Command line: /oak/stanford/groups/akundaje/marinovg/programs/SPAdes-3.14.0-Linux/bin/spades.py --pe1-1 /srv/scratch/marinovg/L1399-Cyclotella_meninghiana_gDNA.H57H5DSXY_L4.read1.paired.fastq.gz --pe1-2 /srv/scratch/marinovg/L1399-Cyclotella_meninghiana_gDNA.H57H5DSXY_L4.read2.paired.fastq.gz --s1 /srv/scratch/marinovg/L1399-Cyclotella_meninghiana_gDNA.H57H5DSXY_L4.read1.unpaired.fastq.gz --s2 /srv/scratch/marinovg/L1399-Cyclotella_meninghiana_gDNA.H57H5DSXY_L4.read2.unpaired.fastq.gz -t 60 -o /srv/scratch/marinovg/SPAdes-3.14-L1399-Cyclotella_meninghiana_gDNA System information: SPAdes version: 3.14.0 Python version: 2.7.17 OS: Linux-4.15.0-74-generic-x86_64-with-Ubuntu-18.04-bionic Output dir: /srv/scratch/marinovg/SPAdes-3.14-L1399-Cyclotella_meninghiana_gDNA Mode: read error correction and assembling Debug mode is turned OFF Dataset parameters: Standard mode For multi-cell/isolate data we recommend to use '--isolate' option; for single-cell MDA data use '--sc'; for metagenomic data use '--meta'; for RNA-Seq use '--rna'. Reads: Library number: 1, library type: single left reads: not specified right reads: not specified interlaced reads: not specified single reads: ['/srv/scratch/marinovg/L1399-Cyclotella_meninghiana_gDNA.H57H5DSXY_L4.read1.unpaired.fastq.gz'] merged reads: not specified Library number: 2, library type: single left reads: not specified right reads: not specified interlaced reads: not specified single reads: ['/srv/scratch/marinovg/L1399-Cyclotella_meninghiana_gDNA.H57H5DSXY_L4.read2.unpaired.fastq.gz'] merged reads: not specified Library number: 3, library type: paired-end orientation: fr left reads: ['/srv/scratch/marinovg/L1399-Cyclotella_meninghiana_gDNA.H57H5DSXY_L4.read1.paired.fastq.gz'] right reads: ['/srv/scratch/marinovg/L1399-Cyclotella_meninghiana_gDNA.H57H5DSXY_L4.read2.paired.fastq.gz'] interlaced reads: not specified single reads: not specified 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-3.14-L1399-Cyclotella_meninghiana_gDNA/tmp Threads: 60 Memory limit (in Gb): 250 ======= SPAdes pipeline started. Log can be found here: /srv/scratch/marinovg/SPAdes-3.14-L1399-Cyclotella_meninghiana_gDNA/spades.log /srv/scratch/marinovg/L1399-Cyclotella_meninghiana_gDNA.H57H5DSXY_L4.read1.unpaired.fastq.gz: max reads length: 150 /srv/scratch/marinovg/L1399-Cyclotella_meninghiana_gDNA.H57H5DSXY_L4.read2.unpaired.fastq.gz: max reads length: 150 /srv/scratch/marinovg/L1399-Cyclotella_meninghiana_gDNA.H57H5DSXY_L4.read2.paired.fastq.gz: max reads length: 150 /srv/scratch/marinovg/L1399-Cyclotella_meninghiana_gDNA.H57H5DSXY_L4.read1.paired.fastq.gz: max reads length: 150 Reads length: 150 Default k-mer sizes were set to [21, 33, 55, 77] because estimated read length (150) is equal to or greater than 150 ===== Read error correction started. ===== Read error correction started. == Running: /oak/stanford/groups/akundaje/marinovg/programs/SPAdes-3.14.0-Linux/bin/spades-hammer /srv/scratch/marinovg/SPAdes-3.14-L1399-Cyclotella_meninghiana_gDNA/corrected/configs/config.info 0:00:00.000 8M / 13M INFO General (main.cpp : 75) Starting BayesHammer, built from refs/heads/spades_3.14.0, git revision c831f9be30a4364383cd4ebe5b78cdfcaad1acc9 0:00:00.001 8M / 13M INFO General (main.cpp : 76) Loading config from /srv/scratch/marinovg/SPAdes-3.14-L1399-Cyclotella_meninghiana_gDNA/corrected/configs/config.info 0:00:00.001 8M / 13M INFO General (main.cpp : 78) Maximum # of threads to use (adjusted due to OMP capabilities): 48 0:00:00.001 8M / 13M INFO General (memory_limit.cpp : 49) Memory limit set to 250 Gb 0:00:00.001 8M / 13M INFO General (main.cpp : 86) Trying to determine PHRED offset 0:00:00.002 8M / 13M INFO General (main.cpp : 92) Determined value is 33 0:00:00.002 8M / 13M INFO General (hammer_tools.cpp : 38) Hamming graph threshold tau=1, k=21, subkmer positions = [ 0 10 ] 0:00:00.002 8M / 13M INFO General (main.cpp : 113) Size of aux. kmer data 24 bytes === ITERATION 0 begins === 0:00:00.003 8M / 13M INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:00:00.003 8M / 13M INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 768 files using 48 threads. This might take a while. 0:00:00.003 9M / 13M INFO General (file_limit.hpp : 32) Open file limit set to 1024 0:00:00.004 9M / 13M INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 1.7361 Gb 0:00:00.004 9M / 13M INFO General (kmer_splitters.hpp : 97) Using cell size of 87381 0:00:00.054 28G / 28G INFO K-mer Splitting (kmer_data.cpp : 97) Processing /srv/scratch/marinovg/L1399-Cyclotella_meninghiana_gDNA.H57H5DSXY_L4.read1.unpaired.fastq.gz 0:00:21.148 28G / 28G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 4182012 reads 0:00:21.153 28G / 28G INFO K-mer Splitting (kmer_data.cpp : 97) Processing /srv/scratch/marinovg/L1399-Cyclotella_meninghiana_gDNA.H57H5DSXY_L4.read2.unpaired.fastq.gz 0:00:25.305 28G / 28G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 5016907 reads 0:00:25.310 28G / 28G INFO K-mer Splitting (kmer_data.cpp : 97) Processing /srv/scratch/marinovg/L1399-Cyclotella_meninghiana_gDNA.H57H5DSXY_L4.read1.paired.fastq.gz 0:01:32.060 28G / 28G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 16946283 reads 0:02:35.785 28G / 28G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 28780550 reads 0:03:39.383 28G / 28G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 40625504 reads 0:04:47.264 28G / 28G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 52424939 reads 0:05:51.401 28G / 28G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 64227649 reads 0:06:56.462 28G / 28G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 76145724 reads 0:08:00.089 28G / 28G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 88029678 reads 0:09:04.192 28G / 28G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 99927047 reads 0:10:07.597 28G / 28G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 111722951 reads 0:11:11.254 28G / 28G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 123496016 reads 0:12:14.542 28G / 28G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 135361693 reads 0:15:58.845 28G / 28G INFO K-mer Splitting (kmer_data.cpp : 97) Processing /srv/scratch/marinovg/L1399-Cyclotella_meninghiana_gDNA.H57H5DSXY_L4.read2.paired.fastq.gz 0:25:10.365 28G / 28G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 278643495 reads 0:31:32.818 28G / 28G INFO K-mer Splitting (kmer_data.cpp : 112) Total 349070985 reads processed 0:31:34.470 561M / 25G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:32:11.832 148M / 25G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 2428722794 kmers in total. 0:32:11.835 148M / 25G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:32:59.216 148M / 25G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:34:18.768 2G / 25G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 0:35:11.512 2G / 25G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 1126233962 bytes occupied (3.70972 bits per kmer). 0:35:11.523 2G / 25G INFO K-mer Counting (kmer_data.cpp : 351) Arranging kmers in hash map order 0:36:41.387 42G / 42G INFO General (main.cpp : 148) Clustering Hamming graph. 1:12:18.946 42G / 42G INFO General (main.cpp : 155) Extracting clusters 1:32:41.569 44G / 94G INFO General (main.cpp : 167) Clustering done. Total clusters: 828454661 1:32:42.864 24G / 94G INFO K-mer Counting (kmer_data.cpp : 371) Collecting K-mer information, this takes a while. 1:33:09.999 80G / 94G INFO K-mer Counting (kmer_data.cpp : 377) Processing /srv/scratch/marinovg/L1399-Cyclotella_meninghiana_gDNA.H57H5DSXY_L4.read1.unpaired.fastq.gz 1:33:35.221 79G / 94G INFO K-mer Counting (kmer_data.cpp : 377) Processing /srv/scratch/marinovg/L1399-Cyclotella_meninghiana_gDNA.H57H5DSXY_L4.read2.unpaired.fastq.gz 1:33:39.524 79G / 94G INFO K-mer Counting (kmer_data.cpp : 377) Processing /srv/scratch/marinovg/L1399-Cyclotella_meninghiana_gDNA.H57H5DSXY_L4.read1.paired.fastq.gz 1:52:53.857 79G / 94G INFO K-mer Counting (kmer_data.cpp : 377) Processing /srv/scratch/marinovg/L1399-Cyclotella_meninghiana_gDNA.H57H5DSXY_L4.read2.paired.fastq.gz 2:12:05.502 79G / 94G INFO K-mer Counting (kmer_data.cpp : 384) Collection done, postprocessing. 2:12:12.138 79G / 94G INFO K-mer Counting (kmer_data.cpp : 398) There are 2428722794 kmers in total. Among them 1410899956 (58.0923%) are singletons. 2:12:12.139 79G / 94G INFO General (main.cpp : 173) Subclustering Hamming graph 4:22:35.679 79G / 94G INFO Hamming Subclustering (kmer_cluster.cpp : 649) Subclustering done. Total 84807 non-read kmers were generated. 4:22:35.681 79G / 94G INFO Hamming Subclustering (kmer_cluster.cpp : 650) Subclustering statistics: 4:22:35.681 79G / 94G INFO Hamming Subclustering (kmer_cluster.cpp : 651) Total singleton hamming clusters: 652844144. Among them 355210278 (54.4097%) are good 4:22:35.682 79G / 94G INFO Hamming Subclustering (kmer_cluster.cpp : 652) Total singleton subclusters: 30396264. Among them 30311379 (99.7207%) are good 4:22:35.682 79G / 94G INFO Hamming Subclustering (kmer_cluster.cpp : 653) Total non-singleton subcluster centers: 231434789. Among them 163026869 (70.4418%) are good 4:22:35.683 79G / 94G INFO Hamming Subclustering (kmer_cluster.cpp : 654) Average size of non-trivial subcluster: 7.67466 kmers 4:22:35.684 79G / 94G INFO Hamming Subclustering (kmer_cluster.cpp : 655) Average number of sub-clusters per non-singleton cluster: 1.49098 4:22:35.684 79G / 94G INFO Hamming Subclustering (kmer_cluster.cpp : 656) Total solid k-mers: 548548526 4:22:35.685 79G / 94G INFO Hamming Subclustering (kmer_cluster.cpp : 657) Substitution probabilities: [4,4]((0.905184,0.0282746,0.0155219,0.051019),(0.0267533,0.946925,0.0144158,0.0119062),(0.0115716,0.0141835,0.947133,0.0271123),(0.0504457,0.0151669,0.0279276,0.90646)) 4:22:36.738 79G / 94G INFO General (main.cpp : 178) Finished clustering. 4:22:36.740 79G / 94G INFO General (main.cpp : 197) Starting solid k-mers expansion in 48 threads. 4:49:15.457 79G / 94G INFO General (main.cpp : 218) Solid k-mers iteration 0 produced 199724851 new k-mers. 5:16:03.896 79G / 94G INFO General (main.cpp : 218) Solid k-mers iteration 1 produced 11132344 new k-mers. 5:42:50.456 79G / 94G INFO General (main.cpp : 218) Solid k-mers iteration 2 produced 466508 new k-mers. 6:09:54.976 79G / 94G INFO General (main.cpp : 218) Solid k-mers iteration 3 produced 25434 new k-mers. 6:36:40.134 79G / 94G INFO General (main.cpp : 218) Solid k-mers iteration 4 produced 2349 new k-mers. 7:03:17.176 79G / 94G INFO General (main.cpp : 218) Solid k-mers iteration 5 produced 149 new k-mers. 7:30:00.622 79G / 94G INFO General (main.cpp : 218) Solid k-mers iteration 6 produced 65 new k-mers. 7:56:43.087 79G / 94G INFO General (main.cpp : 218) Solid k-mers iteration 7 produced 0 new k-mers. 7:56:43.089 79G / 94G INFO General (main.cpp : 222) Solid k-mers finalized 7:56:43.090 79G / 94G INFO General (hammer_tools.cpp : 222) Starting read correction in 48 threads. 7:56:43.090 79G / 94G INFO General (hammer_tools.cpp : 266) Correcting single reads: /srv/scratch/marinovg/L1399-Cyclotella_meninghiana_gDNA.H57H5DSXY_L4.read1.unpaired.fastq.gz 7:56:55.913 81G / 94G INFO General (hammer_tools.cpp : 129) Prepared batch 0 of 4182012 reads. 7:57:08.505 81G / 94G INFO General (hammer_tools.cpp : 134) Processed batch 0 7:57:12.101 81G / 94G INFO General (hammer_tools.cpp : 138) Written batch 0 7:57:13.363 81G / 94G INFO General (hammer_tools.cpp : 266) Correcting single reads: /srv/scratch/marinovg/L1399-Cyclotella_meninghiana_gDNA.H57H5DSXY_L4.read2.unpaired.fastq.gz 7:57:15.627 81G / 94G INFO General (hammer_tools.cpp : 129) Prepared batch 0 of 834895 reads. 7:57:18.534 80G / 94G INFO General (hammer_tools.cpp : 134) Processed batch 0 7:57:19.208 80G / 94G INFO General (hammer_tools.cpp : 138) Written batch 0 7:57:19.493 80G / 94G INFO General (hammer_tools.cpp : 235) Correcting pair of reads: /srv/scratch/marinovg/L1399-Cyclotella_meninghiana_gDNA.H57H5DSXY_L4.read1.paired.fastq.gz and /srv/scratch/marinovg/L1399-Cyclotella_meninghiana_gDNA.H57H5DSXY_L4.read2.paired.fastq.gz 7:57:49.764 84G / 94G INFO General (hammer_tools.cpp : 170) Prepared batch 0 of 4800000 reads. 7:58:17.764 84G / 94G INFO General (hammer_tools.cpp : 177) Processed batch 0 7:58:26.623 84G / 94G INFO General (hammer_tools.cpp : 187) Written batch 0 7:58:54.842 84G / 94G INFO General (hammer_tools.cpp : 170) Prepared batch 1 of 4800000 reads. 7:59:22.708 84G / 94G INFO General (hammer_tools.cpp : 177) Processed batch 1 7:59:30.760 84G / 94G INFO General (hammer_tools.cpp : 187) Written batch 1 7:59:58.750 84G / 94G INFO General (hammer_tools.cpp : 170) Prepared batch 2 of 4800000 reads. 8:00:26.110 84G / 94G INFO General (hammer_tools.cpp : 177) Processed batch 2 8:00:34.330 84G / 94G INFO General (hammer_tools.cpp : 187) Written batch 2 8:01:02.435 84G / 94G INFO General (hammer_tools.cpp : 170) Prepared batch 3 of 4800000 reads. 8:01:30.889 84G / 94G INFO General (hammer_tools.cpp : 177) Processed batch 3 8:01:38.762 84G / 94G INFO General (hammer_tools.cpp : 187) Written batch 3 8:02:06.611 84G / 94G INFO General (hammer_tools.cpp : 170) Prepared batch 4 of 4800000 reads. 8:02:34.344 84G / 94G INFO General (hammer_tools.cpp : 177) Processed batch 4 8:02:42.261 84G / 94G INFO General (hammer_tools.cpp : 187) Written batch 4 8:03:10.455 84G / 94G INFO General (hammer_tools.cpp : 170) Prepared batch 5 of 4800000 reads. 8:03:37.934 84G / 94G INFO General (hammer_tools.cpp : 177) Processed batch 5 8:03:45.999 84G / 94G INFO General (hammer_tools.cpp : 187) Written batch 5 8:04:13.885 84G / 94G INFO General (hammer_tools.cpp : 170) Prepared batch 6 of 4800000 reads. 8:04:43.253 84G / 94G INFO General (hammer_tools.cpp : 177) Processed batch 6 8:04:51.919 84G / 94G INFO General (hammer_tools.cpp : 187) Written batch 6 8:05:20.346 84G / 94G INFO General (hammer_tools.cpp : 170) Prepared batch 7 of 4800000 reads. 8:05:48.688 84G / 94G INFO General (hammer_tools.cpp : 177) Processed batch 7 8:05:56.908 84G / 94G INFO General (hammer_tools.cpp : 187) Written batch 7 8:06:24.639 84G / 94G INFO General (hammer_tools.cpp : 170) Prepared batch 8 of 4800000 reads. 8:06:52.709 84G / 94G INFO General (hammer_tools.cpp : 177) Processed batch 8 8:07:01.476 84G / 94G INFO General (hammer_tools.cpp : 187) Written batch 8 8:07:29.287 84G / 94G INFO General (hammer_tools.cpp : 170) Prepared batch 9 of 4800000 reads. 8:07:58.035 84G / 94G INFO General (hammer_tools.cpp : 177) Processed batch 9 8:08:06.315 84G / 94G INFO General (hammer_tools.cpp : 187) Written batch 9 8:08:34.025 84G / 94G INFO General (hammer_tools.cpp : 170) Prepared batch 10 of 4800000 reads. 8:09:03.718 84G / 94G INFO General (hammer_tools.cpp : 177) Processed batch 10 8:09:11.916 84G / 94G INFO General (hammer_tools.cpp : 187) Written batch 10 8:09:39.721 84G / 94G INFO General (hammer_tools.cpp : 170) Prepared batch 11 of 4800000 reads. 8:10:08.930 84G / 94G INFO General (hammer_tools.cpp : 177) Processed batch 11 8:10:17.248 84G / 94G INFO General (hammer_tools.cpp : 187) Written batch 11 8:10:45.184 84G / 94G INFO General (hammer_tools.cpp : 170) Prepared batch 12 of 4800000 reads. 8:11:14.512 84G / 94G INFO General (hammer_tools.cpp : 177) Processed batch 12 8:11:22.857 84G / 94G INFO General (hammer_tools.cpp : 187) Written batch 12 8:11:50.775 84G / 94G INFO General (hammer_tools.cpp : 170) Prepared batch 13 of 4800000 reads. 8:12:20.115 84G / 94G INFO General (hammer_tools.cpp : 177) Processed batch 13 8:12:28.258 84G / 94G INFO General (hammer_tools.cpp : 187) Written batch 13 8:12:56.173 84G / 94G INFO General (hammer_tools.cpp : 170) Prepared batch 14 of 4800000 reads. 8:13:25.519 84G / 94G INFO General (hammer_tools.cpp : 177) Processed batch 14 8:13:33.747 84G / 94G INFO General (hammer_tools.cpp : 187) Written batch 14 8:14:01.781 84G / 94G INFO General (hammer_tools.cpp : 170) Prepared batch 15 of 4800000 reads. 8:14:31.547 84G / 94G INFO General (hammer_tools.cpp : 177) Processed batch 15 8:14:40.238 84G / 94G INFO General (hammer_tools.cpp : 187) Written batch 15 8:15:08.734 84G / 94G INFO General (hammer_tools.cpp : 170) Prepared batch 16 of 4800000 reads. 8:15:38.351 84G / 94G INFO General (hammer_tools.cpp : 177) Processed batch 16 8:15:46.541 84G / 94G INFO General (hammer_tools.cpp : 187) Written batch 16 8:16:14.725 84G / 94G INFO General (hammer_tools.cpp : 170) Prepared batch 17 of 4800000 reads. 8:16:44.739 84G / 94G INFO General (hammer_tools.cpp : 177) Processed batch 17 8:16:52.906 84G / 94G INFO General (hammer_tools.cpp : 187) Written batch 17 8:17:21.151 84G / 94G INFO General (hammer_tools.cpp : 170) Prepared batch 18 of 4800000 reads. 8:17:50.634 84G / 94G INFO General (hammer_tools.cpp : 177) Processed batch 18 8:17:58.877 84G / 94G INFO General (hammer_tools.cpp : 187) Written batch 18 8:18:26.776 84G / 94G INFO General (hammer_tools.cpp : 170) Prepared batch 19 of 4800000 reads. 