Command line: /data/home/root/SPAdes-3.10.1-Linux/bin/spades.py -k 49 --rna -o /data/home/pitagoras/public_html/gigas/transcriptome/rnaSpades/spadesRNA/output49 --dataset /data/home/pitagoras/public_html/gigas/transcriptome/fastqs.yaml System information: SPAdes version: 3.10.1 Python version: 2.7.5 OS: Linux-3.10.0-862.3.2.el7.x86_64-x86_64-with-centos-7.5.1804-Core Output dir: /data/home/pitagoras/public_html/gigas/transcriptome/rnaSpades/spadesRNA/output49 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: ['/data2/process/RnaPira/trim/Ova_R2.t.fastq', '/data2/process/RnaPira/trim/Cerebro-femea_R2.t.fastq', '/data2/process/RnaPira/trim/Cerebro-macho_R2.t.fastq', '/data2/process/RnaPira/trim/Pulmao-femea_R2.t.fastq', '/data2/process/RnaPira/trim/Pulmao-macho_R2.t.fastq', '/data2/process/RnaPira/trim/Hipofise-femea_R2.t.fastq', '/data2/process/RnaPira/trim/Rim-femea_R2.t.fastq', '/data2/process/RnaPira/trim/Hipofise-macho_R2.t.fastq', '/data2/process/RnaPira/trim/Rim-macho_R2.t.fastq', '/data2/process/RnaPira/trim/Musculo-femea_R2.t.fastq', '/data2/process/RnaPira/trim/Testiculo_R2.t.fastq'] right reads: ['/data2/process/RnaPira/trim/Ova_R1.t.fastq', '/data2/process/RnaPira/trim/Cerebro-femea_R1.t.fastq', '/data2/process/RnaPira/trim/Cerebro-macho_R1.t.fastq', '/data2/process/RnaPira/trim/Pulmao-femea_R1.t.fastq', '/data2/process/RnaPira/trim/Pulmao-macho_R1.t.fastq', '/data2/process/RnaPira/trim/Hipofise-femea_R1.t.fastq', '/data2/process/RnaPira/trim/Rim-femea_R1.t.fastq', '/data2/process/RnaPira/trim/Hipofise-macho_R1.t.fastq', '/data2/process/RnaPira/trim/Rim-macho_R1.t.fastq', '/data2/process/RnaPira/trim/Musculo-femea_R1.t.fastq', '/data2/process/RnaPira/trim/Testiculo_R1.t.fastq'] interlaced reads: not specified single reads: not specified Read error correction parameters: Iterations: 1 PHRED offset will be auto-detected Corrected reads will be compressed (with gzip) Assembly parameters: k: [49] 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: /data/home/pitagoras/public_html/gigas/transcriptome/rnaSpades/spadesRNA/output49/tmp Threads: 16 Memory limit (in Gb): 235 ======= SPAdes pipeline started. Log can be found here: /data/home/pitagoras/public_html/gigas/transcriptome/rnaSpades/spadesRNA/output49/spades.log ===== Read error correction started. == Running read error correction tool: /data/home/root/SPAdes-3.10.1-Linux/bin/hammer /data/home/pitagoras/public_html/gigas/transcriptome/rnaSpades/spadesRNA/output49/corrected/configs/config.info 0:00:00.000 4M / 4M INFO General (main.cpp : 83) Starting BayesHammer, built from N/A, git revision N/A 0:00:00.000 4M / 4M INFO General (main.cpp : 84) Loading config from /data/home/pitagoras/public_html/gigas/transcriptome/rnaSpades/spadesRNA/output49/corrected/configs/config.info 0:00:00.002 4M / 4M INFO General (memory_limit.hpp : 47) Memory limit set to 235 Gb 0:00:00.002 4M / 4M INFO General (main.cpp : 93) Trying to determine PHRED offset 0:00:00.003 4M / 4M INFO General (main.cpp : 99) Determined value is 33 0:00:00.004 4M / 4M INFO General (hammer_tools.cpp : 36) Hamming graph threshold tau=1, k=21, subkmer positions = [ 0 10 ] 0:00:00.004 4M / 4M INFO General (main.cpp : 120) Size of aux. kmer data 24 bytes === ITERATION 0 begins === 0:00:00.008 4M / 4M INFO K-mer Index Building (kmer_index_builder.hpp : 428) Building kmer index 0:00:00.008 4M / 4M INFO K-mer Splitting (kmer_data.cpp : 91) Splitting kmer instances into 256 buckets. This might take a while. 0:00:00.008 4M / 4M INFO General (file_limit.hpp : 30) Open file limit set to 64000 0:00:00.008 4M / 4M INFO General (kmer_index_builder.hpp : 108) Memory available for splitting buffers: 4.89575 Gb 0:00:00.008 4M / 4M INFO General (kmer_index_builder.hpp : 116) Using cell size of 262144 0:00:00.061 8G / 8G INFO K-mer Splitting (kmer_data.cpp : 98) Processing /data2/process/RnaPira/trim/Ova_R2.t.fastq 0:00:24.621 8G / 8G INFO K-mer Splitting (kmer_data.cpp : 108) Processed 1146941 reads 0:00:47.096 8G / 8G INFO K-mer Splitting (kmer_data.cpp : 108) Processed 2304988 reads 0:01:10.693 8G / 8G INFO K-mer Splitting (kmer_data.cpp : 108) Processed 3390313 reads 0:01:34.234 8G / 8G INFO K-mer Splitting (kmer_data.cpp : 108) Processed 4317374 reads 0:01:44.070 8G / 8G INFO K-mer Splitting (kmer_data.cpp : 108) Processed 5431399 reads 0:01:55.238 8G / 8G INFO K-mer Splitting (kmer_data.cpp : 108) Processed 6644863 reads 0:02:12.719 8G / 8G INFO K-mer Splitting (kmer_data.cpp : 108) Processed 7917933 reads 0:02:39.537 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 108) Processed 10386230 reads 0:03:09.434 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 108) Processed 12816845 reads 0:03:58.753 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 108) Processed 17988828 reads 0:05:15.641 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 98) Processing /data2/process/RnaPira/trim/Cerebro-femea_R2.t.fastq 0:06:12.365 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 108) Processed 34128171 reads 0:08:14.446 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 98) Processing /data2/process/RnaPira/trim/Cerebro-macho_R2.t.fastq 0:14:37.064 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 98) Processing /data2/process/RnaPira/trim/Pulmao-femea_R2.t.fastq 0:17:31.438 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 98) Processing /data2/process/RnaPira/trim/Pulmao-macho_R2.t.fastq 0:19:09.428 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 108) Processed 67854607 reads 0:21:37.371 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 98) Processing /data2/process/RnaPira/trim/Hipofise-femea_R2.t.fastq 0:25:27.270 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 98) Processing /data2/process/RnaPira/trim/Rim-femea_R2.t.fastq 0:30:20.506 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 98) Processing /data2/process/RnaPira/trim/Hipofise-macho_R2.t.fastq 0:33:06.915 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 98) Processing /data2/process/RnaPira/trim/Rim-macho_R2.t.fastq 0:38:05.480 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 98) Processing /data2/process/RnaPira/trim/Musculo-femea_R2.t.fastq 0:43:20.038 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 98) Processing /data2/process/RnaPira/trim/Testiculo_R2.t.fastq 0:47:12.605 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 98) Processing /data2/process/RnaPira/trim/Ova_R1.t.fastq 0:47:50.754 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 108) Processed 135061266 reads 0:51:28.972 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 98) Processing /data2/process/RnaPira/trim/Cerebro-femea_R1.t.fastq 0:54:41.192 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 98) Processing /data2/process/RnaPira/trim/Cerebro-macho_R1.t.fastq 0:58:22.819 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 98) Processing /data2/process/RnaPira/trim/Pulmao-femea_R1.t.fastq 1:00:21.360 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 98) Processing /data2/process/RnaPira/trim/Pulmao-macho_R1.t.fastq 1:03:51.932 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 98) Processing /data2/process/RnaPira/trim/Hipofise-femea_R1.t.fastq 1:06:02.058 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 98) Processing /data2/process/RnaPira/trim/Rim-femea_R1.t.fastq 1:07:56.452 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 98) Processing /data2/process/RnaPira/trim/Hipofise-macho_R1.t.fastq 1:10:18.364 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 98) Processing /data2/process/RnaPira/trim/Rim-macho_R1.t.fastq 1:13:04.157 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 98) Processing /data2/process/RnaPira/trim/Musculo-femea_R1.t.fastq 1:14:48.448 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 98) Processing /data2/process/RnaPira/trim/Testiculo_R1.t.fastq 1:16:50.968 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 113) Total 262072356 reads processed 1:16:51.541 64M / 9G INFO General (kmer_index_builder.hpp : 252) Starting k-mer counting. 1:45:10.155 64M / 9G INFO General (kmer_index_builder.hpp : 258) K-mer counting done. There are 853373588 kmers in total. 1:45:10.155 64M / 9G INFO General (kmer_index_builder.hpp : 260) Merging temporary buckets. 1:47:47.868 64M / 9G INFO K-mer Index Building (kmer_index_builder.hpp : 437) Building perfect hash indices 1:49:07.594 320M / 21G INFO General (kmer_index_builder.hpp : 276) Merging final buckets. 1:50:39.466 320M / 21G INFO K-mer Index Building (kmer_index_builder.hpp : 483) Index built. Total 278813288 bytes occupied (2.61375 bits per kmer). 1:50:39.473 320M / 21G INFO K-mer Counting (kmer_data.cpp : 359) Arranging kmers in hash map order 1:52:26.418 13G / 21G INFO General (main.cpp : 155) Clustering Hamming graph. 2:48:56.040 13G / 21G INFO General (main.cpp : 162) Extracting clusters 3:04:11.571 13G / 37G INFO General (main.cpp : 174) Clustering done. Total clusters: 471665404 3:04:12.646 6G / 37G INFO K-mer Counting (kmer_data.cpp : 381) Collecting K-mer information, this takes a while. 3:04:31.628 25G / 37G INFO K-mer Counting (kmer_data.cpp : 387) Processing /data2/process/RnaPira/trim/Ova_R2.t.fastq 3:14:24.189 25G / 37G INFO K-mer Counting (kmer_data.cpp : 387) Processing /data2/process/RnaPira/trim/Cerebro-femea_R2.t.fastq 3:18:37.126 25G / 37G INFO K-mer Counting (kmer_data.cpp : 387) Processing /data2/process/RnaPira/trim/Cerebro-macho_R2.t.fastq 3:22:58.786 25G / 37G INFO K-mer Counting (kmer_data.cpp : 387) Processing /data2/process/RnaPira/trim/Pulmao-femea_R2.t.fastq 3:25:25.689 25G / 37G INFO K-mer Counting (kmer_data.cpp : 387) Processing /data2/process/RnaPira/trim/Pulmao-macho_R2.t.fastq 3:30:35.810 25G / 37G INFO K-mer Counting (kmer_data.cpp : 387) Processing /data2/process/RnaPira/trim/Hipofise-femea_R2.t.fastq 3:33:48.136 25G / 37G INFO K-mer Counting (kmer_data.cpp : 387) Processing /data2/process/RnaPira/trim/Rim-femea_R2.t.fastq 3:36:27.327 25G / 37G INFO K-mer Counting (kmer_data.cpp : 387) Processing /data2/process/RnaPira/trim/Hipofise-macho_R2.t.fastq 3:38:54.351 25G / 37G INFO K-mer Counting (kmer_data.cpp : 387) Processing /data2/process/RnaPira/trim/Rim-macho_R2.t.fastq 3:42:00.157 25G / 37G INFO K-mer Counting (kmer_data.cpp : 387) Processing /data2/process/RnaPira/trim/Musculo-femea_R2.t.fastq 3:45:17.190 25G / 37G INFO K-mer Counting (kmer_data.cpp : 387) Processing /data2/process/RnaPira/trim/Testiculo_R2.t.fastq 3:47:33.555 25G / 37G INFO K-mer Counting (kmer_data.cpp : 387) Processing /data2/process/RnaPira/trim/Ova_R1.t.fastq 3:57:53.250 25G / 37G INFO K-mer Counting (kmer_data.cpp : 387) Processing /data2/process/RnaPira/trim/Cerebro-femea_R1.t.fastq 4:02:46.796 25G / 37G INFO K-mer Counting (kmer_data.cpp : 387) Processing /data2/process/RnaPira/trim/Cerebro-macho_R1.t.fastq 4:07:06.080 25G / 37G INFO K-mer Counting (kmer_data.cpp : 387) Processing /data2/process/RnaPira/trim/Pulmao-femea_R1.t.fastq 4:09:36.395 25G / 37G INFO K-mer Counting (kmer_data.cpp : 387) Processing /data2/process/RnaPira/trim/Pulmao-macho_R1.t.fastq 4:15:06.447 25G / 37G INFO K-mer Counting (kmer_data.cpp : 387) Processing /data2/process/RnaPira/trim/Hipofise-femea_R1.t.fastq 4:18:40.578 25G / 37G INFO K-mer Counting (kmer_data.cpp : 387) Processing /data2/process/RnaPira/trim/Rim-femea_R1.t.fastq 4:21:17.200 25G / 37G INFO K-mer Counting (kmer_data.cpp : 387) Processing /data2/process/RnaPira/trim/Hipofise-macho_R1.t.fastq 4:23:45.856 25G / 37G INFO K-mer Counting (kmer_data.cpp : 387) Processing /data2/process/RnaPira/trim/Rim-macho_R1.t.fastq 4:26:58.018 25G / 37G INFO K-mer Counting (kmer_data.cpp : 387) Processing /data2/process/RnaPira/trim/Musculo-femea_R1.t.fastq 4:30:46.508 25G / 37G INFO K-mer Counting (kmer_data.cpp : 387) Processing /data2/process/RnaPira/trim/Testiculo_R1.t.fastq 4:33:03.358 25G / 37G INFO K-mer Counting (kmer_data.cpp : 394) Collection done, postprocessing. 