Command line: /oak/stanford/groups/akundaje/marinovg/programs/SPAdes-3.13.0-Linux/bin/spades.py --rna --pe1-1 /oak/stanford/groups/akundaje/marinovg/various/2025-04-09-foraminifera-trans-splicing-check/Triloculina_sp._1.read1.paired.fastq.gz --pe1-2 /oak/stanford/groups/akundaje/marinovg/various/2025-04-09-foraminifera-trans-splicing-check/Triloculina_sp._1.read2.paired.fastq.gz -t 20 -o /oak/stanford/groups/akundaje/marinovg/various/2025-04-09-foraminifera-trans-splicing-check/SPAdes-3.13-RNA-Trimmomatic-Triloculina_sp._1 System information: SPAdes version: 3.13.0 Python version: 2.7.16 OS: Linux-3.10.0-1160.119.1.el7.tuxcare.els15.x86_64-x86_64-with-centos-7.9.2009-Core Output dir: /oak/stanford/groups/akundaje/marinovg/various/2025-04-09-foraminifera-trans-splicing-check/SPAdes-3.13-RNA-Trimmomatic-Triloculina_sp._1 Mode: read error correction and assembling Debug mode is turned OFF Dataset parameters: RNA-seq mode Reads: Library number: 1, library type: paired-end orientation: fr left reads: ['/oak/stanford/groups/akundaje/marinovg/various/2025-04-09-foraminifera-trans-splicing-check/Triloculina_sp._1.read1.paired.fastq.gz'] right reads: ['/oak/stanford/groups/akundaje/marinovg/various/2025-04-09-foraminifera-trans-splicing-check/Triloculina_sp._1.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: auto 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: /oak/stanford/groups/akundaje/marinovg/various/2025-04-09-foraminifera-trans-splicing-check/SPAdes-3.13-RNA-Trimmomatic-Triloculina_sp._1/tmp Threads: 20 Memory limit (in Gb): 250 ======= SPAdes pipeline started. Log can be found here: /oak/stanford/groups/akundaje/marinovg/various/2025-04-09-foraminifera-trans-splicing-check/SPAdes-3.13-RNA-Trimmomatic-Triloculina_sp._1/spades.log /oak/stanford/groups/akundaje/marinovg/various/2025-04-09-foraminifera-trans-splicing-check/Triloculina_sp._1.read2.paired.fastq.gz: max reads length: 151 /oak/stanford/groups/akundaje/marinovg/various/2025-04-09-foraminifera-trans-splicing-check/Triloculina_sp._1.read1.paired.fastq.gz: max reads length: 151 Reads length: 151 K values to be used: [49, 73] ===== Read error correction started. == Running read error correction tool: /oak/stanford/groups/akundaje/marinovg/programs/SPAdes-3.13.0-Linux/bin/spades-hammer /oak/stanford/groups/akundaje/marinovg/various/2025-04-09-foraminifera-trans-splicing-check/SPAdes-3.13-RNA-Trimmomatic-Triloculina_sp._1/corrected/configs/config.info 0:00:00.000 4M / 4M INFO General (main.cpp : 75) Starting BayesHammer, built from refs/heads/spades_3.13.0, git revision 8ea46659e9b2aca35444a808db550ac333006f8b 0:00:00.000 4M / 4M INFO General (main.cpp : 76) Loading config from /oak/stanford/groups/akundaje/marinovg/various/2025-04-09-foraminifera-trans-splicing-check/SPAdes-3.13-RNA-Trimmomatic-Triloculina_sp._1/corrected/configs/config.info 0:00:00.002 4M / 4M INFO General (main.cpp : 78) Maximum # of threads to use (adjusted due to OMP capabilities): 1 0:00:00.002 4M / 4M INFO General (memory_limit.cpp : 49) Memory limit set to 250 Gb 0:00:00.002 4M / 4M INFO General (main.cpp : 86) Trying to determine PHRED offset 0:00:00.003 4M / 4M INFO General (main.cpp : 92) Determined value is 33 0:00:00.003 4M / 4M INFO General (hammer_tools.cpp : 36) Hamming graph threshold tau=1, k=21, subkmer positions = [ 0 10 ] 0:00:00.003 4M / 4M INFO General (main.cpp : 113) Size of aux. kmer data 24 bytes === ITERATION 0 begins === 0:00:00.005 4M / 4M INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:00:00.005 4M / 4M INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 16 files using 1 threads. This might take a while. 0:00:00.006 4M / 4M INFO General (file_limit.hpp : 32) Open file limit set to 131072 0:00:00.006 4M / 4M INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 83.332 Gb 0:00:00.006 4M / 4M INFO General (kmer_splitters.hpp : 97) Using cell size of 4194304 0:00:00.006 580M / 616M INFO K-mer Splitting (kmer_data.cpp : 97) Processing /oak/stanford/groups/akundaje/marinovg/various/2025-04-09-foraminifera-trans-splicing-check/Triloculina_sp._1.read1.paired.fastq.gz 0:00:12.548 580M / 616M INFO K-mer Splitting (kmer_data.cpp : 107) Processed 260614 reads 0:00:23.655 580M / 616M INFO K-mer Splitting (kmer_data.cpp : 107) Processed 522714 reads 0:00:34.395 580M / 616M INFO K-mer Splitting (kmer_data.cpp : 107) Processed 786952 reads 0:00:45.250 580M / 616M INFO K-mer Splitting (kmer_data.cpp : 107) Processed 1049727 reads 0:00:55.866 580M / 616M INFO K-mer Splitting (kmer_data.cpp : 107) Processed 1313011 reads 0:01:07.525 580M / 616M INFO K-mer Splitting (kmer_data.cpp : 107) Processed 1576244 reads 0:01:31.680 580M / 616M INFO K-mer Splitting (kmer_data.cpp : 107) Processed 2101553 reads 0:02:45.250 580M / 616M INFO K-mer Splitting (kmer_data.cpp : 97) Processing /oak/stanford/groups/akundaje/marinovg/various/2025-04-09-foraminifera-trans-splicing-check/Triloculina_sp._1.read2.paired.fastq.gz 0:03:06.924 580M / 616M INFO K-mer Splitting (kmer_data.cpp : 107) Processed 4364634 reads 0:05:25.390 580M / 616M INFO K-mer Splitting (kmer_data.cpp : 112) Total 7694032 reads processed 0:05:25.425 4M / 616M INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:06:13.539 4M / 616M INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 128447936 kmers in total. 0:06:13.539 4M / 616M INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:06:17.374 4M / 616M INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:06:39.726 64M / 616M INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 0:06:42.403 64M / 616M INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 59574050 bytes occupied (3.71039 bits per kmer). 0:06:42.406 64M / 616M INFO K-mer Counting (kmer_data.cpp : 356) Arranging kmers in hash map order 0:07:01.229 1G / 1G INFO General (main.cpp : 148) Clustering Hamming graph. 0:31:12.662 1G / 1G INFO General (main.cpp : 155) Extracting clusters 0:32:23.363 1G / 4G INFO General (main.cpp : 167) Clustering done. Total clusters: 52776640 0:32:23.449 1G / 4G INFO K-mer Counting (kmer_data.cpp : 376) Collecting K-mer information, this takes a while. 0:32:25.075 3G / 4G INFO K-mer Counting (kmer_data.cpp : 382) Processing /oak/stanford/groups/akundaje/marinovg/various/2025-04-09-foraminifera-trans-splicing-check/Triloculina_sp._1.read1.paired.fastq.gz 0:42:47.826 3G / 4G INFO K-mer Counting (kmer_data.cpp : 382) Processing /oak/stanford/groups/akundaje/marinovg/various/2025-04-09-foraminifera-trans-splicing-check/Triloculina_sp._1.read2.paired.fastq.gz 0:53:08.166 3G / 4G INFO K-mer Counting (kmer_data.cpp : 389) Collection done, postprocessing. 0:53:08.775 3G / 4G INFO K-mer Counting (kmer_data.cpp : 403) There are 128447936 kmers in total. Among them 64441006 (50.169%) are singletons. 0:53:08.829 3G / 4G INFO General (main.cpp : 173) Subclustering Hamming graph 2:19:49.201 3G / 4G INFO Hamming Subclustering (kmer_cluster.cpp : 649) Subclustering done. Total 19279 non-read kmers were generated. 2:19:49.573 3G / 4G INFO Hamming Subclustering (kmer_cluster.cpp : 650) Subclustering statistics: 2:19:49.884 3G / 4G INFO Hamming Subclustering (kmer_cluster.cpp : 651) Total singleton hamming clusters: 35718492. Among them 22786474 (63.7946%) are good 2:19:49.884 3G / 4G INFO Hamming Subclustering (kmer_cluster.cpp : 652) Total singleton subclusters: 1710523. Among them 1706016 (99.7365%) are good 2:19:49.884 3G / 4G INFO Hamming Subclustering (kmer_cluster.cpp : 653) Total non-singleton subcluster centers: 19918525. Among them 14305410 (71.8196%) are good 2:19:49.884 3G / 4G INFO Hamming Subclustering (kmer_cluster.cpp : 654) Average size of non-trivial subcluster: 4.65721 kmers 2:19:49.884 3G / 4G INFO Hamming Subclustering (kmer_cluster.cpp : 655) Average number of sub-clusters per non-singleton cluster: 1.26796 2:19:49.884 3G / 4G INFO Hamming Subclustering (kmer_cluster.cpp : 656) Total solid k-mers: 38797900 2:19:49.911 3G / 4G INFO Hamming Subclustering (kmer_cluster.cpp : 657) Substitution probabilities: [4,4]((0.925696,0.0213595,0.0158791,0.0370656),(0.0785616,0.879563,0.0104545,0.0314206),(0.0302024,0.0100555,0.879852,0.0798903),(0.036225,0.0155941,0.0209594,0.927222)) 2:19:50.030 3G / 4G INFO General (main.cpp : 178) Finished clustering. 2:19:50.045 3G / 4G INFO General (main.cpp : 197) Starting solid k-mers expansion in 1 threads. 2:26:44.586 3G / 4G INFO General (main.cpp : 218) Solid k-mers iteration 0 produced 11398791 new k-mers. 2:33:37.592 3G / 4G INFO General (main.cpp : 218) Solid k-mers iteration 1 produced 702205 new k-mers. 2:40:30.477 3G / 4G INFO General (main.cpp : 218) Solid k-mers iteration 2 produced 35410 new k-mers. 2:47:22.980 3G / 4G INFO General (main.cpp : 218) Solid k-mers iteration 3 produced 2287 new k-mers. 2:54:15.888 3G / 4G INFO General (main.cpp : 218) Solid k-mers iteration 4 produced 157 new k-mers. 3:01:08.849 3G / 4G INFO General (main.cpp : 218) Solid k-mers iteration 5 produced 97 new k-mers. 3:08:01.539 3G / 4G INFO General (main.cpp : 218) Solid k-mers iteration 6 produced 7 new k-mers. 3:08:01.539 3G / 4G INFO General (main.cpp : 222) Solid k-mers finalized 3:08:01.540 3G / 4G INFO General (hammer_tools.cpp : 220) Starting read correction in 1 threads. 3:08:01.581 3G / 4G INFO General (hammer_tools.cpp : 233) Correcting pair of reads: /oak/stanford/groups/akundaje/marinovg/various/2025-04-09-foraminifera-trans-splicing-check/Triloculina_sp._1.read1.paired.fastq.gz and /oak/stanford/groups/akundaje/marinovg/various/2025-04-09-foraminifera-trans-splicing-check/Triloculina_sp._1.read2.paired.fastq.gz 3:08:02.694 3G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 0 of 100000 reads. 3:08:14.596 3G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 0 3:08:14.981 3G / 4G INFO General (hammer_tools.cpp : 185) Written batch 0 3:08:15.677 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 1 of 100000 reads. 3:08:27.383 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 1 3:08:27.638 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 1 3:08:28.187 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 2 of 100000 reads. 3:08:40.078 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 2 3:08:40.341 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 2 3:08:40.904 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 3 of 100000 reads. 3:08:52.830 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 3 3:08:53.096 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 3 3:08:53.637 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 4 of 100000 reads. 3:09:06.360 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 4 3:09:06.618 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 4 3:09:07.157 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 5 of 100000 reads. 3:09:19.655 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 5 3:09:19.907 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 5 3:09:20.447 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 6 of 100000 reads. 3:09:32.881 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 6 3:09:33.136 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 6 3:09:33.678 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 7 of 100000 reads. 3:09:46.073 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 7 3:09:46.364 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 7 3:09:46.960 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 8 of 100000 reads. 3:09:59.200 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 8 3:09:59.466 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 8 3:10:00.006 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 9 of 100000 reads. 3:10:12.611 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 9 3:10:12.868 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 9 3:10:13.411 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 10 of 100000 reads. 3:10:26.068 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 10 3:10:26.330 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 10 3:10:26.868 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 11 of 100000 reads. 3:10:39.272 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 11 3:10:39.545 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 11 3:10:40.085 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 12 of 100000 reads. 3:10:52.483 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 12 3:10:52.742 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 12 3:10:53.289 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 13 of 100000 reads. 3:11:05.943 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 13 3:11:06.203 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 13 3:11:06.743 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 14 of 100000 reads. 3:11:19.247 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 14 3:11:19.506 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 14 3:11:20.049 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 15 of 100000 reads. 3:11:32.532 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 15 3:11:32.797 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 15 3:11:33.342 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 16 of 100000 reads. 3:11:45.904 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 16 3:11:46.171 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 16 3:11:46.712 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 17 of 100000 reads. 3:11:58.979 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 17 3:11:59.250 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 17 3:11:59.793 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 18 of 100000 reads. 3:12:12.190 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 18 3:12:12.448 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 18 3:12:12.992 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 19 of 100000 reads. 3:12:25.469 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 19 3:12:25.733 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 19 3:12:26.276 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 20 of 100000 reads. 3:12:38.497 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 20 3:12:38.759 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 20 3:12:39.300 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 21 of 100000 reads. 3:12:51.598 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 21 3:12:51.858 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 21 3:12:52.401 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 22 of 100000 reads. 3:13:04.689 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 22 3:13:04.951 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 22 3:13:05.487 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 23 of 100000 reads. 3:13:17.477 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 23 3:13:17.740 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 23 3:13:18.276 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 24 of 100000 reads. 3:13:29.952 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 24 3:13:30.207 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 24 3:13:30.746 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 25 of 100000 reads. 3:13:42.688 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 25 3:13:42.957 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 25 3:13:43.492 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 26 of 100000 reads. 3:13:55.334 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 26 3:13:55.592 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 26 3:13:56.131 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 27 of 100000 reads. 3:14:07.742 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 27 3:14:07.999 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 27 3:14:08.539 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 28 of 100000 reads. 3:14:20.334 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 28 3:14:20.590 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 28 3:14:21.126 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 29 of 100000 reads. 3:14:33.021 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 29 3:14:33.285 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 29 3:14:33.821 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 30 of 100000 reads. 3:14:45.492 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 30 3:14:45.763 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 30 3:14:46.303 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 31 of 100000 reads. 3:14:58.209 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 31 3:14:58.477 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 31 3:14:59.014 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 32 of 100000 reads. 3:15:10.873 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 32 3:15:11.133 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 32 3:15:11.713 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 33 of 100000 reads. 3:15:23.515 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 33 3:15:23.771 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 33 3:15:24.309 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 34 of 100000 reads. 3:15:36.058 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 34 3:15:36.322 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 34 3:15:36.862 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 35 of 100000 reads. 3:15:48.729 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 35 3:15:48.997 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 35 3:15:49.531 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 36 of 100000 reads. 3:16:01.028 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 36 3:16:01.293 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 36 3:16:01.829 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 37 of 100000 reads. 3:16:13.579 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 37 3:16:13.865 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 37 3:16:14.173 4G / 4G INFO General (hammer_tools.cpp : 168) Prepared batch 38 of 47016 reads. 3:16:19.656 4G / 4G INFO General (hammer_tools.cpp : 175) Processed batch 38 3:16:19.785 4G / 4G INFO General (hammer_tools.cpp : 185) Written batch 38 3:16:19.886 3G / 4G INFO General (hammer_tools.cpp : 274) Correction done. Changed 2381601 bases in 1383184 reads. 3:16:19.886 3G / 4G INFO General (hammer_tools.cpp : 275) Failed to correct 3837 bases out of 1014743139. 3:16:20.297 8M / 4G INFO General (main.cpp : 255) Saving corrected dataset description to /oak/stanford/groups/akundaje/marinovg/various/2025-04-09-foraminifera-trans-splicing-check/SPAdes-3.13-RNA-Trimmomatic-Triloculina_sp._1/corrected/corrected.yaml 3:16:20.623 8M / 4G INFO General (main.cpp : 262) All done. Exiting. == Compressing corrected reads (with pigz) == Dataset description file was created: /oak/stanford/groups/akundaje/marinovg/various/2025-04-09-foraminifera-trans-splicing-check/SPAdes-3.13-RNA-Trimmomatic-Triloculina_sp._1/corrected/corrected.yaml ===== Read error correction finished. ===== Assembling started. == Running assembler: K49 0:00:00.000 4M / 4M INFO General (main.cpp : 74) Loaded config from /oak/stanford/groups/akundaje/marinovg/various/2025-04-09-foraminifera-trans-splicing-check/SPAdes-3.13-RNA-Trimmomatic-Triloculina_sp._1/K49/configs/config.info 0:00:00.000 4M / 4M INFO General (main.cpp : 74) Loaded config from /oak/stanford/groups/akundaje/marinovg/various/2025-04-09-foraminifera-trans-splicing-check/SPAdes-3.13-RNA-Trimmomatic-Triloculina_sp._1/K49/configs/mda_mode.info 0:00:00.000 4M / 4M INFO General (main.cpp : 74) Loaded config from /oak/stanford/groups/akundaje/marinovg/various/2025-04-09-foraminifera-trans-splicing-check/SPAdes-3.13-RNA-Trimmomatic-Triloculina_sp._1/K49/configs/rna_mode.info 0:00:00.000 4M / 4M INFO General (memory_limit.cpp : 49) Memory limit set to 250 Gb 0:00:00.000 4M / 4M INFO General (main.cpp : 87) Starting SPAdes, built from refs/heads/spades_3.13.0, git revision 8ea46659e9b2aca35444a808db550ac333006f8b 0:00:00.000 4M / 4M INFO General (main.cpp : 88) Maximum k-mer length: 128 0:00:00.000 4M / 4M INFO General (main.cpp : 89) Assembling dataset (/oak/stanford/groups/akundaje/marinovg/various/2025-04-09-foraminifera-trans-splicing-check/SPAdes-3.13-RNA-Trimmomatic-Triloculina_sp._1/dataset.info) with K=49 0:00:00.000 4M / 4M INFO General (main.cpp : 90) Maximum # of threads to use (adjusted due to OMP capabilities): 1 0:00:00.000 4M / 4M INFO General (launch.hpp : 51) SPAdes started 0:00:00.000 4M / 4M INFO General (launch.hpp : 58) Starting from stage: construction 0:00:00.000 4M / 4M INFO General (launch.hpp : 65) Two-step RR enabled: 0 0:00:00.001 4M / 4M INFO StageManager (stage.cpp : 132) STAGE == de Bruijn graph construction 0:00:00.003 4M / 4M INFO General (read_converter.hpp : 77) Converting reads to binary format for library #0 (takes a while) 0:00:00.003 4M / 4M INFO General (read_converter.hpp : 78) Converting paired reads 0:00:00.364 80M / 132M INFO General (binary_converter.hpp : 93) 16384 reads processed 0:00:00.558 92M / 132M INFO General (binary_converter.hpp : 93) 32768 reads processed 0:00:00.930 120M / 132M INFO General (binary_converter.hpp : 93) 65536 reads processed 0:00:01.564 176M / 176M INFO General (binary_converter.hpp : 93) 131072 reads processed 0:00:02.684 280M / 280M INFO General (binary_converter.hpp : 93) 262144 reads processed 0:00:04.944 496M / 496M INFO General (binary_converter.hpp : 93) 524288 reads processed 0:00:11.850 832M / 832M INFO General (binary_converter.hpp : 93) 1048576 reads processed 0:00:23.101 836M / 836M INFO General (binary_converter.hpp : 93) 2097152 reads processed 0:00:43.608 180M / 844M INFO General (binary_converter.hpp : 117) 3839572 reads written 0:00:43.728 4M / 844M INFO General (read_converter.hpp : 87) Converting single reads 0:00:44.022 132M / 844M INFO General (binary_converter.hpp : 117) 7059 reads written 0:00:44.035 4M / 844M INFO General (read_converter.hpp : 95) Converting merged reads 0:00:44.281 132M / 844M INFO General (binary_converter.hpp : 117) 0 reads written 0:00:44.296 4M / 844M INFO General (construction.cpp : 111) Max read length 151 0:00:44.296 4M / 844M INFO General (construction.cpp : 117) Average read length 131.963 0:00:44.296 4M / 844M INFO General (stage.cpp : 101) PROCEDURE == k+1-mer counting 0:00:44.297 4M / 844M INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 1 files using 1 threads. This might take a while. 0:00:44.298 4M / 844M INFO General (file_limit.hpp : 32) Open file limit set to 131072 0:00:44.298 4M / 844M INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 83.332 Gb 0:00:44.298 4M / 844M INFO General (kmer_splitters.hpp : 97) Using cell size of 33554432 0:00:51.575 568M / 1G INFO General (kmer_splitters.hpp : 289) Processed 812787 reads 0:00:58.727 568M / 1G INFO General (kmer_splitters.hpp : 289) Processed 1612950 reads 0:01:06.063 568M / 1G INFO General (kmer_splitters.hpp : 289) Processed 2429419 reads 0:01:13.096 568M / 1G INFO General (kmer_splitters.hpp : 289) Processed 3241891 reads 0:01:20.193 568M / 1G INFO General (kmer_splitters.hpp : 289) Processed 4049991 reads 0:01:27.292 568M / 1G INFO General (kmer_splitters.hpp : 289) Processed 4858952 reads 0:01:34.399 568M / 1G INFO General (kmer_splitters.hpp : 289) Processed 5664353 reads 0:01:41.727 568M / 1G INFO General (kmer_splitters.hpp : 289) Processed 6471221 reads 0:02:02.817 568M / 1G INFO General (kmer_splitters.hpp : 289) Processed 8892873 reads 0:03:00.150 568M / 1G INFO General (kmer_splitters.hpp : 295) Adding contigs from previous K 0:03:00.212 4M / 1G INFO General (kmer_splitters.hpp : 308) Used 15372406 reads 0:03:00.212 4M / 1G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:03:19.201 4M / 1G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 52159503 kmers in total. 0:03:19.201 4M / 1G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:03:21.911 4M / 1G INFO General (stage.cpp : 101) PROCEDURE == Extension index construction 0:03:21.913 4M / 1G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:03:21.913 4M / 1G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 16 files using 1 threads. This might take a while. 0:03:21.913 4M / 1G INFO General (file_limit.hpp : 32) Open file limit set to 131072 0:03:21.913 4M / 1G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 83.332 Gb 0:03:21.913 4M / 1G INFO General (kmer_splitters.hpp : 97) Using cell size of 2097152 0:03:31.399 580M / 1G INFO General (kmer_splitters.hpp : 380) Processed 16757665 kmers 0:03:39.363 580M / 1G INFO General (kmer_splitters.hpp : 380) Processed 33510486 kmers 0:03:46.839 580M / 1G INFO General (kmer_splitters.hpp : 380) Processed 50265101 kmers 0:03:47.655 580M / 1G INFO General (kmer_splitters.hpp : 380) Processed 52159506 kmers 0:03:47.655 580M / 1G INFO General (kmer_splitters.hpp : 385) Used 52159506 kmers. 0:03:47.705 4M / 1G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:03:53.788 4M / 1G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 52142715 kmers in total. 0:03:53.788 4M / 1G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:03:56.056 4M / 1G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:04:05.675 28M / 1G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 0:04:07.704 28M / 1G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 24186872 bytes occupied (3.71087 bits per kmer). 0:04:07.755 80M / 1G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 99) Building k-mer extensions from k+1-mers 0:04:45.449 80M / 1G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 103) Building k-mer extensions from k+1-mers finished. 