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/Voromonas_pontica_cDNA_sequencing-SRX973460.read1.paired.fastq.gz --pe1-2 /oak/stanford/groups/akundaje/marinovg/various/MMETSP/2018-11-19-trans-splicing/Voromonas_pontica_cDNA_sequencing-SRX973460.read2.paired.fastq.gz --s1 /oak/stanford/groups/akundaje/marinovg/various/MMETSP/2018-11-19-trans-splicing/Voromonas_pontica_cDNA_sequencing-SRX973460.read1.unpaired.fastq.gz --s2 /oak/stanford/groups/akundaje/marinovg/various/MMETSP/2018-11-19-trans-splicing/Voromonas_pontica_cDNA_sequencing-SRX973460.read2.unpaired.fastq.gz -t 20 -o /oak/stanford/groups/akundaje/marinovg/various/MMETSP/2018-11-19-trans-splicing/SPAdes-3.13-RNA-Trimmomatic-Voromonas_pontica_cDNA_sequencing-SRX973460 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-Voromonas_pontica_cDNA_sequencing-SRX973460 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/Voromonas_pontica_cDNA_sequencing-SRX973460.read1.paired.fastq.gz'] right reads: ['/oak/stanford/groups/akundaje/marinovg/various/MMETSP/2018-11-19-trans-splicing/Voromonas_pontica_cDNA_sequencing-SRX973460.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/Voromonas_pontica_cDNA_sequencing-SRX973460.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/Voromonas_pontica_cDNA_sequencing-SRX973460.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-Voromonas_pontica_cDNA_sequencing-SRX973460/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-Voromonas_pontica_cDNA_sequencing-SRX973460/spades.log /oak/stanford/groups/akundaje/marinovg/various/MMETSP/2018-11-19-trans-splicing/Voromonas_pontica_cDNA_sequencing-SRX973460.read2.paired.fastq.gz: max reads length: 100 /oak/stanford/groups/akundaje/marinovg/various/MMETSP/2018-11-19-trans-splicing/Voromonas_pontica_cDNA_sequencing-SRX973460.read1.paired.fastq.gz: max reads length: 100 /oak/stanford/groups/akundaje/marinovg/various/MMETSP/2018-11-19-trans-splicing/Voromonas_pontica_cDNA_sequencing-SRX973460.read1.unpaired.fastq.gz: max reads length: 100 /oak/stanford/groups/akundaje/marinovg/various/MMETSP/2018-11-19-trans-splicing/Voromonas_pontica_cDNA_sequencing-SRX973460.read2.unpaired.fastq.gz: max reads length: 100 Reads length: 100 K values to be used: [33, 49] ===== 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-Voromonas_pontica_cDNA_sequencing-SRX973460/corrected/configs/config.info 0:00:00.003 4M / 4M INFO General (main.cpp : 75) Starting BayesHammer, built from refs/heads/spades_3.13.0, git revision 8ea46659e9b2aca35444a808db550ac333006f8b 0:00:00.015 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-Voromonas_pontica_cDNA_sequencing-SRX973460/corrected/configs/config.info 0:00:00.026 4M / 4M INFO General (main.cpp : 78) Maximum # of threads to use (adjusted due to OMP capabilities): 16 0:00:00.026 4M / 4M INFO General (memory_limit.cpp : 49) Memory limit set to 250 Gb 0:00:00.026 4M / 4M INFO General (main.cpp : 86) Trying to determine PHRED offset 0:00:00.030 4M / 4M INFO General (main.cpp : 92) Determined value is 33 0:00:00.030 4M / 4M INFO General (hammer_tools.cpp : 36) Hamming graph threshold tau=1, k=21, subkmer positions = [ 0 10 ] 0:00:00.030 4M / 4M INFO General (main.cpp : 113) Size of aux. kmer data 24 bytes === ITERATION 0 begins === 0:00:00.031 4M / 4M INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:00:00.031 4M / 4M INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 256 files using 16 threads. This might take a while. 0:00:00.032 4M / 4M INFO General (file_limit.hpp : 32) Open file limit set to 131072 0:00:00.032 4M / 4M INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 5.20825 Gb 0:00:00.032 4M / 4M INFO General (kmer_splitters.hpp : 97) Using cell size of 262144 0:00:00.092 8G / 8G INFO K-mer Splitting (kmer_data.cpp : 97) Processing /oak/stanford/groups/akundaje/marinovg/various/MMETSP/2018-11-19-trans-splicing/Voromonas_pontica_cDNA_sequencing-SRX973460.read1.paired.fastq.gz 0:00:13.743 8G / 8G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 721182 reads 0:00:16.979 8G / 8G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 1373174 reads 0:00:20.078 8G / 8G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 2030011 reads 0:00:23.298 8G / 8G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 2737668 reads 0:00:26.379 8G / 8G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 3417821 reads 0:00:29.607 8G / 8G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 4096945 reads 0:00:32.834 8G / 8G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 4782980 reads 0:00:36.028 8G / 8G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 5371396 reads 0:00:53.952 8G / 8G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 8958998 reads 0:01:03.705 8G / 8G INFO K-mer Splitting (kmer_data.cpp : 97) Processing /oak/stanford/groups/akundaje/marinovg/various/MMETSP/2018-11-19-trans-splicing/Voromonas_pontica_cDNA_sequencing-SRX973460.read2.paired.fastq.gz 0:01:33.853 8G / 8G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 17033203 reads 0:01:58.239 8G / 8G INFO K-mer Splitting (kmer_data.cpp : 97) Processing /oak/stanford/groups/akundaje/marinovg/various/MMETSP/2018-11-19-trans-splicing/Voromonas_pontica_cDNA_sequencing-SRX973460.read1.unpaired.fastq.gz 0:02:07.763 8G / 8G INFO K-mer Splitting (kmer_data.cpp : 97) Processing /oak/stanford/groups/akundaje/marinovg/various/MMETSP/2018-11-19-trans-splicing/Voromonas_pontica_cDNA_sequencing-SRX973460.read2.unpaired.fastq.gz 0:02:10.791 8G / 8G INFO K-mer Splitting (kmer_data.cpp : 112) Total 24391771 reads processed 0:02:11.006 64M / 8G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:02:23.191 64M / 8G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 155979142 kmers in total. 0:02:23.191 64M / 8G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:02:56.501 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:03:00.395 132M / 8G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 0:03:06.433 132M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 72342160 bytes occupied (3.71035 bits per kmer). 0:03:06.436 132M / 8G INFO K-mer Counting (kmer_data.cpp : 356) Arranging kmers in hash map order 0:03:13.102 2G / 8G INFO General (main.cpp : 148) Clustering Hamming graph. 0:06:12.472 2G / 8G INFO General (main.cpp : 155) Extracting clusters 0:07:06.826 2G / 8G INFO General (main.cpp : 167) Clustering done. Total clusters: 94030242 0:07:06.958 1G / 8G INFO K-mer Counting (kmer_data.cpp : 376) Collecting K-mer information, this takes a while. 0:07:09.025 4G / 8G INFO K-mer Counting (kmer_data.cpp : 382) Processing /oak/stanford/groups/akundaje/marinovg/various/MMETSP/2018-11-19-trans-splicing/Voromonas_pontica_cDNA_sequencing-SRX973460.read1.paired.fastq.gz 0:08:21.492 4G / 8G INFO K-mer Counting (kmer_data.cpp : 382) Processing /oak/stanford/groups/akundaje/marinovg/various/MMETSP/2018-11-19-trans-splicing/Voromonas_pontica_cDNA_sequencing-SRX973460.read2.paired.fastq.gz 0:10:21.134 4G / 8G INFO K-mer Counting (kmer_data.cpp : 382) Processing /oak/stanford/groups/akundaje/marinovg/various/MMETSP/2018-11-19-trans-splicing/Voromonas_pontica_cDNA_sequencing-SRX973460.read1.unpaired.fastq.gz 0:10:41.585 4G / 8G INFO K-mer Counting (kmer_data.cpp : 382) Processing /oak/stanford/groups/akundaje/marinovg/various/MMETSP/2018-11-19-trans-splicing/Voromonas_pontica_cDNA_sequencing-SRX973460.read2.unpaired.fastq.gz 0:10:50.300 4G / 8G INFO K-mer Counting (kmer_data.cpp : 389) Collection done, postprocessing. 0:10:50.911 4G / 8G INFO K-mer Counting (kmer_data.cpp : 403) There are 155979142 kmers in total. Among them 99469476 (63.771%) are singletons. 0:10:50.911 4G / 8G INFO General (main.cpp : 173) Subclustering Hamming graph 0:14:08.619 4G / 8G INFO Hamming Subclustering (kmer_cluster.cpp : 649) Subclustering done. Total 4500 non-read kmers were generated. 0:14:08.619 4G / 8G INFO Hamming Subclustering (kmer_cluster.cpp : 650) Subclustering statistics: 0:14:08.619 4G / 8G INFO Hamming Subclustering (kmer_cluster.cpp : 651) Total singleton hamming clusters: 80966488. Among them 46649662 (57.616%) are good 0:14:08.619 4G / 8G INFO Hamming Subclustering (kmer_cluster.cpp : 652) Total singleton subclusters: 216707. Among them 215912 (99.6331%) are good 0:14:08.619 4G / 8G INFO Hamming Subclustering (kmer_cluster.cpp : 653) Total non-singleton subcluster centers: 14367912. Among them 10112704 (70.384%) are good 0:14:08.619 4G / 8G INFO Hamming Subclustering (kmer_cluster.cpp : 654) Average size of non-trivial subcluster: 5.22206 kmers 0:14:08.619 4G / 8G INFO Hamming Subclustering (kmer_cluster.cpp : 655) Average number of sub-clusters per non-singleton cluster: 1.11642 0:14:08.619 4G / 8G INFO Hamming Subclustering (kmer_cluster.cpp : 656) Total solid k-mers: 56978278 0:14:08.619 4G / 8G INFO Hamming Subclustering (kmer_cluster.cpp : 657) Substitution probabilities: [4,4]((0.911698,0.0280351,0.036583,0.0236843),(0.0216491,0.931429,0.0196452,0.027277),(0.0251243,0.0187212,0.932754,0.0234005),(0.0224884,0.0350493,0.0269234,0.915539)) 0:14:08.859 4G / 8G INFO General (main.cpp : 178) Finished clustering. 0:14:08.860 4G / 8G INFO General (main.cpp : 197) Starting solid k-mers expansion in 16 threads. 0:15:32.137 4G / 8G INFO General (main.cpp : 218) Solid k-mers iteration 0 produced 14372613 new k-mers. 0:16:55.533 4G / 8G INFO General (main.cpp : 218) Solid k-mers iteration 1 produced 1430974 new k-mers. 0:18:19.308 4G / 8G INFO General (main.cpp : 218) Solid k-mers iteration 2 produced 55435 new k-mers. 0:19:42.470 4G / 8G INFO General (main.cpp : 218) Solid k-mers iteration 3 produced 2038 new k-mers. 0:21:06.075 4G / 8G INFO General (main.cpp : 218) Solid k-mers iteration 4 produced 109 new k-mers. 0:22:30.043 4G / 8G INFO General (main.cpp : 218) Solid k-mers iteration 5 produced 0 new k-mers. 0:22:30.043 4G / 8G INFO General (main.cpp : 222) Solid k-mers finalized 0:22:30.043 4G / 8G INFO General (hammer_tools.cpp : 220) Starting read correction in 16 threads. 0:22:30.043 4G / 8G INFO General (hammer_tools.cpp : 233) Correcting pair of reads: /oak/stanford/groups/akundaje/marinovg/various/MMETSP/2018-11-19-trans-splicing/Voromonas_pontica_cDNA_sequencing-SRX973460.read1.paired.fastq.gz and /oak/stanford/groups/akundaje/marinovg/various/MMETSP/2018-11-19-trans-splicing/Voromonas_pontica_cDNA_sequencing-SRX973460.read2.paired.fastq.gz 0:22:38.368 5G / 8G INFO General (hammer_tools.cpp : 168) Prepared batch 0 of 1600000 reads. 0:22:44.844 6G / 8G INFO General (hammer_tools.cpp : 175) Processed batch 0 0:22:49.259 6G / 8G INFO General (hammer_tools.cpp : 185) Written batch 0 0:22:57.378 6G / 8G INFO General (hammer_tools.cpp : 168) Prepared batch 1 of 1600000 reads. 0:23:04.125 6G / 8G INFO General (hammer_tools.cpp : 175) Processed batch 1 0:23:08.736 6G / 8G INFO General (hammer_tools.cpp : 185) Written batch 1 0:23:16.617 6G / 8G INFO General (hammer_tools.cpp : 168) Prepared batch 2 of 1600000 reads. 0:23:23.241 6G / 8G INFO General (hammer_tools.cpp : 175) Processed batch 2 0:23:27.456 6G / 8G INFO General (hammer_tools.cpp : 185) Written batch 2 0:23:35.141 6G / 8G INFO General (hammer_tools.cpp : 168) Prepared batch 3 of 1600000 reads. 0:23:42.278 6G / 8G INFO General (hammer_tools.cpp : 175) Processed batch 3 0:23:47.044 6G / 8G INFO General (hammer_tools.cpp : 185) Written batch 3 0:23:55.360 6G / 8G INFO General (hammer_tools.cpp : 168) Prepared batch 4 of 1600000 reads. 0:24:07.946 6G / 8G INFO General (hammer_tools.cpp : 175) Processed batch 4 0:24:12.319 6G / 8G INFO General (hammer_tools.cpp : 185) Written batch 4 0:24:19.418 6G / 8G INFO General (hammer_tools.cpp : 168) Prepared batch 5 of 1600000 reads. 0:24:30.789 6G / 8G INFO General (hammer_tools.cpp : 175) Processed batch 5 0:24:35.225 6G / 8G INFO General (hammer_tools.cpp : 185) Written batch 5 0:24:41.385 6G / 8G INFO General (hammer_tools.cpp : 168) Prepared batch 6 of 1324155 reads. 0:24:46.904 6G / 8G INFO General (hammer_tools.cpp : 175) Processed batch 6 0:24:50.906 6G / 8G INFO General (hammer_tools.cpp : 185) Written batch 6 0:24:52.414 4G / 8G INFO General (hammer_tools.cpp : 264) Correcting single reads: /oak/stanford/groups/akundaje/marinovg/various/MMETSP/2018-11-19-trans-splicing/Voromonas_pontica_cDNA_sequencing-SRX973460.read1.unpaired.fastq.gz 0:24:56.128 5G / 8G INFO General (hammer_tools.cpp : 127) Prepared batch 0 of 1600000 reads. 