Command line: /oak/stanford/groups/akundaje/marinovg/programs/SPAdes-3.13.0-Linux/bin/spades.py --pe1-1 /srv/scratch/marinovg/L1152-L1147-Euplotes_sym_gDNA-reamp.191129_NB551514_0335_AHVFJGBGXC.read1.paired.fastq.gz --pe2-1 /srv/scratch/marinovg/L1152-L1147-Euplotes_sym_gDNA-reamp.191111_NB551514_0319_AHFY5NBGXC.read1.paired.fastq.gz --pe1-2 /srv/scratch/marinovg/L1152-L1147-Euplotes_sym_gDNA-reamp.191129_NB551514_0335_AHVFJGBGXC.read2.paired.fastq.gz --pe2-2 /srv/scratch/marinovg/L1152-L1147-Euplotes_sym_gDNA-reamp.191111_NB551514_0319_AHFY5NBGXC.read2.paired.fastq.gz --s1 /srv/scratch/marinovg/L1152-L1147-Euplotes_sym_gDNA-reamp.191129_NB551514_0335_AHVFJGBGXC.read1.unpaired.fastq.gz --s2 /srv/scratch/marinovg/L1152-L1147-Euplotes_sym_gDNA-reamp.191111_NB551514_0319_AHFY5NBGXC.read1.unpaired.fastq.gz --s3 /srv/scratch/marinovg/L1152-L1147-Euplotes_sym_gDNA-reamp.191111_NB551514_0319_AHFY5NBGXC.read2.unpaired.fastq.gz --s4 /srv/scratch/marinovg/L1152-L1147-Euplotes_sym_gDNA-reamp.191129_NB551514_0335_AHVFJGBGXC.read2.unpaired.fastq.gz -t 40 -o /srv/scratch/marinovg/SPAdes-3.13-L1152-L1147-Euplotes_sym_gDNA-reamp System information: SPAdes version: 3.13.0 Python version: 2.7.13 OS: Linux-4.4.0-161-generic-x86_64-with-debian-stretch-sid Output dir: /srv/scratch/marinovg/SPAdes-3.13-L1152-L1147-Euplotes_sym_gDNA-reamp 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 or --meta flag if processing metagenomic dataset) Reads: Library number: 1, library type: paired-end orientation: fr left reads: ['/srv/scratch/marinovg/L1152-L1147-Euplotes_sym_gDNA-reamp.191129_NB551514_0335_AHVFJGBGXC.read1.paired.fastq.gz'] right reads: ['/srv/scratch/marinovg/L1152-L1147-Euplotes_sym_gDNA-reamp.191129_NB551514_0335_AHVFJGBGXC.read2.paired.fastq.gz'] interlaced reads: not specified single reads: not specified merged reads: not specified Library number: 2, library type: paired-end orientation: fr left reads: ['/srv/scratch/marinovg/L1152-L1147-Euplotes_sym_gDNA-reamp.191111_NB551514_0319_AHFY5NBGXC.read1.paired.fastq.gz'] right reads: ['/srv/scratch/marinovg/L1152-L1147-Euplotes_sym_gDNA-reamp.191111_NB551514_0319_AHFY5NBGXC.read2.paired.fastq.gz'] interlaced reads: not specified single reads: not specified merged reads: not specified Library number: 3, library type: single left reads: not specified right reads: not specified interlaced reads: not specified single reads: ['/srv/scratch/marinovg/L1152-L1147-Euplotes_sym_gDNA-reamp.191129_NB551514_0335_AHVFJGBGXC.read1.unpaired.fastq.gz'] merged reads: not specified Library number: 4, library type: single left reads: not specified right reads: not specified interlaced reads: not specified single reads: ['/srv/scratch/marinovg/L1152-L1147-Euplotes_sym_gDNA-reamp.191111_NB551514_0319_AHFY5NBGXC.read1.unpaired.fastq.gz'] merged reads: not specified Library number: 5, library type: single left reads: not specified right reads: not specified interlaced reads: not specified single reads: ['/srv/scratch/marinovg/L1152-L1147-Euplotes_sym_gDNA-reamp.191111_NB551514_0319_AHFY5NBGXC.read2.unpaired.fastq.gz'] merged reads: not specified Library number: 6, library type: single left reads: not specified right reads: not specified interlaced reads: not specified single reads: ['/srv/scratch/marinovg/L1152-L1147-Euplotes_sym_gDNA-reamp.191129_NB551514_0335_AHVFJGBGXC.read2.unpaired.fastq.gz'] merged reads: not specified Read error correction parameters: Iterations: 1 PHRED offset will be auto-detected Corrected reads will be compressed Assembly parameters: k: automatic selection based on read length Repeat resolution is enabled Mismatch careful mode is turned OFF MismatchCorrector will be SKIPPED Coverage cutoff is turned OFF Other parameters: Dir for temp files: /srv/scratch/marinovg/SPAdes-3.13-L1152-L1147-Euplotes_sym_gDNA-reamp/tmp Threads: 40 Memory limit (in Gb): 250 ======= SPAdes pipeline started. Log can be found here: /srv/scratch/marinovg/SPAdes-3.13-L1152-L1147-Euplotes_sym_gDNA-reamp/spades.log ===== Read error correction started. == Running read error correction tool: /oak/stanford/groups/akundaje/marinovg/programs/SPAdes-3.13.0-Linux/bin/spades-hammer /srv/scratch/marinovg/SPAdes-3.13-L1152-L1147-Euplotes_sym_gDNA-reamp/corrected/configs/config.info 0:00:00.000 4M / 4M INFO General (main.cpp : 75) Starting BayesHammer, built from refs/heads/spades_3.13.0, git revision 8ea46659e9b2aca35444a808db550ac333006f8b 0:00:00.000 4M / 4M INFO General (main.cpp : 76) Loading config from /srv/scratch/marinovg/SPAdes-3.13-L1152-L1147-Euplotes_sym_gDNA-reamp/corrected/configs/config.info 0:00:00.001 4M / 4M INFO General (main.cpp : 78) Maximum # of threads to use (adjusted due to OMP capabilities): 40 0:00:00.001 4M / 4M INFO General (memory_limit.cpp : 49) Memory limit set to 250 Gb 0:00:00.001 4M / 4M INFO General (main.cpp : 86) Trying to determine PHRED offset 0:00:00.001 4M / 4M INFO General (main.cpp : 92) Determined value is 33 0:00:00.001 4M / 4M INFO General (hammer_tools.cpp : 36) Hamming graph threshold tau=1, k=21, subkmer positions = [ 0 10 ] 0:00:00.001 4M / 4M INFO General (main.cpp : 113) Size of aux. kmer data 24 bytes === ITERATION 0 begins === 0:00:00.001 4M / 4M INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:00:00.001 4M / 4M INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 640 files using 40 threads. This might take a while. 0:00:00.002 4M / 4M INFO General (file_limit.hpp : 32) Open file limit set to 1024 0:00:00.002 4M / 4M INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.0833 Gb 0:00:00.002 4M / 4M INFO General (kmer_splitters.hpp : 97) Using cell size of 104857 0:00:00.158 22G / 22G INFO K-mer Splitting (kmer_data.cpp : 97) Processing /srv/scratch/marinovg/L1152-L1147-Euplotes_sym_gDNA-reamp.191129_NB551514_0335_AHVFJGBGXC.read1.paired.fastq.gz 0:00:51.508 22G / 22G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 10607156 reads 0:00:51.508 22G / 22G INFO K-mer Splitting (kmer_data.cpp : 97) Processing /srv/scratch/marinovg/L1152-L1147-Euplotes_sym_gDNA-reamp.191129_NB551514_0335_AHVFJGBGXC.read2.paired.fastq.gz 0:01:42.290 22G / 22G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 21214312 reads 0:01:42.290 22G / 22G INFO K-mer Splitting (kmer_data.cpp : 97) Processing /srv/scratch/marinovg/L1152-L1147-Euplotes_sym_gDNA-reamp.191111_NB551514_0319_AHFY5NBGXC.read1.paired.fastq.gz 0:03:41.878 22G / 23G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 45656257 reads 0:03:58.326 22G / 23G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 48869941 reads 0:03:58.326 22G / 23G INFO K-mer Splitting (kmer_data.cpp : 97) Processing /srv/scratch/marinovg/L1152-L1147-Euplotes_sym_gDNA-reamp.191111_NB551514_0319_AHFY5NBGXC.read2.paired.fastq.gz 0:05:19.743 22G / 23G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 68646689 reads 0:05:47.139 22G / 23G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 76525570 reads 0:05:47.139 22G / 23G INFO K-mer Splitting (kmer_data.cpp : 97) Processing /srv/scratch/marinovg/L1152-L1147-Euplotes_sym_gDNA-reamp.191129_NB551514_0335_AHVFJGBGXC.read1.unpaired.fastq.gz 0:06:17.008 22G / 23G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 86608915 reads 0:06:17.008 22G / 23G INFO K-mer Splitting (kmer_data.cpp : 97) Processing /srv/scratch/marinovg/L1152-L1147-Euplotes_sym_gDNA-reamp.191111_NB551514_0319_AHFY5NBGXC.read1.unpaired.fastq.gz 0:07:12.793 22G / 23G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 104440453 reads 0:07:12.793 22G / 23G INFO K-mer Splitting (kmer_data.cpp : 97) Processing /srv/scratch/marinovg/L1152-L1147-Euplotes_sym_gDNA-reamp.191111_NB551514_0319_AHFY5NBGXC.read2.unpaired.fastq.gz 0:07:19.154 22G / 23G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 105961053 reads 0:07:19.154 22G / 23G INFO K-mer Splitting (kmer_data.cpp : 97) Processing /srv/scratch/marinovg/L1152-L1147-Euplotes_sym_gDNA-reamp.191129_NB551514_0335_AHVFJGBGXC.read2.unpaired.fastq.gz 0:07:19.546 22G / 23G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 106024885 reads 0:07:19.546 22G / 23G INFO K-mer Splitting (kmer_data.cpp : 112) Total 106024885 reads processed 0:07:21.622 160M / 23G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:07:37.568 160M / 23G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 2011963242 kmers in total. 0:07:37.568 160M / 23G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:07:50.467 160M / 23G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:09:04.763 1G / 23G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 0:09:49.042 1G / 23G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 932974748 bytes occupied (3.70971 bits per kmer). 0:09:49.810 1G / 23G INFO K-mer Counting (kmer_data.cpp : 356) Arranging kmers in hash map order 0:11:15.344 31G / 31G INFO General (main.cpp : 148) Clustering Hamming graph. 0:49:28.069 31G / 31G INFO General (main.cpp : 155) Extracting clusters 1:09:53.750 31G / 87G INFO General (main.cpp : 167) Clustering done. Total clusters: 1080788260 1:09:54.874 16G / 87G INFO K-mer Counting (kmer_data.cpp : 376) Collecting K-mer information, this takes a while. 1:10:19.104 61G / 87G INFO K-mer Counting (kmer_data.cpp : 382) Processing /srv/scratch/marinovg/L1152-L1147-Euplotes_sym_gDNA-reamp.191129_NB551514_0335_AHVFJGBGXC.read1.paired.fastq.gz 1:10:58.866 61G / 87G INFO K-mer Counting (kmer_data.cpp : 382) Processing /srv/scratch/marinovg/L1152-L1147-Euplotes_sym_gDNA-reamp.191129_NB551514_0335_AHVFJGBGXC.read2.paired.fastq.gz 1:11:36.025 61G / 87G INFO K-mer Counting (kmer_data.cpp : 382) Processing /srv/scratch/marinovg/L1152-L1147-Euplotes_sym_gDNA-reamp.191111_NB551514_0319_AHFY5NBGXC.read1.paired.fastq.gz 1:13:07.120 61G / 87G INFO K-mer Counting (kmer_data.cpp : 382) Processing /srv/scratch/marinovg/L1152-L1147-Euplotes_sym_gDNA-reamp.191111_NB551514_0319_AHFY5NBGXC.read2.paired.fastq.gz 1:14:37.497 61G / 87G INFO K-mer Counting (kmer_data.cpp : 382) Processing /srv/scratch/marinovg/L1152-L1147-Euplotes_sym_gDNA-reamp.191129_NB551514_0335_AHVFJGBGXC.read1.unpaired.fastq.gz 1:15:02.443 61G / 87G INFO K-mer Counting (kmer_data.cpp : 382) Processing /srv/scratch/marinovg/L1152-L1147-Euplotes_sym_gDNA-reamp.191111_NB551514_0319_AHFY5NBGXC.read1.unpaired.fastq.gz 1:15:47.227 61G / 87G INFO K-mer Counting (kmer_data.cpp : 382) Processing /srv/scratch/marinovg/L1152-L1147-Euplotes_sym_gDNA-reamp.191111_NB551514_0319_AHFY5NBGXC.read2.unpaired.fastq.gz 1:15:51.629 61G / 87G INFO K-mer Counting (kmer_data.cpp : 382) Processing /srv/scratch/marinovg/L1152-L1147-Euplotes_sym_gDNA-reamp.191129_NB551514_0335_AHVFJGBGXC.read2.unpaired.fastq.gz 1:15:52.335 61G / 87G INFO K-mer Counting (kmer_data.cpp : 389) Collection done, postprocessing. 1:16:06.733 61G / 87G INFO K-mer Counting (kmer_data.cpp : 403) There are 2011963242 kmers in total. Among them 1288443678 (64.0391%) are singletons. 1:16:06.733 61G / 87G INFO General (main.cpp : 173) Subclustering Hamming graph 2:21:12.462 61G / 87G INFO Hamming Subclustering (kmer_cluster.cpp : 649) Subclustering done. Total 77553 non-read kmers were generated. 2:21:12.462 61G / 87G INFO Hamming Subclustering (kmer_cluster.cpp : 650) Subclustering statistics: 2:21:12.462 61G / 87G INFO Hamming Subclustering (kmer_cluster.cpp : 651) Total singleton hamming clusters: 825379854. Among them 267734576 (32.4377%) are good 2:21:12.462 61G / 87G INFO Hamming Subclustering (kmer_cluster.cpp : 652) Total singleton subclusters: 6691245. Among them 6582928 (98.3812%) are good 2:21:12.462 61G / 87G INFO Hamming Subclustering (kmer_cluster.cpp : 653) Total non-singleton subcluster centers: 284787775. Among them 165391025 (58.0752%) are good 2:21:12.462 61G / 87G INFO Hamming Subclustering (kmer_cluster.cpp : 654) Average size of non-trivial subcluster: 4.16696 kmers 2:21:12.462 61G / 87G INFO Hamming Subclustering (kmer_cluster.cpp : 655) Average number of sub-clusters per non-singleton cluster: 1.14123 2:21:12.462 61G / 87G INFO Hamming Subclustering (kmer_cluster.cpp : 656) Total solid k-mers: 439708529 2:21:12.462 61G / 87G INFO Hamming Subclustering (kmer_cluster.cpp : 657) Substitution probabilities: [4,4]((0.907156,0.039563,0.0136607,0.03962),(0.021077,0.950554,0.0199358,0.00843275),(0.00779653,0.0190059,0.950787,0.0224111),(0.0374972,0.012828,0.0378756,0.911799)) 2:21:13.780 61G / 87G INFO General (main.cpp : 178) Finished clustering. 2:21:13.780 61G / 87G INFO General (main.cpp : 197) Starting solid k-mers expansion in 40 threads. 2:26:05.280 61G / 87G INFO General (main.cpp : 218) Solid k-mers iteration 0 produced 51054818 new k-mers. 2:30:41.283 61G / 87G INFO General (main.cpp : 218) Solid k-mers iteration 1 produced 1687039 new k-mers. 2:35:17.029 61G / 87G INFO General (main.cpp : 218) Solid k-mers iteration 2 produced 63256 new k-mers. 2:39:52.961 61G / 87G INFO General (main.cpp : 218) Solid k-mers iteration 3 produced 2753 new k-mers. 2:44:28.991 61G / 87G INFO General (main.cpp : 218) Solid k-mers iteration 4 produced 183 new k-mers. 2:49:05.259 61G / 87G INFO General (main.cpp : 218) Solid k-mers iteration 5 produced 18 new k-mers. 2:53:41.943 61G / 87G INFO General (main.cpp : 218) Solid k-mers iteration 6 produced 0 new k-mers. 2:53:41.943 61G / 87G INFO General (main.cpp : 222) Solid k-mers finalized 2:53:41.944 61G / 87G INFO General (hammer_tools.cpp : 220) Starting read correction in 40 threads. 2:53:41.944 61G / 87G INFO General (hammer_tools.cpp : 233) Correcting pair of reads: /srv/scratch/marinovg/L1152-L1147-Euplotes_sym_gDNA-reamp.191129_NB551514_0335_AHVFJGBGXC.read1.paired.fastq.gz and /srv/scratch/marinovg/L1152-L1147-Euplotes_sym_gDNA-reamp.191129_NB551514_0335_AHVFJGBGXC.read2.paired.fastq.gz 2:53:57.901 63G / 87G INFO General (hammer_tools.cpp : 168) Prepared batch 0 of 4000000 reads. 2:54:11.122 64G / 87G INFO General (hammer_tools.cpp : 175) Processed batch 0 2:54:15.924 64G / 87G INFO General (hammer_tools.cpp : 185) Written batch 0 2:54:31.757 64G / 87G INFO General (hammer_tools.cpp : 168) Prepared batch 1 of 4000000 reads. 2:54:46.255 64G / 87G INFO General (hammer_tools.cpp : 175) Processed batch 1 2:54:51.423 64G / 87G INFO General (hammer_tools.cpp : 185) Written batch 1 2:55:00.900 64G / 87G INFO General (hammer_tools.cpp : 168) Prepared batch 2 of 2607156 reads. 2:55:10.636 64G / 87G INFO General (hammer_tools.cpp : 175) Processed batch 2 2:55:18.473 64G / 87G INFO General (hammer_tools.cpp : 185) Written batch 2 2:55:21.389 61G / 87G INFO General (hammer_tools.cpp : 233) Correcting pair of reads: /srv/scratch/marinovg/L1152-L1147-Euplotes_sym_gDNA-reamp.191111_NB551514_0319_AHFY5NBGXC.read1.paired.fastq.gz and /srv/scratch/marinovg/L1152-L1147-Euplotes_sym_gDNA-reamp.191111_NB551514_0319_AHFY5NBGXC.read2.paired.fastq.gz 2:55:38.078 63G / 87G INFO General (hammer_tools.cpp : 168) Prepared batch 0 of 4000000 reads. 