0:04:45.450 80M / 1G INFO General (stage.cpp : 101) PROCEDURE == Early tip clipping 0:04:45.450 80M / 1G INFO General (construction.cpp : 253) Early tip clipper length bound set as (RL - K) 0:04:45.450 80M / 1G INFO Early tip clipping (early_simplification.hpp : 181) Early tip clipping 0:05:54.682 80M / 1G INFO Early tip clipping (early_simplification.hpp : 184) 12750091 50-mers were removed by early tip clipper 0:05:54.683 80M / 1G INFO General (stage.cpp : 101) PROCEDURE == Condensing graph 0:05:54.683 80M / 1G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 355) Extracting unbranching paths 0:06:43.838 156M / 1G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 374) Extracting unbranching paths finished. 1141303 sequences extracted 0:07:03.818 156M / 1G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 310) Collecting perfect loops 0:07:12.983 156M / 1G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 343) Collecting perfect loops finished. 41 loops collected 0:07:15.246 440M / 1G INFO General (stage.cpp : 101) PROCEDURE == Filling coverage indices (PHM) 0:07:15.246 440M / 1G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:07:15.246 440M / 1G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:07:31.516 472M / 1G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 24187000 bytes occupied (3.7097 bits per kmer). 0:07:31.653 672M / 1G INFO General (construction.cpp : 388) Collecting k-mer coverage information from reads, this takes a while. 0:10:21.176 672M / 1G INFO General (construction.cpp : 508) Filling coverage and flanking coverage from PHM 0:10:31.702 672M / 1G INFO General (construction.cpp : 464) Processed 1000000 edges 0:10:42.060 672M / 1G INFO General (construction.cpp : 464) Processed 2000000 edges 0:10:44.984 672M / 1G INFO General (construction.cpp : 464) Processed 2282663 edges 0:10:45.313 384M / 1G INFO StageManager (stage.cpp : 132) STAGE == EC Threshold Finding 0:10:46.844 384M / 1G INFO ThresholdFinder (ec_threshold_finder.hpp : 114) Bucket size: 9 0:10:46.844 384M / 1G INFO General (genomic_info_filler.cpp : 98) Average edge coverage: 15.7976 0:10:46.844 384M / 1G INFO General (genomic_info_filler.cpp : 99) Graph threshold: 137 0:10:47.252 384M / 1G INFO General (genomic_info_filler.cpp : 127) EC coverage threshold value was calculated as 15.7976 0:10:47.253 384M / 1G INFO General (genomic_info_filler.cpp : 128) Trusted kmer low bound: 0 0:10:47.253 384M / 1G INFO StageManager (stage.cpp : 132) STAGE == Raw Simplification 0:10:47.253 384M / 1G INFO General (simplification.cpp : 128) PROCEDURE == InitialCleaning 0:10:47.253 384M / 1G INFO General (graph_simplification.hpp : 662) Flanking coverage based disconnection disabled 0:10:47.253 384M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Self conjugate edge remover 0:10:47.591 384M / 1G INFO Simplification (parallel_processing.hpp : 167) Self conjugate edge remover triggered 0 times 0:10:47.591 384M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Remover of short poly-AT edges 0:10:47.592 384M / 1G INFO General (simplification.cpp : 76) Removing short polyAT 0:10:48.803 384M / 1G INFO Simplification (parallel_processing.hpp : 167) Remover of short poly-AT edges triggered 21385 times 0:10:48.803 384M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Short PolyA/T Edges 0:10:49.222 384M / 1G INFO Simplification (parallel_processing.hpp : 167) Short PolyA/T Edges triggered 0 times 0:10:49.222 384M / 1G INFO Simplification (parallel_processing.hpp : 165) Running AT Tips 0:10:50.511 384M / 1G INFO Simplification (parallel_processing.hpp : 167) AT Tips triggered 73808 times 0:10:50.511 384M / 1G INFO General (graph_simplification.hpp : 701) Removing loops and rc loops with erroneous connections 0:10:52.610 388M / 1G INFO ECLoopRemover (erroneous_connection_remov: 440) Loops: accurately removed/deadend removed/other: 1/95/6 0:10:52.610 388M / 1G INFO ECLoopRemover (erroneous_connection_remov: 441) RC loops: accurately removed/deadend removed/other: 3/6/41 0:10:52.616 384M / 1G INFO StageManager (stage.cpp : 132) STAGE == Simplification 0:10:52.616 384M / 1G INFO General (simplification.cpp : 357) Graph simplification started 0:10:52.616 384M / 1G INFO General (graph_simplification.hpp : 634) Creating parallel br instance 0:10:52.616 384M / 1G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 1 0:10:52.616 384M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:10:53.449 384M / 1G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 14486 times 0:10:53.449 384M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:10:54.502 388M / 1G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 54532 times 0:10:54.502 388M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:11:10.360 408M / 1G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 131967 times 0:11:10.360 408M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:11:10.433 408M / 1G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 432 times 0:11:10.433 408M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:11:10.495 400M / 1G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 231 times 0:11:10.495 400M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:11:10.500 400M / 1G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 23 times 0:11:10.500 400M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:11:10.500 400M / 1G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:11:10.500 400M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:11:10.500 400M / 1G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times 0:11:10.500 400M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:11:10.500 400M / 1G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:11:10.500 400M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:11:12.846 400M / 1G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 68371 times 0:11:12.846 400M / 1G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 2 0:11:12.846 400M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:11:13.239 400M / 1G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 3079 times 0:11:13.239 400M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:11:13.559 396M / 1G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 1702 times 0:11:13.559 396M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:11:15.922 396M / 1G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 10455 times 0:11:15.922 396M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:11:15.927 396M / 1G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 9 times 0:11:15.927 396M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:11:15.930 396M / 1G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times 0:11:15.930 396M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:11:15.930 396M / 1G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:11:15.930 396M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:11:15.930 396M / 1G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:11:15.930 396M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:11:15.930 396M / 1G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times 0:11:15.930 396M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:11:15.930 396M / 1G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:11:15.930 396M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:11:16.241 392M / 1G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 4017 times 0:11:16.241 392M / 1G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 3 0:11:16.241 392M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:11:16.542 392M / 1G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 661 times 0:11:16.542 392M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:11:16.794 392M / 1G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 7 times 0:11:16.794 392M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:11:17.172 392M / 1G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 750 times 0:11:17.172 392M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:11:17.172 392M / 1G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:11:17.172 392M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:11:17.173 392M / 1G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times 0:11:17.173 392M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:11:17.173 392M / 1G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:11:17.173 392M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:11:17.397 392M / 1G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 1262 times 0:11:17.397 392M / 1G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 4 0:11:17.397 392M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:11:17.730 392M / 1G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 151 times 0:11:17.731 392M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:11:17.982 392M / 1G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times 0:11:17.982 392M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:11:18.259 392M / 1G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 199 times 0:11:18.259 392M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:11:18.259 392M / 1G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:11:18.259 392M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:11:18.259 392M / 1G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times 0:11:18.259 392M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:11:18.259 392M / 1G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:11:18.259 392M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:11:18.468 392M / 1G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 594 times 0:11:18.468 392M / 1G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 5 0:11:18.468 392M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:11:18.752 392M / 1G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 61 times 0:11:18.752 392M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:11:19.000 392M / 1G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times 0:11:19.000 392M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:11:19.249 392M / 1G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 72 times 0:11:19.249 392M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:11:19.249 392M / 1G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:11:19.249 392M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:11:19.249 392M / 1G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times 0:11:19.249 392M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:11:19.249 392M / 1G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:11:19.249 392M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:11:19.452 392M / 1G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 349 times 0:11:19.452 392M / 1G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 6 0:11:19.452 392M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:11:19.736 392M / 1G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 33 times 0:11:19.736 392M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:11:19.983 392M / 1G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times 0:11:19.983 392M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:11:20.220 392M / 1G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 33 times 0:11:20.220 392M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:11:20.220 392M / 1G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:11:20.220 392M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:11:20.220 392M / 1G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times 0:11:20.220 392M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:11:20.220 392M / 1G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:11:20.220 392M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:11:20.420 392M / 1G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 264 times 0:11:20.420 392M / 1G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 7 0:11:20.420 392M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:11:20.701 392M / 1G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 18 times 0:11:20.701 392M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:11:20.947 392M / 1G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times 0:11:20.947 392M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:11:21.177 392M / 1G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 19 times 0:11:21.177 392M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:11:21.177 392M / 1G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:11:21.177 392M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:11:21.177 392M / 1G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times 0:11:21.177 392M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:11:21.177 392M / 1G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:11:21.177 392M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:11:21.375 392M / 