0:25:02.080 5G / 8G INFO General (hammer_tools.cpp : 132) Processed batch 0 0:25:04.806 5G / 8G INFO General (hammer_tools.cpp : 136) Written batch 0 0:25:05.496 5G / 8G INFO General (hammer_tools.cpp : 127) Prepared batch 1 of 275414 reads. 0:25:06.257 5G / 8G INFO General (hammer_tools.cpp : 132) Processed batch 1 0:25:06.603 5G / 8G INFO General (hammer_tools.cpp : 136) Written batch 1 0:25:07.244 4G / 8G INFO General (hammer_tools.cpp : 264) Correcting single reads: /oak/stanford/groups/akundaje/marinovg/various/MMETSP/2018-11-19-trans-splicing/Voromonas_pontica_cDNA_sequencing-SRX973460.read2.unpaired.fastq.gz 0:25:08.878 5G / 8G INFO General (hammer_tools.cpp : 127) Prepared batch 0 of 668047 reads. 0:25:10.109 5G / 8G INFO General (hammer_tools.cpp : 132) Processed batch 0 0:25:11.057 5G / 8G INFO General (hammer_tools.cpp : 136) Written batch 0 0:25:11.309 4G / 8G INFO General (hammer_tools.cpp : 274) Correction done. Changed 4454900 bases in 2812760 reads. 0:25:11.309 4G / 8G INFO General (hammer_tools.cpp : 275) Failed to correct 5757989 bases out of 2007121698. 0:25:12.090 64M / 8G 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-Voromonas_pontica_cDNA_sequencing-SRX973460/corrected/corrected.yaml 0:25:12.094 64M / 8G 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-Voromonas_pontica_cDNA_sequencing-SRX973460/corrected/corrected.yaml ===== Read error correction finished. ===== Assembling started. == Running assembler: K33 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-Voromonas_pontica_cDNA_sequencing-SRX973460/K33/configs/config.info 0:00:00.004 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-Voromonas_pontica_cDNA_sequencing-SRX973460/K33/configs/mda_mode.info 0:00:00.004 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-Voromonas_pontica_cDNA_sequencing-SRX973460/K33/configs/rna_mode.info 0:00:00.006 4M / 4M INFO General (memory_limit.cpp : 49) Memory limit set to 250 Gb 0:00:00.006 4M / 4M INFO General (main.cpp : 87) Starting SPAdes, built from refs/heads/spades_3.13.0, git revision 8ea46659e9b2aca35444a808db550ac333006f8b 0:00:00.006 4M / 4M INFO General (main.cpp : 88) Maximum k-mer length: 128 0:00:00.006 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-Voromonas_pontica_cDNA_sequencing-SRX973460/dataset.info) with K=33 0:00:00.006 4M / 4M INFO General (main.cpp : 90) Maximum # of threads to use (adjusted due to OMP capabilities): 16 0:00:00.006 4M / 4M INFO General (launch.hpp : 51) SPAdes started 0:00:00.006 4M / 4M INFO General (launch.hpp : 58) Starting from stage: construction 0:00:00.006 4M / 4M INFO General (launch.hpp : 65) Two-step RR enabled: 0 0:00:00.011 4M / 4M INFO StageManager (stage.cpp : 132) STAGE == de Bruijn graph construction 0:00:00.013 4M / 4M INFO General (read_converter.hpp : 77) Converting reads to binary format for library #0 (takes a while) 0:00:00.013 4M / 4M INFO General (read_converter.hpp : 78) Converting paired reads 0:00:00.333 76M / 76M INFO General (binary_converter.hpp : 93) 16384 reads processed 0:00:00.486 88M / 88M INFO General (binary_converter.hpp : 93) 32768 reads processed 0:00:00.868 108M / 108M INFO General (binary_converter.hpp : 93) 65536 reads processed 0:00:01.490 152M / 152M INFO General (binary_converter.hpp : 93) 131072 reads processed 0:00:02.471 236M / 236M INFO General (binary_converter.hpp : 93) 262144 reads processed 0:00:04.290 408M / 408M INFO General (binary_converter.hpp : 93) 524288 reads processed 0:00:10.065 680M / 680M INFO General (binary_converter.hpp : 93) 1048576 reads processed 0:00:18.970 692M / 692M INFO General (binary_converter.hpp : 93) 2097152 reads processed 0:00:36.936 696M / 696M INFO General (binary_converter.hpp : 93) 4194304 reads processed 0:01:17.243 724M / 724M INFO General (binary_converter.hpp : 93) 8388608 reads processed 0:01:40.717 696M / 732M INFO General (binary_converter.hpp : 117) 10912078 reads written 0:01:41.646 4M / 732M INFO General (read_converter.hpp : 87) Converting single reads 0:01:42.776 136M / 732M INFO General (binary_converter.hpp : 117) 12006 reads written 0:01:42.807 4M / 732M INFO General (read_converter.hpp : 95) Converting merged reads 0:01:43.043 132M / 732M INFO General (binary_converter.hpp : 117) 0 reads written 0:01:43.089 4M / 732M INFO General (read_converter.hpp : 77) Converting reads to binary format for library #1 (takes a while) 0:01:43.089 4M / 732M INFO General (read_converter.hpp : 78) Converting paired reads 0:01:43.417 68M / 732M INFO General (binary_converter.hpp : 117) 0 reads written 0:01:43.430 4M / 732M INFO General (read_converter.hpp : 87) Converting single reads 0:01:43.690 136M / 732M INFO General (binary_converter.hpp : 93) 16384 reads processed 0:01:43.757 140M / 732M INFO General (binary_converter.hpp : 93) 32768 reads processed 0:01:43.954 152M / 732M INFO General (binary_converter.hpp : 93) 65536 reads processed 0:01:44.260 172M / 732M INFO General (binary_converter.hpp : 93) 131072 reads processed 0:01:44.868 212M / 732M INFO General (binary_converter.hpp : 93) 262144 reads processed 0:01:45.808 292M / 732M INFO General (binary_converter.hpp : 93) 524288 reads processed 0:01:47.563 456M / 732M INFO General (binary_converter.hpp : 93) 1048576 reads processed 0:01:51.619 708M / 732M INFO General (binary_converter.hpp : 117) 1868370 reads written 0:01:52.583 4M / 732M INFO General (read_converter.hpp : 95) Converting merged reads 0:01:52.761 132M / 732M INFO General (binary_converter.hpp : 117) 0 reads written 0:01:52.820 4M / 732M INFO General (read_converter.hpp : 77) Converting reads to binary format for library #2 (takes a while) 0:01:52.820 4M / 732M INFO General (read_converter.hpp : 78) Converting paired reads 0:01:53.185 68M / 732M INFO General (binary_converter.hpp : 117) 0 reads written 0:01:53.198 4M / 732M INFO General (read_converter.hpp : 87) Converting single reads 0:01:53.486 136M / 732M INFO General (binary_converter.hpp : 93) 16384 reads processed 0:01:53.546 140M / 732M INFO General (binary_converter.hpp : 93) 32768 reads processed 0:01:53.671 152M / 732M INFO General (binary_converter.hpp : 93) 65536 reads processed 0:01:53.971 172M / 732M INFO General (binary_converter.hpp : 93) 131072 reads processed 0:01:54.545 212M / 732M INFO General (binary_converter.hpp : 93) 262144 reads processed 0:01:55.717 292M / 732M INFO General (binary_converter.hpp : 93) 524288 reads processed 0:01:56.618 336M / 732M INFO General (binary_converter.hpp : 117) 666393 reads written 0:01:56.962 4M / 732M INFO General (read_converter.hpp : 95) Converting merged reads 0:01:57.183 132M / 732M INFO General (binary_converter.hpp : 117) 0 reads written 0:01:57.217 4M / 732M INFO General (construction.cpp : 111) Max read length 100 0:01:57.217 4M / 732M INFO General (construction.cpp : 117) Average read length 82.0988 0:01:57.218 4M / 732M INFO General (stage.cpp : 101) PROCEDURE == k+1-mer counting 0:01:57.218 4M / 732M INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 256 files using 16 threads. This might take a while. 0:01:57.219 4M / 732M INFO General (file_limit.hpp : 32) Open file limit set to 131072 0:01:57.219 4M / 732M INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 5.20825 Gb 0:01:57.219 4M / 732M INFO General (kmer_splitters.hpp : 97) Using cell size of 131072 0:02:09.487 8G / 8G INFO General (kmer_splitters.hpp : 289) Processed 1782031 reads 0:02:10.390 8G / 8G INFO General (kmer_splitters.hpp : 289) Processed 3345158 reads 0:02:13.544 8G / 8G INFO General (kmer_splitters.hpp : 289) Processed 4823020 reads 0:02:14.351 8G / 8G INFO General (kmer_splitters.hpp : 289) Processed 6195342 reads 0:02:15.100 8G / 8G INFO General (kmer_splitters.hpp : 289) Processed 7563517 reads 0:02:16.052 8G / 8G INFO General (kmer_splitters.hpp : 289) Processed 9216724 reads 0:02:19.663 8G / 8G INFO General (kmer_splitters.hpp : 289) Processed 10770791 reads 0:02:20.573 8G / 8G INFO General (kmer_splitters.hpp : 289) Processed 12278290 reads 0:02:21.340 8G / 8G INFO General (kmer_splitters.hpp : 289) Processed 13632267 reads 0:02:23.907 8G / 8G INFO General (kmer_splitters.hpp : 289) Processed 18207341 reads 0:02:32.868 8G / 8G INFO General (kmer_splitters.hpp : 289) Processed 34668908 reads 0:02:40.422 8G / 8G INFO General (kmer_splitters.hpp : 295) Adding contigs from previous K 0:02:40.634 64M / 8G INFO General (kmer_splitters.hpp : 308) Used 48741850 reads 0:02:40.634 64M / 8G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:02:51.212 64M / 8G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 83860711 kmers in total. 0:02:51.212 64M / 8G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:03:25.110 64M / 8G INFO General (stage.cpp : 101) PROCEDURE == Extension index construction 0:03:25.111 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:03:25.111 64M / 8G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 256 files using 16 threads. This might take a while. 0:03:25.112 64M / 8G INFO General (file_limit.hpp : 32) Open file limit set to 131072 0:03:25.112 64M / 8G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 5.20703 Gb 0:03:25.112 64M / 8G INFO General (kmer_splitters.hpp : 97) Using cell size of 131072 0:03:39.779 8G / 8G INFO General (kmer_splitters.hpp : 380) Processed 39738438 kmers 0:03:46.222 8G / 8G INFO General (kmer_splitters.hpp : 380) Processed 79310383 kmers 0:03:46.943 8G / 8G INFO General (kmer_splitters.hpp : 380) Processed 83860743 kmers 0:03:46.943 8G / 8G INFO General (kmer_splitters.hpp : 385) Used 83860743 kmers. 0:03:47.252 64M / 8G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:03:56.939 64M / 8G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 82672651 kmers in total. 0:03:56.939 64M / 8G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:04:28.945 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:04:30.740 68M / 8G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 0:04:38.300 68M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 38343288 bytes occupied (3.71037 bits per kmer). 0:04:38.398 148M / 8G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 99) Building k-mer extensions from k+1-mers 0:04:44.578 148M / 8G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 103) Building k-mer extensions from k+1-mers finished. 0:04:44.583 148M / 8G INFO General (stage.cpp : 101) PROCEDURE == Early tip clipping 0:04:44.583 148M / 8G INFO General (construction.cpp : 253) Early tip clipper length bound set as (RL - K) 0:04:44.583 148M / 8G INFO Early tip clipping (early_simplification.hpp : 181) Early tip clipping 0:04:56.568 148M / 8G INFO Early tip clipping (early_simplification.hpp : 184) 18051677 34-mers were removed by early tip clipper 0:04:56.568 148M / 8G INFO General (stage.cpp : 101) PROCEDURE == Condensing graph 0:04:56.573 148M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 355) Extracting unbranching paths 0:05:03.339 408M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 374) Extracting unbranching paths finished. 4113421 sequences extracted 0:05:06.197 408M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 310) Collecting perfect loops 0:05:07.884 408M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 343) Collecting perfect loops finished. 145 loops collected 0:05:09.905 1G / 8G INFO General (stage.cpp : 101) PROCEDURE == Filling coverage indices (PHM) 0:05:09.905 1G / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:05:09.905 1G / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:05:11.684 1G / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 38894400 bytes occupied (3.71038 bits per kmer). 0:05:11.877 1G / 8G INFO General (construction.cpp : 388) Collecting k-mer coverage information from reads, this takes a while. 