2:55:55.304 64G / 87G INFO General (hammer_tools.cpp : 175) Processed batch 0 2:56:00.523 64G / 87G INFO General (hammer_tools.cpp : 185) Written batch 0 2:56:17.025 65G / 87G INFO General (hammer_tools.cpp : 168) Prepared batch 1 of 4000000 reads. 2:56:35.513 65G / 87G INFO General (hammer_tools.cpp : 175) Processed batch 1 2:56:41.590 65G / 87G INFO General (hammer_tools.cpp : 185) Written batch 1 2:56:56.929 64G / 87G INFO General (hammer_tools.cpp : 168) Prepared batch 2 of 4000000 reads. 2:57:15.154 64G / 87G INFO General (hammer_tools.cpp : 175) Processed batch 2 2:57:21.320 64G / 87G INFO General (hammer_tools.cpp : 185) Written batch 2 2:57:36.391 65G / 87G INFO General (hammer_tools.cpp : 168) Prepared batch 3 of 4000000 reads. 2:57:54.584 65G / 87G INFO General (hammer_tools.cpp : 175) Processed batch 3 2:58:00.743 65G / 87G INFO General (hammer_tools.cpp : 185) Written batch 3 2:58:15.701 65G / 87G INFO General (hammer_tools.cpp : 168) Prepared batch 4 of 4000000 reads. 2:58:33.526 65G / 87G INFO General (hammer_tools.cpp : 175) Processed batch 4 2:58:39.413 65G / 87G INFO General (hammer_tools.cpp : 185) Written batch 4 2:58:54.391 65G / 87G INFO General (hammer_tools.cpp : 168) Prepared batch 5 of 4000000 reads. 2:59:12.000 65G / 87G INFO General (hammer_tools.cpp : 175) Processed batch 5 2:59:17.618 65G / 87G INFO General (hammer_tools.cpp : 185) Written batch 5 2:59:31.579 65G / 87G INFO General (hammer_tools.cpp : 168) Prepared batch 6 of 3655629 reads. 2:59:48.207 65G / 87G INFO General (hammer_tools.cpp : 175) Processed batch 6 2:59:56.213 65G / 87G INFO General (hammer_tools.cpp : 185) Written batch 6 3:00:00.353 61G / 87G INFO General (hammer_tools.cpp : 264) Correcting single reads: /srv/scratch/marinovg/L1152-L1147-Euplotes_sym_gDNA-reamp.191129_NB551514_0335_AHVFJGBGXC.read1.unpaired.fastq.gz 3:00:06.880 62G / 87G INFO General (hammer_tools.cpp : 127) Prepared batch 0 of 4000000 reads. 3:00:11.134 62G / 87G INFO General (hammer_tools.cpp : 132) Processed batch 0 3:00:13.642 62G / 87G INFO General (hammer_tools.cpp : 136) Written batch 0 3:00:20.266 63G / 87G INFO General (hammer_tools.cpp : 127) Prepared batch 1 of 4000000 reads. 3:00:25.337 63G / 87G INFO General (hammer_tools.cpp : 132) Processed batch 1 3:00:27.870 63G / 87G INFO General (hammer_tools.cpp : 136) Written batch 1 3:00:31.045 63G / 87G INFO General (hammer_tools.cpp : 127) Prepared batch 2 of 2083345 reads. 3:00:33.303 63G / 87G INFO General (hammer_tools.cpp : 132) Processed batch 2 3:00:34.668 63G / 87G INFO General (hammer_tools.cpp : 136) Written batch 2 3:00:36.675 61G / 87G INFO General (hammer_tools.cpp : 264) Correcting single reads: /srv/scratch/marinovg/L1152-L1147-Euplotes_sym_gDNA-reamp.191111_NB551514_0319_AHFY5NBGXC.read1.unpaired.fastq.gz 3:00:43.514 62G / 87G INFO General (hammer_tools.cpp : 127) Prepared batch 0 of 4000000 reads. 3:00:48.650 62G / 87G INFO General (hammer_tools.cpp : 132) Processed batch 0 3:00:50.957 62G / 87G INFO General (hammer_tools.cpp : 136) Written batch 0 3:00:57.733 63G / 87G INFO General (hammer_tools.cpp : 127) Prepared batch 1 of 4000000 reads. 3:01:03.966 63G / 87G INFO General (hammer_tools.cpp : 132) Processed batch 1 3:01:06.518 63G / 87G INFO General (hammer_tools.cpp : 136) Written batch 1 3:01:13.264 63G / 87G INFO General (hammer_tools.cpp : 127) Prepared batch 2 of 4000000 reads. 3:01:19.959 63G / 87G INFO General (hammer_tools.cpp : 132) Processed batch 2 3:01:26.679 63G / 87G INFO General (hammer_tools.cpp : 136) Written batch 2 3:01:33.187 63G / 87G INFO General (hammer_tools.cpp : 127) Prepared batch 3 of 4000000 reads. 3:01:39.406 63G / 87G INFO General (hammer_tools.cpp : 132) Processed batch 3 3:01:42.184 63G / 87G INFO General (hammer_tools.cpp : 136) Written batch 3 3:01:45.165 63G / 87G INFO General (hammer_tools.cpp : 127) Prepared batch 4 of 1831538 reads. 3:01:48.248 63G / 87G INFO General (hammer_tools.cpp : 132) Processed batch 4 3:01:49.701 63G / 87G INFO General (hammer_tools.cpp : 136) Written batch 4 3:01:52.059 61G / 87G INFO General (hammer_tools.cpp : 264) Correcting single reads: /srv/scratch/marinovg/L1152-L1147-Euplotes_sym_gDNA-reamp.191111_NB551514_0319_AHFY5NBGXC.read2.unpaired.fastq.gz 3:01:55.081 61G / 87G INFO General (hammer_tools.cpp : 127) Prepared batch 0 of 1520600 reads. 3:01:58.836 61G / 87G INFO General (hammer_tools.cpp : 132) Processed batch 0 3:01:59.976 61G / 87G INFO General (hammer_tools.cpp : 136) Written batch 0 3:02:00.422 61G / 87G INFO General (hammer_tools.cpp : 264) Correcting single reads: /srv/scratch/marinovg/L1152-L1147-Euplotes_sym_gDNA-reamp.191129_NB551514_0335_AHVFJGBGXC.read2.unpaired.fastq.gz 3:02:00.632 61G / 87G INFO General (hammer_tools.cpp : 127) Prepared batch 0 of 63832 reads. 3:02:00.864 61G / 87G INFO General (hammer_tools.cpp : 132) Processed batch 0 3:02:00.914 61G / 87G INFO General (hammer_tools.cpp : 136) Written batch 0 3:02:00.968 61G / 87G INFO General (hammer_tools.cpp : 274) Correction done. Changed 37744709 bases in 22461052 reads. 3:02:00.968 61G / 87G INFO General (hammer_tools.cpp : 275) Failed to correct 60216 bases out of 7182274488. 3:02:07.335 160M / 87G INFO General (main.cpp : 255) Saving corrected dataset description to /srv/scratch/marinovg/SPAdes-3.13-L1152-L1147-Euplotes_sym_gDNA-reamp/corrected/corrected.yaml 3:02:07.335 160M / 87G INFO General (main.cpp : 262) All done. Exiting. == Compressing corrected reads (with pigz) == Dataset description file was created: /srv/scratch/marinovg/SPAdes-3.13-L1152-L1147-Euplotes_sym_gDNA-reamp/corrected/corrected.yaml ===== Read error correction finished. ===== Assembling started. == Running assembler: K21 0:00:00.000 4M / 4M INFO General (main.cpp : 74) Loaded config from /srv/scratch/marinovg/SPAdes-3.13-L1152-L1147-Euplotes_sym_gDNA-reamp/K21/configs/config.info 0:00:00.000 4M / 4M INFO General (memory_limit.cpp : 49) Memory limit set to 250 Gb 0:00:00.000 4M / 4M INFO General (main.cpp : 87) Starting SPAdes, built from refs/heads/spades_3.13.0, git revision 8ea46659e9b2aca35444a808db550ac333006f8b 0:00:00.000 4M / 4M INFO General (main.cpp : 88) Maximum k-mer length: 128 0:00:00.000 4M / 4M INFO General (main.cpp : 89) Assembling dataset (/srv/scratch/marinovg/SPAdes-3.13-L1152-L1147-Euplotes_sym_gDNA-reamp/dataset.info) with K=21 0:00:00.000 4M / 4M INFO General (main.cpp : 90) Maximum # of threads to use (adjusted due to OMP capabilities): 40 0:00:00.000 4M / 4M INFO General (launch.hpp : 51) SPAdes started 0:00:00.000 4M / 4M INFO General (launch.hpp : 58) Starting from stage: construction 0:00:00.000 4M / 4M INFO General (launch.hpp : 65) Two-step RR enabled: 0 0:00:00.000 4M / 4M INFO StageManager (stage.cpp : 132) STAGE == de Bruijn graph construction 0:00:00.000 4M / 4M INFO General (read_converter.hpp : 77) Converting reads to binary format for library #0 (takes a while) 0:00:00.000 4M / 4M INFO General (read_converter.hpp : 78) Converting paired reads 0:00:00.154 76M / 76M INFO General (binary_converter.hpp : 93) 16384 reads processed 0:00:00.261 88M / 88M INFO General (binary_converter.hpp : 93) 32768 reads processed 0:00:00.547 108M / 108M INFO General (binary_converter.hpp : 93) 65536 reads processed 0:00:00.950 152M / 152M INFO General (binary_converter.hpp : 93) 131072 reads processed 0:00:01.760 232M / 232M INFO General (binary_converter.hpp : 93) 262144 reads processed 0:00:03.671 400M / 400M INFO General (binary_converter.hpp : 93) 524288 reads processed 0:00:08.916 656M / 656M INFO General (binary_converter.hpp : 93) 1048576 reads processed 0:00:17.363 660M / 660M INFO General (binary_converter.hpp : 93) 2097152 reads processed 0:00:34.324 660M / 660M INFO General (binary_converter.hpp : 93) 4194304 reads processed 0:01:10.160 660M / 660M INFO General (binary_converter.hpp : 93) 8388608 reads processed 0:01:29.932 360M / 660M INFO General (binary_converter.hpp : 117) 10551147 reads written 0:01:30.350 4M / 660M INFO General (read_converter.hpp : 87) Converting single reads 0:01:30.496 136M / 660M INFO General (binary_converter.hpp : 93) 16384 reads processed 0:01:30.548 140M / 660M INFO General (binary_converter.hpp : 93) 32768 reads processed 0:01:30.641 144M / 660M INFO General (binary_converter.hpp : 117) 42835 reads written 0:01:30.668 4M / 660M INFO General (read_converter.hpp : 95) Converting merged reads 0:01:30.773 132M / 660M INFO General (binary_converter.hpp : 117) 0 reads written 0:01:30.804 4M / 660M INFO General (read_converter.hpp : 77) Converting reads to binary format for library #1 (takes a while) 0:01:30.804 4M / 660M INFO General (read_converter.hpp : 78) Converting paired reads 0:01:30.959 80M / 660M INFO General (binary_converter.hpp : 93) 16384 reads processed 0:01:31.067 88M / 660M INFO General (binary_converter.hpp : 93) 32768 reads processed 0:01:31.281 108M / 660M INFO General (binary_converter.hpp : 93) 65536 reads processed 0:01:31.720 152M / 660M INFO General (binary_converter.hpp : 93) 131072 reads processed 0:01:32.597 232M / 660M INFO General (binary_converter.hpp : 93) 262144 reads processed 0:01:34.322 400M / 660M INFO General (binary_converter.hpp : 93) 524288 reads processed 0:01:39.446 660M / 660M INFO General (binary_converter.hpp : 93) 1048576 reads processed 0:01:47.921 660M / 660M INFO General (binary_converter.hpp : 93) 2097152 reads processed 0:02:05.281 660M / 660M INFO General (binary_converter.hpp : 93) 4194304 reads processed 0:02:43.318 664M / 664M INFO General (binary_converter.hpp : 93) 8388608 reads processed 0:03:59.094 668M / 668M INFO General (binary_converter.hpp : 93) 16777216 reads processed 0:05:28.785 624M / 668M INFO General (binary_converter.hpp : 117) 26328385 reads written 0:05:29.352 8M / 668M INFO General (read_converter.hpp : 87) Converting single reads 0:05:29.497 140M / 668M INFO General (binary_converter.hpp : 93) 16384 reads processed 0:05:29.548 144M / 668M INFO General (binary_converter.hpp : 93) 32768 reads processed 0:05:29.651 152M / 668M INFO General (binary_converter.hpp : 93) 65536 reads processed 0:05:29.856 172M / 668M INFO General (binary_converter.hpp : 93) 131072 reads processed 0:05:30.271 212M / 668M INFO General (binary_converter.hpp : 93) 262144 reads processed 0:05:31.096 292M / 668M INFO General (binary_converter.hpp : 93) 524288 reads processed 0:05:32.717 456M / 668M INFO General (binary_converter.hpp : 93) 1048576 reads processed 0:05:33.692 468M / 668M INFO General (binary_converter.hpp : 117) 1091836 reads written 0:05:34.293 8M / 668M INFO General (read_converter.hpp : 95) Converting merged reads 0:05:34.399 136M / 668M INFO General (binary_converter.hpp : 117) 0 reads written 0:05:34.431 8M / 668M INFO General (read_converter.hpp : 77) Converting reads to binary format for library #2 (takes a while) 0:05:34.431 8M / 668M INFO General (read_converter.hpp : 78) Converting paired reads 0:05:34.498 72M / 668M INFO General (binary_converter.hpp : 117) 0 reads written 0:05:34.503 8M / 668M INFO General (read_converter.hpp : 87) Converting single reads 0:05:34.639 140M / 668M INFO General (binary_converter.hpp : 93) 16384 reads processed 0:05:34.681 144M / 668M INFO General (binary_converter.hpp : 93) 32768 reads processed 0:05:34.766 152M / 668M INFO General (binary_converter.hpp : 93) 65536 reads processed 0:05:34.932 168M / 668M INFO General (binary_converter.hpp : 93) 131072 reads processed 0:05:35.256 204M / 668M INFO General (binary_converter.hpp : 93) 262144 reads processed 0:05:35.915 272M / 668M INFO General (binary_converter.hpp : 93) 524288 reads processed 0:05:37.241 412M / 668M INFO General (binary_converter.hpp : 93) 1048576 reads processed 0:05:39.892 688M / 688M INFO General (binary_converter.hpp : 93) 2097152 reads processed 0:05:48.013 1G / 1G INFO General (binary_converter.hpp : 93) 4194304 reads processed 0:06:01.381 1G / 1G INFO General (binary_converter.hpp : 93) 8388608 reads processed 0:06:07.730 564M / 1G INFO General (binary_converter.hpp : 117) 9933556 reads written 0:06:08.613 8M / 1G INFO General (read_converter.hpp : 95) Converting merged reads 0:06:08.716 136M / 1G INFO General (binary_converter.hpp : 117) 0 reads written 0:06:08.726 8M / 1G INFO General (read_converter.hpp : 77) Converting reads to binary format for library #3 (takes a while) 0:06:08.726 8M / 1G INFO General (read_converter.hpp : 78) Converting paired reads 0:06:08.778 72M / 1G INFO General (binary_converter.hpp : 117) 0 reads written 0:06:08.783 8M / 1G INFO General (read_converter.hpp : 87) Converting single reads 0:06:08.916 140M / 1G INFO General (binary_converter.hpp : 93) 16384 reads processed 0:06:08.961 144M / 1G INFO General (binary_converter.hpp : 93) 32768 reads processed 0:06:09.049 152M / 1G INFO General (binary_converter.hpp : 93) 65536 reads processed 0:06:09.224 172M / 1G INFO General (binary_converter.hpp : 93) 131072 reads processed 0:06:09.582 208M / 1G INFO General (binary_converter.hpp : 93) 262144 reads processed 0:06:10.298 280M / 1G INFO General (binary_converter.hpp : 93) 524288 reads processed 0:06:11.704 420M / 1G INFO General (binary_converter.hpp : 93) 1048576 reads processed 0:06:14.567 708M / 1G INFO General (binary_converter.hpp : 93) 2097152 reads processed 0:06:23.207 1G / 1G INFO General (binary_converter.hpp : 93) 4194304 reads processed 0:06:38.078 1G / 1G INFO General (binary_converter.hpp : 93) 8388608 reads processed 0:07:07.425 1G / 1G INFO General (binary_converter.hpp : 117) 16757217 reads written 0:07:10.173 8M / 1G INFO General (read_converter.hpp : 95) Converting merged reads 0:07:10.279 136M / 1G INFO General (binary_converter.hpp : 117) 0 reads written 0:07:10.289 8M / 1G INFO General (read_converter.hpp : 77) Converting reads to binary format for library #4 (takes a while) 0:07:10.289 8M / 1G INFO General (read_converter.hpp : 78) Converting paired reads 0:07:10.341 72M / 1G INFO General (binary_converter.hpp : 117) 0 reads written 0:07:10.346 8M / 1G INFO General (read_converter.hpp : 87) Converting single reads 0:07:10.490 140M / 1G INFO General (binary_converter.hpp : 93) 16384 reads processed 0:07:10.543 148M / 1G INFO General (binary_converter.hpp : 93) 32768 reads processed 0:07:10.647 156M / 1G INFO General (binary_converter.hpp : 93) 65536 reads processed 0:07:10.857 176M / 1G INFO General (binary_converter.hpp : 93) 131072 reads processed 0:07:11.257 216M / 1G INFO General (binary_converter.hpp : 93) 262144 reads processed 0:07:12.074 296M / 1G INFO General (binary_converter.hpp : 93) 524288 reads processed 0:07:13.655 460M / 1G INFO General (binary_converter.hpp : 93) 1048576 reads processed 0:07:14.995 508M / 1G INFO General (binary_converter.hpp : 117) 1204611 reads written 0:07:15.652 12M / 1G INFO General (read_converter.hpp : 95) Converting merged reads 0:07:15.756 140M / 1G INFO General (binary_converter.hpp : 117) 0 reads written 0:07:15.971 12M / 1G INFO General (read_converter.hpp : 77) Converting reads to binary format for library #5 (takes a while) 0:07:15.971 12M / 1G INFO General (read_converter.hpp : 78) Converting paired reads 0:07:16.061 76M / 1G INFO General (binary_converter.hpp : 117) 0 reads written 0:07:16.066 12M / 1G INFO General (read_converter.hpp : 87) Converting single reads 0:07:16.242 144M / 1G INFO General (binary_converter.hpp : 93) 16384 reads processed 0:07:16.305 148M / 1G INFO General (binary_converter.hpp : 93) 32768 reads processed 0:07:16.438 152M / 1G INFO General (binary_converter.hpp : 117) 52211 reads written 0:07:16.472 12M / 1G INFO General (read_converter.hpp : 95) Converting merged reads 0:07:16.595 140M / 1G INFO General (binary_converter.hpp : 117) 0 reads written 0:07:16.643 12M / 1G INFO General (construction.cpp : 111) Max read length 75 0:07:16.643 12M / 1G INFO General (construction.cpp : 117) Average read length 68.138 0:07:16.643 12M / 1G INFO General (stage.cpp : 101) PROCEDURE == k+1-mer counting 0:07:16.643 12M / 1G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 1600 files using 40 threads. This might take a while. 