1G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 180 times 0:11:21.375 392M / 1G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 8 0:11:21.375 392M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:11:21.655 392M / 1G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 12 times 0:11:21.655 392M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:11:21.901 392M / 1G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times 0:11:21.901 392M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:11:22.127 392M / 1G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 10 times 0:11:22.127 392M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:11:22.127 392M / 1G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:11:22.127 392M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:11:22.127 392M / 1G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times 0:11:22.127 392M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:11:22.127 392M / 1G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:11:22.127 392M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:11:22.324 392M / 1G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 141 times 0:11:22.324 392M / 1G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 9 0:11:22.324 392M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:11:22.604 392M / 1G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 12 times 0:11:22.604 392M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:11:22.849 392M / 1G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times 0:11:22.849 392M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:11:23.072 392M / 1G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 10 times 0:11:23.072 392M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:11:23.072 392M / 1G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:11:23.072 392M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:11:23.072 392M / 1G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times 0:11:23.072 392M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:11:23.072 392M / 1G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:11:23.072 392M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:11:23.268 392M / 1G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 115 times 0:11:23.268 392M / 1G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 10 0:11:23.268 392M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:11:23.550 392M / 1G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 4 times 0:11:23.550 392M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:11:23.795 392M / 1G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times 0:11:23.795 392M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:11:24.018 388M / 1G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 3 times 0:11:24.018 388M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:11:24.018 388M / 1G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:11:24.018 388M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:11:24.018 388M / 1G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times 0:11:24.018 388M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:11:24.018 388M / 1G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:11:24.018 388M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:11:24.214 392M / 1G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 100 times 0:11:24.214 392M / 1G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 11 0:11:24.214 392M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:11:24.494 392M / 1G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 10 times 0:11:24.495 392M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:11:24.737 392M / 1G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times 0:11:24.737 392M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:11:24.959 388M / 1G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 6 times 0:11:24.959 388M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:11:24.959 388M / 1G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:11:24.959 388M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:11:24.959 388M / 1G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times 0:11:24.959 388M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:11:24.959 388M / 1G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:11:24.959 388M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:11:25.153 388M / 1G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:11:25.153 388M / 1G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 12 0:11:25.153 388M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:11:25.153 388M / 1G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:11:25.153 388M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:11:25.153 388M / 1G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times 0:11:25.153 388M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:11:25.153 388M / 1G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:11:25.153 388M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:11:25.153 388M / 1G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:11:25.153 388M / 1G INFO StageManager (stage.cpp : 132) STAGE == Simplification Cleanup 0:11:25.153 388M / 1G INFO General (simplification.cpp : 196) PROCEDURE == Post simplification 0:11:25.153 388M / 1G INFO General (graph_simplification.hpp : 453) Disconnection of relatively low covered edges disabled 0:11:25.153 388M / 1G INFO General (graph_simplification.hpp : 489) Complex tip clipping disabled 0:11:25.153 388M / 1G INFO General (graph_simplification.hpp : 634) Creating parallel br instance 0:11:25.153 388M / 1G INFO General (graph_simplification.hpp : 634) Creating parallel br instance 0:11:25.153 388M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover 0:11:25.513 388M / 1G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 236 times 0:11:25.513 388M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover 0:11:25.943 388M / 1G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 12317 times 0:11:25.943 388M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Complex bulge remover 0:11:27.082 388M / 1G INFO Simplification (parallel_processing.hpp : 167) Complex bulge remover triggered 340 times 0:11:27.082 388M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:11:27.326 388M / 1G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 32 times 0:11:27.326 388M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Final tip clipper 0:11:27.823 376M / 1G INFO Simplification (parallel_processing.hpp : 167) Final tip clipper triggered 19204 times 0:11:27.823 376M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:11:27.989 376M / 1G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 161 times 0:11:27.989 376M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Final bulge remover 0:11:28.145 376M / 1G INFO Simplification (parallel_processing.hpp : 167) Final bulge remover triggered 0 times 0:11:28.145 376M / 1G INFO Simplification (parallel_processing.hpp : 165) Running AT Tips 0:11:28.399 376M / 1G INFO Simplification (parallel_processing.hpp : 167) AT Tips triggered 690 times 0:11:28.399 376M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover 0:11:28.665 376M / 1G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 13 times 0:11:28.665 376M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover 0:11:28.825 376M / 1G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 9 times 0:11:28.825 376M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Complex bulge remover 0:11:29.700 376M / 1G INFO Simplification (parallel_processing.hpp : 167) Complex bulge remover triggered 12 times 0:11:29.700 376M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:11:29.896 376M / 1G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:11:29.896 376M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Final tip clipper 0:11:30.086 376M / 1G INFO Simplification (parallel_processing.hpp : 167) Final tip clipper triggered 22 times 0:11:30.086 376M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:11:30.243 376M / 1G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 1 times 0:11:30.243 376M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Final bulge remover 0:11:30.399 376M / 1G INFO Simplification (parallel_processing.hpp : 167) Final bulge remover triggered 0 times 0:11:30.399 376M / 1G INFO Simplification (parallel_processing.hpp : 165) Running AT Tips 0:11:30.647 376M / 1G INFO Simplification (parallel_processing.hpp : 167) AT Tips triggered 6 times 0:11:30.647 376M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover 0:11:30.647 376M / 1G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 0 times 0:11:30.647 376M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover 0:11:30.807 376M / 1G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 0 times 0:11:30.807 376M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Complex bulge remover 0:11:31.693 376M / 1G INFO Simplification (parallel_processing.hpp : 167) Complex bulge remover triggered 0 times 0:11:31.693 376M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:11:31.693 376M / 1G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:11:31.693 376M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Final tip clipper 0:11:31.693 376M / 1G INFO Simplification (parallel_processing.hpp : 167) Final tip clipper triggered 0 times 0:11:31.693 376M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:11:31.693 376M / 1G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:11:31.693 376M / 1G INFO Simplification (parallel_processing.hpp : 165) Running Final bulge remover 0:11:31.693 376M / 1G INFO Simplification (parallel_processing.hpp : 167) Final bulge remover triggered 0 times 0:11:31.693 376M / 1G INFO Simplification (parallel_processing.hpp : 165) Running AT Tips 0:11:31.693 376M / 1G INFO Simplification (parallel_processing.hpp : 167) AT Tips triggered 0 times 0:11:31.693 376M / 1G INFO General (simplification.cpp : 330) Disrupting self-conjugate edges 0:11:31.927 376M / 1G INFO General (simplification.cpp : 470) Counting average coverage 0:11:32.041 376M / 1G INFO General (simplification.cpp : 476) Average coverage = 22.9258 0:11:32.041 376M / 1G INFO StageManager (stage.cpp : 132) STAGE == Contig Output 0:11:32.041 376M / 1G INFO General (contig_output_stage.cpp : 40) Writing GFA to /oak/stanford/groups/akundaje/marinovg/various/2025-04-09-foraminifera-trans-splicing-check/SPAdes-3.13-RNA-Trimmomatic-Triloculina_sp._1//K49/assembly_graph_with_scaffolds.gfa 0:11:32.828 376M / 1G INFO General (contig_output.hpp : 22) Outputting contigs to /oak/stanford/groups/akundaje/marinovg/various/2025-04-09-foraminifera-trans-splicing-check/SPAdes-3.13-RNA-Trimmomatic-Triloculina_sp._1//K49/before_rr.fasta 0:11:33.713 376M / 1G INFO General (contig_output_stage.cpp : 51) Outputting FastG graph to /oak/stanford/groups/akundaje/marinovg/various/2025-04-09-foraminifera-trans-splicing-check/SPAdes-3.13-RNA-Trimmomatic-Triloculina_sp._1//K49/assembly_graph.fastg 0:11:35.832 376M / 1G INFO General (contig_output.hpp : 22) Outputting contigs to /oak/stanford/groups/akundaje/marinovg/various/2025-04-09-foraminifera-trans-splicing-check/SPAdes-3.13-RNA-Trimmomatic-Triloculina_sp._1//K49/simplified_contigs.fasta 0:11:36.704 376M / 1G INFO General (contig_output.hpp : 22) Outputting contigs to /oak/stanford/groups/akundaje/marinovg/various/2025-04-09-foraminifera-trans-splicing-check/SPAdes-3.13-RNA-Trimmomatic-Triloculina_sp._1//K49/final_contigs.fasta 0:11:37.590 376M / 1G INFO StageManager (stage.cpp : 132) STAGE == Contig Output 0:11:37.590 376M / 1G INFO General (contig_output_stage.cpp : 40) Writing GFA to /oak/stanford/groups/akundaje/marinovg/various/2025-04-09-foraminifera-trans-splicing-check/SPAdes-3.13-RNA-Trimmomatic-Triloculina_sp._1//K49/assembly_graph_with_scaffolds.gfa 0:11:38.319 376M / 1G INFO General (contig_output.hpp : 22) Outputting contigs to /oak/stanford/groups/akundaje/marinovg/various/2025-04-09-foraminifera-trans-splicing-check/SPAdes-3.13-RNA-Trimmomatic-Triloculina_sp._1//K49/before_rr.fasta 0:11:39.211 376M / 1G INFO General (contig_output_stage.cpp : 51) Outputting FastG graph to /oak/stanford/groups/akundaje/marinovg/various/2025-04-09-foraminifera-trans-splicing-check/SPAdes-3.13-RNA-Trimmomatic-Triloculina_sp._1//K49/assembly_graph.fastg 0:11:41.358 376M / 1G INFO General (contig_output.hpp : 22) Outputting contigs to /oak/stanford/groups/akundaje/marinovg/various/2025-04-09-foraminifera-trans-splicing-check/SPAdes-3.13-RNA-Trimmomatic-Triloculina_sp._1//K49/simplified_contigs.fasta 0:11:42.246 376M / 1G INFO General (contig_output.hpp : 22) Outputting contigs to /oak/stanford/groups/akundaje/marinovg/various/2025-04-09-foraminifera-trans-splicing-check/SPAdes-3.13-RNA-Trimmomatic-Triloculina_sp._1//K49/final_contigs.fasta 0:11:43.176 376M / 1G INFO General (launch.hpp : 149) SPAdes finished 0:11:43.836 4M / 1G INFO General (main.cpp : 109) Assembling time: 0 hours 11 minutes 43 seconds Max read length detected as 151 == Running assembler: K73 0:00:00.000 4M / 4M INFO General (main.cpp : 74) Loaded config from /oak/stanford/groups/akundaje/marinovg/various/2025-04-09-foraminifera-trans-splicing-check/SPAdes-3.13-RNA-Trimmomatic-Triloculina_sp._1/K73/configs/config.info 0:00:00.000 4M / 4M INFO General (main.cpp : 74) Loaded config from /oak/stanford/groups/akundaje/marinovg/various/2025-04-09-foraminifera-trans-splicing-check/SPAdes-3.13-RNA-Trimmomatic-Triloculina_sp._1/K73/configs/mda_mode.info 0:00:00.000 4M / 4M INFO General (main.cpp : 74) Loaded config from /oak/stanford/groups/akundaje/marinovg/various/2025-04-09-foraminifera-trans-splicing-check/SPAdes-3.13-RNA-Trimmomatic-Triloculina_sp._1/K73/configs/rna_mode.info 0:00:00.000 4M / 4M INFO General (memory_limit.cpp : 49) Memory limit set to 250 Gb 0:00:00.000 4M / 4M INFO General (main.cpp : 87) Starting SPAdes, built from refs/heads/spades_3.13.0, git revision 8ea46659e9b2aca35444a808db550ac333006f8b 0:00:00.000 4M / 4M INFO General (main.cpp : 88) Maximum k-mer length: 128 0:00:00.000 4M / 4M INFO General (main.cpp : 89) Assembling dataset (/oak/stanford/groups/akundaje/marinovg/various/2025-04-09-foraminifera-trans-splicing-check/SPAdes-3.13-RNA-Trimmomatic-Triloculina_sp._1/dataset.info) with K=73 0:00:00.000 4M / 4M INFO General (main.cpp : 90) Maximum # of threads to use (adjusted due to OMP capabilities): 1 0:00:00.000 4M / 4M INFO General (launch.hpp : 51) SPAdes started 0:00:00.000 4M / 4M INFO General (launch.hpp : 58) Starting from stage: construction 0:00:00.000 4M / 4M INFO General (launch.hpp : 65) Two-step RR enabled: 0 0:00:00.000 4M / 4M INFO General (launch.hpp : 76) Will need read mapping, kmer mapper will be attached 0:00:00.000 4M / 4M INFO StageManager (stage.cpp : 132) STAGE == de Bruijn graph construction 0:00:00.002 4M / 4M INFO General (read_converter.hpp : 59) Binary reads detected 0:00:00.002 4M / 4M INFO General (construction.cpp : 111) Max read length 151 0:00:00.002 4M / 4M INFO General (construction.cpp : 117) Average read length 131.963 0:00:00.002 4M / 4M INFO General (stage.cpp : 101) PROCEDURE == k+1-mer counting 0:00:00.004 4M / 4M INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 1 files using 1 threads. This might take a while. 0:00:00.004 4M / 4M INFO General (file_limit.hpp : 32) Open file limit set to 131072 0:00:00.004 4M / 4M INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 83.332 Gb 0:00:00.004 4M / 4M INFO General (kmer_splitters.hpp : 97) Using cell size of 22369621 0:00:06.101 568M / 1G INFO General (kmer_splitters.hpp : 289) Processed 726854 reads 0:00:11.942 568M / 1G INFO General (kmer_splitters.hpp : 289) Processed 1439452 reads 0:00:17.188 568M / 1G INFO General (kmer_splitters.hpp : 289) Processed 2165416 reads 0:00:22.680 568M / 1G INFO General (kmer_splitters.hpp : 289) Processed 2893526 reads 0:00:28.002 568M / 1G INFO General (kmer_splitters.hpp : 289) Processed 3618310 reads 0:00:33.190 568M / 1G INFO General (kmer_splitters.hpp : 289) Processed 4337804 reads 0:00:38.475 568M / 1G INFO General (kmer_splitters.hpp : 289) Processed 5060251 reads 0:00:43.658 568M / 1G INFO General (kmer_splitters.hpp : 289) Processed 5780029 reads 0:01:05.101 568M / 1G INFO General (kmer_splitters.hpp : 289) Processed 8660778 reads 0:01:54.721 568M / 1G INFO General (kmer_splitters.hpp : 295) Adding contigs from previous K 0:02:02.140 4M / 1G INFO General (kmer_splitters.hpp : 308) Used 15372406 reads 0:02:02.140 4M / 1G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:02:35.500 4M / 1G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 50170781 kmers in total. 0:02:35.500 4M / 1G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:02:39.626 4M / 1G INFO General (stage.cpp : 101) PROCEDURE == Extension index construction 0:02:39.627 4M / 1G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:02:39.627 4M / 1G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 16 files using 1 threads. This might take a while. 0:02:39.628 4M / 1G INFO General (file_limit.hpp : 32) Open file limit set to 131072 0:02:39.628 4M / 1G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 83.332 Gb 0:02:39.628 4M / 1G INFO General (kmer_splitters.hpp : 97) Using cell size of 1398101 0:02:47.059 580M / 1G INFO General (kmer_splitters.hpp : 380) Processed 11169073 kmers 0:02:52.550 580M / 1G INFO General (kmer_splitters.hpp : 380) Processed 22340002 kmers 0:02:57.985 580M / 1G INFO General (kmer_splitters.hpp : 380) Processed 33506653 kmers 0:03:03.452 580M / 1G INFO General (kmer_splitters.hpp : 380) Processed 44675052 kmers 0:03:06.523 580M / 1G INFO General (kmer_splitters.hpp : 380) Processed 50170785 kmers 0:03:06.523 580M / 1G INFO General (kmer_splitters.hpp : 385) Used 50170785 kmers. 0:03:06.593 4M / 1G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:03:14.082 4M / 1G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 50280254 kmers in total. 0:03:14.082 4M / 1G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:03:16.880 4M / 1G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:03:26.823 24M / 1G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 0:03:28.655 24M / 1G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 23323240 bytes occupied (3.71092 bits per kmer). 0:03:28.695 72M / 1G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 99) Building k-mer extensions from k+1-mers 0:04:04.441 72M / 1G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 103) Building k-mer extensions from k+1-mers finished. 0:04:04.442 72M / 1G INFO General (stage.cpp : 101) PROCEDURE == Condensing graph 0:04:04.443 72M / 1G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 355) Extracting unbranching paths 0:04:52.601 236M / 1G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 374) Extracting unbranching paths finished. 2381159 sequences extracted 0:05:15.140 236M / 1G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 310) Collecting perfect loops 0:05:21.671 236M / 1G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 343) Collecting perfect loops finished. 6 loops collected 0:05:26.461 844M / 1G INFO General (stage.cpp : 101) PROCEDURE == Filling coverage indices (PHM) 0:05:26.461 844M / 1G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:05:26.461 844M / 1G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:05:44.412 868M / 1G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 23264808 bytes occupied (3.7097 bits per kmer). 0:05:44.542 1G / 1G INFO General (construction.cpp : 388) Collecting k-mer coverage information from reads, this takes a while. 0:08:11.102 1G / 1G INFO General (construction.cpp : 508) Filling coverage and flanking coverage from PHM 0:08:19.187 1G / 1G INFO General (construction.cpp : 464) Processed 1000000 edges 0:08:26.278 1G / 1G INFO General (construction.cpp : 464) Processed 2000000 edges 0:08:33.340 1G / 1G INFO General (construction.cpp : 464) Processed 3000000 edges 0:08:40.378 1G / 1G INFO General (construction.cpp : 464) Processed 4000000 edges 0:08:45.838 1G / 1G INFO General (construction.cpp : 464) Processed 4762317 edges 0:08:46.216 784M / 1G INFO StageManager (stage.cpp : 132) STAGE == EC Threshold Finding 0:08:49.198 780M / 1G INFO ThresholdFinder (ec_threshold_finder.hpp : 114) Bucket size: 7 0:08:49.199 780M / 1G INFO General (genomic_info_filler.cpp : 98) Average edge coverage: 9.54629 0:08:49.199 780M / 1G INFO General (genomic_info_filler.cpp : 99) Graph threshold: 146 0:08:49.330 780M / 1G INFO General (genomic_info_filler.cpp : 127) EC coverage threshold value was calculated as 9.54629 0:08:49.330 780M / 1G INFO General (genomic_info_filler.cpp : 128) Trusted kmer low bound: 0 0:08:49.330 780M / 1G INFO StageManager (stage.cpp : 132) STAGE == Gap Closer 0:08:49.330 780M / 1G INFO General (graph_pack.hpp : 101) Index refill 0:08:49.332 780M / 1G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:08:49.332 780M / 1G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 16 files using 1 threads. This might take a while. 0:08:49.333 780M / 1G INFO General (file_limit.hpp : 32) Open file limit set to 131072 0:08:49.333 780M / 1G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 83.0794 Gb 0:08:49.333 780M / 1G INFO General (kmer_splitters.hpp : 97) Using cell size of 1398101 0:08:57.418 1G / 1G INFO General (edge_index_builders.hpp : 77) Processed 2071421 edges 0:09:03.725 1G / 1G INFO General (edge_index_builders.hpp : 77) Processed 4139563 edges 0:09:05.480 1G / 1G INFO General (edge_index_builders.hpp : 77) Processed 4762319 edges 0:09:05.480 1G / 1G INFO General (edge_index_builders.hpp : 82) Used 4762319 sequences. 0:09:05.527 780M / 1G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:09:10.443 780M / 1G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 50170781 kmers in total. 0:09:10.443 780M / 1G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:09:14.764 780M / 1G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:09:24.398 804M / 1G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 0:09:26.442 804M / 1G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 23272488 bytes occupied (3.71092 bits per kmer). 0:09:27.087 1G / 1G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while. 0:09:50.115 1G / 1G INFO General (edge_index.hpp : 92) Index refilled 0:09:50.115 1G / 1G INFO General (gap_closer.cpp : 159) Preparing shift maps 0:09:53.111 2G / 2G INFO General (gap_closer.cpp : 119) Processing paired reads (takes a while) 0:11:02.882 2G / 2G INFO General (gap_closer.cpp : 138) Used 3839572 paired reads 0:11:02.882 2G / 2G INFO General (gap_closer.cpp : 140) Merging paired indices 0:11:03.992 1G / 2G INFO GapCloser (gap_closer.cpp : 346) Closing short gaps 0:11:11.200 1G / 2G INFO GapCloser (gap_closer.cpp : 380) Closing short gaps complete: filled 2232 gaps after checking 98844 candidates 0:11:11.807 1G / 2G INFO StageManager (stage.cpp : 132) STAGE == Raw Simplification 0:11:11.882 788M / 2G INFO General (simplification.cpp : 128) PROCEDURE == InitialCleaning 0:11:11.883 788M / 2G INFO General (graph_simplification.hpp : 662) Flanking coverage based disconnection disabled 0:11:11.883 788M / 2G INFO Simplification (parallel_processing.hpp : 165) Running Self conjugate edge remover 0:11:12.605 788M / 2G INFO Simplification (parallel_processing.hpp : 167) Self conjugate edge remover triggered 0 times 0:11:12.605 788M / 2G INFO Simplification (parallel_processing.hpp : 165) Running Remover of short poly-AT edges 0:11:12.605 788M / 2G INFO General (simplification.cpp : 76) Removing short polyAT 0:11:15.228 784M / 2G INFO Simplification (parallel_processing.hpp : 167) Remover of short poly-AT edges triggered 8363 times 0:11:15.228 784M / 2G INFO Simplification (parallel_processing.hpp : 165) Running Short PolyA/T Edges 0:11:16.198 784M / 2G INFO Simplification (parallel_processing.hpp : 167) Short PolyA/T Edges triggered 0 times 0:11:16.198 784M / 2G INFO Simplification (parallel_processing.hpp : 165) Running AT Tips 0:11:20.096 796M / 2G INFO Simplification (parallel_processing.hpp : 167) AT Tips triggered 197720 times 0:11:20.096 796M / 2G INFO General (graph_simplification.hpp : 701) Removing loops and rc loops with erroneous connections 0:11:25.195 796M / 2G INFO ECLoopRemover (erroneous_connection_remov: 440) Loops: accurately removed/deadend removed/other: 0/29/2 0:11:25.195 796M / 2G INFO ECLoopRemover (erroneous_connection_remov: 441) RC loops: accurately removed/deadend removed/other: 0/5/9 0:11:25.227 796M / 2G INFO StageManager (stage.cpp : 132) STAGE == Simplification 0:11:25.227 796M / 2G INFO General (simplification.cpp : 357) Graph simplification started 0:11:25.227 796M / 2G INFO General (graph_simplification.hpp : 634) Creating parallel br instance 0:11:25.227 796M / 2G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 1 0:11:25.227 796M / 2G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:11:34.193 808M / 2G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 530378 times 0:11:34.193 808M / 2G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:11:37.412 808M / 2G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 166934 times 0:11:37.412 808M / 2G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:12:01.989 1G / 2G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 58097 times 0:12:01.989 1G / 2G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:12:02.084 1G / 2G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 537 times 0:12:02.084 1G / 2G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:12:02.136 1G / 2G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 63 times 0:12:02.136 1G / 2G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:12:02.147 1G / 