0:05:40.174 1G / 8G INFO General (construction.cpp : 508) Filling coverage and flanking coverage from PHM 0:05:44.865 1G / 8G INFO General (construction.cpp : 464) Processed 8226896 edges 0:05:46.236 1G / 8G INFO StageManager (stage.cpp : 132) STAGE == EC Threshold Finding 0:05:53.907 1G / 8G INFO ThresholdFinder (ec_threshold_finder.hpp : 114) Bucket size: 10 0:05:53.908 1G / 8G INFO General (genomic_info_filler.cpp : 98) Average edge coverage: 17.8764 0:05:53.908 1G / 8G INFO General (genomic_info_filler.cpp : 99) Graph threshold: 200 0:06:10.031 1G / 8G INFO General (genomic_info_filler.cpp : 127) EC coverage threshold value was calculated as 17.8764 0:06:10.031 1G / 8G INFO General (genomic_info_filler.cpp : 128) Trusted kmer low bound: 0 0:06:10.031 1G / 8G INFO StageManager (stage.cpp : 132) STAGE == Raw Simplification 0:06:10.031 1G / 8G INFO General (simplification.cpp : 128) PROCEDURE == InitialCleaning 0:06:10.031 1G / 8G INFO General (graph_simplification.hpp : 662) Flanking coverage based disconnection disabled 0:06:10.031 1G / 8G INFO Simplification (parallel_processing.hpp : 165) Running Self conjugate edge remover 0:06:10.283 1G / 8G INFO Simplification (parallel_processing.hpp : 167) Self conjugate edge remover triggered 0 times 0:06:10.284 1G / 8G INFO Simplification (parallel_processing.hpp : 165) Running Remover of short poly-AT edges 0:06:10.284 1G / 8G INFO General (simplification.cpp : 76) Removing short polyAT 0:06:14.827 1G / 8G INFO Simplification (parallel_processing.hpp : 167) Remover of short poly-AT edges triggered 76743 times 0:06:14.827 1G / 8G INFO Simplification (parallel_processing.hpp : 165) Running Short PolyA/T Edges 0:06:15.179 1G / 8G INFO Simplification (parallel_processing.hpp : 167) Short PolyA/T Edges triggered 0 times 0:06:15.179 1G / 8G INFO Simplification (parallel_processing.hpp : 165) Running AT Tips 0:06:16.472 1G / 8G INFO Simplification (parallel_processing.hpp : 167) AT Tips triggered 117707 times 0:06:16.472 1G / 8G INFO General (graph_simplification.hpp : 701) Removing loops and rc loops with erroneous connections 0:06:27.001 1G / 8G INFO ECLoopRemover (erroneous_connection_remov: 440) Loops: accurately removed/deadend removed/other: 0/291/8 0:06:27.001 1G / 8G INFO ECLoopRemover (erroneous_connection_remov: 441) RC loops: accurately removed/deadend removed/other: 0/85/215 0:06:27.015 1G / 8G INFO StageManager (stage.cpp : 132) STAGE == Simplification 0:06:27.015 1G / 8G INFO General (simplification.cpp : 357) Graph simplification started 0:06:27.015 1G / 8G INFO General (graph_simplification.hpp : 634) Creating parallel br instance 0:06:27.015 1G / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 1 0:06:27.015 1G / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:06:27.565 1G / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 14777 times 0:06:27.565 1G / 8G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:06:29.336 1G / 8G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 163908 times 0:06:29.336 1G / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:07:24.325 1G / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 35559 times 0:07:24.325 1G / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:07:24.550 1G / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 111 times 0:07:24.551 1G / 8G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:07:24.704 1G / 8G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 780 times 0:07:24.704 1G / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:07:24.969 1G / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 7 times 0:07:24.969 1G / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:07:24.970 1G / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:07:24.970 1G / 8G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:07:24.970 1G / 8G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times 0:07:24.970 1G / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:07:24.970 1G / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:07:24.970 1G / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:08:12.243 1G / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 1122595 times 0:08:12.243 1G / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 2 0:08:12.243 1G / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:08:12.636 1G / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 8436 times 0:08:12.637 1G / 8G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:08:13.055 1G / 8G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 10535 times 0:08:13.055 1G / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:08:36.434 1G / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 26301 times 0:08:36.434 1G / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:08:36.466 1G / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 20 times 0:08:36.466 1G / 8G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:08:36.489 1G / 8G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times 0:08:36.489 1G / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:08:36.489 1G / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:08:36.489 1G / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:08:36.489 1G / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:08:36.489 1G / 8G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:08:36.489 1G / 8G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times 0:08:36.489 1G / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:08:36.489 1G / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:08:36.489 1G / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:08:38.605 1G / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 61512 times 0:08:38.605 1G / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 3 0:08:38.605 1G / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:08:38.741 1G / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 711 times 0:08:38.741 1G / 8G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:08:38.853 1G / 8G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 33 times 0:08:38.853 1G / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:08:45.190 1G / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 4530 times 0:08:45.190 1G / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:08:45.198 1G / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:08:45.198 1G / 8G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:08:45.203 1G / 8G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times 0:08:45.203 1G / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:08:45.203 1G / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:08:45.203 1G / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:08:45.884 1G / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 20435 times 0:08:45.884 1G / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 4 0:08:45.884 1G / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:08:45.993 1G / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 330 times 0:08:45.993 1G / 8G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:08:46.092 1G / 8G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 13 times 0:08:46.092 1G / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:08:49.910 1G / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 1752 times 0:08:49.910 1G / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:08:49.913 1G / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:08:49.913 1G / 8G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:08:49.916 1G / 8G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times 0:08:49.916 1G / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:08:49.916 1G / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:08:49.916 1G / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:08:50.298 1G / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 10007 times 0:08:50.298 1G / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 5 0:08:50.298 1G / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:08:50.415 1G / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 240 times 0:08:50.415 1G / 8G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:08:50.509 1G / 8G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 6 times 0:08:50.510 1G / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:08:53.206 1G / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 844 times 0:08:53.206 1G / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:08:53.208 1G / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:08:53.208 1G / 8G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:08:53.209 1G / 8G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times 0:08:53.209 1G / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:08:53.209 1G / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:08:53.209 1G / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:08:53.475 1G / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 6114 times 0:08:53.475 1G / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 6 0:08:53.475 1G / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:08:53.577 1G / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 150 times 0:08:53.577 1G / 8G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:08:53.670 1G / 8G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times 0:08:53.670 1G / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:08:56.256 1G / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 537 times 0:08:56.256 1G / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:08:56.257 1G / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:08:56.257 1G / 8G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:08:56.258 1G / 8G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times 0:08:56.258 1G / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:08:56.258 1G / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:08:56.258 1G / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:08:56.440 1G / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 4096 times 0:08:56.440 1G / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 7 0:08:56.440 1G / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:08:56.538 1G / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 112 times 0:08:56.538 1G / 8G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:08:56.630 1G / 8G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times 0:08:56.630 1G / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:08:58.629 1G / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 285 times 0:08:58.629 1G / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:08:58.630 1G / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:08:58.630 1G / 8G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:08:58.631 1G / 8G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times 0:08:58.631 1G / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:08:58.631 1G / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:08:58.631 1G / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:08:58.775 1G / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 2832 times 0:08:58.775 1G / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 8 0:08:58.775 1G / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:08:58.872 1G / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 68 times 0:08:58.873 1G / 8G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:08:58.962 1G / 8G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times 0:08:58.963 1G / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:09:00.577 1G / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 197 times 0:09:00.577 1G / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:09:00.577 1G / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:09:00.577 1G / 8G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:09:00.578 1G / 8G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times 0:09:00.578 1G / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:09:00.578 1G / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:09:00.578 1G / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:09:00.718 1G / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 2159 times 0:09:00.718 1G / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 9 0:09:00.718 1G / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:09:00.814 1G / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 59 times 0:09:00.815 1G / 8G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:09:00.905 1G / 8G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 1 times 0:09:00.905 1G / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:09:02.514 1G / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 136 times 0:09:02.514 1G / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:09:02.515 1G / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:09:02.515 1G / 8G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:09:02.515 1G / 8G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times 0:09:02.515 1G / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:09:02.515 1G / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:09:02.515 1G / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:09:02.640 1G / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 1682 times 0:09:02.640 1G / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 10 0:09:02.640 1G / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:09:02.750 1G / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 58 times 0:09:02.750 1G / 8G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:09:02.850 1G / 8G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 1 times 0:09:02.851 1G / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:09:04.385 1G / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 110 times 0:09:04.385 1G / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:09:04.386 1G / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:09:04.386 1G / 8G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:09:04.386 1G / 8G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times 0:09:04.386 1G / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:09:04.386 1G / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:09:04.386 1G / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:09:04.509 1G / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 1331 times 0:09:04.509 1G / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 11 0:09:04.509 1G / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:09:04.630 1G / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 39 times 0:09:04.630 1G / 8G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:09:04.729 1G / 8G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 1 times 0:09:04.729 1G / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:09:06.176 1G / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 78 times 0:09:06.176 1G / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:09:06.176 1G / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:09:06.176 1G / 8G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:09:06.177 1G / 8G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times 0:09:06.177 1G / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:09:06.177 1G / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:09:06.177 1G / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:09:06.272 1G / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:09:06.272 1G / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 12 0:09:06.272 1G / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:09:06.272 1G / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:09:06.273 1G / 8G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:09:06.273 1G / 8G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times 0:09:06.273 1G / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:09:06.273 1G / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:09:06.273 1G / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:09:06.273 1G / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:09:06.274 1G / 8G INFO StageManager (stage.cpp : 132) STAGE == Simplification Cleanup 0:09:06.274 1G / 8G INFO General (simplification.cpp : 196) PROCEDURE == Post simplification 0:09:06.274 1G / 8G INFO General (graph_simplification.hpp : 453) Disconnection of relatively low covered edges disabled 0:09:06.274 1G / 8G INFO General (graph_simplification.hpp : 489) Complex tip clipping disabled 0:09:06.274 1G / 8G INFO General (graph_simplification.hpp : 634) Creating parallel br instance 0:09:06.274 1G / 8G INFO General (graph_simplification.hpp : 634) Creating parallel br instance 0:09:06.274 1G / 8G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover 0:09:06.527 1G / 8G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 7091 times 0:09:06.527 1G / 8G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover 0:09:07.138 1G / 8G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 21833 times 0:09:07.138 1G / 8G INFO Simplification (parallel_processing.hpp : 165) Running Complex bulge remover 0:09:09.442 1G / 8G INFO Simplification (parallel_processing.hpp : 167) Complex bulge remover triggered 45 times 0:09:09.442 1G / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:09:09.544 1G / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 83 times 0:09:09.545 1G / 8G INFO Simplification (parallel_processing.hpp : 165) Running Final tip clipper 0:09:09.972 1G / 8G INFO Simplification (parallel_processing.hpp : 167) Final tip clipper triggered 22262 times 0:09:09.972 1G / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:09:10.941 1G / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 590 times 0:09:10.941 1G / 8G INFO Simplification (parallel_processing.hpp : 165) Running Final bulge remover 0:09:11.653 1G / 8G INFO Simplification (parallel_processing.hpp : 167) Final bulge remover triggered 0 times 0:09:11.653 1G / 8G INFO Simplification (parallel_processing.hpp : 165) Running AT Tips 0:09:11.765 1G / 8G INFO Simplification (parallel_processing.hpp : 167) AT Tips triggered 1397 times 0:09:11.765 1G / 8G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover 0:09:11.899 1G / 8G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 1146 times 0:09:11.899 1G / 8G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover 0:09:12.038 1G / 8G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 905 times 0:09:12.038 1G / 8G INFO Simplification (parallel_processing.hpp : 165) Running Complex bulge remover 0:09:14.176 1G / 8G INFO Simplification (parallel_processing.hpp : 167) Complex bulge remover triggered 3 times 0:09:14.176 1G / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:09:14.280 1G / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:09:14.280 1G / 8G INFO Simplification (parallel_processing.hpp : 165) Running Final tip clipper 0:09:14.359 1G / 8G INFO Simplification (parallel_processing.hpp : 167) Final tip clipper triggered 110 times 0:09:14.359 1G / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:09:14.908 1G / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 40 times 0:09:14.908 1G / 8G INFO Simplification (parallel_processing.hpp : 165) Running Final bulge remover 0:09:15.409 1G / 8G INFO Simplification (parallel_processing.hpp : 167) Final bulge remover triggered 0 times 0:09:15.409 1G / 8G INFO Simplification (parallel_processing.hpp : 165) Running AT Tips 0:09:15.507 1G / 8G INFO Simplification (parallel_processing.hpp : 167) AT Tips triggered 229 times 0:09:15.507 1G / 8G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover 0:09:15.509 1G / 8G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 30 times 0:09:15.509 1G / 8G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover 0:09:15.627 1G / 8G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 32 times 0:09:15.627 1G / 8G INFO Simplification (parallel_processing.hpp : 165) Running Complex bulge remover 0:09:17.830 1G / 8G INFO Simplification (parallel_processing.hpp : 167) Complex bulge remover triggered 0 times 0:09:17.831 1G / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:09:17.831 1G / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:09:17.831 1G / 8G INFO Simplification (parallel_processing.hpp : 165) Running Final tip clipper 0:09:17.832 1G / 8G INFO Simplification (parallel_processing.hpp : 167) Final tip clipper triggered 0 times 0:09:17.832 1G / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:09:17.833 1G / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:09:17.833 1G / 8G INFO Simplification (parallel_processing.hpp : 165) Running Final bulge remover 0:09:17.833 1G / 8G INFO Simplification (parallel_processing.hpp : 167) Final bulge remover triggered 0 times 0:09:17.833 1G / 8G INFO Simplification (parallel_processing.hpp : 165) Running AT Tips 0:09:17.833 1G / 8G INFO Simplification (parallel_processing.hpp : 167) AT Tips triggered 0 times 0:09:17.833 1G / 8G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover 0:09:17.833 1G / 8G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 0 times 0:09:17.833 1G / 8G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover 0:09:17.948 1G / 8G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 0 times 0:09:17.949 1G / 8G INFO Simplification (parallel_processing.hpp : 165) Running Complex bulge remover 0:09:20.162 1G / 8G INFO Simplification (parallel_processing.hpp : 167) Complex bulge remover triggered 0 times 0:09:20.163 1G / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:09:20.163 1G / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:09:20.163 1G / 8G INFO Simplification (parallel_processing.hpp : 165) Running Final tip clipper 0:09:20.163 1G / 8G INFO Simplification (parallel_processing.hpp : 167) Final tip clipper triggered 0 times 0:09:20.163 1G / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:09:20.163 1G / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:09:20.164 1G / 8G INFO Simplification (parallel_processing.hpp : 165) Running Final bulge remover 0:09:20.164 1G / 8G INFO Simplification (parallel_processing.hpp : 167) Final bulge remover triggered 0 times 0:09:20.164 1G / 8G INFO Simplification (parallel_processing.hpp : 165) Running AT Tips 0:09:20.164 1G / 8G INFO Simplification (parallel_processing.hpp : 167) AT Tips triggered 0 times 0:09:20.164 1G / 8G INFO General (simplification.cpp : 330) Disrupting self-conjugate edges 0:09:20.713 1G / 8G INFO General (simplification.cpp : 470) Counting average coverage 0:09:21.004 1G / 8G INFO General (simplification.cpp : 476) Average coverage = 35.2345 0:09:21.004 1G / 8G INFO StageManager (stage.cpp : 132) STAGE == Contig Output 0:09:21.004 1G / 8G 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-Voromonas_pontica_cDNA_sequencing-SRX973460//K33/assembly_graph_with_scaffolds.gfa 0:09:22.436 1G / 8G 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-Voromonas_pontica_cDNA_sequencing-SRX973460//K33/before_rr.fasta 0:09:23.958 1G / 8G 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-Voromonas_pontica_cDNA_sequencing-SRX973460//K33/assembly_graph.fastg 0:09:27.465 1G / 8G 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-Voromonas_pontica_cDNA_sequencing-SRX973460//K33/simplified_contigs.fasta 0:09:29.018 1G / 8G 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-Voromonas_pontica_cDNA_sequencing-SRX973460//K33/final_contigs.fasta 0:09:30.520 1G / 8G INFO StageManager (stage.cpp : 132) STAGE == Contig Output 0:09:30.520 1G / 8G 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-Voromonas_pontica_cDNA_sequencing-SRX973460//K33/assembly_graph_with_scaffolds.gfa 0:09:32.799 1G / 8G 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-Voromonas_pontica_cDNA_sequencing-SRX973460//K33/before_rr.fasta 0:09:34.328 1G / 8G 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-Voromonas_pontica_cDNA_sequencing-SRX973460//K33/assembly_graph.fastg 0:09:37.670 1G / 8G 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-Voromonas_pontica_cDNA_sequencing-SRX973460//K33/simplified_contigs.fasta 0:09:39.196 1G / 8G 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-Voromonas_pontica_cDNA_sequencing-SRX973460//K33/final_contigs.fasta 0:09:40.725 1G / 8G INFO General (launch.hpp : 149) SPAdes finished 0:09:42.790 64M / 8G INFO General (main.cpp : 109) Assembling time: 0 hours 9 minutes 42 seconds Max read length detected as 100 == Running assembler: K49 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-Voromonas_pontica_cDNA_sequencing-SRX973460/K49/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-Voromonas_pontica_cDNA_sequencing-SRX973460/K49/configs/mda_mode.info 0:00:00.000 4M / 4M INFO General (main.cpp : 74) Loaded config from /oak/stanford/groups/akundaje/marinovg/various/MMETSP/2018-11-19-trans-splicing/SPAdes-3.13-RNA-Trimmomatic-Voromonas_pontica_cDNA_sequencing-SRX973460/K49/configs/rna_mode.info 0:00:00.000 4M / 4M INFO General (memory_limit.cpp : 49) Memory limit set to 250 Gb 0:00:00.000 4M / 4M INFO General (main.cpp : 87) Starting SPAdes, built from refs/heads/spades_3.13.0, git revision 8ea46659e9b2aca35444a808db550ac333006f8b 0:00:00.000 4M / 4M INFO General (main.cpp : 88) Maximum k-mer length: 128 0:00:00.000 4M / 4M INFO General (main.cpp : 89) Assembling dataset (/oak/stanford/groups/akundaje/marinovg/various/MMETSP/2018-11-19-trans-splicing/SPAdes-3.13-RNA-Trimmomatic-Voromonas_pontica_cDNA_sequencing-SRX973460/dataset.info) with K=49 0:00:00.000 4M / 4M INFO General (main.cpp : 90) Maximum # of threads to use (adjusted due to OMP capabilities): 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 0:00:00.030 4M / 4M INFO General (read_converter.hpp : 59) Binary reads detected 0:00:00.043 4M / 4M INFO General (read_converter.hpp : 59) Binary reads detected 0:00:00.055 4M / 4M INFO General (read_converter.hpp : 59) Binary reads detected 0:00:00.068 4M / 4M INFO General (construction.cpp : 111) Max read length 100 0:00:00.068 4M / 4M INFO General (construction.cpp : 117) Average read length 82.0988 0:00:00.068 4M / 4M INFO General (stage.cpp : 101) PROCEDURE == k+1-mer counting 0:00:00.069 4M / 4M INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 256 files using 16 threads. This might take a while. 