0:07:16.645 12M / 1G INFO General (file_limit.hpp : 32) Open file limit set to 1680 0:07:16.645 12M / 1G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.08324 Gb 0:07:16.645 12M / 1G INFO General (kmer_splitters.hpp : 97) Using cell size of 41943 0:07:28.373 22G / 22G INFO General (kmer_splitters.hpp : 289) Processed 62344329 reads 0:07:42.121 22G / 22G INFO General (kmer_splitters.hpp : 289) Processed 126684658 reads 0:07:55.237 22G / 22G INFO General (kmer_splitters.hpp : 289) Processed 205682014 reads 0:07:55.338 22G / 22G INFO General (kmer_splitters.hpp : 289) Processed 205682660 reads 0:07:55.338 22G / 22G INFO General (kmer_splitters.hpp : 295) Adding contigs from previous K 0:07:56.634 172M / 22G INFO General (kmer_splitters.hpp : 308) Used 205682660 reads 0:07:56.634 172M / 22G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:08:05.841 172M / 22G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 537725329 kmers in total. 0:08:05.841 172M / 22G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:08:09.605 168M / 22G INFO General (stage.cpp : 101) PROCEDURE == Extension index construction 0:08:09.605 168M / 22G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:08:09.605 168M / 22G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 640 files using 40 threads. This might take a while. 0:08:09.605 168M / 22G INFO General (file_limit.hpp : 32) Open file limit set to 1680 0:08:09.605 168M / 22G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.08197 Gb 0:08:09.605 168M / 22G INFO General (kmer_splitters.hpp : 97) Using cell size of 104857 0:08:16.465 22G / 22G INFO General (kmer_splitters.hpp : 380) Processed 215700773 kmers 0:08:22.929 22G / 22G INFO General (kmer_splitters.hpp : 380) Processed 431432169 kmers 0:08:26.387 22G / 22G INFO General (kmer_splitters.hpp : 380) Processed 537725409 kmers 0:08:26.387 22G / 22G INFO General (kmer_splitters.hpp : 385) Used 537725409 kmers. 0:08:26.879 168M / 22G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:08:35.878 168M / 22G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 538462422 kmers in total. 0:08:35.878 168M / 22G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:08:41.288 168M / 22G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:09:01.156 428M / 22G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 0:09:13.200 428M / 22G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 249693992 bytes occupied (3.70973 bits per kmer). 0:09:13.750 944M / 22G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 99) Building k-mer extensions from k+1-mers 0:09:30.249 944M / 22G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 103) Building k-mer extensions from k+1-mers finished. 0:09:30.252 944M / 22G INFO General (stage.cpp : 101) PROCEDURE == Early tip clipping 0:09:30.252 944M / 22G INFO General (construction.cpp : 253) Early tip clipper length bound set as (RL - K) 0:09:30.252 944M / 22G INFO Early tip clipping (early_simplification.hpp : 181) Early tip clipping 0:10:05.378 944M / 22G INFO Early tip clipping (early_simplification.hpp : 184) 97555738 22-mers were removed by early tip clipper 0:10:05.378 944M / 22G INFO General (stage.cpp : 101) PROCEDURE == Condensing graph 0:10:05.380 944M / 22G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 355) Extracting unbranching paths 0:10:26.931 1G / 22G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 374) Extracting unbranching paths finished. 12203156 sequences extracted 0:10:35.833 1G / 22G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 310) Collecting perfect loops 0:10:42.577 1G / 22G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 343) Collecting perfect loops finished. 995 loops collected 0:10:48.363 4G / 22G INFO General (stage.cpp : 101) PROCEDURE == Filling coverage indices (PHM) 0:10:48.363 4G / 22G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:10:48.363 4G / 22G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:10:58.312 4G / 22G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 249363664 bytes occupied (3.7099 bits per kmer). 0:10:59.506 6G / 22G INFO General (construction.cpp : 388) Collecting k-mer coverage information from reads, this takes a while. 0:12:08.028 6G / 22G INFO General (construction.cpp : 508) Filling coverage and flanking coverage from PHM 0:12:22.774 6G / 22G INFO General (construction.cpp : 464) Processed 24406575 edges 0:12:24.291 3G / 22G INFO StageManager (stage.cpp : 132) STAGE == EC Threshold Finding 0:12:24.355 3G / 22G INFO General (kmer_coverage_model.cpp : 181) Kmer coverage valley at: 164 0:12:24.358 3G / 22G INFO General (kmer_coverage_model.cpp : 201) K-mer histogram maximum: 166 0:12:24.358 3G / 22G INFO General (kmer_coverage_model.cpp : 237) Estimated median coverage: 167. Coverage mad: 2.9652 0:12:24.359 3G / 22G INFO General (kmer_coverage_model.cpp : 259) Fitting coverage model 0:12:24.554 3G / 22G INFO General (kmer_coverage_model.cpp : 295) ... iteration 2 0:12:25.027 3G / 22G INFO General (kmer_coverage_model.cpp : 295) ... iteration 4 0:12:26.075 3G / 22G INFO General (kmer_coverage_model.cpp : 295) ... iteration 8 0:12:27.934 3G / 22G INFO General (kmer_coverage_model.cpp : 295) ... iteration 16 0:12:30.872 3G / 22G INFO General (kmer_coverage_model.cpp : 295) ... iteration 32 0:12:36.193 3G / 22G INFO General (kmer_coverage_model.cpp : 295) ... iteration 64 0:12:42.226 3G / 22G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 145.639. Fitted coverage std. dev: 7.08595 0:12:42.226 3G / 22G WARN General (kmer_coverage_model.cpp : 327) Valley value was estimated improperly, reset to 76 0:12:42.229 3G / 22G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 1 0:12:42.229 3G / 22G WARN General (kmer_coverage_model.cpp : 366) Failed to determine erroneous kmer threshold. Threshold set to: 76 0:12:42.229 3G / 22G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 11007404 0:12:42.230 3G / 22G INFO General (genomic_info_filler.cpp : 114) Failed to estimate mean coverage 0:12:42.230 3G / 22G INFO General (genomic_info_filler.cpp : 127) EC coverage threshold value was calculated as 76 0:12:42.230 3G / 22G INFO General (genomic_info_filler.cpp : 128) Trusted kmer low bound: 0 0:12:42.230 3G / 22G INFO StageManager (stage.cpp : 132) STAGE == Raw Simplification 0:12:42.230 3G / 22G INFO General (simplification.cpp : 128) PROCEDURE == InitialCleaning 0:12:42.230 3G / 22G INFO General (simplification.cpp : 68) Most init cleaning disabled since detected mean 0 was less than activation coverage 10 0:12:42.230 3G / 22G INFO Simplification (parallel_processing.hpp : 165) Running Self conjugate edge remover 0:12:43.276 3G / 22G INFO Simplification (parallel_processing.hpp : 167) Self conjugate edge remover triggered 0 times 0:12:43.276 3G / 22G INFO StageManager (stage.cpp : 132) STAGE == Simplification 0:12:43.276 3G / 22G INFO General (simplification.cpp : 357) Graph simplification started 0:12:43.276 3G / 22G INFO General (graph_simplification.hpp : 634) Creating parallel br instance 0:12:43.276 3G / 22G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 1 0:12:43.276 3G / 22G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:12:58.686 3G / 22G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 1106300 times 0:12:58.686 3G / 22G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:15:04.289 4G / 22G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 837751 times 0:15:04.289 4G / 22G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:16:08.188 4G / 22G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 1431572 times 0:16:08.188 4G / 22G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 2 0:16:08.189 4G / 22G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:16:13.304 4G / 22G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 171475 times 0:16:13.304 4G / 22G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:16:16.898 4G / 22G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 28846 times 0:16:16.898 4G / 22G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:16:18.716 4G / 22G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 51841 times 0:16:18.716 4G / 22G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 3 0:16:18.716 4G / 22G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:16:18.793 4G / 22G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 1217 times 0:16:18.793 4G / 22G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:16:19.184 4G / 22G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 1605 times 0:16:19.184 4G / 22G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:16:19.733 4G / 22G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 17614 times 0:16:19.733 4G / 22G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 4 0:16:19.733 4G / 22G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:16:19.754 4G / 22G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 239 times 0:16:19.754 4G / 22G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:16:20.045 4G / 22G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 613 times 0:16:20.045 4G / 22G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:16:20.294 4G / 22G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 8367 times 0:16:20.294 4G / 22G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 5 0:16:20.294 4G / 22G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:16:20.303 4G / 22G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 93 times 0:16:20.303 4G / 22G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:16:20.413 4G / 22G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 230 times 0:16:20.413 4G / 22G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:16:20.573 4G / 22G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 5437 times 0:16:20.573 4G / 22G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 6 0:16:20.573 4G / 22G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:16:20.578 4G / 22G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 68 times 0:16:20.578 4G / 22G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:16:20.654 4G / 22G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 159 times 0:16:20.654 4G / 22G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:16:20.756 4G / 22G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 3485 times 0:16:20.756 4G / 22G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 7 0:16:20.756 4G / 22G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:16:20.759 4G / 22G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 52 times 0:16:20.760 4G / 22G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:16:20.791 4G / 22G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 65 times 0:16:20.791 4G / 22G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:16:20.854 4G / 22G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 2217 times 0:16:20.854 4G / 22G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 8 0:16:20.854 4G / 22G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:16:20.856 4G / 22G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 29 times 0:16:20.856 4G / 22G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:16:20.873 4G / 22G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 47 times 0:16:20.873 4G / 22G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:16:20.912 4G / 22G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 1388 times 0:16:20.912 4G / 22G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 9 0:16:20.912 4G / 22G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:16:20.913 4G / 22G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 19 times 0:16:20.913 4G / 22G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:16:20.930 4G / 22G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 34 times 0:16:20.931 4G / 22G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:16:20.956 4G / 22G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 1004 times 0:16:20.956 4G / 22G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 10 0:16:20.956 4G / 22G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:16:20.957 4G / 22G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 15 times 0:16:20.957 4G / 22G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:16:20.965 4G / 22G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 16 times 0:16:20.965 4G / 22G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:16:20.986 4G / 22G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 831 times 0:16:20.986 4G / 22G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 11 0:16:20.986 4G / 22G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:16:21.605 4G / 22G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 5161 times 0:16:21.605 4G / 22G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:16:22.074 4G / 22G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 62 times 0:16:22.074 4G / 22G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:16:22.504 4G / 22G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 2 times 0:16:22.504 4G / 22G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 12 0:16:22.504 4G / 22G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:16:22.504 4G / 22G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:16:22.504 4G / 