Command line: /data/home/root/SPAdes-3.10.1-Linux/bin/spades.py --cov-cutoff auto -k 45 --rna -o /data/home/pitagoras/public_html/gigas/transcriptome/rnaSpades/output45 --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/output45 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: [45] Repeat resolution is enabled Mismatch careful mode is turned OFF MismatchCorrector will be SKIPPED Coverage cutoff is turned ON and threshold will be auto-detected Other parameters: Dir for temp files: /data/home/pitagoras/public_html/gigas/transcriptome/rnaSpades/output45/tmp Threads: 16 Memory limit (in Gb): 220 ======= SPAdes pipeline started. Log can be found here: /data/home/pitagoras/public_html/gigas/transcriptome/rnaSpades/output45/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/output45/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/output45/corrected/configs/config.info 0:00:00.003 4M / 4M INFO General (memory_limit.hpp : 47) Memory limit set to 220 Gb 0:00:00.003 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 0:00:00.003 4M / 4M INFO General (hammer_tools.cpp : 36) Hamming graph threshold tau=1, k=21, subkmer positions = [ 0 10 ] 0:00:00.003 4M / 4M INFO General (main.cpp : 120) Size of aux. kmer data 24 bytes === ITERATION 0 begins === 0:00:00.018 4M / 4M INFO K-mer Index Building (kmer_index_builder.hpp : 428) Building kmer index 0:00:00.018 4M / 4M INFO K-mer Splitting (kmer_data.cpp : 91) Splitting kmer instances into 256 buckets. This might take a while. 0:00:00.018 4M / 4M INFO General (file_limit.hpp : 30) Open file limit set to 64000 0:00:00.018 4M / 4M INFO General (kmer_index_builder.hpp : 108) Memory available for splitting buffers: 4.58325 Gb 0:00:00.018 4M / 4M INFO General (kmer_index_builder.hpp : 116) Using cell size of 262144 0:00:00.096 8G / 8G INFO K-mer Splitting (kmer_data.cpp : 98) Processing /data2/process/RnaPira/trim/Ova_R2.t.fastq 0:00:20.201 8G / 8G INFO K-mer Splitting (kmer_data.cpp : 108) Processed 1060500 reads 0:00:38.930 8G / 8G INFO K-mer Splitting (kmer_data.cpp : 108) Processed 2212427 reads 0:00:56.355 8G / 8G INFO K-mer Splitting (kmer_data.cpp : 108) Processed 3419454 reads 0:01:15.894 8G / 8G INFO K-mer Splitting (kmer_data.cpp : 108) Processed 4440726 reads 0:01:33.661 8G / 8G INFO K-mer Splitting (kmer_data.cpp : 108) Processed 5620396 reads 0:01:57.368 8G / 8G INFO K-mer Splitting (kmer_data.cpp : 108) Processed 6809739 reads 0:02:24.385 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 108) Processed 8525114 reads 0:02:51.120 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 108) Processed 11119835 reads 0:03:14.934 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 108) Processed 13885839 reads 0:03:53.834 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 108) Processed 17142000 reads 0:06:40.230 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 98) Processing /data2/process/RnaPira/trim/Cerebro-femea_R2.t.fastq 0:08:15.990 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 108) Processed 34212093 reads 0:10:31.151 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 98) Processing /data2/process/RnaPira/trim/Cerebro-macho_R2.t.fastq 0:14:42.839 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 98) Processing /data2/process/RnaPira/trim/Pulmao-femea_R2.t.fastq 0:17:01.840 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 98) Processing /data2/process/RnaPira/trim/Pulmao-macho_R2.t.fastq 0:18:47.678 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 108) Processed 67252151 reads 0:21:33.412 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 98) Processing /data2/process/RnaPira/trim/Hipofise-femea_R2.t.fastq 0:24:26.273 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 98) Processing /data2/process/RnaPira/trim/Rim-femea_R2.t.fastq 0:26:58.712 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 98) Processing /data2/process/RnaPira/trim/Hipofise-macho_R2.t.fastq 0:29:19.085 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 98) Processing /data2/process/RnaPira/trim/Rim-macho_R2.t.fastq 0:33:56.222 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 98) Processing /data2/process/RnaPira/trim/Musculo-femea_R2.t.fastq 0:36:11.367 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 98) Processing /data2/process/RnaPira/trim/Testiculo_R2.t.fastq 0:38:09.969 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 98) Processing /data2/process/RnaPira/trim/Ova_R1.t.fastq 0:39:09.584 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 108) Processed 134910474 reads 0:44:28.435 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 98) Processing /data2/process/RnaPira/trim/Cerebro-femea_R1.t.fastq 0:48:42.714 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 98) Processing /data2/process/RnaPira/trim/Cerebro-macho_R1.t.fastq 0:52:46.900 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 98) Processing /data2/process/RnaPira/trim/Pulmao-femea_R1.t.fastq 0:54:57.587 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 98) Processing /data2/process/RnaPira/trim/Pulmao-macho_R1.t.fastq 0:59:16.239 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 98) Processing /data2/process/RnaPira/trim/Hipofise-femea_R1.t.fastq 1:01:51.363 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 98) Processing /data2/process/RnaPira/trim/Rim-femea_R1.t.fastq 1:04:08.899 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 98) Processing /data2/process/RnaPira/trim/Hipofise-macho_R1.t.fastq 1:06:25.259 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 98) Processing /data2/process/RnaPira/trim/Rim-macho_R1.t.fastq 1:09:27.953 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 98) Processing /data2/process/RnaPira/trim/Musculo-femea_R1.t.fastq 1:11:28.944 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 98) Processing /data2/process/RnaPira/trim/Testiculo_R1.t.fastq 1:14:31.127 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 113) Total 262072356 reads processed 1:14:31.787 64M / 9G INFO General (kmer_index_builder.hpp : 252) Starting k-mer counting. 1:58:00.821 64M / 9G INFO General (kmer_index_builder.hpp : 258) K-mer counting done. There are 853373588 kmers in total. 1:58:00.821 64M / 9G INFO General (kmer_index_builder.hpp : 260) Merging temporary buckets. 2:02:40.312 64M / 9G INFO K-mer Index Building (kmer_index_builder.hpp : 437) Building perfect hash indices 2:04:10.609 320M / 21G INFO General (kmer_index_builder.hpp : 276) Merging final buckets. 2:07:40.563 320M / 21G INFO K-mer Index Building (kmer_index_builder.hpp : 483) Index built. Total 278813288 bytes occupied (2.61375 bits per kmer). 2:07:40.755 320M / 21G INFO K-mer Counting (kmer_data.cpp : 359) Arranging kmers in hash map order 2:11:34.986 13G / 21G INFO General (main.cpp : 155) Clustering Hamming graph. 3:05:08.136 13G / 21G INFO General (main.cpp : 162) Extracting clusters 3:22:54.035 13G / 37G INFO General (main.cpp : 174) Clustering done. Total clusters: 471673936 3:22:55.660 6G / 37G INFO K-mer Counting (kmer_data.cpp : 381) Collecting K-mer information, this takes a while. 3:23:11.640 25G / 37G INFO K-mer Counting (kmer_data.cpp : 387) Processing /data2/process/RnaPira/trim/Ova_R2.t.fastq 3:31:07.469 25G / 37G INFO K-mer Counting (kmer_data.cpp : 387) Processing /data2/process/RnaPira/trim/Cerebro-femea_R2.t.fastq 3:34:34.737 25G / 37G INFO K-mer Counting (kmer_data.cpp : 387) Processing /data2/process/RnaPira/trim/Cerebro-macho_R2.t.fastq 3:37:43.508 25G / 37G INFO K-mer Counting (kmer_data.cpp : 387) Processing /data2/process/RnaPira/trim/Pulmao-femea_R2.t.fastq 3:39:28.631 25G / 37G INFO K-mer Counting (kmer_data.cpp : 387) Processing /data2/process/RnaPira/trim/Pulmao-macho_R2.t.fastq 3:43:42.138 25G / 37G INFO K-mer Counting (kmer_data.cpp : 387) Processing /data2/process/RnaPira/trim/Hipofise-femea_R2.t.fastq 3:46:29.157 25G / 37G INFO K-mer Counting (kmer_data.cpp : 387) Processing /data2/process/RnaPira/trim/Rim-femea_R2.t.fastq 3:48:39.359 25G / 37G INFO K-mer Counting (kmer_data.cpp : 387) Processing /data2/process/RnaPira/trim/Hipofise-macho_R2.t.fastq 3:50:37.746 25G / 37G INFO K-mer Counting (kmer_data.cpp : 387) Processing /data2/process/RnaPira/trim/Rim-macho_R2.t.fastq 3:53:00.180 25G / 37G INFO K-mer Counting (kmer_data.cpp : 387) Processing /data2/process/RnaPira/trim/Musculo-femea_R2.t.fastq 3:55:53.930 25G / 37G INFO K-mer Counting (kmer_data.cpp : 387) Processing /data2/process/RnaPira/trim/Testiculo_R2.t.fastq 3:57:37.642 25G / 37G INFO K-mer Counting (kmer_data.cpp : 387) Processing /data2/process/RnaPira/trim/Ova_R1.t.fastq 4:05:48.058 25G / 37G INFO K-mer Counting (kmer_data.cpp : 387) Processing /data2/process/RnaPira/trim/Cerebro-femea_R1.t.fastq 4:09:24.860 25G / 37G INFO K-mer Counting (kmer_data.cpp : 387) Processing /data2/process/RnaPira/trim/Cerebro-macho_R1.t.fastq 4:12:43.518 25G / 37G INFO K-mer Counting (kmer_data.cpp : 387) Processing /data2/process/RnaPira/trim/Pulmao-femea_R1.t.fastq 4:14:40.840 25G / 37G INFO K-mer Counting (kmer_data.cpp : 387) Processing /data2/process/RnaPira/trim/Pulmao-macho_R1.t.fastq 4:19:10.237 25G / 37G INFO K-mer Counting (kmer_data.cpp : 387) Processing /data2/process/RnaPira/trim/Hipofise-femea_R1.t.fastq 4:22:03.399 25G / 37G INFO K-mer Counting (kmer_data.cpp : 387) Processing /data2/process/RnaPira/trim/Rim-femea_R1.t.fastq 4:24:18.535 25G / 37G INFO K-mer Counting (kmer_data.cpp : 387) Processing /data2/process/RnaPira/trim/Hipofise-macho_R1.t.fastq 4:26:17.313 25G / 37G INFO K-mer Counting (kmer_data.cpp : 387) Processing /data2/process/RnaPira/trim/Rim-macho_R1.t.fastq 4:28:48.571 25G / 37G INFO K-mer Counting (kmer_data.cpp : 387) Processing /data2/process/RnaPira/trim/Musculo-femea_R1.t.fastq 4:31:54.160 25G / 37G INFO K-mer Counting (kmer_data.cpp : 387) Processing /data2/process/RnaPira/trim/Testiculo_R1.t.fastq 4:33:51.590 25G / 37G INFO K-mer Counting (kmer_data.cpp : 394) Collection done, postprocessing. 4:33:58.725 25G / 37G INFO K-mer Counting (kmer_data.cpp : 408) There are 853373588 kmers in total. Among them 453841768 (53.1821%) are singletons. 4:33:58.726 25G / 37G INFO General (main.cpp : 180) Subclustering Hamming graph 5:02:26.054 25G / 37G INFO Hamming Subclustering (kmer_cluster.cpp : 649) Subclustering done. Total 14721 non-read kmers were generated. 5:02:26.054 25G / 37G INFO Hamming Subclustering (kmer_cluster.cpp : 650) Subclustering statistics: 5:02:26.054 25G / 37G INFO Hamming Subclustering (kmer_cluster.cpp : 651) Total singleton hamming clusters: 373384962. Among them 197438274 (52.8779%) are good 5:02:26.054 25G / 37G INFO Hamming Subclustering (kmer_cluster.cpp : 652) Total singleton subclusters: 4429129. Among them 4416959 (99.7252%) are good 5:02:26.054 25G / 37G INFO Hamming Subclustering (kmer_cluster.cpp : 653) Total non-singleton subcluster centers: 106094099. Among them 76151974 (71.7778%) are good 5:02:26.054 25G / 37G INFO Hamming Subclustering (kmer_cluster.cpp : 654) Average size of non-trivial subcluster: 4.52464 kmers 5:02:26.054 25G / 37G INFO Hamming Subclustering (kmer_cluster.cpp : 655) Average number of sub-clusters per non-singleton cluster: 1.12447 5:02:26.054 25G / 37G INFO Hamming Subclustering (kmer_cluster.cpp : 656) Total solid k-mers: 278007207 5:02:26.054 25G / 37G INFO Hamming Subclustering (kmer_cluster.cpp : 657) Substitution probabilities: [4,4]((0.935096,0.0147379,0.0157104,0.0344558),(0.023117,0.922563,0.0103453,0.0439744),(0.042623,0.00995326,0.923121,0.0243023),(0.0332823,0.0150135,0.0143422,0.937362)) 5:02:27.307 25G / 37G INFO General (main.cpp : 185) Finished clustering. 5:02:27.308 25G / 37G INFO General (main.cpp : 204) Starting solid k-mers expansion in 16 threads. 5:28:44.739 25G / 37G INFO General (main.cpp : 225) Solid k-mers iteration 0 produced 26920448 new k-mers. 5:53:22.319 25G / 37G INFO General (main.cpp : 225) Solid k-mers iteration 1 produced 2198266 new k-mers. 6:17:33.833 25G / 37G INFO General (main.cpp : 225) Solid k-mers iteration 2 produced 175001 new k-mers. 6:41:40.937 25G / 37G INFO General (main.cpp : 225) Solid k-mers iteration 3 produced 21683 new k-mers. 7:06:09.925 25G / 37G INFO General (main.cpp : 225) Solid k-mers iteration 4 produced 3797 new k-mers. 7:30:25.079 25G / 37G INFO General (main.cpp : 225) Solid k-mers iteration 5 produced 595 new k-mers. 7:54:24.456 25G / 37G INFO General (main.cpp : 225) Solid k-mers iteration 6 produced 86 new k-mers. 8:18:51.863 25G / 37G INFO General (main.cpp : 225) Solid k-mers iteration 7 produced 49 new k-mers. 8:43:10.997 25G / 37G INFO General (main.cpp : 225) Solid k-mers iteration 8 produced 15 new k-mers. 9:07:07.481 25G / 37G INFO General (main.cpp : 225) Solid k-mers iteration 9 produced 29 new k-mers. 9:30:44.792 25G / 37G INFO General (main.cpp : 225) Solid k-mers iteration 10 produced 0 new k-mers. 9:30:44.793 25G / 37G INFO General (main.cpp : 229) Solid k-mers finalized 9:30:44.793 25G / 37G INFO General (hammer_tools.cpp : 211) Starting read correction in 16 threads. 9:30:44.793 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 9:30:50.808 26G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 0 of 1600000 reads. 9:31:08.341 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 0 9:31:13.959 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 0 9:31:19.427 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 1 of 1600000 reads. 9:31:37.019 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 1 9:31:42.101 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 1 9:31:46.951 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 2 of 1600000 reads. 9:32:01.885 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 2 9:32:06.640 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 2 9:32:10.794 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 3 of 1600000 reads. 9:32:27.071 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 3 9:32:31.842 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 3 9:32:35.827 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 4 of 1600000 reads. 9:32:51.380 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 4 9:33:10.402 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 4 9:33:15.098 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 5 of 1600000 reads. 9:33:31.625 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 5 9:33:36.445 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 5 9:33:41.053 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 6 of 1600000 reads. 9:33:58.006 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 6 9:34:02.241 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 6 9:34:07.039 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 7 of 1600000 reads. 9:34:24.645 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 7 9:34:34.546 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 7 9:34:39.059 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 8 of 1600000 reads. 9:34:54.255 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 8 9:35:04.786 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 8 9:35:09.557 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 9 of 1600000 reads. 9:35:25.746 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 9 9:35:36.266 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 9 9:35:41.488 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 10 of 1600000 reads. 9:35:56.654 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 10 9:36:05.943 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 10 9:36:10.389 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 11 of 1600000 reads. 9:36:26.746 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 11 9:36:38.621 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 11 9:36:43.152 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 12 of 1600000 reads. 9:36:57.879 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 12 9:37:07.463 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 12 9:37:12.266 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 13 of 1600000 reads. 9:37:28.430 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 13 9:37:39.161 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 13 9:37:44.693 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 14 of 1600000 reads. 9:38:00.304 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 14 9:38:09.242 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 14 9:38:14.004 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 15 of 1600000 reads. 9:38:31.068 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 15 9:38:40.223 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 15 9:38:45.233 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 16 of 1600000 reads. 9:39:00.436 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 16 9:39:12.634 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 16 9:39:17.422 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 17 of 1600000 reads. 9:39:30.900 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 17 9:39:43.531 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 17 9:39:45.906 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 18 of 811697 reads. 9:39:55.931 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 18 9:40:10.320 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 18 9:40:22.242 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 9:40:27.504 26G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 0 of 1600000 reads. 9:40:42.341 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 0 9:40:46.686 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 0 9:40:51.580 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 1 of 1600000 reads. 9:41:05.712 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 1 9:41:10.108 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 1 9:41:14.392 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 2 of 1600000 reads. 9:41:31.196 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 2 9:41:35.061 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 2 9:41:39.071 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 3 of 1600000 reads. 9:41:58.904 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 3 9:42:03.779 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 3 9:42:08.171 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 4 of 1600000 reads. 9:42:21.558 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 4 9:42:31.656 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 4 9:42:36.753 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 5 of 1600000 reads. 9:42:50.860 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 5 9:42:58.343 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 5 9:43:03.391 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 6 of 1600000 reads. 9:43:17.990 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 6 9:43:29.469 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 6 9:43:34.187 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 7 of 1600000 reads. 9:43:49.853 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 7 9:43:59.962 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 7 9:44:02.557 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 8 of 811070 reads. 9:44:12.890 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 8 9:44:15.402 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 8 9:44:37.721 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 9:44:42.971 26G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 0 of 1600000 reads. 9:44:56.399 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 0 9:45:01.256 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 0 9:45:06.857 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 1 of 1600000 reads. 9:45:20.881 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 1 9:45:26.180 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 1 9:45:31.090 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 2 of 1600000 reads. 9:45:44.998 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 2 9:45:54.995 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 2 9:45:59.187 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 3 of 1600000 reads. 9:46:13.336 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 3 9:46:18.654 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 3 9:46:23.884 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 4 of 1600000 reads. 9:46:41.386 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 4 9:46:46.734 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 4 9:46:51.664 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 5 of 1600000 reads. 9:47:06.580 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 5 9:47:26.574 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 5 9:47:31.298 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 6 of 1600000 reads. 9:47:49.000 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 6 9:47:53.216 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 6 9:47:55.321 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 7 of 700384 reads. 9:48:03.508 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 7 9:48:11.636 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 7 9:48:27.888 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 9:48:35.048 26G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 0 of 1600000 reads. 9:48:49.166 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 0 9:48:53.639 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 0 9:48:59.139 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 1 of 1600000 reads. 9:49:14.731 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 1 9:49:18.763 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 1 9:49:23.224 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 2 of 1600000 reads. 9:49:39.366 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 2 9:49:44.278 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 2 9:49:48.185 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 3 of 1600000 reads. 9:50:03.230 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 3 9:50:07.431 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 3 9:50:08.565 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 4 of 442334 reads. 9:50:12.404 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 4 9:50:13.436 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 4 9:50:37.449 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 9:50:42.977 26G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 0 of 1600000 reads. 9:50:58.006 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 0 9:51:04.556 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 0 9:51:09.879 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 1 of 1600000 reads. 9:51:24.445 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 1 9:51:28.807 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 1 9:51:33.837 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 2 of 1600000 reads. 9:51:48.342 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 2 9:51:54.969 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 2 9:51:58.707 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 3 of 1600000 reads. 9:52:15.060 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 3 9:52:26.288 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 3 9:52:30.976 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 4 of 1600000 reads. 9:52:44.983 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 4 9:52:56.711 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 4 9:53:00.726 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 5 of 1600000 reads. 9:53:16.041 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 5 9:53:20.392 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 5 9:53:24.608 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 6 of 1600000 reads. 9:53:40.077 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 6 9:53:49.562 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 6 9:53:53.355 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 7 of 1600000 reads. 9:54:08.699 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 7 9:54:21.558 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 7 9:54:25.967 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 8 of 1600000 reads. 9:54:42.907 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 8 9:54:51.986 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 8 9:54:56.615 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 9 of 1600000 reads. 9:55:10.950 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 9 9:55:22.338 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 9 9:55:22.972 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 10 of 228975 reads. 9:55:25.754 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 10 9:55:26.336 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 10 9:55:50.217 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 9:55:55.751 26G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 0 of 1600000 reads. 9:56:09.414 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 0 9:56:13.635 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 0 9:56:18.702 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 1 of 1600000 reads. 9:56:35.046 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 1 9:56:39.176 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 1 9:56:44.296 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 2 of 1600000 reads. 9:57:02.529 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 2 9:57:06.973 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 2 9:57:11.161 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 3 of 1600000 reads. 9:57:29.674 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 3 9:57:33.548 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 3 9:57:37.684 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 4 of 1600000 reads. 9:57:51.293 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 4 9:57:58.141 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 4 9:58:01.962 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 5 of 1600000 reads. 9:58:15.524 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 5 9:58:26.107 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 5 9:58:28.230 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 6 of 862876 reads. 9:58:36.506 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 6 9:58:39.087 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 6 9:59:02.206 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 9:59:08.122 26G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 0 of 1600000 reads. 9:59:23.842 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 0 9:59:28.279 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 0 9:59:33.828 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 1 of 1600000 reads. 9:59:50.338 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 1 10:00:09.685 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 1 10:00:13.568 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 2 of 1600000 reads. 10:00:26.483 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 2 10:00:32.980 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 2 10:00:37.903 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 3 of 1600000 reads. 10:00:52.712 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 3 10:01:16.368 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 3 10:01:20.544 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 4 of 1600000 reads. 10:01:35.015 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 4 10:01:39.473 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 4 10:01:41.052 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 5 of 531717 reads. 10:01:46.592 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 5 10:01:48.195 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 5 10:02:07.490 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 10:02:12.790 26G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 0 of 1600000 reads. 10:02:27.310 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 0 10:02:31.750 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 0 10:02:37.244 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 1 of 1600000 reads. 10:02:55.103 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 1 10:03:15.949 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 1 10:03:21.141 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 2 of 1600000 reads. 10:03:36.412 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 2 10:03:40.789 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 2 10:03:47.053 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 3 of 1600000 reads. 10:03:59.724 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 3 10:04:03.252 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 3 10:04:05.116 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 4 of 678859 reads. 10:04:11.043 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 4 10:04:22.255 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 4 10:04:33.796 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 10:04:39.675 26G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 0 of 1600000 reads. 10:04:56.257 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 0 10:05:00.748 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 0 10:05:06.494 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 1 of 1600000 reads. 10:05:22.659 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 1 10:05:27.493 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 1 10:05:33.515 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 2 of 1600000 reads. 10:05:50.395 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 2 10:05:54.930 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 2 10:05:59.236 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 3 of 1600000 reads. 10:06:12.770 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 3 10:06:20.035 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 3 10:06:24.916 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 4 of 1600000 reads. 10:06:40.872 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 4 10:06:49.991 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 4 10:06:53.071 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 5 of 880546 reads. 10:07:03.224 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 5 10:07:05.529 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 5 10:07:37.033 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 10:07:45.999 26G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 0 of 1600000 reads. 10:08:01.022 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 0 10:08:04.925 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 0 10:08:16.035 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 1 of 1600000 reads. 10:08:30.288 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 1 10:08:48.932 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 1 10:09:01.317 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 2 of 1600000 reads. 10:09:16.135 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 2 10:09:19.972 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 2 10:09:28.062 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 3 of 1600000 reads. 10:09:43.312 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 3 10:09:48.270 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 3 10:09:56.460 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 4 of 1600000 reads. 10:10:10.554 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 4 10:10:32.483 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 4 10:10:43.194 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 5 of 1600000 reads. 10:10:59.363 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 5 10:11:03.222 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 5 10:11:12.736 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 6 of 1600000 reads. 10:11:28.825 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 6 10:11:33.054 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 6 10:11:34.909 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 7 of 359991 reads. 10:11:39.530 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 7 10:11:54.235 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 7 10:12:04.159 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 10:12:14.881 26G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 0 of 1600000 reads. 10:12:28.613 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 0 10:12:32.368 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 0 10:12:45.432 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 1 of 1600000 reads. 10:13:01.766 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 1 10:13:11.331 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 1 10:13:19.039 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 2 of 1600000 reads. 10:13:35.745 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 2 10:13:42.980 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 2 10:13:53.582 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 3 of 1527729 reads. 10:14:09.970 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 3 10:14:16.579 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 3 10:14:46.392 25G / 37G INFO General (hammer_tools.cpp : 270) Correction done. Changed 15371617 bases in 10325357 reads. 10:14:46.392 25G / 37G INFO General (hammer_tools.cpp : 271) Failed to correct 20707 bases out of 19020763726. 10:14:54.675 64M / 37G INFO General (main.cpp : 262) Saving corrected dataset description to /data/home/pitagoras/public_html/gigas/transcriptome/rnaSpades/output45/corrected/corrected.yaml 10:14:54.850 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/output45/corrected/corrected.yaml ===== Read error correction finished. ===== Assembling started. == Running assembler: K45 0:00:00.000 4M / 4M INFO General (main.cpp : 75) Loading config from /data/home/pitagoras/public_html/gigas/transcriptome/rnaSpades/output45/K45/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/output45/K45/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/output45/K45/configs/rna_mode.info 0:00:00.000 4M / 4M INFO General (memory_limit.hpp : 47) Memory limit set to 220 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/output45/dataset.info) with K=45 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 0:00:00.047 4M / 4M INFO General (launch.hpp : 79) Will need read mapping, kmer mapper will be attached 0:00:00.047 4M / 4M INFO StageManager (stage.cpp : 126) STAGE == Construction 0:00:00.060 4M / 4M INFO General (read_converter.hpp : 84) Converting reads to binary format for library #0 (takes a while) 0:00:00.060 4M / 4M INFO General (read_converter.hpp : 85) Converting paired reads 0:00:00.382 80M / 80M INFO General (binary_converter.hpp : 139) 16384 reads processed 0:00:00.515 88M / 88M INFO General (binary_converter.hpp : 139) 32768 reads processed 0:00:00.769 108M / 108M INFO General (binary_converter.hpp : 139) 65536 reads processed 0:00:01.316 148M / 148M INFO General (binary_converter.hpp : 139) 131072 reads processed 0:00:02.324 228M / 228M INFO General (binary_converter.hpp : 139) 262144 reads processed 0:00:04.491 392M / 392M INFO General (binary_converter.hpp : 139) 524288 reads processed 0:00:10.592 640M / 640M INFO General (binary_converter.hpp : 139) 1048576 reads processed 0:00:20.491 640M / 640M INFO General (binary_converter.hpp : 139) 2097152 reads processed 0:00:38.846 640M / 640M INFO General (binary_converter.hpp : 139) 4194304 reads processed 0:01:16.046 640M / 640M INFO General (binary_converter.hpp : 139) 8388608 reads processed 0:02:33.304 644M / 644M INFO General (binary_converter.hpp : 139) 16777216 reads processed 0:05:07.836 648M / 648M INFO General (binary_converter.hpp : 139) 33554432 reads processed 0:10:32.928 656M / 656M INFO General (binary_converter.hpp : 139) 67108864 reads processed 0:17:53.637 656M / 660M INFO General (binary_converter.hpp : 159) 127434831 reads written 0:17:54.723 8M / 660M INFO General (read_converter.hpp : 94) Converting single reads 0:17:55.057 140M / 660M INFO General (binary_converter.hpp : 139) 16384 reads processed 0:17:55.094 144M / 660M INFO General (binary_converter.hpp : 139) 32768 reads processed 0:17:55.169 152M / 660M INFO General (binary_converter.hpp : 139) 65536 reads processed 0:17:55.319 172M / 660M INFO General (binary_converter.hpp : 139) 131072 reads processed 0:17:55.620 212M / 660M INFO General (binary_converter.hpp : 139) 262144 reads processed 0:17:56.224 292M / 660M INFO General (binary_converter.hpp : 139) 524288 reads processed 0:17:57.426 448M / 660M INFO General (binary_converter.hpp : 139) 1048576 reads processed 0:17:59.815 764M / 764M INFO General (binary_converter.hpp : 139) 2097152 reads processed 0:18:04.463 1G / 1G INFO General (binary_converter.hpp : 159) 3531379 reads written 0:18:11.721 4M / 1G INFO General (graph_construction.hpp : 120) Constructing DeBruijn graph for k=45 0:18:11.803 4M / 1G INFO General (kmer_splitters.hpp : 129) Splitting kmer instances into 256 buckets. This might take a while. 0:18:11.804 4M / 1G INFO General (file_limit.hpp : 30) Open file limit set to 64000 0:18:11.824 4M / 1G INFO General (kmer_index_builder.hpp : 108) Memory available for splitting buffers: 4.58325 Gb 0:18:11.824 4M / 1G INFO General (kmer_index_builder.hpp : 116) Using cell size of 131072 0:18:19.914 8G / 8G INFO General (kmer_splitters.hpp : 153) Processed 2699360 reads 0:18:33.622 8G / 8G INFO General (kmer_splitters.hpp : 153) Processed 6186303 reads 0:18:40.721 8G / 8G INFO General (kmer_splitters.hpp : 153) Processed 8693915 reads 0:18:49.899 8G / 8G INFO General (kmer_splitters.hpp : 153) Processed 12201442 reads 0:19:00.004 8G / 8G INFO General (kmer_splitters.hpp : 153) Processed 15564920 reads 0:19:06.493 8G / 8G INFO General (kmer_splitters.hpp : 153) Processed 17883413 reads 0:19:14.475 8G / 8G INFO General (kmer_splitters.hpp : 153) Processed 20992167 reads 0:19:28.302 8G / 8G INFO General (kmer_splitters.hpp : 153) Processed 23661926 reads 0:19:40.168 8G / 8G INFO General (kmer_splitters.hpp : 153) Processed 26613280 reads 0:19:51.020 8G / 8G INFO General (kmer_splitters.hpp : 153) Processed 29574546 reads 0:20:07.583 8G / 9G INFO General (kmer_splitters.hpp : 153) Processed 40148270 reads 0:21:05.907 8G / 9G INFO General (kmer_splitters.hpp : 153) Processed 67315959 reads 0:24:50.379 8G / 9G INFO General (kmer_splitters.hpp : 153) Processed 140575405 reads 0:34:48.909 8G / 9G INFO General (kmer_splitters.hpp : 153) Processed 269790088 reads 0:51:47.065 8G / 9G INFO General (kmer_splitters.hpp : 159) Adding contigs from previous K 0:51:47.636 64M / 9G INFO General (kmer_splitters.hpp : 172) Used 516802082 reads. Maximum read length 76 0:51:47.636 64M / 9G INFO General (kmer_splitters.hpp : 173) Average read length 73.1881 0:51:47.636 64M / 9G INFO General (kmer_index_builder.hpp : 252) Starting k-mer counting. 0:58:54.394 64M / 9G INFO General (kmer_index_builder.hpp : 258) K-mer counting done. There are 239760688 kmers in total. 0:58:54.394 64M / 9G INFO General (kmer_index_builder.hpp : 260) Merging temporary buckets. 1:00:24.256 64M / 9G INFO K-mer Index Building (kmer_index_builder.hpp : 428) Building kmer index 1:00:24.256 64M / 9G INFO General (kmer_splitters.hpp : 285) Splitting kmer instances into 256 buckets. This might take a while. 1:00:24.256 64M / 9G INFO General (file_limit.hpp : 30) Open file limit set to 64000 1:00:24.256 64M / 9G INFO General (kmer_index_builder.hpp : 108) Memory available for splitting buffers: 4.58203 Gb 1:00:24.256 64M / 9G INFO General (kmer_index_builder.hpp : 116) Using cell size of 131072 1:02:12.055 8G / 9G INFO General (kmer_splitters.hpp : 304) Processed 239760688 kmers 1:02:12.057 8G / 9G INFO General (kmer_splitters.hpp : 309) Used 239760688 kmers. 1:02:13.371 64M / 9G INFO General (kmer_index_builder.hpp : 252) Starting k-mer counting. 1:03:31.362 64M / 9G INFO General (kmer_index_builder.hpp : 258) K-mer counting done. There are 242139293 kmers in total. 1:03:31.363 64M / 9G INFO General (kmer_index_builder.hpp : 260) Merging temporary buckets. 1:06:07.171 64M / 9G INFO K-mer Index Building (kmer_index_builder.hpp : 437) Building perfect hash indices 1:06:17.698 192M / 9G INFO General (kmer_index_builder.hpp : 276) Merging final buckets. 1:09:08.374 192M / 9G INFO K-mer Index Building (kmer_index_builder.hpp : 483) Index built. Total 79111584 bytes occupied (2.61375 bits per kmer). 1:09:08.681 424M / 9G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 85) Building k-mer extensions from k+1-mers 1:09:34.892 424M / 9G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 89) Building k-mer extensions from k+1-mers finished. 1:09:35.227 424M / 9G INFO General (graph_construction.hpp : 136) Condensing graph 1:09:35.227 424M / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 340) Extracting unbranching paths 1:11:56.132 3G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths finished. 33752573 sequences extracted 1:12:15.101 3G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 313) Collecting perfect loops 1:13:16.053 3G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 329) Collecting perfect loops finished. 26 loops collected 1:13:33.288 8G / 10G INFO General (graph_construction.hpp : 141) Building index with from graph 1:13:33.550 8G / 10G INFO K-mer Index Building (kmer_index_builder.hpp : 428) Building kmer index 1:13:33.550 8G / 10G INFO General (kmer_splitters.hpp : 214) Splitting kmer instances into 16 buckets. This might take a while. 1:13:33.550 8G / 10G INFO General (file_limit.hpp : 30) Open file limit set to 64000 1:13:33.550 8G / 10G INFO General (kmer_index_builder.hpp : 108) Memory available for splitting buffers: 70.556 Gb 1:13:33.550 8G / 10G INFO General (kmer_index_builder.hpp : 116) Using cell size of 2097152 1:13:57.759 8G / 10G INFO General (kmer_splitters.hpp : 225) Processed 4097596 edges 1:14:20.900 8G / 10G INFO General (kmer_splitters.hpp : 225) Processed 8203576 edges 1:14:45.229 8G / 10G INFO General (kmer_splitters.hpp : 225) Processed 12304585 edges 1:15:11.061 8G / 10G INFO General (kmer_splitters.hpp : 225) Processed 16406982 edges 1:15:29.974 8G / 10G INFO General (kmer_splitters.hpp : 225) Processed 20505524 edges 1:15:46.443 8G / 10G INFO General (kmer_splitters.hpp : 225) Processed 24597545 edges 1:16:05.073 8G / 10G INFO General (kmer_splitters.hpp : 225) Processed 28703384 edges 1:16:24.603 8G / 10G INFO General (kmer_splitters.hpp : 225) Processed 32801353 edges 1:16:31.360 8G / 10G INFO General (kmer_splitters.hpp : 225) Processed 33752607 edges 1:16:31.360 8G / 10G INFO General (kmer_splitters.hpp : 230) Used 33752607 sequences. 1:16:31.461 8G / 10G INFO General (kmer_index_builder.hpp : 252) Starting k-mer counting. 1:19:28.935 8G / 10G INFO General (kmer_index_builder.hpp : 258) K-mer counting done. There are 239760688 kmers in total. 1:19:28.935 8G / 10G INFO General (kmer_index_builder.hpp : 260) Merging temporary buckets. 1:21:25.189 8G / 10G INFO K-mer Index Building (kmer_index_builder.hpp : 437) Building perfect hash indices 1:23:14.194 8G / 10G INFO General (kmer_index_builder.hpp : 276) Merging final buckets. 1:24:20.243 8G / 10G INFO K-mer Index Building (kmer_index_builder.hpp : 483) Index built. Total 78334464 bytes occupied (2.61376 bits per kmer). 1:24:23.885 13G / 13G INFO General (edge_index_builders.hpp : 27) Collecting k-mer coverage information from graph, this takes a while. 1:24:41.000 13G / 13G INFO General (edge_index.hpp : 91) Index refilled 1:24:42.767 13G / 13G INFO General (graph_construction.hpp : 173) Filling coverage index 1:24:42.767 13G / 13G INFO General (edge_index_builders.hpp : 105) Collecting k-mer coverage information from reads, this takes a while. 1:33:16.365 13G / 13G INFO General (graph_construction.hpp : 175) Filling coverage and flanking coverage from index 1:34:41.068 13G / 13G INFO General (construction.cpp : 30) Figured out: read length = 76 1:34:41.085 13G / 13G INFO StageManager (stage.cpp : 126) STAGE == EC Threshold Finding 1:34:59.122 13G / 13G INFO ThresholdFinder (ec_threshold_finder.hpp : 114) Bucket size: 14 1:34:59.123 13G / 13G INFO General (genomic_info_filler.cpp : 104) Average edge coverage: 30.9566 1:34:59.123 13G / 13G INFO General (genomic_info_filler.cpp : 105) Graph threshold: 451 1:37:52.281 16G / 36G INFO General (genomic_info_filler.cpp : 147) EC coverage threshold value was calculated as 30.9566 1:37:52.281 16G / 36G INFO General (genomic_info_filler.cpp : 148) Trusted kmer low bound: 0 1:37:52.281 16G / 36G INFO StageManager (stage.cpp : 126) STAGE == Gap Closer 1:37:52.313 16G / 36G INFO General (gap_closer.cpp : 159) Preparing shift maps 1:38:27.233 18G / 36G INFO General (gap_closer.cpp : 119) Processing paired reads (takes a while) 1:42:43.484 20G / 36G INFO General (gap_closer.cpp : 138) Used 127434831 paired reads 1:42:43.484 20G / 36G INFO General (gap_closer.cpp : 140) Merging paired indices 1:43:07.331 17G / 36G INFO GapCloser (gap_closer.cpp : 347) Closing short gaps 1:44:52.864 17G / 36G INFO GapCloser (gap_closer.cpp : 381) Closing short gaps complete: filled 348010 gaps after checking 1005111 candidates 1:46:09.113 16G / 36G INFO StageManager (stage.cpp : 126) STAGE == Simplification 1:46:10.038 11G / 36G INFO General (simplification.cpp : 420) Graph simplification started 1:46:10.038 11G / 36G INFO General (simplification.cpp : 76) PROCEDURE == InitialCleaning 1:46:10.038 11G / 36G INFO General (simplification.cpp : 64) Removing short polyAT 1:47:13.702 11G / 36G INFO General (parallel_simplification_al: 806) Parallel compression 1:47:16.422 11G / 36G INFO General (parallel_simplification_al: 815) Launching post-compression to compress loops 1:47:17.633 11G / 36G INFO General (graph_simplification.hpp : 645) Flanking coverage based disconnection disabled 1:47:17.636 11G / 36G INFO General (simplification.cpp : 349) Running Self conjugate edge remover 1:47:19.348 11G / 36G INFO General (simplification.cpp : 351) Triggered 0 times 1:47:19.348 11G / 36G INFO General (simplification.cpp : 349) Running Short PolyA/T Edges 1:47:21.242 11G / 36G INFO General (simplification.cpp : 351) Triggered 0 times 1:47:21.242 11G / 36G INFO General (simplification.cpp : 349) Running AT Tips 1:48:10.493 11G / 36G INFO General (simplification.cpp : 351) Triggered 2481470 times 1:48:10.493 11G / 36G INFO General (graph_simplification.hpp : 666) Removing loops and rc loops with erroneous connections 1:48:58.552 11G / 36G INFO ECLoopRemover (erroneous_connection_remov: 441) Loops: accurately removed/deadend removed/other: 4/88/9 1:48:58.552 11G / 36G INFO ECLoopRemover (erroneous_connection_remov: 442) RC loops: accurately removed/deadend removed/other: 8/331/2741 1:48:59.710 11G / 36G INFO General (graph_simplification.hpp : 617) Creating parallel br instance 1:48:59.710 11G / 36G INFO General (simplification.cpp : 456) PROCEDURE == Tip clipper and bulge removal cycle, iteration 1.0 1:48:59.710 11G / 36G INFO General (simplification.cpp : 349) Running Tip clipper 1:50:30.069 11G / 36G INFO General (simplification.cpp : 351) