Command line: --diploid --pe1-1 SRR1811337_1.paired.fastq.gz --pe1-2 SRR1811337_2.paired.fastq.gz --mp1-1 SRR1811338_1.paired.fastq.gz --mp1-2 SRR1811338_2.paired.fastq.gz -t 16 -o /N/dc2/projects/marinovg/Paramecium/others/2015-10-27-Pseudocohnilembus/Pseudocohnilembus_persalinus-PE+MP-dipSPAdes-3.5.0-trimmed/spades System information: SPAdes version: 3.5.0 Python version: 2.6.6 OS: Linux-2.6.32-573.7.1.el6.x86_64-x86_64-with-redhat-6.7-Santiago Output dir: /N/dc2/projects/marinovg/Paramecium/others/2015-10-27-Pseudocohnilembus/Pseudocohnilembus_persalinus-PE+MP-dipSPAdes-3.5.0-trimmed/spades 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: mate-pairs orientation: rf left reads: ['/N/dc2/projects/marinovg/Paramecium/others/2015-10-27-Pseudocohnilembus/SRR1811338_1.paired.fastq.gz'] right reads: ['/N/dc2/projects/marinovg/Paramecium/others/2015-10-27-Pseudocohnilembus/SRR1811338_2.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/Paramecium/others/2015-10-27-Pseudocohnilembus/SRR1811337_1.paired.fastq.gz'] right reads: ['/N/dc2/projects/marinovg/Paramecium/others/2015-10-27-Pseudocohnilembus/SRR1811337_2.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/Paramecium/others/2015-10-27-Pseudocohnilembus/Pseudocohnilembus_persalinus-PE+MP-dipSPAdes-3.5.0-trimmed/spades/tmp Threads: 16 Memory limit (in Gb): 250 ======= SPAdes pipeline started. Log can be found here: /N/dc2/projects/marinovg/Paramecium/others/2015-10-27-Pseudocohnilembus/Pseudocohnilembus_persalinus-PE+MP-dipSPAdes-3.5.0-trimmed/spades/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/Paramecium/others/2015-10-27-Pseudocohnilembus/Pseudocohnilembus_persalinus-PE+MP-dipSPAdes-3.5.0-trimmed/spades/corrected/configs/config.info 0:00:00.050 4M / 4M INFO General (main.cpp : 82) Loading config from /N/dc2/projects/marinovg/Paramecium/others/2015-10-27-Pseudocohnilembus/Pseudocohnilembus_persalinus-PE+MP-dipSPAdes-3.5.0-trimmed/spades/corrected/configs/config.info 0:00:01.266 4M / 4M INFO General (memory_limit.hpp : 42) Memory limit set to 100 Gb 0:00:01.267 4M / 4M INFO General (main.cpp : 91) Trying to determine PHRED offset 0:00:03.738 4M / 4M INFO General (main.cpp : 97) Determined value is 33 0:00:03.792 4M / 4M INFO General (hammer_tools.cpp : 36) Hamming graph threshold tau=1, k=21, subkmer positions = [ 0 10 ] === ITERATION 0 begins === 0:00:03.793 4M / 4M INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:00:03.793 4M / 4M INFO K-mer Splitting (kmer_data.cpp : 127) Splitting kmer instances into 256 buckets. This might take a while. 0:00:03.794 4M / 4M INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:00:03.794 4M / 4M INFO K-mer Splitting (kmer_data.cpp : 145) Memory available for splitting buffers: 2.08325 Gb 0:00:03.794 4M / 4M INFO K-mer Splitting (kmer_data.cpp : 153) Using cell size of 262144 0:00:07.358 8G / 8G INFO K-mer Splitting (kmer_data.cpp : 167) Processing /N/dc2/projects/marinovg/Paramecium/others/2015-10-27-Pseudocohnilembus/SRR1811338_1.paired.fastq.gz 0:08:14.366 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 176) Processed 5823932 reads 0:11:30.718 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 176) Processed 8831429 reads 0:11:30.720 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 167) Processing /N/dc2/projects/marinovg/Paramecium/others/2015-10-27-Pseudocohnilembus/SRR1811338_2.paired.fastq.gz 0:12:46.430 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 176) Processed 14870380 reads 0:13:21.594 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 176) Processed 17662858 reads 0:13:21.596 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 167) Processing /N/dc2/projects/marinovg/Paramecium/others/2015-10-27-Pseudocohnilembus/SRR1811337_1.paired.fastq.gz 0:24:54.935 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 176) Processed 23756521 reads 0:34:03.146 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 176) Processed 27627723 reads 0:34:03.147 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 167) Processing /N/dc2/projects/marinovg/Paramecium/others/2015-10-27-Pseudocohnilembus/SRR1811337_2.paired.fastq.gz 0:40:47.787 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 176) Processed 33823581 reads 0:52:22.001 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 176) Processed 37592588 reads 0:52:22.002 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 181) Processed 37592588 reads 0:52:22.978 64M / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:55:29.823 64M / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 899759594 kmers in total. 0:55:29.824 64M / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:56:08.967 64M / 9G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:59:47.935 384M / 29G INFO General (kmer_index.hpp : 371) Merging final buckets. 1:01:29.602 384M / 29G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 311260614 bytes occupied (2.7675 bits per kmer). 1:01:29.662 384M / 29G INFO K-mer Counting (kmer_data.cpp : 266) Arranging kmers in hash map order 1:10:04.757 384M / 29G INFO K-mer Counting (kmer_data.cpp : 279) Done. Total swaps: 899759269 1:10:10.125 7G / 29G INFO General (main.cpp : 151) Clustering Hamming graph. 1:10:10.166 7G / 29G INFO Hamming Clustering (hamcluster.cpp : 115) Serializing sub-kmers. 1:10:10.166 7G / 29G INFO Hamming Clustering (hamcluster.cpp : 120) Serializing: [0, 10) 1:17:52.711 7G / 29G INFO Hamming Clustering (hamcluster.cpp : 120) Serializing: [10, 21) 1:25:16.945 7G / 29G INFO Hamming Clustering (hamcluster.cpp : 129) Splitting sub-kmers, pass 1. 1:35:02.734 7G / 29G INFO Hamming Clustering (hamcluster.cpp : 134) Splitting done. Processed 2 blocks. Produced 5242880 blocks. 1:35:02.734 7G / 29G INFO Hamming Clustering (hamcluster.cpp : 145) Merge sub-kmers, pass 1 2:12:17.481 7G / 29G INFO Hamming Clustering (hamcluster.cpp : 170) Merge done, total 5069319 new blocks generated. 2:12:21.634 7G / 29G INFO Hamming Clustering (hamcluster.cpp : 175) Spliting sub-kmers, pass 2. 3:03:03.335 7G / 29G INFO Hamming Clustering (hamcluster.cpp : 180) Splitting done. Processed 10138638 blocks. Produced 2284904999 blocks. 3:03:03.335 7G / 29G INFO Hamming Clustering (hamcluster.cpp : 187) Merge sub-kmers, pass 2 3:34:31.944 7G / 29G INFO Hamming Clustering (hamcluster.cpp : 205) Merge done, saw 1173727 big blocks out of 2284904999 processed. 3:47:19.770 7G / 36G INFO General (main.cpp : 165) Clustering done. Total clusters: 573741332 3:47:19.770 7G / 36G INFO K-mer Counting (kmer_data.cpp : 284) Collecting K-mer information, this takes a while. 3:54:26.910 47G / 47G INFO K-mer Counting (kmer_data.cpp : 290) Processing /N/dc2/projects/marinovg/Paramecium/others/2015-10-27-Pseudocohnilembus/SRR1811338_1.paired.fastq.gz 3:55:52.521 47G / 47G INFO K-mer Counting (kmer_data.cpp : 290) Processing /N/dc2/projects/marinovg/Paramecium/others/2015-10-27-Pseudocohnilembus/SRR1811338_2.paired.fastq.gz 3:57:18.764 47G / 47G INFO K-mer Counting (kmer_data.cpp : 290) Processing /N/dc2/projects/marinovg/Paramecium/others/2015-10-27-Pseudocohnilembus/SRR1811337_1.paired.fastq.gz 3:58:55.447 47G / 47G INFO K-mer Counting (kmer_data.cpp : 290) Processing /N/dc2/projects/marinovg/Paramecium/others/2015-10-27-Pseudocohnilembus/SRR1811337_2.paired.fastq.gz 4:00:26.584 47G / 47G INFO K-mer Counting (kmer_data.cpp : 297) Collection done, postprocessing. 4:00:48.477 47G / 47G INFO K-mer Counting (kmer_data.cpp : 310) There are 899759594 kmers in total. Among them 615427150 (68.3991%) are singletons. 4:00:48.478 47G / 47G INFO General (main.cpp : 203) Subclustering Hamming graph 4:13:24.859 47G / 47G INFO Hamming Subclustering (kmer_cluster.cpp : 626) Subclustering done. Total 113561 non-read kmers were generated. 4:13:24.859 47G / 47G INFO Hamming Subclustering (kmer_cluster.cpp : 627) Subclustering statistics: 4:13:24.859 47G / 47G INFO Hamming Subclustering (kmer_cluster.cpp : 628) Total singleton hamming clusters: 483140689. Among them 197063054 (40.7879%) are good 4:13:24.859 47G / 47G INFO Hamming Subclustering (kmer_cluster.cpp : 629) Total singleton subclusters: 3623323. Among them 3621359 (99.9458%) are good 4:13:24.859 47G / 47G INFO Hamming Subclustering (kmer_cluster.cpp : 630) Total non-singleton subcluster centers: 95756564. Among them 56828850 (59.3472%) are good 4:13:24.859 47G / 47G INFO Hamming Subclustering (kmer_cluster.cpp : 631) Average size of non-trivial subcluster: 4.34341 kmers 4:13:24.859 47G / 47G INFO Hamming Subclustering (kmer_cluster.cpp : 632) Average number of sub-clusters per non-singleton cluster: 1.0969 4:13:24.859 47G / 47G INFO Hamming Subclustering (kmer_cluster.cpp : 633) Total solid k-mers: 257513263 4:13:24.859 47G / 47G INFO Hamming Subclustering (kmer_cluster.cpp : 634) Substitution probabilities: [4,4]((0.890308,0.0281827,0.0257168,0.0557921),(0.0184536,0.941942,0.0208576,0.0187472),(0.016437,0.0193558,0.943849,0.0203585),(0.0560512,0.0249795,0.0276657,0.891304)) 4:13:26.466 47G / 47G INFO General (main.cpp : 208) Finished clustering. 4:13:26.466 47G / 47G INFO General (main.cpp : 228) Starting solid k-mers expansion in 16 threads. 4:18:36.288 47G / 47G INFO General (main.cpp : 249) Solid k-mers iteration 0 produced 81451695 new k-mers. 4:23:43.686 47G / 47G INFO General (main.cpp : 249) Solid k-mers iteration 1 produced 12317295 new k-mers. 4:28:51.845 47G / 47G INFO General (main.cpp : 249) Solid k-mers iteration 2 produced 881104 new k-mers. 4:34:00.701 47G / 47G INFO General (main.cpp : 249) Solid k-mers iteration 3 produced 62176 new k-mers. 4:39:09.415 47G / 47G INFO General (main.cpp : 249) Solid k-mers iteration 4 produced 4769 new k-mers. 4:44:17.793 47G / 47G INFO General (main.cpp : 249) Solid k-mers iteration 5 produced 204 new k-mers. 4:49:26.541 47G / 47G INFO General (main.cpp : 249) Solid k-mers iteration 6 produced 0 new k-mers. 4:49:26.542 47G / 47G INFO General (main.cpp : 253) Solid k-mers finalized 4:49:26.542 47G / 47G INFO General (hammer_tools.cpp : 210) Starting read correction in 16 threads. 4:49:26.542 47G / 47G INFO General (hammer_tools.cpp : 222) Correcting pair of reads: /N/dc2/projects/marinovg/Paramecium/others/2015-10-27-Pseudocohnilembus/SRR1811338_1.paired.fastq.gz and /N/dc2/projects/marinovg/Paramecium/others/2015-10-27-Pseudocohnilembus/SRR1811338_2.paired.fastq.gz 4:51:02.174 48G / 48G INFO General (hammer_tools.cpp : 166) Prepared batch 0 of 1600000 reads. 