22G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:16:22.504 4G / 22G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:16:22.504 4G / 22G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:16:22.504 4G / 22G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:16:22.504 4G / 22G INFO StageManager (stage.cpp : 132) STAGE == Simplification Cleanup 0:16:22.504 4G / 22G INFO General (simplification.cpp : 196) PROCEDURE == Post simplification 0:16:22.504 4G / 22G INFO General (graph_simplification.hpp : 453) Disconnection of relatively low covered edges disabled 0:16:22.504 4G / 22G INFO General (graph_simplification.hpp : 489) Complex tip clipping disabled 0:16:22.504 4G / 22G INFO General (graph_simplification.hpp : 634) Creating parallel br instance 0:16:22.504 4G / 22G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:16:23.109 4G / 22G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:16:23.110 4G / 22G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:16:23.681 4G / 22G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 1 times 0:16:23.681 4G / 22G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:16:24.170 4G / 22G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:16:24.171 4G / 22G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:16:24.735 4G / 22G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:16:24.735 4G / 22G INFO General (simplification.cpp : 330) Disrupting self-conjugate edges 0:16:29.274 4G / 22G INFO Simplification (parallel_processing.hpp : 165) Running Removing isolated edges 0:16:44.389 3G / 22G INFO Simplification (parallel_processing.hpp : 167) Removing isolated edges triggered 2977502 times 0:16:44.390 3G / 22G INFO General (simplification.cpp : 470) Counting average coverage 0:16:44.704 3G / 22G INFO General (simplification.cpp : 476) Average coverage = 23.7074 0:16:44.704 3G / 22G WARN General (simplification.cpp : 479) The determined erroneous connection coverage threshold may be determined improperly 0:16:44.704 3G / 22G INFO StageManager (stage.cpp : 132) STAGE == Contig Output 0:16:44.704 3G / 22G INFO General (contig_output_stage.cpp : 40) Writing GFA to /srv/scratch/marinovg/SPAdes-3.13-L1152-L1147-Euplotes_sym_gDNA-reamp//K21/assembly_graph_with_scaffolds.gfa 0:16:47.222 3G / 22G INFO General (contig_output.hpp : 22) Outputting contigs to /srv/scratch/marinovg/SPAdes-3.13-L1152-L1147-Euplotes_sym_gDNA-reamp//K21/before_rr.fasta 0:16:49.989 3G / 22G INFO General (contig_output_stage.cpp : 51) Outputting FastG graph to /srv/scratch/marinovg/SPAdes-3.13-L1152-L1147-Euplotes_sym_gDNA-reamp//K21/assembly_graph.fastg 0:16:59.047 3G / 22G INFO General (contig_output.hpp : 22) Outputting contigs to /srv/scratch/marinovg/SPAdes-3.13-L1152-L1147-Euplotes_sym_gDNA-reamp//K21/simplified_contigs.fasta 0:17:01.916 3G / 22G INFO General (contig_output.hpp : 22) Outputting contigs to /srv/scratch/marinovg/SPAdes-3.13-L1152-L1147-Euplotes_sym_gDNA-reamp//K21/final_contigs.fasta 0:17:04.690 3G / 22G INFO StageManager (stage.cpp : 132) STAGE == Contig Output 0:17:04.690 3G / 22G INFO General (contig_output_stage.cpp : 40) Writing GFA to /srv/scratch/marinovg/SPAdes-3.13-L1152-L1147-Euplotes_sym_gDNA-reamp//K21/assembly_graph_with_scaffolds.gfa 0:17:07.204 3G / 22G INFO General (contig_output.hpp : 22) Outputting contigs to /srv/scratch/marinovg/SPAdes-3.13-L1152-L1147-Euplotes_sym_gDNA-reamp//K21/before_rr.fasta 0:17:10.102 3G / 22G INFO General (contig_output_stage.cpp : 51) Outputting FastG graph to /srv/scratch/marinovg/SPAdes-3.13-L1152-L1147-Euplotes_sym_gDNA-reamp//K21/assembly_graph.fastg 0:17:19.032 3G / 22G INFO General (contig_output.hpp : 22) Outputting contigs to /srv/scratch/marinovg/SPAdes-3.13-L1152-L1147-Euplotes_sym_gDNA-reamp//K21/simplified_contigs.fasta 0:17:22.133 3G / 22G INFO General (contig_output.hpp : 22) Outputting contigs to /srv/scratch/marinovg/SPAdes-3.13-L1152-L1147-Euplotes_sym_gDNA-reamp//K21/final_contigs.fasta 0:17:25.689 3G / 22G INFO General (launch.hpp : 149) SPAdes finished 0:17:28.946 160M / 22G INFO General (main.cpp : 109) Assembling time: 0 hours 17 minutes 28 seconds Max read length detected as 75 == Running assembler: K33 0:00:00.000 4M / 4M INFO General (main.cpp : 74) Loaded config from /srv/scratch/marinovg/SPAdes-3.13-L1152-L1147-Euplotes_sym_gDNA-reamp/K33/configs/config.info 0:00:00.000 4M / 4M INFO General (memory_limit.cpp : 49) Memory limit set to 250 Gb 0:00:00.000 4M / 4M INFO General (main.cpp : 87) Starting SPAdes, built from refs/heads/spades_3.13.0, git revision 8ea46659e9b2aca35444a808db550ac333006f8b 0:00:00.000 4M / 4M INFO General (main.cpp : 88) Maximum k-mer length: 128 0:00:00.000 4M / 4M INFO General (main.cpp : 89) Assembling dataset (/srv/scratch/marinovg/SPAdes-3.13-L1152-L1147-Euplotes_sym_gDNA-reamp/dataset.info) with K=33 0:00:00.000 4M / 4M INFO General (main.cpp : 90) Maximum # of threads to use (adjusted due to OMP capabilities): 40 0:00:00.000 4M / 4M INFO General (launch.hpp : 51) SPAdes started 0:00:00.000 4M / 4M INFO General (launch.hpp : 58) Starting from stage: construction 0:00:00.000 4M / 4M INFO General (launch.hpp : 65) Two-step RR enabled: 0 0:00:00.000 4M / 4M INFO StageManager (stage.cpp : 132) STAGE == de Bruijn graph construction 0:00:00.000 4M / 4M INFO General (read_converter.hpp : 59) Binary reads detected 0:00:00.003 4M / 4M INFO General (read_converter.hpp : 59) Binary reads detected 0:00:00.005 4M / 4M INFO General (read_converter.hpp : 59) Binary reads detected 0:00:00.007 8M / 8M INFO General (read_converter.hpp : 59) Binary reads detected 0:00:00.009 8M / 8M INFO General (read_converter.hpp : 59) Binary reads detected 0:00:00.011 8M / 8M INFO General (read_converter.hpp : 59) Binary reads detected 0:00:00.013 8M / 8M INFO General (construction.cpp : 111) Max read length 75 0:00:00.013 8M / 8M INFO General (construction.cpp : 117) Average read length 68.138 0:00:00.013 8M / 8M INFO General (stage.cpp : 101) PROCEDURE == k+1-mer counting 0:00:00.013 8M / 8M INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 1600 files using 40 threads. This might take a while. 0:00:00.014 12M / 12M INFO General (file_limit.hpp : 32) Open file limit set to 1680 0:00:00.014 12M / 12M INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.08324 Gb 0:00:00.014 12M / 12M INFO General (kmer_splitters.hpp : 97) Using cell size of 20971 0:00:09.076 22G / 22G INFO General (kmer_splitters.hpp : 289) Processed 40949996 reads 0:00:18.710 22G / 22G INFO General (kmer_splitters.hpp : 289) Processed 82974494 reads 0:00:26.971 22G / 22G INFO General (kmer_splitters.hpp : 289) Processed 126077476 reads 0:00:37.905 22G / 22G INFO General (kmer_splitters.hpp : 289) Processed 203058981 reads 0:00:42.114 22G / 22G INFO General (kmer_splitters.hpp : 289) Processed 205682660 reads 0:00:42.114 22G / 22G INFO General (kmer_splitters.hpp : 295) Adding contigs from previous K 0:01:11.645 172M / 22G INFO General (kmer_splitters.hpp : 308) Used 205682660 reads 0:01:11.645 172M / 22G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:01:21.909 172M / 22G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 495859652 kmers in total. 0:01:21.909 172M / 22G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:01:28.243 164M / 22G INFO General (stage.cpp : 101) PROCEDURE == Extension index construction 0:01:28.243 164M / 22G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:01:28.243 164M / 22G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 640 files using 40 threads. This might take a while. 0:01:28.243 164M / 22G INFO General (file_limit.hpp : 32) Open file limit set to 1680 0:01:28.243 164M / 22G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.082 Gb 0:01:28.243 164M / 22G INFO General (kmer_splitters.hpp : 97) Using cell size of 52428 0:01:32.933 22G / 22G INFO General (kmer_splitters.hpp : 380) Processed 101338723 kmers 0:01:37.305 22G / 22G INFO General (kmer_splitters.hpp : 380) Processed 202713624 kmers 0:01:41.774 22G / 22G INFO General (kmer_splitters.hpp : 380) Processed 304307353 kmers 0:01:46.069 22G / 22G INFO General (kmer_splitters.hpp : 380) Processed 406341620 kmers 0:01:50.153 22G / 22G INFO General (kmer_splitters.hpp : 380) Processed 495859812 kmers 0:01:50.153 22G / 22G INFO General (kmer_splitters.hpp : 385) Used 495859812 kmers. 0:01:50.688 168M / 22G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:01:57.495 168M / 22G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 500721940 kmers in total. 0:01:57.495 168M / 22G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:02:06.883 168M / 22G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:02:26.300 364M / 22G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 0:02:49.347 364M / 22G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 232193784 bytes occupied (3.70974 bits per kmer). 0:02:49.838 844M / 22G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 99) Building k-mer extensions from k+1-mers 0:03:06.416 844M / 22G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 103) Building k-mer extensions from k+1-mers finished. 0:03:06.419 840M / 22G INFO General (stage.cpp : 101) PROCEDURE == Early tip clipping 0:03:06.419 840M / 22G INFO General (construction.cpp : 253) Early tip clipper length bound set as (RL - K) 0:03:06.419 840M / 22G INFO Early tip clipping (early_simplification.hpp : 181) Early tip clipping 0:03:38.189 840M / 22G INFO Early tip clipping (early_simplification.hpp : 184) 77234724 34-mers were removed by early tip clipper 0:03:38.189 840M / 22G INFO General (stage.cpp : 101) PROCEDURE == Condensing graph 0:03:38.190 840M / 22G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 355) Extracting unbranching paths 0:03:59.218 1G / 22G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 374) Extracting unbranching paths finished. 8693025 sequences extracted 0:04:08.481 1G / 22G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 310) Collecting perfect loops 0:04:14.915 1G / 22G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 343) Collecting perfect loops finished. 1079 loops collected 0:04:20.117 3G / 22G INFO General (stage.cpp : 101) PROCEDURE == Filling coverage indices (PHM) 0:04:20.117 3G / 22G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:04:20.117 3G / 22G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:04:28.976 4G / 22G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 229971724 bytes occupied (3.71027 bits per kmer). 0:04:30.126 6G / 22G INFO General (construction.cpp : 388) Collecting k-mer coverage information from reads, this takes a while. 0:05:24.004 6G / 22G INFO General (construction.cpp : 508) Filling coverage and flanking coverage from PHM 0:05:38.336 6G / 22G INFO General (construction.cpp : 464) Processed 17387877 edges 0:05:40.163 3G / 22G INFO StageManager (stage.cpp : 132) STAGE == EC Threshold Finding 0:05:40.207 3G / 22G INFO General (kmer_coverage_model.cpp : 181) Kmer coverage valley at: 218 0:05:40.209 3G / 22G INFO General (kmer_coverage_model.cpp : 201) K-mer histogram maximum: 219 0:05:40.209 3G / 22G WARN General (kmer_coverage_model.cpp : 218) Too many erroneous kmers, the estimates might be unreliable 0:05:40.209 3G / 22G INFO General (kmer_coverage_model.cpp : 237) Estimated median coverage: 219. Coverage mad: 49.0604 0:05:40.210 3G / 22G INFO General (kmer_coverage_model.cpp : 259) Fitting coverage model 0:05:40.354 3G / 22G INFO General (kmer_coverage_model.cpp : 295) ... iteration 2 0:05:40.705 3G / 22G INFO General (kmer_coverage_model.cpp : 295) ... iteration 4 0:05:41.372 3G / 22G INFO General (kmer_coverage_model.cpp : 295) ... iteration 8 0:05:42.643 3G / 22G INFO General (kmer_coverage_model.cpp : 295) ... iteration 16 0:05:45.168 3G / 22G INFO General (kmer_coverage_model.cpp : 295) ... iteration 32 0:05:51.263 3G / 22G INFO General (kmer_coverage_model.cpp : 295) ... iteration 64 0:06:03.238 3G / 22G INFO General (kmer_coverage_model.cpp : 295) ... iteration 128 0:06:04.309 3G / 22G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 28.583. Fitted coverage std. dev: 12.5287 0:06:04.309 3G / 22G WARN General (kmer_coverage_model.cpp : 327) Valley value was estimated improperly, reset to 6 0:06:04.312 3G / 22G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 1 0:06:04.312 3G / 22G WARN General (kmer_coverage_model.cpp : 366) Failed to determine erroneous kmer threshold. Threshold set to: 6 0:06:04.312 3G / 22G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 117891274 0:06:04.313 3G / 22G INFO General (genomic_info_filler.cpp : 114) Failed to estimate mean coverage 0:06:04.313 3G / 22G INFO General (genomic_info_filler.cpp : 127) EC coverage threshold value was calculated as 6 0:06:04.313 3G / 22G INFO General (genomic_info_filler.cpp : 128) Trusted kmer low bound: 0 0:06:04.313 3G / 22G INFO StageManager (stage.cpp : 132) STAGE == Raw Simplification 0:06:04.313 3G / 22G INFO General (simplification.cpp : 128) PROCEDURE == InitialCleaning 0:06:04.313 3G / 22G INFO General (simplification.cpp : 68) Most init cleaning disabled since detected mean 0 was less than activation coverage 10 0:06:04.313 3G / 22G INFO Simplification (parallel_processing.hpp : 165) Running Self conjugate edge remover 0:06:05.341 3G / 22G INFO Simplification (parallel_processing.hpp : 167) Self conjugate edge remover triggered 74 times 0:06:05.341 3G / 22G INFO StageManager (stage.cpp : 132) STAGE == Simplification 0:06:05.341 3G / 22G INFO General (simplification.cpp : 357) Graph simplification started 0:06:05.341 3G / 22G INFO General (graph_simplification.hpp : 634) Creating parallel br instance 0:06:05.341 3G / 22G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 1 0:06:05.341 3G / 22G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:06:19.310 3G / 22G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 834113 times 0:06:19.310 3G / 22G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:06:44.092 3G / 22G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 350713 times 0:06:44.092 3G / 22G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:06:45.354 3G / 22G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 10500 times 0:06:45.354 3G / 22G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 2 0:06:45.354 3G / 22G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:06:45.712 3G / 22G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 9024 times 0:06:45.712 3G / 22G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:06:45.840 3G / 22G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 1533 times 0:06:45.840 3G / 22G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:06:48.184 3G / 22G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 66958 