8:18:56.118 84G / 94G INFO General (hammer_tools.cpp : 177) Processed batch 19 8:19:04.230 84G / 94G INFO General (hammer_tools.cpp : 187) Written batch 19 8:19:32.363 84G / 94G INFO General (hammer_tools.cpp : 170) Prepared batch 20 of 4800000 reads. 8:20:03.406 84G / 94G INFO General (hammer_tools.cpp : 177) Processed batch 20 8:20:11.690 84G / 94G INFO General (hammer_tools.cpp : 187) Written batch 20 8:20:39.822 84G / 94G INFO General (hammer_tools.cpp : 170) Prepared batch 21 of 4800000 reads. 8:21:08.888 84G / 94G INFO General (hammer_tools.cpp : 177) Processed batch 21 8:21:17.135 84G / 94G INFO General (hammer_tools.cpp : 187) Written batch 21 8:21:45.785 84G / 94G INFO General (hammer_tools.cpp : 170) Prepared batch 22 of 4800000 reads. 8:22:16.032 84G / 94G INFO General (hammer_tools.cpp : 177) Processed batch 22 8:22:24.461 84G / 94G INFO General (hammer_tools.cpp : 187) Written batch 22 8:22:52.683 84G / 94G INFO General (hammer_tools.cpp : 170) Prepared batch 23 of 4800000 reads. 8:23:21.445 84G / 94G INFO General (hammer_tools.cpp : 177) Processed batch 23 8:23:29.894 84G / 94G INFO General (hammer_tools.cpp : 187) Written batch 23 8:23:57.922 84G / 94G INFO General (hammer_tools.cpp : 170) Prepared batch 24 of 4800000 reads. 8:24:27.114 84G / 94G INFO General (hammer_tools.cpp : 177) Processed batch 24 8:24:35.451 84G / 94G INFO General (hammer_tools.cpp : 187) Written batch 24 8:25:03.744 84G / 94G INFO General (hammer_tools.cpp : 170) Prepared batch 25 of 4800000 reads. 8:25:34.375 84G / 94G INFO General (hammer_tools.cpp : 177) Processed batch 25 8:25:42.397 84G / 94G INFO General (hammer_tools.cpp : 187) Written batch 25 8:26:10.354 84G / 94G INFO General (hammer_tools.cpp : 170) Prepared batch 26 of 4800000 reads. 8:26:39.481 84G / 94G INFO General (hammer_tools.cpp : 177) Processed batch 26 8:26:47.751 84G / 94G INFO General (hammer_tools.cpp : 187) Written batch 26 8:27:16.599 84G / 94G INFO General (hammer_tools.cpp : 170) Prepared batch 27 of 4800000 reads. 8:27:45.621 84G / 94G INFO General (hammer_tools.cpp : 177) Processed batch 27 8:27:53.967 84G / 94G INFO General (hammer_tools.cpp : 187) Written batch 27 8:28:23.045 84G / 94G INFO General (hammer_tools.cpp : 170) Prepared batch 28 of 4800000 reads. 8:28:52.034 84G / 94G INFO General (hammer_tools.cpp : 177) Processed batch 28 8:29:00.386 84G / 94G INFO General (hammer_tools.cpp : 187) Written batch 28 8:29:29.440 84G / 94G INFO General (hammer_tools.cpp : 170) Prepared batch 29 of 4800000 reads. 8:29:57.698 84G / 94G INFO General (hammer_tools.cpp : 177) Processed batch 29 8:30:06.123 84G / 94G INFO General (hammer_tools.cpp : 187) Written batch 29 8:30:35.036 84G / 94G INFO General (hammer_tools.cpp : 170) Prepared batch 30 of 4800000 reads. 8:31:03.671 84G / 94G INFO General (hammer_tools.cpp : 177) Processed batch 30 8:31:11.838 84G / 94G INFO General (hammer_tools.cpp : 187) Written batch 30 8:31:40.987 84G / 94G INFO General (hammer_tools.cpp : 170) Prepared batch 31 of 4800000 reads. 8:32:09.894 84G / 94G INFO General (hammer_tools.cpp : 177) Processed batch 31 8:32:18.487 84G / 94G INFO General (hammer_tools.cpp : 187) Written batch 31 8:32:47.047 84G / 94G INFO General (hammer_tools.cpp : 170) Prepared batch 32 of 4800000 reads. 8:33:17.017 84G / 94G INFO General (hammer_tools.cpp : 177) Processed batch 32 8:33:25.248 84G / 94G INFO General (hammer_tools.cpp : 187) Written batch 32 8:33:53.627 84G / 94G INFO General (hammer_tools.cpp : 170) Prepared batch 33 of 4800000 reads. 8:34:22.655 84G / 94G INFO General (hammer_tools.cpp : 177) Processed batch 33 8:34:30.632 84G / 94G INFO General (hammer_tools.cpp : 187) Written batch 33 8:34:59.066 84G / 94G INFO General (hammer_tools.cpp : 170) Prepared batch 34 of 4800000 reads. 8:35:28.921 84G / 94G INFO General (hammer_tools.cpp : 177) Processed batch 34 8:35:37.635 84G / 94G INFO General (hammer_tools.cpp : 187) Written batch 34 8:36:02.321 84G / 94G INFO General (hammer_tools.cpp : 170) Prepared batch 35 of 4027039 reads. 8:36:27.260 84G / 94G INFO General (hammer_tools.cpp : 177) Processed batch 35 8:36:34.360 84G / 94G INFO General (hammer_tools.cpp : 187) Written batch 35 8:36:36.498 84G / 94G INFO General (hammer_tools.cpp : 276) Correction done. Changed 60420958 bases in 32327861 reads. 8:36:36.499 84G / 94G INFO General (hammer_tools.cpp : 277) Failed to correct 68556 bases out of 50672565016. 8:36:41.495 7G / 94G INFO General (main.cpp : 255) Saving corrected dataset description to /srv/scratch/marinovg/SPAdes-3.14-L1399-Cyclotella_meninghiana_gDNA/corrected/corrected.yaml 8:36:41.531 7G / 94G INFO General (main.cpp : 262) All done. Exiting. ===== Read error correction finished. ===== corrected reads compression started. == Running: /usr/bin/python /oak/stanford/groups/akundaje/marinovg/programs/SPAdes-3.14.0-Linux/share/spades/spades_pipeline/scripts/compress_all.py --input_file /srv/scratch/marinovg/SPAdes-3.14-L1399-Cyclotella_meninghiana_gDNA/corrected/corrected.yaml --ext_python_modules_home /oak/stanford/groups/akundaje/marinovg/programs/SPAdes-3.14.0-Linux/share/spades --max_threads 60 --output_dir /srv/scratch/marinovg/SPAdes-3.14-L1399-Cyclotella_meninghiana_gDNA/corrected --gzip_output == Compressing corrected reads (with pigz) ===== corrected reads compression finished. ===== Read error correction finished. ===== Assembling started. ===== K21 started. == Running: /oak/stanford/groups/akundaje/marinovg/programs/SPAdes-3.14.0-Linux/bin/spades-core /srv/scratch/marinovg/SPAdes-3.14-L1399-Cyclotella_meninghiana_gDNA/K21/configs/config.info 0:00:00.000 8M / 13M INFO General (main.cpp : 73) Loaded config from /srv/scratch/marinovg/SPAdes-3.14-L1399-Cyclotella_meninghiana_gDNA/K21/configs/config.info 0:00:00.000 8M / 13M INFO General (memory_limit.cpp : 49) Memory limit set to 250 Gb 0:00:00.000 8M / 13M INFO General (main.cpp : 83) Starting SPAdes, built from refs/heads/spades_3.14.0, git revision c831f9be30a4364383cd4ebe5b78cdfcaad1acc9 0:00:00.000 8M / 13M INFO General (main.cpp : 84) Maximum k-mer length: 128 0:00:00.000 8M / 13M INFO General (main.cpp : 85) Assembling dataset (/srv/scratch/marinovg/SPAdes-3.14-L1399-Cyclotella_meninghiana_gDNA/dataset.info) with K=21 0:00:00.000 8M / 13M INFO General (main.cpp : 86) Maximum # of threads to use (adjusted due to OMP capabilities): 48 0:00:00.000 8M / 13M INFO General (launch.hpp : 79) SPAdes started 0:00:00.000 8M / 13M INFO General (launch.hpp : 86) Starting from stage: read_conversion 0:00:00.000 8M / 13M INFO General (launch.hpp : 92) Two-step RR enabled: 0 0:00:00.000 8M / 13M INFO StageManager (stage.cpp : 166) STAGE == Binary Read Conversion 0:00:00.002 8M / 13M INFO General (read_converter.cpp : 72) Converting reads to binary format for library #0 (takes a while) 0:00:00.002 8M / 13M INFO General (read_converter.cpp : 73) Converting paired reads 0:00:00.002 15M / 15M INFO General (binary_converter.cpp : 111) 0 reads written 0:00:00.002 15M / 15M INFO General (read_converter.cpp : 81) Converting single reads 0:00:00.401 65M / 65M INFO General (binary_converter.cpp : 96) 16384 reads processed 0:00:00.421 67M / 67M INFO General (binary_converter.cpp : 96) 32768 reads processed 0:00:00.463 72M / 72M INFO General (binary_converter.cpp : 96) 65536 reads processed 0:00:00.877 112M / 112M INFO General (binary_converter.cpp : 96) 131072 reads processed 0:00:01.336 163M / 163M INFO General (binary_converter.cpp : 96) 262144 reads processed 0:00:02.555 295M / 295M INFO General (binary_converter.cpp : 96) 524288 reads processed 0:00:04.577 464M / 464M INFO General (binary_converter.cpp : 96) 1048576 reads processed 0:00:08.542 617M / 621M INFO General (binary_converter.cpp : 96) 2097152 reads processed 0:00:16.564 948M / 960M INFO General (binary_converter.cpp : 111) 4107115 reads written 0:00:16.565 948M / 960M INFO General (read_converter.cpp : 87) Converting merged reads 0:00:16.566 948M / 960M INFO General (binary_converter.cpp : 111) 0 reads written 0:00:16.636 948M / 960M INFO General (read_converter.cpp : 72) Converting reads to binary format for library #1 (takes a while) 0:00:16.637 948M / 960M INFO General (read_converter.cpp : 73) Converting paired reads 0:00:16.638 948M / 960M INFO General (binary_converter.cpp : 111) 0 reads written 0:00:16.639 948M / 960M INFO General (read_converter.cpp : 81) Converting single reads 0:00:16.994 989M / 989M INFO General (binary_converter.cpp : 96) 16384 reads processed 0:00:17.015 991M / 991M INFO General (binary_converter.cpp : 96) 32768 reads processed 0:00:17.060 953M / 986M INFO General (binary_converter.cpp : 96) 65536 reads processed 0:00:17.394 973M / 986M INFO General (binary_converter.cpp : 96) 131072 reads processed 0:00:17.774 981M / 986M INFO General (binary_converter.cpp : 96) 262144 reads processed 0:00:18.825 984M / 1023M INFO General (binary_converter.cpp : 96) 524288 reads processed 0:00:19.705 958M / 1023M INFO General (binary_converter.cpp : 111) 787141 reads written 0:00:19.706 958M / 1023M INFO General (read_converter.cpp : 87) Converting merged reads 0:00:19.708 958M / 1023M INFO General (binary_converter.cpp : 111) 0 reads written 0:00:19.730 958M / 1023M INFO General (read_converter.cpp : 72) Converting reads to binary format for library #2 (takes a while) 0:00:19.731 958M / 1023M INFO General (read_converter.cpp : 73) Converting paired reads 0:00:20.556 2G / 2G INFO General (binary_converter.cpp : 96) 16384 reads processed 0:00:20.603 2G / 2G INFO General (binary_converter.cpp : 96) 32768 reads processed 0:00:20.699 2G / 2G INFO General (binary_converter.cpp : 96) 65536 reads processed 0:00:20.979 1020M / 2G INFO General (binary_converter.cpp : 96) 131072 reads processed 0:00:21.487 2G / 2G INFO General (binary_converter.cpp : 96) 262144 reads processed 0:00:22.805 2G / 2G INFO General (binary_converter.cpp : 96) 524288 reads processed 0:00:25.214 2G / 2G INFO General (binary_converter.cpp : 96) 1048576 reads processed 0:00:29.509 2G / 2G INFO General (binary_converter.cpp : 96) 2097152 reads processed 0:00:38.398 2G / 2G INFO General (binary_converter.cpp : 96) 4194304 reads processed 0:00:57.320 2G / 2G INFO General (binary_converter.cpp : 96) 8388608 reads processed 0:01:34.017 2G / 3G INFO General (binary_converter.cpp : 96) 16777216 reads processed 0:02:44.497 2G / 3G INFO General (binary_converter.cpp : 96) 33554432 reads processed 0:05:09.212 3G / 3G INFO General (binary_converter.cpp : 96) 67108864 reads processed 0:09:59.014 2G / 3G INFO General (binary_converter.cpp : 96) 134217728 reads processed 0:12:36.215 2G / 3G INFO General (binary_converter.cpp : 111) 171621781 reads written 0:12:36.216 2G / 3G INFO General (read_converter.cpp : 81) Converting single reads 0:12:36.627 2G / 3G INFO General (binary_converter.cpp : 96) 16384 reads processed 0:12:36.647 2G / 3G INFO General (binary_converter.cpp : 96) 32768 reads processed 0:12:36.686 2G / 3G INFO General (binary_converter.cpp : 96) 65536 reads processed 0:12:37.043 2G / 3G INFO General (binary_converter.cpp : 96) 131072 reads processed 0:12:37.469 2G / 3G INFO General (binary_converter.cpp : 96) 262144 reads processed 0:12:37.887 2G / 3G INFO General (binary_converter.cpp : 111) 377985 reads written 0:12:37.888 2G / 3G INFO General (read_converter.cpp : 87) Converting merged reads 0:12:37.888 2G / 3G INFO General (binary_converter.cpp : 111) 0 reads written 0:12:37.958 87M / 3G INFO StageManager (stage.cpp : 166) STAGE == de Bruijn graph construction 0:12:37.980 91M / 3G INFO General (construction.cpp : 150) Max read length 150 0:12:37.981 91M / 3G INFO General (construction.cpp : 156) Average read length 145.292 0:12:37.981 91M / 3G INFO General (stage.cpp : 113) PROCEDURE == k+1-mer counting 0:12:37.982 91M / 3G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 2304 files using 48 threads. This might take a while. 0:12:37.984 91M / 3G INFO General (file_limit.hpp : 32) Open file limit set to 2400 0:12:37.985 91M / 3G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 1.73607 Gb 0:12:37.985 91M / 3G INFO General (kmer_splitters.hpp : 97) Using cell size of 29127 0:12:46.856 28G / 28G INFO General (kmer_splitters.hpp : 287) Processed 23246206 reads 0:13:03.893 28G / 28G INFO General (kmer_splitters.hpp : 287) Processed 64661206 reads 0:13:23.002 28G / 28G INFO General (kmer_splitters.hpp : 287) Processed 106004615 reads 0:13:40.858 28G / 28G INFO General (kmer_splitters.hpp : 287) Processed 147177700 reads 0:13:57.952 28G / 28G INFO General (kmer_splitters.hpp : 287) Processed 188089390 reads 0:14:14.362 28G / 28G INFO General (kmer_splitters.hpp : 287) Processed 228985558 reads 0:14:31.752 28G / 28G INFO General (kmer_splitters.hpp : 287) Processed 270591261 reads 0:14:48.137 28G / 28G INFO General (kmer_splitters.hpp : 287) Processed 312287772 reads 0:15:05.017 28G / 28G INFO General (kmer_splitters.hpp : 287) Processed 354013243 reads 0:15:20.844 28G / 28G INFO General (kmer_splitters.hpp : 287) Processed 394815412 reads 0:15:37.114 28G / 28G INFO General (kmer_splitters.hpp : 287) Processed 436031298 reads 0:15:53.983 28G / 28G INFO General (kmer_splitters.hpp : 287) Processed 477784175 reads 0:16:11.017 28G / 28G INFO General (kmer_splitters.hpp : 287) Processed 518998146 reads 0:16:27.539 28G / 28G INFO General (kmer_splitters.hpp : 287) Processed 560208740 reads 0:16:44.480 28G / 28G INFO General (kmer_splitters.hpp : 287) Processed 601473356 reads 0:17:28.735 547M / 22G INFO General (kmer_splitters.hpp : 293) Used 697031606 reads 0:17:28.736 547M / 22G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:17:44.321 323M / 22G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 587269059 kmers in total. 0:17:44.323 323M / 22G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:17:47.744 310M / 22G INFO General (stage.cpp : 113) PROCEDURE == Extension index construction 0:17:47.745 310M / 22G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:17:47.745 310M / 22G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 768 files using 48 threads. This might take a while. 0:17:47.746 310M / 22G INFO General (file_limit.hpp : 32) Open file limit set to 2400 0:17:47.747 310M / 22G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 1.73604 Gb 0:17:47.747 310M / 22G INFO General (kmer_splitters.hpp : 97) Using cell size of 87381 0:17:55.308 28G / 28G INFO General (kmer_splitters.hpp : 364) Processed 196351557 kmers 0:18:00.774 28G / 28G INFO General (kmer_splitters.hpp : 364) Processed 392750253 kmers 0:18:06.233 28G / 28G INFO General (kmer_splitters.hpp : 364) Processed 587269155 kmers 0:18:06.234 28G / 28G INFO General (kmer_splitters.hpp : 369) Used 587269155 kmers. 0:18:06.545 551M / 22G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:18:10.367 530M / 22G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 573740201 kmers in total. 0:18:10.368 530M / 22G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:18:13.828 530M / 22G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:18:31.210 726M / 22G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 0:18:42.630 726M / 22G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 266057836 bytes occupied (3.7098 bits per kmer). 0:18:43.075 2G / 22G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 99) Building k-mer extensions from k+1-mers 0:19:00.698 2G / 22G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 103) Building k-mer extensions from k+1-mers finished. 0:19:00.705 2G / 22G INFO General (stage.cpp : 113) PROCEDURE == Early tip clipping 0:19:00.707 2G / 22G INFO General (construction.cpp : 293) Early tip clipper length bound set as (RL - K) 0:19:00.708 2G / 22G INFO Early tip clipping (early_simplification.hpp : 28) Early tip clipping 0:19:21.911 2G / 22G INFO Early tip clipping (early_simplification.hpp : 63) #tipped junctions: 7100310 0:19:22.125 2G / 22G INFO Early tip clipping (early_simplification.hpp : 74) Clipped tips: 7201777 0:19:22.354 2G / 22G INFO Early tip clipping (early_simplification.hpp : 30) 70700900 22-mers were removed by early tip clipper 0:19:22.356 2G / 22G INFO General (stage.cpp : 113) PROCEDURE == Condensing graph 0:19:22.359 2G / 22G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths 0:19:47.514 5G / 22G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 36507163 sequences extracted 0:19:59.589 5G / 22G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops 0:20:06.846 5G / 22G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 561 loops collected 0:21:42.829 11G / 22G INFO General (stage.cpp : 113) PROCEDURE == Filling coverage indices (PHM) 0:21:42.831 11G / 22G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:21:42.832 11G / 22G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:21:52.268 11G / 22G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 272355766 bytes occupied (3.71013 bits per kmer). 0:21:53.432 14G / 22G INFO General (construction.cpp : 429) Collecting k-mer coverage information from reads, this takes a while. 0:31:31.257 13G / 22G INFO General (construction.cpp : 549) Filling coverage and flanking coverage from PHM 0:31:43.744 13G / 22G INFO General (construction.cpp : 505) Processed 48000000 edges 0:31:49.785 13G / 22G INFO General (construction.cpp : 505) Processed 73010882 edges 0:31:51.489 10G / 22G INFO StageManager (stage.cpp : 166) STAGE == EC Threshold Finding 0:31:51.717 10G / 22G INFO General (kmer_coverage_model.cpp : 181) Kmer coverage valley at: 98 0:31:51.725 10G / 22G INFO General (kmer_coverage_model.cpp : 201) K-mer histogram maximum: 132 0:31:51.727 10G / 22G INFO General (kmer_coverage_model.cpp : 237) Estimated median coverage: 133. Coverage mad: 23.7216 0:31:51.733 10G / 22G INFO General (kmer_coverage_model.cpp : 259) Fitting coverage model 0:31:51.896 10G / 22G INFO General (kmer_coverage_model.cpp : 295) ... iteration 2 0:31:52.244 10G / 22G INFO General (kmer_coverage_model.cpp : 295) ... iteration 4 0:31:53.816 10G / 22G INFO General (kmer_coverage_model.cpp : 295) ... iteration 8 0:31:57.369 10G / 22G INFO General (kmer_coverage_model.cpp : 295) ... iteration 16 0:32:02.974 10G / 22G INFO General (kmer_coverage_model.cpp : 295) ... iteration 32 0:32:05.661 10G / 22G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 112.621. Fitted coverage std. dev: 43.8565 0:32:05.666 10G / 22G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 0.535978 0:32:05.667 10G / 22G WARN General (kmer_coverage_model.cpp : 366) Failed to determine erroneous kmer threshold. Threshold set to: 98 0:32:05.668 10G / 22G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 40906206 0:32:05.671 10G / 22G INFO General (genomic_info_filler.cpp : 122) Failed to estimate mean coverage 0:32:05.672 10G / 22G INFO General (genomic_info_filler.cpp : 135) EC coverage threshold value was calculated as 98 0:32:05.673 10G / 22G INFO General (genomic_info_filler.cpp : 136) Trusted kmer low bound: 0 0:32:05.674 10G / 22G INFO StageManager (stage.cpp : 166) STAGE == Raw Simplification 0:32:05.675 10G / 22G INFO General (simplification.cpp : 128) PROCEDURE == InitialCleaning 0:32:05.676 10G / 22G INFO General (simplification.cpp : 69) Most init cleaning disabled since detected mean 0 was less than activation coverage 10 0:32:05.677 10G / 22G INFO Simplification (parallel_processing.hpp : 165) Running Self conjugate edge remover 0:32:06.811 10G / 22G INFO Simplification (parallel_processing.hpp : 167) Self conjugate edge remover triggered 0 times 0:32:06.814 10G / 22G INFO StageManager (stage.cpp : 166) STAGE == Simplification 0:32:06.815 10G / 22G INFO General (simplification.cpp : 383) Graph simplification started 0:32:06.816 10G / 22G INFO General (graph_simplification.hpp : 643) Creating parallel br instance 0:32:06.818 10G / 22G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 1 0:32:06.819 10G / 22G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:32:11.365 10G / 22G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 231631 times 0:32:11.366 10G / 22G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:41:10.348 10G / 22G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 3897867 times 0:41:10.352 10G / 22G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:46:25.064 10G / 22G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 7778166 times 0:46:25.067 10G / 22G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 2 0:46:25.068 10G / 22G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:46:30.040 10G / 22G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 53083 times 0:46:30.041 10G / 22G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:47:47.761 10G / 22G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 377934 times 0:47:47.763 10G / 22G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:48:20.142 10G / 22G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 897884 times 0:48:20.143 10G / 22G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 3 0:48:20.144 10G / 22G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:48:21.352 10G / 22G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 428 times 0:48:21.354 10G / 22G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:48:50.240 10G / 22G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 154516 times 0:48:50.242 10G / 22G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:48:59.626 9G / 22G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 262308 times 0:48:59.627 9G / 22G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 4 0:48:59.628 9G / 22G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:49:00.206 9G / 22G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 177 times 0:49:00.208 9G / 22G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:49:09.488 9G / 22G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 60159 times 0:49:09.490 9G / 22G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:49:13.310 9G / 22G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 110985 times 0:49:13.311 9G / 22G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 5 0:49:13.312 9G / 22G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:49:13.592 9G / 22G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 117 times 0:49:13.593 9G / 22G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:49:17.196 9G / 22G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 26325 times 0:49:17.198 9G / 22G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:49:19.222 9G / 22G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 60024 times 0:49:19.224 9G / 22G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 6 0:49:19.225 9G / 22G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:49:19.361 9G / 22G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 61 times 0:49:19.363 9G / 22G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:49:21.331 9G / 22G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 14852 times 0:49:21.333 9G / 22G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:49:22.607 9G / 22G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 39002 times 0:49:22.609 9G / 22G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 7 0:49:22.610 9G / 22G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:49:22.695 9G / 22G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 44 times 0:49:22.697 9G / 22G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:49:23.832 9G / 22G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 9279 times 0:49:23.834 9G / 22G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:49:24.887 9G / 22G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 30278 times 0:49:24.888 9G / 22G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 8 0:49:24.889 9G / 22G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:49:24.953 9G / 22G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 42 times 0:49:24.955 9G / 22G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:49:25.809 9G / 22G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 6697 times 0:49:25.811 9G / 22G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:49:26.662 9G / 22G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 23476 times 0:49:26.664 9G / 22G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 9 0:49:26.664 9G / 22G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:49:26.713 9G / 22G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 34 times 0:49:26.714 9G / 22G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:49:27.279 9G / 22G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 4891 times 0:49:27.281 9G / 22G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:49:27.948 9G / 22G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 17433 times 0:49:27.950 9G / 22G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 10 0:49:27.951 9G / 22G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:49:27.989 9G / 22G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 15 times 0:49:27.991 9G / 22G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:49:28.428 9G / 22G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 3700 times 0:49:28.430 9G / 22G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:49:28.872 8G / 22G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 13107 times 0:49:28.874 8G / 22G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 11 0:49:28.875 8G / 22G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:49:29.220 8G / 22G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 2850 times 0:49:29.222 8G / 22G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:49:30.370 8G / 22G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 4160 times 0:49:30.372 8G / 22G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:49:30.652 8G / 22G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 5 times 0:49:30.654 8G / 22G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 12 0:49:30.655 8G / 22G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:49:30.667 8G / 22G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:49:30.668 8G / 22G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:49:30.669 8G / 22G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:49:30.670 8G / 22G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:49:30.670 8G / 22G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:49:31.196 8G / 22G INFO StageManager (stage.cpp : 166) STAGE == Simplification Cleanup 0:49:31.198 8G / 22G INFO General (simplification.cpp : 196) PROCEDURE == Post simplification 0:49:31.200 8G / 22G INFO General (graph_simplification.hpp : 456) Disconnection of relatively low covered edges disabled 0:49:31.201 8G / 22G INFO General (graph_simplification.hpp : 493) Complex tip clipping disabled 0:49:31.203 8G / 22G INFO General (graph_simplification.hpp : 643) Creating parallel br instance 0:49:31.204 8G / 22G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:49:31.453 8G / 22G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:49:31.455 8G / 22G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:49:32.129 8G / 22G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 26 times 0:49:32.131 8G / 22G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:49:32.396 8G / 22G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:49:32.398 8G / 22G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:49:33.046 8G / 22G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 1 times 0:49:33.048 8G / 22G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:49:33.049 8G / 22G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:49:33.050 8G / 22G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:49:33.051 8G / 22G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:49:33.052 8G / 22G INFO General (simplification.cpp : 343) Disrupting self-conjugate edges 0:49:34.779 8G / 22G INFO Simplification (parallel_processing.hpp : 165) Running Removing isolated edges 0:49:36.106 8G / 22G INFO Simplification (parallel_processing.hpp : 167) Removing isolated edges triggered 339807 times 0:49:36.108 8G / 22G INFO General (simplification.cpp : 496) Counting average coverage 0:49:36.797 8G / 22G INFO General (simplification.cpp : 502) Average coverage = 221.333 0:49:36.798 8G / 22G INFO StageManager (stage.cpp : 166) STAGE == Contig Output 0:49:36.816 8G / 22G INFO General (read_converter.cpp : 102) Outputting contigs to /srv/scratch/marinovg/SPAdes-3.14-L1399-Cyclotella_meninghiana_gDNA/K21/simplified_contigs 0:49:36.830 8G / 22G INFO General (binary_converter.cpp : 96) 16384 reads processed 0:49:36.841 8G / 22G INFO General (binary_converter.cpp : 96) 32768 reads processed 0:49:36.862 8G / 22G INFO General (binary_converter.cpp : 96) 65536 reads processed 0:49:36.914 8G / 22G INFO General (binary_converter.cpp : 96) 131072 reads processed 0:49:37.001 8G / 22G INFO General (binary_converter.cpp : 96) 262144 reads processed 0:49:37.156 8G / 22G INFO General (binary_converter.cpp : 96) 524288 reads processed 0:49:37.329 8G / 22G INFO General (binary_converter.cpp : 111) 776652 reads written 0:49:37.342 8G / 22G INFO General (launch.hpp : 192) SPAdes finished 0:49:42.564 2G / 22G INFO General (main.cpp : 105) Assembling time: 0 hours 49 minutes 42 seconds ===== K21 finished. ===== K33 started. == Running: /oak/stanford/groups/akundaje/marinovg/programs/SPAdes-3.14.0-Linux/bin/spades-core /srv/scratch/marinovg/SPAdes-3.14-L1399-Cyclotella_meninghiana_gDNA/K33/configs/config.info 0:00:00.000 8M / 13M INFO General (main.cpp : 73) Loaded config from /srv/scratch/marinovg/SPAdes-3.14-L1399-Cyclotella_meninghiana_gDNA/K33/configs/config.info 0:00:00.000 8M / 13M INFO General (memory_limit.cpp : 49) Memory limit set to 250 Gb 0:00:00.000 8M / 13M INFO General (main.cpp : 83) Starting SPAdes, built from refs/heads/spades_3.14.0, git revision c831f9be30a4364383cd4ebe5b78cdfcaad1acc9 0:00:00.000 8M / 13M INFO General (main.cpp : 84) Maximum k-mer length: 128 0:00:00.000 8M / 13M INFO General (main.cpp : 85) Assembling dataset (/srv/scratch/marinovg/SPAdes-3.14-L1399-Cyclotella_meninghiana_gDNA/dataset.info) with K=33 0:00:00.000 8M / 13M INFO General (main.cpp : 86) Maximum # of threads to use (adjusted due to OMP capabilities): 48 0:00:00.000 8M / 13M INFO General (launch.hpp : 79) SPAdes started 0:00:00.000 8M / 13M INFO General (launch.hpp : 86) Starting from stage: read_conversion 0:00:00.000 8M / 13M INFO General (launch.hpp : 92) Two-step RR enabled: 0 0:00:00.000 8M / 13M INFO StageManager (stage.cpp : 166) STAGE == Binary Read Conversion 0:00:00.002 8M / 13M INFO General (read_converter.cpp : 53) Binary reads detected 0:00:00.002 8M / 13M INFO General (read_converter.cpp : 53) Binary reads detected 0:00:00.002 8M / 13M INFO General (read_converter.cpp : 53) Binary reads detected 0:00:00.005 8M / 13M INFO StageManager (stage.cpp : 166) STAGE == de Bruijn graph construction 0:00:00.005 8M / 13M INFO General (construction.cpp : 115) Contigs from previous K will be used: /srv/scratch/marinovg/SPAdes-3.14-L1399-Cyclotella_meninghiana_gDNA/K21/simplified_contigs 0:00:00.011 13M / 13M INFO General (construction.cpp : 150) Max read length 150 0:00:00.011 13M / 13M INFO General (construction.cpp : 156) Average read length 145.292 0:00:00.011 13M / 13M INFO General (stage.cpp : 113) PROCEDURE == k+1-mer counting 0:00:00.011 13M / 13M INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 2304 files using 48 threads. This might take a while. 0:00:00.012 13M / 13M INFO General (file_limit.hpp : 32) Open file limit set to 2400 0:00:00.012 13M / 13M INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 1.73607 Gb 0:00:00.012 13M / 13M INFO General (kmer_splitters.hpp : 97) Using cell size of 16384 0:00:04.255 35G / 35G INFO General (kmer_splitters.hpp : 287) Processed 9122686 reads 0:00:14.934 35G / 35G INFO General (kmer_splitters.hpp : 287) Processed 29590271 reads 0:00:27.908 35G / 35G INFO General (kmer_splitters.hpp : 287) Processed 55433861 reads 0:00:40.170 35G / 35G INFO General (kmer_splitters.hpp : 287) Processed 81115373 reads 0:00:53.137 35G / 35G INFO General (kmer_splitters.hpp : 287) Processed 106925590 reads 0:01:04.102 35G / 35G INFO General (kmer_splitters.hpp : 287) Processed 132713627 reads 0:01:16.063 35G / 35G INFO General (kmer_splitters.hpp : 287) Processed 158285919 reads 0:01:27.774 35G / 35G INFO General (kmer_splitters.hpp : 287) Processed 183906254 reads 0:01:39.613 35G / 35G INFO General (kmer_splitters.hpp : 287) Processed 209516946 reads 0:01:51.404 35G / 35G INFO General (kmer_splitters.hpp : 287) Processed 235103001 reads 0:02:02.773 35G / 35G INFO General (kmer_splitters.hpp : 287) Processed 261086580 reads 0:02:14.916 35G / 35G INFO General (kmer_splitters.hpp : 287) Processed 287113375 reads 0:02:26.393 35G / 35G INFO General (kmer_splitters.hpp : 287) Processed 313076327 reads 0:02:40.172 35G / 35G INFO General (kmer_splitters.hpp : 287) Processed 338957278 reads 0:04:13.624 35G / 35G INFO General (kmer_splitters.hpp : 287) Processed 544850511 reads 0:05:31.244 549M / 25G INFO General (kmer_splitters.hpp : 293) Used 698584910 reads 0:05:31.246 549M / 25G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:05:52.772 262M / 25G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 701966976 kmers in total. 0:05:52.774 262M / 25G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:06:01.227 262M / 25G INFO General (stage.cpp : 113) PROCEDURE == Extension index construction 0:06:01.228 262M / 25G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:06:01.228 262M / 25G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 768 files using 48 threads. This might take a while. 