4:33:11.405 25G / 37G INFO K-mer Counting (kmer_data.cpp : 408) There are 853373588 kmers in total. Among them 453841768 (53.1821%) are singletons. 4:33:11.405 25G / 37G INFO General (main.cpp : 180) Subclustering Hamming graph 5:04:25.066 25G / 37G INFO Hamming Subclustering (kmer_cluster.cpp : 649) Subclustering done. Total 14725 non-read kmers were generated. 5:04:25.066 25G / 37G INFO Hamming Subclustering (kmer_cluster.cpp : 650) Subclustering statistics: 5:04:25.066 25G / 37G INFO Hamming Subclustering (kmer_cluster.cpp : 651) Total singleton hamming clusters: 373380040. Among them 197436224 (52.8781%) are good 5:04:25.067 25G / 37G INFO Hamming Subclustering (kmer_cluster.cpp : 652) Total singleton subclusters: 4428047. Among them 4415786 (99.7231%) are good 5:04:25.067 25G / 37G INFO Hamming Subclustering (kmer_cluster.cpp : 653) Total non-singleton subcluster centers: 106087531. Among them 76147115 (71.7776%) are good 5:04:25.067 25G / 37G INFO Hamming Subclustering (kmer_cluster.cpp : 654) Average size of non-trivial subcluster: 4.52497 kmers 5:04:25.067 25G / 37G INFO Hamming Subclustering (kmer_cluster.cpp : 655) Average number of sub-clusters per non-singleton cluster: 1.12444 5:04:25.068 25G / 37G INFO Hamming Subclustering (kmer_cluster.cpp : 656) Total solid k-mers: 277999125 5:04:25.068 25G / 37G INFO Hamming Subclustering (kmer_cluster.cpp : 657) Substitution probabilities: [4,4]((0.935093,0.0147494,0.0157114,0.0344464),(0.0231182,0.922603,0.010326,0.043953),(0.0426235,0.00995275,0.923141,0.0242824),(0.0332819,0.0150219,0.0143522,0.937344)) 5:04:26.000 25G / 37G INFO General (main.cpp : 185) Finished clustering. 5:04:26.000 25G / 37G INFO General (main.cpp : 204) Starting solid k-mers expansion in 16 threads. 5:35:39.793 25G / 37G INFO General (main.cpp : 225) Solid k-mers iteration 0 produced 26913508 new k-mers. 6:04:35.774 25G / 37G INFO General (main.cpp : 225) Solid k-mers iteration 1 produced 2197160 new k-mers. 6:23:55.126 25G / 37G INFO General (main.cpp : 225) Solid k-mers iteration 2 produced 176819 new k-mers. 6:35:51.159 25G / 37G INFO General (main.cpp : 225) Solid k-mers iteration 3 produced 20818 new k-mers. 6:47:22.490 25G / 37G INFO General (main.cpp : 225) Solid k-mers iteration 4 produced 3344 new k-mers. 6:58:53.982 25G / 37G INFO General (main.cpp : 225) Solid k-mers iteration 5 produced 631 new k-mers. 7:10:20.863 25G / 37G INFO General (main.cpp : 225) Solid k-mers iteration 6 produced 116 new k-mers. 7:21:55.062 25G / 37G INFO General (main.cpp : 225) Solid k-mers iteration 7 produced 49 new k-mers. 7:33:31.344 25G / 37G INFO General (main.cpp : 225) Solid k-mers iteration 8 produced 15 new k-mers. 7:45:04.284 25G / 37G INFO General (main.cpp : 225) Solid k-mers iteration 9 produced 29 new k-mers. 7:56:38.973 25G / 37G INFO General (main.cpp : 225) Solid k-mers iteration 10 produced 0 new k-mers. 7:56:38.973 25G / 37G INFO General (main.cpp : 229) Solid k-mers finalized 7:56:38.973 25G / 37G INFO General (hammer_tools.cpp : 211) Starting read correction in 16 threads. 7:56:38.973 25G / 37G INFO General (hammer_tools.cpp : 222) Correcting pair of reads: /data2/process/RnaPira/trim/Ova_R2.t.fastq and /data2/process/RnaPira/trim/Ova_R1.t.fastq 7:56:42.406 26G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 0 of 1600000 reads. 7:56:52.101 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 0 7:56:55.417 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 0 7:56:58.440 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 1 of 1600000 reads. 7:57:08.348 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 1 7:57:10.426 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 1 7:57:12.974 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 2 of 1600000 reads. 7:57:22.928 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 2 7:57:25.415 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 2 7:57:27.904 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 3 of 1600000 reads. 7:57:37.794 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 3 7:57:46.616 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 3 7:57:49.041 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 4 of 1600000 reads. 7:57:59.408 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 4 7:58:11.537 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 4 7:58:13.949 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 5 of 1600000 reads. 7:58:24.062 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 5 7:58:26.603 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 5 7:58:28.997 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 6 of 1600000 reads. 7:58:39.129 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 6 7:58:46.122 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 6 7:58:48.581 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 7 of 1600000 reads. 7:58:58.657 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 7 7:59:15.656 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 7 7:59:18.274 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 8 of 1600000 reads. 7:59:28.490 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 8 7:59:40.321 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 8 7:59:42.861 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 9 of 1600000 reads. 7:59:53.246 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 9 7:59:56.291 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 9 7:59:58.898 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 10 of 1600000 reads. 8:00:09.250 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 10 8:00:12.121 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 10 8:00:15.288 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 11 of 1600000 reads. 8:00:25.451 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 11 8:00:27.759 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 11 8:00:30.245 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 12 of 1600000 reads. 8:00:40.432 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 12 8:00:48.960 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 12 8:00:51.424 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 13 of 1600000 reads. 8:01:01.803 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 13 8:01:13.898 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 13 8:01:16.401 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 14 of 1600000 reads. 8:01:26.600 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 14 8:01:29.218 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 14 8:01:31.720 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 15 of 1600000 reads. 8:01:42.121 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 15 8:01:48.567 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 15 8:01:51.694 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 16 of 1600000 reads. 8:02:01.890 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 16 8:02:16.216 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 16 8:02:18.648 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 17 of 1600000 reads. 8:02:28.809 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 17 8:02:31.072 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 17 8:02:32.330 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 18 of 811697 reads. 8:02:37.688 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 18 8:02:45.821 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 18 8:03:00.681 25G / 37G INFO General (hammer_tools.cpp : 222) Correcting pair of reads: /data2/process/RnaPira/trim/Cerebro-femea_R2.t.fastq and /data2/process/RnaPira/trim/Cerebro-femea_R1.t.fastq 8:03:03.921 26G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 0 of 1600000 reads. 8:03:14.258 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 0 8:03:16.281 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 0 8:03:19.075 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 1 of 1600000 reads. 8:03:29.215 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 1 8:03:31.485 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 1 8:03:34.064 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 2 of 1600000 reads. 8:03:44.304 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 2 8:04:00.139 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 2 8:04:02.620 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 3 of 1600000 reads. 8:04:12.895 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 3 8:04:27.909 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 3 8:04:30.387 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 4 of 1600000 reads. 8:04:40.500 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 4 8:04:42.686 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 4 8:04:45.121 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 5 of 1600000 reads. 8:04:55.213 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 5 8:04:58.362 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 5 8:05:00.813 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 6 of 1600000 reads. 8:05:11.056 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 6 8:05:13.231 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 6 8:05:15.712 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 7 of 1600000 reads. 8:05:25.968 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 7 8:05:32.226 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 7 8:05:33.457 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 8 of 811070 reads. 8:05:38.656 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 8 8:05:39.792 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 8 8:05:59.005 25G / 37G INFO General (hammer_tools.cpp : 222) Correcting pair of reads: /data2/process/RnaPira/trim/Cerebro-macho_R2.t.fastq and /data2/process/RnaPira/trim/Cerebro-macho_R1.t.fastq 8:06:02.333 26G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 0 of 1600000 reads. 8:06:12.446 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 0 8:06:14.558 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 0 8:06:17.382 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 1 of 1600000 reads. 8:06:27.316 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 1 8:06:29.370 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 1 8:06:31.877 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 2 of 1600000 reads. 8:06:42.348 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 2 8:06:44.637 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 2 8:06:47.108 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 3 of 1600000 reads. 8:06:57.598 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 3 8:07:12.062 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 3 8:07:14.603 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 4 of 1600000 reads. 8:07:24.528 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 4 8:07:26.813 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 4 8:07:29.218 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 5 of 1600000 reads. 8:07:39.370 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 5 8:07:41.940 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 5 8:07:44.369 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 6 of 1600000 reads. 8:07:54.813 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 6 8:08:04.140 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 6 8:08:05.197 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 7 of 700384 reads. 