times 0:06:48.184 3G / 22G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 3 0:06:48.184 3G / 22G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:06:48.714 3G / 22G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 20642 times 0:06:48.714 3G / 22G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:06:51.584 3G / 22G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 28562 times 0:06:51.584 3G / 22G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:06:52.392 3G / 22G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 14774 times 0:06:52.392 3G / 22G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 4 0:06:52.392 3G / 22G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:06:52.497 3G / 22G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 2670 times 0:06:52.497 3G / 22G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:06:53.183 3G / 22G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 5179 times 0:06:53.183 3G / 22G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:06:53.865 3G / 22G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 15958 times 0:06:53.865 3G / 22G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 5 0:06:53.865 3G / 22G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:06:53.934 3G / 22G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 2708 times 0:06:53.934 3G / 22G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:06:54.602 3G / 22G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 5114 times 0:06:54.602 3G / 22G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:06:54.876 3G / 22G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 6223 times 0:06:54.876 3G / 22G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 6 0:06:54.876 3G / 22G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:06:54.905 3G / 22G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 920 times 0:06:54.905 3G / 22G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:06:55.241 3G / 22G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 1839 times 0:06:55.241 3G / 22G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:06:55.356 3G / 22G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 2942 times 0:06:55.356 3G / 22G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 7 0:06:55.357 3G / 22G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:06:55.366 3G / 22G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 289 times 0:06:55.366 3G / 22G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:06:55.533 3G / 22G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 686 times 0:06:55.533 3G / 22G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:06:55.644 3G / 22G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 3002 times 0:06:55.644 3G / 22G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 8 0:06:55.644 3G / 22G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:06:55.651 3G / 22G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 253 times 0:06:55.651 3G / 22G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:06:55.766 3G / 22G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 598 times 0:06:55.766 3G / 22G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:06:55.825 3G / 22G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 1727 times 0:06:55.825 3G / 22G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 9 0:06:55.825 3G / 22G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:06:55.829 3G / 22G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 121 times 0:06:55.829 3G / 22G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:06:55.906 3G / 22G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 292 times 0:06:55.906 3G / 22G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:06:55.963 3G / 22G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 1671 times 0:06:55.963 3G / 22G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 10 0:06:55.963 3G / 22G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:06:55.966 3G / 22G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 104 times 0:06:55.966 3G / 22G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:06:56.012 3G / 22G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 193 times 0:06:56.012 3G / 22G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:06:56.056 3G / 22G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 1318 times 0:06:56.056 3G / 22G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 11 0:06:56.056 3G / 22G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:06:56.841 3G / 22G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 1582 times 0:06:56.841 3G / 22G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:06:57.741 3G / 22G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 407 times 0:06:57.742 3G / 22G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:06:58.416 3G / 22G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 7 times 0:06:58.417 3G / 22G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 12 0:06:58.417 3G / 22G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:06:58.417 3G / 22G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:06:58.417 3G / 22G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:06:58.418 3G / 22G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 4 times 0:06:58.418 3G / 22G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:06:58.418 3G / 22G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:06:58.418 3G / 22G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 13 0:06:58.418 3G / 22G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:06:58.418 3G / 22G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:06:58.418 3G / 22G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:06:58.418 3G / 22G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:06:58.418 3G / 22G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:06:58.418 3G / 22G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:06:58.418 3G / 22G INFO StageManager (stage.cpp : 132) STAGE == Simplification Cleanup 0:06:58.418 3G / 22G INFO General (simplification.cpp : 196) PROCEDURE == Post simplification 0:06:58.418 3G / 22G INFO General (graph_simplification.hpp : 453) Disconnection of relatively low covered edges disabled 0:06:58.418 3G / 22G INFO General (graph_simplification.hpp : 489) Complex tip clipping disabled 0:06:58.418 3G / 22G INFO General (graph_simplification.hpp : 634) Creating parallel br instance 0:06:58.418 3G / 22G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:06:59.098 3G / 22G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 1 times 0:06:59.098 3G / 22G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:06:59.843 3G / 22G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 2 times 0:06:59.843 3G / 22G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:07:00.496 3G / 22G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:07:00.496 3G / 22G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:07:01.252 3G / 22G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:07:01.252 3G / 22G INFO General (simplification.cpp : 330) Disrupting self-conjugate edges 0:07:09.525 3G / 22G INFO Simplification (parallel_processing.hpp : 165) Running Removing isolated edges 0:07:36.969 2G / 22G INFO Simplification (parallel_processing.hpp : 167) Removing isolated edges triggered 5159066 times 0:07:36.970 2G / 22G INFO General (simplification.cpp : 470) Counting average coverage 0:07:37.239 2G / 22G INFO General (simplification.cpp : 476) Average coverage = 17.3919 0:07:37.239 2G / 22G INFO StageManager (stage.cpp : 132) STAGE == Contig Output 0:07:37.239 2G / 22G INFO General (contig_output_stage.cpp : 40) Writing GFA to /srv/scratch/marinovg/SPAdes-3.13-L1152-L1147-Euplotes_sym_gDNA-reamp//K33/assembly_graph_with_scaffolds.gfa 0:07:39.708 2G / 22G INFO General (contig_output.hpp : 22) Outputting contigs to /srv/scratch/marinovg/SPAdes-3.13-L1152-L1147-Euplotes_sym_gDNA-reamp//K33/before_rr.fasta 0:07:42.405 2G / 22G INFO General (contig_output_stage.cpp : 51) Outputting FastG graph to /srv/scratch/marinovg/SPAdes-3.13-L1152-L1147-Euplotes_sym_gDNA-reamp//K33/assembly_graph.fastg 0:07:50.795 2G / 22G INFO General (contig_output.hpp : 22) Outputting contigs to /srv/scratch/marinovg/SPAdes-3.13-L1152-L1147-Euplotes_sym_gDNA-reamp//K33/simplified_contigs.fasta 0:07:53.395 2G / 22G INFO General (contig_output.hpp : 22) Outputting contigs to /srv/scratch/marinovg/SPAdes-3.13-L1152-L1147-Euplotes_sym_gDNA-reamp//K33/final_contigs.fasta 0:07:55.945 2G / 22G INFO StageManager (stage.cpp : 132) STAGE == Contig Output 0:07:55.945 2G / 22G INFO General (contig_output_stage.cpp : 40) Writing GFA to /srv/scratch/marinovg/SPAdes-3.13-L1152-L1147-Euplotes_sym_gDNA-reamp//K33/assembly_graph_with_scaffolds.gfa 0:07:58.574 2G / 22G INFO General (contig_output.hpp : 22) Outputting contigs to /srv/scratch/marinovg/SPAdes-3.13-L1152-L1147-Euplotes_sym_gDNA-reamp//K33/before_rr.fasta 0:08:01.333 2G / 22G INFO General (contig_output_stage.cpp : 51) Outputting FastG graph to /srv/scratch/marinovg/SPAdes-3.13-L1152-L1147-Euplotes_sym_gDNA-reamp//K33/assembly_graph.fastg 0:08:10.904 2G / 22G INFO General (contig_output.hpp : 22) Outputting contigs to /srv/scratch/marinovg/SPAdes-3.13-L1152-L1147-Euplotes_sym_gDNA-reamp//K33/simplified_contigs.fasta 0:08:13.958 2G / 22G INFO General (contig_output.hpp : 22) Outputting contigs to /srv/scratch/marinovg/SPAdes-3.13-L1152-L1147-Euplotes_sym_gDNA-reamp//K33/final_contigs.fasta 0:08:16.955 2G / 22G INFO General (launch.hpp : 149) SPAdes finished 0:08:19.610 160M / 22G INFO General (main.cpp : 109) Assembling time: 0 hours 8 minutes 19 seconds == Running assembler: K55 0:00:00.000 4M / 4M INFO General (main.cpp : 74) Loaded config from /srv/scratch/marinovg/SPAdes-3.13-L1152-L1147-Euplotes_sym_gDNA-reamp/K55/configs/config.info 0:00:00.000 4M / 4M INFO General (memory_limit.cpp : 49) Memory limit set to 250 Gb 0:00:00.000 4M / 4M INFO General (main.cpp : 87) Starting SPAdes, built from refs/heads/spades_3.13.0, git revision 8ea46659e9b2aca35444a808db550ac333006f8b 0:00:00.000 4M / 4M INFO General (main.cpp : 88) Maximum k-mer length: 128 0:00:00.000 4M / 4M INFO General (main.cpp : 89) Assembling dataset (/srv/scratch/marinovg/SPAdes-3.13-L1152-L1147-Euplotes_sym_gDNA-reamp/dataset.info) with K=55 0:00:00.000 4M / 4M INFO General (main.cpp : 90) Maximum # of threads to use (adjusted due to OMP capabilities): 40 0:00:00.000 4M / 4M INFO General (launch.hpp : 51) SPAdes started 0:00:00.000 4M / 4M INFO General (launch.hpp : 58) Starting from stage: construction 0:00:00.000 4M / 4M INFO General (launch.hpp : 65) Two-step RR enabled: 0 0:00:00.000 4M / 4M INFO General (launch.hpp : 76) Will need read mapping, kmer mapper will be attached 0:00:00.000 4M / 4M INFO StageManager (stage.cpp : 132) STAGE == de Bruijn graph construction 0:00:00.000 4M / 4M INFO General (read_converter.hpp : 59) Binary reads detected 0:00:00.002 4M / 4M INFO General (read_converter.hpp : 59) Binary reads detected 0:00:00.004 4M / 4M INFO General (read_converter.hpp : 59) Binary reads detected 0:00:00.006 8M / 8M INFO General (read_converter.hpp : 59) Binary reads detected 0:00:00.008 8M / 8M INFO General (read_converter.hpp : 59) Binary reads detected 0:00:00.009 8M / 8M INFO General (read_converter.hpp : 59) Binary reads detected 0:00:00.011 8M / 8M INFO General (construction.cpp : 111) Max read length 75 0:00:00.011 8M / 8M INFO General (construction.cpp : 117) Average read length 68.138 0:00:00.011 8M / 8M INFO General (stage.cpp : 101) PROCEDURE == k+1-mer counting 0:00:00.011 8M / 8M INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 1600 files using 40 threads. This might take a while. 0:00:00.012 12M / 12M INFO General (file_limit.hpp : 32) Open file limit set to 1680 0:00:00.012 12M / 12M INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.08324 Gb 0:00:00.012 12M / 12M INFO General (kmer_splitters.hpp : 97) Using cell size of 20971 0:00:10.869 22G / 22G INFO General (kmer_splitters.hpp : 289) Processed 93709380 reads 0:00:19.271 22G / 22G INFO General (kmer_splitters.hpp : 289) Processed 205682660 reads 0:00:19.271 22G / 22G INFO General (kmer_splitters.hpp : 295) Adding contigs from previous K 0:00:51.559 172M / 22G INFO General (kmer_splitters.hpp : 308) Used 205682660 reads 0:00:51.559 172M / 22G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:00:55.944 172M / 22G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 353598631 kmers in total. 0:00:55.944 172M / 22G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:01:00.322 164M / 22G INFO General (stage.cpp : 101) PROCEDURE == Extension index construction 0:01:00.322 164M / 22G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:01:00.322 164M / 22G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 640 files using 40 threads. This might take a while. 0:01:00.322 168M / 22G INFO General (file_limit.hpp : 32) Open file limit set to 1680 0:01:00.323 168M / 22G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.08197 Gb 0:01:00.323 168M / 22G INFO General (kmer_splitters.hpp : 97) Using cell size of 52428 0:01:03.894 22G / 22G INFO General (kmer_splitters.hpp : 380) Processed 77781501 kmers 0:01:07.390 22G / 22G INFO General (kmer_splitters.hpp : 380) Processed 157308045 kmers 0:01:10.797 22G / 22G INFO General (kmer_splitters.hpp : 380) Processed 236877552 kmers 0:01:14.423 22G / 22G INFO General (kmer_splitters.hpp : 380) Processed 316433341 kmers 0:01:16.181 22G / 22G INFO General (kmer_splitters.hpp : 380) Processed 353598791 kmers 0:01:16.181 22G / 22G INFO General (kmer_splitters.hpp : 385) Used 353598791 kmers. 0:01:16.520 168M / 22G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:01:19.843 168M / 22G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 360631943 kmers in total. 0:01:19.843 168M / 22G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:01:24.315 168M / 22G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:01:36.521 360M / 22G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 0:01:52.530 360M / 22G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 167233664 bytes occupied (3.70979 bits per kmer). 0:01:52.865 704M / 22G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 99) Building k-mer extensions from k+1-mers 0:02:04.050 704M / 22G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 103) Building k-mer extensions from k+1-mers finished. 0:02:04.052 704M / 22G INFO General (stage.cpp : 101) PROCEDURE == Condensing graph 0:02:04.101 704M / 22G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 355) Extracting unbranching paths 0:02:21.392 2G / 22G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 374) Extracting unbranching paths finished. 