0:06:01.229 262M / 25G INFO General (file_limit.hpp : 32) Open file limit set to 2400 0:06:01.230 262M / 25G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 1.73604 Gb 0:06:01.231 262M / 25G INFO General (kmer_splitters.hpp : 97) Using cell size of 43690 0:06:01.672 28G / 28G INFO General (kmer_splitters.hpp : 364) Processed 7158772 kmers 0:06:02.425 28G / 28G INFO General (kmer_splitters.hpp : 364) Processed 21726316 kmers 0:06:03.109 28G / 28G INFO General (kmer_splitters.hpp : 364) Processed 36344592 kmers 0:06:03.781 28G / 28G INFO General (kmer_splitters.hpp : 364) Processed 50971214 kmers 0:06:04.460 28G / 28G INFO General (kmer_splitters.hpp : 364) Processed 65592957 kmers 0:06:05.158 28G / 28G INFO General (kmer_splitters.hpp : 364) Processed 80225689 kmers 0:06:05.875 28G / 28G INFO General (kmer_splitters.hpp : 364) Processed 94851447 kmers 0:06:06.569 28G / 28G INFO General (kmer_splitters.hpp : 364) Processed 109464653 kmers 0:06:07.329 28G / 28G INFO General (kmer_splitters.hpp : 364) Processed 124098852 kmers 0:06:08.064 28G / 28G INFO General (kmer_splitters.hpp : 364) Processed 138727579 kmers 0:06:08.737 28G / 28G INFO General (kmer_splitters.hpp : 364) Processed 153347094 kmers 0:06:09.442 28G / 28G INFO General (kmer_splitters.hpp : 364) Processed 167963952 kmers 0:06:10.109 28G / 28G INFO General (kmer_splitters.hpp : 364) Processed 182600207 kmers 0:06:10.848 28G / 28G INFO General (kmer_splitters.hpp : 364) Processed 197222766 kmers 0:06:11.684 28G / 28G INFO General (kmer_splitters.hpp : 364) Processed 211846223 kmers 0:06:12.529 28G / 28G INFO General (kmer_splitters.hpp : 364) Processed 226466070 kmers 0:06:13.223 28G / 28G INFO General (kmer_splitters.hpp : 364) Processed 241091529 kmers 0:06:13.875 28G / 28G INFO General (kmer_splitters.hpp : 364) Processed 255722021 kmers 0:06:14.580 28G / 28G INFO General (kmer_splitters.hpp : 364) Processed 270344226 kmers 0:06:29.072 28G / 28G INFO General (kmer_splitters.hpp : 364) Processed 548187585 kmers 0:06:37.446 28G / 28G INFO General (kmer_splitters.hpp : 369) Used 701969280 kmers. 0:06:37.658 369M / 25G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:06:46.248 361M / 25G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 694166163 kmers in total. 0:06:46.250 361M / 25G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:06:55.235 361M / 25G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:07:15.538 681M / 25G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 0:07:47.092 681M / 25G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 321901562 bytes occupied (3.70979 bits per kmer). 0:07:47.660 2G / 25G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 99) Building k-mer extensions from k+1-mers 0:08:09.796 2G / 25G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 103) Building k-mer extensions from k+1-mers finished. 0:08:09.801 2G / 25G INFO General (stage.cpp : 113) PROCEDURE == Early tip clipping 0:08:09.802 2G / 25G INFO General (construction.cpp : 293) Early tip clipper length bound set as (RL - K) 0:08:09.803 2G / 25G INFO Early tip clipping (early_simplification.hpp : 28) Early tip clipping 0:08:33.608 3G / 25G INFO Early tip clipping (early_simplification.hpp : 63) #tipped junctions: 10145267 0:08:34.012 3G / 25G INFO Early tip clipping (early_simplification.hpp : 74) Clipped tips: 10328290 0:08:34.433 2G / 25G INFO Early tip clipping (early_simplification.hpp : 30) 111892090 34-mers were removed by early tip clipper 0:08:34.434 2G / 25G INFO General (stage.cpp : 113) PROCEDURE == Condensing graph 0:08:34.437 2G / 25G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths 0:09:03.449 4G / 25G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 25121985 sequences extracted 0:09:17.178 4G / 25G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops 0:09:25.781 4G / 25G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 636 loops collected 0:10:45.111 8G / 25G INFO General (stage.cpp : 113) PROCEDURE == Filling coverage indices (PHM) 0:10:45.113 8G / 25G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:10:45.113 8G / 25G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:10:57.232 9G / 25G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 325552074 bytes occupied (3.71017 bits per kmer). 0:10:58.635 12G / 25G INFO General (construction.cpp : 429) Collecting k-mer coverage information from reads, this takes a while. 0:19:59.228 12G / 25G INFO General (construction.cpp : 549) Filling coverage and flanking coverage from PHM 0:20:18.647 12G / 25G INFO General (construction.cpp : 505) Processed 48000000 edges 0:20:19.643 12G / 25G INFO General (construction.cpp : 505) Processed 50244561 edges 0:20:22.201 8G / 25G INFO StageManager (stage.cpp : 166) STAGE == EC Threshold Finding 0:20:22.379 8G / 25G INFO General (kmer_coverage_model.cpp : 181) Kmer coverage valley at: 90 0:20:22.386 8G / 25G INFO General (kmer_coverage_model.cpp : 201) K-mer histogram maximum: 121 0:20:22.388 8G / 25G INFO General (kmer_coverage_model.cpp : 237) Estimated median coverage: 121. Coverage mad: 20.7564 0:20:22.393 8G / 25G INFO General (kmer_coverage_model.cpp : 259) Fitting coverage model 0:20:22.573 8G / 25G INFO General (kmer_coverage_model.cpp : 295) ... iteration 2 0:20:22.991 8G / 25G INFO General (kmer_coverage_model.cpp : 295) ... iteration 4 0:20:24.197 8G / 25G INFO General (kmer_coverage_model.cpp : 295) ... iteration 8 0:20:27.519 8G / 25G INFO General (kmer_coverage_model.cpp : 295) ... iteration 16 0:20:33.705 8G / 25G INFO General (kmer_coverage_model.cpp : 295) ... iteration 32 0:20:47.761 8G / 25G INFO General (kmer_coverage_model.cpp : 295) ... iteration 64 0:20:58.562 8G / 25G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 105.248. Fitted coverage std. dev: 37.4776 0:20:58.567 8G / 25G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 0.565225 0:20:58.568 8G / 25G WARN General (kmer_coverage_model.cpp : 366) Failed to determine erroneous kmer threshold. Threshold set to: 90 0:20:58.569 8G / 25G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 40513018 0:20:58.572 8G / 25G INFO General (genomic_info_filler.cpp : 122) Failed to estimate mean coverage 0:20:58.573 8G / 25G INFO General (genomic_info_filler.cpp : 135) EC coverage threshold value was calculated as 90 0:20:58.574 8G / 25G INFO General (genomic_info_filler.cpp : 136) Trusted kmer low bound: 0 0:20:58.575 8G / 25G INFO StageManager (stage.cpp : 166) STAGE == Raw Simplification 0:20:58.576 8G / 25G INFO General (simplification.cpp : 128) PROCEDURE == InitialCleaning 0:20:58.577 8G / 25G INFO General (simplification.cpp : 69) Most init cleaning disabled since detected mean 0 was less than activation coverage 10 0:20:58.578 8G / 25G INFO Simplification (parallel_processing.hpp : 165) Running Self conjugate edge remover 0:20:59.463 8G / 25G INFO Simplification (parallel_processing.hpp : 167) Self conjugate edge remover triggered 155 times 0:20:59.465 8G / 25G INFO StageManager (stage.cpp : 166) STAGE == Simplification 0:20:59.466 8G / 25G INFO General (simplification.cpp : 383) Graph simplification started 0:20:59.466 8G / 25G INFO General (graph_simplification.hpp : 643) Creating parallel br instance 0:20:59.467 8G / 25G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 1 0:20:59.468 8G / 25G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:21:06.962 7G / 25G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 558284 times 0:21:06.964 7G / 25G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:28:21.713 7G / 25G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 3716395 times 0:28:21.717 7G / 25G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:30:53.935 7G / 25G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 3639897 times 0:30:53.938 7G / 25G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 2 0:30:53.939 7G / 25G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:30:58.096 7G / 25G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 79613 times 0:30:58.098 7G / 25G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:32:10.068 7G / 25G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 291790 times 0:32:10.069 7G / 25G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:32:29.242 7G / 25G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 482846 times 0:32:29.243 7G / 25G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 3 0:32:29.244 7G / 25G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:32:29.949 7G / 25G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 394 times 0:32:29.950 7G / 25G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:32:49.408 7G / 25G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 93621 times 0:32:49.410 7G / 25G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:32:54.016 7G / 25G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 128363 times 0:32:54.018 7G / 25G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 4 0:32:54.019 7G / 25G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:32:54.350 7G / 25G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 96 times 0:32:54.351 7G / 25G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:32:59.600 7G / 25G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 33017 times 0:32:59.602 7G / 25G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:33:01.368 7G / 25G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 51023 times 0:33:01.369 7G / 25G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 5 0:33:01.370 7G / 25G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:33:01.506 7G / 25G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 40 times 0:33:01.507 7G / 25G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:33:03.479 7G / 25G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 14279 times 0:33:03.480 7G / 25G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:33:04.416 7G / 25G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 27759 times 0:33:04.418 7G / 25G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 6 0:33:04.418 7G / 25G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:33:04.492 7G / 25G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 30 times 0:33:04.494 7G / 25G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:33:05.516 7G / 25G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 7750 times 0:33:05.518 7G / 25G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:33:06.176 7G / 25G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 18343 times 0:33:06.177 7G / 25G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 7 0:33:06.178 7G / 25G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:33:06.223 7G / 25G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 16 times 0:33:06.224 7G / 25G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:33:06.838 7G / 25G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 5033 times 0:33:06.841 7G / 25G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:33:07.302 7G / 25G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 13222 times 0:33:07.304 7G / 25G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 8 0:33:07.305 7G / 25G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:33:07.340 7G / 25G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 16 times 0:33:07.341 7G / 25G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:33:07.774 7G / 25G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 3401 times 0:33:07.775 7G / 25G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:33:08.107 7G / 25G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 9856 times 0:33:08.109 7G / 25G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 9 0:33:08.110 7G / 25G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:33:08.137 7G / 25G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 14 times 0:33:08.138 7G / 25G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:33:08.506 7G / 25G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 2445 times 0:33:08.508 7G / 25G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:33:08.743 7G / 25G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 7500 times 0:33:08.745 7G / 25G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 10 0:33:08.746 7G / 25G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:33:08.763 7G / 25G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 9 times 0:33:08.764 7G / 25G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:33:09.024 7G / 25G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 1775 times 0:33:09.026 7G / 25G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:33:09.212 7G / 25G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 5877 times 0:33:09.214 7G / 25G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 11 0:33:09.215 7G / 25G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:33:09.509 7G / 25G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 666 times 0:33:09.511 7G / 25G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:33:10.138 7G / 25G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 1991 times 0:33:10.140 7G / 25G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:33:10.359 7G / 25G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:33:10.361 7G / 25G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 12 0:33:10.362 7G / 25G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:33:10.370 7G / 25G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:33:10.371 7G / 25G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:33:10.372 7G / 25G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:33:10.373 7G / 25G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:33:10.374 7G / 25G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:33:10.891 7G / 25G INFO StageManager (stage.cpp : 166) STAGE == Simplification Cleanup 0:33:10.893 7G / 25G INFO General (simplification.cpp : 196) PROCEDURE == Post simplification 0:33:10.895 7G / 25G INFO General (graph_simplification.hpp : 456) Disconnection of relatively low covered edges disabled 0:33:10.897 7G / 25G INFO General (graph_simplification.hpp : 493) Complex tip clipping disabled 0:33:10.898 7G / 25G INFO General (graph_simplification.hpp : 643) Creating parallel br instance 0:33:10.900 7G / 25G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:33:11.115 7G / 25G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:33:11.117 7G / 25G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:33:11.523 7G / 25G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 12 times 0:33:11.525 7G / 25G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:33:11.832 7G / 25G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:33:11.834 7G / 25G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:33:12.240 7G / 25G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:33:12.242 7G / 25G INFO General (simplification.cpp : 343) Disrupting self-conjugate edges 0:33:14.036 7G / 25G INFO Simplification (parallel_processing.hpp : 165) Running Removing isolated edges 0:33:16.211 7G / 25G INFO Simplification (parallel_processing.hpp : 167) Removing isolated edges triggered 648956 times 0:33:16.213 7G / 25G INFO General (simplification.cpp : 496) Counting average coverage 0:33:16.757 7G / 25G INFO General (simplification.cpp : 502) Average coverage = 155.63 0:33:16.758 7G / 25G INFO StageManager (stage.cpp : 166) STAGE == Contig Output 0:33:16.759 7G / 25G INFO General (read_converter.cpp : 102) Outputting contigs to /srv/scratch/marinovg/SPAdes-3.14-L1399-Cyclotella_meninghiana_gDNA/K33/simplified_contigs 0:33:16.771 7G / 25G INFO General (binary_converter.cpp : 96) 16384 reads processed 0:33:16.781 7G / 25G INFO General (binary_converter.cpp : 96) 32768 reads processed 0:33:16.799 7G / 25G INFO General (binary_converter.cpp : 96) 65536 reads processed 0:33:16.839 7G / 25G INFO General (binary_converter.cpp : 96) 131072 reads processed 0:33:16.921 7G / 25G INFO General (binary_converter.cpp : 96) 262144 reads processed 0:33:17.084 7G / 25G INFO General (binary_converter.cpp : 96) 524288 reads processed 0:33:17.128 7G / 25G INFO General (binary_converter.cpp : 111) 538230 reads written 0:33:17.137 7G / 25G INFO General (launch.hpp : 192) SPAdes finished 0:33:20.805 2G / 25G INFO General (main.cpp : 105) Assembling time: 0 hours 33 minutes 20 seconds ===== K33 finished. ===== K55 started. == Running: /oak/stanford/groups/akundaje/marinovg/programs/SPAdes-3.14.0-Linux/bin/spades-core /srv/scratch/marinovg/SPAdes-3.14-L1399-Cyclotella_meninghiana_gDNA/K55/configs/config.info 0:00:00.000 8M / 13M INFO General (main.cpp : 73) Loaded config from /srv/scratch/marinovg/SPAdes-3.14-L1399-Cyclotella_meninghiana_gDNA/K55/configs/config.info 0:00:00.000 8M / 13M INFO General (memory_limit.cpp : 49) Memory limit set to 250 Gb 0:00:00.000 8M / 13M INFO General (main.cpp : 83) Starting SPAdes, built from refs/heads/spades_3.14.0, git revision c831f9be30a4364383cd4ebe5b78cdfcaad1acc9 0:00:00.000 8M / 13M INFO General (main.cpp : 84) Maximum k-mer length: 128 0:00:00.000 8M / 13M INFO General (main.cpp : 85) Assembling dataset (/srv/scratch/marinovg/SPAdes-3.14-L1399-Cyclotella_meninghiana_gDNA/dataset.info) with K=55 0:00:00.000 8M / 13M INFO General (main.cpp : 86) Maximum # of threads to use (adjusted due to OMP capabilities): 48 0:00:00.000 8M / 13M INFO General (launch.hpp : 79) SPAdes started 0:00:00.000 8M / 13M INFO General (launch.hpp : 86) Starting from stage: read_conversion 0:00:00.000 8M / 13M INFO General (launch.hpp : 92) Two-step RR enabled: 0 0:00:00.000 8M / 13M INFO General (launch.hpp : 103) Will need read mapping, kmer mapper will be attached 0:00:00.000 8M / 13M INFO StageManager (stage.cpp : 166) STAGE == Binary Read Conversion 0:00:00.002 8M / 13M INFO General (read_converter.cpp : 53) Binary reads detected 0:00:00.002 8M / 13M INFO General (read_converter.cpp : 53) Binary reads detected 0:00:00.002 8M / 13M INFO General (read_converter.cpp : 53) Binary reads detected 0:00:00.003 8M / 13M INFO StageManager (stage.cpp : 166) STAGE == de Bruijn graph construction 0:00:00.003 8M / 13M INFO General (construction.cpp : 115) Contigs from previous K will be used: /srv/scratch/marinovg/SPAdes-3.14-L1399-Cyclotella_meninghiana_gDNA/K33/simplified_contigs 0:00:00.009 13M / 13M INFO General (construction.cpp : 150) Max read length 150 0:00:00.009 13M / 13M INFO General (construction.cpp : 156) Average read length 145.292 0:00:00.009 13M / 13M INFO General (stage.cpp : 113) PROCEDURE == k+1-mer counting 0:00:00.009 13M / 13M INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 2304 files using 48 threads. This might take a while. 