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/MMETSP/2018-11-19-trans-splicing/Telonema_subtile_mixed_culture_with_Procryptobia-SRX4244210.read1.paired.fastq.gz --pe1-2 /oak/stanford/groups/akundaje/marinovg/various/MMETSP/2018-11-19-trans-splicing/Telonema_subtile_mixed_culture_with_Procryptobia-SRX4244210.read2.paired.fastq.gz --s1 /oak/stanford/groups/akundaje/marinovg/various/MMETSP/2018-11-19-trans-splicing/Telonema_subtile_mixed_culture_with_Procryptobia-SRX4244210.read1.unpaired.fastq.gz --s2 /oak/stanford/groups/akundaje/marinovg/various/MMETSP/2018-11-19-trans-splicing/Telonema_subtile_mixed_culture_with_Procryptobia-SRX4244210.read2.unpaired.fastq.gz -t 20 -o /oak/stanford/groups/akundaje/marinovg/various/MMETSP/2018-11-19-trans-splicing/SPAdes-3.13-RNA-Trimmomatic-Telonema_subtile_mixed_culture_with_Procryptobia-SRX4244210 System information: SPAdes version: 3.13.0 Python version: 2.7.15 OS: Linux-3.10.0-957.10.1.el7.x86_64-x86_64-with-centos-7.6.1810-Core Output dir: /oak/stanford/groups/akundaje/marinovg/various/MMETSP/2018-11-19-trans-splicing/SPAdes-3.13-RNA-Trimmomatic-Telonema_subtile_mixed_culture_with_Procryptobia-SRX4244210 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/MMETSP/2018-11-19-trans-splicing/Telonema_subtile_mixed_culture_with_Procryptobia-SRX4244210.read1.paired.fastq.gz'] right reads: ['/oak/stanford/groups/akundaje/marinovg/various/MMETSP/2018-11-19-trans-splicing/Telonema_subtile_mixed_culture_with_Procryptobia-SRX4244210.read2.paired.fastq.gz'] interlaced reads: not specified single reads: not specified merged reads: not specified Library number: 2, library type: single left reads: not specified right reads: not specified interlaced reads: not specified single reads: ['/oak/stanford/groups/akundaje/marinovg/various/MMETSP/2018-11-19-trans-splicing/Telonema_subtile_mixed_culture_with_Procryptobia-SRX4244210.read1.unpaired.fastq.gz'] merged reads: not specified Library number: 3, library type: single left reads: not specified right reads: not specified interlaced reads: not specified single reads: ['/oak/stanford/groups/akundaje/marinovg/various/MMETSP/2018-11-19-trans-splicing/Telonema_subtile_mixed_culture_with_Procryptobia-SRX4244210.read2.unpaired.fastq.gz'] merged reads: not specified Read error correction parameters: Iterations: 1 PHRED offset will be auto-detected Corrected reads will be compressed Assembly parameters: k: 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/MMETSP/2018-11-19-trans-splicing/SPAdes-3.13-RNA-Trimmomatic-Telonema_subtile_mixed_culture_with_Procryptobia-SRX4244210/tmp Threads: 20 Memory limit (in Gb): 250 ======= SPAdes pipeline started. Log can be found here: /oak/stanford/groups/akundaje/marinovg/various/MMETSP/2018-11-19-trans-splicing/SPAdes-3.13-RNA-Trimmomatic-Telonema_subtile_mixed_culture_with_Procryptobia-SRX4244210/spades.log /oak/stanford/groups/akundaje/marinovg/various/MMETSP/2018-11-19-trans-splicing/Telonema_subtile_mixed_culture_with_Procryptobia-SRX4244210.read2.paired.fastq.gz: max reads length: 251 /oak/stanford/groups/akundaje/marinovg/various/MMETSP/2018-11-19-trans-splicing/Telonema_subtile_mixed_culture_with_Procryptobia-SRX4244210.read1.paired.fastq.gz: max reads length: 251 /oak/stanford/groups/akundaje/marinovg/various/MMETSP/2018-11-19-trans-splicing/Telonema_subtile_mixed_culture_with_Procryptobia-SRX4244210.read1.unpaired.fastq.gz: max reads length: 251 /oak/stanford/groups/akundaje/marinovg/various/MMETSP/2018-11-19-trans-splicing/Telonema_subtile_mixed_culture_with_Procryptobia-SRX4244210.read2.unpaired.fastq.gz: max reads length: 251 Reads length: 251 K values to be used: [55, 123] ===== 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/MMETSP/2018-11-19-trans-splicing/SPAdes-3.13-RNA-Trimmomatic-Telonema_subtile_mixed_culture_with_Procryptobia-SRX4244210/corrected/configs/config.info 0:00:00.018 4M / 4M INFO General (main.cpp : 75) Starting BayesHammer, built from refs/heads/spades_3.13.0, git revision 8ea46659e9b2aca35444a808db550ac333006f8b 0:00:00.119 4M / 4M INFO General (main.cpp : 76) Loading config from /oak/stanford/groups/akundaje/marinovg/various/MMETSP/2018-11-19-trans-splicing/SPAdes-3.13-RNA-Trimmomatic-Telonema_subtile_mixed_culture_with_Procryptobia-SRX4244210/corrected/configs/config.info 0:00:00.189 4M / 4M INFO General (main.cpp : 78) Maximum # of threads to use (adjusted due to OMP capabilities): 16 0:00:00.190 4M / 4M INFO General (memory_limit.cpp : 49) Memory limit set to 250 Gb 0:00:00.190 4M / 4M INFO General (main.cpp : 86) Trying to determine PHRED offset 0:00:00.269 4M / 4M INFO General (main.cpp : 92) Determined value is 33 0:00:00.269 4M / 4M INFO General (hammer_tools.cpp : 36) Hamming graph threshold tau=1, k=21, subkmer positions = [ 0 10 ] 0:00:00.269 4M / 4M INFO General (main.cpp : 113) Size of aux. kmer data 24 bytes === ITERATION 0 begins === 0:00:00.271 4M / 4M INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:00:00.271 4M / 4M INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 256 files using 16 threads. This might take a while. 0:00:00.272 4M / 4M INFO General (file_limit.hpp : 32) Open file limit set to 131072 0:00:00.272 4M / 4M INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 5.20825 Gb 0:00:00.272 4M / 4M INFO General (kmer_splitters.hpp : 97) Using cell size of 262144 0:00:00.339 8G / 8G INFO K-mer Splitting (kmer_data.cpp : 97) Processing /oak/stanford/groups/akundaje/marinovg/various/MMETSP/2018-11-19-trans-splicing/Telonema_subtile_mixed_culture_with_Procryptobia-SRX4244210.read1.paired.fastq.gz 0:00:27.211 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 1922497 reads 0:00:48.323 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 3846168 reads 0:00:50.203 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 4001822 reads 0:00:50.203 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 97) Processing /oak/stanford/groups/akundaje/marinovg/various/MMETSP/2018-11-19-trans-splicing/Telonema_subtile_mixed_culture_with_Procryptobia-SRX4244210.read2.paired.fastq.gz 0:01:12.362 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 6057577 reads 0:01:32.145 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 8003644 reads 0:01:32.147 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 97) Processing /oak/stanford/groups/akundaje/marinovg/various/MMETSP/2018-11-19-trans-splicing/Telonema_subtile_mixed_culture_with_Procryptobia-SRX4244210.read1.unpaired.fastq.gz 0:01:52.073 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 10894772 reads 0:01:52.074 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 97) Processing /oak/stanford/groups/akundaje/marinovg/various/MMETSP/2018-11-19-trans-splicing/Telonema_subtile_mixed_culture_with_Procryptobia-SRX4244210.read2.unpaired.fastq.gz 0:01:52.407 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 10914040 reads 0:01:52.408 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 112) Total 10914040 reads processed 0:01:53.401 64M / 9G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:02:04.130 64M / 9G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 223475990 kmers in total. 0:02:04.131 64M / 9G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:02:37.682 64M / 9G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:02:43.994 132M / 9G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 0:02:55.035 132M / 9G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 103635326 bytes occupied (3.70994 bits per kmer). 0:02:55.039 132M / 9G INFO K-mer Counting (kmer_data.cpp : 356) Arranging kmers in hash map order 0:03:05.654 3G / 9G INFO General (main.cpp : 148) Clustering Hamming graph. 0:07:43.249 3G / 9G INFO General (main.cpp : 155) Extracting clusters 0:09:10.748 3G / 10G INFO General (main.cpp : 167) Clustering done. Total clusters: 135119010 0:09:10.918 1G / 10G INFO K-mer Counting (kmer_data.cpp : 376) Collecting K-mer information, this takes a while. 0:09:13.729 6G / 10G INFO K-mer Counting (kmer_data.cpp : 382) Processing /oak/stanford/groups/akundaje/marinovg/various/MMETSP/2018-11-19-trans-splicing/Telonema_subtile_mixed_culture_with_Procryptobia-SRX4244210.read1.paired.fastq.gz 0:10:54.902 6G / 10G INFO K-mer Counting (kmer_data.cpp : 382) Processing /oak/stanford/groups/akundaje/marinovg/various/MMETSP/2018-11-19-trans-splicing/Telonema_subtile_mixed_culture_with_Procryptobia-SRX4244210.read2.paired.fastq.gz 0:12:24.758 6G / 10G INFO K-mer Counting (kmer_data.cpp : 382) Processing /oak/stanford/groups/akundaje/marinovg/various/MMETSP/2018-11-19-trans-splicing/Telonema_subtile_mixed_culture_with_Procryptobia-SRX4244210.read1.unpaired.fastq.gz 0:13:04.212 6G / 10G INFO K-mer Counting (kmer_data.cpp : 382) Processing /oak/stanford/groups/akundaje/marinovg/various/MMETSP/2018-11-19-trans-splicing/Telonema_subtile_mixed_culture_with_Procryptobia-SRX4244210.read2.unpaired.fastq.gz 0:13:04.357 6G / 10G INFO K-mer Counting (kmer_data.cpp : 389) Collection done, postprocessing. 0:13:05.132 6G / 10G INFO K-mer Counting (kmer_data.cpp : 403) There are 223475990 kmers in total. Among them 119291078 (53.3798%) are singletons. 0:13:05.132 6G / 10G INFO General (main.cpp : 173) Subclustering Hamming graph 0:16:12.614 6G / 10G INFO Hamming Subclustering (kmer_cluster.cpp : 649) Subclustering done. Total 2227 non-read kmers were generated. 0:16:12.614 6G / 10G INFO Hamming Subclustering (kmer_cluster.cpp : 650) Subclustering statistics: 0:16:12.614 6G / 10G INFO Hamming Subclustering (kmer_cluster.cpp : 651) Total singleton hamming clusters: 106338384. Among them 75373368 (70.8807%) are good 0:16:12.614 6G / 10G INFO Hamming Subclustering (kmer_cluster.cpp : 652) Total singleton subclusters: 1197612. Among them 1196431 (99.9014%) are good 0:16:12.614 6G / 10G INFO Hamming Subclustering (kmer_cluster.cpp : 653) Total non-singleton subcluster centers: 30035691. Among them 19523112 (64.9997%) are good 0:16:12.614 6G / 10G INFO Hamming Subclustering (kmer_cluster.cpp : 654) Average size of non-trivial subcluster: 3.90012 kmers 0:16:12.614 6G / 10G INFO Hamming Subclustering (kmer_cluster.cpp : 655) Average number of sub-clusters per non-singleton cluster: 1.08522 0:16:12.614 6G / 10G INFO Hamming Subclustering (kmer_cluster.cpp : 656) Total solid k-mers: 96092911 0:16:12.614 6G / 10G INFO Hamming Subclustering (kmer_cluster.cpp : 657) Substitution probabilities: [4,4]((0.931127,0.0347632,0.0211856,0.0129243),(0.0262585,0.94848,0.00711763,0.0181436),(0.0171603,0.0068549,0.948761,0.0272239),(0.0123943,0.0202987,0.033718,0.933589)) 0:16:12.938 6G / 10G INFO General (main.cpp : 178) Finished clustering. 0:16:12.939 6G / 10G INFO General (main.cpp : 197) Starting solid k-mers expansion in 16 threads. 0:17:33.611 6G / 10G INFO General (main.cpp : 218) Solid k-mers iteration 0 produced 4170607 new k-mers. 0:18:53.236 6G / 10G INFO General (main.cpp : 218) Solid k-mers iteration 1 produced 313939 new k-mers. 0:20:13.301 6G / 10G INFO General (main.cpp : 218) Solid k-mers iteration 2 produced 17146 new k-mers. 0:21:33.423 6G / 10G INFO General (main.cpp : 218) Solid k-mers iteration 3 produced 1593 new k-mers. 0:22:52.691 6G / 10G INFO General (main.cpp : 218) Solid k-mers iteration 4 produced 142 new k-mers. 0:24:12.611 6G / 10G INFO General (main.cpp : 218) Solid k-mers iteration 5 produced 3 new k-mers. 0:24:12.612 6G / 10G INFO General (main.cpp : 222) Solid k-mers finalized 0:24:12.612 6G / 10G INFO General (hammer_tools.cpp : 220) Starting read correction in 16 threads. 0:24:12.612 6G / 10G INFO General (hammer_tools.cpp : 233) Correcting pair of reads: /oak/stanford/groups/akundaje/marinovg/various/MMETSP/2018-11-19-trans-splicing/Telonema_subtile_mixed_culture_with_Procryptobia-SRX4244210.read1.paired.fastq.gz and /oak/stanford/groups/akundaje/marinovg/various/MMETSP/2018-11-19-trans-splicing/Telonema_subtile_mixed_culture_with_Procryptobia-SRX4244210.read2.paired.fastq.gz 0:24:31.473 8G / 10G INFO General (hammer_tools.cpp : 168) Prepared batch 0 of 1600000 reads. 0:25:04.595 9G / 10G INFO General (hammer_tools.cpp : 175) Processed batch 0 0:25:12.710 9G / 10G INFO General (hammer_tools.cpp : 185) Written batch 0 0:25:31.751 9G / 10G INFO General (hammer_tools.cpp : 168) Prepared batch 1 of 1600000 reads. 0:26:06.426 9G / 10G INFO General (hammer_tools.cpp : 175) Processed batch 1 0:26:14.315 9G / 10G INFO General (hammer_tools.cpp : 185) Written batch 1 0:26:24.098 9G / 10G INFO General (hammer_tools.cpp : 168) Prepared batch 2 of 801822 reads. 0:26:42.170 9G / 10G INFO General (hammer_tools.cpp : 175) Processed batch 2 0:26:46.496 9G / 10G INFO General (hammer_tools.cpp : 185) Written batch 2 0:26:49.085 6G / 10G INFO General (hammer_tools.cpp : 264) Correcting single reads: /oak/stanford/groups/akundaje/marinovg/various/MMETSP/2018-11-19-trans-splicing/Telonema_subtile_mixed_culture_with_Procryptobia-SRX4244210.read1.unpaired.fastq.gz 0:26:55.859 7G / 10G INFO General (hammer_tools.cpp : 127) Prepared batch 0 of 1600000 reads. 