2G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 27 times 0:12:02.147 1G / 2G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:12:02.147 1G / 2G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:12:02.147 1G / 2G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:12:02.148 1G / 2G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times 0:12:02.148 1G / 2G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:12:02.148 1G / 2G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:12:02.148 1G / 2G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:12:03.617 1G / 2G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 33527 times 0:12:03.617 1G / 2G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 2 0:12:03.617 1G / 2G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:12:04.338 1G / 2G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 7805 times 0:12:04.338 1G / 2G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:12:04.792 1G / 2G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 1426 times 0:12:04.792 1G / 2G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:12:08.710 1G / 2G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 4842 times 0:12:08.710 1G / 2G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:12:08.717 1G / 2G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 6 times 0:12:08.717 1G / 2G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:12:08.721 1G / 2G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times 0:12:08.721 1G / 2G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:12:08.721 1G / 2G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:12:08.721 1G / 2G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:12:08.721 1G / 2G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:12:08.721 1G / 2G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:12:08.721 1G / 2G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times 0:12:08.721 1G / 2G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:12:08.721 1G / 2G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:12:08.721 1G / 2G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:12:09.154 1G / 2G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 2955 times 0:12:09.154 1G / 2G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 3 0:12:09.154 1G / 2G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:12:09.664 1G / 2G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 731 times 0:12:09.664 1G / 2G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:12:10.065 1G / 2G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 2 times 0:12:10.065 1G / 2G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:12:10.733 1G / 2G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 297 times 0:12:10.734 1G / 2G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:12:10.734 1G / 2G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:12:10.734 1G / 2G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:12:10.735 1G / 2G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times 0:12:10.735 1G / 2G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:12:10.735 1G / 2G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:12:10.735 1G / 2G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:12:11.101 1G / 2G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 1370 times 0:12:11.101 1G / 2G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 4 0:12:11.101 1G / 2G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:12:11.594 1G / 2G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 151 times 0:12:11.594 1G / 2G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:12:11.991 1G / 2G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times 0:12:11.991 1G / 2G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:12:12.473 1G / 2G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 63 times 0:12:12.473 1G / 2G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:12:12.473 1G / 2G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:12:12.473 1G / 2G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:12:12.473 1G / 2G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times 0:12:12.473 1G / 2G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:12:12.473 1G / 2G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:12:12.473 1G / 2G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:12:12.820 1G / 2G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 897 times 0:12:12.820 1G / 2G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 5 0:12:12.820 1G / 2G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:12:13.307 1G / 2G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 48 times 0:12:13.307 1G / 2G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:12:13.701 1G / 2G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times 0:12:13.702 1G / 2G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:12:14.127 1G / 2G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 24 times 0:12:14.127 1G / 2G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:12:14.127 1G / 2G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:12:14.127 1G / 2G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:12:14.127 1G / 2G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times 0:12:14.127 1G / 2G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:12:14.127 1G / 2G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:12:14.127 1G / 2G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:12:14.469 1G / 2G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 657 times 0:12:14.469 1G / 2G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 6 0:12:14.469 1G / 2G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:12:14.955 1G / 2G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 39 times 0:12:14.955 1G / 2G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:12:15.348 1G / 2G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times 0:12:15.348 1G / 2G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:12:15.758 1G / 2G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 9 times 0:12:15.758 1G / 2G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:12:15.758 1G / 2G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:12:15.758 1G / 2G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:12:15.758 1G / 2G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times 0:12:15.758 1G / 2G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:12:15.758 1G / 2G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:12:15.758 1G / 2G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:12:16.094 1G / 2G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 564 times 0:12:16.094 1G / 2G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 7 0:12:16.094 1G / 2G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:12:16.579 1G / 2G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 22 times 0:12:16.579 1G / 2G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:12:16.972 1G / 2G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times 0:12:16.972 1G / 2G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:12:17.372 1G / 2G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 9 times 0:12:17.372 1G / 2G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:12:17.372 1G / 2G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:12:17.372 1G / 2G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:12:17.372 1G / 2G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times 0:12:17.372 1G / 2G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:12:17.372 1G / 2G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:12:17.372 1G / 2G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:12:17.701 1G / 2G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 436 times 0:12:17.701 1G / 2G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 8 0:12:17.701 1G / 2G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:12:18.184 1G / 2G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 29 times 0:12:18.184 1G / 2G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:12:18.573 1G / 2G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times 0:12:18.573 1G / 2G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:12:18.967 1G / 2G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 6 times 0:12:18.967 1G / 2G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:12:18.967 1G / 2G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:12:18.967 1G / 2G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:12:18.967 1G / 2G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times 0:12:18.967 1G / 2G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:12:18.967 1G / 2G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:12:18.967 1G / 2G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:12:19.294 1G / 2G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 387 times 0:12:19.294 1G / 2G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 9 0:12:19.294 1G / 2G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:12:19.775 1G / 2G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 23 times 0:12:19.775 1G / 2G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:12:20.164 1G / 2G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times 0:12:20.164 1G / 2G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:12:20.551 1G / 2G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 6 times 0:12:20.551 1G / 2G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:12:20.551 1G / 2G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:12:20.551 1G / 2G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:12:20.551 1G / 2G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times 0:12:20.551 1G / 2G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:12:20.551 1G / 2G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:12:20.551 1G / 2G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:12:20.875 1G / 2G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 336 times 0:12:20.875 1G / 2G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 10 0:12:20.875 1G / 2G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:12:21.355 1G / 2G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 24 times 0:12:21.355 1G / 2G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:12:21.769 1G / 2G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times 0:12:21.769 1G / 2G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:12:22.153 1G / 2G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:12:22.153 1G / 2G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:12:22.153 1G / 2G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:12:22.153 1G / 2G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:12:22.153 1G / 2G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times 0:12:22.153 1G / 2G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:12:22.153 1G / 2G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:12:22.153 1G / 2G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:12:22.476 1G / 2G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 304 times 0:12:22.476 1G / 2G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 11 0:12:22.476 1G / 2G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:12:22.964 1G / 2G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 7 times 0:12:22.964 1G / 2G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:12:23.351 1G / 2G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times 0:12:23.351 1G / 2G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:12:23.732 1G / 2G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:12:23.732 1G / 2G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:12:23.732 1G / 2G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:12:23.732 1G / 2G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:12:23.732 1G / 2G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times 0:12:23.732 1G / 2G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:12:23.732 1G / 2G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:12:23.732 1G / 2G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:12:24.045 1G / 2G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:12:24.045 1G / 2G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 12 0:12:24.045 1G / 2G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:12:24.045 1G / 2G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:12:24.045 1G / 2G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:12:24.045 1G / 2G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times 0:12:24.045 1G / 2G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:12:24.045 1G / 2G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:12:24.045 1G / 2G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:12:24.045 1G / 2G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:12:24.045 1G / 2G INFO StageManager (stage.cpp : 132) STAGE == Gap Closer 0:12:24.045 1G / 2G INFO General (graph_pack.hpp : 101) Index refill 0:12:24.047 1G / 2G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:12:24.047 1G / 2G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 16 files using 1 threads. This might take a while. 