0:00:00.010 13M / 13M INFO General (file_limit.hpp : 32) Open file limit set to 2400 0:00:00.010 13M / 13M INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 1.73607 Gb 0:00:00.010 13M / 13M INFO General (kmer_splitters.hpp : 97) Using cell size of 16384 0:00:06.657 35G / 35G INFO General (kmer_splitters.hpp : 287) Processed 17068480 reads 0:00:20.301 35G / 35G INFO General (kmer_splitters.hpp : 287) Processed 49638509 reads 0:00:32.681 35G / 35G INFO General (kmer_splitters.hpp : 287) Processed 82088676 reads 0:00:45.007 35G / 35G INFO General (kmer_splitters.hpp : 287) Processed 114615426 reads 0:00:56.522 35G / 35G INFO General (kmer_splitters.hpp : 287) Processed 147107739 reads 0:01:08.790 35G / 35G INFO General (kmer_splitters.hpp : 287) Processed 179948609 reads 0:01:22.110 35G / 35G INFO General (kmer_splitters.hpp : 287) Processed 212189191 reads 0:01:34.214 35G / 35G INFO General (kmer_splitters.hpp : 287) Processed 244699005 reads 0:01:48.259 35G / 35G INFO General (kmer_splitters.hpp : 287) Processed 277607434 reads 0:02:00.254 35G / 35G INFO General (kmer_splitters.hpp : 287) Processed 310386955 reads 0:02:12.674 35G / 35G INFO General (kmer_splitters.hpp : 287) Processed 343103772 reads 0:02:24.473 35G / 35G INFO General (kmer_splitters.hpp : 287) Processed 375547622 reads 0:02:37.028 35G / 35G INFO General (kmer_splitters.hpp : 287) Processed 408106112 reads 0:02:49.673 35G / 35G INFO General (kmer_splitters.hpp : 287) Processed 440576120 reads 0:03:30.737 35G / 35G INFO General (kmer_splitters.hpp : 287) Processed 538719458 reads 0:04:40.497 493M / 25G INFO General (kmer_splitters.hpp : 293) Used 698108066 reads 0:04:40.499 493M / 25G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:05:01.475 430M / 25G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 828424885 kmers in total. 0:05:01.476 430M / 25G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:05:11.486 204M / 25G INFO General (stage.cpp : 113) PROCEDURE == Extension index construction 0:05:11.487 204M / 25G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:05:11.488 204M / 25G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 768 files using 48 threads. This might take a while. 0:05:11.488 204M / 25G INFO General (file_limit.hpp : 32) Open file limit set to 2400 0:05:11.489 204M / 25G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 1.73604 Gb 0:05:11.490 204M / 25G INFO General (kmer_splitters.hpp : 97) Using cell size of 43690 0:05:11.963 28G / 28G INFO General (kmer_splitters.hpp : 364) Processed 7718630 kmers 0:05:12.392 28G / 28G INFO General (kmer_splitters.hpp : 364) Processed 16114908 kmers 0:05:12.835 28G / 28G INFO General (kmer_splitters.hpp : 364) Processed 24974336 kmers 0:05:13.250 28G / 28G INFO General (kmer_splitters.hpp : 364) Processed 33365702 kmers 0:05:13.711 28G / 28G INFO General (kmer_splitters.hpp : 364) Processed 42222606 kmers 0:05:14.152 28G / 28G INFO General (kmer_splitters.hpp : 364) Processed 50615139 kmers 0:05:14.595 28G / 28G INFO General (kmer_splitters.hpp : 364) Processed 59491867 kmers 0:05:15.042 28G / 28G INFO General (kmer_splitters.hpp : 364) Processed 67875945 kmers 0:05:15.495 28G / 28G INFO General (kmer_splitters.hpp : 364) Processed 76750366 kmers 0:05:15.963 28G / 28G INFO General (kmer_splitters.hpp : 364) Processed 85145323 kmers 0:05:16.450 28G / 28G INFO General (kmer_splitters.hpp : 364) Processed 94002442 kmers 0:05:16.895 28G / 28G INFO General (kmer_splitters.hpp : 364) Processed 102392971 kmers 0:05:17.354 28G / 28G INFO General (kmer_splitters.hpp : 364) Processed 111251216 kmers 0:05:17.788 28G / 28G INFO General (kmer_splitters.hpp : 364) Processed 119651380 kmers 0:05:18.244 28G / 28G INFO General (kmer_splitters.hpp : 364) Processed 128524740 kmers 0:05:18.686 28G / 28G INFO General (kmer_splitters.hpp : 364) Processed 136925124 kmers 0:05:19.139 28G / 28G INFO General (kmer_splitters.hpp : 364) Processed 145777560 kmers 0:05:19.570 28G / 28G INFO General (kmer_splitters.hpp : 364) Processed 154174676 kmers 0:05:26.153 28G / 28G INFO General (kmer_splitters.hpp : 364) Processed 274989101 kmers 0:05:41.081 28G / 28G INFO General (kmer_splitters.hpp : 364) Processed 542748462 kmers 0:05:56.899 28G / 28G INFO General (kmer_splitters.hpp : 369) Used 828429493 kmers. 0:05:57.036 362M / 25G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:06:09.427 359M / 25G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 824331646 kmers in total. 0:06:09.429 359M / 25G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:06:20.390 359M / 25G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:06:45.885 709M / 25G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 0:07:34.182 709M / 25G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 382270656 bytes occupied (3.70987 bits per kmer). 0:07:34.805 2G / 25G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 99) Building k-mer extensions from k+1-mers 0:08:01.596 2G / 25G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 103) Building k-mer extensions from k+1-mers finished. 0:08:01.606 2G / 25G INFO General (stage.cpp : 113) PROCEDURE == Condensing graph 0:08:01.612 2G / 25G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths 0:08:39.428 6G / 25G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 39669535 sequences extracted 0:08:58.222 6G / 25G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops 0:09:08.731 6G / 25G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 41 loops collected 0:11:32.654 13G / 25G INFO General (stage.cpp : 113) PROCEDURE == Filling coverage indices (PHM) 0:11:32.656 13G / 25G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:11:32.657 13G / 25G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:11:48.242 14G / 26G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 384169018 bytes occupied (3.70987 bits per kmer). 0:11:49.858 17G / 26G INFO General (construction.cpp : 429) Collecting k-mer coverage information from reads, this takes a while. 0:19:32.895 17G / 26G INFO General (construction.cpp : 549) Filling coverage and flanking coverage from PHM 0:19:51.431 17G / 26G INFO General (construction.cpp : 505) Processed 48000000 edges 0:20:02.934 17G / 26G INFO General (construction.cpp : 505) Processed 79339052 edges 0:20:05.955 12G / 26G INFO StageManager (stage.cpp : 166) STAGE == EC Threshold Finding 0:20:06.113 12G / 26G INFO General (kmer_coverage_model.cpp : 181) Kmer coverage valley at: 71 0:20:06.119 12G / 26G INFO General (kmer_coverage_model.cpp : 201) K-mer histogram maximum: 95 0:20:06.121 12G / 26G INFO General (kmer_coverage_model.cpp : 237) Estimated median coverage: 96. Coverage mad: 17.7912 0:20:06.125 12G / 26G INFO General (kmer_coverage_model.cpp : 259) Fitting coverage model 0:20:06.252 12G / 26G INFO General (kmer_coverage_model.cpp : 295) ... iteration 2 0:20:06.541 12G / 26G INFO General (kmer_coverage_model.cpp : 295) ... iteration 4 0:20:07.504 12G / 26G INFO General (kmer_coverage_model.cpp : 295) ... iteration 8 0:20:10.726 12G / 26G INFO General (kmer_coverage_model.cpp : 295) ... iteration 16 0:20:15.383 12G / 26G INFO General (kmer_coverage_model.cpp : 295) ... iteration 32 0:20:16.508 12G / 26G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 102.403. Fitted coverage std. dev: 20.0148 0:20:16.512 12G / 26G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 0.714419 0:20:16.513 12G / 26G WARN General (kmer_coverage_model.cpp : 366) Failed to determine erroneous kmer threshold. Threshold set to: 71 0:20:16.514 12G / 26G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 40224764 0:20:16.516 12G / 26G INFO General (genomic_info_filler.cpp : 122) Failed to estimate mean coverage 0:20:16.517 12G / 26G INFO General (genomic_info_filler.cpp : 135) EC coverage threshold value was calculated as 71 0:20:16.518 12G / 26G INFO General (genomic_info_filler.cpp : 136) Trusted kmer low bound: 0 0:20:16.519 12G / 26G INFO StageManager (stage.cpp : 166) STAGE == Gap Closer 0:20:16.520 12G / 26G INFO General (graph_pack.hpp : 105) Index refill 0:20:16.521 12G / 26G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:20:16.522 12G / 26G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 768 files using 48 threads. This might take a while. 0:20:16.525 12G / 26G INFO General (file_limit.hpp : 32) Open file limit set to 2400 0:20:16.526 12G / 26G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 1.66181 Gb 0:20:16.527 12G / 26G INFO General (kmer_splitters.hpp : 97) Using cell size of 43690 0:20:34.407 39G / 39G INFO General (edge_index_builders.hpp : 77) Processed 79339052 edges 0:20:34.410 39G / 39G INFO General (edge_index_builders.hpp : 82) Used 79339052 sequences. 0:20:35.395 12G / 26G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:20:39.862 12G / 26G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 828424885 kmers in total. 0:20:39.865 12G / 26G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:20:50.137 12G / 26G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:21:18.552 12G / 26G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 0:22:01.279 12G / 26G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 384150632 bytes occupied (3.7097 bits per kmer). 0:22:07.429 26G / 26G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while. 0:22:26.207 26G / 26G INFO General (edge_index.hpp : 92) Index refilled 0:22:26.210 26G / 26G INFO General (gap_closer.cpp : 147) Preparing shift maps 0:23:14.105 28G / 28G INFO General (gap_closer.cpp : 107) Processing paired reads (takes a while) 0:30:22.317 29G / 29G INFO General (gap_closer.cpp : 126) Used 171621781 paired reads 0:30:22.321 29G / 29G INFO General (gap_closer.cpp : 128) Merging paired indices 0:30:41.126 29G / 29G INFO GapCloser (gap_closer.cpp : 332) Closing short gaps 0:32:02.812 29G / 29G INFO GapCloser (gap_closer.cpp : 366) Closing short gaps complete: filled 18887 gaps after checking 1067710 candidates 0:32:13.314 28G / 28G INFO StageManager (stage.cpp : 166) STAGE == Raw Simplification 0:32:13.822 13G / 28G INFO General (simplification.cpp : 128) PROCEDURE == InitialCleaning 0:32:13.824 13G / 28G INFO General (simplification.cpp : 69) Most init cleaning disabled since detected mean 0 was less than activation coverage 10 0:32:13.825 13G / 28G INFO Simplification (parallel_processing.hpp : 165) Running Self conjugate edge remover 0:32:15.435 13G / 28G INFO Simplification (parallel_processing.hpp : 167) Self conjugate edge remover triggered 27 times 0:32:15.437 13G / 28G INFO StageManager (stage.cpp : 166) STAGE == Simplification 0:32:15.439 13G / 28G INFO General (simplification.cpp : 383) Graph simplification started 0:32:15.440 13G / 28G INFO General (graph_simplification.hpp : 643) Creating parallel br instance 0:32:15.441 13G / 28G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 1 0:32:15.442 13G / 28G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:34:57.703 12G / 28G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 12810445 times 0:34:57.705 12G / 28G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:49:48.114 25G / 28G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 2398309 times 0:49:48.117 25G / 28G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:51:33.042 25G / 28G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 2223954 times 0:51:33.043 25G / 28G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 2 0:51:33.044 25G / 28G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:51:37.704 25G / 28G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 126518 times 0:51:37.705 25G / 28G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:53:24.695 26G / 28G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 178273 times 0:53:24.698 26G / 28G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:53:37.154 26G / 28G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 276315 times 0:53:37.156 26G / 28G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 3 0:53:37.157 26G / 28G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:53:37.653 26G / 28G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 498 times 0:53:37.655 26G / 28G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:54:01.942 27G / 28G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 43470 times 0:54:01.944 27G / 28G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:54:04.731 27G / 28G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 71065 times 0:54:04.733 27G / 28G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 4 0:54:04.734 27G / 28G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:54:04.932 27G / 28G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 64 times 0:54:04.933 27G / 28G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:54:12.380 27G / 28G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 15394 times 0:54:12.382 27G / 28G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:54:13.391 27G / 28G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 26274 times 0:54:13.393 27G / 28G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 5 0:54:13.394 27G / 28G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:54:13.468 27G / 28G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 28 times 0:54:13.470 27G / 28G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:54:16.550 27G / 28G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 6375 times 0:54:16.552 27G / 28G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:54:17.061 27G / 28G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 14438 times 0:54:17.063 27G / 28G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 6 0:54:17.064 27G / 28G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:54:17.104 27G / 28G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 31 times 0:54:17.106 27G / 28G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:54:18.767 27G / 28G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 3487 times 0:54:18.769 27G / 28G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:54:19.064 27G / 28G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 9324 times 0:54:19.066 27G / 28G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 7 0:54:19.067 27G / 28G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:54:19.091 27G / 28G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 17 times 0:54:19.092 27G / 28G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:54:20.263 27G / 28G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 2301 times 0:54:20.265 27G / 28G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:54:20.477 27G / 28G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 6552 times 0:54:20.478 27G / 28G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 8 0:54:20.479 27G / 28G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:54:20.496 27G / 28G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 8 times 0:54:20.497 27G / 28G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:54:21.259 27G / 28G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 1537 times 0:54:21.260 27G / 28G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:54:21.412 27G / 28G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 4763 times 0:54:21.414 27G / 28G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 9 0:54:21.415 27G / 28G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:54:21.427 27G / 28G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 12 times 0:54:21.427 27G / 28G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:54:21.950 27G / 28G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 1148 times 0:54:21.951 27G / 28G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:54:22.103 27G / 28G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 3760 times 0:54:22.104 27G / 28G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 10 0:54:22.105 27G / 28G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:54:22.116 27G / 28G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 7 times 0:54:22.117 27G / 28G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:54:22.524 27G / 28G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 875 times 0:54:22.526 27G / 28G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:54:22.625 27G / 28G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 2996 times 0:54:22.627 27G / 28G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 11 0:54:22.627 27G / 28G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:54:23.064 27G / 28G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 321 times 0:54:23.065 27G / 28G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:54:23.887 27G / 28G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 959 times 0:54:23.889 27G / 28G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:54:24.292 27G / 28G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 3 times 0:54:24.293 27G / 28G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 12 0:54:24.295 27G / 28G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:54:24.301 27G / 28G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:54:24.302 27G / 28G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:54:24.304 27G / 28G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:54:24.305 27G / 28G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:54:24.307 27G / 28G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:54:25.061 27G / 28G INFO StageManager (stage.cpp : 166) STAGE == Gap Closer 0:54:25.064 27G / 28G INFO General (graph_pack.hpp : 105) Index refill 0:54:25.067 27G / 28G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:54:25.069 27G / 28G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 768 files using 48 threads. This might take a while. 