8:08:09.754 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 7 8:08:10.962 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 7 8:08:30.156 25G / 37G INFO General (hammer_tools.cpp : 222) Correcting pair of reads: /data2/process/RnaPira/trim/Pulmao-femea_R2.t.fastq and /data2/process/RnaPira/trim/Pulmao-femea_R1.t.fastq 8:08:33.287 26G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 0 of 1600000 reads. 8:08:41.353 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 0 8:08:43.498 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 0 8:08:46.262 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 1 of 1600000 reads. 8:08:55.268 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 1 8:08:57.441 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 1 8:08:59.994 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 2 of 1600000 reads. 8:09:08.860 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 2 8:09:11.228 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 2 8:09:13.716 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 3 of 1600000 reads. 8:09:22.958 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 3 8:09:37.194 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 3 8:09:37.854 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 4 of 442334 reads. 8:09:40.447 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 4 8:09:41.072 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 4 8:10:00.598 25G / 37G INFO General (hammer_tools.cpp : 222) Correcting pair of reads: /data2/process/RnaPira/trim/Pulmao-macho_R2.t.fastq and /data2/process/RnaPira/trim/Pulmao-macho_R1.t.fastq 8:10:04.018 26G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 0 of 1600000 reads. 8:10:12.611 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 0 8:10:14.731 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 0 8:10:17.534 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 1 of 1600000 reads. 8:10:26.110 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 1 8:10:28.268 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 1 8:10:30.867 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 2 of 1600000 reads. 8:10:39.528 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 2 8:10:41.745 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 2 8:10:44.255 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 3 of 1600000 reads. 8:10:53.271 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 3 8:11:09.059 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 3 8:11:11.494 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 4 of 1600000 reads. 8:11:20.571 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 4 8:11:24.411 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 4 8:11:26.840 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 5 of 1600000 reads. 8:11:35.509 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 5 8:11:37.723 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 5 8:11:40.142 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 6 of 1600000 reads. 8:11:48.705 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 6 8:12:02.521 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 6 8:12:04.915 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 7 of 1600000 reads. 8:12:13.573 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 7 8:12:30.270 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 7 8:12:32.827 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 8 of 1600000 reads. 8:12:41.522 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 8 8:12:43.864 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 8 8:12:46.333 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 9 of 1600000 reads. 8:12:55.432 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 9 8:12:58.391 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 9 8:12:58.775 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 10 of 228975 reads. 8:13:00.097 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 10 8:13:00.429 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 10 8:13:20.287 25G / 37G INFO General (hammer_tools.cpp : 222) Correcting pair of reads: /data2/process/RnaPira/trim/Hipofise-femea_R2.t.fastq and /data2/process/RnaPira/trim/Hipofise-femea_R1.t.fastq 8:13:23.499 26G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 0 of 1600000 reads. 8:13:32.882 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 0 8:13:34.992 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 0 8:13:37.838 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 1 of 1600000 reads. 8:13:47.358 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 1 8:13:49.514 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 1 8:13:52.092 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 2 of 1600000 reads. 8:14:01.669 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 2 8:14:04.234 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 2 8:14:06.809 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 3 of 1600000 reads. 8:14:16.453 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 3 8:14:32.883 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 3 8:14:35.348 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 4 of 1600000 reads. 8:14:44.727 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 4 8:14:47.828 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 4 8:14:50.344 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 5 of 1600000 reads. 8:14:59.941 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 5 8:15:02.611 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 5 8:15:03.976 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 6 of 862876 reads. 8:15:09.143 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 6 8:15:24.046 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 6 8:15:40.421 25G / 37G INFO General (hammer_tools.cpp : 222) Correcting pair of reads: /data2/process/RnaPira/trim/Rim-femea_R2.t.fastq and /data2/process/RnaPira/trim/Rim-femea_R1.t.fastq 8:15:43.551 26G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 0 of 1600000 reads. 8:15:53.368 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 0 8:15:55.779 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 0 8:15:58.643 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 1 of 1600000 reads. 8:16:08.698 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 1 8:16:11.080 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 1 8:16:14.024 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 2 of 1600000 reads. 8:16:24.028 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 2 8:16:34.596 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 2 8:16:37.087 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 3 of 1600000 reads. 8:16:46.752 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 3 8:17:03.824 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 3 8:17:06.273 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 4 of 1600000 reads. 8:17:16.273 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 4 8:17:29.425 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 4 8:17:30.242 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 5 of 531717 reads. 8:17:33.697 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 5 8:17:34.470 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 5 8:17:46.116 25G / 37G INFO General (hammer_tools.cpp : 222) Correcting pair of reads: /data2/process/RnaPira/trim/Hipofise-macho_R2.t.fastq and /data2/process/RnaPira/trim/Hipofise-macho_R1.t.fastq 8:17:49.347 26G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 0 of 1600000 reads. 8:17:58.327 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 0 8:18:00.660 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 0 8:18:03.509 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 1 of 1600000 reads. 8:18:13.088 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 1 8:18:15.704 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 1 8:18:18.380 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 2 of 1600000 reads. 8:18:27.668 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 2 8:18:40.963 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 2 8:18:43.434 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 3 of 1600000 reads. 8:18:52.796 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 3 8:19:09.775 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 3 8:19:10.855 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 4 of 678859 reads. 8:19:15.034 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 4 8:19:16.002 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 4 8:19:29.193 25G / 37G INFO General (hammer_tools.cpp : 222) Correcting pair of reads: /data2/process/RnaPira/trim/Rim-macho_R2.t.fastq and /data2/process/RnaPira/trim/Rim-macho_R1.t.fastq 8:19:32.657 26G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 0 of 1600000 reads. 8:19:42.152 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 0 8:19:44.371 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 0 8:19:47.263 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 1 of 1600000 reads. 8:19:57.228 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 1 8:19:59.470 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 1 8:20:02.225 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 2 of 1600000 reads. 8:20:12.325 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 2 8:20:14.698 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 2 8:20:17.338 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 3 of 1600000 reads. 8:20:26.782 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 3 8:20:41.654 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 3 8:20:44.251 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 4 of 1600000 reads. 8:20:54.101 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 4 8:20:56.612 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 4 8:20:58.040 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 5 of 880546 reads. 8:21:03.430 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 5 8:21:04.749 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 5 8:21:28.069 25G / 37G INFO General (hammer_tools.cpp : 222) Correcting pair of reads: /data2/process/RnaPira/trim/Musculo-femea_R2.t.fastq and /data2/process/RnaPira/trim/Musculo-femea_R1.t.fastq 8:21:31.312 26G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 0 of 1600000 reads. 8:21:39.791 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 0 8:21:42.618 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 0 8:21:45.470 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 1 of 1600000 reads. 8:21:54.246 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 1 8:21:56.607 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 1 8:21:59.207 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 2 of 1600000 reads. 8:22:07.714 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 2 8:22:10.093 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 2 8:22:12.689 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 3 of 1600000 reads. 8:22:21.628 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 3 8:22:38.150 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 3 8:22:40.632 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 4 of 1600000 reads. 8:22:49.031 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 4 8:22:52.552 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 4 8:22:55.330 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 5 of 1600000 reads. 8:23:03.640 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 5 8:23:06.098 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 5 8:23:08.520 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 6 of 1600000 reads. 