0:27:04.942 7G / 10G INFO General (hammer_tools.cpp : 132) Processed batch 0 0:27:07.369 7G / 10G INFO General (hammer_tools.cpp : 136) Written batch 0 0:27:11.976 7G / 10G INFO General (hammer_tools.cpp : 127) Prepared batch 1 of 1291128 reads. 0:27:19.651 7G / 10G INFO General (hammer_tools.cpp : 132) Processed batch 1 0:27:21.933 7G / 10G INFO General (hammer_tools.cpp : 136) Written batch 1 0:27:22.933 6G / 10G INFO General (hammer_tools.cpp : 264) Correcting single reads: /oak/stanford/groups/akundaje/marinovg/various/MMETSP/2018-11-19-trans-splicing/Telonema_subtile_mixed_culture_with_Procryptobia-SRX4244210.read2.unpaired.fastq.gz 0:27:23.029 6G / 10G INFO General (hammer_tools.cpp : 127) Prepared batch 0 of 19268 reads. 0:27:23.338 6G / 10G INFO General (hammer_tools.cpp : 132) Processed batch 0 0:27:23.398 6G / 10G INFO General (hammer_tools.cpp : 136) Written batch 0 0:27:23.422 6G / 10G INFO General (hammer_tools.cpp : 274) Correction done. Changed 4222684 bases in 2291349 reads. 0:27:23.422 6G / 10G INFO General (hammer_tools.cpp : 275) Failed to correct 7633 bases out of 2264805754. 0:27:24.478 64M / 10G INFO General (main.cpp : 255) Saving corrected dataset description to /oak/stanford/groups/akundaje/marinovg/various/MMETSP/2018-11-19-trans-splicing/SPAdes-3.13-RNA-Trimmomatic-Telonema_subtile_mixed_culture_with_Procryptobia-SRX4244210/corrected/corrected.yaml 0:27:24.511 64M / 10G INFO General (main.cpp : 262) All done. Exiting. == Compressing corrected reads (with pigz) == Dataset description file was created: /oak/stanford/groups/akundaje/marinovg/various/MMETSP/2018-11-19-trans-splicing/SPAdes-3.13-RNA-Trimmomatic-Telonema_subtile_mixed_culture_with_Procryptobia-SRX4244210/corrected/corrected.yaml ===== Read error correction finished. ===== Assembling started. == Running assembler: K55 0:00:00.000 4M / 4M INFO General (main.cpp : 74) Loaded config from /oak/stanford/groups/akundaje/marinovg/various/MMETSP/2018-11-19-trans-splicing/SPAdes-3.13-RNA-Trimmomatic-Telonema_subtile_mixed_culture_with_Procryptobia-SRX4244210/K55/configs/config.info 0:00:00.031 4M / 4M INFO General (main.cpp : 74) Loaded config from /oak/stanford/groups/akundaje/marinovg/various/MMETSP/2018-11-19-trans-splicing/SPAdes-3.13-RNA-Trimmomatic-Telonema_subtile_mixed_culture_with_Procryptobia-SRX4244210/K55/configs/mda_mode.info 0:00:00.031 4M / 4M INFO General (main.cpp : 74) Loaded config from /oak/stanford/groups/akundaje/marinovg/various/MMETSP/2018-11-19-trans-splicing/SPAdes-3.13-RNA-Trimmomatic-Telonema_subtile_mixed_culture_with_Procryptobia-SRX4244210/K55/configs/rna_mode.info 0:00:00.035 4M / 4M INFO General (memory_limit.cpp : 49) Memory limit set to 250 Gb 0:00:00.035 4M / 4M INFO General (main.cpp : 87) Starting SPAdes, built from refs/heads/spades_3.13.0, git revision 8ea46659e9b2aca35444a808db550ac333006f8b 0:00:00.035 4M / 4M INFO General (main.cpp : 88) Maximum k-mer length: 128 0:00:00.035 4M / 4M INFO General (main.cpp : 89) Assembling dataset (/oak/stanford/groups/akundaje/marinovg/various/MMETSP/2018-11-19-trans-splicing/SPAdes-3.13-RNA-Trimmomatic-Telonema_subtile_mixed_culture_with_Procryptobia-SRX4244210/dataset.info) with K=55 0:00:00.035 4M / 4M INFO General (main.cpp : 90) Maximum # of threads to use (adjusted due to OMP capabilities): 16 0:00:00.035 4M / 4M INFO General (launch.hpp : 51) SPAdes started 0:00:00.035 4M / 4M INFO General (launch.hpp : 58) Starting from stage: construction 0:00:00.035 4M / 4M INFO General (launch.hpp : 65) Two-step RR enabled: 0 0:00:00.080 4M / 4M INFO General (launch.hpp : 76) Will need read mapping, kmer mapper will be attached 0:00:00.080 4M / 4M INFO StageManager (stage.cpp : 132) STAGE == de Bruijn graph construction 0:00:00.082 4M / 4M INFO General (read_converter.hpp : 77) Converting reads to binary format for library #0 (takes a while) 0:00:00.082 4M / 4M INFO General (read_converter.hpp : 78) Converting paired reads 0:00:00.564 88M / 88M INFO General (binary_converter.hpp : 93) 16384 reads processed 0:00:00.919 108M / 108M INFO General (binary_converter.hpp : 93) 32768 reads processed 0:00:01.438 152M / 152M INFO General (binary_converter.hpp : 93) 65536 reads processed 0:00:02.471 240M / 240M INFO General (binary_converter.hpp : 93) 131072 reads processed 0:00:04.539 416M / 416M INFO General (binary_converter.hpp : 93) 262144 reads processed 0:00:08.678 764M / 764M INFO General (binary_converter.hpp : 93) 524288 reads processed 0:00:21.641 1G / 1G INFO General (binary_converter.hpp : 93) 1048576 reads processed 0:00:42.737 1G / 1G INFO General (binary_converter.hpp : 93) 2097152 reads processed 0:01:22.236 484M / 1G INFO General (binary_converter.hpp : 117) 3959819 reads written 0:01:22.556 8M / 1G INFO General (read_converter.hpp : 87) Converting single reads 0:01:22.759 140M / 1G INFO General (binary_converter.hpp : 93) 16384 reads processed 0:01:22.848 148M / 1G INFO General (binary_converter.hpp : 93) 32768 reads processed 0:01:23.884 152M / 1G INFO General (binary_converter.hpp : 117) 41437 reads written 0:01:23.937 4M / 1G INFO General (read_converter.hpp : 95) Converting merged reads 0:01:24.138 132M / 1G INFO General (binary_converter.hpp : 117) 0 reads written 0:01:24.566 4M / 1G INFO General (read_converter.hpp : 77) Converting reads to binary format for library #1 (takes a while) 0:01:24.566 4M / 1G INFO General (read_converter.hpp : 78) Converting paired reads 0:01:24.754 68M / 1G INFO General (binary_converter.hpp : 117) 0 reads written 0:01:24.766 4M / 1G INFO General (read_converter.hpp : 87) Converting single reads 0:01:25.027 140M / 1G INFO General (binary_converter.hpp : 93) 16384 reads processed 0:01:25.138 144M / 1G INFO General (binary_converter.hpp : 93) 32768 reads processed 0:01:25.367 160M / 1G INFO General (binary_converter.hpp : 93) 65536 reads processed 0:01:25.787 188M / 1G INFO General (binary_converter.hpp : 93) 131072 reads processed 0:01:26.430 244M / 1G INFO General (binary_converter.hpp : 93) 262144 reads processed 0:01:27.734 356M / 1G INFO General (binary_converter.hpp : 93) 524288 reads processed 0:01:30.349 588M / 1G INFO General (binary_converter.hpp : 93) 1048576 reads processed 0:01:35.542 1G / 1G INFO General (binary_converter.hpp : 93) 2097152 reads processed 0:01:43.493 1G / 1G INFO General (binary_converter.hpp : 117) 2889643 reads written 0:01:45.113 4M / 1G INFO General (read_converter.hpp : 95) Converting merged reads 0:01:45.348 132M / 1G INFO General (binary_converter.hpp : 117) 0 reads written 0:01:45.400 4M / 1G INFO General (read_converter.hpp : 77) Converting reads to binary format for library #2 (takes a while) 0:01:45.400 4M / 1G INFO General (read_converter.hpp : 78) Converting paired reads 0:01:45.614 68M / 1G INFO General (binary_converter.hpp : 117) 0 reads written 0:01:45.624 4M / 1G INFO General (read_converter.hpp : 87) Converting single reads 0:01:46.117 136M / 1G INFO General (binary_converter.hpp : 117) 6396 reads written 0:01:46.143 4M / 1G INFO General (read_converter.hpp : 95) Converting merged reads 0:01:46.769 132M / 1G INFO General (binary_converter.hpp : 117) 0 reads written 0:01:46.820 4M / 1G INFO General (construction.cpp : 111) Max read length 251 0:01:46.820 4M / 1G INFO General (construction.cpp : 117) Average read length 208.302 0:01:46.820 4M / 1G INFO General (stage.cpp : 101) PROCEDURE == k+1-mer counting 0:01:46.821 4M / 1G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 256 files using 16 threads. This might take a while. 0:01:46.822 8M / 1G INFO General (file_limit.hpp : 32) Open file limit set to 131072 0:01:46.822 8M / 1G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 5.20817 Gb 0:01:46.822 8M / 1G INFO General (kmer_splitters.hpp : 97) Using cell size of 131072 0:02:04.521 8G / 9G INFO General (kmer_splitters.hpp : 289) Processed 5283794 reads 0:02:12.542 8G / 9G INFO General (kmer_splitters.hpp : 289) Processed 10598890 reads 0:02:21.177 8G / 9G INFO General (kmer_splitters.hpp : 289) Processed 16610356 reads 0:02:26.478 8G / 9G INFO General (kmer_splitters.hpp : 289) Processed 21714228 reads 0:02:26.478 8G / 9G INFO General (kmer_splitters.hpp : 295) Adding contigs from previous K 0:02:27.547 64M / 9G INFO General (kmer_splitters.hpp : 308) Used 21714228 reads 0:02:27.547 64M / 9G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:02:33.315 64M / 9G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 79301191 kmers in total. 0:02:33.315 64M / 9G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:03:09.183 64M / 9G INFO General (stage.cpp : 101) PROCEDURE == Extension index construction 0:03:09.183 64M / 9G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:03:09.183 64M / 9G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 256 files using 16 threads. This might take a while. 0:03:09.184 64M / 9G INFO General (file_limit.hpp : 32) Open file limit set to 131072 0:03:09.184 64M / 9G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 5.20703 Gb 0:03:09.184 64M / 9G INFO General (kmer_splitters.hpp : 97) Using cell size of 131072 0:03:33.646 8G / 9G INFO General (kmer_splitters.hpp : 380) Processed 79301191 kmers 0:03:33.646 8G / 9G INFO General (kmer_splitters.hpp : 385) Used 79301191 kmers. 0:03:34.104 64M / 9G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:03:41.210 64M / 9G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 79150630 kmers in total. 0:03:41.210 64M / 9G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:04:15.660 64M / 9G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:04:17.925 68M / 9G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 0:04:22.098 68M / 9G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 36710192 bytes occupied (3.71041 bits per kmer). 0:04:22.188 144M / 9G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 99) Building k-mer extensions from k+1-mers 0:04:27.756 144M / 9G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 103) Building k-mer extensions from k+1-mers finished. 0:04:27.759 144M / 9G INFO General (stage.cpp : 101) PROCEDURE == Condensing graph 0:04:27.772 144M / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 355) Extracting unbranching paths 0:04:35.127 316M / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 374) Extracting unbranching paths finished. 2331706 sequences extracted 0:04:38.436 316M / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 310) Collecting perfect loops 0:04:39.882 316M / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 343) Collecting perfect loops finished. 9 loops collected 0:04:41.049 896M / 9G INFO General (stage.cpp : 101) PROCEDURE == Filling coverage indices (PHM) 0:04:41.049 896M / 9G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:04:41.049 896M / 9G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:04:42.640 912M / 9G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 36780000 bytes occupied (3.71041 bits per kmer). 0:04:42.866 1G / 9G INFO General (construction.cpp : 388) Collecting k-mer coverage information from reads, this takes a while. 0:05:26.434 1G / 9G INFO General (construction.cpp : 508) Filling coverage and flanking coverage from PHM 0:05:31.272 1G / 9G INFO General (construction.cpp : 464) Processed 4663329 edges 0:05:31.873 772M / 9G INFO StageManager (stage.cpp : 132) STAGE == EC Threshold Finding 0:05:35.637 772M / 9G INFO ThresholdFinder (ec_threshold_finder.hpp : 114) Bucket size: 11 0:05:35.637 772M / 9G INFO General (genomic_info_filler.cpp : 98) Average edge coverage: 21.0201 0:05:35.637 772M / 9G INFO General (genomic_info_filler.cpp : 99) Graph threshold: 256 0:05:35.666 768M / 9G INFO General (genomic_info_filler.cpp : 127) EC coverage threshold value was calculated as 21.0201 0:05:35.666 768M / 9G INFO General (genomic_info_filler.cpp : 128) Trusted kmer low bound: 0 0:05:35.666 768M / 9G INFO StageManager (stage.cpp : 132) STAGE == Gap Closer 0:05:35.666 768M / 9G INFO General (graph_pack.hpp : 101) Index refill 0:05:35.667 768M / 9G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:05:35.667 768M / 9G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 256 files using 16 threads. This might take a while. 0:05:35.667 772M / 9G INFO General (file_limit.hpp : 32) Open file limit set to 131072 0:05:35.667 772M / 9G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 5.19263 Gb 0:05:35.667 772M / 9G INFO General (kmer_splitters.hpp : 97) Using cell size of 131072 0:05:50.666 9G / 9G INFO General (edge_index_builders.hpp : 77) Processed 4663329 edges 0:05:50.666 9G / 9G INFO General (edge_index_builders.hpp : 82) Used 4663329 sequences. 0:05:50.951 772M / 9G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:06:00.018 772M / 9G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 79301191 kmers in total. 