4:51:16.943 48G / 48G INFO General (hammer_tools.cpp : 175) Processed batch 0 4:51:26.204 48G / 48G INFO General (hammer_tools.cpp : 185) Written batch 0 4:51:41.708 48G / 48G INFO General (hammer_tools.cpp : 166) Prepared batch 1 of 1600000 reads. 4:51:56.247 48G / 48G INFO General (hammer_tools.cpp : 175) Processed batch 1 4:52:05.549 48G / 48G INFO General (hammer_tools.cpp : 185) Written batch 1 4:52:20.535 48G / 48G INFO General (hammer_tools.cpp : 166) Prepared batch 2 of 1600000 reads. 4:52:35.010 48G / 48G INFO General (hammer_tools.cpp : 175) Processed batch 2 4:52:44.351 48G / 48G INFO General (hammer_tools.cpp : 185) Written batch 2 4:52:59.321 48G / 48G INFO General (hammer_tools.cpp : 166) Prepared batch 3 of 1600000 reads. 4:53:13.710 48G / 48G INFO General (hammer_tools.cpp : 175) Processed batch 3 4:53:22.989 48G / 48G INFO General (hammer_tools.cpp : 185) Written batch 3 4:53:37.973 48G / 48G INFO General (hammer_tools.cpp : 166) Prepared batch 4 of 1600000 reads. 4:53:52.206 48G / 48G INFO General (hammer_tools.cpp : 175) Processed batch 4 4:54:01.568 48G / 48G INFO General (hammer_tools.cpp : 185) Written batch 4 4:54:09.509 48G / 48G INFO General (hammer_tools.cpp : 166) Prepared batch 5 of 831429 reads. 4:54:17.011 48G / 48G INFO General (hammer_tools.cpp : 175) Processed batch 5 4:54:21.886 48G / 48G INFO General (hammer_tools.cpp : 185) Written batch 5 4:54:23.607 47G / 48G INFO General (hammer_tools.cpp : 222) Correcting pair of reads: /N/dc2/projects/marinovg/Paramecium/others/2015-10-27-Pseudocohnilembus/SRR1811337_1.paired.fastq.gz and /N/dc2/projects/marinovg/Paramecium/others/2015-10-27-Pseudocohnilembus/SRR1811337_2.paired.fastq.gz 4:55:07.376 48G / 48G INFO General (hammer_tools.cpp : 166) Prepared batch 0 of 1600000 reads. 4:55:21.152 48G / 48G INFO General (hammer_tools.cpp : 175) Processed batch 0 4:55:30.981 48G / 48G INFO General (hammer_tools.cpp : 185) Written batch 0 4:55:47.197 48G / 48G INFO General (hammer_tools.cpp : 166) Prepared batch 1 of 1600000 reads. 4:56:00.949 48G / 48G INFO General (hammer_tools.cpp : 175) Processed batch 1 4:56:10.830 48G / 48G INFO General (hammer_tools.cpp : 185) Written batch 1 4:56:26.575 48G / 48G INFO General (hammer_tools.cpp : 166) Prepared batch 2 of 1600000 reads. 4:56:40.453 48G / 48G INFO General (hammer_tools.cpp : 175) Processed batch 2 4:56:50.391 48G / 48G INFO General (hammer_tools.cpp : 185) Written batch 2 4:57:06.017 48G / 48G INFO General (hammer_tools.cpp : 166) Prepared batch 3 of 1600000 reads. 4:57:19.744 48G / 48G INFO General (hammer_tools.cpp : 175) Processed batch 3 4:57:29.757 48G / 48G INFO General (hammer_tools.cpp : 185) Written batch 3 4:57:45.287 48G / 48G INFO General (hammer_tools.cpp : 166) Prepared batch 4 of 1600000 reads. 4:57:59.018 48G / 48G INFO General (hammer_tools.cpp : 175) Processed batch 4 4:58:08.887 48G / 48G INFO General (hammer_tools.cpp : 185) Written batch 4 4:58:24.380 48G / 48G INFO General (hammer_tools.cpp : 166) Prepared batch 5 of 1600000 reads. 4:58:38.170 48G / 48G INFO General (hammer_tools.cpp : 175) Processed batch 5 4:58:48.048 48G / 48G INFO General (hammer_tools.cpp : 185) Written batch 5 4:58:51.639 48G / 48G INFO General (hammer_tools.cpp : 166) Prepared batch 6 of 364865 reads. 4:58:54.742 48G / 48G INFO General (hammer_tools.cpp : 175) Processed batch 6 4:58:57.023 48G / 48G INFO General (hammer_tools.cpp : 185) Written batch 6 4:58:58.665 47G / 48G INFO General (hammer_tools.cpp : 269) Correction done. Changed 10057307 bases in 7311550 reads. 4:58:58.665 47G / 48G INFO General (hammer_tools.cpp : 270) Failed to correct 494958399 bases out of 3695880866. 4:58:59.325 6G / 48G INFO General (main.cpp : 286) Saving corrected dataset description to /N/dc2/projects/marinovg/Paramecium/others/2015-10-27-Pseudocohnilembus/Pseudocohnilembus_persalinus-PE+MP-dipSPAdes-3.5.0-trimmed/spades/corrected/corrected.yaml 4:58:59.352 6G / 48G INFO General (main.cpp : 293) All done. Exiting. == Compressing corrected reads (with gzip) == Dataset description file was created: /N/dc2/projects/marinovg/Paramecium/others/2015-10-27-Pseudocohnilembus/Pseudocohnilembus_persalinus-PE+MP-dipSPAdes-3.5.0-trimmed/spades/corrected/corrected.yaml ===== Read error correction finished. ===== Assembling started. == Running assembler: K21 0:00:00.015 4M / 4M INFO General (memory_limit.hpp : 42) Memory limit set to 100 Gb 0:00:00.064 4M / 4M INFO General (main.cpp : 146) Assembling dataset (/N/dc2/projects/marinovg/Paramecium/others/2015-10-27-Pseudocohnilembus/Pseudocohnilembus_persalinus-PE+MP-dipSPAdes-3.5.0-trimmed/spades/dataset.info) with K=21 0:00:00.072 4M / 4M INFO General (launch.hpp : 28) SPAdes started 0:00:00.072 4M / 4M INFO General (launch.hpp : 29) Starting from stage: construction 0:00:00.117 4M / 4M INFO StageManager (stage.cpp : 125) STAGE == Construction 0:00:00.124 4M / 4M INFO General (read_converter.hpp : 79) Converting reads to binary format (takes a while) 0:00:00.124 4M / 4M INFO General (read_converter.hpp : 81) Paired reads for library #0 0:00:00.925 76M / 76M INFO General (binary_converter.hpp : 138) 16384 reads processed 0:00:01.170 84M / 84M INFO General (binary_converter.hpp : 138) 32768 reads processed 0:00:01.658 104M / 104M INFO General (binary_converter.hpp : 138) 65536 reads processed 0:00:02.639 144M / 144M INFO General (binary_converter.hpp : 138) 131072 reads processed 0:00:04.599 220M / 220M INFO General (binary_converter.hpp : 138) 262144 reads processed 0:00:08.518 376M / 376M INFO General (binary_converter.hpp : 138) 524288 reads processed 0:00:18.193 616M / 616M INFO General (binary_converter.hpp : 138) 1048576 reads processed 0:00:35.858 616M / 616M INFO General (binary_converter.hpp : 138) 2097152 reads processed 0:01:11.210 616M / 616M INFO General (binary_converter.hpp : 138) 4194304 reads processed 0:02:23.566 616M / 616M INFO General (binary_converter.hpp : 138) 8388608 reads processed 0:02:30.831 312M / 616M INFO General (binary_converter.hpp : 158) 8766042 reads written 0:02:31.344 4M / 616M INFO General (read_converter.hpp : 91) Single reads for library #0 0:02:32.660 136M / 616M INFO General (binary_converter.hpp : 138) 16384 reads processed 0:02:32.775 140M / 616M INFO General (binary_converter.hpp : 138) 32768 reads processed 0:02:33.120 148M / 616M INFO General (binary_converter.hpp : 158) 64944 reads written 0:02:33.190 4M / 616M INFO General (read_converter.hpp : 81) Paired reads for library #1 0:02:33.999 76M / 616M INFO General (binary_converter.hpp : 138) 16384 reads processed 0:02:34.252 84M / 616M INFO General (binary_converter.hpp : 138) 32768 reads processed 0:02:34.750 104M / 616M INFO General (binary_converter.hpp : 138) 65536 reads processed 0:02:35.754 144M / 616M INFO General (binary_converter.hpp : 138) 131072 reads processed 0:02:37.763 220M / 616M INFO General (binary_converter.hpp : 138) 262144 reads processed 0:02:41.754 372M / 616M INFO General (binary_converter.hpp : 138) 524288 reads processed 0:02:51.627 608M / 616M INFO General (binary_converter.hpp : 138) 1048576 reads processed 0:03:09.425 612M / 616M INFO General (binary_converter.hpp : 138) 2097152 reads processed 0:03:45.118 612M / 616M INFO General (binary_converter.hpp : 138) 4194304 reads processed 0:04:59.945 624M / 624M INFO General (binary_converter.hpp : 138) 8388608 reads processed 0:05:21.454 284M / 624M INFO General (binary_converter.hpp : 158) 9562605 reads written 0:05:21.841 4M / 624M INFO General (read_converter.hpp : 91) Single reads for library #1 0:05:23.161 136M / 624M INFO General (binary_converter.hpp : 138) 16384 reads processed 0:05:23.270 140M / 624M INFO General (binary_converter.hpp : 138) 32768 reads processed 0:05:23.485 148M / 624M INFO General (binary_converter.hpp : 138) 65536 reads processed 0:05:23.918 164M / 624M INFO General (binary_converter.hpp : 138) 131072 reads processed 0:05:24.790 200M / 624M INFO General (binary_converter.hpp : 138) 262144 reads processed 0:05:25.612 220M / 624M INFO General (binary_converter.hpp : 158) 335791 reads written 0:05:25.895 4M / 624M INFO General (graph_construction.hpp : 129) Constructing DeBruijn graph for k=21 0:05:25.898 4M / 624M INFO General (kmer_splitters.hpp : 172) Splitting kmer instances into 256 buckets. This might take a while. 0:05:25.899 4M / 624M INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:05:25.899 4M / 624M INFO General (kmer_splitters.hpp : 190) Memory available for splitting buffers: 2.08325 Gb 0:05:25.899 4M / 624M INFO General (kmer_splitters.hpp : 199) Using cell size of 262144 0:06:21.299 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 27836134 reads 0:06:33.686 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 38922002 reads 0:06:33.686 8G / 9G INFO General (kmer_splitters.hpp : 234) Adding contigs from previous K 0:06:33.686 8G / 9G INFO General (kmer_splitters.hpp : 245) Used 38922002 reads. Maximum read length 101 0:06:33.686 8G / 9G INFO General (kmer_splitters.hpp : 246) Average read length 97.7662 0:06:35.341 64M / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:06:45.114 64M / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 254042175 kmers in total. 0:06:45.114 64M / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:06:54.704 64M / 9G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:06:54.714 64M / 9G INFO General (kmer_splitters.hpp : 379) Splitting kmer instances into 256 buckets. This might take a while. 0:06:54.714 64M / 9G INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:06:54.714 64M / 9G INFO General (kmer_splitters.hpp : 397) Memory available for splitting buffers: 2.08203 Gb 0:06:54.715 64M / 9G INFO General (kmer_splitters.hpp : 405) Using cell size of 262144 0:07:23.520 8G / 9G INFO General (kmer_splitters.hpp : 428) Processed 254042175 kmers 0:07:23.521 8G / 9G INFO General (kmer_splitters.hpp : 437) Used 254042175 kmers. 0:07:24.267 64M / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:07:31.239 64M / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 247328578 kmers in total. 0:07:31.239 64M / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:07:39.899 64M / 9G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:08:13.189 192M / 9G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:08:21.147 192M / 9G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 85560276 bytes occupied (2.7675 bits per kmer). 