0:54:25.072 27G / 28G INFO General (file_limit.hpp : 32) Open file limit set to 2400 0:54:25.075 27G / 28G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 1.55878 Gb 0:54:25.076 27G / 28G INFO General (kmer_splitters.hpp : 97) Using cell size of 43690 0:54:31.100 54G / 54G INFO General (edge_index_builders.hpp : 77) Processed 2831713 edges 0:54:31.102 54G / 54G INFO General (edge_index_builders.hpp : 82) Used 2831713 sequences. 0:54:31.510 27G / 32G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:54:33.806 27G / 32G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 339236865 kmers in total. 0:54:33.809 27G / 32G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:54:37.899 27G / 32G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:54:47.303 27G / 32G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 0:55:05.152 27G / 32G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 157315496 bytes occupied (3.70987 bits per kmer). 0:55:09.283 33G / 33G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while. 0:55:15.748 33G / 33G INFO General (edge_index.hpp : 92) Index refilled 0:55:15.751 33G / 33G INFO General (gap_closer.cpp : 147) Preparing shift maps 0:55:20.706 34G / 34G INFO General (gap_closer.cpp : 107) Processing paired reads (takes a while) 0:58:09.094 33G / 33G INFO General (gap_closer.cpp : 126) Used 171621781 paired reads 0:58:09.100 33G / 33G INFO General (gap_closer.cpp : 128) Merging paired indices 0:58:11.969 33G / 33G INFO GapCloser (gap_closer.cpp : 332) Closing short gaps 0:58:15.965 33G / 33G INFO GapCloser (gap_closer.cpp : 366) Closing short gaps complete: filled 2088 gaps after checking 85573 candidates 0:58:22.030 33G / 33G INFO StageManager (stage.cpp : 166) STAGE == Simplification Cleanup 0:58:22.032 33G / 33G INFO General (simplification.cpp : 196) PROCEDURE == Post simplification 0:58:22.033 33G / 33G INFO General (graph_simplification.hpp : 456) Disconnection of relatively low covered edges disabled 0:58:22.034 33G / 33G INFO General (graph_simplification.hpp : 493) Complex tip clipping disabled 0:58:22.035 33G / 33G INFO General (graph_simplification.hpp : 643) Creating parallel br instance 0:58:22.036 33G / 33G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:58:22.397 33G / 33G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:58:22.399 33G / 33G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:58:22.826 33G / 33G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 4 times 0:58:22.827 33G / 33G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:58:23.160 33G / 33G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:58:23.161 33G / 33G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:58:23.655 33G / 33G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:58:23.656 33G / 33G INFO General (simplification.cpp : 343) Disrupting self-conjugate edges 0:58:26.128 33G / 33G INFO Simplification (parallel_processing.hpp : 165) Running Removing isolated edges 0:59:20.151 33G / 33G INFO Simplification (parallel_processing.hpp : 167) Removing isolated edges triggered 1041846 times 0:59:20.152 33G / 33G INFO General (simplification.cpp : 496) Counting average coverage 0:59:20.991 33G / 33G INFO General (simplification.cpp : 502) Average coverage = 111.641 0:59:20.993 33G / 33G INFO StageManager (stage.cpp : 166) STAGE == Contig Output 0:59:21.023 33G / 33G INFO General (read_converter.cpp : 102) Outputting contigs to /srv/scratch/marinovg/SPAdes-3.14-L1399-Cyclotella_meninghiana_gDNA/K55/simplified_contigs 0:59:21.044 33G / 33G INFO General (binary_converter.cpp : 96) 16384 reads processed 0:59:21.061 33G / 33G INFO General (binary_converter.cpp : 96) 32768 reads processed 0:59:21.094 33G / 33G INFO General (binary_converter.cpp : 96) 65536 reads processed 0:59:21.157 33G / 33G INFO General (binary_converter.cpp : 96) 131072 reads processed 0:59:21.269 33G / 33G INFO General (binary_converter.cpp : 96) 262144 reads processed 0:59:21.469 33G / 33G INFO General (binary_converter.cpp : 111) 371924 reads written 0:59:21.473 33G / 33G INFO General (launch.hpp : 192) SPAdes finished 1:01:40.154 7G / 32G INFO General (main.cpp : 105) Assembling time: 1 hours 1 minutes 40 seconds ===== K55 finished. ===== K77 started. == Running: /oak/stanford/groups/akundaje/marinovg/programs/SPAdes-3.14.0-Linux/bin/spades-core /srv/scratch/marinovg/SPAdes-3.14-L1399-Cyclotella_meninghiana_gDNA/K77/configs/config.info 0:00:00.000 8M / 13M INFO General (main.cpp : 73) Loaded config from /srv/scratch/marinovg/SPAdes-3.14-L1399-Cyclotella_meninghiana_gDNA/K77/configs/config.info 0:00:00.000 8M / 13M INFO General (memory_limit.cpp : 49) Memory limit set to 250 Gb 0:00:00.000 8M / 13M INFO General (main.cpp : 83) Starting SPAdes, built from refs/heads/spades_3.14.0, git revision c831f9be30a4364383cd4ebe5b78cdfcaad1acc9 0:00:00.000 8M / 13M INFO General (main.cpp : 84) Maximum k-mer length: 128 0:00:00.000 8M / 13M INFO General (main.cpp : 85) Assembling dataset (/srv/scratch/marinovg/SPAdes-3.14-L1399-Cyclotella_meninghiana_gDNA/dataset.info) with K=77 0:00:00.000 8M / 13M INFO General (main.cpp : 86) Maximum # of threads to use (adjusted due to OMP capabilities): 48 0:00:00.000 8M / 13M INFO General (launch.hpp : 79) SPAdes started 0:00:00.000 8M / 13M INFO General (launch.hpp : 86) Starting from stage: read_conversion 0:00:00.000 8M / 13M INFO General (launch.hpp : 92) Two-step RR enabled: 0 0:00:00.000 8M / 13M INFO General (launch.hpp : 103) Will need read mapping, kmer mapper will be attached 0:00:00.000 8M / 13M INFO StageManager (stage.cpp : 166) STAGE == Binary Read Conversion 0:00:00.002 8M / 13M INFO General (read_converter.cpp : 53) Binary reads detected 0:00:00.002 8M / 13M INFO General (read_converter.cpp : 53) Binary reads detected 0:00:00.002 8M / 13M INFO General (read_converter.cpp : 53) Binary reads detected 0:00:00.003 8M / 13M INFO StageManager (stage.cpp : 166) STAGE == de Bruijn graph construction 0:00:00.003 8M / 13M INFO General (construction.cpp : 115) Contigs from previous K will be used: /srv/scratch/marinovg/SPAdes-3.14-L1399-Cyclotella_meninghiana_gDNA/K55/simplified_contigs 0:00:00.012 13M / 13M INFO General (construction.cpp : 150) Max read length 150 0:00:00.012 13M / 13M INFO General (construction.cpp : 156) Average read length 145.292 0:00:00.012 13M / 13M INFO General (stage.cpp : 113) PROCEDURE == k+1-mer counting 0:00:00.012 13M / 13M INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 2304 files using 48 threads. This might take a while. 0:00:00.013 13M / 13M INFO General (file_limit.hpp : 32) Open file limit set to 2400 0:00:00.013 13M / 13M INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 1.73607 Gb 0:00:00.013 13M / 13M INFO General (kmer_splitters.hpp : 97) Using cell size of 16384 0:00:11.381 48G / 48G INFO General (kmer_splitters.hpp : 287) Processed 28762986 reads 0:00:29.863 48G / 48G INFO General (kmer_splitters.hpp : 287) Processed 71421848 reads 0:00:44.403 48G / 48G INFO General (kmer_splitters.hpp : 287) Processed 114043264 reads 0:00:59.969 48G / 48G INFO General (kmer_splitters.hpp : 287) Processed 156669641 reads 0:01:15.552 48G / 48G INFO General (kmer_splitters.hpp : 287) Processed 199284607 reads 0:01:31.818 48G / 48G INFO General (kmer_splitters.hpp : 287) Processed 241713794 reads 0:01:47.503 48G / 48G INFO General (kmer_splitters.hpp : 287) Processed 284605359 reads 0:02:02.671 48G / 48G INFO General (kmer_splitters.hpp : 287) Processed 327430685 reads 0:02:17.549 48G / 48G INFO General (kmer_splitters.hpp : 287) Processed 370066452 reads 0:02:32.277 48G / 48G INFO General (kmer_splitters.hpp : 287) Processed 412748063 reads 0:02:46.878 48G / 48G INFO General (kmer_splitters.hpp : 287) Processed 455438153 reads 0:03:01.598 48G / 48G INFO General (kmer_splitters.hpp : 287) Processed 498101730 reads 0:03:16.451 48G / 48G INFO General (kmer_splitters.hpp : 287) Processed 540724316 reads 0:03:31.837 48G / 48G INFO General (kmer_splitters.hpp : 287) Processed 583421145 reads 0:03:47.901 48G / 48G INFO General (kmer_splitters.hpp : 287) Processed 626003857 reads 0:04:29.825 405M / 37G INFO General (kmer_splitters.hpp : 293) Used 697775454 reads 0:04:29.826 405M / 37G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:05:17.010 353M / 37G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 877398735 kmers in total. 0:05:17.013 353M / 37G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:05:52.860 219M / 37G INFO General (stage.cpp : 113) PROCEDURE == Extension index construction 0:05:52.862 219M / 37G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:05:52.862 219M / 37G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 768 files using 48 threads. This might take a while. 0:05:52.863 219M / 37G INFO General (file_limit.hpp : 32) Open file limit set to 2400 0:05:52.864 219M / 37G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 1.73604 Gb 0:05:52.865 219M / 37G INFO General (kmer_splitters.hpp : 97) Using cell size of 29127 0:05:53.306 28G / 37G INFO General (kmer_splitters.hpp : 364) Processed 5007389 kmers 0:05:53.695 28G / 37G INFO General (kmer_splitters.hpp : 364) Processed 10532456 kmers 0:05:54.287 28G / 37G INFO General (kmer_splitters.hpp : 364) Processed 16001524 kmers 0:05:54.821 28G / 37G INFO General (kmer_splitters.hpp : 364) Processed 23267247 kmers 0:05:55.207 28G / 37G INFO General (kmer_splitters.hpp : 364) Processed 28801683 kmers 0:05:55.584 28G / 37G INFO General (kmer_splitters.hpp : 364) Processed 34269735 kmers 0:05:56.058 28G / 37G INFO General (kmer_splitters.hpp : 364) Processed 41553962 kmers 0:05:56.430 28G / 37G INFO General (kmer_splitters.hpp : 364) Processed 47082806 kmers 0:05:56.828 28G / 37G INFO General (kmer_splitters.hpp : 364) Processed 52555659 kmers 0:05:57.293 28G / 37G INFO General (kmer_splitters.hpp : 364) Processed 59831958 kmers 0:05:57.661 28G / 37G INFO General (kmer_splitters.hpp : 364) Processed 65363361 kmers 0:05:58.051 28G / 37G INFO General (kmer_splitters.hpp : 364) Processed 70829771 kmers 0:05:58.556 28G / 37G INFO General (kmer_splitters.hpp : 364) Processed 78113187 kmers 0:05:58.939 28G / 37G INFO General (kmer_splitters.hpp : 364) Processed 83649220 kmers 0:05:59.476 28G / 37G INFO General (kmer_splitters.hpp : 364) Processed 89116441 kmers 0:05:59.951 28G / 37G INFO General (kmer_splitters.hpp : 364) Processed 96396770 kmers 0:06:00.353 28G / 37G INFO General (kmer_splitters.hpp : 364) Processed 101931893 kmers 0:06:02.980 28G / 37G INFO General (kmer_splitters.hpp : 364) Processed 138486626 kmers 0:06:12.402 28G / 37G INFO General (kmer_splitters.hpp : 364) Processed 271900552 kmers 0:06:32.162 28G / 37G INFO General (kmer_splitters.hpp : 364) Processed 540608328 kmers 0:06:56.627 28G / 37G INFO General (kmer_splitters.hpp : 369) Used 877405647 kmers. 0:06:56.805 325M / 37G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:07:23.296 169M / 37G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 876745974 kmers in total. 0:07:23.298 169M / 37G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:08:09.829 169M / 37G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:08:43.607 811M / 37G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 0:09:47.572 811M / 37G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 406570294 bytes occupied (3.70981 bits per kmer). 0:09:48.232 2G / 37G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 99) Building k-mer extensions from k+1-mers 0:10:16.335 2G / 37G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 103) Building k-mer extensions from k+1-mers finished. 0:10:16.345 2G / 37G INFO General (stage.cpp : 113) PROCEDURE == Condensing graph 0:10:16.350 2G / 37G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths 0:10:56.412 6G / 37G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 35829590 sequences extracted 0:11:18.989 6G / 37G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops 0:11:29.366 6G / 37G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 47 loops collected 0:13:49.645 12G / 37G INFO General (stage.cpp : 113) PROCEDURE == Filling coverage indices (PHM) 0:13:49.647 12G / 37G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:13:49.648 12G / 37G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:14:05.983 13G / 37G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 406889078 bytes occupied (3.70996 bits per kmer). 0:14:07.759 17G / 37G INFO General (construction.cpp : 429) Collecting k-mer coverage information from reads, this takes a while. 0:20:08.655 16G / 37G INFO General (construction.cpp : 549) Filling coverage and flanking coverage from PHM 0:20:30.458 16G / 37G INFO General (construction.cpp : 505) Processed 48000000 edges 0:20:40.601 16G / 37G INFO General (construction.cpp : 505) Processed 71659245 edges 0:20:45.063 12G / 37G INFO StageManager (stage.cpp : 166) STAGE == EC Threshold Finding 0:20:45.196 12G / 37G INFO General (kmer_coverage_model.cpp : 181) Kmer coverage valley at: 54 0:20:45.202 12G / 37G INFO General (kmer_coverage_model.cpp : 201) K-mer histogram maximum: 73 0:20:45.204 12G / 37G INFO General (kmer_coverage_model.cpp : 237) Estimated median coverage: 73. Coverage mad: 13.3434 0:20:45.208 12G / 37G INFO General (kmer_coverage_model.cpp : 259) Fitting coverage model 0:20:45.352 12G / 37G INFO General (kmer_coverage_model.cpp : 295) ... iteration 2 0:20:45.661 12G / 37G INFO General (kmer_coverage_model.cpp : 295) ... iteration 4 0:20:46.415 12G / 37G INFO General (kmer_coverage_model.cpp : 295) ... iteration 8 0:20:48.665 12G / 37G INFO General (kmer_coverage_model.cpp : 295) ... iteration 16 0:20:52.750 12G / 37G INFO General (kmer_coverage_model.cpp : 295) ... iteration 32 0:20:56.610 12G / 37G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 77.0302. Fitted coverage std. dev: 18.5952 0:20:56.614 12G / 37G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 0.619488 0:20:56.615 12G / 37G WARN General (kmer_coverage_model.cpp : 366) Failed to determine erroneous kmer threshold. Threshold set to: 54 0:20:56.616 12G / 37G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 39897036 0:20:56.618 12G / 37G INFO General (genomic_info_filler.cpp : 122) Failed to estimate mean coverage 0:20:56.619 12G / 37G INFO General (genomic_info_filler.cpp : 135) EC coverage threshold value was calculated as 54 0:20:56.620 12G / 37G INFO General (genomic_info_filler.cpp : 136) Trusted kmer low bound: 0 0:20:56.621 12G / 37G INFO StageManager (stage.cpp : 166) STAGE == Gap Closer 0:20:56.622 12G / 37G INFO General (graph_pack.hpp : 105) Index refill 0:20:56.623 12G / 37G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:20:56.624 12G / 37G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 768 files using 48 threads. This might take a while. 