0:00:00.070 4M / 4M INFO General (file_limit.hpp : 32) Open file limit set to 131072 0:00:00.070 4M / 4M INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 5.20825 Gb 0:00:00.070 4M / 4M INFO General (kmer_splitters.hpp : 97) Using cell size of 131072 0:00:15.408 8G / 8G INFO General (kmer_splitters.hpp : 289) Processed 3061299 reads 0:00:16.525 8G / 8G INFO General (kmer_splitters.hpp : 289) Processed 5667505 reads 0:00:17.504 8G / 8G INFO General (kmer_splitters.hpp : 289) Processed 8236819 reads 0:00:18.562 8G / 8G INFO General (kmer_splitters.hpp : 289) Processed 11092197 reads 0:00:19.571 8G / 8G INFO General (kmer_splitters.hpp : 289) Processed 13661893 reads 0:00:20.703 8G / 8G INFO General (kmer_splitters.hpp : 289) Processed 16406629 reads 0:00:21.863 8G / 8G INFO General (kmer_splitters.hpp : 289) Processed 19136936 reads 0:00:22.811 8G / 8G INFO General (kmer_splitters.hpp : 289) Processed 21566883 reads 0:00:23.996 8G / 8G INFO General (kmer_splitters.hpp : 289) Processed 24802858 reads 0:00:25.152 8G / 8G INFO General (kmer_splitters.hpp : 289) Processed 27695207 reads 0:00:27.548 8G / 8G INFO General (kmer_splitters.hpp : 289) Processed 34552130 reads 0:00:34.913 8G / 8G INFO General (kmer_splitters.hpp : 295) Adding contigs from previous K 0:00:40.561 64M / 8G INFO General (kmer_splitters.hpp : 308) Used 48741850 reads 0:00:40.562 64M / 8G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:00:49.296 64M / 8G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 89398712 kmers in total. 0:00:49.296 64M / 8G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:01:25.230 64M / 8G INFO General (stage.cpp : 101) PROCEDURE == Extension index construction 0:01:25.230 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:01:25.230 64M / 8G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 256 files using 16 threads. This might take a while. 0:01:25.231 64M / 8G INFO General (file_limit.hpp : 32) Open file limit set to 131072 0:01:25.231 64M / 8G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 5.20703 Gb 0:01:25.231 64M / 8G INFO General (kmer_splitters.hpp : 97) Using cell size of 131072 0:01:41.636 8G / 8G INFO General (kmer_splitters.hpp : 380) Processed 22323280 kmers 0:01:49.372 8G / 8G INFO General (kmer_splitters.hpp : 380) Processed 44270703 kmers 0:01:52.178 8G / 8G INFO General (kmer_splitters.hpp : 380) Processed 66441371 kmers 0:01:54.615 8G / 8G INFO General (kmer_splitters.hpp : 380) Processed 88617772 kmers 0:01:54.974 8G / 8G INFO General (kmer_splitters.hpp : 380) Processed 89398772 kmers 0:01:54.974 8G / 8G INFO General (kmer_splitters.hpp : 385) Used 89398772 kmers. 0:01:55.265 64M / 8G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:02:07.625 64M / 8G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 89536936 kmers in total. 0:02:07.625 64M / 8G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:02:41.475 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:02:43.549 68M / 8G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 0:02:53.139 68M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 41526680 bytes occupied (3.71035 bits per kmer). 0:02:53.226 156M / 8G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 99) Building k-mer extensions from k+1-mers 0:02:59.419 156M / 8G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 103) Building k-mer extensions from k+1-mers finished. 0:02:59.421 156M / 8G INFO General (stage.cpp : 101) PROCEDURE == Condensing graph 0:02:59.434 156M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 355) Extracting unbranching paths 0:03:08.107 516M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 374) Extracting unbranching paths finished. 5420837 sequences extracted 0:03:12.499 516M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 310) Collecting perfect loops 0:03:14.222 516M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 343) Collecting perfect loops finished. 27 loops collected 0:03:16.797 1G / 8G INFO General (stage.cpp : 101) PROCEDURE == Filling coverage indices (PHM) 0:03:16.797 1G / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:03:16.797 1G / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:03:18.652 1G / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 41462440 bytes occupied (3.71034 bits per kmer). 0:03:18.912 2G / 8G INFO General (construction.cpp : 388) Collecting k-mer coverage information from reads, this takes a while. 0:03:40.965 2G / 8G INFO General (construction.cpp : 508) Filling coverage and flanking coverage from PHM 0:03:47.201 2G / 8G INFO General (construction.cpp : 464) Processed 10841579 edges 0:03:48.174 1G / 8G INFO StageManager (stage.cpp : 132) STAGE == EC Threshold Finding 0:03:56.964 1G / 8G INFO ThresholdFinder (ec_threshold_finder.hpp : 114) Bucket size: 7 0:03:56.964 1G / 8G INFO General (genomic_info_filler.cpp : 98) Average edge coverage: 9.15243 0:03:56.964 1G / 8G INFO General (genomic_info_filler.cpp : 99) Graph threshold: 183 0:04:05.241 1G / 8G INFO General (genomic_info_filler.cpp : 127) EC coverage threshold value was calculated as 9.15243 0:04:05.241 1G / 8G INFO General (genomic_info_filler.cpp : 128) Trusted kmer low bound: 0 0:04:05.241 1G / 8G INFO StageManager (stage.cpp : 132) STAGE == Gap Closer 0:04:05.241 1G / 8G INFO General (graph_pack.hpp : 101) Index refill 0:04:05.242 1G / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:04:05.242 1G / 8G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 256 files using 16 threads. This might take a while. 0:04:05.243 1G / 8G INFO General (file_limit.hpp : 32) Open file limit set to 131072 0:04:05.243 1G / 8G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 5.16756 Gb 0:04:05.243 1G / 8G INFO General (kmer_splitters.hpp : 97) Using cell size of 131072 0:04:17.214 10G / 10G INFO General (edge_index_builders.hpp : 77) Processed 10841579 edges 0:04:17.214 10G / 10G INFO General (edge_index_builders.hpp : 82) Used 10841579 sequences. 0:04:17.519 1G / 10G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:04:27.633 1G / 10G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 89398712 kmers in total. 0:04:27.633 1G / 10G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:04:58.995 1G / 10G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:05:01.176 2G / 10G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 0:05:08.634 2G / 10G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 41462440 bytes occupied (3.71034 bits per kmer). 0:05:09.912 4G / 10G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while. 0:05:14.089 4G / 10G INFO General (edge_index.hpp : 92) Index refilled 0:05:14.093 4G / 10G INFO General (gap_closer.cpp : 159) Preparing shift maps 0:05:22.791 4G / 10G INFO General (gap_closer.cpp : 119) Processing paired reads (takes a while) 0:05:49.434 4G / 10G INFO General (gap_closer.cpp : 138) Used 10912078 paired reads 0:05:49.434 4G / 10G INFO General (gap_closer.cpp : 140) Merging paired indices 0:05:51.690 4G / 10G INFO GapCloser (gap_closer.cpp : 346) Closing short gaps 0:06:08.215 4G / 10G INFO GapCloser (gap_closer.cpp : 380) Closing short gaps complete: filled 4711 gaps after checking 80587 candidates 0:06:09.536 4G / 10G INFO StageManager (stage.cpp : 132) STAGE == Raw Simplification 0:06:09.787 1G / 10G INFO General (simplification.cpp : 128) PROCEDURE == InitialCleaning 0:06:09.787 1G / 10G INFO General (graph_simplification.hpp : 662) Flanking coverage based disconnection disabled 0:06:09.787 1G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Self conjugate edge remover 0:06:10.238 1G / 10G INFO Simplification (parallel_processing.hpp : 167) Self conjugate edge remover triggered 0 times 0:06:10.238 1G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Remover of short poly-AT edges 0:06:10.238 1G / 10G INFO General (simplification.cpp : 76) Removing short polyAT 0:06:16.838 1G / 10G INFO Simplification (parallel_processing.hpp : 167) Remover of short poly-AT edges triggered 76176 times 0:06:16.838 1G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Short PolyA/T Edges 0:06:17.300 1G / 10G INFO Simplification (parallel_processing.hpp : 167) Short PolyA/T Edges triggered 0 times 0:06:17.301 1G / 10G INFO Simplification (parallel_processing.hpp : 165) Running AT Tips 0:06:21.679 1G / 10G INFO Simplification (parallel_processing.hpp : 167) AT Tips triggered 378199 times 0:06:21.679 1G / 10G INFO General (graph_simplification.hpp : 701) Removing loops and rc loops with erroneous connections 0:06:36.149 1G / 10G INFO ECLoopRemover (erroneous_connection_remov: 440) Loops: accurately removed/deadend removed/other: 1/121/4 0:06:36.149 1G / 10G INFO ECLoopRemover (erroneous_connection_remov: 441) RC loops: accurately removed/deadend removed/other: 0/60/92 0:06:36.196 1G / 10G INFO StageManager (stage.cpp : 132) STAGE == Simplification 0:06:36.196 1G / 10G INFO General (simplification.cpp : 357) Graph simplification started 0:06:36.196 1G / 10G INFO General (graph_simplification.hpp : 634) Creating parallel br instance 0:06:36.197 1G / 10G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 1 0:06:36.197 1G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:06:52.275 2G / 10G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 1262012 times 0:06:52.275 2G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:06:56.651 2G / 10G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 325308 times 0:06:56.651 2G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:07:19.448 2G / 10G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 22526 times 0:07:19.448 2G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:07:19.626 2G / 10G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 329 times 0:07:19.626 2G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:07:19.696 2G / 10G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 40 times 0:07:19.696 2G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:07:19.698 2G / 10G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:07:19.698 2G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:07:19.698 2G / 10G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:07:19.698 2G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:07:19.698 2G / 10G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times 0:07:19.698 2G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:07:19.698 2G / 10G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:07:19.698 2G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:07:33.654 2G / 10G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 337706 times 0:07:33.654 2G / 10G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 2 0:07:33.654 2G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:07:34.192 2G / 10G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 14076 times 0:07:34.192 2G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:07:34.549 2G / 10G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 6876 times 0:07:34.549 2G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:07:50.901 2G / 10G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 13908 times 0:07:50.901 2G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:07:50.927 2G / 10G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 19 times 0:07:50.927 2G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:07:50.946 2G / 10G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times 0:07:50.946 2G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:07:50.947 2G / 10G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:07:50.947 2G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:07:50.947 2G / 10G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:07:50.947 2G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:07:50.947 