0:06:00.018 772M / 9G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:06:33.547 772M / 9G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:06:35.388 820M / 9G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 0:06:39.680 820M / 9G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 36780000 bytes occupied (3.71041 bits per kmer). 0:06:40.846 2G / 9G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while. 0:06:44.466 2G / 9G INFO General (edge_index.hpp : 92) Index refilled 0:06:44.470 2G / 9G INFO General (gap_closer.cpp : 159) Preparing shift maps 0:06:48.623 2G / 9G INFO General (gap_closer.cpp : 119) Processing paired reads (takes a while) 0:07:15.948 2G / 9G INFO General (gap_closer.cpp : 138) Used 3959819 paired reads 0:07:15.948 2G / 9G INFO General (gap_closer.cpp : 140) Merging paired indices 0:07:16.917 2G / 9G INFO GapCloser (gap_closer.cpp : 346) Closing short gaps 0:07:23.415 2G / 9G INFO GapCloser (gap_closer.cpp : 380) Closing short gaps complete: filled 1373 gaps after checking 45966 candidates 0:07:24.554 2G / 9G INFO StageManager (stage.cpp : 132) STAGE == Raw Simplification 0:07:24.778 776M / 9G INFO General (simplification.cpp : 128) PROCEDURE == InitialCleaning 0:07:24.779 776M / 9G INFO General (graph_simplification.hpp : 662) Flanking coverage based disconnection disabled 0:07:24.779 776M / 9G INFO Simplification (parallel_processing.hpp : 165) Running Self conjugate edge remover 0:07:24.974 776M / 9G INFO Simplification (parallel_processing.hpp : 167) Self conjugate edge remover triggered 0 times 0:07:24.974 776M / 9G INFO Simplification (parallel_processing.hpp : 165) Running Remover of short poly-AT edges 0:07:24.974 776M / 9G INFO General (simplification.cpp : 76) Removing short polyAT 0:07:27.713 772M / 9G INFO Simplification (parallel_processing.hpp : 167) Remover of short poly-AT edges triggered 1371 times 0:07:27.713 772M / 9G INFO Simplification (parallel_processing.hpp : 165) Running Short PolyA/T Edges 0:07:27.921 772M / 9G INFO Simplification (parallel_processing.hpp : 167) Short PolyA/T Edges triggered 0 times 0:07:27.921 772M / 9G INFO Simplification (parallel_processing.hpp : 165) Running AT Tips 0:07:29.473 780M / 9G INFO Simplification (parallel_processing.hpp : 167) AT Tips triggered 109121 times 0:07:29.473 780M / 9G INFO General (graph_simplification.hpp : 701) Removing loops and rc loops with erroneous connections 0:07:35.090 784M / 9G INFO ECLoopRemover (erroneous_connection_remov: 440) Loops: accurately removed/deadend removed/other: 0/95/13 0:07:35.090 784M / 9G INFO ECLoopRemover (erroneous_connection_remov: 441) RC loops: accurately removed/deadend removed/other: 1/20/161 0:07:35.115 780M / 9G INFO StageManager (stage.cpp : 132) STAGE == Simplification 0:07:35.115 780M / 9G INFO General (simplification.cpp : 357) Graph simplification started 0:07:35.116 780M / 9G INFO General (graph_simplification.hpp : 634) Creating parallel br instance 0:07:35.116 780M / 9G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 1 0:07:35.116 780M / 9G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:07:42.529 800M / 9G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 523522 times 0:07:42.529 800M / 9G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:07:43.485 800M / 9G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 72196 times 0:07:43.485 800M / 9G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:08:17.680 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 76408 times 0:08:17.680 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:08:17.772 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 149 times 0:08:17.772 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:08:17.849 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 246 times 0:08:17.849 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:08:17.865 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 18 times 0:08:17.865 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:08:17.866 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 1 times 0:08:17.866 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:08:17.866 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times 0:08:17.866 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:08:17.866 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:08:17.866 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:08:17.866 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:08:17.866 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:08:17.866 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times 0:08:17.866 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:08:17.866 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:08:17.866 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:08:25.443 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 174997 times 0:08:25.443 1G / 9G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 2 0:08:25.443 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:08:25.660 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 5302 times 0:08:25.660 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:08:25.777 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 1758 times 0:08:25.777 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:08:48.301 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 25246 times 0:08:48.301 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:08:48.309 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 2 times 0:08:48.309 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:08:48.316 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times 0:08:48.316 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:08:48.317 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 1 times 0:08:48.317 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:08:48.317 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:08:48.317 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:08:48.317 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times 0:08:48.317 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:08:48.317 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:08:48.317 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:08:48.666 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 8758 times 0:08:48.666 1G / 9G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 3 0:08:48.666 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:08:48.738 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 787 times 0:08:48.738 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:08:48.793 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 15 times 0:08:48.794 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:08:50.639 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 2413 times 0:08:50.639 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:08:50.642 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:08:50.642 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:08:50.644 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times 0:08:50.644 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:08:50.644 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:08:50.644 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:08:50.818 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 3991 times 0:08:50.818 1G / 9G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 4 0:08:50.818 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:08:50.875 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 239 times 0:08:50.875 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:08:50.926 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 4 times 0:08:50.926 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:08:51.695 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 898 times 0:08:51.695 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:08:51.696 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:08:51.696 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:08:51.698 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times 0:08:51.698 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:08:51.698 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:08:51.698 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:08:51.818 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 2418 times 0:08:51.818 1G / 9G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 5 0:08:51.818 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:08:51.870 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 102 times 0:08:51.870 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:08:51.920 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 1 times 0:08:51.920 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:08:52.279 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 350 times 0:08:52.279 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:08:52.280 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:08:52.280 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:08:52.281 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times 0:08:52.281 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:08:52.281 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:08:52.281 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:08:52.376 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 1692 times 0:08:52.376 1G / 9G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 6 0:08:52.376 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:08:52.426 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 51 times 0:08:52.426 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:08:52.474 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 1 times 0:08:52.474 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:08:52.699 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 168 times 0:08:52.699 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:08:52.700 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:08:52.700 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:08:52.700 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times 0:08:52.700 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:08:52.700 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:08:52.700 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:08:52.783 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 1209 times 0:08:52.783 1G / 9G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 7 0:08:52.783 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:08:52.846 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 29 times 0:08:52.847 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:08:52.896 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times 0:08:52.896 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:08:53.093 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 113 times 0:08:53.093 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:08:53.094 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:08:53.094 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:08:53.094 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times 0:08:53.094 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:08:53.094 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:08:53.094 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:08:53.167 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 893 times 0:08:53.167 1G / 9G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 8 0:08:53.167 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:08:53.221 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 31 times 0:08:53.222 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:08:53.268 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times 0:08:53.269 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:08:53.431 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 63 times 0:08:53.431 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:08:53.431 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:08:53.431 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:08:53.431 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times 0:08:53.431 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:08:53.431 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:08:53.431 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:08:53.501 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 725 times 0:08:53.501 1G / 9G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 9 0:08:53.501 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:08:53.560 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 17 times 0:08:53.561 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:08:53.610 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times 0:08:53.610 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:08:53.779 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 45 times 0:08:53.780 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:08:53.780 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:08:53.780 