0:20:56.627 12G / 37G INFO General (file_limit.hpp : 32) Open file limit set to 2400 0:20:56.628 12G / 37G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 1.66575 Gb 0:20:56.629 12G / 37G INFO General (kmer_splitters.hpp : 97) Using cell size of 29127 0:21:21.132 39G / 39G INFO General (edge_index_builders.hpp : 77) Processed 71659245 edges 0:21:21.135 39G / 39G INFO General (edge_index_builders.hpp : 82) Used 71659245 sequences. 0:21:22.556 12G / 37G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:21:31.134 11G / 37G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 877398735 kmers in total. 0:21:31.137 11G / 37G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:22:16.621 11G / 37G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:22:49.502 12G / 37G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 0:23:51.805 12G / 37G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 406860048 bytes occupied (3.70969 bits per kmer). 0:23:58.695 26G / 37G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while. 0:24:17.836 26G / 37G INFO General (edge_index.hpp : 92) Index refilled 0:24:17.838 26G / 37G INFO General (gap_closer.cpp : 147) Preparing shift maps 0:25:13.768 28G / 37G INFO General (gap_closer.cpp : 107) Processing paired reads (takes a while) 0:29:52.013 29G / 37G INFO General (gap_closer.cpp : 126) Used 171621781 paired reads 0:29:52.015 29G / 37G INFO General (gap_closer.cpp : 128) Merging paired indices 0:30:13.379 29G / 37G INFO GapCloser (gap_closer.cpp : 332) Closing short gaps 0:31:38.036 28G / 37G INFO GapCloser (gap_closer.cpp : 366) Closing short gaps complete: filled 26451 gaps after checking 1113095 candidates 0:31:50.448 27G / 37G INFO StageManager (stage.cpp : 166) STAGE == Raw Simplification 0:31:51.036 13G / 37G INFO General (simplification.cpp : 128) PROCEDURE == InitialCleaning 0:31:51.037 13G / 37G INFO General (simplification.cpp : 69) Most init cleaning disabled since detected mean 0 was less than activation coverage 10 0:31:51.038 13G / 37G INFO Simplification (parallel_processing.hpp : 165) Running Self conjugate edge remover 0:31:52.656 13G / 37G INFO Simplification (parallel_processing.hpp : 167) Self conjugate edge remover triggered 6 times 0:31:52.658 13G / 37G INFO StageManager (stage.cpp : 166) STAGE == Simplification 0:31:52.660 13G / 37G INFO General (simplification.cpp : 383) Graph simplification started 0:31:52.661 13G / 37G INFO General (graph_simplification.hpp : 643) Creating parallel br instance 0:31:52.662 13G / 37G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 1 0:31:52.664 13G / 37G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:35:08.424 12G / 37G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 14279337 times 0:35:08.426 12G / 37G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:45:01.470 25G / 37G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 1185986 times 0:45:01.473 25G / 37G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:45:46.185 25G / 37G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 917966 times 0:45:46.187 25G / 37G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 2 0:45:46.188 25G / 37G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:45:51.249 25G / 37G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 167353 times 0:45:51.250 25G / 37G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:47:03.393 27G / 37G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 94365 times 0:47:03.396 27G / 37G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:47:11.335 27G / 37G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 168814 times 0:47:11.336 27G / 37G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 3 0:47:11.337 27G / 37G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:47:11.655 27G / 37G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 860 times 0:47:11.657 27G / 37G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:47:30.486 27G / 37G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 25018 times 0:47:30.488 27G / 37G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:47:32.388 27G / 37G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 42514 times 0:47:32.389 27G / 37G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 4 0:47:32.390 27G / 37G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:47:32.498 27G / 37G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 96 times 0:47:32.500 27G / 37G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:47:38.626 27G / 37G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 8979 times 0:47:38.627 27G / 37G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:47:39.310 27G / 37G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 15927 times 0:47:39.311 27G / 37G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 5 0:47:39.312 27G / 37G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:47:39.357 27G / 37G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 28 times 0:47:39.358 27G / 37G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:47:41.892 27G / 37G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 3782 times 0:47:41.894 27G / 37G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:47:42.317 27G / 37G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 9059 times 0:47:42.318 27G / 37G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 6 0:47:42.319 27G / 37G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:47:42.349 27G / 37G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 20 times 0:47:42.351 27G / 37G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:47:44.035 27G / 37G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 2218 times 0:47:44.037 27G / 37G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:47:44.255 27G / 37G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 5550 times 0:47:44.256 27G / 37G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 7 0:47:44.257 27G / 37G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:47:44.272 27G / 37G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 11 times 0:47:44.273 27G / 37G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:47:45.248 27G / 37G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 1353 times 0:47:45.250 27G / 37G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:47:45.418 27G / 37G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 3844 times 0:47:45.419 27G / 37G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 8 0:47:45.420 27G / 37G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:47:45.431 27G / 37G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 7 times 0:47:45.432 27G / 37G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:47:46.086 27G / 37G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 931 times 0:47:46.087 27G / 37G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:47:46.195 27G / 37G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 2900 times 0:47:46.197 27G / 37G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 9 0:47:46.198 27G / 37G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:47:46.205 27G / 37G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 7 times 0:47:46.206 27G / 37G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:47:46.644 27G / 37G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 649 times 0:47:46.645 27G / 37G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:47:46.724 27G / 37G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 2177 times 0:47:46.725 27G / 37G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 10 0:47:46.726 27G / 37G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:47:46.732 27G / 37G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 4 times 0:47:46.732 27G / 37G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:47:47.100 27G / 37G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 492 times 0:47:47.102 27G / 37G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:47:47.177 27G / 37G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 1716 times 0:47:47.179 27G / 37G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 11 0:47:47.180 27G / 37G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:47:47.809 27G / 37G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 394 times 0:47:47.811 27G / 37G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:47:48.661 27G / 37G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 592 times 0:47:48.662 27G / 37G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:47:48.995 27G / 37G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 4 times 0:47:48.997 27G / 37G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 12 0:47:48.999 27G / 37G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:47:49.002 27G / 37G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:47:49.003 27G / 37G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:47:49.005 27G / 37G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:47:49.006 27G / 37G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:47:49.007 27G / 37G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:47:49.732 27G / 37G INFO StageManager (stage.cpp : 166) STAGE == Gap Closer 0:47:49.735 27G / 37G INFO General (graph_pack.hpp : 105) Index refill 0:47:49.763 27G / 37G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:47:49.764 27G / 37G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 768 files using 48 threads. This might take a while. 0:47:49.765 27G / 37G INFO General (file_limit.hpp : 32) Open file limit set to 2400 0:47:49.767 27G / 37G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 1.55669 Gb 0:47:49.768 27G / 37G INFO General (kmer_splitters.hpp : 97) Using cell size of 29127 0:48:00.877 54G / 54G INFO General (edge_index_builders.hpp : 77) Processed 3947547 edges 0:48:00.880 54G / 54G INFO General (edge_index_builders.hpp : 82) Used 3947547 sequences. 0:48:01.572 27G / 37G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:48:06.160 27G / 37G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 376649519 kmers in total. 0:48:06.162 27G / 37G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:48:13.588 27G / 37G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:48:26.278 27G / 37G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 0:48:54.978 27G / 37G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 174683560 bytes occupied (3.71026 bits per kmer). 0:49:00.510 33G / 37G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while. 0:49:09.652 33G / 37G INFO General (edge_index.hpp : 92) Index refilled 0:49:09.655 33G / 37G INFO General (gap_closer.cpp : 147) Preparing shift maps 0:49:16.754 34G / 37G INFO General (gap_closer.cpp : 107) Processing paired reads (takes a while) 0:51:39.627 34G / 37G INFO General (gap_closer.cpp : 126) Used 171621781 paired reads 0:51:39.633 34G / 37G INFO General (gap_closer.cpp : 128) Merging paired indices 0:51:43.652 34G / 37G INFO GapCloser (gap_closer.cpp : 332) Closing short gaps 0:51:49.499 34G / 37G INFO GapCloser (gap_closer.cpp : 366) Closing short gaps complete: filled 1833 gaps after checking 106607 candidates 0:51:58.224 34G / 37G INFO StageManager (stage.cpp : 166) STAGE == Simplification Cleanup 0:51:58.226 34G / 37G INFO General (simplification.cpp : 196) PROCEDURE == Post simplification 0:51:58.227 34G / 37G INFO General (graph_simplification.hpp : 456) Disconnection of relatively low covered edges disabled 0:51:58.228 34G / 37G INFO General (graph_simplification.hpp : 493) Complex tip clipping disabled 0:51:58.228 34G / 37G INFO General (graph_simplification.hpp : 643) Creating parallel br instance 0:51:58.229 34G / 37G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:51:58.642 34G / 37G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:51:58.645 34G / 37G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:51:59.106 34G / 37G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 3 times 0:51:59.108 34G / 37G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:51:59.553 34G / 37G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:51:59.555 34G / 37G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:52:00.000 34G / 37G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:52:00.001 34G / 37G INFO General (simplification.cpp : 343) Disrupting self-conjugate edges 0:52:03.053 33G / 37G INFO Simplification (parallel_processing.hpp : 165) Running Removing isolated edges 0:53:32.152 32G / 37G INFO Simplification (parallel_processing.hpp : 167) Removing isolated edges triggered 1680550 times 0:53:32.154 32G / 37G INFO General (simplification.cpp : 496) Counting average coverage 0:53:32.878 32G / 37G INFO General (simplification.cpp : 502) Average coverage = 80.1129 0:53:32.880 32G / 37G INFO StageManager (stage.cpp : 166) STAGE == Mismatch Correction 0:53:32.881 32G / 37G INFO General (graph_pack.hpp : 113) Normalizing k-mer map. Total 224688239 kmers to process 0:54:41.945 32G / 38G INFO General (graph_pack.hpp : 115) Normalizing done 1:09:49.587 60G / 60G INFO General (mismatch_shall_not_pass.hp: 195) Finished collecting potential mismatches positions 1:10:16.233 33G / 58G INFO General (mismatch_shall_not_pass.hp: 303) All edges processed 1:10:16.288 33G / 58G INFO General (mismatch_correction.cpp : 27) Corrected 1271 nucleotides 1:10:16.291 33G / 58G INFO StageManager (stage.cpp : 166) STAGE == Contig Output 1:10:16.291 33G / 58G INFO General (contig_output_stage.cpp : 107) Writing GFA to /srv/scratch/marinovg/SPAdes-3.14-L1399-Cyclotella_meninghiana_gDNA/K77/assembly_graph_with_scaffolds.gfa 1:10:20.250 33G / 58G INFO General (contig_output.hpp : 21) Outputting contigs to /srv/scratch/marinovg/SPAdes-3.14-L1399-Cyclotella_meninghiana_gDNA/K77/before_rr.fasta 1:10:24.261 33G / 58G INFO General (contig_output_stage.cpp : 118) Outputting FastG graph to /srv/scratch/marinovg/SPAdes-3.14-L1399-Cyclotella_meninghiana_gDNA/K77/assembly_graph.fastg 1:10:37.040 33G / 58G INFO General (contig_output.hpp : 21) Outputting contigs to /srv/scratch/marinovg/SPAdes-3.14-L1399-Cyclotella_meninghiana_gDNA/K77/final_contigs.fasta 1:10:40.911 33G / 58G INFO StageManager (stage.cpp : 166) STAGE == Paired Information Counting 1:10:47.353 33G / 58G INFO General (graph_pack.hpp : 113) Normalizing k-mer map. Total 224816037 kmers to process 1:11:59.133 33G / 58G INFO General (graph_pack.hpp : 115) Normalizing done 1:11:59.617 33G / 58G INFO General (pair_info_count.cpp : 322) Min edge length for estimation: 5767 1:11:59.619 33G / 58G INFO General (pair_info_count.cpp : 394) Mapping single reads of library #0 1:11:59.620 33G / 58G INFO General (pair_info_count.cpp : 39) Selecting usual mapper 1:12:04.614 33G / 58G INFO General (sequence_mapper_notifier.h: 94) Total 4107115 reads processed 1:12:04.616 33G / 58G INFO General (pair_info_count.cpp : 396) Total paths obtained from single reads: 377029 1:12:04.617 33G / 58G INFO General (pair_info_count.cpp : 394) Mapping single reads of library #1 1:12:04.618 33G / 58G INFO General (pair_info_count.cpp : 39) Selecting usual mapper 1:12:05.255 33G / 58G INFO General (sequence_mapper_notifier.h: 94) Total 787141 reads processed 1:12:05.257 33G / 58G INFO General (pair_info_count.cpp : 396) Total paths obtained from single reads: 47444 1:12:05.258 33G / 58G INFO General (pair_info_count.cpp : 333) Estimating insert size for library #2 1:12:05.259 33G / 58G INFO General (pair_info_count.cpp : 190) Estimating insert size (takes a while) 1:12:05.779 34G / 58G INFO General (pair_info_count.cpp : 39) Selecting usual mapper 1:12:12.364 34G / 58G INFO General (sequence_mapper_notifier.h: 76) Processed 200000 reads 1:12:12.462 34G / 58G INFO General (sequence_mapper_notifier.h: 76) Processed 400000 reads 1:12:12.515 34G / 58G INFO General (sequence_mapper_notifier.h: 76) Processed 600000 reads 1:12:12.568 34G / 58G INFO General (sequence_mapper_notifier.h: 76) Processed 800000 reads 1:12:12.615 34G / 58G INFO General (sequence_mapper_notifier.h: 76) Processed 1000000 reads 1:12:12.668 34G / 58G INFO General (sequence_mapper_notifier.h: 76) Processed 1200000 reads 1:12:12.987 34G / 58G INFO General (sequence_mapper_notifier.h: 76) Processed 2200000 reads 1:12:13.484 34G / 58G INFO General (sequence_mapper_notifier.h: 76) Processed 4200000 reads 1:12:14.736 34G / 58G INFO General (sequence_mapper_notifier.h: 76) Processed 8400000 reads 1:12:22.412 34G / 58G INFO General (sequence_mapper_notifier.h: 76) Processed 