0:12:24.048 1G / 2G INFO General (file_limit.hpp : 32) Open file limit set to 131072 0:12:24.048 1G / 2G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 82.9258 Gb 0:12:24.048 1G / 2G INFO General (kmer_splitters.hpp : 97) Using cell size of 1398101 0:12:31.573 1G / 2G INFO General (edge_index_builders.hpp : 77) Processed 613905 edges 0:12:32.929 1G / 2G INFO General (edge_index_builders.hpp : 77) Processed 762731 edges 0:12:32.929 1G / 2G INFO General (edge_index_builders.hpp : 82) Used 762731 sequences. 0:12:32.971 1G / 2G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:12:36.708 1G / 2G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 27752942 kmers in total. 0:12:36.708 1G / 2G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:12:38.536 1G / 2G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:12:43.886 1G / 2G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 0:12:45.087 1G / 2G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 12877400 bytes occupied (3.71201 bits per kmer). 0:12:45.908 1G / 2G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while. 0:12:55.342 1G / 2G INFO General (edge_index.hpp : 92) Index refilled 0:12:55.342 1G / 2G INFO General (gap_closer.cpp : 159) Preparing shift maps 0:12:56.222 1G / 2G INFO General (gap_closer.cpp : 119) Processing paired reads (takes a while) 0:15:06.594 1G / 2G INFO General (gap_closer.cpp : 138) Used 3839572 paired reads 0:15:06.594 1G / 2G INFO General (gap_closer.cpp : 140) Merging paired indices 0:15:07.024 1G / 2G INFO GapCloser (gap_closer.cpp : 346) Closing short gaps 0:15:08.893 1G / 2G INFO GapCloser (gap_closer.cpp : 380) Closing short gaps complete: filled 533 gaps after checking 76164 candidates 0:15:09.212 1G / 2G INFO StageManager (stage.cpp : 132) STAGE == Simplification Cleanup 0:15:09.212 1G / 2G INFO General (simplification.cpp : 196) PROCEDURE == Post simplification 0:15:09.212 1G / 2G INFO General (graph_simplification.hpp : 453) Disconnection of relatively low covered edges disabled 0:15:09.212 1G / 2G INFO General (graph_simplification.hpp : 489) Complex tip clipping disabled 0:15:09.212 1G / 2G INFO General (graph_simplification.hpp : 634) Creating parallel br instance 0:15:09.212 1G / 2G INFO General (graph_simplification.hpp : 634) Creating parallel br instance 0:15:09.212 1G / 2G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover 0:15:09.827 1G / 2G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 143 times 0:15:09.827 1G / 2G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover 0:15:13.922 1G / 2G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 35906 times 0:15:13.922 1G / 2G INFO Simplification (parallel_processing.hpp : 165) Running Complex bulge remover 0:15:16.092 1G / 2G INFO Simplification (parallel_processing.hpp : 167) Complex bulge remover triggered 436 times 0:15:16.092 1G / 2G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:15:16.545 1G / 2G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 198 times 0:15:16.545 1G / 2G INFO Simplification (parallel_processing.hpp : 165) Running Final tip clipper 0:15:35.996 1G / 2G INFO Simplification (parallel_processing.hpp : 167) Final tip clipper triggered 52163 times 0:15:35.996 1G / 2G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:15:36.627 1G / 2G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 303 times 0:15:36.627 1G / 2G INFO Simplification (parallel_processing.hpp : 165) Running Final bulge remover 0:15:36.811 1G / 2G INFO Simplification (parallel_processing.hpp : 167) Final bulge remover triggered 0 times 0:15:36.811 1G / 2G INFO Simplification (parallel_processing.hpp : 165) Running AT Tips 0:15:37.118 1G / 2G INFO Simplification (parallel_processing.hpp : 167) AT Tips triggered 1225 times 0:15:37.118 1G / 2G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover 0:15:37.419 1G / 2G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 3 times 0:15:37.419 1G / 2G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover 0:15:37.619 1G / 2G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 4 times 0:15:37.619 1G / 2G INFO Simplification (parallel_processing.hpp : 165) Running Complex bulge remover 0:15:38.609 1G / 2G INFO Simplification (parallel_processing.hpp : 167) Complex bulge remover triggered 11 times 0:15:38.609 1G / 2G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:15:38.838 1G / 2G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:15:38.838 1G / 2G INFO Simplification (parallel_processing.hpp : 165) Running Final tip clipper 0:15:39.070 1G / 2G INFO Simplification (parallel_processing.hpp : 167) Final tip clipper triggered 17 times 0:15:39.070 1G / 2G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:15:39.256 1G / 2G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 2 times 0:15:39.256 1G / 2G INFO Simplification (parallel_processing.hpp : 165) Running Final bulge remover 0:15:39.439 1G / 2G INFO Simplification (parallel_processing.hpp : 167) Final bulge remover triggered 0 times 0:15:39.439 1G / 2G INFO Simplification (parallel_processing.hpp : 165) Running AT Tips 0:15:39.714 1G / 2G INFO Simplification (parallel_processing.hpp : 167) AT Tips triggered 0 times 0:15:39.714 1G / 2G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover 0:15:39.714 1G / 2G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 0 times 0:15:39.714 1G / 2G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover 0:15:39.905 1G / 2G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 0 times 0:15:39.905 1G / 2G INFO Simplification (parallel_processing.hpp : 165) Running Complex bulge remover 0:15:40.834 1G / 2G INFO Simplification (parallel_processing.hpp : 167) Complex bulge remover triggered 0 times 0:15:40.834 1G / 2G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:15:40.834 1G / 2G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:15:40.834 1G / 2G INFO Simplification (parallel_processing.hpp : 165) Running Final tip clipper 0:15:40.835 1G / 2G INFO Simplification (parallel_processing.hpp : 167) Final tip clipper triggered 1 times 0:15:40.835 1G / 2G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:15:40.835 1G / 2G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:15:40.835 1G / 2G INFO Simplification (parallel_processing.hpp : 165) Running Final bulge remover 0:15:40.835 1G / 2G INFO Simplification (parallel_processing.hpp : 167) Final bulge remover triggered 0 times 0:15:40.835 1G / 2G INFO Simplification (parallel_processing.hpp : 165) Running AT Tips 0:15:40.835 1G / 2G INFO Simplification (parallel_processing.hpp : 167) AT Tips triggered 0 times 0:15:40.835 1G / 2G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover 0:15:40.835 1G / 2G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 0 times 0:15:40.835 1G / 2G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover 0:15:41.024 1G / 2G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 0 times 0:15:41.024 1G / 2G INFO Simplification (parallel_processing.hpp : 165) Running Complex bulge remover 0:15:41.940 1G / 2G INFO Simplification (parallel_processing.hpp : 167) Complex bulge remover triggered 0 times 0:15:41.940 1G / 2G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:15:41.940 1G / 2G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:15:41.940 1G / 2G INFO Simplification (parallel_processing.hpp : 165) Running Final tip clipper 0:15:41.940 1G / 2G INFO Simplification (parallel_processing.hpp : 167) Final tip clipper triggered 0 times 0:15:41.940 1G / 2G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:15:41.940 1G / 2G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:15:41.940 1G / 2G INFO Simplification (parallel_processing.hpp : 165) Running Final bulge remover 0:15:41.940 1G / 2G INFO Simplification (parallel_processing.hpp : 167) Final bulge remover triggered 0 times 0:15:41.940 1G / 2G INFO Simplification (parallel_processing.hpp : 165) Running AT Tips 0:15:41.940 1G / 2G INFO Simplification (parallel_processing.hpp : 167) AT Tips triggered 0 times 0:15:41.940 1G / 2G INFO General (simplification.cpp : 330) Disrupting self-conjugate edges 0:15:42.193 1G / 2G INFO General (simplification.cpp : 470) Counting average coverage 0:15:42.332 1G / 2G INFO General (simplification.cpp : 476) Average coverage = 17.24 0:15:42.332 1G / 2G INFO StageManager (stage.cpp : 132) STAGE == Mismatch Correction 0:15:42.332 1G / 2G INFO General (graph_pack.hpp : 109) Normalizing k-mer map. Total 9801046 kmers to process 0:15:49.340 1G / 2G INFO General (graph_pack.hpp : 111) Normalizing done 0:21:06.552 1G / 2G INFO General (mismatch_shall_not_pass.hp: 189) Finished collecting potential mismatches positions 0:21:09.123 1G / 2G INFO General (mismatch_shall_not_pass.hp: 290) All edges processed 0:21:09.296 1G / 2G INFO General (mismatch_correction.cpp : 27) Corrected 947 nucleotides 0:21:09.296 1G / 2G INFO StageManager (stage.cpp : 132) STAGE == Contig Output 0:21:09.296 1G / 2G INFO General (contig_output_stage.cpp : 40) Writing GFA to /oak/stanford/groups/akundaje/marinovg/various/2025-04-09-foraminifera-trans-splicing-check/SPAdes-3.13-RNA-Trimmomatic-Triloculina_sp._1//K73/assembly_graph_with_scaffolds.gfa 0:21:10.121 1G / 2G INFO General (contig_output.hpp : 22) Outputting contigs to /oak/stanford/groups/akundaje/marinovg/various/2025-04-09-foraminifera-trans-splicing-check/SPAdes-3.13-RNA-Trimmomatic-Triloculina_sp._1//K73/before_rr.fasta 0:21:11.065 1G / 2G INFO General (contig_output_stage.cpp : 51) Outputting FastG graph to /oak/stanford/groups/akundaje/marinovg/various/2025-04-09-foraminifera-trans-splicing-check/SPAdes-3.13-RNA-Trimmomatic-Triloculina_sp._1//K73/assembly_graph.fastg 0:21:13.330 1G / 2G INFO General (contig_output.hpp : 22) Outputting contigs to /oak/stanford/groups/akundaje/marinovg/various/2025-04-09-foraminifera-trans-splicing-check/SPAdes-3.13-RNA-Trimmomatic-Triloculina_sp._1//K73/simplified_contigs.fasta 0:21:14.251 1G / 2G INFO General (contig_output.hpp : 22) Outputting contigs to /oak/stanford/groups/akundaje/marinovg/various/2025-04-09-foraminifera-trans-splicing-check/SPAdes-3.13-RNA-Trimmomatic-Triloculina_sp._1//K73/intermediate_contigs.fasta 0:21:15.276 1G / 2G INFO StageManager (stage.cpp : 132) STAGE == Paired Information Counting 0:21:16.305 1G / 2G INFO General (graph_pack.hpp : 109) Normalizing k-mer map. Total 9847260 kmers to process 0:21:23.175 1G / 2G INFO General (graph_pack.hpp : 111) Normalizing done 0:21:23.330 1G / 2G INFO General (pair_info_count.cpp : 320) Min edge length for estimation: 427 0:21:23.330 1G / 2G INFO General (pair_info_count.cpp : 331) Estimating insert size for library #0 0:21:23.330 1G / 2G INFO General (pair_info_count.cpp : 190) Estimating insert size (takes a while) 0:21:23.350 1G / 2G INFO General (pair_info_count.cpp : 39) Selecting usual mapper 0:21:30.495 1G / 2G INFO General (sequence_mapper_notifier.h: 80) Processed 200000 reads 0:21:37.735 1G / 2G INFO General (sequence_mapper_notifier.h: 80) Processed 400000 reads 0:21:44.958 1G / 2G INFO General (sequence_mapper_notifier.h: 80) Processed 600000 reads 0:21:52.221 1G / 2G INFO General (sequence_mapper_notifier.h: 80) Processed 800000 reads 0:21:59.471 1G / 2G INFO General (sequence_mapper_notifier.h: 80) Processed 1000000 reads 0:22:06.758 1G / 2G INFO General (sequence_mapper_notifier.h: 80) Processed 1200000 reads 0:22:43.041 1G / 2G INFO General (sequence_mapper_notifier.h: 80) Processed 2200000 reads 0:23:42.236 1G / 2G INFO General (sequence_mapper_notifier.h: 98) Total 3839572 reads processed 0:23:43.453 1G / 2G INFO General (pair_info_count.cpp : 209) Edge pairs: 67108864 (rough upper limit) 0:23:43.453 1G / 2G INFO General (pair_info_count.cpp : 213) 2093381 paired reads (54.5212% of all) aligned to long edges 0:23:43.456 1G / 2G INFO General (pair_info_count.cpp : 354) Insert size = 221.171, deviation = 69.1694, left quantile = 153, right quantile = 318, read length = 151 0:23:43.456 1G / 2G INFO General (pair_info_count.cpp : 383) Mapping library #0 0:23:43.456 1G / 2G INFO General (pair_info_count.cpp : 385) Mapping paired reads (takes a while) 0:23:43.456 1G / 2G INFO General (pair_info_count.cpp : 289) Left insert size quantile 153, right insert size quantile 318, filtering threshold 0, rounding threshold 0 0:23:43.462 1G / 2G INFO General (pair_info_count.cpp : 39) Selecting usual mapper 0:23:50.804 1G / 2G INFO General (sequence_mapper_notifier.h: 80) Processed 200000 reads 0:23:58.185 1G / 2G INFO General (sequence_mapper_notifier.h: 80) Processed 400000 reads 0:24:05.606 1G / 2G INFO General (sequence_mapper_notifier.h: 80) Processed 600000 reads 0:24:13.036 1G / 2G INFO General (sequence_mapper_notifier.h: 80) Processed 800000 reads 0:24:20.477 1G / 2G INFO General (sequence_mapper_notifier.h: 80) Processed 1000000 reads 0:24:27.942 1G / 2G INFO General (sequence_mapper_notifier.h: 80) Processed 1200000 reads 0:25:05.165 1G / 2G INFO General (sequence_mapper_notifier.h: 80) Processed 2200000 reads 0:26:06.049 1G / 2G INFO General (sequence_mapper_notifier.h: 98) Total 3839572 reads processed 0:26:06.088 1G / 2G INFO General (pair_info_count.cpp : 392) Mapping single reads of library #0 0:26:06.088 1G / 2G INFO General (pair_info_count.cpp : 255) Will calculate lib coverage as well 0:26:06.088 1G / 2G INFO General (pair_info_count.cpp : 39) Selecting usual mapper 0:26:09.715 1G / 2G INFO General (sequence_mapper_notifier.h: 80) Processed 200000 reads 0:26:13.335 1G / 2G INFO General (sequence_mapper_notifier.h: 80) Processed 400000 reads 0:26:17.009 1G / 2G INFO General (sequence_mapper_notifier.h: 80) Processed 600000 reads 0:26:20.645 1G / 2G INFO General (sequence_mapper_notifier.h: 80) Processed 800000 reads 0:26:24.352 1G / 2G INFO General (sequence_mapper_notifier.h: 80) Processed 1000000 reads 0:26:27.967 1G / 2G INFO General (sequence_mapper_notifier.h: 80) Processed 1200000 reads 0:26:46.354 1G / 2G INFO General (sequence_mapper_notifier.h: 80) Processed 2200000 reads 0:27:23.237 1G / 2G INFO General (sequence_mapper_notifier.h: 80) Processed 4200000 reads 0:28:26.928 1G / 2G INFO General (sequence_mapper_notifier.h: 98) Total 7686203 reads processed 0:28:26.955 1G / 2G INFO General (pair_info_count.cpp : 394) Total paths obtained from single reads: 0 0:28:26.955 1G / 2G INFO StageManager (stage.cpp : 132) STAGE == Distance Estimation 0:28:26.955 1G / 2G INFO General (distance_estimation.cpp : 173) Processing library #0 0:28:26.955 1G / 2G INFO General (distance_estimation.cpp : 149) Weight Filter Done 0:28:26.955 1G / 2G INFO DistanceEstimator (distance_estimation.hpp : 116) Using SIMPLE distance estimator 0:28:27.774 1G / 2G INFO General (distance_estimation.cpp : 34) Filtering info 0:28:27.774 1G / 2G INFO General (pair_info_filters.hpp : 242) Start filtering; index size: 408786 0:28:28.145 1G / 2G INFO General (pair_info_filters.hpp : 263) Done filtering 0:28:28.146 1G / 2G INFO General (distance_estimation.cpp : 156) Refining clustered pair information 0:28:28.190 1G / 2G INFO General (distance_estimation.cpp : 158) The refining of clustered pair information has been finished 0:28:28.190 1G / 2G INFO General (distance_estimation.cpp : 160) Improving paired information 0:28:28.664 1G / 2G INFO PairInfoImprover (pair_info_improver.hpp : 103) Paired info stats: missing = 41; contradictional = 0 0:28:29.139 1G / 2G INFO PairInfoImprover (pair_info_improver.hpp : 103) Paired info stats: missing = 0; contradictional = 0 0:28:29.139 1G / 2G INFO StageManager (stage.cpp : 132) STAGE == Repeat Resolving 0:28:29.139 1G / 2G INFO General (repeat_resolving.cpp : 69) Using Path-Extend repeat resolving 0:28:29.139 1G / 2G INFO General (launcher.cpp : 477) ExSPAnder repeat resolving tool started 0:28:30.399 2G / 2G INFO General (launcher.cpp : 392) Creating main extenders, unique edge length = 2000 0:28:30.826 2G / 2G INFO General (extenders_logic.cpp : 472) Using 1 paired-end library 0:28:30.826 2G / 2G INFO General (extenders_logic.cpp : 473) Using 1 paired-end scaffolding library 0:28:30.826 2G / 2G INFO General (extenders_logic.cpp : 474) Using 0 single read libraries 0:28:30.826 2G / 2G INFO General (launcher.cpp : 420) Total number of extenders is 5 0:28:30.826 2G / 2G INFO General (path_extender.hpp : 885) Processed 0 paths from 200867 (0%) 0:28:30.857 2G / 2G INFO General (path_extender.hpp : 883) Processed 128 paths from 200867 (0%) 0:28:30.881 2G / 2G INFO General (path_extender.hpp : 883) Processed 256 paths from 200867 (0%) 0:28:30.924 2G / 2G INFO General (path_extender.hpp : 883) Processed 512 paths from 200867 (0%) 0:28:30.998 2G / 2G INFO General (path_extender.hpp : 883) Processed 1024 paths from 200867 (0%) 0:28:31.145 2G / 2G INFO General (path_extender.hpp : 883) Processed 2048 paths from 200867 (1%) 0:28:31.409 2G / 2G INFO General (path_extender.hpp : 883) Processed 4096 paths from 200867 (2%) 0:28:31.918 2G / 2G INFO General (path_extender.hpp : 883) Processed 8192 paths from 200867 (4%) 0:28:32.836 2G / 2G INFO General (path_extender.hpp : 883) Processed 16384 paths from 200867 (8%) 0:28:33.217 2G / 2G INFO General (path_extender.hpp : 885) Processed 20087 paths from 200867 (10%) 0:28:34.444 2G / 2G INFO General (path_extender.hpp : 883) Processed 32768 paths from 200867 (16%) 0:28:35.031 2G / 2G INFO General (path_extender.hpp : 885) Processed 40174 paths from 200867 (20%) 0:28:36.448 3G / 3G INFO General (path_extender.hpp : 885) Processed 60261 paths from 200867 (30%) 0:28:36.832 3G / 3G INFO General (path_extender.hpp : 883) Processed 65536 paths from 200867 (32%) 0:28:37.843 3G / 3G INFO General (path_extender.hpp : 885) Processed 80348 paths from 200867 (40%) 0:28:39.181 3G / 3G INFO General (path_extender.hpp : 885) Processed 100435 paths from 200867 (50%) 0:28:40.460 3G / 3G INFO General (path_extender.hpp : 885) Processed 120522 paths from 200867 (60%) 0:28:41.130 3G / 3G INFO General (path_extender.hpp : 883) Processed 131072 paths from 200867 (65%) 0:28:41.743 3G / 3G INFO General (path_extender.hpp : 885) Processed 140609 paths from 200867 (70%) 0:28:42.994 3G / 3G INFO General (path_extender.hpp : 885) Processed 160696 paths from 200867 (80%) 0:28:44.204 4G / 4G INFO General (path_extender.hpp : 885) Processed 180783 paths from 200867 (90%) 0:28:45.398 4G / 4G INFO General (launcher.cpp : 234) Finalizing paths 0:28:45.398 4G / 4G INFO General (launcher.cpp : 236) Deduplicating paths 0:28:45.884 4G / 4G INFO General (launcher.cpp : 240) Paths deduplicated 0:28:45.884 4G / 4G INFO PEResolver (pe_resolver.hpp : 295) Removing overlaps 0:28:45.884 4G / 4G INFO PEResolver (pe_resolver.hpp : 305) Marking overlaps 0:28:45.884 4G / 4G INFO OverlapRemover (pe_resolver.hpp : 130) Marking start/end overlaps 0:28:46.170 4G / 4G INFO PEResolver (pe_resolver.hpp : 308) Splitting paths 0:28:46.194 4G / 4G INFO PEResolver (pe_resolver.hpp : 313) Deduplicating paths 0:28:46.346 4G / 4G INFO PEResolver (pe_resolver.hpp : 315) Overlaps removed 0:28:46.837 4G / 4G INFO General (launcher.cpp : 257) Paths finalized 0:28:46.837 4G / 4G INFO General (launcher.cpp : 427) Closing gaps in paths 0:28:47.837 4G / 4G INFO General (launcher.cpp : 455) Gap closing completed 0:28:48.158 4G / 4G INFO General (launcher.cpp : 286) Traversing tandem repeats 0:28:49.560 4G / 4G INFO General (launcher.cpp : 296) Traversed 0 loops 0:28:49.560 4G / 4G INFO General (launcher.cpp : 234) Finalizing paths 0:28:49.560 4G / 4G INFO General (launcher.cpp : 236) Deduplicating paths 0:28:49.713 4G / 4G INFO General (launcher.cpp : 240) Paths deduplicated 0:28:49.713 4G / 4G INFO PEResolver (pe_resolver.hpp : 295) Removing overlaps 0:28:49.713 4G / 4G INFO PEResolver (pe_resolver.hpp : 305) Marking overlaps 0:28:49.713 4G / 4G INFO OverlapRemover (pe_resolver.hpp : 130) Marking start/end overlaps 0:28:49.999 4G / 4G INFO PEResolver (pe_resolver.hpp : 308) Splitting paths 0:28:50.017 4G / 4G INFO PEResolver (pe_resolver.hpp : 313) Deduplicating paths 0:28:50.170 4G / 4G INFO PEResolver (pe_resolver.hpp : 315) Overlaps removed 0:28:50.607 4G / 4G INFO General (launcher.cpp : 257) Paths finalized 0:28:51.168 4G / 4G INFO General (launcher.cpp : 462) Finalizing main paths 0:28:51.168 4G / 4G INFO General (launcher.cpp : 279) Read length relative cutoff 1.3 converted to 123 0:28:51.168 4G / 4G INFO General (launcher.cpp : 280) Read length absolute cutoff 110 bp converted to 123 0:28:51.168 4G / 4G INFO General (launcher.cpp : 281) Length cutoff: 123 0:28:51.296 4G / 4G INFO General (launcher.cpp : 279) Read length relative cutoff 1.6 converted to 168 0:28:51.296 4G / 4G INFO General (launcher.cpp : 280) Read length absolute cutoff 140 bp converted to 168 0:28:51.296 4G / 4G INFO General (launcher.cpp : 281) Length cutoff: 168 0:28:51.310 4G / 4G INFO General (launcher.cpp : 279) Read length relative cutoff 1.5 converted to 153 0:28:51.310 4G / 4G INFO General (launcher.cpp : 280) Read length absolute cutoff 130 bp converted to 153 0:28:51.310 4G / 4G INFO General (launcher.cpp : 281) Length cutoff: 153 0:28:51.351 4G / 4G INFO General (launcher.cpp : 467) Finalizing paths - hard 0:28:51.715 5G / 5G INFO General (launcher.cpp : 279) Read length relative cutoff 1.5 converted to 153 0:28:51.715 5G / 5G INFO General (launcher.cpp : 280) Read length absolute cutoff 130 bp converted to 153 0:28:51.715 5G / 5G INFO General (launcher.cpp : 281) Length cutoff: 153 0:28:51.860 4G / 5G INFO General (launcher.cpp : 279) Read length relative cutoff 2 converted to 229 0:28:51.860 4G / 5G INFO General (launcher.cpp : 280) Read length absolute cutoff 180 bp converted to 229 0:28:51.860 4G / 5G INFO General (launcher.cpp : 281) Length cutoff: 229 0:28:51.876 4G / 5G INFO General (launcher.cpp : 279) Read length relative cutoff 2 converted to 229 0:28:51.876 4G / 5G INFO General (launcher.cpp : 280) Read length absolute cutoff 180 bp converted to 229 0:28:51.877 4G / 5G INFO General (launcher.cpp : 281) Length cutoff: 229 0:28:52.559 4G / 5G INFO General (launcher.cpp : 467) Finalizing paths - soft 0:28:52.913 5G / 5G INFO General (launcher.cpp : 279) Read length relative cutoff 1.05 converted to 85 0:28:52.914 5G / 5G INFO General (launcher.cpp : 280) Read length absolute cutoff 85 bp converted to 85 0:28:52.914 5G / 5G INFO General (launcher.cpp : 281) Length cutoff: 85 0:28:53.047 4G / 5G INFO General (launcher.cpp : 279) Read length relative cutoff 1.5 converted to 153 0:28:53.047 4G / 5G INFO General (launcher.cpp : 280) Read length absolute cutoff 130 bp converted to 153 0:28:53.047 4G / 5G INFO General (launcher.cpp : 281) Length cutoff: 153 0:28:53.060 4G / 5G INFO General (launcher.cpp : 279) Read length relative cutoff 1.2 converted to 108 0:28:53.060 4G / 5G INFO General (launcher.cpp : 280) Read length absolute cutoff 100 bp converted to 108 0:28:53.060 4G / 5G INFO General (launcher.cpp : 281) Length cutoff: 108 0:28:54.258 4G / 5G INFO General (launcher.cpp : 529) ExSPAnder repeat resolving tool finished 0:28:55.520 2G / 5G INFO StageManager (stage.cpp : 132) STAGE == Contig Output 0:28:55.520 2G / 5G INFO General (contig_output_stage.cpp : 40) Writing GFA to /oak/stanford/groups/akundaje/marinovg/various/2025-04-09-foraminifera-trans-splicing-check/SPAdes-3.13-RNA-Trimmomatic-Triloculina_sp._1//K73/assembly_graph_with_scaffolds.gfa 0:28:56.357 2G / 5G INFO General (contig_output.hpp : 22) Outputting contigs to /oak/stanford/groups/akundaje/marinovg/various/2025-04-09-foraminifera-trans-splicing-check/SPAdes-3.13-RNA-Trimmomatic-Triloculina_sp._1//K73/before_rr.fasta 0:28:57.306 2G / 5G INFO General (contig_output_stage.cpp : 51) Outputting FastG graph to /oak/stanford/groups/akundaje/marinovg/various/2025-04-09-foraminifera-trans-splicing-check/SPAdes-3.13-RNA-Trimmomatic-Triloculina_sp._1//K73/assembly_graph.fastg 0:28:59.554 2G / 5G INFO General (contig_output_stage.cpp : 20) Outputting FastG paths to /oak/stanford/groups/akundaje/marinovg/various/2025-04-09-foraminifera-trans-splicing-check/SPAdes-3.13-RNA-Trimmomatic-Triloculina_sp._1//K73/transcripts.paths 0:29:00.412 2G / 5G INFO General (launch.hpp : 149) SPAdes finished 0:29:04.973 4M / 5G INFO General (main.cpp : 109) Assembling time: 0 hours 29 minutes 4 seconds ===== Assembling finished. Used k-mer sizes: 49, 73 * Corrected reads are in /oak/stanford/groups/akundaje/marinovg/various/2025-04-09-foraminifera-trans-splicing-check/SPAdes-3.13-RNA-Trimmomatic-Triloculina_sp._1/corrected/ * Assembled transcripts are in /oak/stanford/groups/akundaje/marinovg/various/2025-04-09-foraminifera-trans-splicing-check/SPAdes-3.13-RNA-Trimmomatic-Triloculina_sp._1/transcripts.fasta * Paths in the assembly graph corresponding to the transcripts are in /oak/stanford/groups/akundaje/marinovg/various/2025-04-09-foraminifera-trans-splicing-check/SPAdes-3.13-RNA-Trimmomatic-Triloculina_sp._1/transcripts.paths * Hard filtered transcripts are in /oak/stanford/groups/akundaje/marinovg/various/2025-04-09-foraminifera-trans-splicing-check/SPAdes-3.13-RNA-Trimmomatic-Triloculina_sp._1/hard_filtered_transcripts.fasta * Soft filtered transcripts are in /oak/stanford/groups/akundaje/marinovg/various/2025-04-09-foraminifera-trans-splicing-check/SPAdes-3.13-RNA-Trimmomatic-Triloculina_sp._1/soft_filtered_transcripts.fasta ======= SPAdes pipeline finished. SPAdes log can be found here: /oak/stanford/groups/akundaje/marinovg/various/2025-04-09-foraminifera-trans-splicing-check/SPAdes-3.13-RNA-Trimmomatic-Triloculina_sp._1/spades.log Thank you for using SPAdes!