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:08:53.780 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times 0:08:53.780 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:08:53.780 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:08:53.780 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:08:53.847 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 616 times 0:08:53.847 1G / 9G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 10 0:08:53.847 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:08:53.899 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 9 times 0:08:53.900 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:08:53.952 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times 0:08:53.952 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:08:54.084 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 26 times 0:08:54.084 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:08:54.084 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:08:54.084 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:08:54.084 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times 0:08:54.084 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:08:54.084 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:08:54.084 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:08:54.139 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 468 times 0:08:54.139 1G / 9G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 11 0:08:54.139 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:08:54.185 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 15 times 0:08:54.186 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:08:54.230 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times 0:08:54.231 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:08:54.367 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 35 times 0:08:54.367 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:08:54.367 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:08:54.367 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:08:54.367 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times 0:08:54.367 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:08:54.367 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:08:54.367 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:08:54.415 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:08:54.416 1G / 9G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 12 0:08:54.416 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:08:54.416 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:08:54.416 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:08:54.416 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times 0:08:54.416 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:08:54.416 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:08:54.416 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:08:54.416 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:08:54.416 1G / 9G INFO StageManager (stage.cpp : 132) STAGE == Gap Closer 0:08:54.416 1G / 9G INFO General (graph_pack.hpp : 101) Index refill 0:08:54.417 1G / 9G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:08:54.417 1G / 9G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 256 files using 16 threads. This might take a while. 0:08:54.418 1G / 9G INFO General (file_limit.hpp : 32) Open file limit set to 131072 0:08:54.418 1G / 9G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 5.18164 Gb 0:08:54.418 1G / 9G INFO General (kmer_splitters.hpp : 97) Using cell size of 131072 0:09:07.074 10G / 10G INFO General (edge_index_builders.hpp : 77) Processed 434700 edges 0:09:07.075 10G / 10G INFO General (edge_index_builders.hpp : 82) Used 434700 sequences. 0:09:07.294 1G / 10G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:09:15.493 1G / 10G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 53503716 kmers in total. 0:09:15.494 1G / 10G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:09:48.339 1G / 10G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:09:49.361 1G / 10G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 0:09:52.495 1G / 10G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 24817960 bytes occupied (3.71084 bits per kmer). 0:09:53.684 2G / 10G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while. 0:09:55.388 2G / 10G INFO General (edge_index.hpp : 92) Index refilled 0:09:55.392 2G / 10G INFO General (gap_closer.cpp : 159) Preparing shift maps 0:09:56.279 2G / 10G INFO General (gap_closer.cpp : 119) Processing paired reads (takes a while) 0:10:16.729 2G / 10G INFO General (gap_closer.cpp : 138) Used 3959819 paired reads 0:10:16.729 2G / 10G INFO General (gap_closer.cpp : 140) Merging paired indices 0:10:17.375 2G / 10G INFO GapCloser (gap_closer.cpp : 346) Closing short gaps 0:10:18.117 2G / 10G INFO GapCloser (gap_closer.cpp : 380) Closing short gaps complete: filled 447 gaps after checking 19337 candidates 0:10:19.053 2G / 10G INFO StageManager (stage.cpp : 132) STAGE == Simplification Cleanup 0:10:19.053 2G / 10G INFO General (simplification.cpp : 196) PROCEDURE == Post simplification 0:10:19.053 2G / 10G INFO General (graph_simplification.hpp : 453) Disconnection of relatively low covered edges disabled 0:10:19.053 2G / 10G INFO General (graph_simplification.hpp : 489) Complex tip clipping disabled 0:10:19.053 2G / 10G INFO General (graph_simplification.hpp : 634) Creating parallel br instance 0:10:19.053 2G / 10G INFO General (graph_simplification.hpp : 634) Creating parallel br instance 0:10:19.053 2G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover 0:10:19.212 2G / 10G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 319 times 0:10:19.212 2G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover 0:10:21.551 2G / 10G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 9118 times 0:10:21.551 2G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Complex bulge remover 0:10:23.484 2G / 10G INFO Simplification (parallel_processing.hpp : 167) Complex bulge remover triggered 274 times 0:10:23.484 2G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:10:23.545 2G / 10G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 27 times 0:10:23.545 2G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Final tip clipper 0:10:29.868 2G / 10G INFO Simplification (parallel_processing.hpp : 167) Final tip clipper triggered 10241 times 0:10:29.868 2G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:10:30.130 2G / 10G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 221 times 0:10:30.131 2G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Final bulge remover 0:10:30.205 2G / 10G INFO Simplification (parallel_processing.hpp : 167) Final bulge remover triggered 0 times 0:10:30.205 2G / 10G INFO Simplification (parallel_processing.hpp : 165) Running AT Tips 0:10:30.251 2G / 10G INFO Simplification (parallel_processing.hpp : 167) AT Tips triggered 45 times 0:10:30.252 2G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover 0:10:30.305 2G / 10G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 15 times 0:10:30.305 2G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover 0:10:30.353 2G / 10G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 7 times 0:10:30.353 2G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Complex bulge remover 0:10:31.450 2G / 10G INFO Simplification (parallel_processing.hpp : 167) Complex bulge remover triggered 11 times 0:10:31.450 2G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:10:31.493 2G / 10G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:10:31.493 2G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Final tip clipper 0:10:31.538 2G / 10G INFO Simplification (parallel_processing.hpp : 167) Final tip clipper triggered 7 times 0:10:31.538 2G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:10:31.626 2G / 10G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 6 times 0:10:31.626 2G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Final bulge remover 0:10:31.712 2G / 10G INFO Simplification (parallel_processing.hpp : 167) Final bulge remover triggered 0 times 0:10:31.712 2G / 10G INFO Simplification (parallel_processing.hpp : 165) Running AT Tips 0:10:31.762 2G / 10G INFO Simplification (parallel_processing.hpp : 167) AT Tips triggered 0 times 0:10:31.762 2G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover 0:10:31.762 2G / 10G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 0 times 0:10:31.763 2G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover 0:10:31.821 2G / 10G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 0 times 0:10:31.821 2G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Complex bulge remover 0:10:32.935 2G / 10G INFO Simplification (parallel_processing.hpp : 167) Complex bulge remover triggered 1 times 0:10:32.935 2G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:10:32.935 2G / 10G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:10:32.935 2G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Final tip clipper 0:10:32.935 2G / 10G INFO Simplification (parallel_processing.hpp : 167) Final tip clipper triggered 0 times 0:10:32.935 2G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:10:32.935 2G / 10G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:10:32.935 2G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Final bulge remover 0:10:32.935 2G / 10G INFO Simplification (parallel_processing.hpp : 167) Final bulge remover triggered 0 times 0:10:32.935 2G / 10G INFO Simplification (parallel_processing.hpp : 165) Running AT Tips 0:10:32.935 2G / 10G INFO Simplification (parallel_processing.hpp : 167) AT Tips triggered 0 times 0:10:32.935 2G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover 0:10:32.935 2G / 10G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 0 times 0:10:32.935 2G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover 0:10:32.974 2G / 10G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 0 times 0:10:32.974 2G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Complex bulge remover 0:10:34.022 2G / 10G INFO Simplification (parallel_processing.hpp : 167) Complex bulge remover triggered 0 times 0:10:34.023 2G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:10:34.023 2G / 10G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:10:34.023 2G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Final tip clipper 0:10:34.023 2G / 10G INFO Simplification (parallel_processing.hpp : 167) Final tip clipper triggered 0 times 0:10:34.023 2G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:10:34.024 2G / 10G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:10:34.024 2G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Final bulge remover 0:10:34.024 2G / 10G INFO Simplification (parallel_processing.hpp : 167) Final bulge remover triggered 0 times 0:10:34.024 2G / 10G INFO Simplification (parallel_processing.hpp : 165) Running AT Tips 0:10:34.024 2G / 10G INFO Simplification (parallel_processing.hpp : 167) AT Tips triggered 0 times 0:10:34.024 2G / 10G INFO General (simplification.cpp : 330) Disrupting self-conjugate edges 0:10:34.286 2G / 10G INFO General (simplification.cpp : 470) Counting average coverage 0:10:34.428 2G / 10G INFO General (simplification.cpp : 476) Average coverage = 30.6285 0:10:34.428 2G / 10G INFO StageManager (stage.cpp : 132) STAGE == Contig Output 0:10:34.428 2G / 10G INFO General (contig_output_stage.cpp : 40) Writing GFA to /oak/stanford/groups/akundaje/marinovg/various/MMETSP/2018-11-19-trans-splicing/SPAdes-3.13-RNA-Trimmomatic-Telonema_subtile_mixed_culture_with_Procryptobia-SRX4244210//K55/assembly_graph_with_scaffolds.gfa 0:10:35.588 2G / 10G INFO General (contig_output.hpp : 22) Outputting contigs to /oak/stanford/groups/akundaje/marinovg/various/MMETSP/2018-11-19-trans-splicing/SPAdes-3.13-RNA-Trimmomatic-Telonema_subtile_mixed_culture_with_Procryptobia-SRX4244210//K55/before_rr.fasta 0:10:36.836 2G / 10G INFO General (contig_output_stage.cpp : 51) Outputting FastG graph to /oak/stanford/groups/akundaje/marinovg/various/MMETSP/2018-11-19-trans-splicing/SPAdes-3.13-RNA-Trimmomatic-Telonema_subtile_mixed_culture_with_Procryptobia-SRX4244210//K55/assembly_graph.fastg 0:10:40.067 2G / 10G INFO General (contig_output.hpp : 22) Outputting contigs to /oak/stanford/groups/akundaje/marinovg/various/MMETSP/2018-11-19-trans-splicing/SPAdes-3.13-RNA-Trimmomatic-Telonema_subtile_mixed_culture_with_Procryptobia-SRX4244210//K55/simplified_contigs.fasta 0:10:41.379 2G / 10G INFO General (contig_output.hpp : 22) Outputting contigs to /oak/stanford/groups/akundaje/marinovg/various/MMETSP/2018-11-19-trans-splicing/SPAdes-3.13-RNA-Trimmomatic-Telonema_subtile_mixed_culture_with_Procryptobia-SRX4244210//K55/final_contigs.fasta 0:10:42.615 2G / 10G INFO StageManager (stage.cpp : 132) STAGE == Contig Output 0:10:42.615 2G / 10G INFO General (contig_output_stage.cpp : 40) Writing GFA to /oak/stanford/groups/akundaje/marinovg/various/MMETSP/2018-11-19-trans-splicing/SPAdes-3.13-RNA-Trimmomatic-Telonema_subtile_mixed_culture_with_Procryptobia-SRX4244210//K55/assembly_graph_with_scaffolds.gfa 0:10:43.754 2G / 10G INFO General (contig_output.hpp : 22) Outputting contigs to /oak/stanford/groups/akundaje/marinovg/various/MMETSP/2018-11-19-trans-splicing/SPAdes-3.13-RNA-Trimmomatic-Telonema_subtile_mixed_culture_with_Procryptobia-SRX4244210//K55/before_rr.fasta 0:10:45.033 2G / 10G INFO General (contig_output_stage.cpp : 51) Outputting FastG graph to /oak/stanford/groups/akundaje/marinovg/various/MMETSP/2018-11-19-trans-splicing/SPAdes-3.13-RNA-Trimmomatic-Telonema_subtile_mixed_culture_with_Procryptobia-SRX4244210//K55/assembly_graph.fastg 0:10:48.642 2G / 10G INFO General (contig_output.hpp : 22) Outputting contigs to /oak/stanford/groups/akundaje/marinovg/various/MMETSP/2018-11-19-trans-splicing/SPAdes-3.13-RNA-Trimmomatic-Telonema_subtile_mixed_culture_with_Procryptobia-SRX4244210//K55/simplified_contigs.fasta 0:10:49.920 2G / 10G INFO General (contig_output.hpp : 22) Outputting contigs to /oak/stanford/groups/akundaje/marinovg/various/MMETSP/2018-11-19-trans-splicing/SPAdes-3.13-RNA-Trimmomatic-Telonema_subtile_mixed_culture_with_Procryptobia-SRX4244210//K55/final_contigs.fasta 0:10:51.210 2G / 10G INFO General (launch.hpp : 149) SPAdes finished 0:10:57.382 64M / 10G INFO General (main.cpp : 109) Assembling time: 0 hours 10 minutes 57 seconds Max read length detected as 251 == Running assembler: K123 0:00:00.000 4M / 4M INFO General (main.cpp : 74) Loaded config from /oak/stanford/groups/akundaje/marinovg/various/MMETSP/2018-11-19-trans-splicing/SPAdes-3.13-RNA-Trimmomatic-Telonema_subtile_mixed_culture_with_Procryptobia-SRX4244210/K123/configs/config.info 0:00:00.000 4M / 4M INFO General (main.cpp : 74) Loaded config from /oak/stanford/groups/akundaje/marinovg/various/MMETSP/2018-11-19-trans-splicing/SPAdes-3.13-RNA-Trimmomatic-Telonema_subtile_mixed_culture_with_Procryptobia-SRX4244210/K123/configs/mda_mode.info 0:00:00.000 4M / 4M INFO General (main.cpp : 74) Loaded config from /oak/stanford/groups/akundaje/marinovg/various/MMETSP/2018-11-19-trans-splicing/SPAdes-3.13-RNA-Trimmomatic-Telonema_subtile_mixed_culture_with_Procryptobia-SRX4244210/K123/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/MMETSP/2018-11-19-trans-splicing/SPAdes-3.13-RNA-Trimmomatic-Telonema_subtile_mixed_culture_with_Procryptobia-SRX4244210/dataset.info) with K=123 0:00:00.000 4M / 4M INFO General (main.cpp : 90) Maximum # of threads to use (adjusted due to OMP capabilities): 16 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 0:00:00.001 4M / 4M INFO General (read_converter.hpp : 59) Binary reads detected 0:00:00.013 4M / 4M INFO General (read_converter.hpp : 59) Binary reads detected 0:00:00.036 4M / 4M INFO General (read_converter.hpp : 59) Binary reads detected 0:00:00.048 4M / 4M INFO General (construction.cpp : 111) Max read length 251 0:00:00.048 4M / 4M INFO General (construction.cpp : 117) Average read length 208.302 0:00:00.048 4M / 4M INFO General (stage.cpp : 101) PROCEDURE == k+1-mer counting 0:00:00.049 4M / 4M INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 256 files using 16 threads. This might take a while. 0:00:00.049 4M / 4M INFO General (file_limit.hpp : 32) Open file limit set to 131072 0:00:00.049 4M / 4M INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 5.20825 Gb 0:00:00.049 4M / 4M INFO General (kmer_splitters.hpp : 97) Using cell size of 65536 0:00:15.290 8G / 9G INFO General (kmer_splitters.hpp : 289) Processed 4176413 reads 0:00:21.232 8G / 9G INFO General (kmer_splitters.hpp : 289) Processed 8357910 reads 0:00:26.766 8G / 9G INFO General (kmer_splitters.hpp : 289) Processed 12819795 reads 0:00:32.198 8G / 9G INFO General (kmer_splitters.hpp : 289) Processed 20397229 reads 0:00:33.276 8G / 9G INFO General (kmer_splitters.hpp : 289) Processed 21714228 reads 0:00:33.276 8G / 9G INFO General (kmer_splitters.hpp : 295) Adding contigs from previous K 0:00:49.945 64M / 9G INFO General (kmer_splitters.hpp : 308) Used 21714228 reads 0:00:49.945 64M / 9G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:01:00.934 64M / 9G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 80344095 kmers in total. 0:01:00.934 64M / 9G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:01:33.424 64M / 9G INFO General (stage.cpp : 101) PROCEDURE == Extension index construction 0:01:33.425 64M / 9G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:01:33.425 64M / 9G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 256 files using 16 threads. This might take a while. 0:01:33.425 64M / 9G INFO General (file_limit.hpp : 32) Open file limit set to 131072 0:01:33.425 64M / 9G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 5.20703 Gb 0:01:33.425 64M / 9G INFO General (kmer_splitters.hpp : 97) Using cell size of 65536 0:01:42.998 8G / 9G INFO General (kmer_splitters.hpp : 380) Processed 4198806 kmers 0:01:44.293 8G / 9G INFO General (kmer_splitters.hpp : 380) Processed 9183210 kmers 0:01:45.484 8G / 9G INFO General (kmer_splitters.hpp : 380) Processed 14215915 kmers 0:01:46.919 8G / 9G INFO General (kmer_splitters.hpp : 380) Processed 19236056 kmers 0:01:48.149 8G / 9G INFO General (kmer_splitters.hpp : 380) Processed 24257121 kmers 0:01:49.340 8G / 9G INFO General (kmer_splitters.hpp : 380) Processed 29280782 kmers 0:01:50.630 8G / 9G INFO General (kmer_splitters.hpp : 380) Processed 34296333 kmers 0:01:51.949 8G / 9G INFO General (kmer_splitters.hpp : 380) Processed 39325768 kmers 0:01:53.245 8G / 9G INFO General (kmer_splitters.hpp : 380) Processed 44343209 kmers 0:01:54.407 8G / 9G INFO General (kmer_splitters.hpp : 380) Processed 49355824 kmers 0:01:55.619 8G / 9G INFO General (kmer_splitters.hpp : 380) Processed 54378769 kmers 0:01:57.049 8G / 9G INFO General (kmer_splitters.hpp : 380) Processed 59401556 kmers 0:01:58.346 8G / 9G INFO General (kmer_splitters.hpp : 380) Processed 64421747 kmers 0:01:59.658 8G / 9G INFO General (kmer_splitters.hpp : 380) Processed 69449241 kmers 0:02:00.889 8G / 9G INFO General (kmer_splitters.hpp : 380) Processed 74477049 kmers 0:02:02.081 8G / 9G INFO General (kmer_splitters.hpp : 380) Processed 79493255 kmers 0:02:02.464 8G / 9G INFO General (kmer_splitters.hpp : 380) Processed 80344351 kmers 0:02:02.464 8G / 9G INFO General (kmer_splitters.hpp : 385) Used 80344351 kmers. 0:02:02.669 64M / 9G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:02:11.857 64M / 9G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 80436831 kmers in total. 0:02:11.857 64M / 9G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:02:42.950 64M / 9G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:02:46.115 72M / 9G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 0:02:52.962 72M / 9G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 37314814 bytes occupied (3.71122 bits per kmer). 0:02:53.039 152M / 9G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 99) Building k-mer extensions from k+1-mers 0:02:58.918 152M / 9G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 103) Building k-mer extensions from k+1-mers finished. 0:02:58.920 152M / 9G INFO General (stage.cpp : 101) PROCEDURE == Condensing graph 0:02:58.934 152M / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 355) Extracting unbranching paths 0:03:06.544 336M / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 374) Extracting unbranching paths finished. 1933350 sequences extracted 0:03:10.129 336M / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 310) Collecting perfect loops 0:03:11.676 336M / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 343) Collecting perfect loops finished. 15 loops collected 0:03:12.839 832M / 9G INFO General (stage.cpp : 101) PROCEDURE == Filling coverage indices (PHM) 0:03:12.839 832M / 9G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:03:12.839 832M / 9G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:03:14.828 860M / 9G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 37263688 bytes occupied (3.71041 bits per kmer). 0:03:15.059 1G / 9G INFO General (construction.cpp : 388) Collecting k-mer coverage information from reads, this takes a while. 0:03:41.666 1G / 9G INFO General (construction.cpp : 508) Filling coverage and flanking coverage from PHM 0:03:46.738 1G / 9G INFO General (construction.cpp : 464) Processed 3866714 edges 0:03:47.627 696M / 9G INFO StageManager (stage.cpp : 132) STAGE == EC Threshold Finding 0:03:50.433 696M / 9G INFO ThresholdFinder (ec_threshold_finder.hpp : 114) Bucket size: 8 0:03:50.433 696M / 9G INFO General (genomic_info_filler.cpp : 98) Average edge coverage: 12.2715 0:03:50.433 696M / 9G INFO General (genomic_info_filler.cpp : 99) Graph threshold: 104 0:03:50.447 696M / 9G INFO General (genomic_info_filler.cpp : 127) EC coverage threshold value was calculated as 12.2715 0:03:50.447 696M / 9G INFO General (genomic_info_filler.cpp : 128) Trusted kmer low bound: 0 0:03:50.447 696M / 9G INFO StageManager (stage.cpp : 132) STAGE == Gap Closer 0:03:50.447 696M / 9G INFO General (graph_pack.hpp : 101) Index refill 0:03:50.448 696M / 9G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:03:50.448 696M / 9G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 256 files using 16 threads. This might take a while. 0:03:50.449 696M / 9G INFO General (file_limit.hpp : 32) Open file limit set to 131072 0:03:50.449 696M / 9G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 5.19417 Gb 0:03:50.449 696M / 9G INFO General (kmer_splitters.hpp : 97) Using cell size of 65536 0:04:05.995 9G / 9G INFO General (edge_index_builders.hpp : 77) Processed 3866714 edges 0:04:05.995 9G / 9G INFO General (edge_index_builders.hpp : 82) Used 3866714 sequences. 0:04:06.450 696M / 9G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:04:17.190 696M / 9G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 80344095 kmers in total. 0:04:17.191 696M / 9G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:04:53.165 696M / 9G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:04:55.917 752M / 9G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 0:05:06.536 752M / 9G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 37263688 bytes occupied (3.71041 bits per kmer). 0:05:07.708 2G / 9G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while. 0:05:11.027 2G / 9G INFO General (edge_index.hpp : 92) Index refilled 0:05:11.029 2G / 9G INFO General (gap_closer.cpp : 159) Preparing shift maps 0:05:15.011 2G / 9G INFO General (gap_closer.cpp : 119) Processing paired reads (takes a while) 0:05:32.572 2G / 9G INFO General (gap_closer.cpp : 138) Used 3959819 paired reads 0:05:32.572 2G / 9G INFO General (gap_closer.cpp : 140) Merging paired indices 0:05:33.690 2G / 9G INFO GapCloser (gap_closer.cpp : 346) Closing short gaps 0:05:39.733 2G / 9G INFO GapCloser (gap_closer.cpp : 380) Closing short gaps complete: filled 520 gaps after checking 40242 candidates 0:05:40.199 2G / 9G INFO StageManager (stage.cpp : 132) STAGE == Raw Simplification 0:05:40.403 720M / 9G INFO General (simplification.cpp : 128) PROCEDURE == InitialCleaning 0:05:40.403 720M / 9G INFO General (graph_simplification.hpp : 662) Flanking coverage based disconnection disabled 0:05:40.403 720M / 9G INFO Simplification (parallel_processing.hpp : 165) Running Self conjugate edge remover 0:05:40.580 720M / 9G INFO Simplification (parallel_processing.hpp : 167) Self conjugate edge remover triggered 0 times 0:05:40.580 720M / 9G INFO Simplification (parallel_processing.hpp : 165) Running Remover of short poly-AT edges 0:05:40.580 720M / 9G INFO General (simplification.cpp : 76) Removing short polyAT 0:05:42.804 716M / 9G INFO Simplification (parallel_processing.hpp : 167) Remover of short poly-AT edges triggered 145 times 0:05:42.804 716M / 9G INFO Simplification (parallel_processing.hpp : 165) Running Short PolyA/T Edges 0:05:43.009 716M / 9G INFO Simplification (parallel_processing.hpp : 167) Short PolyA/T Edges triggered 0 times 0:05:43.009 716M / 9G INFO Simplification (parallel_processing.hpp : 165) Running AT Tips 0:05:44.704 720M / 9G INFO Simplification (parallel_processing.hpp : 167) AT Tips triggered 97478 times 0:05:44.704 720M / 9G INFO General (graph_simplification.hpp : 701) Removing loops and rc loops with erroneous connections 0:05:49.103 724M / 9G INFO ECLoopRemover (erroneous_connection_remov: 440) Loops: accurately removed/deadend removed/other: 2/61/4 0:05:49.103 724M / 9G INFO ECLoopRemover (erroneous_connection_remov: 441) RC loops: accurately removed/deadend removed/other: 0/2/15 0:05:49.162 720M / 9G INFO StageManager (stage.cpp : 132) STAGE == Simplification 0:05:49.162 720M / 9G INFO General (simplification.cpp : 357) Graph simplification started 0:05:49.162 720M / 9G INFO General (graph_simplification.hpp : 634) Creating parallel br instance 0:05:49.162 720M / 9G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 1 0:05:49.162 720M / 9G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:05:57.975 748M / 9G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 557821 times 0:05:57.975 748M / 9G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:05:59.359 748M / 9G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 90198 times 0:05:59.360 748M / 9G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:06:32.425 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 29202 times 0:06:32.425 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:06:32.483 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 311 times 0:06:32.483 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:06:32.511 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 15 times 0:06:32.511 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:06:32.528 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 3 times 0:06:32.528 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:06:32.528 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:06:32.528 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:06:32.528 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times 0:06:32.528 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:06:32.528 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:06:32.528 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:06:34.396 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 48746 times 0:06:34.396 1G / 9G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 2 0:06:34.396 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:06:34.596 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 5694 times 0:06:34.596 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:06:34.687 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 1109 times 0:06:34.687 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:06:58.505 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 11934 times 0:06:58.505 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:06:58.512 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 3 times 0:06:58.512 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:06:58.518 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times 0:06:58.518 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:06:58.518 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:06:58.518 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:06:58.518 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:06:58.518 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:06:58.518 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times 0:06:58.518 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:06:58.518 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:06:58.518 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:06:58.748 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 5311 times 0:06:58.748 1G / 9G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 3 0:06:58.748 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:06:58.822 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 730 times 0:06:58.822 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:06:58.879 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 10 times 0:06:58.880 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:07:00.111 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 760 times 0:07:00.111 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:07:00.113 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:07:00.113 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:07:00.115 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times 0:07:00.115 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:07:00.115 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:07:00.115 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:07:00.232 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 2148 times 0:07:00.232 1G / 9G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 4 0:07:00.232 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:07:00.294 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 220 times 0:07:00.294 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:07:00.351 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 4 times 0:07:00.352 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:07:00.701 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 146 times 0:07:00.701 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:07:00.702 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:07:00.702 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:07:00.703 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times 0:07:00.703 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:07:00.703 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:07:00.703 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:07:00.787 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 1137 times 0:07:00.787 1G / 9G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 5 0:07:00.787 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:07:00.845 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 113 times 0:07:00.845 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:07:00.903 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 2 times 0:07:00.903 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:07:01.126 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 66 times 0:07:01.126 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:07:01.126 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:07:01.126 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:07:01.127 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times 0:07:01.127 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:07:01.127 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:07:01.127 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:07:01.194 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 646 times 0:07:01.194 1G / 9G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 6 0:07:01.194 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:07:01.254 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 60 times 0:07:01.254 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:07:01.310 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times 0:07:01.310 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:07:01.476 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 41 times 0:07:01.476 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:07:01.476 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:07:01.476 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:07:01.476 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times 0:07:01.476 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:07:01.476 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:07:01.476 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:07:01.538 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 456 times 0:07:01.538 1G / 9G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 7 0:07:01.538 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:07:01.596 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 32 times 0:07:01.596 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:07:01.651 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times 0:07:01.651 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:07:01.867 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 25 times 0:07:01.867 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:07:01.867 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:07:01.867 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:07:01.868 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times 0:07:01.868 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:07:01.868 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:07:01.868 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:07:01.933 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 241 times 0:07:01.933 1G / 9G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 8 0:07:01.933 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:07:01.997 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 18 times 0:07:01.998 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:07:02.057 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times 0:07:02.057 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:07:02.195 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 14 times 0:07:02.195 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:07:02.195 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:07:02.195 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:07:02.195 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times 0:07:02.195 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:07:02.195 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:07:02.195 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:07:02.255 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 181 times 0:07:02.255 1G / 9G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 9 0:07:02.255 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:07:02.320 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 11 times 0:07:02.320 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:07:02.380 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times 0:07:02.380 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:07:02.516 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 7 times 0:07:02.516 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:07:02.516 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:07:02.516 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:07:02.516 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times 0:07:02.516 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:07:02.516 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:07:02.516 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:07:02.575 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 136 times 0:07:02.575 1G / 9G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 10 0:07:02.575 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:07:02.637 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 7 times 0:07:02.637 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:07:02.699 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times 0:07:02.699 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:07:02.827 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 6 times 0:07:02.827 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:07:02.827 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:07:02.827 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:07:02.827 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times 0:07:02.827 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:07:02.827 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:07:02.827 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:07:02.885 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 108 times 0:07:02.885 1G / 9G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 11 0:07:02.885 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:07:02.945 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 17 times 0:07:02.945 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:07:03.002 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times 0:07:03.002 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:07:03.115 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 2 times 0:07:03.115 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:07:03.115 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:07:03.115 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:07:03.115 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times 0:07:03.115 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:07:03.115 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:07:03.115 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:07:03.168 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:07:03.168 1G / 9G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 12 0:07:03.168 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:07:03.169 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:07:03.169 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:07:03.169 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times 0:07:03.169 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:07:03.169 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:07:03.170 1G / 9G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:07:03.170 1G / 9G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:07:03.170 1G / 9G INFO StageManager (stage.cpp : 132) STAGE == Gap Closer 0:07:03.170 1G / 9G INFO General (graph_pack.hpp : 101) Index refill 0:07:03.172 1G / 9G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:07:03.172 1G / 9G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 256 files using 16 threads. This might take a while. 