8:23:17.105 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 6 8:23:30.829 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 6 8:23:31.593 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 7 of 359991 reads. 8:23:33.591 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 7 8:23:34.120 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 7 8:23:54.341 25G / 37G INFO General (hammer_tools.cpp : 222) Correcting pair of reads: /data2/process/RnaPira/trim/Testiculo_R2.t.fastq and /data2/process/RnaPira/trim/Testiculo_R1.t.fastq 8:23:57.786 26G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 0 of 1600000 reads. 8:24:06.729 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 0 8:24:09.322 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 0 8:24:12.129 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 1 of 1600000 reads. 8:24:21.888 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 1 8:24:25.673 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 1 8:24:28.291 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 2 of 1600000 reads. 8:24:37.556 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 2 8:24:44.627 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 2 8:24:47.023 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 3 of 1527729 reads. 8:24:56.195 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 3 8:24:58.743 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 3 8:25:22.994 25G / 37G INFO General (hammer_tools.cpp : 270) Correction done. Changed 15372871 bases in 10325499 reads. 8:25:22.994 25G / 37G INFO General (hammer_tools.cpp : 271) Failed to correct 20826 bases out of 19020763726. 8:25:27.684 64M / 37G INFO General (main.cpp : 262) Saving corrected dataset description to /data/home/pitagoras/public_html/gigas/transcriptome/rnaSpades/spadesRNA/output49/corrected/corrected.yaml 8:25:27.717 64M / 37G INFO General (main.cpp : 269) All done. Exiting. == Compressing corrected reads (with gzip) == Dataset description file was created: /data/home/pitagoras/public_html/gigas/transcriptome/rnaSpades/spadesRNA/output49/corrected/corrected.yaml ===== Read error correction finished. ===== Assembling started. == Running assembler: K49 0:00:00.000 4M / 4M INFO General (main.cpp : 75) Loading config from /data/home/pitagoras/public_html/gigas/transcriptome/rnaSpades/spadesRNA/output49/K49/configs/config.info 0:00:00.000 4M / 4M INFO General (main.cpp : 75) Loading config from /data/home/pitagoras/public_html/gigas/transcriptome/rnaSpades/spadesRNA/output49/K49/configs/mda_mode.info 0:00:00.000 4M / 4M INFO General (main.cpp : 75) Loading config from /data/home/pitagoras/public_html/gigas/transcriptome/rnaSpades/spadesRNA/output49/K49/configs/rna_mode.info 0:00:00.000 4M / 4M INFO General (memory_limit.hpp : 47) Memory limit set to 235 Gb 0:00:00.000 4M / 4M INFO General (main.cpp : 88) Starting SPAdes, built from N/A, git revision N/A 0:00:00.000 4M / 4M INFO General (main.cpp : 89) Maximum k-mer length: 128 0:00:00.000 4M / 4M INFO General (main.cpp : 90) Assembling dataset (/data/home/pitagoras/public_html/gigas/transcriptome/rnaSpades/spadesRNA/output49/dataset.info) with K=49 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 : 61) Two-step RR enabled: 0 0:00:00.003 4M / 4M INFO General (launch.hpp : 79) Will need read mapping, kmer mapper will be attached 0:00:00.003 4M / 4M INFO StageManager (stage.cpp : 126) STAGE == Construction 0:00:00.015 4M / 4M INFO General (read_converter.hpp : 84) Converting reads to binary format for library #0 (takes a while) 0:00:00.015 4M / 4M INFO General (read_converter.hpp : 85) Converting paired reads 0:00:00.261 80M / 80M INFO General (binary_converter.hpp : 139) 16384 reads processed 0:00:00.371 88M / 88M INFO General (binary_converter.hpp : 139) 32768 reads processed 0:00:00.621 108M / 108M INFO General (binary_converter.hpp : 139) 65536 reads processed 0:00:01.041 148M / 148M INFO General (binary_converter.hpp : 139) 131072 reads processed 0:00:01.722 228M / 228M INFO General (binary_converter.hpp : 139) 262144 reads processed 0:00:02.952 392M / 392M INFO General (binary_converter.hpp : 139) 524288 reads processed 0:00:06.454 640M / 640M INFO General (binary_converter.hpp : 139) 1048576 reads processed 0:00:12.219 640M / 640M INFO General (binary_converter.hpp : 139) 2097152 reads processed 0:00:23.601 640M / 640M INFO General (binary_converter.hpp : 139) 4194304 reads processed 0:00:47.053 640M / 640M INFO General (binary_converter.hpp : 139) 8388608 reads processed 0:01:33.825 644M / 644M INFO General (binary_converter.hpp : 139) 16777216 reads processed 0:03:20.940 648M / 648M INFO General (binary_converter.hpp : 139) 33554432 reads processed 0:06:58.332 656M / 656M INFO General (binary_converter.hpp : 139) 67108864 reads processed 0:13:31.214 656M / 660M INFO General (binary_converter.hpp : 159) 127432194 reads written 0:13:32.486 8M / 660M INFO General (read_converter.hpp : 94) Converting single reads 0:13:32.712 140M / 660M INFO General (binary_converter.hpp : 139) 16384 reads processed 0:13:32.760 144M / 660M INFO General (binary_converter.hpp : 139) 32768 reads processed 0:13:32.856 152M / 660M INFO General (binary_converter.hpp : 139) 65536 reads processed 0:13:33.039 172M / 660M INFO General (binary_converter.hpp : 139) 131072 reads processed 0:13:33.341 212M / 660M INFO General (binary_converter.hpp : 139) 262144 reads processed 0:13:34.107 292M / 660M INFO General (binary_converter.hpp : 139) 524288 reads processed 0:13:35.374 448M / 660M INFO General (binary_converter.hpp : 139) 1048576 reads processed 0:13:37.847 764M / 764M INFO General (binary_converter.hpp : 139) 2097152 reads processed 0:13:42.943 1G / 1G INFO General (binary_converter.hpp : 159) 3534009 reads written 0:13:48.488 4M / 1G INFO General (graph_construction.hpp : 120) Constructing DeBruijn graph for k=49 0:13:48.572 4M / 1G INFO General (kmer_splitters.hpp : 129) Splitting kmer instances into 256 buckets. This might take a while. 0:13:48.573 4M / 1G INFO General (file_limit.hpp : 30) Open file limit set to 64000 0:13:48.591 4M / 1G INFO General (kmer_index_builder.hpp : 108) Memory available for splitting buffers: 4.89575 Gb 0:13:48.591 4M / 1G INFO General (kmer_index_builder.hpp : 116) Using cell size of 131072 0:13:57.460 8G / 8G INFO General (kmer_splitters.hpp : 153) Processed 3273079 reads 0:14:04.352 8G / 8G INFO General (kmer_splitters.hpp : 153) Processed 6827753 reads 0:14:11.810 8G / 8G INFO General (kmer_splitters.hpp : 153) Processed 11067998 reads 0:14:18.297 8G / 8G INFO General (kmer_splitters.hpp : 153) Processed 14171447 reads 0:14:24.960 8G / 8G INFO General (kmer_splitters.hpp : 153) Processed 17207142 reads 0:14:32.428 8G / 8G INFO General (kmer_splitters.hpp : 153) Processed 20895553 reads 0:14:39.351 8G / 8G INFO General (kmer_splitters.hpp : 153) Processed 24013687 reads 0:14:46.255 8G / 8G INFO General (kmer_splitters.hpp : 153) Processed 27226567 reads 0:14:56.153 8G / 9G INFO General (kmer_splitters.hpp : 153) Processed 33976618 reads 0:15:09.915 8G / 9G INFO General (kmer_splitters.hpp : 153) Processed 46946661 reads 0:15:22.731 8G / 9G INFO General (kmer_splitters.hpp : 153) Processed 58388842 reads 0:15:39.462 8G / 9G INFO General (kmer_splitters.hpp : 153) Processed 67711769 reads 0:17:53.338 8G / 9G INFO General (kmer_splitters.hpp : 153) Processed 136333281 reads 0:24:23.043 8G / 9G INFO General (kmer_splitters.hpp : 153) Processed 271740050 reads 0:37:09.909 8G / 9G INFO General (kmer_splitters.hpp : 159) Adding contigs from previous K 0:37:10.400 64M / 9G INFO General (kmer_splitters.hpp : 172) Used 516796794 reads. Maximum read length 76 0:37:10.400 64M / 9G INFO General (kmer_splitters.hpp : 173) Average read length 73.1885 0:37:10.400 64M / 9G INFO General (kmer_index_builder.hpp : 252) Starting k-mer counting. 0:41:30.757 64M / 9G INFO General (kmer_index_builder.hpp : 258) K-mer counting done. There are 228302751 kmers in total. 0:41:30.757 64M / 9G INFO General (kmer_index_builder.hpp : 260) Merging temporary buckets. 0:43:01.349 64M / 9G INFO K-mer Index Building (kmer_index_builder.hpp : 428) Building kmer index 0:43:01.349 64M / 9G INFO General (kmer_splitters.hpp : 285) Splitting kmer instances into 256 buckets. This might take a while. 0:43:01.350 64M / 9G INFO General (file_limit.hpp : 30) Open file limit set to 64000 0:43:01.350 64M / 9G INFO General (kmer_index_builder.hpp : 108) Memory available for splitting buffers: 4.89453 Gb 0:43:01.350 64M / 9G INFO General (kmer_index_builder.hpp : 116) Using cell size of 131072 0:44:47.978 8G / 9G INFO General (kmer_splitters.hpp : 304) Processed 228302751 kmers 0:44:47.978 8G / 9G INFO General (kmer_splitters.hpp : 309) Used 228302751 kmers. 0:44:49.112 64M / 9G INFO General (kmer_index_builder.hpp : 252) Starting k-mer counting. 0:46:06.477 64M / 9G INFO General (kmer_index_builder.hpp : 258) K-mer counting done. There are 231362997 kmers in total. 0:46:06.477 64M / 9G INFO General (kmer_index_builder.hpp : 260) Merging temporary buckets. 0:47:35.962 64M / 9G INFO K-mer Index Building (kmer_index_builder.hpp : 437) Building perfect hash indices 0:47:45.975 192M / 9G INFO General (kmer_index_builder.hpp : 276) Merging final buckets. 0:48:51.425 192M / 9G INFO K-mer Index Building (kmer_index_builder.hpp : 483) Index built. Total 75590752 bytes occupied (2.61375 bits per kmer). 0:48:51.698 416M / 9G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 85) Building k-mer extensions from k+1-mers 0:49:13.503 416M / 9G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 89) Building k-mer extensions from k+1-mers finished. 0:49:13.517 416M / 9G INFO General (graph_construction.hpp : 136) Condensing graph 0:49:13.517 416M / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 340) Extracting unbranching paths 0:51:28.666 3G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths finished. 32734475 sequences extracted 0:51:46.333 3G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 313) Collecting perfect loops 0:52:48.449 3G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 329) Collecting perfect loops finished. 20 loops collected 0:53:07.096 8G / 10G INFO General (graph_construction.hpp : 141) Building index with from graph 0:53:07.106 8G / 10G INFO K-mer Index Building (kmer_index_builder.hpp : 428) Building kmer index 0:53:07.106 8G / 10G INFO General (kmer_splitters.hpp : 214) Splitting kmer instances into 16 buckets. This might take a while. 0:53:07.106 8G / 10G INFO General (file_limit.hpp : 30) Open file limit set to 64000 0:53:07.106 8G / 10G INFO General (kmer_index_builder.hpp : 108) Memory available for splitting buffers: 75.5872 Gb 0:53:07.106 8G / 10G INFO General (kmer_index_builder.hpp : 116) Using cell size of 2097152 0:53:25.138 8G / 10G INFO General (kmer_splitters.hpp : 225) Processed 4198897 edges 0:53:41.584 8G / 10G INFO General (kmer_splitters.hpp : 225) Processed 8398122 edges 0:53:57.123 8G / 10G INFO General (kmer_splitters.hpp : 225) Processed 12602268 edges 0:54:12.353 8G / 10G INFO General (kmer_splitters.hpp : 225) Processed 16808110 edges 0:54:27.123 8G / 10G INFO General (kmer_splitters.hpp : 225) Processed 21010296 edges 0:54:41.957 8G / 10G INFO General (kmer_splitters.hpp : 225) Processed 25209415 edges 0:54:57.256 8G / 10G INFO General (kmer_splitters.hpp : 225) Processed 29407411 edges 0:55:09.347 8G / 10G INFO General (kmer_splitters.hpp : 225) Processed 32734502 edges 0:55:09.347 8G / 10G INFO General (kmer_splitters.hpp : 230) Used 32734502 sequences. 0:55:09.424 8G / 10G INFO General (kmer_index_builder.hpp : 252) Starting k-mer counting. 