0:08:21.485 428M / 9G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 382) Building k-mer extensions from k+1-mers 0:08:49.589 428M / 9G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 386) Building k-mer extensions from k+1-mers finished. 0:08:49.594 428M / 9G INFO Early tip clipping (early_simplification.hpp : 236) Early tip clipping 0:21:33.938 428M / 9G INFO Early tip clipping (early_simplification.hpp : 239) 35256225 22-mers were removed by early tip clipper 0:21:33.939 428M / 9G INFO General (graph_construction.hpp : 145) Condensing graph 0:21:33.951 428M / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 337) Extracting unbranching paths 0:24:48.508 3G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 351) Extracting unbranching paths finished. 37975319 sequences extracted 0:25:10.367 3G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 311) Collecting perfect loops 0:26:17.572 3G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 326) Collecting perfect loops finished. 5376 loops collected 0:26:40.608 7G / 10G INFO General (graph_construction.hpp : 150) Building index with from graph 0:26:40.609 7G / 10G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:26:40.609 7G / 10G INFO General (kmer_splitters.hpp : 289) Splitting kmer instances into 16 buckets. This might take a while. 0:26:40.609 7G / 10G INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:26:40.610 7G / 10G INFO General (kmer_splitters.hpp : 307) Memory available for splitting buffers: 30.8138 Gb 0:26:40.610 7G / 10G INFO General (kmer_splitters.hpp : 312) Using cell size of 4194304 0:26:56.823 8G / 10G INFO General (kmer_splitters.hpp : 325) Processed 11629711 edges 0:27:12.999 8G / 10G INFO General (kmer_splitters.hpp : 325) Processed 23290210 edges 0:27:28.949 8G / 10G INFO General (kmer_splitters.hpp : 325) Processed 34946224 edges 0:27:33.104 8G / 10G INFO General (kmer_splitters.hpp : 325) Processed 37980695 edges 0:27:33.105 8G / 10G INFO General (kmer_splitters.hpp : 330) Used 37980695 sequences. 0:27:33.171 7G / 10G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:28:11.835 7G / 10G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 218785950 kmers in total. 0:28:11.835 7G / 10G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:28:18.800 7G / 10G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:33:32.143 7G / 10G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:33:39.815 7G / 10G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 75686298 bytes occupied (2.7675 bits per kmer). 0:33:43.113 12G / 12G INFO General (edge_index_builders.hpp : 21) Collecting k-mer coverage information from graph, this takes a while. 0:40:58.762 12G / 12G INFO General (graph_construction.hpp : 182) Filling coverage index 0:40:58.762 12G / 12G INFO General (edge_index_builders.hpp : 99) Collecting k-mer coverage information from reads, this takes a while. 0:43:08.672 12G / 12G INFO General (graph_construction.hpp : 184) Filling coverage and flanking coverage from index 0:44:12.224 12G / 12G INFO General (construction.cpp : 33) Figured out: read length = 101 0:44:12.239 12G / 12G INFO StageManager (stage.cpp : 125) STAGE == EC Threshold Finding 0:44:18.901 12G / 12G INFO General (kmer_coverage_model.cpp : 178) Kmer coverage valley at: 4 0:44:18.917 12G / 12G INFO General (kmer_coverage_model.cpp : 198) K-mer histogram maximum: 17 0:44:18.917 12G / 12G INFO General (kmer_coverage_model.cpp : 234) Estimated median coverage: 18. Coverage mad: 8.8956 0:44:18.917 12G / 12G INFO General (kmer_coverage_model.cpp : 261) Fitting coverage model 0:44:19.052 12G / 12G INFO General (kmer_coverage_model.cpp : 296) ... iteration 2 0:44:19.179 12G / 12G INFO General (kmer_coverage_model.cpp : 296) ... iteration 4 0:44:19.605 12G / 12G INFO General (kmer_coverage_model.cpp : 296) ... iteration 8 0:44:20.565 12G / 12G INFO General (kmer_coverage_model.cpp : 296) ... iteration 16 0:44:22.315 12G / 12G INFO General (kmer_coverage_model.cpp : 296) ... iteration 32 0:44:24.251 12G / 12G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 19.1017. Fitted coverage std. dev: 6.76984 0:44:24.252 12G / 12G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 0.831528 0:44:24.252 12G / 12G INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 14 0:44:24.252 12G / 12G INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 11 0:44:24.252 12G / 12G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 53498491 0:44:24.264 12G / 12G INFO General (genomic_info_filler.cpp : 103) Mean coverage was calculated as 19.1017 0:44:24.265 12G / 12G INFO General (genomic_info_filler.cpp : 117) EC coverage threshold value was calculated as 11 0:44:24.265 12G / 12G INFO General (genomic_info_filler.cpp : 118) Trusted kmer low bound: 0 0:44:24.265 12G / 12G INFO StageManager (stage.cpp : 125) STAGE == Simplification 0:44:24.683 7G / 12G INFO General (graph_simplification.hpp : 911) Graph simplification started 0:44:24.707 7G / 12G INFO General (graph_simplification.hpp : 924) Fast simplification mode enabled 0:44:24.711 7G / 12G INFO General (graph_simplification.hpp : 771) PROCEDURE == Presimplification 0:44:24.715 7G / 12G INFO General (graph_simplification.hpp : 211) Removing short low covered self-conjugate connections 0:44:27.063 7G / 12G INFO General (graph_simplification.hpp : 403) Removing isolated edges 0:44:27.065 7G / 12G INFO General (graph_simplification.hpp : 404) All edges shorter than 150 will be removed 0:44:27.065 7G / 12G INFO General (graph_simplification.hpp : 405) Also edges shorter than 0 and coverage smaller than 0 will be removed 0:44:43.051 7G / 12G INFO General (graph_simplification.hpp : 687) Non parallel mode 0:46:58.810 8G / 12G INFO General (graph_simplification.hpp : 93) Clipping tips 0:51:48.560 8G / 12G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:58:34.247 7G / 12G INFO General (graph_simplification.hpp : 644) Using permanent iterators 0:58:34.268 7G / 12G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 1 0:59:01.292 7G / 12G INFO General (graph_simplification.hpp : 93) Clipping tips 1:00:50.500 7G / 12G INFO General (graph_simplification.hpp : 187) Removing low covered connections 1:01:00.652 7G / 12G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 2 1:01:00.652 7G / 12G INFO General (graph_simplification.hpp : 93) Clipping tips 1:01:01.235 7G / 12G INFO General (graph_simplification.hpp : 187) Removing low covered connections 1:01:10.609 7G / 12G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 3 1:01:10.609 7G / 12G INFO General (graph_simplification.hpp : 93) Clipping tips 1:01:11.022 7G / 12G INFO General (graph_simplification.hpp : 187) Removing low covered connections 1:01:31.553 7G / 12G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 4 1:01:31.553 7G / 12G INFO General (graph_simplification.hpp : 93) Clipping tips 1:01:32.216 7G / 12G INFO General (graph_simplification.hpp : 187) Removing low covered connections 1:01:39.207 7G / 12G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 5 1:01:39.207 7G / 12G INFO General (graph_simplification.hpp : 93) Clipping tips 1:01:39.448 7G / 12G INFO General (graph_simplification.hpp : 187) Removing low covered connections 1:01:43.156 7G / 12G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 6 1:01:43.156 7G / 12G INFO General (graph_simplification.hpp : 93) Clipping tips 1:01:43.281 7G / 12G INFO General (graph_simplification.hpp : 187) Removing low covered connections 1:01:45.685 7G / 12G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 7 1:01:45.685 7G / 12G INFO General (graph_simplification.hpp : 93) Clipping tips 1:01:45.767 7G / 12G INFO General (graph_simplification.hpp : 187) Removing low covered connections 1:01:47.985 7G / 12G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 8 1:01:47.985 7G / 12G INFO General (graph_simplification.hpp : 93) Clipping tips 1:01:48.060 7G / 12G INFO General (graph_simplification.hpp : 187) Removing low covered connections 1:01:50.471 7G / 12G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 9 1:01:50.471 7G / 12G INFO General (graph_simplification.hpp : 93) Clipping tips 1:01:50.552 7G / 12G INFO General (graph_simplification.hpp : 187) Removing low covered connections 1:01:53.338 7G / 12G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 10 1:01:53.338 7G / 12G INFO General (graph_simplification.hpp : 93) Clipping tips 1:01:53.432 7G / 12G INFO General (graph_simplification.hpp : 187) Removing low covered connections 1:01:58.621 7G / 12G INFO General (graph_simplification.hpp : 796) PROCEDURE == Post simplification 1:01:58.622 7G / 12G INFO General (graph_simplification.hpp : 644) Using permanent iterators 1:01:58.622 7G / 12G INFO General (graph_simplification.hpp : 806) Iteration 0 1:01:58.626 7G / 12G INFO General (graph_simplification.hpp : 247) Removal of relatively low covered connections disabled 1:02:17.103 7G / 12G INFO General (graph_simplification.hpp : 93) Clipping tips 1:02:57.306 7G / 12G INFO General (graph_simplification.hpp : 806) Iteration 1 1:02:57.306 7G / 12G INFO General (graph_simplification.hpp : 247) Removal of relatively low covered connections disabled 1:02:57.306 7G / 12G INFO General (graph_simplification.hpp : 93) Clipping tips 1:03:08.649 7G / 12G INFO StageManager (stage.cpp : 125) STAGE == Simplification Cleanup 1:03:08.650 7G / 12G INFO General (graph_simplification.hpp : 403) Removing isolated edges 1:03:08.650 7G / 12G INFO General (graph_simplification.hpp : 404) All edges shorter than 150 will be removed 1:03:08.650 7G / 12G INFO General (graph_simplification.hpp : 405) Also edges shorter than 0 and coverage smaller than 2 will be removed 1:03:09.722 7G / 12G INFO General (simplification.cpp : 56) Removing all the edges having coverage 0 and less 1:03:41.005 7G / 12G INFO General (simplification.cpp : 68) Counting average coverage 1:03:44.131 7G / 12G INFO General (simplification.cpp : 71) Average coverage = 16.082 1:03:44.131 7G / 12G INFO StageManager (stage.cpp : 125) STAGE == Contig Output 1:03:44.165 7G / 12G INFO General (contig_output.hpp : 283) Outputting contigs to /N/dc2/projects/marinovg/Paramecium/others/2015-10-27-Pseudocohnilembus/Pseudocohnilembus_persalinus-PE+MP-dipSPAdes-3.5.0-trimmed/spades//K21/simplified_contigs.fasta 1:05:43.281 7G / 12G INFO General (contig_output.hpp : 283) Outputting contigs to /N/dc2/projects/marinovg/Paramecium/others/2015-10-27-Pseudocohnilembus/Pseudocohnilembus_persalinus-PE+MP-dipSPAdes-3.5.0-trimmed/spades//K21/before_rr.fasta 1:11:31.620 7G / 12G INFO General (contig_output.hpp : 283) Outputting contigs to /N/dc2/projects/marinovg/Paramecium/others/2015-10-27-Pseudocohnilembus/Pseudocohnilembus_persalinus-PE+MP-dipSPAdes-3.5.0-trimmed/spades//K21/final_contigs.fasta 1:17:13.958 7G / 12G INFO General (launch.hpp : 82) SPAdes finished 1:17:38.058 64M / 12G INFO General (main.cpp : 166) Assembling time: 1 hours 17 minutes 38 seconds == Running assembler: K33 0:00:00.000 4M / 4M INFO General (memory_limit.hpp : 42) Memory limit set to 100 Gb 0:00:00.001 4M / 4M INFO General (main.cpp : 146) Assembling dataset (/N/dc2/projects/marinovg/Paramecium/others/2015-10-27-Pseudocohnilembus/Pseudocohnilembus_persalinus-PE+MP-dipSPAdes-3.5.0-trimmed/spades/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 0:00:00.001 4M / 4M INFO StageManager (stage.cpp : 125) STAGE == Construction 0:00:00.001 4M / 4M INFO General (construction.cpp : 44) Contigs from previous K will be used 0:00:00.005 4M / 4M INFO General (read_converter.hpp : 49) Binary reads detected 0:00:00.026 4M / 4M INFO General (graph_construction.hpp : 129) Constructing DeBruijn graph for k=33 0:00:00.029 4M / 4M INFO General (kmer_splitters.hpp : 172) Splitting kmer instances into 256 buckets. This might take a while. 0:00:00.029 4M / 4M INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:00:00.029 4M / 4M INFO General (kmer_splitters.hpp : 190) Memory available for splitting buffers: 2.08325 Gb 0:00:00.029 4M / 4M INFO General (kmer_splitters.hpp : 199) Using cell size of 131072 0:02:06.603 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 16431990 reads 0:05:41.178 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 32991399 reads 0:07:17.294 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 38922002 reads 0:07:17.294 8G / 9G INFO General (kmer_splitters.hpp : 234) Adding contigs from previous K 0:07:46.372 8G / 9G INFO General (kmer_splitters.hpp : 245) Used 38922002 reads. Maximum read length 101 0:07:46.373 8G / 9G INFO General (kmer_splitters.hpp : 246) Average read length 97.7662 0:07:48.028 64M / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:08:10.552 64M / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 263236174 kmers in total. 0:08:10.552 64M / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:08:50.329 64M / 9G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:08:50.329 64M / 9G INFO General (kmer_splitters.hpp : 379) Splitting kmer instances into 256 buckets. This might take a while. 0:08:50.329 64M / 9G INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:08:50.329 64M / 9G INFO General (kmer_splitters.hpp : 397) Memory available for splitting buffers: 2.08203 Gb 0:08:50.330 64M / 9G INFO General (kmer_splitters.hpp : 405) Using cell size of 131072 0:09:26.780 8G / 9G INFO General (kmer_splitters.hpp : 428) Processed 263236174 kmers 0:09:26.782 8G / 9G INFO General (kmer_splitters.hpp : 437) Used 263236174 kmers. 0:09:28.005 64M / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:09:42.012 64M / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 263880901 kmers in total. 0:09:42.013 64M / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:10:01.839 64M / 9G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:10:42.920 192M / 9G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:11:02.677 192M / 9G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 91286334 bytes occupied (2.7675 bits per kmer). 0:11:03.003 444M / 9G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 382) Building k-mer extensions from k+1-mers 0:11:33.544 444M / 9G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 386) Building k-mer extensions from k+1-mers finished. 0:11:33.548 444M / 9G INFO Early tip clipping (early_simplification.hpp : 236) Early tip clipping 0:22:21.661 444M / 9G INFO Early tip clipping (early_simplification.hpp : 239) 59350122 34-mers were removed by early tip clipper 0:22:21.661 444M / 9G INFO General (graph_construction.hpp : 145) Condensing graph 0:22:21.661 444M / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 337) Extracting unbranching paths 0:25:07.779 1G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 351) Extracting unbranching paths finished. 8785406 sequences extracted 0:25:27.221 1G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 311) Collecting perfect loops 0:26:47.530 1G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 326) Collecting perfect loops finished. 7238 loops collected 0:26:54.925 2G / 9G INFO General (graph_construction.hpp : 150) Building index with from graph 0:26:54.927 2G / 9G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:26:54.927 2G / 9G INFO General (kmer_splitters.hpp : 289) Splitting kmer instances into 16 buckets. This might take a while. 0:26:54.927 2G / 9G INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:26:54.927 2G / 9G INFO General (kmer_splitters.hpp : 307) Memory available for splitting buffers: 32.4922 Gb 0:26:54.927 2G / 9G INFO General (kmer_splitters.hpp : 312) Using cell size of 2097152 0:27:01.138 3G / 9G INFO General (kmer_splitters.hpp : 325) Processed 1447215 edges 0:27:07.298 3G / 9G INFO General (kmer_splitters.hpp : 325) Processed 2895536 edges 0:27:13.668 3G / 9G INFO General (kmer_splitters.hpp : 325) Processed 4345392 edges 0:27:19.893 3G / 9G INFO General (kmer_splitters.hpp : 325) Processed 5789932 edges 0:27:25.956 3G / 9G INFO General (kmer_splitters.hpp : 325) Processed 7233359 edges 0:27:32.047 3G / 9G INFO General (kmer_splitters.hpp : 325) Processed 8682352 edges 0:27:32.552 3G / 9G INFO General (kmer_splitters.hpp : 325) Processed 8792644 edges 0:27:32.553 3G / 9G INFO General (kmer_splitters.hpp : 330) Used 8792644 sequences. 0:27:32.622 2G / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:28:42.108 2G / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 203886052 kmers in total. 0:28:42.108 2G / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:28:55.906 2G / 9G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:33:48.029 2G / 9G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:34:01.334 2G / 9G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 70531873 bytes occupied (2.7675 bits per kmer). 0:34:04.334 7G / 9G INFO General (edge_index_builders.hpp : 21) Collecting k-mer coverage information from graph, this takes a while. 0:39:50.527 6G / 9G INFO General (graph_construction.hpp : 182) Filling coverage index 0:39:50.527 6G / 9G INFO General (edge_index_builders.hpp : 99) Collecting k-mer coverage information from reads, this takes a while. 0:41:29.681 6G / 9G INFO General (graph_construction.hpp : 184) Filling coverage and flanking coverage from index 0:42:18.670 6G / 9G INFO General (construction.cpp : 33) Figured out: read length = 101 0:42:18.688 6G / 9G INFO StageManager (stage.cpp : 125) STAGE == EC Threshold Finding 0:42:25.459 6G / 9G INFO General (kmer_coverage_model.cpp : 178) Kmer coverage valley at: 3 0:42:25.460 6G / 9G INFO General (kmer_coverage_model.cpp : 198) K-mer histogram maximum: 14 0:42:25.460 6G / 9G INFO General (kmer_coverage_model.cpp : 234) Estimated median coverage: 15. Coverage mad: 7.413 0:42:25.460 6G / 9G INFO General (kmer_coverage_model.cpp : 261) Fitting coverage model 0:42:25.500 6G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 2 0:42:25.606 6G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 4 0:42:25.912 6G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 8 0:42:26.567 6G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 16 0:42:27.714 6G / 9G INFO General (kmer_coverage_model.cpp : 296) ... iteration 32 0:42:27.920 6G / 9G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 15.8651. Fitted coverage std. dev: 5.95525 0:42:27.921 6G / 9G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 0.825022 0:42:27.921 6G / 9G INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 11 0:42:27.921 6G / 9G INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 9 0:42:27.921 6G / 9G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 54901970 0:42:27.921 6G / 9G INFO General (genomic_info_filler.cpp : 103) Mean coverage was calculated as 15.8651 0:42:27.921 6G / 9G INFO General (genomic_info_filler.cpp : 117) EC coverage threshold value was calculated as 9 0:42:27.921 6G / 9G INFO General (genomic_info_filler.cpp : 118) Trusted kmer low bound: 0 0:42:27.921 6G / 9G INFO StageManager (stage.cpp : 125) STAGE == Simplification 0:42:28.257 2G / 9G INFO General (graph_simplification.hpp : 911) Graph simplification started 0:42:28.258 2G / 9G INFO General (graph_simplification.hpp : 924) Fast simplification mode enabled 0:42:28.258 2G / 9G INFO General (graph_simplification.hpp : 771) PROCEDURE == Presimplification 0:42:28.258 2G / 9G INFO General (graph_simplification.hpp : 211) Removing short low covered self-conjugate connections 0:42:29.069 2G / 9G INFO General (graph_simplification.hpp : 403) Removing isolated edges 0:42:29.069 2G / 9G INFO General (graph_simplification.hpp : 404) All edges shorter than 150 will be removed 0:42:29.069 2G / 9G INFO General (graph_simplification.hpp : 405) Also edges shorter than 0 and coverage smaller than 0 will be removed 0:42:45.062 2G / 9G INFO General (graph_simplification.hpp : 687) Non parallel mode 0:42:58.458 2G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:43:31.542 2G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:44:33.018 2G / 9G INFO General (graph_simplification.hpp : 644) Using permanent iterators 0:44:33.018 2G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 1 0:44:34.361 2G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:44:39.709 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:44:39.762 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 2 0:44:39.762 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:44:39.768 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:44:43.740 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 3 0:44:43.740 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:44:43.813 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:44:45.529 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 4 0:44:45.530 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:44:45.553 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:44:46.610 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 5 0:44:46.610 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:44:46.621 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:44:47.391 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 6 0:44:47.391 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:44:47.397 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:44:48.009 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 7 0:44:48.009 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:44:48.013 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:44:48.575 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 8 0:44:48.575 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:44:48.578 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:44:49.083 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 9 0:44:49.083 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:44:49.086 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:44:49.497 1G / 9G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 10 0:44:49.497 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:44:49.500 1G / 9G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:44:49.790 1G / 9G INFO General (graph_simplification.hpp : 796) PROCEDURE == Post simplification 0:44:49.790 1G / 9G INFO General (graph_simplification.hpp : 644) Using permanent iterators 0:44:49.790 1G / 9G INFO General (graph_simplification.hpp : 806) Iteration 0 0:44:49.790 1G / 9G INFO General (graph_simplification.hpp : 247) Removal of relatively low covered connections disabled 0:44:50.206 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:44:51.063 1G / 9G INFO General (graph_simplification.hpp : 806) Iteration 1 0:44:51.063 1G / 9G INFO General (graph_simplification.hpp : 247) Removal of relatively low covered connections disabled 0:44:51.063 1G / 9G INFO General (graph_simplification.hpp : 93) Clipping tips 0:44:51.356 1G / 9G INFO StageManager (stage.cpp : 125) STAGE == Simplification Cleanup 0:44:51.357 1G / 9G INFO General (graph_simplification.hpp : 403) Removing isolated edges 0:44:51.357 1G / 9G INFO General (graph_simplification.hpp : 404) All edges shorter than 150 will be removed 0:44:51.357 1G / 9G INFO General (graph_simplification.hpp : 405) Also edges shorter than 0 and coverage smaller than 2 will be removed 0:44:51.726 1G / 9G INFO General (simplification.cpp : 56) Removing all the edges having coverage 0 and less 0:44:52.322 1G / 9G INFO General (simplification.cpp : 68) Counting average coverage 0:44:52.470 1G / 9G INFO General (simplification.cpp : 71) Average coverage = 13.1317 0:44:52.470 1G / 9G INFO StageManager (stage.cpp : 125) STAGE == Contig Output 0:44:52.470 1G / 9G INFO General (contig_output.hpp : 283) Outputting contigs to /N/dc2/projects/marinovg/Paramecium/others/2015-10-27-Pseudocohnilembus/Pseudocohnilembus_persalinus-PE+MP-dipSPAdes-3.5.0-trimmed/spades//K33/simplified_contigs.fasta 0:45:07.248 1G / 9G INFO General (contig_output.hpp : 283) Outputting contigs to /N/dc2/projects/marinovg/Paramecium/others/2015-10-27-Pseudocohnilembus/Pseudocohnilembus_persalinus-PE+MP-dipSPAdes-3.5.0-trimmed/spades//K33/before_rr.fasta 0:45:49.941 1G / 9G INFO General (contig_output.hpp : 283) Outputting contigs to /N/dc2/projects/marinovg/Paramecium/others/2015-10-27-Pseudocohnilembus/Pseudocohnilembus_persalinus-PE+MP-dipSPAdes-3.5.0-trimmed/spades//K33/final_contigs.fasta 0:46:33.825 1G / 9G INFO General (launch.hpp : 82) SPAdes finished 0:46:37.188 64M / 9G INFO General (main.cpp : 166) Assembling time: 0 hours 46 minutes 37 seconds == Running assembler: K55 0:00:00.000 4M / 4M INFO General (memory_limit.hpp : 42) Memory limit set to 100 Gb 0:00:00.001 4M / 4M INFO General (main.cpp : 146) Assembling dataset (/N/dc2/projects/marinovg/Paramecium/others/2015-10-27-Pseudocohnilembus/Pseudocohnilembus_persalinus-PE+MP-dipSPAdes-3.5.0-trimmed/spades/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 0:00:00.001 4M / 4M INFO General (launch.hpp : 44) Will need read mapping, kmer mapper will be attached 0:00:00.001 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 0:00:00.005 4M / 4M INFO General (read_converter.hpp : 49) Binary reads detected 0:00:00.024 4M / 4M INFO General (graph_construction.hpp : 129) Constructing DeBruijn graph for k=55 0:00:00.026 4M / 4M INFO General (kmer_splitters.hpp : 172) Splitting kmer instances into 256 buckets. This might take a while. 0:00:00.027 4M / 4M INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:00:00.027 4M / 4M INFO General (kmer_splitters.hpp : 190) Memory available for splitting buffers: 2.08325 Gb 0:00:00.027 4M / 4M INFO General (kmer_splitters.hpp : 199) Using cell size of 131072 0:00:21.123 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 24695721 reads 0:01:12.437 8G / 9G INFO General (kmer_splitters.hpp : 228) Processed 38922002 reads 0:01:12.437 8G / 9G INFO General (kmer_splitters.hpp : 234) Adding contigs from previous K 0:01:48.516 8G / 9G INFO General (kmer_splitters.hpp : 245) Used 38922002 reads. Maximum read length 101 0:01:48.516 8G / 9G INFO General (kmer_splitters.hpp : 246) Average read length 97.7662 0:01:50.129 64M / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:02:09.939 64M / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 231756152 kmers in total. 0:02:09.939 64M / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:02:26.786 64M / 9G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:02:26.786 64M / 9G INFO General (kmer_splitters.hpp : 379) Splitting kmer instances into 256 buckets. This might take a while. 0:02:26.786 64M / 9G INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:02:26.786 64M / 9G INFO General (kmer_splitters.hpp : 397) Memory available for splitting buffers: 2.08203 Gb 0:02:26.786 64M / 9G INFO General (kmer_splitters.hpp : 405) Using cell size of 131072 0:03:03.286 8G / 9G INFO General (kmer_splitters.hpp : 428) Processed 231756152 kmers 0:03:03.287 8G / 9G INFO General (kmer_splitters.hpp : 437) Used 231756152 kmers. 0:03:04.352 64M / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:03:16.828 64M / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 233704811 kmers in total. 0:03:16.829 64M / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:03:33.399 64M / 9G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:04:07.550 192M / 9G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:04:24.243 192M / 9G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 80847289 bytes occupied (2.7675 bits per kmer). 0:04:24.563 416M / 9G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 382) Building k-mer extensions from k+1-mers 0:04:55.938 416M / 9G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 386) Building k-mer extensions from k+1-mers finished. 0:04:55.944 416M / 9G INFO General (graph_construction.hpp : 145) Condensing graph 0:04:55.944 416M / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 337) Extracting unbranching paths 0:07:30.699 2G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 351) Extracting unbranching paths finished. 17919403 sequences extracted 0:07:54.237 2G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 311) Collecting perfect loops 0:09:05.201 2G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 326) Collecting perfect loops finished. 988 loops collected 0:09:20.892 4G / 9G INFO General (graph_construction.hpp : 150) Building index with from graph 0:09:20.894 4G / 9G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:09:20.894 4G / 9G INFO General (kmer_splitters.hpp : 289) Splitting kmer instances into 16 buckets. This might take a while. 0:09:20.894 4G / 9G INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:09:20.894 4G / 9G INFO General (kmer_splitters.hpp : 307) Memory available for splitting buffers: 31.7031 Gb 0:09:20.894 4G / 9G INFO General (kmer_splitters.hpp : 312) Using cell size of 2097152 0:09:28.358 5G / 9G INFO General (kmer_splitters.hpp : 325) Processed 2598161 edges 0:09:35.640 5G / 9G INFO General (kmer_splitters.hpp : 325) Processed 5191303 edges 0:09:42.966 5G / 9G INFO General (kmer_splitters.hpp : 325) Processed 7787052 edges 0:09:50.474 5G / 9G INFO General (kmer_splitters.hpp : 325) Processed 10382312 edges 0:09:57.790 5G / 9G INFO General (kmer_splitters.hpp : 325) Processed 12975107 edges 0:10:05.041 5G / 9G INFO General (kmer_splitters.hpp : 325) Processed 15567943 edges 0:10:11.619 5G / 9G INFO General (kmer_splitters.hpp : 325) Processed 17920391 edges 0:10:11.619 5G / 9G INFO General (kmer_splitters.hpp : 330) Used 17920391 sequences. 0:10:11.689 4G / 9G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:11:29.530 4G / 9G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 231756152 kmers in total. 0:11:29.530 4G / 9G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:11:46.565 4G / 9G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:16:53.594 5G / 9G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:17:08.259 5G / 9G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 80173172 bytes occupied (2.7675 bits per kmer). 0:17:11.743 10G / 10G INFO General (edge_index_builders.hpp : 21) Collecting k-mer coverage information from graph, this takes a while. 0:24:23.869 9G / 10G INFO General (graph_construction.hpp : 182) Filling coverage index 0:24:23.869 9G / 10G INFO General (edge_index_builders.hpp : 99) Collecting k-mer coverage information from reads, this takes a while. 0:25:37.630 9G / 10G INFO General (graph_construction.hpp : 184) Filling coverage and flanking coverage from index 0:26:29.887 9G / 10G INFO General (construction.cpp : 33) Figured out: read length = 101 0:26:29.902 9G / 10G INFO StageManager (stage.cpp : 125) STAGE == EC Threshold Finding 0:26:36.086 9G / 10G INFO General (kmer_coverage_model.cpp : 178) Kmer coverage valley at: 0 0:26:36.086 9G / 10G INFO General (kmer_coverage_model.cpp : 198) K-mer histogram maximum: 1 0:26:36.086 9G / 10G INFO General (kmer_coverage_model.cpp : 234) Estimated median coverage: 1. Coverage mad: 3.31519 0:26:36.086 9G / 10G INFO General (kmer_coverage_model.cpp : 261) Fitting coverage model 0:26:36.089 9G / 10G INFO General (kmer_coverage_model.cpp : 296) ... iteration 2 0:26:36.097 9G / 10G INFO General (kmer_coverage_model.cpp : 296) ... iteration 4 0:26:36.115 9G / 10G INFO General (kmer_coverage_model.cpp : 296) ... iteration 8 0:26:36.144 9G / 10G INFO General (kmer_coverage_model.cpp : 296) ... iteration 16 0:26:36.193 9G / 10G INFO General (kmer_coverage_model.cpp : 296) ... iteration 32 0:26:36.244 9G / 10G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 7.72195. Fitted coverage std. dev: 2.87185 0:26:36.244 9G / 10G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 0.996204 0:26:36.244 9G / 10G INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 4 0:26:36.244 9G / 10G INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 3 0:26:36.244 9G / 10G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 47172740 0:26:36.244 9G / 10G INFO General (genomic_info_filler.cpp : 103) Mean coverage was calculated as 7.72195 0:26:36.244 9G / 10G INFO General (genomic_info_filler.cpp : 117) EC coverage threshold value was calculated as 3 0:26:36.244 9G / 10G INFO General (genomic_info_filler.cpp : 118) Trusted kmer low bound: 0 0:26:36.244 9G / 10G INFO StageManager (stage.cpp : 125) STAGE == Gap Closer 0:26:36.301 9G / 10G INFO General (gap_closer.cpp : 157) Preparing shift maps 0:27:01.806 10G / 10G INFO General (gap_closer.cpp : 117) Processing paired reads (takes a while) 0:27:23.475 12G / 12G INFO General (gap_closer.cpp : 136) Used 19125210 paired reads 0:27:23.476 12G / 12G INFO General (gap_closer.cpp : 138) Merging paired indices 0:27:40.262 10G / 12G INFO GapCloser (gap_closer.cpp : 395) Closing short gaps 0:28:32.488 10G / 12G INFO GapCloser (gap_closer.cpp : 424) Closing short gaps complete: filled 4996 gaps after checking 136163 candidates 0:28:40.165 9G / 12G INFO StageManager (stage.cpp : 125) STAGE == Simplification 0:28:40.587 4G / 12G INFO General (graph_simplification.hpp : 911) Graph simplification started 0:28:40.587 4G / 12G INFO General (graph_simplification.hpp : 899) Estimated mean coverage 7.72195 is less than fast mode activation coverage 10 0:28:40.587 4G / 12G INFO General (graph_simplification.hpp : 926) Fast simplification mode disabled 0:28:40.587 4G / 12G INFO General (graph_simplification.hpp : 771) PROCEDURE == Presimplification 0:28:40.587 4G / 12G INFO General (graph_simplification.hpp : 211) Removing short low covered self-conjugate connections 0:28:42.115 4G / 12G INFO General (graph_simplification.hpp : 775) Further presimplification is disabled 0:28:42.115 4G / 12G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 1 0:29:35.433 5G / 12G INFO General (graph_simplification.hpp : 93) Clipping tips 0:32:28.975 4G / 12G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:32:30.132 4G / 12G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 2 0:32:41.025 4G / 12G INFO General (graph_simplification.hpp : 93) Clipping tips 0:33:20.291 4G / 12G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:33:21.447 4G / 12G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 3 0:33:32.319 4G / 12G INFO General (graph_simplification.hpp : 93) Clipping tips 0:34:11.536 4G / 12G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:34:12.808 4G / 12G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 4 0:34:23.651 4G / 12G INFO General (graph_simplification.hpp : 93) Clipping tips 0:35:02.818 4G / 12G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:35:11.716 4G / 12G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 5 0:35:22.152 4G / 12G INFO General (graph_simplification.hpp : 93) Clipping tips 0:35:59.704 4G / 12G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:36:08.030 4G / 12G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 6 0:36:18.231 4G / 12G INFO General (graph_simplification.hpp : 93) Clipping tips 0:36:54.707 4G / 12G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:37:02.310 4G / 12G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 7 0:37:12.396 4G / 12G INFO General (graph_simplification.hpp : 93) Clipping tips 0:37:48.593 4G / 12G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:37:56.020 4G / 12G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 8 0:38:06.070 4G / 12G INFO General (graph_simplification.hpp : 93) Clipping tips 0:38:42.066 4G / 12G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:38:49.389 4G / 12G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 9 0:38:59.392 4G / 12G INFO General (graph_simplification.hpp : 93) Clipping tips 0:39:35.043 4G / 12G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:39:42.318 4G / 12G INFO General (graph_simplification.hpp : 857) PROCEDURE == Simplification cycle, iteration 10 0:39:52.163 4G / 12G INFO General (graph_simplification.hpp : 93) Clipping tips 0:40:27.560 4G / 12G INFO General (graph_simplification.hpp : 187) Removing low covered connections 0:40:34.746 4G / 12G INFO General (graph_simplification.hpp : 796) PROCEDURE == Post simplification 0:40:34.747 4G / 12G INFO General (graph_simplification.hpp : 806) Iteration 0 0:40:34.747 4G / 12G INFO General (graph_simplification.hpp : 247) Removal of relatively low covered connections disabled 0:40:44.530 4G / 12G INFO General (graph_simplification.hpp : 93) Clipping tips 0:41:05.007 4G / 12G INFO General (graph_simplification.hpp : 806) Iteration 1 0:41:05.007 4G / 12G INFO General (graph_simplification.hpp : 247) Removal of relatively low covered connections disabled 0:41:14.794 4G / 12G INFO General (graph_simplification.hpp : 93) Clipping tips 0:41:37.519 4G / 12G INFO StageManager (stage.cpp : 125) STAGE == Gap Closer 0:41:37.519 4G / 12G INFO General (graph_pack.hpp : 84) Index refill 0:41:37.520 4G / 12G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:41:37.521 4G / 12G INFO General (kmer_splitters.hpp : 289) Splitting kmer instances into 16 buckets. This might take a while. 0:41:37.521 4G / 12G INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:41:37.521 4G / 12G INFO General (kmer_splitters.hpp : 307) Memory available for splitting buffers: 31.7982 Gb 0:41:37.521 4G / 12G INFO General (kmer_splitters.hpp : 312) Using cell size of 2097152 0:41:43.626 5G / 12G INFO General (kmer_splitters.hpp : 325) Processed 859269 edges 0:41:49.585 5G / 12G INFO General (kmer_splitters.hpp : 325) Processed 1740498 edges 0:41:55.514 5G / 12G INFO General (kmer_splitters.hpp : 325) Processed 2595274 edges 0:42:01.425 5G / 12G INFO General (kmer_splitters.hpp : 325) Processed 3465132 edges 0:42:05.645 5G / 12G INFO General (kmer_splitters.hpp : 325) Processed 4090761 edges 0:42:05.646 5G / 12G INFO General (kmer_splitters.hpp : 330) Used 4090761 sequences. 0:42:05.717 4G / 12G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:42:43.353 4G / 12G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 158461996 kmers in total. 0:42:43.353 4G / 12G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:42:53.253 4G / 12G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:46:32.827 4G / 12G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:46:44.173 4G / 12G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 54817996 bytes occupied (2.7675 bits per kmer). 0:46:46.526 8G / 12G INFO General (edge_index_builders.hpp : 21) Collecting k-mer coverage information from graph, this takes a while. 0:51:13.431 8G / 12G INFO General (gap_closer.cpp : 157) Preparing shift maps 0:51:23.353 8G / 12G INFO General (gap_closer.cpp : 117) Processing paired reads (takes a while) 0:51:48.647 9G / 12G INFO General (gap_closer.cpp : 136) Used 19125210 paired reads 0:51:48.648 9G / 12G INFO General (gap_closer.cpp : 138) Merging paired indices 0:52:00.209 8G / 12G INFO GapCloser (gap_closer.cpp : 395) Closing short gaps 0:52:11.218 8G / 12G INFO GapCloser (gap_closer.cpp : 424) Closing short gaps complete: filled 348 gaps after checking 64516 candidates 0:52:17.594 8G / 12G INFO StageManager (stage.cpp : 125) STAGE == Simplification Cleanup 0:52:17.595 8G / 12G INFO General (graph_simplification.hpp : 403) Removing isolated edges 0:52:17.595 8G / 12G INFO General (graph_simplification.hpp : 404) All edges shorter than 150 will be removed 0:52:17.595 8G / 12G INFO General (graph_simplification.hpp : 405) Also edges shorter than 0 and coverage smaller than 2 will be removed 0:54:20.174 5G / 12G INFO General (simplification.cpp : 56) Removing all the edges having coverage 0 and less 0:54:20.739 5G / 12G INFO General (simplification.cpp : 68) Counting average coverage 0:54:20.887 5G / 12G INFO General (simplification.cpp : 71) Average coverage = 8.58257 0:54:20.887 5G / 12G INFO StageManager (stage.cpp : 125) STAGE == Mismatch Correction 0:56:12.256 5G / 12G INFO General (mismatch_shall_not_pass.hp: 188) Finished collecting potential mismatches positions 0:56:12.619 5G / 12G INFO General (mismatch_shall_not_pass.hp: 291) All edges processed 0:56:12.628 5G / 12G INFO General (mismatch_correction.cpp : 18) Corrected 0 nucleotides 0:56:12.665 5G / 12G INFO StageManager (stage.cpp : 125) STAGE == Paired Information Counting 0:56:13.922 5G / 12G INFO General (pair_info_count.cpp : 150) Graph N50: 6820 0:56:13.939 5G / 12G INFO General (pair_info_count.cpp : 152) Estimating insert size for library #0 0:56:13.939 5G / 12G INFO General (pair_info_count.cpp : 31) Estimating insert size (takes a while) 0:56:13.952 5G / 12G INFO General (short_read_mapper.hpp : 81) Mapping mate-pair library, selecting sensitive read mapper with k=19 0:56:13.952 5G / 12G INFO General (edge_multi_index.hpp : 97) DeBruijnEdgeMultiIndex constructing 0:56:13.954 5G / 12G INFO K-mer Index Building (kmer_index.hpp : 467) Building kmer index 0:56:13.954 5G / 12G INFO General (kmer_splitters.hpp : 289) Splitting kmer instances into 16 buckets. This might take a while. 0:56:13.954 5G / 12G INFO General (file_limit.hpp : 29) Open file limit set to 32768 0:56:13.954 5G / 12G INFO General (kmer_splitters.hpp : 307) Memory available for splitting buffers: 31.5339 Gb 0:56:13.954 5G / 12G INFO General (kmer_splitters.hpp : 312) Using cell size of 4194304 0:56:20.171 5G / 12G INFO General (kmer_splitters.hpp : 325) Processed 73570 edges 0:56:26.357 5G / 12G INFO General (kmer_splitters.hpp : 325) Processed 145434 edges 0:56:29.168 5G / 12G INFO General (kmer_splitters.hpp : 325) Processed 177815 edges 0:56:29.168 5G / 12G INFO General (kmer_splitters.hpp : 330) Used 177815 sequences. 0:56:29.242 5G / 12G INFO General (kmer_index.hpp : 345) Starting k-mer counting. 0:56:55.820 5G / 12G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 142188034 kmers in total. 0:56:55.820 5G / 12G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:57:00.707 5G / 12G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 1:00:10.425 5G / 12G INFO General (kmer_index.hpp : 371) Merging final buckets. 1:00:15.237 5G / 12G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 49188211 bytes occupied (2.7675 bits per kmer). 1:00:17.372 8G / 12G INFO General (perfect_hash_map.hpp : 178) Arranging kmers in hash map order 1:01:23.079 8G / 12G INFO General (perfect_hash_map.hpp : 190) Done. Total swaps: 142187775 1:01:23.083 8G / 12G INFO General (edge_index_builders.hpp : 21) Collecting k-mer coverage information from graph, this takes a while. 1:05:31.418 13G / 13G INFO General (sequence_mapper_notifier.h: 81) Processed 200000 reads 1:05:31.600 13G / 13G INFO General (sequence_mapper_notifier.h: 81) Processed 400000 reads 1:05:31.860 13G / 13G INFO General (sequence_mapper_notifier.h: 81) Processed 600000 reads 1:05:32.574 13G / 13G INFO General (sequence_mapper_notifier.h: 81) Processed 800000 reads 1:05:32.841 13G / 13G INFO General (sequence_mapper_notifier.h: 81) Processed 1000000 reads 1:05:32.892 13G / 13G INFO General (sequence_mapper_notifier.h: 81) Processed 1200000 reads 1:05:37.686 13G / 13G INFO General (sequence_mapper_notifier.h: 81) Processed 2200000 reads 1:07:22.467 13G / 13G INFO General (sequence_mapper_notifier.h: 81) Processed 4200000 reads 1:09:00.277 13G / 13G INFO General (sequence_mapper_notifier.h: 81) Processed 8470287 reads 1:09:03.386 13G / 13G INFO General (sequence_mapper_notifier.h: 89) Processed 8766042 reads 1:09:03.387 13G / 13G INFO General (pair_info_count.cpp : 41) 3074347 paired reads (35.0711% of all) aligned to long edges 1:09:03.401 13G / 13G INFO General (pair_info_count.cpp : 170) Estimated insert size for paired library #0 1:09:03.401 13G / 13G INFO General (pair_info_count.cpp : 175) Insert size = 2001.34, deviation = 166.919, left quantile = 1790, right quantile = 2221, read length = 101 1:09:03.401 13G / 13G INFO General (pair_info_count.cpp : 152) Estimating insert size for library #1 1:09:03.401 13G / 13G INFO General (pair_info_count.cpp : 31) Estimating insert size (takes a while) 1:09:03.410 13G / 13G INFO General (short_read_mapper.hpp : 91) Selecting usual mapper 1:09:08.720 13G / 13G INFO General (sequence_mapper_notifier.h: 81) Processed 200000 reads 1:09:08.729 13G / 13G INFO General (sequence_mapper_notifier.h: 81) Processed 400000 reads 1:09:08.758 13G / 13G INFO General (sequence_mapper_notifier.h: 81) Processed 600000 reads 1:09:08.765 13G / 13G INFO General (sequence_mapper_notifier.h: 81) Processed 800000 reads 1:09:08.766 13G / 13G INFO General (sequence_mapper_notifier.h: 81) Processed 1000000 reads 1:09:08.847 13G / 13G INFO General (sequence_mapper_notifier.h: 81) Processed 1200000 reads 1:09:10.150 13G / 13G INFO General (sequence_mapper_notifier.h: 81) Processed 2200000 reads 1:09:14.357 13G / 13G INFO General (sequence_mapper_notifier.h: 81) Processed 4200000 reads 1:09:23.141 13G / 13G INFO General (sequence_mapper_notifier.h: 81) Processed 8574290 reads 1:09:24.118 13G / 13G INFO General (sequence_mapper_notifier.h: 89) Processed 9562605 reads 1:09:24.119 13G / 13G INFO General (pair_info_count.cpp : 41) 4289202 paired reads (44.8539% of all) aligned to long edges 1:09:24.136 13G / 13G INFO General (pair_info_count.cpp : 170) Estimated insert size for paired library #1 1:09:24.136 13G / 13G INFO General (pair_info_count.cpp : 175) Insert size = 193.495, deviation = 34.278, left quantile = 149, right quantile = 237, read length = 101 1:09:24.137 13G / 13G INFO General (pair_info_count.cpp : 187) Mapping library #0 1:09:24.137 13G / 13G INFO General (pair_info_count.cpp : 189) Mapping paired reads (takes a while) 1:09:24.137 13G / 13G INFO General (pair_info_count.cpp : 73) Left insert size qauntile 1790, right insert size quantile 2221 1:09:24.147 13G / 13G INFO General (short_read_mapper.hpp : 81) Mapping mate-pair library, selecting sensitive read mapper with k=19 1:11:15.066 13G / 13G INFO General (sequence_mapper_notifier.h: 81) Processed 200000 reads 1:11:15.576 13G / 13G INFO General (sequence_mapper_notifier.h: 81) Processed 400000 reads 1:11:15.893 13G / 13G INFO General (sequence_mapper_notifier.h: 81) Processed 600000 reads 1:11:16.267 13G / 13G INFO General (sequence_mapper_notifier.h: 81) Processed 800000 reads 1:11:16.766 13G / 13G INFO General (sequence_mapper_notifier.h: 81) Processed 1000000 reads 1:11:17.232 13G / 13G INFO General (sequence_mapper_notifier.h: 81) Processed 1200000 reads 1:11:24.273 13G / 13G INFO General (sequence_mapper_notifier.h: 81) Processed 2200000 reads 1:13:07.650 13G / 13G INFO General (sequence_mapper_notifier.h: 81) Processed 4200000 reads 1:15:20.063 13G / 13G INFO General (sequence_mapper_notifier.h: 81) Processed 8400000 reads 1:19:53.919 13G / 13G INFO General (sequence_mapper_notifier.h: 81) Processed 16861798 reads 1:20:14.282 13G / 13G INFO General (sequence_mapper_notifier.h: 89) Processed 17532084 reads 1:20:14.302 13G / 13G INFO General (pair_info_count.cpp : 187) Mapping library #1 1:20:14.302 13G / 13G INFO General (pair_info_count.cpp : 189) Mapping paired reads (takes a while) 1:20:14.302 13G / 13G INFO General (pair_info_count.cpp : 73) Left insert size qauntile 149, right insert size quantile 237 1:20:14.310 13G / 13G INFO General (short_read_mapper.hpp : 91) Selecting usual mapper 1:20:23.464 14G / 14G INFO General (sequence_mapper_notifier.h: 81) Processed 200000 reads 1:20:24.357 14G / 15G INFO General (sequence_mapper_notifier.h: 81) Processed 400000 reads 1:20:25.027 14G / 15G INFO General (sequence_mapper_notifier.h: 81) Processed 600000 reads 1:20:25.928 14G / 15G INFO General (sequence_mapper_notifier.h: 81) Processed 800000 reads 1:20:26.911 14G / 15G INFO General (sequence_mapper_notifier.h: 81) Processed 1000000 reads 1:20:27.938 15G / 15G INFO General (sequence_mapper_notifier.h: 81) Processed 1200000 reads 1:20:34.094 15G / 15G INFO General (sequence_mapper_notifier.h: 81) Processed 2200000 reads 1:20:47.557 15G / 15G INFO General (sequence_mapper_notifier.h: 81) Processed 4200000 reads 1:21:16.712 15G / 15G INFO General (sequence_mapper_notifier.h: 81) Processed 8400000 reads 1:22:17.782 15G / 15G INFO General (sequence_mapper_notifier.h: 81) Processed 16781302 reads 1:22:35.238 13G / 15G INFO General (sequence_mapper_notifier.h: 89) Processed 19125210 reads 1:22:51.905 14G / 15G INFO General (split_graph_pair_info.hpp : 344) Threshold for paired information 0.0764237 1:24:14.710 5G / 15G INFO StageManager (stage.cpp : 125) STAGE == Distance Estimation 1:24:14.726 5G / 15G INFO General (distance_estimation.cpp : 234) Processing library #1 1:24:14.727 5G / 15G INFO General (distance_estimation.cpp : 136) Weight Filter Done 1:24:14.727 5G / 15G INFO DistanceEstimator (distance_estimation.hpp : 187) Using SIMPLE distance estimator 1:24:33.827 5G / 15G INFO DistanceEstimator (distance_estimation.hpp : 208) Merging maps 1:24:37.349 5G / 15G INFO General (distance_estimation.cpp : 38) Filtering info 1:24:46.580 5G / 15G INFO General (pair_info_filters.hpp : 354) Pruning the index 1:24:46.769 5G / 15G INFO General (distance_estimation.cpp : 184) Refining clustered pair information 1:24:46.998 5G / 15G INFO General (distance_estimation.cpp : 186) The refining of clustered pair information has been finished 1:24:46.998 5G / 15G INFO General (distance_estimation.cpp : 188) Filling paired information 1:25:01.684 5G / 15G INFO PairInfoImprover (pair_info_improver.hpp : 61) Paired info stats: missing = 118228; contradictional = 14254 1:25:14.773 5G / 15G INFO PairInfoImprover (pair_info_improver.hpp : 61) Paired info stats: missing = 48876; contradictional = 8 1:25:14.773 5G / 15G INFO General (distance_estimation.cpp : 193) Filling scaffolding index 1:25:14.773 5G / 15G INFO DistanceEstimator (distance_estimation.hpp : 187) Using SMOOTHING distance estimator 1:25:34.546 5G / 15G INFO DistanceEstimator (distance_estimation.hpp : 208) Merging maps 1:25:34.578 5G / 15G INFO General (distance_estimation.cpp : 38) Filtering info 1:25:35.065 5G / 15G INFO General (pair_info_filters.hpp : 354) Pruning the index 1:25:35.745 5G / 15G INFO StageManager (stage.cpp : 125) STAGE == Repeat Resolving 1:25:35.745 5G / 15G INFO General (contig_output.hpp : 283) Outputting contigs to /N/dc2/projects/marinovg/Paramecium/others/2015-10-27-Pseudocohnilembus/Pseudocohnilembus_persalinus-PE+MP-dipSPAdes-3.5.0-trimmed/spades//K55/before_rr.fasta 1:26:17.785 5G / 15G INFO General (repeat_resolving.cpp : 59) Using Path-Extend repeat resolving 1:26:17.786 5G / 15G INFO General (path_extend_launch.hpp : 459) Threshold for library #1 is 0.0764237 1:26:17.786 5G / 15G INFO General (path_extend_launch.hpp : 298) Path-Extend repeat resolving tool started 1:26:17.963 5G / 15G INFO General (path_extend_launch.hpp : 316) Using 1 paired-end library 1:26:17.963 5G / 15G INFO General (path_extend_launch.hpp : 317) Using 1 paired-end scaffolding library 1:26:17.963 5G / 15G INFO General (path_extend_launch.hpp : 318) Using 1 mate-pair library 1:26:17.963 5G / 15G INFO General (path_extend_launch.hpp : 319) Using 0 single read libraries 1:26:17.963 5G / 15G INFO General (path_extend_launch.hpp : 320) Scaffolder is on 1:26:19.178 6G / 15G INFO General (path_extend_launch.hpp : 332) Growing paths using paired-end and long single reads 1:26:19.178 6G / 15G INFO PathExtender (path_extender.hpp : 611) Processed 0 paths from 86198 (0%) 1:26:19.250 6G / 15G INFO PathExtender (path_extender.hpp : 609) Processed 128 paths from 86198 (0%) 1:26:19.319 6G / 15G INFO PathExtender (path_extender.hpp : 609) Processed 256 paths from 86198 (0%) 1:26:19.521 6G / 15G INFO PathExtender (path_extender.hpp : 609) Processed 512 paths from 86198 (0%) 1:26:19.862 6G / 15G INFO PathExtender (path_extender.hpp : 609) Processed 1024 paths from 86198 (1%) 1:26:20.462 6G / 15G INFO PathExtender (path_extender.hpp : 609) Processed 2048 paths from 86198 (2%) 1:26:21.738 6G / 15G INFO PathExtender (path_extender.hpp : 609) Processed 4096 paths from 86198 (4%) 1:26:23.883 6G / 15G INFO PathExtender (path_extender.hpp : 609) Processed 8192 paths from 86198 (9%) 1:26:24.138 6G / 15G INFO PathExtender (path_extender.hpp : 611) Processed 8620 paths from 86198 (10%) 1:26:25.598 6G / 15G INFO PathExtender (path_extender.hpp : 609) Processed 16384 paths from 86198 (19%) 1:26:25.697 6G / 15G INFO PathExtender (path_extender.hpp : 611) Processed 17240 paths from 86198 (20%) 1:26:26.334 6G / 15G INFO PathExtender (path_extender.hpp : 611) Processed 25860 paths from 86198 (30%) 1:26:26.688 6G / 15G INFO PathExtender (path_extender.hpp : 609) Processed 32768 paths from 86198 (38%) 1:26:26.767 6G / 15G INFO PathExtender (path_extender.hpp : 611) Processed 34480 paths from 86198 (40%) 1:26:27.110 6G / 15G INFO PathExtender (path_extender.hpp : 611) Processed 43100 paths from 86198 (50%) 1:26:27.507 6G / 15G INFO PathExtender (path_extender.hpp : 611) Processed 51720 paths from 86198 (60%) 1:26:29.915 6G / 15G INFO PathExtender (path_extender.hpp : 611) Processed 60340 paths from 86198 (70%) 1:26:32.459 6G / 15G INFO PathExtender (path_extender.hpp : 609) Processed 65536 paths from 86198 (76%) 1:26:34.078 6G / 15G INFO PathExtender (path_extender.hpp : 611) Processed 68960 paths from 86198 (80%) 1:26:40.247 6G / 15G INFO PathExtender (path_extender.hpp : 611) Processed 77580 paths from 86198 (90%) 1:26:48.933 6G / 15G INFO PathExtendIO (pe_io.hpp : 339) Constructing FASTG file from paths 1:26:51.295 6G / 15G INFO PathExtendIO (pe_io.hpp : 342) Writing contigs in FASTG to /N/dc2/projects/marinovg/Paramecium/others/2015-10-27-Pseudocohnilembus/Pseudocohnilembus_persalinus-PE+MP-dipSPAdes-3.5.0-trimmed/spades//K55/pe_contigs.fastg 1:26:51.295 6G / 15G INFO PathExtendIO (pe_io.hpp : 343) Writing contigs in FASTA to /N/dc2/projects/marinovg/Paramecium/others/2015-10-27-Pseudocohnilembus/Pseudocohnilembus_persalinus-PE+MP-dipSPAdes-3.5.0-trimmed/spades//K55/pe_contigs.fasta 1:27:31.471 6G / 15G INFO PathExtendIO (pe_io.hpp : 339) Constructing FASTG file from paths 1:27:33.938 6G / 15G INFO PathExtendIO (pe_io.hpp : 342) Writing contigs in FASTG to /N/dc2/projects/marinovg/Paramecium/others/2015-10-27-Pseudocohnilembus/Pseudocohnilembus_persalinus-PE+MP-dipSPAdes-3.5.0-trimmed/spades//K55/path_extend/pe_before_traversal.fastg 1:27:33.938 6G / 15G INFO PathExtendIO (pe_io.hpp : 343) Writing contigs in FASTA to /N/dc2/projects/marinovg/Paramecium/others/2015-10-27-Pseudocohnilembus/Pseudocohnilembus_persalinus-PE+MP-dipSPAdes-3.5.0-trimmed/spades//K55/path_extend/pe_before_traversal.fasta 1:28:14.423 6G / 15G INFO General (path_extend_launch.hpp : 281) Traversing tandem repeats 1:28:17.219 6G / 15G INFO PathExtendIO (pe_io.hpp : 339) Constructing FASTG file from paths 1:28:19.377 6G / 15G INFO PathExtendIO (pe_io.hpp : 342) Writing contigs in FASTG to /N/dc2/projects/marinovg/Paramecium/others/2015-10-27-Pseudocohnilembus/Pseudocohnilembus_persalinus-PE+MP-dipSPAdes-3.5.0-trimmed/spades//K55/pe_scaffolds.fastg 1:28:19.377 6G / 15G INFO PathExtendIO (pe_io.hpp : 343) Writing contigs in FASTA to /N/dc2/projects/marinovg/Paramecium/others/2015-10-27-Pseudocohnilembus/Pseudocohnilembus_persalinus-PE+MP-dipSPAdes-3.5.0-trimmed/spades//K55/pe_scaffolds.fasta 1:28:59.444 6G / 15G INFO General (path_extend_launch.hpp : 367) Adding mate-pairs 1:28:59.776 6G / 15G INFO General (path_extend_launch.hpp : 379) Growing paths using mate-pairs 1:29:00.026 6G / 15G INFO PathExtender (path_extender.hpp : 611) Processed 0 paths from 71452 (0%) 1:30:04.786 6G / 15G INFO PathExtender (path_extender.hpp : 609) Processed 128 paths from 71452 (0%) 1:30:20.587 6G / 15G INFO PathExtender (path_extender.hpp : 609) Processed 256 paths from 71452 (0%) 1:31:10.209 6G / 15G INFO PathExtender (path_extender.hpp : 609) Processed 512 paths from 71452 (0%) 1:33:48.004 6G / 15G INFO PathExtender (path_extender.hpp : 609) Processed 1024 paths from 71452 (1%) 1:35:19.544 6G / 15G INFO PathExtender (path_extender.hpp : 609) Processed 2048 paths from 71452 (2%) 1:36:58.388 6G / 15G INFO PathExtender (path_extender.hpp : 609) Processed 4096 paths from 71452 (5%) 1:39:35.056 6G / 15G INFO PathExtender (path_extender.hpp : 611) Processed 7146 paths from 71452 (10%) 1:40:29.826 6G / 15G INFO PathExtender (path_extender.hpp : 609) Processed 8192 paths from 71452 (11%) 1:46:55.147 6G / 15G INFO PathExtender (path_extender.hpp : 611) Processed 14292 paths from 71452 (20%) 1:48:14.768 6G / 15G INFO PathExtender (path_extender.hpp : 609) Processed 16384 paths from 71452 (22%) 1:52:50.037 6G / 15G INFO PathExtender (path_extender.hpp : 611) Processed 21438 paths from 71452 (30%) 1:52:53.335 6G / 15G INFO PathExtender (path_extender.hpp : 611) Processed 28584 paths from 71452 (40%) 1:52:53.568 6G / 15G INFO PathExtender (path_extender.hpp : 609) Processed 32768 paths from 71452 (45%) 1:52:53.737 6G / 15G INFO PathExtender (path_extender.hpp : 611) Processed 35730 paths from 71452 (50%) 1:52:54.077 6G / 15G INFO PathExtender (path_extender.hpp : 611) Processed 42876 paths from 71452 (60%) 1:52:55.292 6G / 15G INFO PathExtender (path_extender.hpp : 611) Processed 50022 paths from 71452 (70%) 1:52:55.579 6G / 15G INFO PathExtender (path_extender.hpp : 611) Processed 57168 paths from 71452 (80%) 1:52:56.142 7G / 15G INFO PathExtender (path_extender.hpp : 611) Processed 64314 paths from 71452 (90%) 1:52:56.187 7G / 15G INFO PathExtender (path_extender.hpp : 609) Processed 65536 paths from 71452 (91%) 1:53:09.935 7G / 15G INFO PathExtendIO (pe_io.hpp : 339) Constructing FASTG file from paths 1:53:11.718 7G / 15G INFO PathExtendIO (pe_io.hpp : 342) Writing contigs in FASTG to /N/dc2/projects/marinovg/Paramecium/others/2015-10-27-Pseudocohnilembus/Pseudocohnilembus_persalinus-PE+MP-dipSPAdes-3.5.0-trimmed/spades//K55/path_extend/mp_prefinal.fastg 1:53:11.718 7G / 15G INFO PathExtendIO (pe_io.hpp : 343) Writing contigs in FASTA to /N/dc2/projects/marinovg/Paramecium/others/2015-10-27-Pseudocohnilembus/Pseudocohnilembus_persalinus-PE+MP-dipSPAdes-3.5.0-trimmed/spades//K55/path_extend/mp_prefinal.fasta 1:53:50.370 7G / 15G INFO PathExtender (path_extender.hpp : 611) Processed 0 paths from 53992 (0%) 1:53:51.041 7G / 15G INFO PathExtender (path_extender.hpp : 609) Processed 128 paths from 53992 (0%) 1:53:51.500 7G / 15G INFO PathExtender (path_extender.hpp : 609) Processed 256 paths from 53992 (0%) 1:53:52.100 7G / 15G INFO PathExtender (path_extender.hpp : 609) Processed 512 paths from 53992 (0%) 1:53:52.734 7G / 15G INFO PathExtender (path_extender.hpp : 609) Processed 1024 paths from 53992 (1%) 1:53:53.232 7G / 15G INFO PathExtender (path_extender.hpp : 609) Processed 2048 paths from 53992 (3%) 1:53:53.340 7G / 15G INFO PathExtender (path_extender.hpp : 609) Processed 4096 paths from 53992 (7%) 1:53:53.396 7G / 15G INFO PathExtender (path_extender.hpp : 611) Processed 5400 paths from 53992 (10%) 1:53:53.511 7G / 15G INFO PathExtender (path_extender.hpp : 609) Processed 8192 paths from 53992 (15%) 1:53:53.629 7G / 15G INFO PathExtender (path_extender.hpp : 611) Processed 10800 paths from 53992 (20%) 1:53:53.854 7G / 15G INFO PathExtender (path_extender.hpp : 611) Processed 16200 paths from 53992 (30%) 1:53:53.861 7G / 15G INFO PathExtender (path_extender.hpp : 609) Processed 16384 paths from 53992 (30%) 1:53:54.075 7G / 15G INFO PathExtender (path_extender.hpp : 611) Processed 21600 paths from 53992 (40%) 1:53:54.275 7G / 15G INFO PathExtender (path_extender.hpp : 611) Processed 27000 paths from 53992 (50%) 1:53:54.442 7G / 15G INFO PathExtender (path_extender.hpp : 611) Processed 32400 paths from 53992 (60%) 1:53:54.453 7G / 15G INFO PathExtender (path_extender.hpp : 609) Processed 32768 paths from 53992 (60%) 1:53:54.615 7G / 15G INFO PathExtender (path_extender.hpp : 611) Processed 37800 paths from 53992 (70%) 1:53:54.794 7G / 15G INFO PathExtender (path_extender.hpp : 611) Processed 43200 paths from 53992 (80%) 1:53:55.803 7G / 15G INFO PathExtender (path_extender.hpp : 611) Processed 48600 paths from 53992 (90%) 1:54:00.570 7G / 15G INFO PathExtendIO (pe_io.hpp : 339) Constructing FASTG file from paths 1:54:02.801 7G / 15G INFO PathExtendIO (pe_io.hpp : 342) Writing contigs in FASTG to /N/dc2/projects/marinovg/Paramecium/others/2015-10-27-Pseudocohnilembus/Pseudocohnilembus_persalinus-PE+MP-dipSPAdes-3.5.0-trimmed/spades//K55/path_extend/mp_before_traversal.fastg 1:54:02.801 7G / 15G INFO PathExtendIO (pe_io.hpp : 343) Writing contigs in FASTA to /N/dc2/projects/marinovg/Paramecium/others/2015-10-27-Pseudocohnilembus/Pseudocohnilembus_persalinus-PE+MP-dipSPAdes-3.5.0-trimmed/spades//K55/path_extend/mp_before_traversal.fasta 1:54:43.525 7G / 15G INFO General (path_extend_launch.hpp : 281) Traversing tandem repeats 1:54:45.524 7G / 15G INFO PathExtendIO (pe_io.hpp : 339) Constructing FASTG file from paths 1:54:47.879 7G / 15G INFO PathExtendIO (pe_io.hpp : 342) Writing contigs in FASTG to /N/dc2/projects/marinovg/Paramecium/others/2015-10-27-Pseudocohnilembus/Pseudocohnilembus_persalinus-PE+MP-dipSPAdes-3.5.0-trimmed/spades//K55/final_contigs.fastg 1:54:47.879 7G / 15G INFO PathExtendIO (pe_io.hpp : 343) Writing contigs in FASTA to /N/dc2/projects/marinovg/Paramecium/others/2015-10-27-Pseudocohnilembus/Pseudocohnilembus_persalinus-PE+MP-dipSPAdes-3.5.0-trimmed/spades//K55/final_contigs.fasta 1:55:29.428 7G / 15G INFO PathExtendIO (pe_io.hpp : 339) Constructing FASTG file from paths 1:55:31.613 7G / 15G INFO PathExtendIO (pe_io.hpp : 342) Writing contigs in FASTG to /N/dc2/projects/marinovg/Paramecium/others/2015-10-27-Pseudocohnilembus/Pseudocohnilembus_persalinus-PE+MP-dipSPAdes-3.5.0-trimmed/spades//K55/scaffolds.fastg 1:55:31.613 7G / 15G INFO PathExtendIO (pe_io.hpp : 343) Writing contigs in FASTA to /N/dc2/projects/marinovg/Paramecium/others/2015-10-27-Pseudocohnilembus/Pseudocohnilembus_persalinus-PE+MP-dipSPAdes-3.5.0-trimmed/spades//K55/scaffolds.fasta 1:56:13.882 6G / 15G INFO General (path_extend_launch.hpp : 418) Path-Extend repeat resolving tool finished 1:56:16.528 6G / 15G INFO General (launch.hpp : 82) SPAdes finished 1:56:22.726 1G / 15G INFO General (main.cpp : 166) Assembling time: 1 hours 56 minutes 22 seconds ===== Assembling finished. * Corrected reads are in /N/dc2/projects/marinovg/Paramecium/others/2015-10-27-Pseudocohnilembus/Pseudocohnilembus_persalinus-PE+MP-dipSPAdes-3.5.0-trimmed/spades/corrected/ * Assembled contigs are in /N/dc2/projects/marinovg/Paramecium/others/2015-10-27-Pseudocohnilembus/Pseudocohnilembus_persalinus-PE+MP-dipSPAdes-3.5.0-trimmed/spades/contigs.fasta (contigs.fastg) * Assembled scaffolds are in /N/dc2/projects/marinovg/Paramecium/others/2015-10-27-Pseudocohnilembus/Pseudocohnilembus_persalinus-PE+MP-dipSPAdes-3.5.0-trimmed/spades/scaffolds.fasta (scaffolds.fastg) ======= SPAdes pipeline finished. SPAdes log can be found here: /N/dc2/projects/marinovg/Paramecium/others/2015-10-27-Pseudocohnilembus/Pseudocohnilembus_persalinus-PE+MP-dipSPAdes-3.5.0-trimmed/spades/spades.log Thank you for using SPAdes!