0:07:03.172 1G / 9G INFO General (file_limit.hpp : 32) Open file limit set to 131072 0:07:03.172 1G / 9G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 5.17814 Gb 0:07:03.172 1G / 9G INFO General (kmer_splitters.hpp : 97) Using cell size of 65536 0:07:16.703 10G / 10G INFO General (edge_index_builders.hpp : 77) Processed 524396 edges 0:07:16.703 10G / 10G INFO General (edge_index_builders.hpp : 82) Used 524396 sequences. 0:07:17.040 1G / 10G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:07:25.752 1G / 10G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 51733541 kmers in total. 0:07:25.752 1G / 10G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:08:01.876 1G / 10G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:08:03.447 1G / 10G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 0:08:09.143 1G / 10G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 23996904 bytes occupied (3.71085 bits per kmer). 0:08:10.635 2G / 10G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while. 0:08:12.331 2G / 10G INFO General (edge_index.hpp : 92) Index refilled 0:08:12.334 2G / 10G INFO General (gap_closer.cpp : 159) Preparing shift maps 0:08:12.921 2G / 10G INFO General (gap_closer.cpp : 119) Processing paired reads (takes a while) 0:08:33.085 2G / 10G INFO General (gap_closer.cpp : 138) Used 3959819 paired reads 0:08:33.085 2G / 10G INFO General (gap_closer.cpp : 140) Merging paired indices 0:08:33.792 2G / 10G INFO GapCloser (gap_closer.cpp : 346) Closing short gaps 0:08:35.072 2G / 10G INFO GapCloser (gap_closer.cpp : 380) Closing short gaps complete: filled 121 gaps after checking 21247 candidates 0:08:35.393 2G / 10G INFO StageManager (stage.cpp : 132) STAGE == Simplification Cleanup 0:08:35.393 2G / 10G INFO General (simplification.cpp : 196) PROCEDURE == Post simplification 0:08:35.393 2G / 10G INFO General (graph_simplification.hpp : 453) Disconnection of relatively low covered edges disabled 0:08:35.393 2G / 10G INFO General (graph_simplification.hpp : 489) Complex tip clipping disabled 0:08:35.393 2G / 10G INFO General (graph_simplification.hpp : 634) Creating parallel br instance 0:08:35.393 2G / 10G INFO General (graph_simplification.hpp : 634) Creating parallel br instance 0:08:35.393 2G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover 0:08:35.496 2G / 10G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 49 times 0:08:35.496 2G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover 0:08:38.674 2G / 10G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 18104 times 0:08:38.674 2G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Complex bulge remover 0:08:40.821 2G / 10G INFO Simplification (parallel_processing.hpp : 167) Complex bulge remover triggered 117 times 0:08:40.821 2G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:08:40.887 2G / 10G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 15 times 0:08:40.887 2G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Final tip clipper 0:08:50.926 2G / 10G INFO Simplification (parallel_processing.hpp : 167) Final tip clipper triggered 11411 times 0:08:50.926 2G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:08:51.221 2G / 10G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 118 times 0:08:51.221 2G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Final bulge remover 0:08:51.281 2G / 10G INFO Simplification (parallel_processing.hpp : 167) Final bulge remover triggered 0 times 0:08:51.281 2G / 10G INFO Simplification (parallel_processing.hpp : 165) Running AT Tips 0:08:51.336 2G / 10G INFO Simplification (parallel_processing.hpp : 167) AT Tips triggered 15 times 0:08:51.336 2G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover 0:08:51.401 2G / 10G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 11 times 0:08:51.401 2G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover 0:08:51.448 2G / 10G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 2 times 0:08:51.449 2G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Complex bulge remover 0:08:52.847 2G / 10G INFO Simplification (parallel_processing.hpp : 167) Complex bulge remover triggered 10 times 0:08:52.847 2G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:08:52.894 2G / 10G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:08:52.895 2G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Final tip clipper 0:08:52.943 2G / 10G INFO Simplification (parallel_processing.hpp : 167) Final tip clipper triggered 5 times 0:08:52.943 2G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:08:53.011 2G / 10G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 2 times 0:08:53.011 2G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Final bulge remover 0:08:53.081 2G / 10G INFO Simplification (parallel_processing.hpp : 167) Final bulge remover triggered 0 times 0:08:53.081 2G / 10G INFO Simplification (parallel_processing.hpp : 165) Running AT Tips 0:08:53.144 2G / 10G INFO Simplification (parallel_processing.hpp : 167) AT Tips triggered 0 times 0:08:53.144 2G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover 0:08:53.144 2G / 10G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 0 times 0:08:53.144 2G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover 0:08:53.199 2G / 10G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 0 times 0:08:53.199 2G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Complex bulge remover 0:08:54.733 2G / 10G INFO Simplification (parallel_processing.hpp : 167) Complex bulge remover triggered 0 times 0:08:54.734 2G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:08:54.734 2G / 10G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:08:54.734 2G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Final tip clipper 0:08:54.734 2G / 10G INFO Simplification (parallel_processing.hpp : 167) Final tip clipper triggered 0 times 0:08:54.734 2G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:08:54.735 2G / 10G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:08:54.735 2G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Final bulge remover 0:08:54.735 2G / 10G INFO Simplification (parallel_processing.hpp : 167) Final bulge remover triggered 0 times 0:08:54.735 2G / 10G INFO Simplification (parallel_processing.hpp : 165) Running AT Tips 0:08:54.735 2G / 10G INFO Simplification (parallel_processing.hpp : 167) AT Tips triggered 0 times 0:08:54.735 2G / 10G INFO General (simplification.cpp : 330) Disrupting self-conjugate edges 0:08:55.034 2G / 10G INFO General (simplification.cpp : 470) Counting average coverage 0:08:55.179 2G / 10G INFO General (simplification.cpp : 476) Average coverage = 18.55 0:08:55.179 2G / 10G INFO StageManager (stage.cpp : 132) STAGE == Mismatch Correction 0:08:55.179 2G / 10G INFO General (graph_pack.hpp : 109) Normalizing k-mer map. Total 11064834 kmers to process 0:09:03.732 2G / 10G INFO General (graph_pack.hpp : 111) Normalizing done 0:10:36.024 3G / 10G INFO General (mismatch_shall_not_pass.hp: 189) Finished collecting potential mismatches positions 0:10:38.698 2G / 10G INFO General (mismatch_shall_not_pass.hp: 290) All edges processed 0:10:38.792 2G / 10G INFO General (mismatch_correction.cpp : 27) Corrected 147 nucleotides 0:10:38.812 2G / 10G INFO StageManager (stage.cpp : 132) STAGE == Contig Output 0:10:38.813 2G / 10G INFO General (contig_output_stage.cpp : 40) Writing GFA to /oak/stanford/groups/akundaje/marinovg/various/MMETSP/2018-11-19-trans-splicing/SPAdes-3.13-RNA-Trimmomatic-Telonema_subtile_mixed_culture_with_Procryptobia-SRX4244210//K123/assembly_graph_with_scaffolds.gfa 0:10:40.085 2G / 10G INFO General (contig_output.hpp : 22) Outputting contigs to /oak/stanford/groups/akundaje/marinovg/various/MMETSP/2018-11-19-trans-splicing/SPAdes-3.13-RNA-Trimmomatic-Telonema_subtile_mixed_culture_with_Procryptobia-SRX4244210//K123/before_rr.fasta 0:10:41.806 2G / 10G INFO General (contig_output_stage.cpp : 51) Outputting FastG graph to /oak/stanford/groups/akundaje/marinovg/various/MMETSP/2018-11-19-trans-splicing/SPAdes-3.13-RNA-Trimmomatic-Telonema_subtile_mixed_culture_with_Procryptobia-SRX4244210//K123/assembly_graph.fastg 0:10:45.538 2G / 10G INFO General (contig_output.hpp : 22) Outputting contigs to /oak/stanford/groups/akundaje/marinovg/various/MMETSP/2018-11-19-trans-splicing/SPAdes-3.13-RNA-Trimmomatic-Telonema_subtile_mixed_culture_with_Procryptobia-SRX4244210//K123/simplified_contigs.fasta 0:10:47.150 2G / 10G INFO General (contig_output.hpp : 22) Outputting contigs to /oak/stanford/groups/akundaje/marinovg/various/MMETSP/2018-11-19-trans-splicing/SPAdes-3.13-RNA-Trimmomatic-Telonema_subtile_mixed_culture_with_Procryptobia-SRX4244210//K123/intermediate_contigs.fasta 0:10:48.637 2G / 10G INFO StageManager (stage.cpp : 132) STAGE == Paired Information Counting 0:10:51.894 2G / 10G INFO General (graph_pack.hpp : 109) Normalizing k-mer map. Total 11083002 kmers to process 0:11:00.542 2G / 10G INFO General (graph_pack.hpp : 111) Normalizing done 0:11:00.715 2G / 10G INFO General (pair_info_count.cpp : 320) Min edge length for estimation: 793 0:11:00.715 2G / 10G INFO General (pair_info_count.cpp : 331) Estimating insert size for library #0 0:11:00.715 2G / 10G INFO General (pair_info_count.cpp : 190) Estimating insert size (takes a while) 0:11:00.901 3G / 10G INFO General (pair_info_count.cpp : 39) Selecting usual mapper 0:11:13.208 3G / 10G INFO General (sequence_mapper_notifier.h: 80) Processed 200000 reads 0:11:13.242 3G / 10G INFO General (sequence_mapper_notifier.h: 80) Processed 400000 reads 0:11:13.272 3G / 10G INFO General (sequence_mapper_notifier.h: 80) Processed 600000 reads 0:11:13.314 3G / 10G INFO General (sequence_mapper_notifier.h: 80) Processed 800000 reads 0:11:13.344 3G / 10G INFO General (sequence_mapper_notifier.h: 80) Processed 1000000 reads 0:11:13.372 3G / 10G INFO General (sequence_mapper_notifier.h: 80) Processed 1200000 reads 0:11:15.197 3G / 10G INFO General (sequence_mapper_notifier.h: 80) Processed 2200000 reads 0:11:19.943 3G / 10G INFO General (sequence_mapper_notifier.h: 98) Total 3959819 reads processed 0:11:21.303 3G / 10G INFO General (pair_info_count.cpp : 209) Edge pairs: 67108864 (rough upper limit) 0:11:21.303 3G / 10G INFO General (pair_info_count.cpp : 213) 1745557 paired reads (44.0817% of all) aligned to long edges 0:11:21.341 2G / 10G INFO General (pair_info_count.cpp : 354) Insert size = 420.183, deviation = 144.176, left quantile = 269, right quantile = 625, read length = 251 0:11:21.341 2G / 10G INFO General (pair_info_count.cpp : 383) Mapping library #0 0:11:21.341 2G / 10G INFO General (pair_info_count.cpp : 385) Mapping paired reads (takes a while) 0:11:21.341 2G / 10G INFO General (pair_info_count.cpp : 289) Left insert size quantile 269, right insert size quantile 625, filtering threshold 0, rounding threshold 0 0:11:21.354 2G / 10G INFO General (pair_info_count.cpp : 39) Selecting usual mapper 0:11:34.411 2G / 10G INFO General (sequence_mapper_notifier.h: 80) Processed 200000 reads 0:11:34.453 2G / 10G INFO General (sequence_mapper_notifier.h: 80) Processed 400000 reads 0:11:34.609 2G / 10G INFO General (sequence_mapper_notifier.h: 80) Processed 600000 reads 0:11:34.631 2G / 10G INFO General (sequence_mapper_notifier.h: 80) Processed 800000 reads 0:11:34.696 2G / 10G INFO General (sequence_mapper_notifier.h: 80) Processed 1000000 reads 0:11:34.697 2G / 10G INFO General (sequence_mapper_notifier.h: 80) Processed 1200000 reads 0:11:36.054 2G / 10G INFO General (sequence_mapper_notifier.h: 80) Processed 2200000 reads 0:11:40.538 2G / 10G INFO General (sequence_mapper_notifier.h: 98) Total 3959819 reads processed 0:11:40.633 2G / 10G INFO General (pair_info_count.cpp : 392) Mapping single reads of library #0 0:11:40.633 2G / 10G INFO General (pair_info_count.cpp : 255) Will calculate lib coverage as well 0:11:40.633 2G / 10G INFO General (pair_info_count.cpp : 39) Selecting usual mapper 0:11:46.981 2G / 10G INFO General (sequence_mapper_notifier.h: 80) Processed 200000 reads 0:11:47.193 2G / 10G INFO General (sequence_mapper_notifier.h: 80) Processed 400000 reads 0:11:47.224 2G / 10G INFO General (sequence_mapper_notifier.h: 80) Processed 600000 reads 0:11:47.251 2G / 10G INFO General (sequence_mapper_notifier.h: 80) Processed 800000 reads 0:11:47.261 2G / 10G INFO General (sequence_mapper_notifier.h: 80) Processed 1000000 reads 0:11:47.293 2G / 10G INFO General (sequence_mapper_notifier.h: 80) Processed 1200000 reads 0:11:48.092 2G / 10G INFO General (sequence_mapper_notifier.h: 80) Processed 2200000 reads 0:11:53.834 2G / 10G INFO General (sequence_mapper_notifier.h: 80) Processed 4200000 reads 0:11:59.931 2G / 10G INFO General (sequence_mapper_notifier.h: 98) Total 