G INFO K-mer Splitting (kmer_data.cpp : 167) Processing /N/dc2/projects/marinovg/2015-01-29-P-assem/biaurelia-100709_IRIS_0005-s_7_1_sequence.trimmed.paired.fastq.gz 0:01:17.873 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 176) Processed 5601810 reads 0:01:52.217 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 176) Processed 8210252 reads 0:01:52.219 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 167) Processing /N/dc2/projects/marinovg/2015-01-29-P-assem/biaurelia-100709_IRIS_0005-s_7_2_sequence.trimmed.paired.fastq.gz 0:05:28.196 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 176) Processed 14066270 reads 0:07:35.339 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 176) Processed 16420504 reads 0:07:35.342 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 167) Processing /N/dc2/projects/marinovg/2015-01-29-P-assem/biaurelia-100727_IRIS_0006-pbia_1_sequence.paired.fastq.gz 0:08:49.609 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 176) Processed 21848828 reads 0:09:38.784 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 176) Processed 25450116 reads 0:09:38.786 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 167) Processing /N/dc2/projects/marinovg/2015-01-29-P-assem/biaurelia-100727_IRIS_0006-pbia_2_sequence.paired.fastq.gz 0:10:54.421 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 176) Processed 30957304 reads 0:11:42.582 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 176) Processed 34479728 reads 0:11:42.586 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 181) Processed 34479728 reads 0:11:43.750 64M / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:12:36.711 64M / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 475865712 kmers in total. 0:12:36.713 64M / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:12:58.657 64M / 9G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:14:01.758 256M / 15G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:14:22.356 256M / 15G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 164619835 bytes occupied (2.7675 bits per kmer). 0:14:22.358 256M / 15G INFO K-mer Counting (kmer_data.cpp : 266) Arranging kmers in hash map order 0:19:12.882 256M / 15G INFO K-mer Counting (kmer_data.cpp : 279) Done. Total swaps: 475865419 0:19:16.068 3G / 15G INFO General (main.cpp : 151) Clustering Hamming graph. 0:19:16.069 3G / 15G INFO Hamming Clustering (hamcluster.cpp : 115) Serializing sub-kmers. 0:19:16.069 3G / 15G INFO Hamming Clustering (hamcluster.cpp : 120) Serializing: [0, 10) 0:24:35.462 3G / 15G INFO Hamming Clustering (hamcluster.cpp : 120) Serializing: [10, 21) 0:29:55.099 3G / 15G INFO Hamming Clustering (hamcluster.cpp : 129) Splitting sub-kmers, pass 1. 0:36:22.672 3G / 15G INFO Hamming Clustering (hamcluster.cpp : 134) Splitting done. Processed 2 blocks. Produced 5242557 blocks. 0:36:22.672 3G / 15G INFO Hamming Clustering (hamcluster.cpp : 145) Merge sub-kmers, pass 1 1:01:07.943 3G / 15G INFO Hamming Clustering (hamcluster.cpp : 170) Merge done, total 3311089 new blocks generated. 1:01:10.549 3G / 15G INFO Hamming Clustering (hamcluster.cpp : 175) Spliting sub-kmers, pass 2. 1:22:29.961 3G / 15G INFO Hamming Clustering (hamcluster.cpp : 180) Splitting done. Processed 6622178 blocks. Produced 1123527312 blocks. 1:22:29.961 3G / 15G INFO Hamming Clustering (hamcluster.cpp : 187) Merge sub-kmers, pass 2 1:36:55.488 3G / 15G INFO Hamming Clustering (hamcluster.cpp : 205) Merge done, saw 201952 big blocks out of 1123527312 processed. 1:43:32.789 3G / 18G INFO General (main.cpp : 165) Clustering done. Total clusters: 291820123 1:43:32.789 3G / 18G INFO K-mer Counting (kmer_data.cpp : 284) Collecting K-mer information, this takes a while. 1:43:44.496 25G / 25G INFO K-mer Counting (kmer_data.cpp : 290) Processing /N/dc2/projects/marinovg/2015-01-29-P-assem/biaurelia-100709_IRIS_0005-s_7_1_sequence.trimmed.paired.fastq.gz 1:45:10.293 25G / 25G INFO K-mer Counting (kmer_data.cpp : 290) Processing /N/dc2/projects/marinovg/2015-01-29-P-assem/biaurelia-100709_IRIS_0005-s_7_2_sequence.trimmed.paired.fastq.gz 1:46:34.014 25G / 25G INFO K-mer Counting (kmer_data.cpp : 290) Processing /N/dc2/projects/marinovg/2015-01-29-P-assem/biaurelia-100727_IRIS_0006-pbia_1_sequence.paired.fastq.gz 1:48:13.876 25G / 25G INFO K-mer Counting (kmer_data.cpp : 290) Processing /N/dc2/projects/marinovg/2015-01-29-P-assem/biaurelia-100727_IRIS_0006-pbia_2_sequence.paired.fastq.gz 1:49:52.901 25G / 25G INFO K-mer Counting (kmer_data.cpp : 297) Collection done, postprocessing. 1:50:08.558 25G / 25G INFO K-mer Counting (kmer_data.cpp : 310) There are 475865712 kmers in total. Among them 213977630 (44.966%) are singletons. 1:50:08.558 25G / 25G INFO General (main.cpp : 203) Subclustering Hamming graph 1:53:13.476 25G / 25G INFO Hamming Subclustering (kmer_cluster.cpp : 626) Subclustering done. Total 80343 non-read kmers were generated. 1:53:13.476 25G / 25G INFO Hamming Subclustering (kmer_cluster.cpp : 627) Subclustering statistics: 1:53:13.476 25G / 25G INFO Hamming Subclustering (kmer_cluster.cpp : 628) Total singleton hamming clusters: 214207933. Among them 169673484 (79.2097%) are good 1:53:13.476 25G / 25G INFO Hamming Subclustering (kmer_cluster.cpp : 629) Total singleton subclusters: 11601426. Among them 11601274 (99.9987%) are good 1:53:13.476 25G / 25G INFO Hamming Subclustering (kmer_cluster.cpp : 630) Total non-singleton subcluster centers: 81550607. Among them 68344925 (83.8068%) are good 1:53:13.476 25G / 25G INFO Hamming Subclustering (kmer_cluster.cpp : 631) Average size of non-trivial subcluster: 3.16873 kmers 1:53:13.476 25G / 25G INFO Hamming Subclustering (kmer_cluster.cpp : 632) Average number of sub-clusters per non-singleton cluster: 1.20022 1:53:13.476 25G / 25G INFO Hamming Subclustering (kmer_cluster.cpp : 633) Total solid k-mers: 249619683 1:53:13.476 25G / 25G INFO Hamming Subclustering (kmer_cluster.cpp : 634) Substitution probabilities: [4,4]((0.899468,0.0221924,0.0384704,0.0398693),(0.0149042,0.954044,0.00954876,0.0215028),(0.019833,0.00891455,0.95553,0.0157225),(0.0391207,0.038331,0.022127,0.900421)) 1:53:14.446 25G / 25G INFO General (main.cpp : 208) Finished clustering. 1:53:14.446 25G / 25G INFO General (main.cpp : 228) Starting solid k-mers expansion in 16 threads. 1:58:08.656 25G / 25G INFO General (main.cpp : 249) Solid k-mers iteration 0 produced 50735776 new k-mers. 2:03:04.473 25G / 25G INFO General (main.cpp : 249) Solid k-mers iteration 1 produced 1631934 new k-mers. 2:08:00.827 25G / 25G INFO General (main.cpp : 249) Solid k-mers iteration 2 produced 59499 new k-mers. 2:12:57.176 25G / 25G INFO General (main.cpp : 249) Solid k-mers iteration 3 produced 5104 new k-mers. 2:17:52.453 25G / 25G INFO General (main.cpp : 249) Solid k-mers iteration 4 produced 672 new k-mers. 2:22:47.972 25G / 25G INFO General (main.cpp : 249) Solid k-mers iteration 5 produced 66 new k-mers. 2:27:43.472 25G / 25G INFO General (main.cpp : 249) Solid k-mers iteration 6 produced 0 new k-mers. 2:27:43.473 25G / 25G INFO General (main.cpp : 253) Solid k-mers finalized 2:27:43.473 25G / 25G INFO General (hammer_tools.cpp : 210) Starting read correction in 16 threads. 2:27:43.474 25G / 25G INFO General (hammer_tools.cpp : 222) Correcting pair of reads: /N/dc2/projects/marinovg/2015-01-29-P-assem/biaurelia-100709_IRIS_0005-s_7_1_sequence.trimmed.paired.fastq.gz and /N/dc2/projects/marinovg/2015-01-29-P-assem/biaurelia-100709_IRIS_0005-s_7_2_sequence.trimmed.paired.fastq.gz 2:28:05.501 26G / 26G INFO General (hammer_tools.cpp : 166) Prepared batch 0 of 1600000 reads. 2:28:19.517 26G / 26G INFO General (hammer_tools.cpp : 175) Processed batch 0 2:28:33.110 26G / 26G INFO General (hammer_tools.cpp : 185) Written batch 0 2:28:53.626 26G / 26G INFO General (hammer_tools.cpp : 166) Prepared batch 1 of 1600000 reads. 2:29:07.560 26G / 26G INFO General (hammer_tools.cpp : 175) Processed batch 1 2:29:21.187 26G / 26G INFO General (hammer_tools.cpp : 185) Written batch 1 2:29:41.269 26G / 26G INFO General (hammer_tools.cpp : 166) Prepared batch 2 of 1600000 reads. 2:29:55.287 26G / 26G INFO General (hammer_tools.cpp : 175) Processed batch 2 2:30:09.024 26G / 26G INFO General (hammer_tools.cpp : 185) Written batch 2 2:30:29.007 26G / 26G INFO General (hammer_tools.cpp : 166) Prepared batch 3 of 1600000 reads. 2:30:43.137 26G / 26G INFO General (hammer_tools.cpp : 175) Processed batch 3 2:30:57.057 26G / 26G INFO General (hammer_tools.cpp : 185) Written batch 3 2:31:17.884 26G / 26G INFO General (hammer_tools.cpp : 166) Prepared batch 4 of 1600000 reads. 2:31:32.080 26G / 26G INFO General (hammer_tools.cpp : 175) Processed batch 4 2:31:45.946 26G / 26G INFO General (hammer_tools.cpp : 185) Written batch 4 2:31:48.608 26G / 26G INFO General (hammer_tools.cpp : 166) Prepared batch 5 of 210252 reads. 2:31:50.497 26G / 26G INFO General (hammer_tools.cpp : 175) Processed batch 5 2:31:52.312 26G / 26G INFO General (hammer_tools.cpp : 185) Written batch 5 2:31:55.154 25G / 26G INFO General (hammer_tools.cpp : 222) Correcting pair of reads: /N/dc2/projects/marinovg/2015-01-29-P-assem/biaurelia-100727_IRIS_0006-pbia_1_sequence.paired.fastq.gz and /N/dc2/projects/marinovg/2015-01-29-P-assem/biaurelia-100727_IRIS_0006-pbia_2_sequence.paired.fastq.gz 2:32:17.583 26G / 26G INFO General (hammer_tools.cpp : 166) Prepared batch 0 of 1600000 reads. 