16800000 reads 1:12:37.722 34G / 58G INFO General (sequence_mapper_notifier.h: 76) Processed 33600000 reads 1:13:05.520 34G / 58G INFO General (sequence_mapper_notifier.h: 76) Processed 67200000 reads 1:14:00.298 34G / 58G INFO General (sequence_mapper_notifier.h: 76) Processed 134400000 reads 1:14:32.634 34G / 58G INFO General (sequence_mapper_notifier.h: 94) Total 171621781 reads processed 1:14:33.916 34G / 58G INFO General (pair_info_count.cpp : 208) Edge pairs: 17867368 1:14:33.918 34G / 58G INFO General (pair_info_count.cpp : 212) 143461651 paired reads (83.5918% of all) aligned to long edges 1:14:33.968 33G / 58G INFO General (pair_info_count.cpp : 356) Insert size = 335.434, deviation = 155.963, left quantile = 163, right quantile = 555, read length = 150 1:14:33.997 33G / 58G INFO General (pair_info_count.cpp : 373) Filtering data for library #2 1:14:34.001 33G / 58G INFO General (pair_info_count.cpp : 39) Selecting usual mapper 1:14:41.167 33G / 58G INFO General (sequence_mapper_notifier.h: 76) Processed 200000 reads 1:14:41.169 33G / 58G INFO General (sequence_mapper_notifier.h: 76) Processed 400000 reads 1:14:41.347 33G / 58G INFO General (sequence_mapper_notifier.h: 76) Processed 600000 reads 1:14:41.431 33G / 58G INFO General (sequence_mapper_notifier.h: 76) Processed 800000 reads 1:14:41.452 33G / 58G INFO General (sequence_mapper_notifier.h: 76) Processed 1000000 reads 1:14:41.541 33G / 58G INFO General (sequence_mapper_notifier.h: 76) Processed 1200000 reads 1:14:41.691 33G / 58G INFO General (sequence_mapper_notifier.h: 76) Processed 2200000 reads 1:14:42.034 33G / 58G INFO General (sequence_mapper_notifier.h: 76) Processed 4200000 reads 1:14:43.161 33G / 58G INFO General (sequence_mapper_notifier.h: 76) Processed 8400000 reads 1:14:51.410 33G / 58G INFO General (sequence_mapper_notifier.h: 76) Processed 16800000 reads 1:15:08.020 33G / 58G INFO General (sequence_mapper_notifier.h: 76) Processed 33600000 reads 1:15:37.632 33G / 58G INFO General (sequence_mapper_notifier.h: 76) Processed 67200000 reads 1:16:38.294 33G / 58G INFO General (sequence_mapper_notifier.h: 76) Processed 134400000 reads 1:17:13.625 33G / 58G INFO General (sequence_mapper_notifier.h: 94) Total 171621781 reads processed 1:17:13.629 33G / 58G INFO General (pair_info_count.cpp : 385) Mapping library #2 1:17:13.631 33G / 58G INFO General (pair_info_count.cpp : 387) Mapping paired reads (takes a while) 1:17:13.633 33G / 58G INFO General (pair_info_count.cpp : 288) Left insert size quantile 163, right insert size quantile 555, filtering threshold 2, rounding threshold 0 1:17:13.644 33G / 58G INFO General (pair_info_count.cpp : 39) Selecting usual mapper 1:17:29.758 33G / 58G INFO General (sequence_mapper_notifier.h: 76) Processed 200000 reads 1:17:30.019 33G / 58G INFO General (sequence_mapper_notifier.h: 76) Processed 400000 reads 1:17:30.545 33G / 58G INFO General (sequence_mapper_notifier.h: 76) Processed 600000 reads 1:17:30.904 33G / 58G INFO General (sequence_mapper_notifier.h: 76) Processed 800000 reads 1:17:31.233 33G / 58G INFO General (sequence_mapper_notifier.h: 76) Processed 1000000 reads 1:17:31.388 33G / 58G INFO General (sequence_mapper_notifier.h: 76) Processed 1200000 reads 1:17:32.064 33G / 58G INFO General (sequence_mapper_notifier.h: 76) Processed 2200000 reads 1:17:32.786 33G / 58G INFO General (sequence_mapper_notifier.h: 76) Processed 4200000 reads 1:17:34.524 33G / 58G INFO General (sequence_mapper_notifier.h: 76) Processed 8400000 reads 1:17:53.777 34G / 58G INFO General (sequence_mapper_notifier.h: 76) Processed 16800000 reads 1:18:31.234 34G / 58G INFO General (sequence_mapper_notifier.h: 76) Processed 33600000 reads 1:19:37.699 34G / 58G INFO General (sequence_mapper_notifier.h: 76) Processed 67200000 reads 1:21:54.671 35G / 58G INFO General (sequence_mapper_notifier.h: 76) Processed 134400000 reads 1:22:57.897 35G / 58G INFO General (sequence_mapper_notifier.h: 94) Total 171621781 reads processed 1:22:58.011 35G / 58G INFO StageManager (stage.cpp : 166) STAGE == Distance Estimation 1:22:58.013 35G / 58G INFO General (distance_estimation.cpp : 174) Processing library #2 1:22:58.014 35G / 58G INFO General (distance_estimation.cpp : 150) Weight Filter Done 1:22:58.015 35G / 58G INFO DistanceEstimator (distance_estimation.hpp : 116) Using SIMPLE distance estimator 1:26:53.875 37G / 58G INFO General (distance_estimation.cpp : 35) Filtering info 1:26:53.877 37G / 58G INFO General (pair_info_filters.hpp : 242) Start filtering; index size: 120750690 1:27:27.379 37G / 58G INFO General (pair_info_filters.hpp : 263) Done filtering 1:27:27.388 37G / 58G INFO General (distance_estimation.cpp : 157) Refining clustered pair information 1:27:31.672 37G / 58G INFO General (distance_estimation.cpp : 159) The refining of clustered pair information has been finished 1:27:31.674 37G / 58G INFO General (distance_estimation.cpp : 161) Improving paired information 1:28:11.386 36G / 58G INFO PairInfoImprover (pair_info_improver.hpp : 103) Paired info stats: missing = 3657708; contradictional = 15356 1:29:02.478 37G / 58G INFO PairInfoImprover (pair_info_improver.hpp : 103) Paired info stats: missing = 763752; contradictional = 202 1:29:02.480 37G / 58G INFO General (distance_estimation.cpp : 104) Filling scaffolding index 1:29:02.481 37G / 58G INFO DistanceEstimator (distance_estimation.hpp : 116) Using SMOOTHING distance estimator 1:32:51.716 36G / 58G INFO General (distance_estimation.cpp : 35) Filtering info 1:32:51.718 36G / 58G INFO General (pair_info_filters.hpp : 242) Start filtering; index size: 2184140 1:32:52.648 37G / 58G INFO General (pair_info_filters.hpp : 263) Done filtering 1:32:52.652 36G / 58G INFO General (distance_estimation.cpp : 183) Clearing raw paired index 1:32:56.082 36G / 58G INFO StageManager (stage.cpp : 166) STAGE == Repeat Resolving 1:32:56.084 36G / 58G INFO General (repeat_resolving.cpp : 69) Using Path-Extend repeat resolving 1:32:56.085 36G / 58G INFO General (launcher.cpp : 538) ExSPAnder repeat resolving tool started 1:32:57.055 36G / 58G INFO General (coverage_uniformity_analyz: 25) genomic coverage is 7.86599 calculated of length 233987854 1:33:00.079 38G / 58G INFO General (launcher.cpp : 404) Creating main extenders, unique edge length = 2000 1:33:00.338 38G / 58G INFO General (launcher.cpp : 336) filling path container 1:33:05.003 39G / 58G INFO General (launcher.cpp : 336) filling path container 1:33:05.431 40G / 58G INFO General (extenders_logic.cpp : 35) resolvable_repeat_length_bound set to 10000 1:33:12.316 40G / 58G INFO General (extenders_logic.cpp : 35) resolvable_repeat_length_bound set to 10000 1:33:14.934 40G / 58G INFO General (extenders_logic.cpp : 311) Estimated coverage of library #2 is 79.0985 1:33:15.189 40G / 58G INFO General (extenders_logic.cpp : 311) Estimated coverage of library #2 is 79.0985 1:33:16.297 40G / 58G INFO General (extenders_logic.cpp : 519) Using 1 paired-end library 1:33:16.298 40G / 58G INFO General (extenders_logic.cpp : 520) Using 1 paired-end scaffolding library 1:33:16.299 40G / 58G INFO General (extenders_logic.cpp : 521) Using 2 single read libraries 1:33:16.300 40G / 58G INFO General (launcher.cpp : 432) Total number of extenders is 5 1:33:16.301 40G / 58G INFO General (path_extender.hpp : 894) Processed 0 paths from 285739 (0%) 1:33:16.857 40G / 58G INFO General (path_extender.hpp : 892) Processed 128 paths from 285739 (0%) 1:33:17.232 40G / 58G INFO General (path_extender.hpp : 892) Processed 256 paths from 285739 (0%) 1:33:17.619 40G / 58G INFO General (path_extender.hpp : 892) Processed 512 paths from 285739 (0%) 1:33:18.645 40G / 58G INFO General (path_extender.hpp : 892) Processed 1024 paths from 285739 (0%) 1:33:22.387 40G / 58G INFO General (path_extender.hpp : 892) Processed 2048 paths from 285739 (0%) 1:33:31.385 40G / 58G INFO General (path_extender.hpp : 892) Processed 4096 paths from 285739 (1%) 1:33:42.383 40G / 58G INFO General (path_extender.hpp : 892) Processed 8192 paths from 285739 (2%) 1:34:04.793 40G / 58G INFO General (path_extender.hpp : 892) Processed 16384 paths from 285739 (5%) 1:34:33.645 40G / 58G INFO General (path_extender.hpp : 894) Processed 28574 paths from 285739 (10%) 1:34:40.215 40G / 58G INFO General (path_extender.hpp : 892) Processed 32768 paths from 285739 (11%) 1:35:14.106 40G / 58G INFO General (path_extender.hpp : 894) Processed 57148 paths from 285739 (20%) 1:35:17.068 40G / 58G INFO General (path_extender.hpp : 892) Processed 65536 paths from 285739 (22%) 1:35:20.072 40G / 58G INFO General (path_extender.hpp : 894) Processed 85722 paths from 285739 (30%) 1:35:24.705 41G / 58G INFO General (path_extender.hpp : 894) Processed 114296 paths from 285739 (40%) 1:35:27.060 41G / 58G INFO General (path_extender.hpp : 892) Processed 131072 paths from 285739 (45%) 1:35:28.045 41G / 58G INFO General (path_extender.hpp : 894) Processed 142870 paths from 285739 (50%) 1:35:30.207 41G / 58G INFO General (path_extender.hpp : 894) Processed 171444 paths from 285739 (60%) 1:35:32.444 41G / 58G INFO General (path_extender.hpp : 894) Processed 200018 paths from 285739 (70%) 1:41:30.375 42G / 58G INFO General (path_extender.hpp : 894) Processed 228592 paths from 285739 (80%) 1:45:02.101 42G / 58G INFO General (path_extender.hpp : 894) Processed 257166 paths from 285739 (90%) 1:45:15.119 42G / 58G INFO General (path_extender.hpp : 892) Processed 262144 paths from 285739 (91%) 1:45:40.119 42G / 58G INFO General (launcher.cpp : 244) Finalizing paths 1:45:40.121 42G / 58G INFO General (launcher.cpp : 246) Deduplicating paths 1:45:48.290 42G / 58G INFO General (launcher.cpp : 250) Paths deduplicated 1:45:48.291 42G / 58G INFO PEResolver (pe_resolver.hpp : 295) Removing overlaps 1:45:48.292 42G / 58G INFO PEResolver (pe_resolver.hpp : 298) Sorting paths 1:45:48.616 42G / 58G INFO PEResolver (pe_resolver.hpp : 305) Marking overlaps 1:45:48.618 42G / 58G INFO OverlapRemover (pe_resolver.hpp : 130) Marking start/end overlaps 1:45:53.771 42G / 58G INFO OverlapRemover (pe_resolver.hpp : 133) Marking remaining overlaps 1:45:59.019 42G / 58G INFO PEResolver (pe_resolver.hpp : 308) Splitting paths 1:45:59.473 42G / 58G INFO PEResolver (pe_resolver.hpp : 313) Deduplicating paths 1:46:00.328 42G / 58G INFO PEResolver (pe_resolver.hpp : 315) Overlaps removed 1:46:02.304 42G / 58G INFO General (launcher.cpp : 267) Paths finalized 1:46:02.305 42G / 58G INFO General (launcher.cpp : 439) Closing gaps in paths 1:46:03.921 42G / 58G INFO General (launcher.cpp : 467) Gap closing completed 1:46:04.475 42G / 58G INFO General (launcher.cpp : 296) Traversing tandem repeats 1:46:07.103 42G / 58G INFO General (launcher.cpp : 306) Traversed 93 loops 1:46:07.105 42G / 58G INFO General (launcher.cpp : 244) Finalizing paths 1:46:07.105 42G / 58G INFO General (launcher.cpp : 246) Deduplicating paths 1:46:07.338 42G / 58G INFO General (launcher.cpp : 250) Paths deduplicated 1:46:07.340 42G / 58G INFO PEResolver (pe_resolver.hpp : 295) Removing overlaps 1:46:07.341 42G / 58G INFO PEResolver (pe_resolver.hpp : 298) Sorting paths 1:46:07.581 42G / 58G INFO PEResolver (pe_resolver.hpp : 305) Marking overlaps 1:46:07.583 42G / 58G INFO OverlapRemover (pe_resolver.hpp : 130) Marking start/end overlaps 1:46:08.006 42G / 58G INFO OverlapRemover (pe_resolver.hpp : 133) Marking remaining overlaps 1:46:08.478 42G / 58G INFO PEResolver (pe_resolver.hpp : 308) Splitting paths 1:46:08.507 42G / 58G INFO PEResolver (pe_resolver.hpp : 313) Deduplicating paths 1:46:08.735 42G / 58G INFO PEResolver (pe_resolver.hpp : 315) Overlaps removed 1:46:09.789 42G / 58G INFO General (launcher.cpp : 267) Paths finalized 1:46:09.791 42G / 58G INFO General (launcher.cpp : 596) ExSPAnder repeat resolving tool finished 1:46:13.106 41G / 58G INFO StageManager (stage.cpp : 166) STAGE == Contig Output 1:46:13.108 41G / 58G INFO General (contig_output_stage.cpp : 107) Writing GFA to /srv/scratch/marinovg/SPAdes-3.14-L1399-Cyclotella_meninghiana_gDNA/K77/assembly_graph_with_scaffolds.gfa 1:46:17.846 39G / 58G INFO General (contig_output.hpp : 21) Outputting contigs to /srv/scratch/marinovg/SPAdes-3.14-L1399-Cyclotella_meninghiana_gDNA/K77/before_rr.fasta 1:46:23.001 38G / 58G INFO General (contig_output_stage.cpp : 118) Outputting FastG graph to /srv/scratch/marinovg/SPAdes-3.14-L1399-Cyclotella_meninghiana_gDNA/K77/assembly_graph.fastg 1:46:39.667 38G / 58G INFO General (contig_output_stage.cpp : 80) Outputting FastG paths to /srv/scratch/marinovg/SPAdes-3.14-L1399-Cyclotella_meninghiana_gDNA/K77/final_contigs.paths 1:46:46.819 39G / 58G INFO General (contig_output_stage.cpp : 80) Outputting FastG paths to /srv/scratch/marinovg/SPAdes-3.14-L1399-Cyclotella_meninghiana_gDNA/K77/scaffolds.paths 1:46:53.853 38G / 58G INFO General (launch.hpp : 192) SPAdes finished 1:48:58.936 5G / 58G INFO General (main.cpp : 105) Assembling time: 1 hours 48 minutes 58 seconds ===== K77 finished. ===== Copy files started. == Running: /usr/bin/python /oak/stanford/groups/akundaje/marinovg/programs/SPAdes-3.14.0-Linux/share/spades/spades_pipeline/scripts/copy_files.py /srv/scratch/marinovg/SPAdes-3.14-L1399-Cyclotella_meninghiana_gDNA/K77/before_rr.fasta /srv/scratch/marinovg/SPAdes-3.14-L1399-Cyclotella_meninghiana_gDNA/before_rr.fasta /srv/scratch/marinovg/SPAdes-3.14-L1399-Cyclotella_meninghiana_gDNA/K77/final_contigs.fasta /srv/scratch/marinovg/SPAdes-3.14-L1399-Cyclotella_meninghiana_gDNA/contigs.fasta /srv/scratch/marinovg/SPAdes-3.14-L1399-Cyclotella_meninghiana_gDNA/K77/first_pe_contigs.fasta /srv/scratch/marinovg/SPAdes-3.14-L1399-Cyclotella_meninghiana_gDNA/first_pe_contigs.fasta /srv/scratch/marinovg/SPAdes-3.14-L1399-Cyclotella_meninghiana_gDNA/K77/scaffolds.fasta /srv/scratch/marinovg/SPAdes-3.14-L1399-Cyclotella_meninghiana_gDNA/scaffolds.fasta /srv/scratch/marinovg/SPAdes-3.14-L1399-Cyclotella_meninghiana_gDNA/K77/scaffolds.paths /srv/scratch/marinovg/SPAdes-3.14-L1399-Cyclotella_meninghiana_gDNA/scaffolds.paths /srv/scratch/marinovg/SPAdes-3.14-L1399-Cyclotella_meninghiana_gDNA/K77/assembly_graph_with_scaffolds.gfa /srv/scratch/marinovg/SPAdes-3.14-L1399-Cyclotella_meninghiana_gDNA/assembly_graph_with_scaffolds.gfa /srv/scratch/marinovg/SPAdes-3.14-L1399-Cyclotella_meninghiana_gDNA/K77/assembly_graph.fastg /srv/scratch/marinovg/SPAdes-3.14-L1399-Cyclotella_meninghiana_gDNA/assembly_graph.fastg /srv/scratch/marinovg/SPAdes-3.14-L1399-Cyclotella_meninghiana_gDNA/K77/final_contigs.paths /srv/scratch/marinovg/SPAdes-3.14-L1399-Cyclotella_meninghiana_gDNA/contigs.paths ===== Copy files finished. ===== Assembling finished. ===== Breaking scaffolds started. == Running: /usr/bin/python /oak/stanford/groups/akundaje/marinovg/programs/SPAdes-3.14.0-Linux/share/spades/spades_pipeline/scripts/breaking_scaffolds_script.py --result_scaffolds_filename /srv/scratch/marinovg/SPAdes-3.14-L1399-Cyclotella_meninghiana_gDNA/scaffolds.fasta --misc_dir /srv/scratch/marinovg/SPAdes-3.14-L1399-Cyclotella_meninghiana_gDNA/misc --threshold_for_breaking_scaffolds 3 ===== Breaking scaffolds finished. ===== Terminate started. ===== Terminate finished. * Corrected reads are in /srv/scratch/marinovg/SPAdes-3.14-L1399-Cyclotella_meninghiana_gDNA/corrected/ * Assembled contigs are in /srv/scratch/marinovg/SPAdes-3.14-L1399-Cyclotella_meninghiana_gDNA/contigs.fasta * Assembled scaffolds are in /srv/scratch/marinovg/SPAdes-3.14-L1399-Cyclotella_meninghiana_gDNA/scaffolds.fasta * Paths in the assembly graph corresponding to the contigs are in /srv/scratch/marinovg/SPAdes-3.14-L1399-Cyclotella_meninghiana_gDNA/contigs.paths * Paths in the assembly graph corresponding to the scaffolds are in /srv/scratch/marinovg/SPAdes-3.14-L1399-Cyclotella_meninghiana_gDNA/scaffolds.paths * Assembly graph is in /srv/scratch/marinovg/SPAdes-3.14-L1399-Cyclotella_meninghiana_gDNA/assembly_graph.fastg * Assembly graph in GFA format is in /srv/scratch/marinovg/SPAdes-3.14-L1399-Cyclotella_meninghiana_gDNA/assembly_graph_with_scaffolds.gfa ======= SPAdes pipeline finished WITH WARNINGS! === Error correction and assembling warnings: * 0:32:05.667 10G / 22G WARN General (kmer_coverage_model.cpp : 366) Failed to determine erroneous kmer threshold. Threshold set to: 98 * 0:20:58.568 8G / 25G WARN General (kmer_coverage_model.cpp : 366) Failed to determine erroneous kmer threshold. Threshold set to: 90 * 0:20:16.513 12G / 26G WARN General (kmer_coverage_model.cpp : 366) Failed to determine erroneous kmer threshold. Threshold set to: 71 * 0:20:56.615 12G / 37G WARN General (kmer_coverage_model.cpp : 366) Failed to determine erroneous kmer threshold. Threshold set to: 54 ======= Warnings saved to /srv/scratch/marinovg/SPAdes-3.14-L1399-Cyclotella_meninghiana_gDNA/warnings.log SPAdes log can be found here: /srv/scratch/marinovg/SPAdes-3.14-L1399-Cyclotella_meninghiana_gDNA/spades.log Thank you for using SPAdes!