0:56:48.427 8G / 10G INFO General (kmer_index_builder.hpp : 258) K-mer counting done. There are 228302751 kmers in total. 0:56:48.427 8G / 10G INFO General (kmer_index_builder.hpp : 260) Merging temporary buckets. 0:57:59.677 8G / 10G INFO K-mer Index Building (kmer_index_builder.hpp : 437) Building perfect hash indices 0:59:38.568 8G / 10G INFO General (kmer_index_builder.hpp : 276) Merging final buckets. 1:00:26.759 8G / 10G INFO K-mer Index Building (kmer_index_builder.hpp : 483) Index built. Total 74590912 bytes occupied (2.61375 bits per kmer). 1:00:29.805 13G / 13G INFO General (edge_index_builders.hpp : 27) Collecting k-mer coverage information from graph, this takes a while. 1:00:44.806 13G / 13G INFO General (edge_index.hpp : 91) Index refilled 1:00:46.156 13G / 13G INFO General (graph_construction.hpp : 173) Filling coverage index 1:00:46.157 13G / 13G INFO General (edge_index_builders.hpp : 105) Collecting k-mer coverage information from reads, this takes a while. 1:08:00.010 13G / 13G INFO General (graph_construction.hpp : 175) Filling coverage and flanking coverage from index 1:09:19.273 13G / 13G INFO General (construction.cpp : 30) Figured out: read length = 76 1:09:19.290 13G / 13G INFO StageManager (stage.cpp : 126) STAGE == EC Threshold Finding 1:09:37.806 13G / 13G INFO ThresholdFinder (ec_threshold_finder.hpp : 114) Bucket size: 13 1:09:37.807 13G / 13G INFO General (genomic_info_filler.cpp : 104) Average edge coverage: 28.1797 1:09:37.807 13G / 13G INFO General (genomic_info_filler.cpp : 105) Graph threshold: 503 1:11:58.462 15G / 33G INFO General (genomic_info_filler.cpp : 147) EC coverage threshold value was calculated as 28.1797 1:11:58.462 15G / 33G INFO General (genomic_info_filler.cpp : 148) Trusted kmer low bound: 0 1:11:58.462 15G / 33G INFO StageManager (stage.cpp : 126) STAGE == Gap Closer 1:11:58.502 15G / 33G INFO General (gap_closer.cpp : 159) Preparing shift maps 1:12:28.930 17G / 33G INFO General (gap_closer.cpp : 119) Processing paired reads (takes a while) 1:15:46.015 19G / 33G INFO General (gap_closer.cpp : 138) Used 127432194 paired reads 1:15:46.015 19G / 33G INFO General (gap_closer.cpp : 140) Merging paired indices 1:16:09.920 16G / 33G INFO GapCloser (gap_closer.cpp : 347) Closing short gaps 1:17:39.031 16G / 33G INFO GapCloser (gap_closer.cpp : 381) Closing short gaps complete: filled 409730 gaps after checking 1128248 candidates 1:18:50.663 16G / 33G INFO StageManager (stage.cpp : 126) STAGE == Simplification 1:18:51.450 10G / 33G INFO General (simplification.cpp : 420) Graph simplification started 1:18:51.450 10G / 33G INFO General (simplification.cpp : 76) PROCEDURE == InitialCleaning 1:18:51.450 10G / 33G INFO General (simplification.cpp : 64) Removing short polyAT 1:19:55.792 10G / 33G INFO General (parallel_simplification_al: 806) Parallel compression 1:19:58.538 10G / 33G INFO General (parallel_simplification_al: 815) Launching post-compression to compress loops 1:20:00.094 10G / 33G INFO General (graph_simplification.hpp : 645) Flanking coverage based disconnection disabled 1:20:00.095 10G / 33G INFO General (simplification.cpp : 349) Running Self conjugate edge remover 1:20:01.853 10G / 33G INFO General (simplification.cpp : 351) Triggered 0 times 1:20:01.853 10G / 33G INFO General (simplification.cpp : 349) Running Short PolyA/T Edges 1:20:03.884 10G / 33G INFO General (simplification.cpp : 351) Triggered 0 times 1:20:03.884 10G / 33G INFO General (simplification.cpp : 349) Running AT Tips 1:20:50.098 10G / 33G INFO General (simplification.cpp : 351) Triggered 2443064 times 1:20:50.098 10G / 33G INFO General (graph_simplification.hpp : 666) Removing loops and rc loops with erroneous connections 1:21:40.221 10G / 33G INFO ECLoopRemover (erroneous_connection_remov: 441) Loops: accurately removed/deadend removed/other: 6/72/8 1:21:40.221 10G / 33G INFO ECLoopRemover (erroneous_connection_remov: 442) RC loops: accurately removed/deadend removed/other: 8/254/2379 1:21:41.389 10G / 33G INFO General (graph_simplification.hpp : 617) Creating parallel br instance 1:21:41.389 10G / 33G INFO General (simplification.cpp : 456) PROCEDURE == Tip clipper and bulge removal cycle, iteration 1.0 1:21:41.389 10G / 33G INFO General (simplification.cpp : 349) Running Tip clipper 1:23:15.355 10G / 33G INFO General (simplification.cpp : 351) Triggered 4082294 times 1:23:15.355 10G / 33G INFO General (simplification.cpp : 349) Running Dead end clipper 1:23:17.171 10G / 33G INFO General (simplification.cpp : 351) Triggered 50725 times 1:23:17.171 10G / 33G INFO General (simplification.cpp : 349) Running Bulge remover 1:24:32.596 11G / 33G INFO General (simplification.cpp : 351) Triggered 96828 times 1:24:32.596 11G / 33G INFO General (simplification.cpp : 456) PROCEDURE == Tip clipper and bulge removal cycle, iteration 1.1 1:24:32.596 11G / 33G INFO General (simplification.cpp : 349) Running Tip clipper 1:24:32.858 11G / 33G INFO General (simplification.cpp : 351) Triggered 3168 times 1:24:32.858 11G / 33G INFO General (simplification.cpp : 349) Running Dead end clipper 1:24:32.986 11G / 33G INFO General (simplification.cpp : 351) Triggered 22 times 1:24:32.986 11G / 33G INFO General (simplification.cpp : 349) Running Bulge remover 1:24:33.062 11G / 33G INFO General (simplification.cpp : 351) Triggered 87 times 1:24:33.062 11G / 33G INFO General (simplification.cpp : 456) PROCEDURE == Tip clipper and bulge removal cycle, iteration 1.2 1:24:33.062 11G / 33G INFO General (simplification.cpp : 349) Running Tip clipper 1:24:33.063 11G / 33G INFO General (simplification.cpp : 351) Triggered 7 times 1:24:33.063 11G / 33G INFO General (simplification.cpp : 349) Running Dead end clipper 1:24:33.064 11G / 33G INFO General (simplification.cpp : 351) Triggered 0 times 1:24:33.064 11G / 33G INFO General (simplification.cpp : 349) Running Bulge remover 1:24:33.064 11G / 33G INFO General (simplification.cpp : 351) Triggered 0 times 1:24:33.064 11G / 33G INFO General (simplification.cpp : 456) PROCEDURE == Tip clipper and bulge removal cycle, iteration 1.3 1:24:33.064 11G / 33G INFO General (simplification.cpp : 349) Running Tip clipper 1:24:33.064 11G / 33G INFO General (simplification.cpp : 351) Triggered 0 times 1:24:33.064 11G / 33G INFO General (simplification.cpp : 349) Running Dead end clipper 1:24:33.064 11G / 33G INFO General (simplification.cpp : 351) Triggered 0 times 1:24:33.064 11G / 33G INFO General (simplification.cpp : 349) Running Bulge remover 1:24:33.064 11G / 33G INFO General (simplification.cpp : 351) Triggered 0 times 1:24:33.064 11G / 33G INFO General (simplification.cpp : 460) PROCEDURE == Erroneous connection, iteration 1 1:24:33.064 11G / 33G INFO General (simplification.cpp : 349) Running Low coverage edge remover 1:24:47.838 11G / 33G INFO General (simplification.cpp : 351) Triggered 193216 times 1:24:48.048 11G / 33G INFO General (graph_simplification.hpp : 617) Creating parallel br instance 1:24:48.048 11G / 33G INFO General (simplification.cpp : 456) PROCEDURE == Tip clipper and bulge removal cycle, iteration 2.0 1:24:48.048 11G / 33G INFO General (simplification.cpp : 349) Running Tip clipper 1:24:51.158 11G / 33G INFO General (simplification.cpp : 351) Triggered 60681 times 1:24:51.158 11G / 33G INFO General (simplification.cpp : 349) Running Dead end clipper 1:24:52.297 11G / 33G INFO General (simplification.cpp : 351) Triggered 26 times 1:24:52.297 11G / 33G INFO General (simplification.cpp : 349) Running Bulge remover 1:25:28.091 11G / 33G INFO General (simplification.cpp : 351) Triggered 39244 times 1:25:28.091 11G / 33G INFO General (simplification.cpp : 456) PROCEDURE == Tip clipper and bulge removal cycle, iteration 2.1 1:25:28.091 11G / 33G INFO General (simplification.cpp : 349) Running Tip clipper 1:25:28.123 11G / 33G INFO General (simplification.cpp : 351) Triggered 220 times 1:25:28.123 11G / 33G INFO General (simplification.cpp : 349) Running Dead end clipper 1:25:28.141 11G / 33G INFO General (simplification.cpp : 351) Triggered 0 times 1:25:28.141 11G / 33G INFO General (simplification.cpp : 349) Running Bulge remover 1:25:28.152 11G / 33G INFO General (simplification.cpp : 351) Triggered 15 times 1:25:28.152 11G / 33G INFO General (simplification.cpp : 456) PROCEDURE == Tip clipper and bulge removal cycle, iteration 2.2 1:25:28.152 11G / 33G INFO General (simplification.cpp : 349) Running Tip clipper 1:25:28.152 11G / 33G INFO General (simplification.cpp : 351) Triggered 0 times 1:25:28.152 11G / 33G INFO General (simplification.cpp : 349) Running Dead end clipper 1:25:28.152 11G / 33G INFO General (simplification.cpp : 351) Triggered 0 times 1:25:28.152 11G / 33G INFO General (simplification.cpp : 349) Running Bulge remover 1:25:28.152 11G / 33G INFO General (simplification.cpp : 351) Triggered 0 times 1:25:28.152 11G / 33G INFO General (simplification.cpp : 460) PROCEDURE == Erroneous connection, iteration 2 1:25:28.152 11G / 33G INFO General (simplification.cpp : 349) Running Low coverage edge remover 1:25:29.244 11G / 33G INFO General (simplification.cpp : 351) Triggered 17185 times 1:25:29.270 11G / 33G INFO General (graph_simplification.hpp : 617) Creating parallel br instance 1:25:29.270 11G / 33G INFO General (simplification.cpp : 456) PROCEDURE == Tip clipper and bulge removal cycle, iteration 3.0 1:25:29.270 11G / 33G INFO General (simplification.cpp : 349) Running Tip clipper 1:25:30.850 11G / 33G INFO General (simplification.cpp : 351) Triggered 2421 times 1:25:30.850 11G / 33G INFO General (simplification.cpp : 349) Running Dead end clipper 1:25:31.970 11G / 33G INFO General (simplification.cpp : 351) Triggered 0 times 1:25:31.971 11G / 33G INFO General (simplification.cpp : 349) Running Bulge remover 1:25:34.790 11G / 33G INFO General (simplification.cpp : 351) Triggered 2755 times 1:25:34.790 11G / 33G INFO General (simplification.cpp : 456) PROCEDURE == Tip clipper and bulge removal cycle, iteration 3.1 1:25:34.790 11G / 33G INFO General (simplification.cpp : 349) Running Tip clipper 1:25:34.797 11G / 33G INFO General (simplification.cpp : 351) Triggered 9 times 1:25:34.797 11G / 33G INFO General (simplification.cpp : 349) Running Dead end clipper 1:25:34.801 11G / 33G INFO General (simplification.cpp : 351) Triggered 0 times 1:25:34.801 11G / 33G INFO General (simplification.cpp : 349) Running Bulge remover 1:25:34.801 11G / 33G INFO General (simplification.cpp : 351) Triggered 0 times 1:25:34.801 11G / 33G INFO General (simplification.cpp : 456) PROCEDURE == Tip clipper and bulge removal cycle, iteration 3.2 1:25:34.801 11G / 33G INFO General (simplification.cpp : 349) Running Tip clipper 1:25:34.801 11G / 33G INFO General (simplification.cpp : 351) Triggered 0 times 1:25:34.801 11G / 33G INFO General (simplification.cpp : 349) Running Dead end clipper 1:25:34.801 11G / 33G INFO General (simplification.cpp : 351) Triggered 0 times 1:25:34.801 11G / 33G INFO General (simplification.cpp : 349) Running Bulge remover 1:25:34.802 11G / 33G INFO General (simplification.cpp : 351) Triggered 0 times 1:25:34.802 11G / 33G INFO General (simplification.cpp : 460) PROCEDURE == Erroneous connection, iteration 3 1:25:34.802 11G / 33G INFO General (simplification.cpp : 349) Running Low coverage edge remover 1:25:35.197 11G / 33G INFO General (simplification.cpp : 351) Triggered 6287 times 1:25:35.210 11G / 33G INFO General (graph_simplification.hpp : 617) Creating parallel br instance 1:25:35.210 11G / 33G INFO General (simplification.cpp : 456) PROCEDURE == Tip clipper and bulge removal cycle, iteration 4.0 1:25:35.210 11G / 33G INFO General (simplification.cpp : 349) Running Tip clipper 1:25:36.549 11G / 33G INFO General (simplification.cpp : 351) Triggered 469 times 1:25:36.549 11G / 33G INFO General (simplification.cpp : 349) Running Dead end clipper 1:25:37.827 11G / 33G INFO General (simplification.cpp : 351) Triggered 0 times 1:25:37.827 11G / 33G INFO General (simplification.cpp : 349) Running Bulge remover 1:25:39.469 11G / 33G INFO General (simplification.cpp : 351) Triggered 866 times 1:25:39.469 11G / 33G INFO General (simplification.cpp : 456) PROCEDURE == Tip clipper and bulge removal cycle, iteration 4.1 1:25:39.469 11G / 33G INFO General (simplification.cpp : 349) Running Tip clipper 1:25:39.471 11G / 33G INFO General (simplification.cpp : 351) Triggered 1 times 1:25:39.471 11G / 33G INFO General (simplification.cpp : 349) Running Dead end clipper 1:25:39.473 11G / 33G INFO General (simplification.cpp : 351) Triggered 0 times 1:25:39.473 11G / 33G INFO General (simplification.cpp : 349) Running Bulge remover 1:25:39.473 11G / 33G INFO General (simplification.cpp : 351) Triggered 0 times 1:25:39.473 11G / 33G INFO General (simplification.cpp : 456) PROCEDURE == Tip clipper and bulge removal cycle, iteration 4.2 1:25:39.473 11G / 33G INFO General (simplification.cpp : 349) Running Tip clipper 1:25:39.473 11G / 33G INFO General (simplification.cpp : 351) Triggered 0 times 1:25:39.473 11G / 33G INFO General (simplification.cpp : 349) Running Dead end clipper 1:25:39.473 11G / 33G INFO General (simplification.cpp : 351) Triggered 0 times 1:25:39.473 11G / 33G INFO General (simplification.cpp : 349) Running Bulge remover 1:25:39.473 11G / 33G INFO General (simplification.cpp : 351) Triggered 0 times 1:25:39.473 11G / 33G INFO General (simplification.cpp : 460) PROCEDURE == Erroneous connection, iteration 4 1:25:39.473 11G / 33G INFO General (simplification.cpp : 349) Running Low coverage edge remover 1:25:39.654 11G / 33G INFO General (simplification.cpp : 351) Triggered 3338 times 1:25:39.659 11G / 33G INFO General (graph_simplification.hpp : 617) Creating parallel br instance 1:25:39.659 11G / 33G INFO General (simplification.cpp : 456) PROCEDURE == Tip clipper and bulge removal cycle, iteration 5.0 1:25:39.659 11G / 33G INFO General (simplification.cpp : 349) Running Tip clipper 1:25:40.651 11G / 33G INFO General (simplification.cpp : 351) Triggered 170 times 1:25:40.651 11G / 33G INFO General (simplification.cpp : 349) Running Dead end clipper 1:25:41.679 11G / 33G INFO General (simplification.cpp : 351) Triggered 0 times 1:25:41.679 11G / 33G INFO General (simplification.cpp : 349) Running Bulge remover 1:25:43.008 11G / 33G INFO General (simplification.cpp : 351) Triggered 378 times 1:25:43.008 11G / 33G INFO General (simplification.cpp : 456) PROCEDURE == Tip clipper and bulge removal cycle, iteration 5.1 1:25:43.008 11G / 33G INFO General (simplification.cpp : 349) Running Tip clipper 1:25:43.010 11G / 33G INFO General (simplification.cpp : 351) Triggered 0 times 1:25:43.010 11G / 33G INFO General (simplification.cpp : 349) Running Dead end clipper 1:25:43.011 11G / 33G INFO General (simplification.cpp : 351) Triggered 0 times 1:25:43.011 11G / 33G INFO General (simplification.cpp : 349) Running Bulge remover 1:25:43.011 11G / 33G INFO General (simplification.cpp : 351) Triggered 0 times 1:25:43.011 11G / 33G INFO General (simplification.cpp : 460) PROCEDURE == Erroneous connection, iteration 5 1:25:43.011 11G / 33G INFO General (simplification.cpp : 349) Running Low coverage edge remover 1:25:43.131 11G / 33G INFO General (simplification.cpp : 351) Triggered 2013 times 1:25:43.135 11G / 33G INFO General (graph_simplification.hpp : 617) Creating parallel br instance 1:25:43.135 11G / 33G INFO General (simplification.cpp : 456) PROCEDURE == Tip clipper and bulge removal cycle, iteration 6.0 1:25:43.135 11G / 33G INFO General (simplification.cpp : 349) Running Tip clipper 1:25:44.198 11G / 33G INFO General (simplification.cpp : 351) Triggered 56 times 1:25:44.198 11G / 33G INFO General (simplification.cpp : 349) Running Dead end clipper 1:25:45.252 11G / 33G INFO General (simplification.cpp : 351) Triggered 0 times 1:25:45.252 11G / 33G INFO General (simplification.cpp : 349) Running Bulge remover 1:25:46.533 11G / 33G INFO General (simplification.cpp : 351) Triggered 236 times 1:25:46.534 11G / 33G INFO General (simplification.cpp : 456) PROCEDURE == Tip clipper and bulge removal cycle, iteration 6.1 1:25:46.534 11G / 33G INFO General (simplification.cpp : 349) Running Tip clipper 1:25:46.537 11G / 33G INFO General (simplification.cpp : 351) Triggered 0 times 1:25:46.537 11G / 33G INFO General (simplification.cpp : 349) Running Dead end clipper 1:25:46.538 11G / 33G INFO General (simplification.cpp : 351) Triggered 0 times 1:25:46.538 11G / 33G INFO General (simplification.cpp : 349) Running Bulge remover 1:25:46.538 11G / 33G INFO General (simplification.cpp : 351) Triggered 0 times 1:25:46.538 11G / 33G INFO General (simplification.cpp : 460) PROCEDURE == Erroneous connection, iteration 6 1:25:46.538 11G / 33G INFO General (simplification.cpp : 349) Running Low coverage edge remover 1:25:46.630 11G / 33G INFO General (simplification.cpp : 351) Triggered 1470 times 1:25:46.633 11G / 33G INFO General (graph_simplification.hpp : 617) Creating parallel br instance 1:25:46.633 11G / 33G INFO General (simplification.cpp : 456) PROCEDURE == Tip clipper and bulge removal cycle, iteration 7.0 1:25:46.633 11G / 33G INFO General (simplification.cpp : 349) Running Tip clipper 1:25:47.731 11G / 33G INFO General (simplification.cpp : 351) Triggered 34 times 1:25:47.731 11G / 33G INFO General (simplification.cpp : 349) Running Dead end clipper 1:25:48.712 11G / 33G INFO General (simplification.cpp : 351) Triggered 0 times 1:25:48.712 11G / 33G INFO General (simplification.cpp : 349) Running Bulge remover 1:25:49.847 11G / 33G INFO General (simplification.cpp : 351) Triggered 137 times 1:25:49.847 11G / 33G INFO General (simplification.cpp : 456) PROCEDURE == Tip clipper and bulge removal cycle, iteration 7.1 1:25:49.847 11G / 33G INFO General (simplification.cpp : 349) Running Tip clipper 1:25:49.848 11G / 33G INFO General (simplification.cpp : 351) Triggered 0 times 1:25:49.848 11G / 33G INFO General (simplification.cpp : 349) Running Dead end clipper 1:25:49.848 11G / 33G INFO General (simplification.cpp : 351) Triggered 0 times 1:25:49.848 11G / 33G INFO General (simplification.cpp : 349) Running Bulge remover 1:25:49.848 11G / 33G INFO General (simplification.cpp : 351) Triggered 0 times 1:25:49.848 11G / 33G INFO General (simplification.cpp : 460) PROCEDURE == Erroneous connection, iteration 7 1:25:49.848 11G / 33G INFO General (simplification.cpp : 349) Running Low coverage edge remover 1:25:49.905 11G / 33G INFO General (simplification.cpp : 351) Triggered 1099 times 1:25:49.907 11G / 33G INFO General (graph_simplification.hpp : 617) Creating parallel br instance 1:25:49.907 11G / 33G INFO General (simplification.cpp : 456) PROCEDURE == Tip clipper and bulge removal cycle, iteration 8.0 1:25:49.907 11G / 33G INFO General (simplification.cpp : 349) Running Tip clipper 1:25:50.891 11G / 33G INFO General (simplification.cpp : 351) Triggered 29 times 1:25:50.891 11G / 33G INFO General (simplification.cpp : 349) Running Dead end clipper 1:25:51.905 11G / 33G INFO General (simplification.cpp : 351) Triggered 0 times 1:25:51.905 11G / 33G INFO General (simplification.cpp : 349) Running Bulge remover 1:25:52.996 11G / 33G INFO General (simplification.cpp : 351) Triggered 90 times 1:25:52.996 11G / 33G INFO General (simplification.cpp : 456) PROCEDURE == Tip clipper and bulge removal cycle, iteration 8.1 1:25:52.996 11G / 33G INFO General (simplification.cpp : 349) Running Tip clipper 1:25:52.996 11G / 33G INFO General (simplification.cpp : 351) Triggered 0 times 1:25:52.996 11G / 33G INFO General (simplification.cpp : 349) Running Dead end clipper 1:25:52.997 11G / 33G INFO General (simplification.cpp : 351) Triggered 0 times 1:25:52.997 11G / 33G INFO General (simplification.cpp : 349) Running Bulge remover 1:25:52.997 11G / 33G INFO General (simplification.cpp : 351) Triggered 0 times 1:25:52.997 11G / 33G INFO General (simplification.cpp : 460) PROCEDURE == Erroneous connection, iteration 8 1:25:52.997 11G / 33G INFO General (simplification.cpp : 349) Running Low coverage edge remover 1:25:53.040 11G / 33G INFO General (simplification.cpp : 351) Triggered 889 times 1:25:53.042 11G / 33G INFO General (graph_simplification.hpp : 617) Creating parallel br instance 1:25:53.042 11G / 33G INFO General (simplification.cpp : 456) PROCEDURE == Tip clipper and bulge removal cycle, iteration 9.0 1:25:53.042 11G / 33G INFO General (simplification.cpp : 349) Running Tip clipper 1:25:54.071 11G / 33G INFO General (simplification.cpp : 351) Triggered 22 times 1:25:54.071 11G / 33G INFO General (simplification.cpp : 349) Running Dead end clipper 1:25:55.059 11G / 33G INFO General (simplification.cpp : 351) Triggered 0 times 1:25:55.059 11G / 33G INFO General (simplification.cpp : 349) Running Bulge remover 1:25:56.153 11G / 33G INFO General (simplification.cpp : 351) Triggered 54 times 1:25:56.153 11G / 33G INFO General (simplification.cpp : 456) PROCEDURE == Tip clipper and bulge removal cycle, iteration 9.1 1:25:56.153 11G / 33G INFO General (simplification.cpp : 349) Running Tip clipper 1:25:56.153 11G / 33G INFO General (simplification.cpp : 351) Triggered 1 times 1:25:56.153 11G / 33G INFO General (simplification.cpp : 349) Running Dead end clipper 1:25:56.153 11G / 33G INFO General (simplification.cpp : 351) Triggered 0 times 1:25:56.153 11G / 33G INFO General (simplification.cpp : 349) Running Bulge remover 1:25:56.153 11G / 33G INFO General (simplification.cpp : 351) Triggered 0 times 1:25:56.153 11G / 33G INFO General (simplification.cpp : 456) PROCEDURE == Tip clipper and bulge removal cycle, iteration 9.2 1:25:56.153 11G / 33G INFO General (simplification.cpp : 349) Running Tip clipper 1:25:56.153 11G / 33G INFO General (simplification.cpp : 351) Triggered 0 times 1:25:56.153 11G / 33G INFO General (simplification.cpp : 349) Running Dead end clipper 1:25:56.153 11G / 33G INFO General (simplification.cpp : 351) Triggered 0 times 1:25:56.153 11G / 33G INFO General (simplification.cpp : 349) Running Bulge remover 1:25:56.153 11G / 33G INFO General (simplification.cpp : 351) Triggered 0 times 1:25:56.153 11G / 33G INFO General (simplification.cpp : 460) PROCEDURE == Erroneous connection, iteration 9 1:25:56.153 11G / 33G INFO General (simplification.cpp : 349) Running Low coverage edge remover 1:25:56.196 11G / 33G INFO General (simplification.cpp : 351) Triggered 742 times 1:25:56.197 11G / 33G INFO General (graph_simplification.hpp : 617) Creating parallel br instance 1:25:56.197 11G / 33G INFO General (simplification.cpp : 456) PROCEDURE == Tip clipper and bulge removal cycle, iteration 10.0 1:25:56.197 11G / 33G INFO General (simplification.cpp : 349) Running Tip clipper 1:25:57.222 11G / 33G INFO General (simplification.cpp : 351) Triggered 16 times 1:25:57.222 11G / 33G INFO General (simplification.cpp : 349) Running Dead end clipper 1:25:58.283 11G / 33G INFO General (simplification.cpp : 351) Triggered 0 times 1:25:58.283 11G / 33G INFO General (simplification.cpp : 349) Running Bulge remover 1:25:59.496 11G / 33G INFO General (simplification.cpp : 351) Triggered 38 times 1:25:59.496 11G / 33G INFO General (simplification.cpp : 456) PROCEDURE == Tip clipper and bulge removal cycle, iteration 10.1 1:25:59.496 11G / 33G INFO General (simplification.cpp : 349) Running Tip clipper 1:25:59.496 11G / 33G INFO General (simplification.cpp : 351) Triggered 0 times 1:25:59.496 11G / 33G INFO General (simplification.cpp : 349) Running Dead end clipper 1:25:59.496 11G / 33G INFO General (simplification.cpp : 351) Triggered 0 times 1:25:59.496 