7961075 reads processed 0:11:59.963 2G / 10G INFO General (pair_info_count.cpp : 394) Total paths obtained from single reads: 0 0:11:59.963 2G / 10G INFO General (pair_info_count.cpp : 392) Mapping single reads of library #1 0:11:59.963 2G / 10G INFO General (pair_info_count.cpp : 255) Will calculate lib coverage as well 0:11:59.963 2G / 10G INFO General (pair_info_count.cpp : 39) Selecting usual mapper 0:12:03.202 2G / 10G INFO General (sequence_mapper_notifier.h: 98) Total 2889643 reads processed 0:12:03.220 2G / 10G INFO General (pair_info_count.cpp : 394) Total paths obtained from single reads: 125498 0:12:03.220 2G / 10G INFO General (pair_info_count.cpp : 392) Mapping single reads of library #2 0:12:03.220 2G / 10G INFO General (pair_info_count.cpp : 255) Will calculate lib coverage as well 0:12:03.220 2G / 10G INFO General (pair_info_count.cpp : 39) Selecting usual mapper 0:12:03.257 2G / 10G INFO General (sequence_mapper_notifier.h: 98) Total 6396 reads processed 0:12:03.267 2G / 10G INFO General (pair_info_count.cpp : 394) Total paths obtained from single reads: 2160 0:12:03.267 2G / 10G INFO StageManager (stage.cpp : 132) STAGE == Distance Estimation 0:12:03.267 2G / 10G INFO General (distance_estimation.cpp : 173) Processing library #0 0:12:03.267 2G / 10G INFO General (distance_estimation.cpp : 149) Weight Filter Done 0:12:03.267 2G / 10G INFO DistanceEstimator (distance_estimation.hpp : 116) Using SIMPLE distance estimator 0:12:03.674 2G / 10G INFO General (distance_estimation.cpp : 34) Filtering info 0:12:03.674 2G / 10G INFO General (pair_info_filters.hpp : 242) Start filtering; index size: 462650 0:12:04.154 2G / 10G INFO General (pair_info_filters.hpp : 263) Done filtering 0:12:04.156 2G / 10G INFO General (distance_estimation.cpp : 156) Refining clustered pair information 0:12:04.209 2G / 10G INFO General (distance_estimation.cpp : 158) The refining of clustered pair information has been finished 0:12:04.209 2G / 10G INFO General (distance_estimation.cpp : 160) Improving paired information 0:12:04.788 2G / 10G INFO PairInfoImprover (pair_info_improver.hpp : 103) Paired info stats: missing = 980; contradictional = 6 0:12:05.360 2G / 10G INFO PairInfoImprover (pair_info_improver.hpp : 103) Paired info stats: missing = 36; contradictional = 0 0:12:05.360 2G / 10G INFO StageManager (stage.cpp : 132) STAGE == Repeat Resolving 0:12:05.361 2G / 10G INFO General (repeat_resolving.cpp : 69) Using Path-Extend repeat resolving 0:12:05.361 2G / 10G INFO General (launcher.cpp : 477) ExSPAnder repeat resolving tool started 0:12:06.817 3G / 10G INFO General (launcher.cpp : 392) Creating main extenders, unique edge length = 2000 0:12:07.670 3G / 10G INFO General (extenders_logic.cpp : 34) resolvable_repeat_length_bound set to 10000 0:12:08.283 3G / 10G INFO General (extenders_logic.cpp : 34) resolvable_repeat_length_bound set to 10000 0:12:08.783 3G / 10G INFO General (extenders_logic.cpp : 472) Using 1 paired-end library 0:12:08.783 3G / 10G INFO General (extenders_logic.cpp : 473) Using 1 paired-end scaffolding library 0:12:08.783 3G / 10G INFO General (extenders_logic.cpp : 474) Using 2 single read libraries 0:12:08.783 3G / 10G INFO General (launcher.cpp : 420) Total number of extenders is 7 0:12:08.783 3G / 10G INFO General (path_extender.hpp : 885) Processed 0 paths from 201582 (0%) 0:12:08.832 3G / 10G INFO General (path_extender.hpp : 883) Processed 128 paths from 201582 (0%) 0:12:08.868 3G / 10G INFO General (path_extender.hpp : 883) Processed 256 paths from 201582 (0%) 0:12:08.915 3G / 10G INFO General (path_extender.hpp : 883) Processed 512 paths from 201582 (0%) 0:12:09.007 3G / 10G INFO General (path_extender.hpp : 883) Processed 1024 paths from 201582 (0%) 0:12:09.186 3G / 10G INFO General (path_extender.hpp : 883) Processed 2048 paths from 201582 (1%) 0:12:09.578 3G / 10G INFO General (path_extender.hpp : 883) Processed 4096 paths from 201582 (2%) 0:12:10.376 3G / 10G INFO General (path_extender.hpp : 883) Processed 8192 paths from 201582 (4%) 0:12:11.921 4G / 10G INFO General (path_extender.hpp : 883) Processed 16384 paths from 201582 (8%) 0:12:12.670 4G / 10G INFO General (path_extender.hpp : 885) Processed 20159 paths from 201582 (10%) 0:12:15.077 4G / 10G INFO General (path_extender.hpp : 883) Processed 32768 paths from 201582 (16%) 0:12:16.335 4G / 10G INFO General (path_extender.hpp : 885) Processed 40318 paths from 201582 (20%) 0:12:19.089 4G / 10G INFO General (path_extender.hpp : 885) Processed 60477 paths from 201582 (30%) 0:12:19.635 4G / 10G INFO General (path_extender.hpp : 883) Processed 65536 paths from 201582 (32%) 0:12:21.562 4G / 10G INFO General (path_extender.hpp : 885) Processed 80636 paths from 201582 (40%) 0:12:23.663 4G / 10G INFO General (path_extender.hpp : 885) Processed 100795 paths from 201582 (50%) 0:12:25.602 4G / 10G INFO General (path_extender.hpp : 885) Processed 120954 paths from 201582 (60%) 0:12:26.475 4G / 10G INFO General (path_extender.hpp : 883) Processed 131072 paths from 201582 (65%) 0:12:27.289 4G / 10G INFO General (path_extender.hpp : 885) Processed 141113 paths from 201582 (70%) 0:12:28.944 5G / 10G INFO General (path_extender.hpp : 885) Processed 161272 paths from 201582 (80%) 0:12:30.488 5G / 10G INFO General (path_extender.hpp : 885) Processed 181431 paths from 201582 (90%) 0:12:32.025 5G / 10G INFO General (launcher.cpp : 234) Finalizing paths 0:12:32.026 5G / 10G INFO General (launcher.cpp : 236) Deduplicating paths 0:12:32.708 5G / 10G INFO General (launcher.cpp : 240) Paths deduplicated 0:12:32.708 5G / 10G INFO PEResolver (pe_resolver.hpp : 295) Removing overlaps 0:12:32.708 5G / 10G INFO PEResolver (pe_resolver.hpp : 305) Marking overlaps 0:12:32.708 5G / 10G INFO OverlapRemover (pe_resolver.hpp : 130) Marking start/end overlaps 0:12:33.009 5G / 10G INFO PEResolver (pe_resolver.hpp : 308) Splitting paths 0:12:33.040 5G / 10G INFO PEResolver (pe_resolver.hpp : 313) Deduplicating paths 0:12:33.196 5G / 10G INFO PEResolver (pe_resolver.hpp : 315) Overlaps removed 0:12:33.746 5G / 10G INFO General (launcher.cpp : 257) Paths finalized 0:12:33.747 5G / 10G INFO General (launcher.cpp : 427) Closing gaps in paths 0:12:34.779 5G / 10G INFO General (launcher.cpp : 455) Gap closing completed 0:12:35.097 5G / 10G INFO General (launcher.cpp : 286) Traversing tandem repeats 0:12:36.528 5G / 10G INFO General (launcher.cpp : 296) Traversed 2 loops 0:12:36.528 5G / 10G INFO General (launcher.cpp : 234) Finalizing paths 0:12:36.528 5G / 10G INFO General (launcher.cpp : 236) Deduplicating paths 0:12:36.684 5G / 10G INFO General (launcher.cpp : 240) Paths deduplicated 0:12:36.684 5G / 10G INFO PEResolver (pe_resolver.hpp : 295) Removing overlaps 0:12:36.684 5G / 10G INFO PEResolver (pe_resolver.hpp : 305) Marking overlaps 0:12:36.684 5G / 10G INFO OverlapRemover (pe_resolver.hpp : 130) Marking start/end overlaps 0:12:36.973 5G / 10G INFO PEResolver (pe_resolver.hpp : 308) Splitting paths 0:12:36.991 5G / 10G INFO PEResolver (pe_resolver.hpp : 313) Deduplicating paths 0:12:37.177 5G / 10G INFO PEResolver (pe_resolver.hpp : 315) Overlaps removed 0:12:37.698 5G / 10G INFO General (launcher.cpp : 257) Paths finalized 0:12:38.260 6G / 10G INFO General (launcher.cpp : 462) Finalizing main paths 0:12:38.260 6G / 10G INFO General (launcher.cpp : 279) Read length relative cutoff 1.3 converted to 203 0:12:38.260 6G / 10G INFO General (launcher.cpp : 280) Read length absolute cutoff 110 bp converted to 203 0:12:38.260 6G / 10G INFO General (launcher.cpp : 281) Length cutoff: 203 0:12:38.383 6G / 10G INFO General (launcher.cpp : 279) Read length relative cutoff 1.6 converted to 278 0:12:38.383 6G / 10G INFO General (launcher.cpp : 280) Read length absolute cutoff 140 bp converted to 278 0:12:38.383 6G / 10G INFO General (launcher.cpp : 281) Length cutoff: 278 0:12:38.405 6G / 10G INFO General (launcher.cpp : 279) Read length relative cutoff 1.5 converted to 253 0:12:38.406 6G / 10G INFO General (launcher.cpp : 280) Read length absolute cutoff 130 bp converted to 253 0:12:38.406 6G / 10G INFO General (launcher.cpp : 281) Length cutoff: 253 0:12:38.449 6G / 10G INFO General (launcher.cpp : 467) Finalizing paths - hard 0:12:38.816 6G / 10G INFO General (launcher.cpp : 279) Read length relative cutoff 1.5 converted to 253 0:12:38.816 6G / 10G INFO General (launcher.cpp : 280) Read length absolute cutoff 130 bp converted to 253 0:12:38.816 6G / 10G INFO General (launcher.cpp : 281) Length cutoff: 253 0:12:38.955 6G / 10G INFO General (launcher.cpp : 279) Read length relative cutoff 2 converted to 379 0:12:38.955 6G / 10G INFO General (launcher.cpp : 280) Read length absolute cutoff 180 bp converted to 379 0:12:38.955 6G / 10G INFO General (launcher.cpp : 281) Length cutoff: 379 0:12:38.981 6G / 10G INFO General (launcher.cpp : 279) Read length relative cutoff 2 converted to 379 0:12:38.981 6G / 10G INFO General (launcher.cpp : 280) Read length absolute cutoff 180 bp converted to 379 0:12:38.981 6G / 10G INFO General (launcher.cpp : 281) Length cutoff: 379 0:12:40.092 6G / 10G INFO General (launcher.cpp : 467) Finalizing paths - soft 0:12:40.511 6G / 10G INFO General (launcher.cpp : 279) Read length relative cutoff 1.05 converted to 140 0:12:40.511 6G / 10G INFO General (launcher.cpp : 280) Read length absolute cutoff 85 bp converted to 140 0:12:40.511 6G / 10G INFO General (launcher.cpp : 281) Length cutoff: 140 0:12:40.634 6G / 10G INFO General (launcher.cpp : 279) Read length relative cutoff 1.5 converted to 253 0:12:40.634 6G / 10G INFO General (launcher.cpp : 280) Read length absolute cutoff 130 bp converted to 253 0:12:40.634 6G / 10G INFO General (launcher.cpp : 281) Length cutoff: 253 0:12:40.655 6G / 10G INFO General (launcher.cpp : 279) Read length relative cutoff 1.2 converted to 178 0:12:40.655 6G / 10G INFO General (launcher.cpp : 280) Read length absolute cutoff 100 bp converted to 178 0:12:40.655 6G / 10G INFO General (launcher.cpp : 281) Length cutoff: 178 0:12:42.251 5G / 10G INFO General (launcher.cpp : 529) ExSPAnder repeat resolving tool finished 0:12:43.788 3G / 10G INFO StageManager (stage.cpp : 132) STAGE == Contig Output 0:12:43.788 3G / 10G INFO General (contig_output_stage.cpp : 40) Writing GFA to /oak/stanford/groups/akundaje/marinovg/various/MMETSP/2018-11-19-trans-splicing/SPAdes-3.13-RNA-Trimmomatic-Telonema_subtile_mixed_culture_with_Procryptobia-SRX4244210//K123/assembly_graph_with_scaffolds.gfa 0:12:45.058 3G / 10G INFO General (contig_output.hpp : 22) Outputting contigs to /oak/stanford/groups/akundaje/marinovg/various/MMETSP/2018-11-19-trans-splicing/SPAdes-3.13-RNA-Trimmomatic-Telonema_subtile_mixed_culture_with_Procryptobia-SRX4244210//K123/before_rr.fasta 0:12:46.549 3G / 10G INFO General (contig_output_stage.cpp : 51) Outputting FastG graph to /oak/stanford/groups/akundaje/marinovg/various/MMETSP/2018-11-19-trans-splicing/SPAdes-3.13-RNA-Trimmomatic-Telonema_subtile_mixed_culture_with_Procryptobia-SRX4244210//K123/assembly_graph.fastg 0:12:50.437 3G / 10G INFO General (contig_output_stage.cpp : 20) Outputting FastG paths to /oak/stanford/groups/akundaje/marinovg/various/MMETSP/2018-11-19-trans-splicing/SPAdes-3.13-RNA-Trimmomatic-Telonema_subtile_mixed_culture_with_Procryptobia-SRX4244210//K123/transcripts.paths 0:12:51.814 3G / 10G INFO General (launch.hpp : 149) SPAdes finished 0:12:58.952 68M / 10G INFO General (main.cpp : 109) Assembling time: 0 hours 12 minutes 58 seconds ===== Assembling finished. Used k-mer sizes: 55, 123 * Corrected reads are in /oak/stanford/groups/akundaje/marinovg/various/MMETSP/2018-11-19-trans-splicing/SPAdes-3.13-RNA-Trimmomatic-Telonema_subtile_mixed_culture_with_Procryptobia-SRX4244210/corrected/ * Assembled transcripts are in /oak/stanford/groups/akundaje/marinovg/various/MMETSP/2018-11-19-trans-splicing/SPAdes-3.13-RNA-Trimmomatic-Telonema_subtile_mixed_culture_with_Procryptobia-SRX4244210/transcripts.fasta * Paths in the assembly graph corresponding to the transcripts are in /oak/stanford/groups/akundaje/marinovg/various/MMETSP/2018-11-19-trans-splicing/SPAdes-3.13-RNA-Trimmomatic-Telonema_subtile_mixed_culture_with_Procryptobia-SRX4244210/transcripts.paths * Hard filtered transcripts are in /oak/stanford/groups/akundaje/marinovg/various/MMETSP/2018-11-19-trans-splicing/SPAdes-3.13-RNA-Trimmomatic-Telonema_subtile_mixed_culture_with_Procryptobia-SRX4244210/hard_filtered_transcripts.fasta * Soft filtered transcripts are in /oak/stanford/groups/akundaje/marinovg/various/MMETSP/2018-11-19-trans-splicing/SPAdes-3.13-RNA-Trimmomatic-Telonema_subtile_mixed_culture_with_Procryptobia-SRX4244210/soft_filtered_transcripts.fasta ======= SPAdes pipeline finished. SPAdes log can be found here: /oak/stanford/groups/akundaje/marinovg/various/MMETSP/2018-11-19-trans-splicing/SPAdes-3.13-RNA-Trimmomatic-Telonema_subtile_mixed_culture_with_Procryptobia-SRX4244210/spades.log Thank you for using SPAdes!