25449647 sequences extracted 0:02:30.566 2G / 22G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 310) Collecting perfect loops 0:02:34.735 2G / 22G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 343) Collecting perfect loops finished. 72 loops collected 0:02:47.023 9G / 22G INFO General (stage.cpp : 101) PROCEDURE == Filling coverage indices (PHM) 0:02:47.023 9G / 22G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:02:47.023 9G / 22G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:02:52.639 9G / 22G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 163992204 bytes occupied (3.71025 bits per kmer). 0:02:53.476 10G / 22G INFO General (construction.cpp : 388) Collecting k-mer coverage information from reads, this takes a while. 0:03:17.698 10G / 22G INFO General (construction.cpp : 508) Filling coverage and flanking coverage from PHM 0:03:28.648 10G / 22G INFO General (construction.cpp : 464) Processed 40000000 edges 0:03:31.646 10G / 22G INFO General (construction.cpp : 464) Processed 50899417 edges 0:03:33.137 8G / 22G INFO StageManager (stage.cpp : 132) STAGE == EC Threshold Finding 0:03:33.152 8G / 22G INFO General (kmer_coverage_model.cpp : 181) Kmer coverage valley at: 177 0:03:33.152 8G / 22G INFO General (kmer_coverage_model.cpp : 201) K-mer histogram maximum: 178 0:03:33.152 8G / 22G WARN General (kmer_coverage_model.cpp : 218) Too many erroneous kmers, the estimates might be unreliable 0:03:33.152 8G / 22G INFO General (kmer_coverage_model.cpp : 237) Estimated median coverage: 178. Coverage mad: 44.2302 0:03:33.153 8G / 22G INFO General (kmer_coverage_model.cpp : 259) Fitting coverage model 0:03:33.209 8G / 22G INFO General (kmer_coverage_model.cpp : 295) ... iteration 2 0:03:33.330 8G / 22G INFO General (kmer_coverage_model.cpp : 295) ... iteration 4 0:03:33.631 8G / 22G INFO General (kmer_coverage_model.cpp : 295) ... iteration 8 0:03:34.266 8G / 22G INFO General (kmer_coverage_model.cpp : 295) ... iteration 16 0:03:35.706 8G / 22G INFO General (kmer_coverage_model.cpp : 295) ... iteration 32 0:03:39.437 8G / 22G INFO General (kmer_coverage_model.cpp : 295) ... iteration 64 0:03:44.672 8G / 22G INFO General (kmer_coverage_model.cpp : 295) ... iteration 128 0:03:56.887 8G / 22G INFO General (kmer_coverage_model.cpp : 295) ... iteration 256 0:04:04.525 8G / 22G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 13.5589. Fitted coverage std. dev: 5.03161 0:04:04.525 8G / 22G WARN General (kmer_coverage_model.cpp : 327) Valley value was estimated improperly, reset to 7 0:04:04.529 8G / 22G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 0.93792 0:04:04.529 8G / 22G WARN General (kmer_coverage_model.cpp : 366) Failed to determine erroneous kmer threshold. Threshold set to: 7 0:04:04.529 8G / 22G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 50394963 0:04:04.530 8G / 22G INFO General (genomic_info_filler.cpp : 114) Failed to estimate mean coverage 0:04:04.530 8G / 22G INFO General (genomic_info_filler.cpp : 127) EC coverage threshold value was calculated as 7 0:04:04.530 8G / 22G INFO General (genomic_info_filler.cpp : 128) Trusted kmer low bound: 0 0:04:04.530 8G / 22G INFO StageManager (stage.cpp : 132) STAGE == Gap Closer 0:04:04.530 8G / 22G INFO General (graph_pack.hpp : 101) Index refill 0:04:04.530 8G / 22G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:04:04.530 8G / 22G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 640 files using 40 threads. This might take a while. 0:04:04.530 8G / 22G INFO General (file_limit.hpp : 32) Open file limit set to 1680 0:04:04.530 8G / 22G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.01178 Gb 0:04:04.530 8G / 22G INFO General (kmer_splitters.hpp : 97) Using cell size of 52428 0:04:14.150 30G / 31G INFO General (edge_index_builders.hpp : 77) Processed 50899417 edges 0:04:14.150 30G / 31G INFO General (edge_index_builders.hpp : 82) Used 50899417 sequences. 0:04:14.743 8G / 31G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:04:17.994 8G / 31G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 353598631 kmers in total. 0:04:17.994 8G / 31G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:04:22.749 8G / 31G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:04:35.492 8G / 31G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 0:04:53.057 8G / 31G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 163972512 bytes occupied (3.7098 bits per kmer). 0:04:57.493 16G / 31G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while. 0:05:08.191 16G / 31G INFO General (edge_index.hpp : 92) Index refilled 0:05:08.192 16G / 31G INFO General (gap_closer.cpp : 159) Preparing shift maps 0:06:07.376 20G / 31G INFO General (gap_closer.cpp : 119) Processing paired reads (takes a while) 0:06:11.462 21G / 31G INFO General (gap_closer.cpp : 138) Used 10551147 paired reads 0:06:11.462 21G / 31G INFO General (gap_closer.cpp : 140) Merging paired indices 0:06:30.914 17G / 31G INFO GapCloser (gap_closer.cpp : 346) Closing short gaps 0:08:15.499 17G / 31G INFO GapCloser (gap_closer.cpp : 380) Closing short gaps complete: filled 45709 gaps after checking 410151 candidates 0:08:24.920 16G / 31G INFO General (gap_closer.cpp : 159) Preparing shift maps 0:09:17.257 20G / 31G INFO General (gap_closer.cpp : 119) Processing paired reads (takes a while) 0:09:25.786 21G / 31G INFO General (gap_closer.cpp : 138) Used 26328385 paired reads 0:09:25.786 21G / 31G INFO General (gap_closer.cpp : 140) Merging paired indices 0:09:56.354 17G / 31G INFO GapCloser (gap_closer.cpp : 346) Closing short gaps 0:11:49.170 17G / 31G INFO GapCloser (gap_closer.cpp : 380) Closing short gaps complete: filled 109721 gaps after checking 1109302 candidates 0:12:07.147 16G / 31G INFO StageManager (stage.cpp : 132) STAGE == Raw Simplification 0:12:07.564 8G / 31G INFO General (simplification.cpp : 128) PROCEDURE == InitialCleaning 0:12:07.565 8G / 31G INFO General (simplification.cpp : 68) Most init cleaning disabled since detected mean 0 was less than activation coverage 10 0:12:07.565 8G / 31G INFO Simplification (parallel_processing.hpp : 165) Running Self conjugate edge remover 0:12:09.627 8G / 31G INFO Simplification (parallel_processing.hpp : 167) Self conjugate edge remover triggered 9 times 0:12:09.628 8G / 31G INFO StageManager (stage.cpp : 132) STAGE == Simplification 0:12:09.628 8G / 31G INFO General (simplification.cpp : 357) Graph simplification started 0:12:09.628 8G / 31G INFO General (graph_simplification.hpp : 634) Creating parallel br instance 0:12:09.628 8G / 31G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 1 0:12:09.628 8G / 31G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:14:55.256 9G / 31G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 9374766 times 0:14:55.256 9G / 31G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:15:02.432 9G / 31G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 27899 times 0:15:02.433 9G / 31G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:15:03.549 9G / 31G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 889 times 0:15:03.549 9G / 31G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 2 0:15:03.549 9G / 31G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:15:03.573 9G / 31G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 492 times 0:15:03.573 9G / 31G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:15:03.711 9G / 31G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 366 times 0:15:03.711 9G / 31G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:15:03.865 9G / 31G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 4340 times 0:15:03.865 9G / 31G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 3 0:15:03.865 9G / 31G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:15:04.016 9G / 31G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 4823 times 0:15:04.016 9G / 31G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:15:04.301 9G / 31G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 970 times 0:15:04.301 9G / 31G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:15:04.324 9G / 31G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 471 times 0:15:04.324 9G / 31G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 4 0:15:04.324 9G / 31G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:15:04.341 9G / 31G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 390 times 0:15:04.341 9G / 31G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:15:04.392 9G / 31G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 158 times 0:15:04.392 9G / 31G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:15:04.399 9G / 31G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 151 times 0:15:04.399 9G / 31G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 5 0:15:04.399 9G / 31G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:15:04.401 9G / 31G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 65 times 0:15:04.401 9G / 31G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:15:04.413 9G / 31G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 35 times 0:15:04.413 9G / 31G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:15:04.422 9G / 31G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 167 times 0:15:04.422 9G / 31G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 6 0:15:04.422 9G / 31G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:15:04.424 9G / 31G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 52 times 0:15:04.424 9G / 31G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:15:04.437 9G / 31G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 35 times 0:15:04.437 9G / 31G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:15:04.441 9G / 31G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 99 times 0:15:04.441 9G / 31G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 7 0:15:04.441 9G / 31G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:15:04.442 9G / 31G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 17 times 0:15:04.442 9G / 31G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:15:04.449 9G / 31G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 10 times 0:15:04.449 9G / 31G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:15:04.454 9G / 31G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 100 times 0:15:04.454 9G / 31G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 8 0:15:04.454 9G / 31G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:15:04.455 9G / 31G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 9 times 0:15:04.455 9G / 31G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:15:04.458 9G / 31G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 12 times 0:15:04.458 9G / 31G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:15:04.463 9G / 31G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 84 times 0:15:04.463 9G / 31G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 9 0:15:04.463 9G / 31G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:15:04.463 9G / 31G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 5 times 0:15:04.463 9G / 31G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:15:04.469 9G / 31G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 5 times 0:15:04.469 9G / 31G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:15:04.473 9G / 31G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 90 times 0:15:04.473 9G / 31G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 10 0:15:04.473 9G / 31G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:15:04.474 9G / 31G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 8 times 0:15:04.474 9G / 31G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:15:04.478 9G / 31G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 15 times 0:15:04.478 9G / 31G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:15:04.484 9G / 31G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 92 times 0:15:04.484 9G / 31G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 11 0:15:04.484 9G / 31G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:15:05.963 9G / 31G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 1147 times 0:15:05.963 9G / 31G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:15:06.978 9G / 31G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 108 times 0:15:06.978 9G / 31G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:15:07.894 9G / 31G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:15:07.894 9G / 31G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 12 0:15:07.894 9G / 31G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:15:07.894 9G / 31G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 1 times 0:15:07.894 9G / 31G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:15:07.894 9G / 31G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:15:07.894 9G / 31G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:15:07.894 9G / 31G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:15:07.894 9G / 31G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 13 0:15:07.894 9G / 31G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:15:07.894 9G / 31G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:15:07.894 9G / 31G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:15:07.894 9G / 31G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:15:07.894 9G / 31G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:15:07.894 9G / 31G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:15:07.894 9G / 31G INFO StageManager (stage.cpp : 132) STAGE == Gap Closer 0:15:07.895 9G / 31G INFO General (graph_pack.hpp : 101) Index refill 0:15:07.895 9G / 31G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:15:07.895 9G / 31G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 640 files using 40 threads. This might take a while. 0:15:07.895 9G / 31G INFO General (file_limit.hpp : 32) Open file limit set to 1680 0:15:07.895 9G / 31G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.00739 Gb 0:15:07.895 9G / 31G INFO General (kmer_splitters.hpp : 97) Using cell size of 52428 0:15:14.480 31G / 31G INFO General (edge_index_builders.hpp : 77) Processed 13846367 edges 0:15:14.480 31G / 31G INFO General (edge_index_builders.hpp : 82) Used 13846367 sequences. 0:15:15.011 9G / 31G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:15:17.251 9G / 31G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 304997206 kmers in total. 0:15:17.251 9G / 31G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:15:21.021 9G / 31G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:15:30.752 9G / 31G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 0:15:44.845 9G / 31G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 141448208 bytes occupied (3.71015 bits per kmer). 