11G / 33G INFO General (simplification.cpp : 349) Running Bulge remover 1:25:59.496 11G / 33G INFO General (simplification.cpp : 351) Triggered 0 times 1:25:59.496 11G / 33G INFO General (simplification.cpp : 460) PROCEDURE == Erroneous connection, iteration 10 1:25:59.496 11G / 33G INFO General (simplification.cpp : 349) Running Low coverage edge remover 1:25:59.528 11G / 33G INFO General (simplification.cpp : 351) Triggered 597 times 1:25:59.529 11G / 33G INFO General (graph_simplification.hpp : 617) Creating parallel br instance 1:25:59.529 11G / 33G INFO General (simplification.cpp : 456) PROCEDURE == Tip clipper and bulge removal cycle, iteration 11.0 1:25:59.529 11G / 33G INFO General (simplification.cpp : 349) Running Tip clipper 1:26:00.504 11G / 33G INFO General (simplification.cpp : 351) Triggered 10 times 1:26:00.504 11G / 33G INFO General (simplification.cpp : 349) Running Dead end clipper 1:26:01.526 11G / 33G INFO General (simplification.cpp : 351) Triggered 0 times 1:26:01.526 11G / 33G INFO General (simplification.cpp : 349) Running Bulge remover 1:26:02.544 11G / 33G INFO General (simplification.cpp : 351) Triggered 31 times 1:26:02.544 11G / 33G INFO General (simplification.cpp : 456) PROCEDURE == Tip clipper and bulge removal cycle, iteration 11.1 1:26:02.544 11G / 33G INFO General (simplification.cpp : 349) Running Tip clipper 1:26:02.545 11G / 33G INFO General (simplification.cpp : 351) Triggered 0 times 1:26:02.545 11G / 33G INFO General (simplification.cpp : 349) Running Dead end clipper 1:26:02.545 11G / 33G INFO General (simplification.cpp : 351) Triggered 0 times 1:26:02.545 11G / 33G INFO General (simplification.cpp : 349) Running Bulge remover 1:26:02.545 11G / 33G INFO General (simplification.cpp : 351) Triggered 0 times 1:26:02.545 11G / 33G INFO General (simplification.cpp : 460) PROCEDURE == Erroneous connection, iteration 11 1:26:02.545 11G / 33G INFO General (simplification.cpp : 349) Running Low coverage edge remover 1:26:02.545 11G / 33G INFO General (simplification.cpp : 351) Triggered 0 times 1:26:02.545 11G / 33G INFO General (simplification.cpp : 162) PROCEDURE == Post simplification 1:26:02.545 11G / 33G INFO General (graph_simplification.hpp : 446) Disconnection of relatively low covered edges disabled 1:26:02.545 11G / 33G INFO General (graph_simplification.hpp : 476) Complex tip clipping disabled 1:26:02.545 11G / 33G INFO General (graph_simplification.hpp : 617) Creating parallel br instance 1:26:02.545 11G / 33G INFO General (graph_simplification.hpp : 617) Creating parallel br instance 1:26:02.545 11G / 33G INFO General (simplification.cpp : 294) Iteration 0 1:26:02.545 11G / 33G INFO General (simplification.cpp : 349) Running Relative coverage component remover 1:26:03.809 11G / 33G INFO General (simplification.cpp : 351) Triggered 533 times 1:26:03.809 11G / 33G INFO General (simplification.cpp : 349) Running Relative coverage component remover 1:26:04.987 11G / 33G INFO General (simplification.cpp : 351) Triggered 5528 times 1:26:04.987 11G / 33G INFO General (simplification.cpp : 349) Running Complex bulge remover 1:26:26.338 11G / 33G INFO General (simplification.cpp : 351) Triggered 118 times 1:26:26.338 11G / 33G INFO General (simplification.cpp : 349) Running Tip clipper 1:26:27.669 11G / 33G INFO General (simplification.cpp : 351) Triggered 19 times 1:26:27.669 11G / 33G INFO General (simplification.cpp : 349) Running Final tip clipper 1:26:29.153 11G / 33G INFO General (simplification.cpp : 351) Triggered 9601 times 1:26:29.153 11G / 33G INFO General (simplification.cpp : 349) Running Bulge remover 1:26:30.346 11G / 33G INFO General (simplification.cpp : 351) Triggered 160 times 1:26:30.346 11G / 33G INFO General (simplification.cpp : 349) Running Final bulge remover 1:26:31.459 11G / 33G INFO General (simplification.cpp : 351) Triggered 0 times 1:26:31.459 11G / 33G INFO General (simplification.cpp : 349) Running AT Tips 1:26:32.699 11G / 33G INFO General (simplification.cpp : 351) Triggered 2101 times 1:26:32.699 11G / 33G INFO General (simplification.cpp : 294) Iteration 1 1:26:32.699 11G / 33G INFO General (simplification.cpp : 349) Running Relative coverage component remover 1:26:32.723 11G / 33G INFO General (simplification.cpp : 351) Triggered 18 times 1:26:32.723 11G / 33G INFO General (simplification.cpp : 349) Running Relative coverage component remover 1:26:33.706 11G / 33G INFO General (simplification.cpp : 351) Triggered 28 times 1:26:33.706 11G / 33G INFO General (simplification.cpp : 349) Running Complex bulge remover 1:26:54.981 11G / 33G INFO General (simplification.cpp : 351) Triggered 8 times 1:26:54.981 11G / 33G INFO General (simplification.cpp : 349) Running Tip clipper 1:26:55.013 11G / 33G INFO General (simplification.cpp : 351) Triggered 0 times 1:26:55.013 11G / 33G INFO General (simplification.cpp : 349) Running Final tip clipper 1:26:55.016 11G / 33G INFO General (simplification.cpp : 351) Triggered 7 times 1:26:55.016 11G / 33G INFO General (simplification.cpp : 349) Running Bulge remover 1:26:55.024 11G / 33G INFO General (simplification.cpp : 351) Triggered 3 times 1:26:55.024 11G / 33G INFO General (simplification.cpp : 349) Running Final bulge remover 1:26:55.026 11G / 33G INFO General (simplification.cpp : 351) Triggered 0 times 1:26:55.026 11G / 33G INFO General (simplification.cpp : 349) Running AT Tips 1:26:55.026 11G / 33G INFO General (simplification.cpp : 351) Triggered 0 times 1:26:55.026 11G / 33G INFO General (simplification.cpp : 294) Iteration 2 1:26:55.026 11G / 33G INFO General (simplification.cpp : 349) Running Relative coverage component remover 1:26:55.026 11G / 33G INFO General (simplification.cpp : 351) Triggered 0 times 1:26:55.026 11G / 33G INFO General (simplification.cpp : 349) Running Relative coverage component remover 1:26:56.496 11G / 33G INFO General (simplification.cpp : 351) Triggered 1 times 1:26:56.496 11G / 33G INFO General (simplification.cpp : 349) Running Complex bulge remover 1:27:18.522 11G / 33G INFO General (simplification.cpp : 351) Triggered 0 times 1:27:18.523 11G / 33G INFO General (simplification.cpp : 349) Running Tip clipper 1:27:18.523 11G / 33G INFO General (simplification.cpp : 351) Triggered 0 times 1:27:18.523 11G / 33G INFO General (simplification.cpp : 349) Running Final tip clipper 1:27:18.523 11G / 33G INFO General (simplification.cpp : 351) Triggered 0 times 1:27:18.523 11G / 33G INFO General (simplification.cpp : 349) Running Bulge remover 1:27:18.523 11G / 33G INFO General (simplification.cpp : 351) Triggered 0 times 1:27:18.523 11G / 33G INFO General (simplification.cpp : 349) Running Final bulge remover 1:27:18.523 11G / 33G INFO General (simplification.cpp : 351) Triggered 0 times 1:27:18.523 11G / 33G INFO General (simplification.cpp : 349) Running AT Tips 1:27:18.523 11G / 33G INFO General (simplification.cpp : 351) Triggered 0 times 1:27:18.523 11G / 33G INFO General (simplification.cpp : 294) Iteration 3 1:27:18.523 11G / 33G INFO General (simplification.cpp : 349) Running Relative coverage component remover 1:27:18.523 11G / 33G INFO General (simplification.cpp : 351) Triggered 0 times 1:27:18.523 11G / 33G INFO General (simplification.cpp : 349) Running Relative coverage component remover 1:27:19.840 11G / 33G INFO General (simplification.cpp : 351) Triggered 0 times 1:27:19.840 11G / 33G INFO General (simplification.cpp : 349) Running Complex bulge remover 1:27:41.060 11G / 33G INFO General (simplification.cpp : 351) Triggered 0 times 1:27:41.060 11G / 33G INFO General (simplification.cpp : 349) Running Tip clipper 1:27:41.061 11G / 33G INFO General (simplification.cpp : 351) Triggered 0 times 1:27:41.061 11G / 33G INFO General (simplification.cpp : 349) Running Final tip clipper 1:27:41.061 11G / 33G INFO General (simplification.cpp : 351) Triggered 0 times 1:27:41.061 11G / 33G INFO General (simplification.cpp : 349) Running Bulge remover 1:27:41.061 11G / 33G INFO General (simplification.cpp : 351) Triggered 0 times 1:27:41.061 11G / 33G INFO General (simplification.cpp : 349) Running Final bulge remover 1:27:41.061 11G / 33G INFO General (simplification.cpp : 351) Triggered 0 times 1:27:41.061 11G / 33G INFO General (simplification.cpp : 349) Running AT Tips 1:27:41.061 11G / 33G INFO General (simplification.cpp : 351) Triggered 0 times 1:27:41.061 11G / 33G INFO General (simplification.cpp : 326) Disrupting self-conjugate edges 1:27:47.286 11G / 33G INFO StageManager (stage.cpp : 126) STAGE == Gap Closer 1:27:47.286 11G / 33G INFO General (graph_pack.hpp : 96) Index refill 1:27:47.297 11G / 33G INFO K-mer Index Building (kmer_index_builder.hpp : 428) Building kmer index 1:27:47.297 11G / 33G INFO General (kmer_splitters.hpp : 214) Splitting kmer instances into 16 buckets. This might take a while. 1:27:47.297 11G / 33G INFO General (file_limit.hpp : 30) Open file limit set to 64000 1:27:47.297 11G / 33G INFO General (kmer_index_builder.hpp : 108) Memory available for splitting buffers: 74.5703 Gb 1:27:47.297 11G / 33G INFO General (kmer_index_builder.hpp : 116) Using cell size of 2097152 1:28:04.099 11G / 33G INFO General (kmer_splitters.hpp : 225) Processed 1181615 edges 1:28:21.239 11G / 33G INFO General (kmer_splitters.hpp : 225) Processed 2364800 edges 1:28:40.840 11G / 33G INFO General (kmer_splitters.hpp : 225) Processed 3548521 edges 1:28:57.336 11G / 33G INFO General (kmer_splitters.hpp : 225) Processed 4721813 edges 1:29:14.653 11G / 33G INFO General (kmer_splitters.hpp : 225) Processed 5891553 edges 1:29:16.385 11G / 33G INFO General (kmer_splitters.hpp : 225) Processed 5987031 edges 1:29:16.385 11G / 33G INFO General (kmer_splitters.hpp : 230) Used 5987031 sequences. 1:29:16.454 11G / 33G INFO General (kmer_index_builder.hpp : 252) Starting k-mer counting. 1:30:41.120 11G / 33G INFO General (kmer_index_builder.hpp : 258) K-mer counting done. There are 166037298 kmers in total. 1:30:41.120 11G / 33G INFO General (kmer_index_builder.hpp : 260) Merging temporary buckets. 1:31:45.442 11G / 33G INFO K-mer Index Building (kmer_index_builder.hpp : 437) Building perfect hash indices 1:32:59.336 11G / 33G INFO General (kmer_index_builder.hpp : 276) Merging final buckets. 1:33:52.787 11G / 33G INFO K-mer Index Building (kmer_index_builder.hpp : 483) Index built. Total 54247640 bytes occupied (2.61376 bits per kmer). 1:33:55.166 15G / 33G INFO General (edge_index_builders.hpp : 27) Collecting k-mer coverage information from graph, this takes a while. 