2:32:32.585 26G / 26G INFO General (hammer_tools.cpp : 175) Processed batch 0 2:32:46.305 26G / 26G INFO General (hammer_tools.cpp : 185) Written batch 0 2:33:07.220 26G / 26G INFO General (hammer_tools.cpp : 166) Prepared batch 1 of 1600000 reads. 2:33:22.128 26G / 26G INFO General (hammer_tools.cpp : 175) Processed batch 1 2:33:35.933 26G / 26G INFO General (hammer_tools.cpp : 185) Written batch 1 2:33:56.497 26G / 26G INFO General (hammer_tools.cpp : 166) Prepared batch 2 of 1600000 reads. 2:34:11.413 26G / 26G INFO General (hammer_tools.cpp : 175) Processed batch 2 2:34:25.274 26G / 26G INFO General (hammer_tools.cpp : 185) Written batch 2 2:34:45.693 26G / 26G INFO General (hammer_tools.cpp : 166) Prepared batch 3 of 1600000 reads. 2:35:00.653 26G / 26G INFO General (hammer_tools.cpp : 175) Processed batch 3 2:35:34.665 26G / 26G INFO General (hammer_tools.cpp : 185) Written batch 3 2:35:55.253 26G / 26G INFO General (hammer_tools.cpp : 166) Prepared batch 4 of 1600000 reads. 2:36:10.244 26G / 26G INFO General (hammer_tools.cpp : 175) Processed batch 4 2:36:24.166 26G / 26G INFO General (hammer_tools.cpp : 185) Written batch 4 2:36:37.434 26G / 26G INFO General (hammer_tools.cpp : 166) Prepared batch 5 of 1029612 reads. 2:36:47.151 26G / 26G INFO General (hammer_tools.cpp : 175) Processed batch 5 2:36:56.108 26G / 26G INFO General (hammer_tools.cpp : 185) Written batch 5 2:36:58.960 25G / 26G INFO General (hammer_tools.cpp : 269) Correction done. Changed 4488691 bases in 4055562 reads. 2:36:58.960 25G / 26G INFO General (hammer_tools.cpp : 270) Failed to correct 210007333 bases out of 3661851635. 2:36:59.128 3G / 26G INFO General (main.cpp : 286) Saving corrected dataset description to /N/dc2/projects/marinovg/2015-01-29-P-assem/Paramecium_biaurelia-SPAdes-3.5.0-trimmed/corrected/corrected.yaml 2:36:59.131 3G / 26G INFO General (main.cpp : 293) All done. Exiting. == Compressing corrected reads (with gzip) == Dataset description file was created: /N/dc2/projects/marinovg/2015-01-29-P-assem/Paramecium_biaurelia-SPAdes-3.5.0-trimmed/corrected/corrected.yaml ===== Read error correction finished. ===== Assembling started. == Running assembler: K21 0:00:00.000 4M / 4M INFO General (memory_limit.hpp : 42) Memory limit set to 250 Gb 0:00:00.001 4M / 4M INFO General (main.cpp : 146) Assembling dataset (/N/dc2/projects/marinovg/2015-01-29-P-assem/Paramecium_biaurelia-SPAdes-3.5.0-trimmed/dataset.info) with K=21 0:00:00.001 4M / 4M INFO General (launch.hpp : 28) SPAdes started 0:00:00.001 4M / 4M INFO General (launch.hpp : 29) Starting from stage: construction 0:00:00.002 4M / 4M INFO StageManager (stage.cpp : 125) STAGE == Construction 0:00:00.005 4M / 4M INFO General (read_converter.hpp : 79) Converting reads to binary format (takes a while) 0:00:00.005 4M / 4M INFO General (read_converter.hpp : 81) Paired reads for library #0 0:00:01.073 80M / 80M INFO General (binary_converter.hpp : 138) 16384 reads processed 0:00:01.423 92M / 92M INFO General (binary_converter.hpp : 138) 32768 reads processed 0:00:02.119 112M / 112M INFO General (binary_converter.hpp : 138) 65536 reads processed 0:00:03.513 160M / 160M INFO General (binary_converter.hpp : 138) 131072 reads processed 0:00:06.302 252M / 252M INFO General (binary_converter.hpp : 138) 262144 reads processed 0:00:11.887 440M / 440M INFO General (binary_converter.hpp : 138) 524288 reads processed 0:00:25.414 732M / 732M INFO General (binary_converter.hpp : 138) 1048576 reads processed 0:00:50.196 736M / 736M INFO General (binary_converter.hpp : 138) 2097152 reads processed 0:01:39.994 740M / 740M INFO General (binary_converter.hpp : 138) 4194304 reads processed 0:03:17.348 636M / 744M INFO General (binary_converter.hpp : 158) 8149676 reads written 0:03:18.738 4M / 744M INFO General (read_converter.hpp : 91) Single reads for library #0 0:03:20.553 136M / 744M INFO General (binary_converter.hpp : 138) 16384 reads processed 0:03:20.735 140M / 744M INFO General (binary_converter.hpp : 138) 32768 reads processed 0:03:21.131 148M / 744M INFO General (binary_converter.hpp : 158) 56278 reads written 0:03:21.207 4M / 744M INFO General (read_converter.hpp : 81) Paired reads for library #1 0:03:22.310 80M / 744M INFO General (binary_converter.hpp : 138) 16384 reads processed 0:03:22.671 92M / 744M INFO General (binary_converter.hpp : 138) 32768 reads processed 0:03:23.391 116M / 744M INFO General (binary_converter.hpp : 138) 65536 reads processed 0:03:24.833 160M / 744M INFO General (binary_converter.hpp : 138) 131072 reads processed 0:03:27.717 256M / 744M INFO General (binary_converter.hpp : 138) 262144 reads processed 0:03:33.481 444M / 744M INFO General (binary_converter.hpp : 138) 524288 reads processed 0:03:47.360 740M / 744M INFO General (binary_converter.hpp : 138) 1048576 reads processed 0:04:12.581 744M / 744M INFO General (binary_converter.hpp : 138) 2097152 reads processed 0:05:03.189 744M / 744M INFO General (binary_converter.hpp : 138) 4194304 reads processed 0:06:47.766 748M / 748M INFO General (binary_converter.hpp : 138) 8388608 reads processed 0:07:03.199 576M / 748M INFO General (binary_converter.hpp : 158) 8983143 reads written 0:07:04.419 4M / 748M INFO General (read_converter.hpp : 91) Single reads for library #1 0:07:06.187 136M / 748M INFO General (binary_converter.hpp : 138) 16384 reads processed 0:07:06.336 140M / 748M INFO General (binary_converter.hpp : 138) 32768 reads processed 0:07:06.565 144M / 748M INFO General (binary_converter.hpp : 158) 45439 reads written 0:07:06.672 4M / 748M INFO General (graph_construction.hpp : 129) Constructing DeBruijn graph for k=21 0:07:06.675 4M / 748M INFO General (kmer_splitters.hpp : 172) Splitting kmer instances into 256 buckets. This might take a while. 0:07:06.675 4M / 748M INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:07:06.675 4M / 748M INFO General (kmer_splitters.hpp : 190) Memory available for splitting buffers: 5.20825 Gb 0:07:06.675 4M / 748M INFO General (kmer_splitters.hpp : 199) Using cell size of 262144 0:07:36.020 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 25723318 reads 0:08:02.413 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 50636019 reads 0:08:21.967 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 68734710 reads 0:08:21.967 8G / 9G INFO General (kmer_splitters.hpp : 234) Adding contigs from previous K 0:08:21.968 8G / 9G INFO General (kmer_splitters.hpp : 245) Used 68734710 reads. Maximum read length 112 0:08:21.968 8G / 9G INFO General (kmer_splitters.hpp : 246) Average read length 106.502 0:08:24.134 64M / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:08:35.940 64M / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 201572913 kmers in total. 0:08:35.941 64M / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:08:44.869 64M / 9G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:08:44.869 64M / 9G INFO General (kmer_splitters.hpp : 379) Splitting kmer instances into 256 buckets. This might take a while. 0:08:44.870 64M / 9G INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:08:44.870 64M / 9G INFO General (kmer_splitters.hpp : 397) Memory available for splitting buffers: 5.20703 Gb 0:08:44.870 64M / 9G INFO General (kmer_splitters.hpp : 405) Using cell size of 262144 0:09:08.989 8G / 9G INFO General (kmer_splitters.hpp : 428) Processed 201572913 kmers 0:09:08.990 8G / 9G INFO General (kmer_splitters.hpp : 437) Used 201572913 kmers. 0:09:09.655 64M / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:09:17.782 64M / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 198338046 kmers in total. 0:09:17.782 64M / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:09:26.729 64M / 9G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:09:52.673 128M / 9G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:10:20.888 128M / 9G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 68612610 bytes occupied (2.7675 bits per kmer). 0:10:21.217 320M / 9G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 382) Building k-mer extensions from k+1-mers 0:10:43.517 320M / 9G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 386) Building k-mer extensions from k+1-mers finished. 0:10:43.524 320M / 9G INFO Early tip clipping (early_simplification.hpp : 236) Early tip clipping 0:21:04.633 320M / 9G INFO Early tip clipping (early_simplification.hpp : 239) 18683808 22-mers were removed by early tip clipper 0:21:04.633 320M / 9G INFO General (graph_construction.hpp : 145) Condensing graph 0:21:04.633 320M / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 337) Extracting unbranching paths 0:23:27.986 2G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 351) Extracting unbranching paths finished. 19541849 sequences extracted 0:23:45.091 2G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 311) Collecting perfect loops 0:24:47.250 2G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 326) Collecting perfect loops finished. 194 loops collected 0:25:01.620 4G / 9G INFO General (graph_construction.hpp : 150) Building index with from graph 0:25:01.621 4G / 9G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:25:01.621 4G / 9G INFO General (kmer_splitters.hpp : 289) Splitting kmer instances into 16 buckets. This might take a while. 0:25:01.621 4G / 9G INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:25:01.621 4G / 9G INFO General (kmer_splitters.hpp : 307) Memory available for splitting buffers: 81.9935 Gb 0:25:01.621 4G / 9G INFO General (kmer_splitters.hpp : 312) Using cell size of 4194304 0:26:18.231 4G / 9G INFO General (kmer_splitters.hpp : 325) Processed 7179102 edges 0:28:16.281 4G / 9G INFO General (kmer_splitters.hpp : 325) Processed 14343347 edges 0:29:50.640 4G / 9G INFO General (kmer_splitters.hpp : 325) Processed 19542043 edges 0:29:50.640 4G / 9G INFO General (kmer_splitters.hpp : 330) Used 19542043 sequences. 0:29:50.691 4G / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:31:11.784 4G / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 182889105 kmers in total. 0:31:11.785 4G / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:31:19.176 4G / 9G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:36:03.555 4G / 9G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:36:10.729 4G / 9G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 63268245 bytes occupied (2.7675 bits per kmer). 0:36:13.919 8G / 9G INFO General (edge_index_builders.hpp : 21) Collecting k-mer coverage information from graph, this takes a while. 0:41:47.412 7G / 9G INFO General (graph_construction.hpp : 182) Filling coverage index 0:41:47.413 7G / 9G INFO General (edge_index_builders.hpp : 99) Collecting k-mer coverage information from reads, this takes a while. 0:45:18.340 7G / 9G INFO General (graph_construction.hpp : 184) Filling coverage and flanking coverage from index 0:46:04.288 7G / 9G INFO General (construction.cpp : 33) Figured out: read length = 112 0:46:04.316 7G / 9G INFO StageManager (stage.cpp : 125) STAGE == EC Threshold Finding 0:46:15.458 7G / 9G INFO General (kmer_coverage_model.cpp : 178) Kmer coverage valley at: 11 0:46:15.458 7G / 9G INFO General (kmer_coverage_model.cpp : 198) K-mer histogram maximum: 26 0:46:15.458 7G / 9G INFO General (kmer_coverage_model.cpp : 234) Estimated median coverage: 27. Coverage mad: 10.3782 0:46:15.458 7G / 9G INFO General (kmer_coverage_model.cpp : 261) Fitting coverage model 0:46:15.561 7G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 2 0:46:15.818 7G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 4 0:46:16.684 7G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 8 0:46:18.536 7G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 16 0:46:22.053 7G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 32 0:46:24.645 7G / 9G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 31.1459. Fitted coverage std. dev: 12.5308 0:46:24.647 7G / 9G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 0.489278 0:46:24.647 7G / 9G INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 27 0:46:24.647 7G / 9G INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 21 0:46:24.647 7G / 9G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 61941700 0:46:24.647 7G / 9G INFO General (genomic_info_filler.cpp : 103) Mean coverage was calculated as 31.1459 0:46:24.648 7G / 9G INFO General (genomic_info_filler.cpp : 117) EC coverage threshold value was calculated as 21 0:46:24.648 7G / 9G INFO General (genomic_info_filler.cpp : 118) Trusted kmer low bound: 0 0:46:24.648 7G / 9G INFO StageManager (stage.cpp : 125) STAGE == Simplification 0:46:25.011 3G / 9G INFO General (graph_simplification.hpp : 911) Graph simplification started 0:46:25.011 3G / 9G INFO General (graph_simplification.hpp : 924) Fast simplification mode enabled 0:46:25.011 3G / 9G INFO General (graph_simplification.hpp : 771) PROCEDURE == Presimplification 0:46:25.011 3G / 9G INFO General (graph_simplification.hpp : 211) Removing short low covered self-conjugate connections 0:46:26.179 3G / 9G INFO General (graph_simplification.hpp : 403) Removing isolated edges 0:46:26.182 3G / 9G INFO General (graph_simplification.hpp : 404) All edges shorter than 150 will be removed 0:46:26.182 3G / 9G INFO General (graph_simplification.hpp : 405) Also edges shorter than 0 and coverage smaller than 0 will be removed 0:46:29.733 3G / 9G INFO General (graph_simplification.hpp : 687) Non parallel mode 0:47:27.735 4G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:49:50.566 4G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:53:55.286 4G / 9G INFO General (graph_simplification.hpp : 644) Using permanent iterators 0:53:55.286 4G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 1 0:54:06.681 4G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:54:33.448 4G / 9G INFO General (graph_simplification.hpp : 147) Removing bulges 0:59:50.233 4G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:59:59.090 3G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 2 0:59:59.091 3G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:59:59.835 3G / 9G INFO General (graph_simplification.hpp : 147) Removing bulges 1:00:20.972 3G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 1:00:33.254 3G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 3 1:00:33.254 3G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 1:00:33.528 3G / 9G INFO General (graph_simplification.hpp : 147) Removing bulges 1:00:56.734 3G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 1:01:00.223 3G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 4 1:01:00.223 3G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 1:01:00.345 3G / 9G INFO General (graph_simplification.hpp : 147) Removing bulges 1:01:07.951 3G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 1:01:10.060 3G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 5 1:01:10.060 3G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 1:01:10.133 3G / 9G INFO General (graph_simplification.hpp : 147) Removing bulges 1:01:14.596 3G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 1:01:16.303 3G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 6 1:01:16.303 3G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 1:01:16.359 3G / 9G INFO General (graph_simplification.hpp : 147) Removing bulges 1:01:19.226 3G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 1:01:20.858 3G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 7 1:01:20.858 3G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 1:01:20.907 3G / 9G INFO General (graph_simplification.hpp : 147) Removing bulges 1:01:23.143 3G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 1:01:25.000 3G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 8 1:01:25.000 3G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 1:01:25.051 3G / 9G INFO General (graph_simplification.hpp : 147) Removing bulges 1:01:26.992 3G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 1:01:29.182 3G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 9 1:01:29.182 3G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 1:01:29.237 3G / 9G INFO General (graph_simplification.hpp : 147) Removing bulges 1:01:30.938 3G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 1:01:33.420 3G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 10 1:01:33.420 3G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 1:01:33.478 3G / 9G INFO General (graph_simplification.hpp : 147) Removing bulges 1:01:34.817 3G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 1:01:37.659 3G / 9G INFO General (graph_simplification.hpp : 796) PROCEDURE == Post simplification 1:01:37.659 3G / 9G INFO General (graph_simplification.hpp : 644) Using permanent iterators 1:01:37.659 3G / 9G INFO General (graph_simplification.hpp : 806) Iteration 0 1:01:37.659 3G / 9G INFO General (graph_simplification.hpp : 247) Removal of relatively low covered connections disabled 1:01:40.826 3G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 1:01:47.712 3G / 9G INFO General (graph_simplification.hpp : 147) Removing bulges 1:02:04.564 3G / 9G INFO General (graph_simplification.hpp : 806) Iteration 1 1:02:04.564 3G / 9G INFO General (graph_simplification.hpp : 247) Removal of relatively low covered connections disabled 1:02:04.564 3G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 1:02:04.570 3G / 9G INFO General (graph_simplification.hpp : 147) Removing bulges 1:02:05.929 3G / 9G INFO StageManager (stage.cpp : 125) STAGE == Simplification Cleanup 1:02:05.930 3G / 9G INFO General (graph_simplification.hpp : 403) Removing isolated edges 1:02:05.930 3G / 9G INFO General (graph_simplification.hpp : 404) All edges shorter than 150 will be removed 1:02:05.930 3G / 9G INFO General (graph_simplification.hpp : 405) Also edges shorter than 0 and coverage smaller than 2 will be removed 1:02:06.232 3G / 9G INFO General (simplification.cpp : 56) Removing all the edges having coverage 0 and less 1:02:11.941 3G / 9G INFO General (simplification.cpp : 68) Counting average coverage 1:02:12.650 3G / 9G INFO General (simplification.cpp : 71) Average coverage = 26.029 1:02:12.650 3G / 9G INFO StageManager (stage.cpp : 125) STAGE == Contig Output 1:02:12.650 3G / 9G INFO General (contig_output.hpp : 283) Outputting contigs to /N/dc2/projects/marinovg/2015-01-29-P-assem/Paramecium_biaurelia-SPAdes-3.5.0-trimmed//K21/simplified_contigs.fasta 1:03:02.073 3G / 9G INFO General (contig_output.hpp : 283) Outputting contigs to /N/dc2/projects/marinovg/2015-01-29-P-assem/Paramecium_biaurelia-SPAdes-3.5.0-trimmed//K21/before_rr.fasta 1:05:20.559 3G / 9G INFO General (contig_output.hpp : 283) Outputting contigs to /N/dc2/projects/marinovg/2015-01-29-P-assem/Paramecium_biaurelia-SPAdes-3.5.0-trimmed//K21/final_contigs.fasta 1:07:38.131 3G / 9G INFO General (launch.hpp : 82) SPAdes finished 1:07:48.002 64M / 9G INFO General (main.cpp : 166) Assembling time: 1 hours 7 minutes 48 seconds == Running assembler: K33 0:00:00.000 4M / 4M INFO General (memory_limit.hpp : 42) Memory limit set to 250 Gb 0:00:00.001 4M / 4M INFO General (main.cpp : 146) Assembling dataset (/N/dc2/projects/marinovg/2015-01-29-P-assem/Paramecium_biaurelia-SPAdes-3.5.0-trimmed/dataset.info) with K=33 0:00:00.001 4M / 4M INFO General (launch.hpp : 28) SPAdes started 0:00:00.001 4M / 4M INFO General (launch.hpp : 29) Starting from stage: construction 0:00:00.002 4M / 4M INFO StageManager (stage.cpp : 125) STAGE == Construction 0:00:00.002 4M / 4M INFO General (construction.cpp : 44) Contigs from previous K will be used 0:00:00.006 4M / 4M INFO General (read_converter.hpp : 49) Binary reads detected 0:00:00.041 4M / 4M INFO General (graph_construction.hpp : 129) Constructing DeBruijn graph for k=33 0:00:00.043 4M / 4M INFO General (kmer_splitters.hpp : 172) Splitting kmer instances into 256 buckets. This might take a while. 0:00:00.044 4M / 4M INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:00:00.044 4M / 4M INFO General (kmer_splitters.hpp : 190) Memory available for splitting buffers: 5.20825 Gb 0:00:00.044 4M / 4M INFO General (kmer_splitters.hpp : 199) Using cell size of 131072 0:01:17.490 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 15050542 reads 0:01:43.975 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 30021144 reads 0:02:00.128 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 44409162 reads 0:04:12.233 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 58695311 reads 0:05:03.942 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 68734710 reads 0:05:03.943 8G / 9G INFO General (kmer_splitters.hpp : 234) Adding contigs from previous K 0:05:33.909 8G / 9G INFO General (kmer_splitters.hpp : 245) Used 68734710 reads. Maximum read length 112 0:05:33.910 8G / 9G INFO General (kmer_splitters.hpp : 246) Average read length 106.502 0:05:36.117 64M / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:06:28.905 64M / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 222388043 kmers in total. 0:06:28.906 64M / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:06:47.445 64M / 9G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:06:47.446 64M / 9G INFO General (kmer_splitters.hpp : 379) Splitting kmer instances into 256 buckets. This might take a while. 0:06:47.446 64M / 9G INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:06:47.446 64M / 9G INFO General (kmer_splitters.hpp : 397) Memory available for splitting buffers: 5.20703 Gb 0:06:47.446 64M / 9G INFO General (kmer_splitters.hpp : 405) Using cell size of 131072 0:07:20.682 8G / 9G INFO General (kmer_splitters.hpp : 428) Processed 222388043 kmers 0:07:20.682 8G / 9G INFO General (kmer_splitters.hpp : 437) Used 222388043 kmers. 0:07:21.881 64M / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:07:35.678 64M / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 221201814 kmers in total. 0:07:35.679 64M / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:08:11.162 64M / 9G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:08:43.140 192M / 9G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:09:00.335 192M / 9G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 76522035 bytes occupied (2.7675 bits per kmer). 0:09:00.718 404M / 9G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 382) Building k-mer extensions from k+1-mers 0:09:27.977 404M / 9G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 386) Building k-mer extensions from k+1-mers finished. 0:09:27.983 404M / 9G INFO Early tip clipping (early_simplification.hpp : 236) Early tip clipping 0:22:11.317 404M / 9G INFO Early tip clipping (early_simplification.hpp : 239) 35799924 34-mers were removed by early tip clipper 0:22:11.317 404M / 9G INFO General (graph_construction.hpp : 145) Condensing graph 0:22:11.317 404M / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 337) Extracting unbranching paths 0:24:57.136 1G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 351) Extracting unbranching paths finished. 9936506 sequences extracted 0:25:16.408 1G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 311) Collecting perfect loops 0:26:38.823 1G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 326) Collecting perfect loops finished. 252 loops collected 0:26:46.689 2G / 9G INFO General (graph_construction.hpp : 150) Building index with from graph 0:26:46.690 2G / 9G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:26:46.691 2G / 9G INFO General (kmer_splitters.hpp : 289) Splitting kmer instances into 16 buckets. This might take a while. 0:26:46.691 2G / 9G INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:26:46.691 2G / 9G INFO General (kmer_splitters.hpp : 307) Memory available for splitting buffers: 82.5378 Gb 0:26:46.691 2G / 9G INFO General (kmer_splitters.hpp : 312) Using cell size of 2097152 0:27:14.642 2G / 9G INFO General (kmer_splitters.hpp : 325) Processed 1786358 edges 0:28:22.293 2G / 9G INFO General (kmer_splitters.hpp : 325) Processed 3575868 edges 0:29:08.815 2G / 9G INFO General (kmer_splitters.hpp : 325) Processed 5360872 edges 0:29:16.517 2G / 9G INFO General (kmer_splitters.hpp : 325) Processed 7152097 edges 0:29:24.062 2G / 9G INFO General (kmer_splitters.hpp : 325) Processed 8936553 edges 0:29:28.331 2G / 9G INFO General (kmer_splitters.hpp : 325) Processed 9936758 edges 0:29:28.332 2G / 9G INFO General (kmer_splitters.hpp : 330) Used 9936758 sequences. 0:29:28.406 2G / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:30:24.100 2G / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 186588119 kmers in total. 0:30:24.100 2G / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:30:39.085 2G / 9G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:35:35.452 2G / 9G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:35:49.926 2G / 9G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 64547872 bytes occupied (2.7675 bits per kmer). 0:35:53.123 6G / 9G INFO General (edge_index_builders.hpp : 21) Collecting k-mer coverage information from graph, this takes a while. 0:41:55.176 6G / 9G INFO General (graph_construction.hpp : 182) Filling coverage index 0:41:55.176 6G / 9G INFO General (edge_index_builders.hpp : 99) Collecting k-mer coverage information from reads, this takes a while. 0:45:15.351 6G / 9G INFO General (graph_construction.hpp : 184) Filling coverage and flanking coverage from index 0:46:00.324 6G / 9G INFO General (construction.cpp : 33) Figured out: read length = 112 0:46:00.355 6G / 9G INFO StageManager (stage.cpp : 125) STAGE == EC Threshold Finding 0:46:11.615 6G / 9G INFO General (kmer_coverage_model.cpp : 178) Kmer coverage valley at: 9 0:46:11.615 6G / 9G INFO General (kmer_coverage_model.cpp : 198) K-mer histogram maximum: 22 0:46:11.615 6G / 9G INFO General (kmer_coverage_model.cpp : 234) Estimated median coverage: 23. Coverage mad: 10.3782 0:46:11.615 6G / 9G INFO General (kmer_coverage_model.cpp : 261) Fitting coverage model 0:46:11.702 6G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 2 0:46:11.919 6G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 4 0:46:12.688 6G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 8 0:46:14.270 6G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 16 0:46:17.313 6G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 32 0:46:19.478 6G / 9G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 26.6247. Fitted coverage std. dev: 10.8492 0:46:19.480 6G / 9G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 0.502611 0:46:19.480 6G / 9G INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 22 0:46:19.480 6G / 9G INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 17 0:46:19.480 6G / 9G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 64865951 0:46:19.480 6G / 9G INFO General (genomic_info_filler.cpp : 103) Mean coverage was calculated as 26.6247 0:46:19.481 6G / 9G INFO General (genomic_info_filler.cpp : 117) EC coverage threshold value was calculated as 17 0:46:19.481 6G / 9G INFO General (genomic_info_filler.cpp : 118) Trusted kmer low bound: 0 0:46:19.481 6G / 9G INFO StageManager (stage.cpp : 125) STAGE == Simplification 0:46:19.862 2G / 9G INFO General (graph_simplification.hpp : 911) Graph simplification started 0:46:19.862 2G / 9G INFO General (graph_simplification.hpp : 924) Fast simplification mode enabled 0:46:19.862 2G / 9G INFO General (graph_simplification.hpp : 771) PROCEDURE == Presimplification 0:46:19.862 2G / 9G INFO General (graph_simplification.hpp : 211) Removing short low covered self-conjugate connections 0:46:20.524 2G / 9G INFO General (graph_simplification.hpp : 403) Removing isolated edges 0:46:20.524 2G / 9G INFO General (graph_simplification.hpp : 404) All edges shorter than 150 will be removed 0:46:20.524 2G / 9G INFO General (graph_simplification.hpp : 405) Also edges shorter than 0 and coverage smaller than 0 will be removed 0:46:25.120 2G / 9G INFO General (graph_simplification.hpp : 687) Non parallel mode 0:46:52.695 2G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:47:58.897 2G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:50:09.643 2G / 9G INFO General (graph_simplification.hpp : 644) Using permanent iterators 0:50:09.644 2G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 1 0:50:12.913 2G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:50:20.985 2G / 9G INFO General (graph_simplification.hpp : 147) Removing bulges 0:51:17.170 2G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:51:21.597 2G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 2 0:51:21.597 2G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:51:21.825 2G / 9G INFO General (graph_simplification.hpp : 147) Removing bulges 0:51:24.495 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:51:29.297 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 3 0:51:29.297 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:51:29.364 1G / 9G INFO General (graph_simplification.hpp : 147) Removing bulges 0:51:34.177 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:51:35.477 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 4 0:51:35.477 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:51:35.515 1G / 9G INFO General (graph_simplification.hpp : 147) Removing bulges 0:51:38.856 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:51:39.349 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 5 0:51:39.349 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:51:39.371 1G / 9G INFO General (graph_simplification.hpp : 147) Removing bulges 0:51:41.130 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:51:41.457 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 6 0:51:41.457 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:51:41.472 1G / 9G INFO General (graph_simplification.hpp : 147) Removing bulges 0:51:42.417 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:51:42.641 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 7 0:51:42.641 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:51:42.651 1G / 9G INFO General (graph_simplification.hpp : 147) Removing bulges 0:51:43.356 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:51:43.528 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 8 0:51:43.528 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:51:43.536 1G / 9G INFO General (graph_simplification.hpp : 147) Removing bulges 0:51:43.978 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:51:44.134 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 9 0:51:44.134 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:51:44.140 1G / 9G INFO General (graph_simplification.hpp : 147) Removing bulges 0:51:44.457 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:51:44.618 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 10 0:51:44.618 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:51:44.624 1G / 9G INFO General (graph_simplification.hpp : 147) Removing bulges 0:51:44.847 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:51:45.033 1G / 9G INFO General (graph_simplification.hpp : 796) PROCEDURE == Post simplification 0:51:45.033 1G / 9G INFO General (graph_simplification.hpp : 644) Using permanent iterators 0:51:45.033 1G / 9G INFO General (graph_simplification.hpp : 806) Iteration 0 0:51:45.033 1G / 9G INFO General (graph_simplification.hpp : 247) Removal of relatively low covered connections disabled 0:51:45.982 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:51:47.990 1G / 9G INFO General (graph_simplification.hpp : 147) Removing bulges 0:51:49.883 1G / 9G INFO General (graph_simplification.hpp : 806) Iteration 1 0:51:49.883 1G / 9G INFO General (graph_simplification.hpp : 247) Removal of relatively low covered connections disabled 0:51:49.883 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:51:49.885 1G / 9G INFO General (graph_simplification.hpp : 147) Removing bulges 0:51:50.360 1G / 9G INFO StageManager (stage.cpp : 125) STAGE == Simplification Cleanup 0:51:50.361 1G / 9G INFO General (graph_simplification.hpp : 403) Removing isolated edges 0:51:50.361 1G / 9G INFO General (graph_simplification.hpp : 404) All edges shorter than 150 will be removed 0:51:50.361 1G / 9G INFO General (graph_simplification.hpp : 405) Also edges shorter than 0 and coverage smaller than 2 will be removed 0:51:50.524 1G / 9G INFO General (simplification.cpp : 56) Removing all the edges having coverage 0 and less 0:51:52.162 1G / 9G INFO General (simplification.cpp : 68) Counting average coverage 0:51:52.452 1G / 9G INFO General (simplification.cpp : 71) Average coverage = 20.4617 0:51:52.452 1G / 9G INFO StageManager (stage.cpp : 125) STAGE == Contig Output 0:51:52.452 1G / 9G INFO General (contig_output.hpp : 283) Outputting contigs to /N/dc2/projects/marinovg/2015-01-29-P-assem/Paramecium_biaurelia-SPAdes-3.5.0-trimmed//K33/simplified_contigs.fasta 0:52:25.800 1G / 9G INFO General (contig_output.hpp : 283) Outputting contigs to /N/dc2/projects/marinovg/2015-01-29-P-assem/Paramecium_biaurelia-SPAdes-3.5.0-trimmed//K33/before_rr.fasta 0:54:00.488 1G / 9G INFO General (contig_output.hpp : 283) Outputting contigs to /N/dc2/projects/marinovg/2015-01-29-P-assem/Paramecium_biaurelia-SPAdes-3.5.0-trimmed//K33/final_contigs.fasta 0:55:35.262 1G / 9G INFO General (launch.hpp : 82) SPAdes finished 0:55:40.010 64M / 9G INFO General (main.cpp : 166) Assembling time: 0 hours 55 minutes 40 seconds == Running assembler: K55 0:00:00.000 4M / 4M INFO General (memory_limit.hpp : 42) Memory limit set to 250 Gb 0:00:00.001 4M / 4M INFO General (main.cpp : 146) Assembling dataset (/N/dc2/projects/marinovg/2015-01-29-P-assem/Paramecium_biaurelia-SPAdes-3.5.0-trimmed/dataset.info) with K=55 0:00:00.001 4M / 4M INFO General (launch.hpp : 28) SPAdes started 0:00:00.001 4M / 4M INFO General (launch.hpp : 29) Starting from stage: construction 0:00:00.002 4M / 4M INFO General (launch.hpp : 44) Will need read mapping, kmer mapper will be attached 0:00:00.002 4M / 4M INFO StageManager (stage.cpp : 125) STAGE == Construction 0:00:00.002 4M / 4M INFO General (construction.cpp : 44) Contigs from previous K will be used 0:00:00.006 4M / 4M INFO General (read_converter.hpp : 49) Binary reads detected 0:00:00.043 4M / 4M INFO General (graph_construction.hpp : 129) Constructing DeBruijn graph for k=55 0:00:00.045 4M / 4M INFO General (kmer_splitters.hpp : 172) Splitting kmer instances into 256 buckets. This might take a while. 0:00:00.046 4M / 4M INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:00:00.046 4M / 4M INFO General (kmer_splitters.hpp : 190) Memory available for splitting buffers: 5.20825 Gb 0:00:00.046 4M / 4M INFO General (kmer_splitters.hpp : 199) Using cell size of 131072 0:00:20.575 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 21623165 reads 0:00:37.706 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 42453924 reads 0:00:54.745 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 62571437 reads 0:01:01.434 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 68734710 reads 0:01:01.434 8G / 9G INFO General (kmer_splitters.hpp : 234) Adding contigs from previous K 0:01:29.457 8G / 9G INFO General (kmer_splitters.hpp : 245) Used 68734710 reads. Maximum read length 112 0:01:29.457 8G / 9G INFO General (kmer_splitters.hpp : 246) Average read length 106.502 0:01:31.643 64M / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:01:59.557 64M / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 229099371 kmers in total. 0:01:59.558 64M / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:02:31.691 64M / 9G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:02:31.691 64M / 9G INFO General (kmer_splitters.hpp : 379) Splitting kmer instances into 256 buckets. This might take a while. 0:02:31.692 64M / 9G INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:02:31.692 64M / 9G INFO General (kmer_splitters.hpp : 397) Memory available for splitting buffers: 5.20703 Gb 0:02:31.692 64M / 9G INFO General (kmer_splitters.hpp : 405) Using cell size of 131072 0:03:38.245 8G / 9G INFO General (kmer_splitters.hpp : 428) Processed 229099371 kmers 0:03:38.246 8G / 9G INFO General (kmer_splitters.hpp : 437) Used 229099371 kmers. 0:03:39.538 64M / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:04:14.096 64M / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 229504284 kmers in total. 0:04:14.096 64M / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:04:54.464 64M / 9G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:05:25.736 192M / 9G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:05:44.253 192M / 9G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 79394174 bytes occupied (2.7675 bits per kmer). 0:05:44.646 412M / 9G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 382) Building k-mer extensions from k+1-mers 0:06:18.405 412M / 9G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 386) Building k-mer extensions from k+1-mers finished. 0:06:18.411 412M / 9G INFO General (graph_construction.hpp : 145) Condensing graph 0:06:18.411 412M / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 337) Extracting unbranching paths 0:08:51.526 2G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 351) Extracting unbranching paths finished. 14330047 sequences extracted 0:09:14.486 2G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 311) Collecting perfect loops 0:10:37.758 2G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 326) Collecting perfect loops finished. 26 loops collected 0:10:51.740 3G / 9G INFO General (graph_construction.hpp : 150) Building index with from graph 0:10:51.741 3G / 9G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:10:51.741 3G / 9G INFO General (kmer_splitters.hpp : 289) Splitting kmer instances into 16 buckets. This might take a while. 0:10:51.741 3G / 9G INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:10:51.741 3G / 9G INFO General (kmer_splitters.hpp : 307) Memory available for splitting buffers: 82.0794 Gb 0:10:51.741 3G / 9G INFO General (kmer_splitters.hpp : 312) Using cell size of 2097152 0:11:20.387 4G / 9G INFO General (kmer_splitters.hpp : 325) Processed 2098829 edges 0:11:35.456 4G / 9G INFO General (kmer_splitters.hpp : 325) Processed 4198271 edges 0:11:43.557 4G / 9G INFO General (kmer_splitters.hpp : 325) Processed 6297567 edges 0:12:04.623 4G / 9G INFO General (kmer_splitters.hpp : 325) Processed 8397203 edges 0:13:01.773 4G / 9G INFO General (kmer_splitters.hpp : 325) Processed 10495908 edges 0:14:59.334 4G / 9G INFO General (kmer_splitters.hpp : 325) Processed 12592220 edges 0:15:26.260 4G / 9G INFO General (kmer_splitters.hpp : 325) Processed 14330073 edges 0:15:26.260 4G / 9G INFO General (kmer_splitters.hpp : 330) Used 14330073 sequences. 0:15:26.314 3G / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:16:36.073 3G / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 229099371 kmers in total. 0:16:36.074 3G / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:16:54.407 3G / 9G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:22:40.877 3G / 9G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:22:58.622 3G / 9G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 79254102 bytes occupied (2.7675 bits per kmer). 0:23:02.530 9G / 9G INFO General (edge_index_builders.hpp : 21) Collecting k-mer coverage information from graph, this takes a while. 0:31:06.385 8G / 9G INFO General (graph_construction.hpp : 182) Filling coverage index 0:31:06.385 8G / 9G INFO General (edge_index_builders.hpp : 99) Collecting k-mer coverage information from reads, this takes a while. 0:33:45.371 8G / 9G INFO General (graph_construction.hpp : 184) Filling coverage and flanking coverage from index 0:34:44.360 8G / 9G INFO General (construction.cpp : 33) Figured out: read length = 112 0:34:44.393 8G / 9G INFO StageManager (stage.cpp : 125) STAGE == EC Threshold Finding 0:34:56.368 8G / 9G INFO General (kmer_coverage_model.cpp : 178) Kmer coverage valley at: 6 0:34:56.368 8G / 9G INFO General (kmer_coverage_model.cpp : 198) K-mer histogram maximum: 14 0:34:56.368 8G / 9G INFO General (kmer_coverage_model.cpp : 234) Estimated median coverage: 15. Coverage mad: 7.413 0:34:56.368 8G / 9G INFO General (kmer_coverage_model.cpp : 261) Fitting coverage model 0:34:56.418 8G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 2 0:34:56.556 8G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 4 0:34:57.053 8G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 8 0:34:58.079 8G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 16 0:34:59.948 8G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 32 0:35:01.221 8G / 9G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 18.5029. Fitted coverage std. dev: 8.02794 0:35:01.223 8G / 9G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 0.443739 0:35:01.223 8G / 9G INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 15 0:35:01.223 8G / 9G INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 12 0:35:01.223 8G / 9G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 63751429 0:35:01.223 8G / 9G INFO General (genomic_info_filler.cpp : 103) Mean coverage was calculated as 18.5029 0:35:01.223 8G / 9G INFO General (genomic_info_filler.cpp : 117) EC coverage threshold value was calculated as 12 0:35:01.223 8G / 9G INFO General (genomic_info_filler.cpp : 118) Trusted kmer low bound: 0 0:35:01.223 8G / 9G INFO StageManager (stage.cpp : 125) STAGE == Gap Closer 0:35:01.233 8G / 9G INFO General (gap_closer.cpp : 157) Preparing shift maps 0:35:18.718 9G / 9G INFO General (gap_closer.cpp : 117) Processing paired reads (takes a while) 0:35:35.899 9G / 9G INFO General (gap_closer.cpp : 136) Used 16299352 paired reads 0:35:35.901 9G / 9G INFO General (gap_closer.cpp : 138) Merging paired indices 0:35:42.571 8G / 9G INFO GapCloser (gap_closer.cpp : 395) Closing short gaps 0:36:23.961 8G / 9G INFO GapCloser (gap_closer.cpp : 424) Closing short gaps complete: filled 7476 gaps after checking 53217 candidates 0:36:31.297 8G / 9G INFO General (gap_closer.cpp : 157) Preparing shift maps 0:36:49.308 9G / 9G INFO General (gap_closer.cpp : 117) Processing paired reads (takes a while) 0:37:09.173 9G / 9G INFO General (gap_closer.cpp : 136) Used 17966286 paired reads 0:37:09.174 9G / 9G INFO General (gap_closer.cpp : 138) Merging paired indices 0:37:15.874 8G / 9G INFO GapCloser (gap_closer.cpp : 395) Closing short gaps 0:37:57.061 8G / 9G INFO GapCloser (gap_closer.cpp : 424) Closing short gaps complete: filled 6287 gaps after checking 53120 candidates 0:38:03.995 8G / 9G INFO StageManager (stage.cpp : 125) STAGE == Simplification 0:38:04.441 3G / 9G INFO General (graph_simplification.hpp : 911) Graph simplification started 0:38:04.441 3G / 9G INFO General (graph_simplification.hpp : 924) Fast simplification mode enabled 0:38:04.441 3G / 9G INFO General (graph_simplification.hpp : 771) PROCEDURE == Presimplification 0:38:04.442 3G / 9G INFO General (graph_simplification.hpp : 211) Removing short low covered self-conjugate connections 0:38:05.793 3G / 9G INFO General (graph_simplification.hpp : 403) Removing isolated edges 0:38:05.793 3G / 9G INFO General (graph_simplification.hpp : 404) All edges shorter than 150 will be removed 0:38:05.793 3G / 9G INFO General (graph_simplification.hpp : 405) Also edges shorter than 0 and coverage smaller than 0 will be removed 0:38:15.783 3G / 9G INFO General (graph_simplification.hpp : 687) Non parallel mode 0:39:01.551 3G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:41:25.382 3G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:41:51.889 2G / 9G INFO General (graph_simplification.hpp : 644) Using permanent iterators 0:41:51.890 2G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 1 0:41:53.099 2G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:41:56.110 2G / 9G INFO General (graph_simplification.hpp : 147) Removing bulges 0:42:19.807 2G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:42:20.217 2G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 2 0:42:20.217 2G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:42:20.270 2G / 9G INFO General (graph_simplification.hpp : 147) Removing bulges 0:42:20.464 2G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:42:21.418 2G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 3 0:42:21.418 2G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:42:21.433 2G / 9G INFO General (graph_simplification.hpp : 147) Removing bulges 0:42:22.673 2G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:42:23.461 2G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 4 0:42:23.461 2G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:42:23.483 2G / 9G INFO General (graph_simplification.hpp : 147) Removing bulges 0:42:25.757 2G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:42:26.100 2G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 5 0:42:26.100 2G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:42:26.112 2G / 9G INFO General (graph_simplification.hpp : 147) Removing bulges 0:42:27.122 2G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:42:27.297 2G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 6 0:42:27.298 2G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:42:27.306 2G / 9G INFO General (graph_simplification.hpp : 147) Removing bulges 0:42:27.894 2G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:42:28.029 2G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 7 0:42:28.029 2G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:42:28.035 2G / 9G INFO General (graph_simplification.hpp : 147) Removing bulges 0:42:28.461 2G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:42:28.565 2G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 8 0:42:28.566 2G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:42:28.571 2G / 9G INFO General (graph_simplification.hpp : 147) Removing bulges 0:42:28.832 2G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:42:28.902 2G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 9 0:42:28.902 2G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:42:28.905 2G / 9G INFO General (graph_simplification.hpp : 147) Removing bulges 0:42:29.027 2G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:42:29.092 2G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 10 0:42:29.092 2G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:42:29.095 2G / 9G INFO General (graph_simplification.hpp : 147) Removing bulges 0:42:29.180 2G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:42:29.246 2G / 9G INFO General (graph_simplification.hpp : 796) PROCEDURE == Post simplification 0:42:29.246 2G / 9G INFO General (graph_simplification.hpp : 644) Using permanent iterators 0:42:29.247 2G / 9G INFO General (graph_simplification.hpp : 806) Iteration 0 0:42:29.247 2G / 9G INFO General (graph_simplification.hpp : 247) Removal of relatively low covered connections disabled 0:42:29.929 2G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:42:31.339 2G / 9G INFO General (graph_simplification.hpp : 147) Removing bulges 0:42:32.260 2G / 9G INFO General (graph_simplification.hpp : 806) Iteration 1 0:42:32.260 2G / 9G INFO General (graph_simplification.hpp : 247) Removal of relatively low covered connections disabled 0:42:32.260 2G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:42:32.261 2G / 9G INFO General (graph_simplification.hpp : 147) Removing bulges 0:42:32.721 2G / 9G INFO StageManager (stage.cpp : 125) STAGE == Gap Closer 0:42:32.721 2G / 9G INFO General (graph_pack.hpp : 84) Index refill 0:42:32.722 2G / 9G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:42:32.722 2G / 9G INFO General (kmer_splitters.hpp : 289) Splitting kmer instances into 16 buckets. This might take a while. 0:42:32.722 2G / 9G INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:42:32.722 2G / 9G INFO General (kmer_splitters.hpp : 307) Memory available for splitting buffers: 82.4648 Gb 0:42:32.722 2G / 9G INFO General (kmer_splitters.hpp : 312) Using cell size of 2097152 0:42:59.513 3G / 9G INFO General (kmer_splitters.hpp : 325) Processed 77489 edges 0:43:05.711 3G / 9G INFO General (kmer_splitters.hpp : 325) Processed 155435 edges 0:43:11.910 3G / 9G INFO General (kmer_splitters.hpp : 325) Processed 234561 edges 0:43:15.642 3G / 9G INFO General (kmer_splitters.hpp : 325) Processed 280653 edges 0:43:15.643 3G / 9G INFO General (kmer_splitters.hpp : 330) Used 280653 sequences. 0:43:15.728 2G / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:43:52.480 2G / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 120630969 kmers in total. 0:43:52.481 2G / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:44:02.344 2G / 9G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:46:59.068 2G / 9G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:47:08.614 2G / 9G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 41730810 bytes occupied (2.7675 bits per kmer). 0:47:10.715 5G / 9G INFO General (edge_index_builders.hpp : 21) Collecting k-mer coverage information from graph, this takes a while. 0:50:52.293 5G / 9G INFO General (gap_closer.cpp : 157) Preparing shift maps 0:50:52.876 5G / 9G INFO General (gap_closer.cpp : 117) Processing paired reads (takes a while) 0:51:23.377 5G / 9G INFO General (gap_closer.cpp : 136) Used 16299352 paired reads 0:51:23.378 5G / 9G INFO General (gap_closer.cpp : 138) Merging paired indices 0:51:24.531 5G / 9G INFO GapCloser (gap_closer.cpp : 395) Closing short gaps 0:51:25.432 5G / 9G INFO GapCloser (gap_closer.cpp : 424) Closing short gaps complete: filled 340 gaps after checking 11995 candidates 0:51:27.239 5G / 9G INFO General (gap_closer.cpp : 157) Preparing shift maps 0:51:27.815 5G / 9G INFO General (gap_closer.cpp : 117) Processing paired reads (takes a while) 0:52:01.705 5G / 9G INFO General (gap_closer.cpp : 136) Used 17966286 paired reads 0:52:01.707 5G / 9G INFO General (gap_closer.cpp : 138) Merging paired indices 0:52:02.757 5G / 9G INFO GapCloser (gap_closer.cpp : 395) Closing short gaps 0:52:03.642 5G / 9G INFO GapCloser (gap_closer.cpp : 424) Closing short gaps complete: filled 285 gaps after checking 10967 candidates 0:52:05.451 5G / 9G INFO StageManager (stage.cpp : 125) STAGE == Simplification Cleanup 0:52:05.452 5G / 9G INFO General (graph_simplification.hpp : 403) Removing isolated edges 0:52:05.452 5G / 9G INFO General (graph_simplification.hpp : 404) All edges shorter than 150 will be removed 0:52:05.452 5G / 9G INFO General (graph_simplification.hpp : 405) Also edges shorter than 0 and coverage smaller than 2 will be removed 0:52:09.433 5G / 9G INFO General (simplification.cpp : 56) Removing all the edges having coverage 0 and less 0:52:10.319 5G / 9G INFO General (simplification.cpp : 68) Counting average coverage 0:52:10.515 5G / 9G INFO General (simplification.cpp : 71) Average coverage = 13.9085 0:52:10.515 5G / 9G INFO StageManager (stage.cpp : 125) STAGE == Mismatch Correction 0:53:39.090 5G / 9G INFO General (mismatch_shall_not_pass.hp: 188) Finished collecting potential mismatches positions 0:53:42.030 5G / 9G INFO General (mismatch_shall_not_pass.hp: 291) All edges processed 0:53:42.125 5G / 9G INFO General (mismatch_correction.cpp : 18) Corrected 74 nucleotides 0:53:42.156 5G / 9G INFO StageManager (stage.cpp : 125) STAGE == Paired Information Counting 0:53:43.949 5G / 9G INFO General (pair_info_count.cpp : 150) Graph N50: 4335 0:53:43.949 5G / 9G INFO General (pair_info_count.cpp : 152) Estimating insert size for library #0 0:53:43.949 5G / 9G INFO General (pair_info_count.cpp : 31) Estimating insert size (takes a while) 0:53:43.959 5G / 9G INFO General (short_read_mapper.hpp : 91) Selecting usual mapper 0:53:50.232 5G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 200000 reads 0:53:50.250 5G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 400000 reads 0:53:50.258 5G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 600000 reads 0:53:50.287 5G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 800000 reads 0:53:50.366 5G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 1000000 reads 0:53:50.376 5G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 1200000 reads 0:53:50.960 5G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 2200000 reads 0:53:56.566 5G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 4200000 reads 0:54:01.905 5G / 9G INFO General (sequence_mapper_notifier.h: 89) Processed 8149676 reads 0:54:01.906 5G / 9G INFO General (pair_info_count.cpp : 41) 4206995 paired reads (51.6216% of all) aligned to long edges 0:54:01.916 5G / 9G INFO General (pair_info_count.cpp : 170) Estimated insert size for paired library #0 0:54:01.916 5G / 9G INFO General (pair_info_count.cpp : 175) Insert size = 211.862, deviation = 35.0027, left quantile = 169, right quantile = 254, read length = 108 0:54:01.916 5G / 9G INFO General (pair_info_count.cpp : 152) Estimating insert size for library #1 0:54:01.916 5G / 9G INFO General (pair_info_count.cpp : 31) Estimating insert size (takes a while) 0:54:01.925 5G / 9G INFO General (short_read_mapper.hpp : 91) Selecting usual mapper 0:54:08.246 5G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 200000 reads 0:54:08.336 5G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 400000 reads 0:54:08.346 5G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 600000 reads 0:54:08.528 5G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 800000 reads 0:54:08.595 5G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 1000000 reads 0:54:08.651 5G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 1200000 reads 0:54:08.977 5G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 2200000 reads 0:54:14.870 5G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 4200000 reads 0:54:21.694 5G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 8498802 reads 0:54:21.752 5G / 9G INFO General (sequence_mapper_notifier.h: 89) Processed 8983143 reads 0:54:21.753 5G / 9G INFO General (pair_info_count.cpp : 41) 4688163 paired reads (52.1884% of all) aligned to long edges 0:54:21.762 5G / 9G INFO General (pair_info_count.cpp : 170) Estimated insert size for paired library #1 0:54:21.763 5G / 9G INFO General (pair_info_count.cpp : 175) Insert size = 211.899, deviation = 34.5033, left quantile = 170, right quantile = 254, read length = 112 0:54:21.763 5G / 9G INFO General (pair_info_count.cpp : 187) Mapping library #0 0:54:21.763 5G / 9G INFO General (pair_info_count.cpp : 189) Mapping paired reads (takes a while) 0:54:21.763 5G / 9G INFO General (pair_info_count.cpp : 73) Left insert size qauntile 169, right insert size quantile 254 0:54:21.772 5G / 9G INFO General (short_read_mapper.hpp : 91) Selecting usual mapper 0:54:35.123 7G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 200000 reads 0:54:36.104 7G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 400000 reads 0:54:36.988 7G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 600000 reads 0:54:38.021 7G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 800000 reads 0:54:39.185 7G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 1000000 reads 0:54:40.373 7G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 1200000 reads 0:54:46.867 7G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 2200000 reads 0:55:01.970 7G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 4200000 reads 0:55:36.566 7G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 8400000 reads 0:56:47.296 6G / 9G INFO General (sequence_mapper_notifier.h: 89) Processed 16299352 reads 0:57:22.324 6G / 9G INFO General (split_graph_pair_info.hpp : 344) Threshold for paired information 0.0484345 0:57:26.388 5G / 9G INFO General (pair_info_count.cpp : 187) Mapping library #1 0:57:26.388 5G / 9G INFO General (pair_info_count.cpp : 189) Mapping paired reads (takes a while) 0:57:26.388 5G / 9G INFO General (pair_info_count.cpp : 73) Left insert size qauntile 170, right insert size quantile 254 0:57:26.398 5G / 9G INFO General (short_read_mapper.hpp : 91) Selecting usual mapper 0:57:40.018 7G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 200000 reads 0:57:41.050 7G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 400000 reads 0:57:42.039 7G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 600000 reads 0:57:43.201 7G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 800000 reads 0:57:44.376 7G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 1000000 reads 0:57:45.614 7G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 1200000 reads 0:57:52.753 7G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 2200000 reads 0:58:08.816 7G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 4200000 reads 0:58:45.224 8G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 8400000 reads 1:00:03.542 7G / 9G INFO General (sequence_mapper_notifier.h: 81) Processed 16860250 reads 1:00:15.663 6G / 9G INFO General (sequence_mapper_notifier.h: 89) Processed 17966286 reads 1:00:52.924 6G / 9G INFO General (split_graph_pair_info.hpp : 344) Threshold for paired information 0.0537194 1:00:57.216 5G / 9G INFO StageManager (stage.cpp : 125) STAGE == Distance Estimation 1:00:57.217 5G / 9G INFO General (distance_estimation.cpp : 234) Processing library #0 1:00:57.217 5G / 9G INFO General (distance_estimation.cpp : 136) Weight Filter Done 1:00:57.217 5G / 9G INFO DistanceEstimator (distance_estimation.hpp : 187) Using SIMPLE distance estimator 1:02:09.495 5G / 9G INFO DistanceEstimator (distance_estimation.hpp : 208) Merging maps 1:02:13.269 5G / 9G INFO General (distance_estimation.cpp : 38) Filtering info 1:02:15.901 5G / 9G INFO General (pair_info_filters.hpp : 354) Pruning the index 1:02:16.263 5G / 9G INFO General (distance_estimation.cpp : 184) Refining clustered pair information 1:02:16.616 5G / 9G INFO General (distance_estimation.cpp : 186) The refining of clustered pair information has been finished 1:02:16.616 5G / 9G INFO General (distance_estimation.cpp : 188) Filling paired information 1:02:38.689 5G / 9G INFO PairInfoImprover (pair_info_improver.hpp : 61) Paired info stats: missing = 135531; contradictional = 524 1:03:01.497 5G / 9G INFO PairInfoImprover (pair_info_improver.hpp : 61) Paired info stats: missing = 36672; contradictional = 0 1:03:01.497 5G / 9G INFO General (distance_estimation.cpp : 193) Filling scaffolding index 1:03:01.497 5G / 9G INFO DistanceEstimator (distance_estimation.hpp : 187) Using SMOOTHING distance estimator 1:04:16.542 5G / 9G INFO DistanceEstimator (distance_estimation.hpp : 208) Merging maps 1:04:16.574 5G / 9G INFO General (distance_estimation.cpp : 38) Filtering info 1:04:16.720 5G / 9G INFO General (pair_info_filters.hpp : 354) Pruning the index 1:04:17.766 5G / 9G INFO General (distance_estimation.cpp : 234) Processing library #1 1:04:17.767 5G / 9G INFO General (distance_estimation.cpp : 136) Weight Filter Done 1:04:17.767 5G / 9G INFO DistanceEstimator (distance_estimation.hpp : 187) Using SIMPLE distance estimator 1:05:42.890 5G / 9G INFO DistanceEstimator (distance_estimation.hpp : 208) Merging maps 1:05:47.036 5G / 9G INFO General (distance_estimation.cpp : 38) Filtering info 1:05:49.946 5G / 9G INFO General (pair_info_filters.hpp : 354) Pruning the index 1:05:50.336 5G / 9G INFO General (distance_estimation.cpp : 184) Refining clustered pair information 1:05:50.743 5G / 9G INFO General (distance_estimation.cpp : 186) The refining of clustered pair information has been finished 1:05:50.743 5G / 9G INFO General (distance_estimation.cpp : 188) Filling paired information 1:06:15.597 5G / 9G INFO PairInfoImprover (pair_info_improver.hpp : 61) Paired info stats: missing = 148508; contradictional = 728 1:06:41.434 5G / 9G INFO PairInfoImprover (pair_info_improver.hpp : 61) Paired info stats: missing = 38328; contradictional = 0 1:06:41.435 5G / 9G INFO General (distance_estimation.cpp : 193) Filling scaffolding index 1:06:41.435 5G / 9G INFO DistanceEstimator (distance_estimation.hpp : 187) Using SMOOTHING distance estimator 1:08:07.529 5G / 9G INFO DistanceEstimator (distance_estimation.hpp : 208) Merging maps 1:08:07.563 5G / 9G INFO General (distance_estimation.cpp : 38) Filtering info 1:08:07.709 5G / 9G INFO General (pair_info_filters.hpp : 354) Pruning the index 1:08:09.024 5G / 9G INFO StageManager (stage.cpp : 125) STAGE == Repeat Resolving 1:08:09.024 5G / 9G INFO General (contig_output.hpp : 283) Outputting contigs to /N/dc2/projects/marinovg/2015-01-29-P-assem/Paramecium_biaurelia-SPAdes-3.5.0-trimmed//K55/before_rr.fasta 1:09:35.039 5G / 9G INFO General (repeat_resolving.cpp : 59) Using Path-Extend repeat resolving 1:09:35.039 5G / 9G INFO General (path_extend_launch.hpp : 459) Threshold for library #0 is 0.0484345 1:09:35.040 5G / 9G INFO General (path_extend_launch.hpp : 459) Threshold for library #1 is 0.0537194 1:09:35.040 5G / 9G INFO General (path_extend_launch.hpp : 298) Path-Extend repeat resolving tool started 1:09:35.544 5G / 9G INFO General (path_extend_launch.hpp : 316) Using 2 paired-end libraries 1:09:35.544 5G / 9G INFO General (path_extend_launch.hpp : 317) Using 2 paired-end scaffolding libraries 1:09:35.544 5G / 9G INFO General (path_extend_launch.hpp : 318) Using 0 mate-pair libraries 1:09:35.544 5G / 9G INFO General (path_extend_launch.hpp : 319) Using 0 single read libraries 1:09:35.544 5G / 9G INFO General (path_extend_launch.hpp : 320) Scaffolder is on 1:09:37.536 5G / 9G INFO General (path_extend_launch.hpp : 332) Growing paths using paired-end and long single reads 1:09:37.537 5G / 9G INFO PathExtender (path_extender.hpp : 611) Processed 0 paths from 113617 (0%) 1:09:37.705 5G / 9G INFO PathExtender (path_extender.hpp : 609) Processed 128 paths from 113617 (0%) 1:09:37.976 5G / 9G INFO PathExtender (path_extender.hpp : 609) Processed 256 paths from 113617 (0%) 1:09:38.641 5G / 9G INFO PathExtender (path_extender.hpp : 609) Processed 512 paths from 113617 (0%) 1:09:40.742 5G / 9G INFO PathExtender (path_extender.hpp : 609) Processed 1024 paths from 113617 (0%) 1:09:44.006 5G / 9G INFO PathExtender (path_extender.hpp : 609) Processed 2048 paths from 113617 (1%) 1:09:47.802 5G / 9G INFO PathExtender (path_extender.hpp : 609) Processed 4096 paths from 113617 (3%) 1:09:52.261 5G / 9G INFO PathExtender (path_extender.hpp : 609) Processed 8192 paths from 113617 (7%) 1:09:54.103 5G / 9G INFO PathExtender (path_extender.hpp : 611) Processed 11362 paths from 113617 (10%) 1:09:56.208 5G / 9G INFO PathExtender (path_extender.hpp : 609) Processed 16384 paths from 113617 (14%) 1:09:57.776 5G / 9G INFO PathExtender (path_extender.hpp : 611) Processed 22724 paths from 113617 (20%) 1:09:59.813 5G / 9G INFO PathExtender (path_extender.hpp : 609) Processed 32768 paths from 113617 (28%) 1:10:00.029 5G / 9G INFO PathExtender (path_extender.hpp : 611) Processed 34086 paths from 113617 (30%) 1:10:01.686 5G / 9G INFO PathExtender (path_extender.hpp : 611) Processed 45448 paths from 113617 (40%) 1:10:03.246 5G / 9G INFO PathExtender (path_extender.hpp : 611) Processed 56810 paths from 113617 (50%) 1:10:04.646 5G / 9G INFO PathExtender (path_extender.hpp : 609) Processed 65536 paths from 113617 (57%) 1:10:04.960 5G / 9G INFO PathExtender (path_extender.hpp : 611) Processed 68172 paths from 113617 (60%) 1:10:06.175 6G / 9G INFO PathExtender (path_extender.hpp : 611) Processed 79534 paths from 113617 (70%) 1:10:07.441 6G / 9G INFO PathExtender (path_extender.hpp : 611) Processed 90896 paths from 113617 (80%) 1:10:26.680 6G / 9G INFO PathExtender (path_extender.hpp : 611) Processed 102258 paths from 113617 (90%) 1:10:43.746 6G / 9G INFO PathExtendIO (pe_io.hpp : 339) Constructing FASTG file from paths 1:10:46.901 6G / 9G INFO PathExtendIO (pe_io.hpp : 342) Writing contigs in FASTG to /N/dc2/projects/marinovg/2015-01-29-P-assem/Paramecium_biaurelia-SPAdes-3.5.0-trimmed//K55/final_contigs.fastg 1:10:46.901 6G / 9G INFO PathExtendIO (pe_io.hpp : 343) Writing contigs in FASTA to /N/dc2/projects/marinovg/2015-01-29-P-assem/Paramecium_biaurelia-SPAdes-3.5.0-trimmed//K55/final_contigs.fasta 1:12:09.543 6G / 9G INFO PathExtendIO (pe_io.hpp : 339) Constructing FASTG file from paths 1:12:12.707 6G / 9G INFO PathExtendIO (pe_io.hpp : 342) Writing contigs in FASTG to /N/dc2/projects/marinovg/2015-01-29-P-assem/Paramecium_biaurelia-SPAdes-3.5.0-trimmed//K55/path_extend/pe_before_traversal.fastg 1:12:12.707 6G / 9G INFO PathExtendIO (pe_io.hpp : 343) Writing contigs in FASTA to /N/dc2/projects/marinovg/2015-01-29-P-assem/Paramecium_biaurelia-SPAdes-3.5.0-trimmed//K55/path_extend/pe_before_traversal.fasta 1:13:33.524 6G / 9G INFO General (path_extend_launch.hpp : 281) Traversing tandem repeats 1:13:35.564 6G / 9G INFO PathExtendIO (pe_io.hpp : 339) Constructing FASTG file from paths 1:13:38.729 6G / 9G INFO PathExtendIO (pe_io.hpp : 342) Writing contigs in FASTG to /N/dc2/projects/marinovg/2015-01-29-P-assem/Paramecium_biaurelia-SPAdes-3.5.0-trimmed//K55/scaffolds.fastg 1:13:38.729 6G / 9G INFO PathExtendIO (pe_io.hpp : 343) Writing contigs in FASTA to /N/dc2/projects/marinovg/2015-01-29-P-assem/Paramecium_biaurelia-SPAdes-3.5.0-trimmed//K55/scaffolds.fasta 1:15:01.374 6G / 9G INFO General (launch.hpp : 82) SPAdes finished 1:15:10.524 1000M / 9G INFO General (main.cpp : 166) Assembling time: 1 hours 15 minutes 10 seconds ===== Assembling finished. * Corrected reads are in /N/dc2/projects/marinovg/2015-01-29-P-assem/Paramecium_biaurelia-SPAdes-3.5.0-trimmed/corrected/ * Assembled contigs are in /N/dc2/projects/marinovg/2015-01-29-P-assem/Paramecium_biaurelia-SPAdes-3.5.0-trimmed/contigs.fasta (contigs.fastg) * Assembled scaffolds are in /N/dc2/projects/marinovg/2015-01-29-P-assem/Paramecium_biaurelia-SPAdes-3.5.0-trimmed/scaffolds.fasta (scaffolds.fastg) ======= SPAdes pipeline finished. SPAdes log can be found here: /N/dc2/projects/marinovg/2015-01-29-P-assem/Paramecium_biaurelia-SPAdes-3.5.0-trimmed/spades.log Thank you for using SPAdes!