0:15:49.285 16G / 31G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while. 0:15:56.510 16G / 31G INFO General (edge_index.hpp : 92) Index refilled 0:15:56.511 16G / 31G INFO General (gap_closer.cpp : 159) Preparing shift maps 0:16:21.070 18G / 31G INFO General (gap_closer.cpp : 119) Processing paired reads (takes a while) 0:16:24.660 18G / 31G INFO General (gap_closer.cpp : 138) Used 10551147 paired reads 0:16:24.660 18G / 31G INFO General (gap_closer.cpp : 140) Merging paired indices 0:16:39.366 16G / 31G INFO GapCloser (gap_closer.cpp : 346) Closing short gaps 0:17:04.733 16G / 31G INFO GapCloser (gap_closer.cpp : 380) Closing short gaps complete: filled 2754 gaps after checking 57665 candidates 0:17:19.549 16G / 31G INFO General (gap_closer.cpp : 159) Preparing shift maps 0:17:44.243 18G / 31G INFO General (gap_closer.cpp : 119) Processing paired reads (takes a while) 0:17:52.833 19G / 31G INFO General (gap_closer.cpp : 138) Used 26328385 paired reads 0:17:52.833 19G / 31G INFO General (gap_closer.cpp : 140) Merging paired indices 0:18:18.755 16G / 31G INFO GapCloser (gap_closer.cpp : 346) Closing short gaps 0:18:49.872 16G / 31G INFO GapCloser (gap_closer.cpp : 380) Closing short gaps complete: filled 10418 gaps after checking 214681 candidates 0:19:08.624 16G / 31G INFO StageManager (stage.cpp : 132) STAGE == Simplification Cleanup 0:19:08.624 16G / 31G INFO General (simplification.cpp : 196) PROCEDURE == Post simplification 0:19:08.624 16G / 31G INFO General (graph_simplification.hpp : 453) Disconnection of relatively low covered edges disabled 0:19:08.624 16G / 31G INFO General (graph_simplification.hpp : 489) Complex tip clipping disabled 0:19:08.624 16G / 31G INFO General (graph_simplification.hpp : 634) Creating parallel br instance 0:19:08.624 16G / 31G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:19:09.698 16G / 31G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 3 times 0:19:09.698 16G / 31G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:19:10.592 16G / 31G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:19:10.592 16G / 31G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:19:11.561 16G / 31G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:19:11.561 16G / 31G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:19:12.449 16G / 31G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:19:12.449 16G / 31G INFO General (simplification.cpp : 330) Disrupting self-conjugate edges 0:19:23.363 16G / 31G INFO Simplification (parallel_processing.hpp : 165) Running Removing isolated edges 0:22:03.269 11G / 31G INFO Simplification (parallel_processing.hpp : 167) Removing isolated edges triggered 6694422 times 0:22:03.270 11G / 31G INFO General (simplification.cpp : 470) Counting average coverage 0:22:03.519 11G / 31G INFO General (simplification.cpp : 476) Average coverage = 7.35071 0:22:03.519 11G / 31G INFO StageManager (stage.cpp : 132) STAGE == Mismatch Correction 0:22:03.519 11G / 31G INFO General (graph_pack.hpp : 109) Normalizing k-mer map. Total 3825445 kmers to process 0:22:05.732 11G / 31G INFO General (graph_pack.hpp : 111) Normalizing done 0:22:45.355 11G / 31G INFO General (mismatch_shall_not_pass.hp: 189) Finished collecting potential mismatches positions 0:22:47.473 11G / 31G INFO General (mismatch_shall_not_pass.hp: 290) All edges processed 0:22:47.513 11G / 31G INFO General (mismatch_correction.cpp : 27) Corrected 27 nucleotides 0:22:47.517 11G / 31G INFO StageManager (stage.cpp : 132) STAGE == Contig Output 0:22:47.517 11G / 31G INFO General (contig_output_stage.cpp : 40) Writing GFA to /srv/scratch/marinovg/SPAdes-3.13-L1152-L1147-Euplotes_sym_gDNA-reamp//K55/assembly_graph_with_scaffolds.gfa 0:22:49.725 11G / 31G INFO General (contig_output.hpp : 22) Outputting contigs to /srv/scratch/marinovg/SPAdes-3.13-L1152-L1147-Euplotes_sym_gDNA-reamp//K55/before_rr.fasta 0:22:52.068 11G / 31G INFO General (contig_output_stage.cpp : 51) Outputting FastG graph to /srv/scratch/marinovg/SPAdes-3.13-L1152-L1147-Euplotes_sym_gDNA-reamp//K55/assembly_graph.fastg 0:22:59.182 11G / 31G INFO General (contig_output.hpp : 22) Outputting contigs to /srv/scratch/marinovg/SPAdes-3.13-L1152-L1147-Euplotes_sym_gDNA-reamp//K55/simplified_contigs.fasta 0:23:01.566 11G / 31G INFO General (contig_output.hpp : 22) Outputting contigs to /srv/scratch/marinovg/SPAdes-3.13-L1152-L1147-Euplotes_sym_gDNA-reamp//K55/intermediate_contigs.fasta 0:23:04.003 11G / 31G INFO StageManager (stage.cpp : 132) STAGE == Paired Information Counting 0:23:12.677 11G / 31G INFO General (graph_pack.hpp : 109) Normalizing k-mer map. Total 3827751 kmers to process 0:23:15.112 11G / 31G INFO General (graph_pack.hpp : 111) Normalizing done 0:23:15.420 11G / 31G INFO General (pair_info_count.cpp : 320) Min edge length for estimation: 2163 0:23:15.420 11G / 31G INFO General (pair_info_count.cpp : 331) Estimating insert size for library #0 0:23:15.420 11G / 31G INFO General (pair_info_count.cpp : 190) Estimating insert size (takes a while) 0:23:15.821 11G / 31G INFO General (pair_info_count.cpp : 39) Selecting usual mapper 0:23:21.655 11G / 31G INFO General (sequence_mapper_notifier.h: 80) Processed 200000 reads 0:23:21.722 11G / 31G INFO General (sequence_mapper_notifier.h: 80) Processed 400000 reads 0:23:21.753 11G / 31G INFO General (sequence_mapper_notifier.h: 80) Processed 600000 reads 0:23:21.776 11G / 31G INFO General (sequence_mapper_notifier.h: 80) Processed 800000 reads 0:23:21.799 11G / 31G INFO General (sequence_mapper_notifier.h: 80) Processed 1000000 reads 0:23:21.821 11G / 31G INFO General (sequence_mapper_notifier.h: 80) Processed 1200000 reads 0:23:21.950 11G / 31G INFO General (sequence_mapper_notifier.h: 80) Processed 2200000 reads 0:23:22.290 11G / 31G INFO General (sequence_mapper_notifier.h: 80) Processed 4200000 reads 0:23:22.935 11G / 31G INFO General (sequence_mapper_notifier.h: 80) Processed 8629121 reads 0:23:24.701 11G / 31G INFO General (sequence_mapper_notifier.h: 98) Total 10551147 reads processed 0:23:25.873 11G / 31G INFO General (pair_info_count.cpp : 209) Edge pairs: 67108864 (rough upper limit) 0:23:25.873 11G / 31G INFO General (pair_info_count.cpp : 213) 7332542 paired reads (69.4952% of all) aligned to long edges 0:23:25.913 11G / 31G INFO General (pair_info_count.cpp : 354) Insert size = 125.576, deviation = 64.0447, left quantile = 73, right quantile = 208, read length = 75 0:23:26.014 11G / 31G INFO General (pair_info_count.cpp : 371) Filtering data for library #0 0:23:26.016 11G / 31G INFO General (pair_info_count.cpp : 39) Selecting usual mapper 0:23:31.567 11G / 31G INFO General (sequence_mapper_notifier.h: 80) Processed 200000 reads 0:23:31.568 11G / 31G INFO General (sequence_mapper_notifier.h: 80) Processed 400000 reads 0:23:31.581 11G / 31G INFO General (sequence_mapper_notifier.h: 80) Processed 600000 reads 0:23:31.582 11G / 31G INFO General (sequence_mapper_notifier.h: 80) Processed 800000 reads 0:23:31.603 11G / 31G INFO General (sequence_mapper_notifier.h: 80) Processed 1000000 reads 0:23:31.642 11G / 31G INFO General (sequence_mapper_notifier.h: 80) Processed 1200000 reads 0:23:31.690 11G / 31G INFO General (sequence_mapper_notifier.h: 80) Processed 2200000 reads 0:23:31.763 11G / 31G INFO General (sequence_mapper_notifier.h: 80) Processed 4200000 reads 0:23:33.562 11G / 31G INFO General (sequence_mapper_notifier.h: 98) Total 10551147 reads processed 0:23:33.562 11G / 31G INFO General (pair_info_count.cpp : 383) Mapping library #0 0:23:33.562 11G / 31G INFO General (pair_info_count.cpp : 385) Mapping paired reads (takes a while) 0:23:33.562 11G / 31G INFO General (pair_info_count.cpp : 289) Left insert size quantile 73, right insert size quantile 208, filtering threshold 2, rounding threshold 0 0:23:33.570 11G / 31G INFO General (pair_info_count.cpp : 39) Selecting usual mapper 0:23:38.459 11G / 31G INFO General (sequence_mapper_notifier.h: 80) Processed 200000 reads 0:23:38.490 11G / 31G INFO General (sequence_mapper_notifier.h: 80) Processed 400000 reads 0:23:38.519 11G / 31G INFO General (sequence_mapper_notifier.h: 80) Processed 600000 reads 0:23:38.552 11G / 31G INFO General (sequence_mapper_notifier.h: 80) Processed 800000 reads 0:23:38.557 11G / 31G INFO General (sequence_mapper_notifier.h: 80) Processed 1000000 reads 0:23:38.564 11G / 31G INFO General (sequence_mapper_notifier.h: 80) Processed 1200000 reads 0:23:38.582 11G / 31G INFO General (sequence_mapper_notifier.h: 80) Processed 2200000 reads 0:23:38.642 11G / 31G INFO General (sequence_mapper_notifier.h: 80) Processed 4200000 reads 0:23:40.352 11G / 31G INFO General (sequence_mapper_notifier.h: 98) Total 10551147 reads processed 0:23:40.438 11G / 31G INFO General (pair_info_count.cpp : 331) Estimating insert size for library #1 0:23:40.438 11G / 31G INFO General (pair_info_count.cpp : 190) Estimating insert size (takes a while) 0:23:40.849 12G / 31G INFO General (pair_info_count.cpp : 39) Selecting usual mapper 0:23:45.527 12G / 31G INFO General (sequence_mapper_notifier.h: 80) Processed 200000 reads 0:23:45.571 12G / 31G INFO General (sequence_mapper_notifier.h: 80) Processed 400000 reads 0:23:45.606 12G / 31G INFO General (sequence_mapper_notifier.h: 80) Processed 600000 reads 0:23:45.635 12G / 31G INFO General (sequence_mapper_notifier.h: 80) Processed 800000 reads 0:23:45.658 12G / 31G INFO General (sequence_mapper_notifier.h: 80) Processed 1000000 reads 0:23:45.681 12G / 31G INFO General (sequence_mapper_notifier.h: 80) Processed 1200000 reads 0:23:45.798 12G / 31G INFO General (sequence_mapper_notifier.h: 80) Processed 2200000 reads 0:23:46.206 12G / 31G INFO General (sequence_mapper_notifier.h: 80) Processed 4200000 reads 0:23:49.858 12G / 31G INFO General (sequence_mapper_notifier.h: 80) Processed 8400000 reads 0:23:55.082 12G / 31G INFO General (sequence_mapper_notifier.h: 80) Processed 16800000 reads 0:23:58.928 12G / 31G INFO General (sequence_mapper_notifier.h: 98) Total 26328385 reads processed 0:24:00.103 12G / 31G INFO General (pair_info_count.cpp : 209) Edge pairs: 67108864 (rough upper limit) 0:24:00.103 12G / 31G INFO General (pair_info_count.cpp : 213) 16048790 paired reads (60.9562% of all) aligned to long edges 0:24:00.149 11G / 31G INFO General (pair_info_count.cpp : 354) Insert size = 127.194, deviation = 58.7942, left quantile = 74, right quantile = 207, read length = 75 0:24:00.249 11G / 31G INFO General (pair_info_count.cpp : 371) Filtering data for library #1 0:24:00.250 11G / 31G INFO General (pair_info_count.cpp : 39) Selecting usual mapper 0:24:05.182 11G / 31G INFO General (sequence_mapper_notifier.h: 80) Processed 200000 reads 0:24:05.353 11G / 31G INFO General (sequence_mapper_notifier.h: 80) Processed 400000 reads 0:24:05.353 11G / 31G INFO General (sequence_mapper_notifier.h: 80) Processed 600000 reads 0:24:05.390 11G / 31G INFO General (sequence_mapper_notifier.h: 80) Processed 800000 reads 0:24:05.421 11G / 31G INFO General (sequence_mapper_notifier.h: 80) Processed 1000000 reads 0:24:05.438 11G / 31G INFO General (sequence_mapper_notifier.h: 80) Processed 1200000 reads 0:24:05.506 11G / 31G INFO General (sequence_mapper_notifier.h: 80) Processed 2200000 reads 0:24:05.573 11G / 31G INFO General (sequence_mapper_notifier.h: 80) Processed 4200000 reads 0:24:10.653 11G / 31G INFO General (sequence_mapper_notifier.h: 80) Processed 8400000 reads 0:24:16.284 11G / 31G INFO General (sequence_mapper_notifier.h: 80) Processed 16800000 reads 0:24:18.034 11G / 31G INFO General (sequence_mapper_notifier.h: 98) Total 26328385 reads processed 0:24:18.035 11G / 31G INFO General (pair_info_count.cpp : 383) Mapping library #1 0:24:18.035 11G / 31G INFO General (pair_info_count.cpp : 385) Mapping paired reads (takes a while) 0:24:18.035 11G / 31G INFO General (pair_info_count.cpp : 289) Left insert size quantile 74, right insert size quantile 207, filtering threshold 2, rounding threshold 0 0:24:18.048 11G / 31G INFO General (pair_info_count.cpp : 39) Selecting usual mapper 0:24:22.475 11G / 31G INFO General (sequence_mapper_notifier.h: 80) Processed 200000 reads 0:24:22.477 11G / 31G INFO General (sequence_mapper_notifier.h: 80) Processed 400000 reads 0:24:22.481 11G / 31G INFO General (sequence_mapper_notifier.h: 80) Processed 600000 reads 0:24:22.497 11G / 31G INFO General (sequence_mapper_notifier.h: 80) Processed 800000 reads 0:24:22.514 11G / 31G INFO General (sequence_mapper_notifier.h: 80) Processed 1000000 reads 0:24:22.515 11G / 31G INFO General (sequence_mapper_notifier.h: 80) Processed 1200000 reads 0:24:22.547 11G / 31G INFO General (sequence_mapper_notifier.h: 80) Processed 2200000 reads 0:24:22.597 11G / 31G INFO General (sequence_mapper_notifier.h: 80) Processed 4200000 reads 0:24:27.315 11G / 31G INFO General (sequence_mapper_notifier.h: 80) Processed 8400000 reads 0:24:31.911 11G / 31G INFO General (sequence_mapper_notifier.h: 80) Processed 16800000 reads 0:24:33.491 11G / 31G INFO General (sequence_mapper_notifier.h: 98) Total 26328385 reads processed 0:24:33.614 11G / 31G INFO General (pair_info_count.cpp : 392) Mapping single reads of library #2 0:24:33.614 11G / 31G INFO General (pair_info_count.cpp : 39) Selecting usual mapper 0:24:40.162 11G / 31G INFO General (sequence_mapper_notifier.h: 80) Processed 200000 reads 0:24:40.187 11G / 31G INFO General (sequence_mapper_notifier.h: 80) Processed 400000 reads 0:24:40.204 11G / 31G INFO General (sequence_mapper_notifier.h: 80) Processed 600000 reads 0:24:40.223 11G / 31G INFO General (sequence_mapper_notifier.h: 80) Processed 800000 reads 0:24:40.239 11G / 31G INFO General (sequence_mapper_notifier.h: 80) Processed 1000000 reads 0:24:40.255 11G / 31G INFO General (sequence_mapper_notifier.h: 80) Processed 1200000 reads 0:24:40.346 11G / 31G INFO General (sequence_mapper_notifier.h: 80) Processed 2345017 reads 0:24:40.544 11G / 31G INFO General (sequence_mapper_notifier.h: 80) Processed 4228406 reads 0:24:40.933 11G / 31G INFO General (sequence_mapper_notifier.h: 80) Processed 8601828 reads 0:24:41.362 11G / 31G INFO General (sequence_mapper_notifier.h: 98) Total 9933556 reads processed 0:24:41.363 11G / 31G INFO General (pair_info_count.cpp : 394) Total paths obtained from single reads: 206619 0:24:41.363 11G / 31G INFO General (pair_info_count.cpp : 392) Mapping single reads of library #3 0:24:41.363 11G / 31G INFO General (pair_info_count.cpp : 39) Selecting usual mapper 0:24:46.858 11G / 31G INFO General (sequence_mapper_notifier.h: 80) Processed 200000 reads 0:24:46.883 11G / 31G INFO General (sequence_mapper_notifier.h: 80) Processed 400000 reads 0:24:46.908 11G / 31G INFO General (sequence_mapper_notifier.h: 80) Processed 600000 reads 0:24:46.935 11G / 31G INFO General (sequence_mapper_notifier.h: 80) Processed 800000 reads 0:24:46.967 11G / 31G INFO General (sequence_mapper_notifier.h: 80) Processed 1000000 reads 0:24:46.988 11G / 31G INFO General (sequence_mapper_notifier.h: 80) Processed 1200000 reads 0:24:47.123 11G / 31G INFO General (sequence_mapper_notifier.h: 80) Processed 2200000 reads 0:24:47.449 11G / 31G INFO General (sequence_mapper_notifier.h: 80) Processed 4200000 reads 0:24:48.959 11G / 31G INFO General (sequence_mapper_notifier.h: 80) Processed 8400000 reads 0:24:53.041 11G / 31G INFO General (sequence_mapper_notifier.h: 98) Total 16757217 reads processed 0:24:53.042 11G / 31G INFO General (pair_info_count.cpp : 394) Total paths obtained from single reads: 286124 0:24:53.042 11G / 31G INFO General (pair_info_count.cpp : 392) Mapping single reads of library #4 0:24:53.042 11G / 31G INFO General (pair_info_count.cpp : 39) Selecting usual mapper 0:24:54.182 11G / 31G INFO General (sequence_mapper_notifier.h: 98) Total 1204611 reads processed 0:24:54.182 11G / 31G INFO General (pair_info_count.cpp : 394) Total paths obtained from single reads: 93631 0:24:54.182 11G / 31G INFO General (pair_info_count.cpp : 392) Mapping single reads of library #5 0:24:54.182 11G / 31G INFO General (pair_info_count.cpp : 39) Selecting usual mapper 0:24:54.243 11G / 31G INFO General (sequence_mapper_notifier.h: 98) Total 52211 reads processed 0:24:54.244 11G / 31G INFO General (pair_info_count.cpp : 394) Total paths obtained from single reads: 10020 0:24:54.244 11G / 31G INFO StageManager (stage.cpp : 132) STAGE == Distance Estimation 0:24:54.244 11G / 31G INFO General (distance_estimation.cpp : 173) Processing library #0 0:24:54.244 11G / 31G INFO General (distance_estimation.cpp : 149) Weight Filter Done 0:24:54.244 11G / 31G INFO DistanceEstimator (distance_estimation.hpp : 116) Using SIMPLE distance estimator 0:24:55.161 11G / 31G INFO General (distance_estimation.cpp : 34) Filtering info 0:24:55.161 11G / 31G INFO General (pair_info_filters.hpp : 242) Start filtering; index size: 453150 0:24:55.562 11G / 31G INFO General (pair_info_filters.hpp : 263) Done filtering 0:24:55.563 11G / 31G INFO General (distance_estimation.cpp : 156) Refining clustered pair information 0:24:55.703 11G / 31G INFO General (distance_estimation.cpp : 158) The refining of clustered pair information has been finished 0:24:55.704 11G / 31G INFO General (distance_estimation.cpp : 160) Improving paired information 0:24:56.230 11G / 31G INFO PairInfoImprover (pair_info_improver.hpp : 103) Paired info stats: missing = 2333; contradictional = 454 0:24:56.712 11G / 31G INFO PairInfoImprover (pair_info_improver.hpp : 103) Paired info stats: missing = 263; contradictional = 2 0:24:56.712 11G / 31G INFO General (distance_estimation.cpp : 103) Filling scaffolding index 0:24:56.712 11G / 31G INFO DistanceEstimator (distance_estimation.hpp : 116) Using SMOOTHING distance estimator 0:24:56.949 11G / 31G INFO General (distance_estimation.cpp : 34) Filtering info 0:24:56.949 11G / 31G INFO General (pair_info_filters.hpp : 242) Start filtering; index size: 434686 0:24:57.203 11G / 31G INFO General (pair_info_filters.hpp : 263) Done filtering 0:24:57.205 11G / 31G INFO General (distance_estimation.cpp : 182) Clearing raw paired index 0:24:57.337 11G / 31G INFO General (distance_estimation.cpp : 173) Processing library #1 0:24:57.337 11G / 31G INFO General (distance_estimation.cpp : 149) Weight Filter Done 0:24:57.337 11G / 31G INFO DistanceEstimator (distance_estimation.hpp : 116) Using SIMPLE distance estimator 0:24:57.979 11G / 31G INFO General (distance_estimation.cpp : 34) Filtering info 0:24:57.979 11G / 31G INFO General (pair_info_filters.hpp : 242) Start filtering; index size: 457866 0:24:58.363 11G / 31G INFO General (pair_info_filters.hpp : 263) Done filtering 0:24:58.364 11G / 31G INFO General (distance_estimation.cpp : 156) Refining clustered pair information 0:24:58.578 11G / 31G INFO General (distance_estimation.cpp : 158) The refining of clustered pair information has been finished 0:24:58.578 11G / 31G INFO General (distance_estimation.cpp : 160) Improving paired information 0:24:59.564 11G / 31G INFO PairInfoImprover (pair_info_improver.hpp : 103) Paired info stats: missing = 2659; contradictional = 524 0:25:00.186 11G / 31G INFO PairInfoImprover (pair_info_improver.hpp : 103) Paired info stats: missing = 224; contradictional = 2 0:25:00.186 11G / 31G INFO General (distance_estimation.cpp : 103) Filling scaffolding index 0:25:00.186 11G / 31G INFO DistanceEstimator (distance_estimation.hpp : 116) Using SMOOTHING distance estimator 0:25:00.545 11G / 31G INFO General (distance_estimation.cpp : 34) Filtering info 0:25:00.545 11G / 31G INFO General (pair_info_filters.hpp : 242) Start filtering; index size: 440791 0:25:00.843 11G / 31G INFO General (pair_info_filters.hpp : 263) Done filtering 0:25:00.845 11G / 31G INFO General (distance_estimation.cpp : 182) Clearing raw paired index 0:25:01.179 11G / 31G INFO StageManager (stage.cpp : 132) STAGE == Repeat Resolving 0:25:01.179 11G / 31G INFO General (repeat_resolving.cpp : 69) Using Path-Extend repeat resolving 0:25:01.179 11G / 31G INFO General (launcher.cpp : 477) ExSPAnder repeat resolving tool started 0:25:02.940 12G / 31G INFO General (launcher.cpp : 392) Creating main extenders, unique edge length = 2000 0:25:03.729 12G / 31G INFO General (extenders_logic.cpp : 275) Estimated coverage of library #0 is 1.65299 0:25:03.836 12G / 31G INFO General (extenders_logic.cpp : 275) Estimated coverage of library #0 is 1.65299 0:25:04.375 12G / 31G INFO General (extenders_logic.cpp : 275) Estimated coverage of library #1 is 4.09129 0:25:04.460 12G / 31G INFO General (extenders_logic.cpp : 275) Estimated coverage of library #1 is 4.09129 0:25:04.937 12G / 31G INFO General (extenders_logic.cpp : 34) resolvable_repeat_length_bound set to 10000 0:25:06.184 12G / 31G INFO General (extenders_logic.cpp : 34) resolvable_repeat_length_bound set to 10000 0:25:07.441 12G / 31G INFO General (extenders_logic.cpp : 34) resolvable_repeat_length_bound set to 10000 0:25:08.739 12G / 31G INFO General (extenders_logic.cpp : 34) resolvable_repeat_length_bound set to 10000 0:25:09.996 12G / 31G INFO General (extenders_logic.cpp : 472) Using 2 paired-end libraries 0:25:09.996 12G / 31G INFO General (extenders_logic.cpp : 473) Using 2 paired-end scaffolding libraries 0:25:09.996 12G / 31G INFO General (extenders_logic.cpp : 474) Using 4 single read libraries 0:25:09.996 12G / 31G INFO General (launcher.cpp : 420) Total number of extenders is 10 0:25:09.996 12G / 31G INFO General (path_extender.hpp : 885) Processed 0 paths from 214778 (0%) 0:25:10.378 12G / 31G INFO General (path_extender.hpp : 883) Processed 128 paths from 214778 (0%) 0:25:10.546 12G / 31G INFO General (path_extender.hpp : 883) Processed 256 paths from 214778 (0%) 0:25:10.748 12G / 31G INFO General (path_extender.hpp : 883) Processed 512 paths from 214778 (0%) 0:25:11.019 12G / 31G INFO General (path_extender.hpp : 883) Processed 1024 paths from 214778 (0%) 0:25:11.439 12G / 31G INFO General (path_extender.hpp : 883) Processed 2048 paths from 214778 (0%) 0:25:11.832 12G / 31G INFO General (path_extender.hpp : 883) Processed 4096 paths from 214778 (1%) 0:25:12.357 12G / 31G INFO General (path_extender.hpp : 883) Processed 8192 paths from 214778 (3%) 0:25:13.298 12G / 31G INFO General (path_extender.hpp : 883) Processed 16384 paths from 214778 (7%) 0:25:13.829 12G / 31G INFO General (path_extender.hpp : 885) Processed 21478 paths from 214778 (10%) 0:25:15.017 12G / 31G INFO General (path_extender.hpp : 883) Processed 32768 paths from 214778 (15%) 0:25:16.064 12G / 31G INFO General (path_extender.hpp : 885) Processed 42956 paths from 214778 (20%) 0:25:18.179 13G / 31G INFO General (path_extender.hpp : 885) Processed 64434 paths from 214778 (30%) 0:25:18.289 13G / 31G INFO General (path_extender.hpp : 883) Processed 65536 paths from 214778 (30%) 0:25:20.307 13G / 31G INFO General (path_extender.hpp : 885) Processed 85912 paths from 214778 (40%) 0:25:22.349 13G / 31G INFO General (path_extender.hpp : 885) Processed 107390 paths from 214778 (50%) 0:25:26.635 13G / 31G INFO General (path_extender.hpp : 885) Processed 128868 paths from 214778 (60%) 0:25:26.840 13G / 31G INFO General (path_extender.hpp : 883) Processed 131072 paths from 214778 (61%) 0:25:28.972 13G / 31G INFO General (path_extender.hpp : 885) Processed 150346 paths from 214778 (70%) 0:25:30.966 13G / 31G INFO General (path_extender.hpp : 885) Processed 171824 paths from 214778 (80%) 0:25:32.954 14G / 31G INFO General (path_extender.hpp : 885) Processed 193302 paths from 214778 (90%) 0:26:02.016 14G / 31G INFO General (launcher.cpp : 234) Finalizing paths 0:26:02.016 14G / 31G INFO General (launcher.cpp : 236) Deduplicating paths 0:26:03.157 14G / 31G INFO General (launcher.cpp : 240) Paths deduplicated 0:26:03.158 14G / 31G INFO PEResolver (pe_resolver.hpp : 295) Removing overlaps 0:26:03.158 14G / 31G INFO PEResolver (pe_resolver.hpp : 298) Sorting paths 0:26:03.549 14G / 31G INFO PEResolver (pe_resolver.hpp : 305) Marking overlaps 0:26:03.549 14G / 31G INFO OverlapRemover (pe_resolver.hpp : 130) Marking start/end overlaps 0:26:03.945 14G / 31G INFO OverlapRemover (pe_resolver.hpp : 133) Marking remaining overlaps 0:26:04.319 14G / 31G INFO PEResolver (pe_resolver.hpp : 308) Splitting paths 0:26:04.365 14G / 31G INFO PEResolver (pe_resolver.hpp : 313) Deduplicating paths 0:26:04.563 14G / 31G INFO PEResolver (pe_resolver.hpp : 315) Overlaps removed 0:26:05.741 14G / 31G INFO General (launcher.cpp : 257) Paths finalized 0:26:05.741 14G / 31G INFO General (launcher.cpp : 427) Closing gaps in paths 0:26:06.868 14G / 31G INFO General (launcher.cpp : 455) Gap closing completed 0:26:07.276 14G / 31G INFO General (launcher.cpp : 286) Traversing tandem repeats 0:26:09.078 14G / 31G INFO General (launcher.cpp : 296) Traversed 162 loops 0:26:09.078 14G / 31G INFO General (launcher.cpp : 234) Finalizing paths 0:26:09.078 14G / 31G INFO General (launcher.cpp : 236) Deduplicating paths 0:26:09.301 14G / 31G INFO General (launcher.cpp : 240) Paths deduplicated 0:26:09.301 14G / 31G INFO PEResolver (pe_resolver.hpp : 295) Removing overlaps 0:26:09.301 14G / 31G INFO PEResolver (pe_resolver.hpp : 298) Sorting paths 0:26:09.575 14G / 31G INFO PEResolver (pe_resolver.hpp : 305) Marking overlaps 0:26:09.575 14G / 31G INFO OverlapRemover (pe_resolver.hpp : 130) Marking start/end overlaps 0:26:09.910 14G / 31G INFO OverlapRemover (pe_resolver.hpp : 133) Marking remaining overlaps 0:26:10.296 14G / 31G INFO PEResolver (pe_resolver.hpp : 308) Splitting paths 0:26:10.318 14G / 31G INFO PEResolver (pe_resolver.hpp : 313) Deduplicating paths 0:26:10.501 14G / 31G INFO PEResolver (pe_resolver.hpp : 315) Overlaps removed 0:26:11.155 14G / 31G INFO General (launcher.cpp : 257) Paths finalized 0:26:11.948 14G / 31G INFO General (launcher.cpp : 529) ExSPAnder repeat resolving tool finished 0:26:13.640 13G / 31G INFO StageManager (stage.cpp : 132) STAGE == Contig Output 0:26:13.640 13G / 31G INFO General (contig_output_stage.cpp : 40) Writing GFA to /srv/scratch/marinovg/SPAdes-3.13-L1152-L1147-Euplotes_sym_gDNA-reamp//K55/assembly_graph_with_scaffolds.gfa 0:26:15.952 13G / 31G INFO General (contig_output.hpp : 22) Outputting contigs to /srv/scratch/marinovg/SPAdes-3.13-L1152-L1147-Euplotes_sym_gDNA-reamp//K55/before_rr.fasta 0:26:18.455 13G / 31G INFO General (contig_output_stage.cpp : 51) Outputting FastG graph to /srv/scratch/marinovg/SPAdes-3.13-L1152-L1147-Euplotes_sym_gDNA-reamp//K55/assembly_graph.fastg 0:26:27.989 13G / 31G INFO General (contig_output_stage.cpp : 20) Outputting FastG paths to /srv/scratch/marinovg/SPAdes-3.13-L1152-L1147-Euplotes_sym_gDNA-reamp//K55/final_contigs.paths 0:26:32.451 13G / 31G INFO General (contig_output_stage.cpp : 20) Outputting FastG paths to /srv/scratch/marinovg/SPAdes-3.13-L1152-L1147-Euplotes_sym_gDNA-reamp//K55/scaffolds.paths 0:26:36.719 13G / 31G INFO General (launch.hpp : 149) SPAdes finished 0:26:45.427 168M / 31G INFO General (main.cpp : 109) Assembling time: 0 hours 26 minutes 45 seconds ===== Assembling finished. Used k-mer sizes: 21, 33, 55 * Corrected reads are in /srv/scratch/marinovg/SPAdes-3.13-L1152-L1147-Euplotes_sym_gDNA-reamp/corrected/ * Assembled contigs are in /srv/scratch/marinovg/SPAdes-3.13-L1152-L1147-Euplotes_sym_gDNA-reamp/contigs.fasta * Assembled scaffolds are in /srv/scratch/marinovg/SPAdes-3.13-L1152-L1147-Euplotes_sym_gDNA-reamp/scaffolds.fasta * Assembly graph is in /srv/scratch/marinovg/SPAdes-3.13-L1152-L1147-Euplotes_sym_gDNA-reamp/assembly_graph.fastg * Assembly graph in GFA format is in /srv/scratch/marinovg/SPAdes-3.13-L1152-L1147-Euplotes_sym_gDNA-reamp/assembly_graph_with_scaffolds.gfa * Paths in the assembly graph corresponding to the contigs are in /srv/scratch/marinovg/SPAdes-3.13-L1152-L1147-Euplotes_sym_gDNA-reamp/contigs.paths * Paths in the assembly graph corresponding to the scaffolds are in /srv/scratch/marinovg/SPAdes-3.13-L1152-L1147-Euplotes_sym_gDNA-reamp/scaffolds.paths ======= SPAdes pipeline finished WITH WARNINGS! === Error correction and assembling warnings: * 0:12:42.226 3G / 22G WARN General (kmer_coverage_model.cpp : 327) Valley value was estimated improperly, reset to 76 * 0:12:42.229 3G / 22G WARN General (kmer_coverage_model.cpp : 366) Failed to determine erroneous kmer threshold. Threshold set to: 76 * 0:16:44.704 3G / 22G WARN General (simplification.cpp : 479) The determined erroneous connection coverage threshold may be determined improperly * 0:05:40.209 3G / 22G WARN General (kmer_coverage_model.cpp : 218) Too many erroneous kmers, the estimates might be unreliable * 0:06:04.309 3G / 22G WARN General (kmer_coverage_model.cpp : 327) Valley value was estimated improperly, reset to 6 * 0:06:04.312 3G / 22G WARN General (kmer_coverage_model.cpp : 366) Failed to determine erroneous kmer threshold. Threshold set to: 6 * 0:04:04.525 8G / 22G WARN General (kmer_coverage_model.cpp : 327) Valley value was estimated improperly, reset to 7 * 0:04:04.529 8G / 22G WARN General (kmer_coverage_model.cpp : 366) Failed to determine erroneous kmer threshold. Threshold set to: 7 ======= Warnings saved to /srv/scratch/marinovg/SPAdes-3.13-L1152-L1147-Euplotes_sym_gDNA-reamp/warnings.log SPAdes log can be found here: /srv/scratch/marinovg/SPAdes-3.13-L1152-L1147-Euplotes_sym_gDNA-reamp/spades.log Thank you for using SPAdes!