1:34:04.730 15G / 33G INFO General (edge_index.hpp : 91) Index refilled 1:34:04.793 15G / 33G INFO General (gap_closer.cpp : 159) Preparing shift maps 1:34:17.997 15G / 33G INFO General (gap_closer.cpp : 119) Processing paired reads (takes a while) 1:35:53.573 16G / 33G INFO General (gap_closer.cpp : 138) Used 127432194 paired reads 1:35:53.573 16G / 33G INFO General (gap_closer.cpp : 140) Merging paired indices 1:36:20.022 15G / 33G INFO GapCloser (gap_closer.cpp : 347) Closing short gaps 1:36:45.283 15G / 33G INFO GapCloser (gap_closer.cpp : 381) Closing short gaps complete: filled 63443 gaps after checking 1253916 candidates 1:37:39.329 15G / 33G INFO StageManager (stage.cpp : 126) STAGE == Simplification Cleanup 1:37:39.329 15G / 33G INFO General (simplification.cpp : 561) Counting average coverage 1:37:42.716 15G / 33G INFO General (simplification.cpp : 566) Average coverage = 35.0483 1:37:42.716 15G / 33G INFO StageManager (stage.cpp : 126) STAGE == Mismatch Correction 1:37:42.716 15G / 33G INFO General (graph_pack.hpp : 105) Normalizing k-mer map. Total 13894959 kmers to process 1:37:53.959 15G / 33G INFO General (graph_pack.hpp : 107) Normalizing done 1:42:26.616 15G / 33G INFO General (mismatch_shall_not_pass.hp: 187) Finished collecting potential mismatches positions 1:42:44.574 15G / 33G INFO General (mismatch_shall_not_pass.hp: 284) All edges processed 1:42:45.561 15G / 33G INFO General (mismatch_correction.cpp : 26) Corrected 373 nucleotides 1:42:45.569 15G / 33G INFO StageManager (stage.cpp : 126) STAGE == Contig Output 1:42:45.569 15G / 33G INFO General (contig_output.hpp : 478) Outputting contigs to /data/home/pitagoras/public_html/gigas/transcriptome/rnaSpades/spadesRNA/output49//K49/pre_pe_before_rr.fasta 1:43:15.970 15G / 33G INFO General (contig_output.hpp : 518) Outputting graph to /data/home/pitagoras/public_html/gigas/transcriptome/rnaSpades/spadesRNA/output49//K49/pre_pe_assembly_graph.fastg 1:44:24.594 15G / 33G INFO General (contig_output.hpp : 478) Outputting contigs to /data/home/pitagoras/public_html/gigas/transcriptome/rnaSpades/spadesRNA/output49//K49/pre_pe_simplified_contigs.fasta 1:44:55.836 15G / 33G INFO General (contig_output.hpp : 478) Outputting contigs to /data/home/pitagoras/public_html/gigas/transcriptome/rnaSpades/spadesRNA/output49//K49/pre_pe_final_contigs.fasta 1:45:26.944 15G / 33G INFO StageManager (stage.cpp : 126) STAGE == Paired Information Counting 1:45:51.695 15G / 33G INFO General (graph_pack.hpp : 105) Normalizing k-mer map. Total 13911625 kmers to process 1:46:02.197 15G / 33G INFO General (graph_pack.hpp : 107) Normalizing done 1:46:04.644 15G / 33G INFO General (pair_info_count.cpp : 300) Min edge length for estimation: 153 1:46:04.644 15G / 33G INFO General (pair_info_count.cpp : 311) Estimating insert size for library #0 1:46:04.644 15G / 33G INFO General (pair_info_count.cpp : 116) Estimating insert size (takes a while) 1:46:04.834 15G / 33G INFO General (short_read_mapper.hpp : 88) Selecting usual mapper 1:46:07.247 15G / 33G INFO General (sequence_mapper_notifier.h: 82) Processed 200000 reads 1:46:07.281 15G / 33G INFO General (sequence_mapper_notifier.h: 82) Processed 400000 reads 1:46:07.313 15G / 33G INFO General (sequence_mapper_notifier.h: 82) Processed 600000 reads 1:46:07.345 15G / 33G INFO General (sequence_mapper_notifier.h: 82) Processed 800000 reads 1:46:07.377 15G / 33G INFO General (sequence_mapper_notifier.h: 82) Processed 1000000 reads 1:46:07.410 15G / 33G INFO General (sequence_mapper_notifier.h: 82) Processed 1200000 reads 1:46:07.572 15G / 33G INFO General (sequence_mapper_notifier.h: 82) Processed 2200000 reads 1:46:09.616 15G / 33G INFO General (sequence_mapper_notifier.h: 82) Processed 4200000 reads 1:46:12.011 15G / 33G INFO General (sequence_mapper_notifier.h: 82) Processed 8400000 reads 1:46:17.914 15G / 33G INFO General (sequence_mapper_notifier.h: 82) Processed 16800000 reads 1:46:29.220 15G / 33G INFO General (sequence_mapper_notifier.h: 82) Processed 33600000 reads 1:46:53.216 15G / 33G INFO General (sequence_mapper_notifier.h: 82) Processed 67200000 reads 1:47:37.817 15G / 33G INFO General (sequence_mapper_notifier.h: 100) Total 127432194 reads processed 1:47:39.203 15G / 33G INFO General (pair_info_count.cpp : 134) Edge pairs: 67108864 (rough upper limit) 1:47:39.203 15G / 33G INFO General (pair_info_count.cpp : 138) 72708186 paired reads (57.0564% of all) aligned to long edges 1:47:39.248 15G / 33G INFO General (pair_info_count.cpp : 334) Insert size = 155.689, deviation = 44.7431, left quantile = 110, right quantile = 214, read length = 76 1:47:39.248 15G / 33G INFO General (pair_info_count.cpp : 363) Mapping library #0 1:47:39.248 15G / 33G INFO General (pair_info_count.cpp : 365) Mapping paired reads (takes a while) 1:47:39.248 15G / 33G INFO General (pair_info_count.cpp : 204) Left insert size quantile 110, right insert size quantile 214, filtering threshold 0, rounding threshold 0 1:47:39.261 15G / 33G INFO General (short_read_mapper.hpp : 88) Selecting usual mapper 1:47:41.733 15G / 33G INFO General (sequence_mapper_notifier.h: 82) Processed 200000 reads 1:47:41.739 15G / 33G INFO General (sequence_mapper_notifier.h: 82) Processed 400000 reads 1:47:41.754 15G / 33G INFO General (sequence_mapper_notifier.h: 82) Processed 600000 reads 1:47:41.754 15G / 33G INFO General (sequence_mapper_notifier.h: 82) Processed 800000 reads 1:47:41.756 15G / 33G INFO General (sequence_mapper_notifier.h: 82) Processed 1000000 reads 1:47:41.762 15G / 33G INFO General (sequence_mapper_notifier.h: 82) Processed 1200000 reads 1:47:41.784 15G / 33G INFO General (sequence_mapper_notifier.h: 82) Processed 2200000 reads 1:47:44.271 15G / 33G INFO General (sequence_mapper_notifier.h: 82) Processed 4200000 reads 1:47:46.770 15G / 33G INFO General (sequence_mapper_notifier.h: 82) Processed 8400000 reads 1:47:54.293 15G / 33G INFO General (sequence_mapper_notifier.h: 82) Processed 16800000 reads 1:48:06.736 15G / 33G INFO General (sequence_mapper_notifier.h: 82) Processed 33600000 reads 1:48:37.682 16G / 33G INFO General (sequence_mapper_notifier.h: 82) Processed 67200000 reads 1:49:33.088 16G / 33G INFO General (sequence_mapper_notifier.h: 100) Total 127432194 reads processed 1:49:34.267 16G / 33G INFO StageManager (stage.cpp : 126) STAGE == Distance Estimation 1:49:34.267 16G / 33G INFO General (distance_estimation.cpp : 224) Processing library #0 1:49:34.267 16G / 33G INFO General (distance_estimation.cpp : 130) Weight Filter Done 1:49:34.267 16G / 33G INFO DistanceEstimator (distance_estimation.hpp : 176) Using SIMPLE distance estimator 1:49:39.047 16G / 33G INFO General (distance_estimation.cpp : 35) Filtering info 1:49:39.047 16G / 33G INFO General (pair_info_filters.hpp : 242) Start filtering; index size: 6320221 1:49:46.425 16G / 33G INFO General (pair_info_filters.hpp : 263) Done filtering 1:49:46.444 16G / 33G INFO General (distance_estimation.cpp : 172) Refining clustered pair information 1:49:46.942 16G / 33G INFO General (distance_estimation.cpp : 174) The refining of clustered pair information has been finished 1:49:46.942 16G / 33G INFO General (distance_estimation.cpp : 176) Improving paired information 1:49:55.426 16G / 33G INFO PairInfoImprover (pair_info_improver.hpp : 103) Paired info stats: missing = 36383; contradictional = 40 1:50:01.643 16G / 33G INFO PairInfoImprover (pair_info_improver.hpp : 103) Paired info stats: missing = 10455; contradictional = 24 1:50:01.643 16G / 33G INFO StageManager (stage.cpp : 126) STAGE == Repeat Resolving 1:50:01.643 16G / 33G INFO General (repeat_resolving.cpp : 68) Using Path-Extend repeat resolving 1:50:17.868 16G / 33G INFO General (launcher.cpp : 399) ExSPAnder repeat resolving tool started 1:50:54.942 28G / 33G INFO General (launcher.cpp : 357) Creating main extenders, unique edge length = 2000 1:51:00.165 28G / 33G INFO General (extenders_logic.cpp : 415) Using 1 paired-end library 1:51:00.165 28G / 33G INFO General (extenders_logic.cpp : 416) Using 1 paired-end scaffolding library 1:51:00.165 28G / 33G INFO General (extenders_logic.cpp : 417) Using 0 single read libraries 1:51:00.165 28G / 33G INFO General (launcher.cpp : 385) Total number of extenders is 4 1:51:00.165 28G / 33G INFO PathExtender (path_extender.hpp :1031) Processed 0 paths from 2929776 (0%) 1:51:00.210 28G / 33G INFO PathExtender (path_extender.hpp :1029) Processed 128 paths from 2929776 (0%) 1:51:00.241 28G / 33G INFO PathExtender (path_extender.hpp :1029) Processed 256 paths from 2929776 (0%) 1:51:00.286 28G / 33G INFO PathExtender (path_extender.hpp :1029) Processed 512 paths from 2929776 (0%) 1:51:00.372 28G / 33G INFO PathExtender (path_extender.hpp :1029) Processed 1024 paths from 2929776 (0%) 1:51:00.547 28G / 33G INFO PathExtender (path_extender.hpp :1029) Processed 2048 paths from 2929776 (0%) 1:51:00.923 28G / 33G INFO PathExtender (path_extender.hpp :1029) Processed 4096 paths from 2929776 (0%) 1:51:01.555 28G / 33G INFO PathExtender (path_extender.hpp :1029) Processed 8192 paths from 2929776 (0%) 1:51:02.673 28G / 33G INFO PathExtender (path_extender.hpp :1029) Processed 16384 paths from 2929776 (0%) 1:51:04.543 28G / 33G INFO PathExtender (path_extender.hpp :1029) Processed 32768 paths from 2929776 (1%) 1:51:07.441 29G / 33G INFO PathExtender (path_extender.hpp :1029) Processed 65536 paths from 2929776 (2%) 1:51:11.914 29G / 33G INFO PathExtender (path_extender.hpp :1029) Processed 131072 paths from 2929776 (4%) 1:51:16.859 29G / 33G INFO PathExtender (path_extender.hpp :1029) Processed 262144 paths from 2929776 (8%) 1:51:17.610 29G / 33G INFO PathExtender (path_extender.hpp :1031) Processed 292978 paths from 2929776 (10%) 1:51:25.480 30G / 33G INFO PathExtender (path_extender.hpp :1029) Processed 524288 paths from 2929776 (17%) 1:51:27.573 31G / 33G INFO PathExtender (path_extender.hpp :1031) Processed 585956 paths from 2929776 (20%) 1:51:34.167 32G / 33G INFO PathExtender (path_extender.hpp :1031) Processed 878934 paths from 2929776 (30%) 1:51:37.559 32G / 33G INFO PathExtender (path_extender.hpp :1029) Processed 1048576 paths from 2929776 (35%) 1:51:40.039 33G / 33G INFO PathExtender (path_extender.hpp :1031) Processed 1171912 paths from 2929776 (40%) 1:51:45.911 34G / 34G INFO PathExtender (path_extender.hpp :1031) Processed 1464890 paths from 2929776 (50%) 1:51:51.741 35G / 35G INFO PathExtender (path_extender.hpp :1031) Processed 1757868 paths from 2929776 (60%) 1:51:57.533 36G / 36G INFO PathExtender (path_extender.hpp :1031) Processed 2050846 paths from 2929776 (70%) 1:51:58.497 36G / 36G INFO PathExtender (path_extender.hpp :1029) Processed 2097152 paths from 2929776 (71%) 1:52:03.193 37G / 37G INFO PathExtender (path_extender.hpp :1031) Processed 2343824 paths from 2929776 (80%) 1:52:08.549 38G / 38G INFO PathExtender (path_extender.hpp :1031) Processed 2636802 paths from 2929776 (90%) 2:55:07.482 40G / 40G INFO General (launcher.cpp : 248) Traversing tandem repeats 2:56:19.734 40G / 40G INFO General (launcher.cpp : 258) Traversed 8 loops 2:56:19.734 40G / 40G INFO General (launcher.cpp : 391) Closing gaps in paths 2:56:23.197 41G / 41G INFO General (launcher.cpp : 395) Gap closing completed 4:46:24.690 52G / 52G INFO General (launcher.cpp : 445) ExSPAnder repeat resolving tool finished 4:46:59.719 38G / 52G INFO StageManager (stage.cpp : 126) STAGE == Contig Output 4:46:59.719 38G / 52G INFO General (contig_output.hpp : 478) Outputting contigs to /data/home/pitagoras/public_html/gigas/transcriptome/rnaSpades/spadesRNA/output49//K49/before_rr.fasta 4:47:41.682 38G / 52G INFO General (contig_output.hpp : 518) Outputting graph to /data/home/pitagoras/public_html/gigas/transcriptome/rnaSpades/spadesRNA/output49//K49/assembly_graph.fastg 4:49:43.962 39G / 52G INFO PathExtendIO (bidirectional_path_output.: 31) Writing contigs to /data/home/pitagoras/public_html/gigas/transcriptome/rnaSpades/spadesRNA/output49//K49/transcripts 4:49:56.718 39G / 52G INFO General (contig_output.hpp : 509) Outputting graph to /data/home/pitagoras/public_html/gigas/transcriptome/rnaSpades/spadesRNA/output49//K49/assembly_graph.gfa 4:50:29.210 38G / 52G INFO General (launch.hpp : 136) SPAdes finished 4:51:17.999 22G / 52G INFO General (main.cpp : 109) Assembling time: 4 hours 51 minutes 18 seconds ===== Assembling finished. Used k-mer sizes: 49 * Corrected reads are in /data/home/pitagoras/public_html/gigas/transcriptome/rnaSpades/spadesRNA/output49/corrected/ * Assembled transcripts are in /data/home/pitagoras/public_html/gigas/transcriptome/rnaSpades/spadesRNA/output49/transcripts.fasta * Paths in the assembly graph corresponding to the transcripts are in /data/home/pitagoras/public_html/gigas/transcriptome/rnaSpades/spadesRNA/output49/transcripts.paths ======= SPAdes pipeline finished. SPAdes log can be found here: /data/home/pitagoras/public_html/gigas/transcriptome/rnaSpades/spadesRNA/output49/spades.log Thank you for using SPAdes!