2G / 10G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times 0:07:50.947 2G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:07:50.947 2G / 10G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:07:50.947 2G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:07:51.803 2G / 10G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 22150 times 0:07:51.803 2G / 10G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 3 0:07:51.803 2G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:07:52.022 2G / 10G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 1297 times 0:07:52.022 2G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:07:52.207 2G / 10G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 13 times 0:07:52.207 2G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:07:55.838 2G / 10G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 1950 times 0:07:55.838 2G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:07:55.843 2G / 10G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:07:55.843 2G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:07:55.847 2G / 10G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times 0:07:55.847 2G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:07:55.847 2G / 10G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:07:55.847 2G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:07:56.280 2G / 10G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 8261 times 0:07:56.280 2G / 10G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 4 0:07:56.280 2G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:07:56.500 2G / 10G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 444 times 0:07:56.500 2G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:07:56.681 2G / 10G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 2 times 0:07:56.681 2G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:07:58.689 2G / 10G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 703 times 0:07:58.689 2G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:07:58.691 2G / 10G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:07:58.691 2G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:07:58.693 2G / 10G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times 0:07:58.693 2G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:07:58.693 2G / 10G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:07:58.693 2G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:07:58.970 2G / 10G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 4463 times 0:07:58.970 2G / 10G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 5 0:07:58.970 2G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:07:59.163 2G / 10G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 246 times 0:07:59.163 2G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:07:59.340 2G / 10G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times 0:07:59.341 2G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:08:00.843 2G / 10G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 296 times 0:08:00.843 2G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:08:00.844 2G / 10G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:08:00.844 2G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:08:00.846 2G / 10G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times 0:08:00.846 2G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:08:00.846 2G / 10G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:08:00.846 2G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:08:01.087 2G / 10G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 2877 times 0:08:01.087 2G / 10G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 6 0:08:01.087 2G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:08:01.271 2G / 10G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 152 times 0:08:01.271 2G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:08:01.449 2G / 10G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 1 times 0:08:01.449 2G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:08:02.651 2G / 10G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 174 times 0:08:02.651 2G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:08:02.652 2G / 10G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:08:02.652 2G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:08:02.653 2G / 10G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times 0:08:02.653 2G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:08:02.653 2G / 10G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:08:02.653 2G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:08:02.865 2G / 10G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 1995 times 0:08:02.865 2G / 10G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 7 0:08:02.865 2G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:08:03.068 2G / 10G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 121 times 0:08:03.068 2G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:08:03.247 2G / 10G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times 0:08:03.247 2G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:08:04.336 2G / 10G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 102 times 0:08:04.336 2G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:08:04.336 2G / 10G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:08:04.336 2G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:08:04.337 2G / 10G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times 0:08:04.337 2G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:08:04.337 2G / 10G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:08:04.337 2G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:08:04.550 2G / 10G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 1499 times 0:08:04.550 2G / 10G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 8 0:08:04.550 2G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:08:04.750 2G / 10G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 81 times 0:08:04.750 2G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:08:04.929 2G / 10G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times 0:08:04.930 2G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:08:05.864 2G / 10G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 40 times 0:08:05.864 2G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:08:05.864 2G / 10G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:08:05.864 2G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:08:05.864 2G / 10G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times 0:08:05.864 2G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:08:05.864 2G / 10G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:08:05.864 2G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:08:06.051 2G / 10G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 1119 times 0:08:06.051 2G / 10G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 9 0:08:06.051 2G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:08:06.241 2G / 10G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 61 times 0:08:06.241 2G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:08:06.421 2G / 10G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 1 times 0:08:06.421 2G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:08:07.266 2G / 10G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 27 times 0:08:07.266 2G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:08:07.266 2G / 10G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:08:07.266 2G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:08:07.267 2G / 10G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times 0:08:07.267 2G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:08:07.267 2G / 10G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:08:07.267 2G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:08:07.439 2G / 10G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 867 times 0:08:07.439 2G / 10G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 10 0:08:07.439 2G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:08:07.629 2G / 10G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 51 times 0:08:07.629 2G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:08:07.805 2G / 10G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times 0:08:07.805 2G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:08:08.626 2G / 10G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 22 times 0:08:08.626 2G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:08:08.626 2G / 10G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:08:08.626 2G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:08:08.627 2G / 10G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times 0:08:08.627 2G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:08:08.627 2G / 10G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:08:08.627 2G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:08:08.794 2G / 10G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 708 times 0:08:08.794 2G / 10G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 11 0:08:08.794 2G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:08:08.982 2G / 10G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 47 times 0:08:08.982 2G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:08:09.158 2G / 10G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times 0:08:09.158 2G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:08:09.951 2G / 10G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 16 times 0:08:09.951 2G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:08:09.951 2G / 10G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:08:09.951 2G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:08:09.952 2G / 10G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times 0:08:09.952 2G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:08:09.952 2G / 10G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:08:09.952 2G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:08:10.104 2G / 10G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:08:10.104 2G / 10G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 12 0:08:10.105 2G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:08:10.105 2G / 10G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:08:10.105 2G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:08:10.105 2G / 10G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times 0:08:10.105 2G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:08:10.106 2G / 10G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:08:10.106 2G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:08:10.106 2G / 10G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:08:10.106 2G / 10G INFO StageManager (stage.cpp : 132) STAGE == Gap Closer 0:08:10.106 2G / 10G INFO General (graph_pack.hpp : 101) Index refill 0:08:10.107 2G / 10G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:08:10.107 2G / 10G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 256 files using 16 threads. This might take a while. 0:08:10.108 2G / 10G INFO General (file_limit.hpp : 32) Open file limit set to 131072 0:08:10.108 2G / 10G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 5.16357 Gb 0:08:10.108 2G / 10G INFO General (kmer_splitters.hpp : 97) Using cell size of 131072 0:08:20.884 10G / 10G INFO General (edge_index_builders.hpp : 77) Processed 1902928 edges 0:08:20.884 10G / 10G INFO General (edge_index_builders.hpp : 82) Used 1902928 sequences. 0:08:21.086 2G / 10G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:08:28.491 2G / 10G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 40659666 kmers in total. 0:08:28.491 2G / 10G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:08:51.271 2G / 10G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:08:52.020 2G / 10G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 0:08:55.462 2G / 10G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 18864396 bytes occupied (3.71167 bits per kmer). 0:08:56.495 3G / 10G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while. 0:08:58.037 3G / 10G INFO General (edge_index.hpp : 92) Index refilled 0:08:58.040 3G / 10G INFO General (gap_closer.cpp : 159) Preparing shift maps 0:09:00.620 3G / 10G INFO General (gap_closer.cpp : 119) Processing paired reads (takes a while) 0:09:28.144 3G / 10G INFO General (gap_closer.cpp : 138) Used 10912078 paired reads 0:09:28.145 3G / 10G INFO General (gap_closer.cpp : 140) Merging paired indices 0:09:29.644 3G / 10G INFO GapCloser (gap_closer.cpp : 346) Closing short gaps 0:09:33.068 3G / 10G INFO GapCloser (gap_closer.cpp : 380) Closing short gaps complete: filled 826 gaps after checking 59080 candidates 0:09:33.783 3G / 10G INFO StageManager (stage.cpp : 132) STAGE == Simplification Cleanup 0:09:33.783 3G / 10G INFO General (simplification.cpp : 196) PROCEDURE == Post simplification 0:09:33.783 3G / 10G INFO General (graph_simplification.hpp : 453) Disconnection of relatively low covered edges disabled 0:09:33.783 3G / 10G INFO General (graph_simplification.hpp : 489) Complex tip clipping disabled 0:09:33.783 3G / 10G INFO General (graph_simplification.hpp : 634) Creating parallel br instance 0:09:33.783 3G / 10G INFO General (graph_simplification.hpp : 634) Creating parallel br instance 0:09:33.783 3G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover 0:09:34.153 3G / 10G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 1330 times 0:09:34.153 3G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover 0:09:40.372 3G / 10G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 87328 times 0:09:40.372 3G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Complex bulge remover 0:09:45.311 3G / 10G INFO Simplification (parallel_processing.hpp : 167) Complex bulge remover triggered 58 times 0:09:45.311 3G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:09:45.535 3G / 10G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 266 times 0:09:45.535 3G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Final tip clipper 0:10:06.493 3G / 10G INFO Simplification (parallel_processing.hpp : 167) Final tip clipper triggered 65326 times 0:10:06.493 3G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:10:08.834 3G / 10G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 1108 times 0:10:08.834 3G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Final bulge remover 0:10:09.188 3G / 10G INFO Simplification (parallel_processing.hpp : 167) Final bulge remover triggered 0 times 0:10:09.188 3G / 10G INFO Simplification (parallel_processing.hpp : 165) Running AT Tips 0:10:09.445 3G / 10G INFO Simplification (parallel_processing.hpp : 167) AT Tips triggered 1385 times 0:10:09.445 3G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover 0:10:09.706 3G / 10G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 255 times 0:10:09.706 3G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover 0:10:09.929 3G / 10G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 110 times 0:10:09.929 3G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Complex bulge remover 0:10:14.361 3G / 10G INFO Simplification (parallel_processing.hpp : 167) Complex bulge remover triggered 4 times 0:10:14.361 3G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:10:14.565 3G / 10G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 1 times 0:10:14.565 3G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Final tip clipper 0:10:14.853 3G / 10G INFO Simplification (parallel_processing.hpp : 167) Final tip clipper triggered 54 times 0:10:14.853 3G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:10:15.164 3G / 10G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 29 times 0:10:15.164 3G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Final bulge remover 0:10:15.412 3G / 10G INFO Simplification (parallel_processing.hpp : 167) Final bulge remover triggered 0 times 0:10:15.412 3G / 10G INFO Simplification (parallel_processing.hpp : 165) Running AT Tips 0:10:15.637 3G / 10G INFO Simplification (parallel_processing.hpp : 167) AT Tips triggered 11 times 0:10:15.637 3G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover 0:10:15.638 3G / 10G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 2 times 0:10:15.638 3G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover 0:10:15.800 3G / 10G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 2 times 0:10:15.800 3G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Complex bulge remover 0:10:20.074 3G / 10G INFO Simplification (parallel_processing.hpp : 167) Complex bulge remover triggered 0 times 0:10:20.074 3G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:10:20.075 3G / 10G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:10:20.075 3G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Final tip clipper 0:10:20.076 3G / 10G INFO Simplification (parallel_processing.hpp : 167) Final tip clipper triggered 1 times 0:10:20.076 3G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:10:20.080 3G / 10G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 1 times 0:10:20.080 3G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Final bulge remover 0:10:20.080 3G / 10G INFO Simplification (parallel_processing.hpp : 167) Final bulge remover triggered 0 times 0:10:20.080 3G / 10G INFO Simplification (parallel_processing.hpp : 165) Running AT Tips 0:10:20.080 3G / 10G INFO Simplification (parallel_processing.hpp : 167) AT Tips triggered 0 times 0:10:20.080 3G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover 0:10:20.080 3G / 10G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 0 times 0:10:20.080 3G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover 0:10:20.279 3G / 10G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 0 times 0:10:20.279 3G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Complex bulge remover 0:10:24.483 3G / 10G INFO Simplification (parallel_processing.hpp : 167) Complex bulge remover triggered 0 times 0:10:24.483 3G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:10:24.483 3G / 10G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:10:24.483 3G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Final tip clipper 0:10:24.483 3G / 10G INFO Simplification (parallel_processing.hpp : 167) Final tip clipper triggered 0 times 0:10:24.483 3G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:10:24.483 3G / 10G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:10:24.483 3G / 10G INFO Simplification (parallel_processing.hpp : 165) Running Final bulge remover 0:10:24.483 3G / 10G INFO Simplification (parallel_processing.hpp : 167) Final bulge remover triggered 0 times 0:10:24.483 3G / 10G INFO Simplification (parallel_processing.hpp : 165) Running AT Tips 0:10:24.483 3G / 10G INFO Simplification (parallel_processing.hpp : 167) AT Tips triggered 0 times 0:10:24.483 3G / 10G INFO General (simplification.cpp : 330) Disrupting self-conjugate edges 0:10:25.535 3G / 10G INFO General (simplification.cpp : 470) Counting average coverage 0:10:26.084 3G / 10G INFO General (simplification.cpp : 476) Average coverage = 17.5681 0:10:26.084 3G / 10G INFO StageManager (stage.cpp : 132) STAGE == Mismatch Correction 0:10:26.084 3G / 10G INFO General (graph_pack.hpp : 109) Normalizing k-mer map. Total 4149558 kmers to process 0:10:29.303 3G / 10G INFO General (graph_pack.hpp : 111) Normalizing done 0:11:21.716 3G / 10G INFO General (mismatch_shall_not_pass.hp: 189) Finished collecting potential mismatches positions 0:11:24.819 3G / 10G INFO General (mismatch_shall_not_pass.hp: 290) All edges processed 0:11:24.958 3G / 10G INFO General (mismatch_correction.cpp : 27) Corrected 92 nucleotides 0:11:24.984 3G / 10G INFO StageManager (stage.cpp : 132) STAGE == Contig Output 0:11:24.984 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-Voromonas_pontica_cDNA_sequencing-SRX973460//K49/assembly_graph_with_scaffolds.gfa 0:11:27.505 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-Voromonas_pontica_cDNA_sequencing-SRX973460//K49/before_rr.fasta 0:11:30.244 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-Voromonas_pontica_cDNA_sequencing-SRX973460//K49/assembly_graph.fastg 0:11:35.804 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-Voromonas_pontica_cDNA_sequencing-SRX973460//K49/simplified_contigs.fasta 0:11:38.601 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-Voromonas_pontica_cDNA_sequencing-SRX973460//K49/intermediate_contigs.fasta 0:11:41.368 3G / 10G INFO StageManager (stage.cpp : 132) STAGE == Paired Information Counting 0:11:54.083 3G / 10G INFO General (graph_pack.hpp : 109) Normalizing k-mer map. Total 4153432 kmers to process 0:11:56.950 3G / 10G INFO General (graph_pack.hpp : 111) Normalizing done 0:11:57.537 3G / 10G INFO General (pair_info_count.cpp : 320) Min edge length for estimation: 55 0:11:57.537 3G / 10G INFO General (pair_info_count.cpp : 331) Estimating insert size for library #0 0:11:57.537 3G / 10G INFO General (pair_info_count.cpp : 190) Estimating insert size (takes a while) 0:11:57.717 3G / 10G INFO General (pair_info_count.cpp : 39) Selecting usual mapper 0:12:03.171 3G / 10G INFO General (sequence_mapper_notifier.h: 80) Processed 200000 reads 0:12:03.199 3G / 10G INFO General (sequence_mapper_notifier.h: 80) Processed 400000 reads 0:12:03.226 3G / 10G INFO General (sequence_mapper_notifier.h: 80) Processed 600000 reads 0:12:03.275 3G / 10G INFO General (sequence_mapper_notifier.h: 80) Processed 800000 reads 0:12:03.327 3G / 10G INFO General (sequence_mapper_notifier.h: 80) Processed 1000000 reads 0:12:03.376 3G / 10G INFO General (sequence_mapper_notifier.h: 80) Processed 1200000 reads 0:12:03.989 3G / 10G INFO General (sequence_mapper_notifier.h: 80) Processed 2200000 reads 0:12:09.180 3G / 10G INFO General (sequence_mapper_notifier.h: 80) Processed 4200000 reads 0:12:17.928 3G / 10G INFO General (sequence_mapper_notifier.h: 80) Processed 8400000 reads 0:12:22.513 3G / 10G INFO General (sequence_mapper_notifier.h: 98) Total 10912078 reads processed 0:12:23.843 3G / 10G INFO General (pair_info_count.cpp : 209) Edge pairs: 67108864 (rough upper limit) 0:12:23.843 3G / 10G INFO General (pair_info_count.cpp : 213) 964801 paired reads (8.84159% of all) aligned to long edges 0:12:23.892 3G / 10G INFO General (pair_info_count.cpp : 354) Insert size = 271.664, deviation = 88.3692, left quantile = 139, right quantile = 362, read length = 100 0:12:23.892 3G / 10G INFO General (pair_info_count.cpp : 383) Mapping library #0 0:12:23.892 3G / 10G INFO General (pair_info_count.cpp : 385) Mapping paired reads (takes a while) 0:12:23.892 3G / 10G INFO General (pair_info_count.cpp : 289) Left insert size quantile 139, right insert size quantile 362, filtering threshold 0, rounding threshold 0 0:12:23.911 3G / 10G INFO General (pair_info_count.cpp : 39) Selecting usual mapper 0:12:54.269 3G / 10G INFO General (sequence_mapper_notifier.h: 80) Processed 200000 reads 0:12:54.350 3G / 10G INFO General (sequence_mapper_notifier.h: 80) Processed 400000 reads 0:12:54.519 4G / 10G INFO General (sequence_mapper_notifier.h: 80) Processed 600000 reads 0:12:54.570 3G / 10G INFO General (sequence_mapper_notifier.h: 80) Processed 800000 reads 0:12:54.665 4G / 10G INFO General (sequence_mapper_notifier.h: 80) Processed 1000000 reads 0:12:55.487 4G / 10G INFO General (sequence_mapper_notifier.h: 80) Processed 1200000 reads 0:12:57.467 4G / 10G INFO General (sequence_mapper_notifier.h: 80) Processed 2200000 reads 0:13:26.339 4G / 10G INFO General (sequence_mapper_notifier.h: 80) Processed 4200000 reads 0:13:50.858 4G / 10G INFO General (sequence_mapper_notifier.h: 80) Processed 8400000 reads 0:14:03.070 4G / 10G INFO General (sequence_mapper_notifier.h: 98) Total 10912078 reads processed 0:14:03.323 4G / 10G INFO General (pair_info_count.cpp : 392) Mapping single reads of library #0 0:14:03.323 4G / 10G INFO General (pair_info_count.cpp : 255) Will calculate lib coverage as well 0:14:03.323 4G / 10G INFO General (pair_info_count.cpp : 39) Selecting usual mapper 0:14:06.066 4G / 10G INFO General (sequence_mapper_notifier.h: 80) Processed 200000 reads 0:14:06.083 4G / 10G INFO General (sequence_mapper_notifier.h: 80) Processed 400000 reads 0:14:06.093 4G / 10G INFO General (sequence_mapper_notifier.h: 80) Processed 600000 reads 0:14:06.104 4G / 10G INFO General (sequence_mapper_notifier.h: 80) Processed 800000 reads 0:14:06.113 4G / 10G INFO General (sequence_mapper_notifier.h: 80) Processed 1000000 reads 0:14:06.123 4G / 10G INFO General (sequence_mapper_notifier.h: 80) Processed 1200000 reads 0:14:06.513 4G / 10G INFO General (sequence_mapper_notifier.h: 80) Processed 2200000 reads 0:14:08.940 4G / 10G INFO General (sequence_mapper_notifier.h: 80) Processed 4200000 reads 0:14:12.238 4G / 10G INFO General (sequence_mapper_notifier.h: 80) Processed 8400000 reads 0:14:21.324 4G / 10G INFO General (sequence_mapper_notifier.h: 80) Processed 16800000 reads 0:14:27.454 4G / 10G INFO General (sequence_mapper_notifier.h: 98) Total 21836162 reads processed 0:14:27.572 4G / 10G INFO General (pair_info_count.cpp : 394) Total paths obtained from single reads: 0 0:14:27.572 4G / 10G INFO General (pair_info_count.cpp : 392) Mapping single reads of library #1 0:14:27.572 4G / 10G INFO General (pair_info_count.cpp : 255) Will calculate lib coverage as well 0:14:27.572 4G / 10G INFO General (pair_info_count.cpp : 39) Selecting usual mapper 0:14:29.984 4G / 10G INFO General (sequence_mapper_notifier.h: 98) Total 1868370 reads processed 0:14:30.040 4G / 10G INFO General (pair_info_count.cpp : 394) Total paths obtained from single reads: 185273 0:14:30.040 4G / 10G INFO General (pair_info_count.cpp : 392) Mapping single reads of library #2 0:14:30.040 4G / 10G INFO General (pair_info_count.cpp : 255) Will calculate lib coverage as well 0:14:30.040 4G / 10G INFO General (pair_info_count.cpp : 39) Selecting usual mapper 0:14:31.101 4G / 10G INFO General (sequence_mapper_notifier.h: 98) Total 666393 reads processed 0:14:31.117 4G / 10G INFO General (pair_info_count.cpp : 394) Total paths obtained from single reads: 60345 0:14:31.117 4G / 10G INFO StageManager (stage.cpp : 132) STAGE == Distance Estimation 0:14:31.117 4G / 10G INFO General (distance_estimation.cpp : 173) Processing library #0 0:14:31.117 4G / 10G INFO General (distance_estimation.cpp : 149) Weight Filter Done 0:14:31.117 4G / 10G INFO DistanceEstimator (distance_estimation.hpp : 116) Using SIMPLE distance estimator 0:15:55.104 4G / 10G INFO General (distance_estimation.cpp : 34) Filtering info 0:15:55.104 4G / 10G INFO General (pair_info_filters.hpp : 242) Start filtering; index size: 23923880 0:16:03.088 4G / 10G INFO General (pair_info_filters.hpp : 263) Done filtering 0:16:03.095 4G / 10G INFO General (distance_estimation.cpp : 156) Refining clustered pair information 0:16:03.482 4G / 10G INFO General (distance_estimation.cpp : 158) The refining of clustered pair information has been finished 0:16:03.482 4G / 10G INFO General (distance_estimation.cpp : 160) Improving paired information 0:16:09.903 4G / 10G INFO PairInfoImprover (pair_info_improver.hpp : 103) Paired info stats: missing = 547831; contradictional = 2 0:16:24.013 4G / 10G INFO PairInfoImprover (pair_info_improver.hpp : 103) Paired info stats: missing = 160021; contradictional = 0 0:16:24.013 4G / 10G INFO StageManager (stage.cpp : 132) STAGE == Repeat Resolving 0:16:24.013 4G / 10G INFO General (repeat_resolving.cpp : 69) Using Path-Extend repeat resolving 0:16:24.013 4G / 10G INFO General (launcher.cpp : 477) ExSPAnder repeat resolving tool started 0:16:28.546 7G / 10G INFO General (launcher.cpp : 392) Creating main extenders, unique edge length = 2000 0:16:31.029 7G / 10G INFO General (extenders_logic.cpp : 34) resolvable_repeat_length_bound set to 10000 0:16:33.777 7G / 10G INFO General (extenders_logic.cpp : 34) resolvable_repeat_length_bound set to 10000 0:16:36.185 7G / 10G INFO General (extenders_logic.cpp : 472) Using 1 paired-end library 0:16:36.185 7G / 10G INFO General (extenders_logic.cpp : 473) Using 1 paired-end scaffolding library 0:16:36.185 7G / 10G INFO General (extenders_logic.cpp : 474) Using 2 single read libraries 0:16:36.185 7G / 10G INFO General (launcher.cpp : 420) Total number of extenders is 7 0:16:36.185 7G / 10G INFO General (path_extender.hpp : 885) Processed 0 paths from 640563 (0%) 0:16:36.475 7G / 10G INFO General (path_extender.hpp : 883) Processed 128 paths from 640563 (0%) 0:16:36.599 7G / 10G INFO General (path_extender.hpp : 883) Processed 256 paths from 640563 (0%) 0:16:37.154 7G / 10G INFO General (path_extender.hpp : 883) Processed 512 paths from 640563 (0%) 0:16:38.356 7G / 10G INFO General (path_extender.hpp : 883) Processed 1024 paths from 640563 (0%) 0:16:40.002 7G / 10G INFO General (path_extender.hpp : 883) Processed 2048 paths from 640563 (0%) 0:16:42.781 7G / 10G INFO General (path_extender.hpp : 883) Processed 4096 paths from 640563 (0%) 0:16:47.323 7G / 10G INFO General (path_extender.hpp : 883) Processed 8192 paths from 640563 (1%) 0:17:18.939 8G / 10G INFO General (path_extender.hpp : 883) Processed 16384 paths from 640563 (2%) 0:17:42.399 8G / 10G INFO General (path_extender.hpp : 883) Processed 32768 paths from 640563 (5%) 0:18:08.538 8G / 10G INFO General (path_extender.hpp : 885) Processed 64057 paths from 640563 (10%) 0:18:09.110 8G / 10G INFO General (path_extender.hpp : 883) Processed 65536 paths from 640563 (10%) 0:18:24.588 8G / 10G INFO General (path_extender.hpp : 885) Processed 128114 paths from 640563 (20%) 0:18:25.225 8G / 10G INFO General (path_extender.hpp : 883) Processed 131072 paths from 640563 (20%) 0:18:33.095 9G / 10G INFO General (path_extender.hpp : 885) Processed 192171 paths from 640563 (30%) 0:18:48.879 9G / 10G INFO General (path_extender.hpp : 885) Processed 256228 paths from 640563 (40%) 0:18:49.673 10G / 10G INFO General (path_extender.hpp : 883) Processed 262144 paths from 640563 (40%) 0:18:59.154 10G / 10G INFO General (path_extender.hpp : 885) Processed 320285 paths from 640563 (50%) 0:20:50.677 11G / 11G INFO General (path_extender.hpp : 885) Processed 384342 paths from 640563 (60%) 0:21:08.283 11G / 11G INFO General (path_extender.hpp : 885) Processed 448399 paths from 640563 (70%) 0:21:19.333 12G / 12G INFO General (path_extender.hpp : 885) Processed 512456 paths from 640563 (80%) 0:21:20.548 12G / 12G INFO General (path_extender.hpp : 883) Processed 524288 paths from 640563 (81%) 0:21:27.465 12G / 12G INFO General (path_extender.hpp : 885) Processed 576513 paths from 640563 (90%) 0:21:45.124 13G / 13G INFO General (launcher.cpp : 234) Finalizing paths 0:21:45.124 13G / 13G INFO General (launcher.cpp : 236) Deduplicating paths 0:21:48.820 13G / 13G INFO General (launcher.cpp : 240) Paths deduplicated 0:21:48.820 13G / 13G INFO PEResolver (pe_resolver.hpp : 295) Removing overlaps 0:21:48.820 13G / 13G INFO PEResolver (pe_resolver.hpp : 305) Marking overlaps 0:21:48.820 13G / 13G INFO OverlapRemover (pe_resolver.hpp : 130) Marking start/end overlaps 0:21:52.526 13G / 13G INFO PEResolver (pe_resolver.hpp : 308) Splitting paths 0:21:52.827 13G / 13G INFO PEResolver (pe_resolver.hpp : 313) Deduplicating paths 0:21:54.857 13G / 13G INFO PEResolver (pe_resolver.hpp : 315) Overlaps removed 0:21:57.099 13G / 13G INFO General (launcher.cpp : 257) Paths finalized 0:21:57.099 13G / 13G INFO General (launcher.cpp : 427) Closing gaps in paths 0:22:00.838 13G / 13G INFO General (launcher.cpp : 455) Gap closing completed 0:22:02.037 13G / 13G INFO General (launcher.cpp : 286) Traversing tandem repeats 0:22:09.121 13G / 13G INFO General (launcher.cpp : 296) Traversed 0 loops 0:22:09.121 13G / 13G INFO General (launcher.cpp : 234) Finalizing paths 0:22:09.121 13G / 13G INFO General (launcher.cpp : 236) Deduplicating paths 0:22:10.171 13G / 13G INFO General (launcher.cpp : 240) Paths deduplicated 0:22:10.171 13G / 13G INFO PEResolver (pe_resolver.hpp : 295) Removing overlaps 0:22:10.171 13G / 13G INFO PEResolver (pe_resolver.hpp : 305) Marking overlaps 0:22:10.171 13G / 13G INFO OverlapRemover (pe_resolver.hpp : 130) Marking start/end overlaps 0:22:12.409 13G / 13G INFO PEResolver (pe_resolver.hpp : 308) Splitting paths 0:22:12.531 13G / 13G INFO PEResolver (pe_resolver.hpp : 313) Deduplicating paths 0:22:13.623 13G / 13G INFO PEResolver (pe_resolver.hpp : 315) Overlaps removed 0:22:15.730 13G / 13G INFO General (launcher.cpp : 257) Paths finalized 0:22:17.860 15G / 15G INFO General (launcher.cpp : 462) Finalizing main paths 0:22:17.860 15G / 15G INFO General (launcher.cpp : 279) Read length relative cutoff 1.3 converted to 81 0:22:17.860 15G / 15G INFO General (launcher.cpp : 280) Read length absolute cutoff 110 bp converted to 81 0:22:17.860 15G / 15G INFO General (launcher.cpp : 281) Length cutoff: 81 0:22:18.463 15G / 15G INFO General (launcher.cpp : 279) Read length relative cutoff 1.6 converted to 111 0:22:18.463 15G / 15G INFO General (launcher.cpp : 280) Read length absolute cutoff 140 bp converted to 111 0:22:18.463 15G / 15G INFO General (launcher.cpp : 281) Length cutoff: 111 0:22:18.528 15G / 15G INFO General (launcher.cpp : 279) Read length relative cutoff 1.5 converted to 101 0:22:18.528 15G / 15G INFO General (launcher.cpp : 280) Read length absolute cutoff 130 bp converted to 101 0:22:18.528 15G / 15G INFO General (launcher.cpp : 281) Length cutoff: 101 0:22:18.599 15G / 15G INFO General (launcher.cpp : 467) Finalizing paths - hard 0:22:19.883 15G / 15G INFO General (launcher.cpp : 279) Read length relative cutoff 1.5 converted to 101 0:22:19.883 15G / 15G INFO General (launcher.cpp : 280) Read length absolute cutoff 130 bp converted to 101 0:22:19.883 15G / 15G INFO General (launcher.cpp : 281) Length cutoff: 101 0:22:20.515 15G / 15G INFO General (launcher.cpp : 279) Read length relative cutoff 2 converted to 151 0:22:20.515 15G / 15G INFO General (launcher.cpp : 280) Read length absolute cutoff 180 bp converted to 151 0:22:20.515 15G / 15G INFO General (launcher.cpp : 281) Length cutoff: 151 0:22:20.569 15G / 15G INFO General (launcher.cpp : 279) Read length relative cutoff 2 converted to 151 0:22:20.569 15G / 15G INFO General (launcher.cpp : 280) Read length absolute cutoff 180 bp converted to 151 0:22:20.569 15G / 15G INFO General (launcher.cpp : 281) Length cutoff: 151 0:22:21.370 15G / 15G INFO General (launcher.cpp : 467) Finalizing paths - soft 0:22:22.648 15G / 15G INFO General (launcher.cpp : 279) Read length relative cutoff 1.05 converted to 56 0:22:22.649 15G / 15G INFO General (launcher.cpp : 280) Read length absolute cutoff 85 bp converted to 56 0:22:22.649 15G / 15G INFO General (launcher.cpp : 281) Length cutoff: 56 0:22:23.228 15G / 15G INFO General (launcher.cpp : 279) Read length relative cutoff 1.5 converted to 101 0:22:23.228 15G / 15G INFO General (launcher.cpp : 280) Read length absolute cutoff 130 bp converted to 101 0:22:23.228 15G / 15G INFO General (launcher.cpp : 281) Length cutoff: 101 0:22:23.271 15G / 15G INFO General (launcher.cpp : 279) Read length relative cutoff 1.2 converted to 71 0:22:23.271 15G / 15G INFO General (launcher.cpp : 280) Read length absolute cutoff 100 bp converted to 71 0:22:23.271 15G / 15G INFO General (launcher.cpp : 281) Length cutoff: 71 0:22:25.485 13G / 15G INFO General (launcher.cpp : 529) ExSPAnder repeat resolving tool finished 0:22:33.324 5G / 15G INFO StageManager (stage.cpp : 132) STAGE == Contig Output 0:22:33.324 5G / 15G 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-Voromonas_pontica_cDNA_sequencing-SRX973460//K49/assembly_graph_with_scaffolds.gfa 0:22:35.828 5G / 15G 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-Voromonas_pontica_cDNA_sequencing-SRX973460//K49/before_rr.fasta 0:22:38.979 5G / 15G 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-Voromonas_pontica_cDNA_sequencing-SRX973460//K49/assembly_graph.fastg 0:22:45.067 5G / 15G 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-Voromonas_pontica_cDNA_sequencing-SRX973460//K49/transcripts.paths 0:22:46.349 5G / 15G INFO General (launch.hpp : 149) SPAdes finished 0:23:01.478 64M / 15G INFO General (main.cpp : 109) Assembling time: 0 hours 23 minutes 1 seconds ===== Assembling finished. Used k-mer sizes: 33, 49 * Corrected reads are in /oak/stanford/groups/akundaje/marinovg/various/MMETSP/2018-11-19-trans-splicing/SPAdes-3.13-RNA-Trimmomatic-Voromonas_pontica_cDNA_sequencing-SRX973460/corrected/ * Assembled transcripts are in /oak/stanford/groups/akundaje/marinovg/various/MMETSP/2018-11-19-trans-splicing/SPAdes-3.13-RNA-Trimmomatic-Voromonas_pontica_cDNA_sequencing-SRX973460/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-Voromonas_pontica_cDNA_sequencing-SRX973460/transcripts.paths * Hard filtered transcripts are in /oak/stanford/groups/akundaje/marinovg/various/MMETSP/2018-11-19-trans-splicing/SPAdes-3.13-RNA-Trimmomatic-Voromonas_pontica_cDNA_sequencing-SRX973460/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-Voromonas_pontica_cDNA_sequencing-SRX973460/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-Voromonas_pontica_cDNA_sequencing-SRX973460/spades.log Thank you for using SPAdes!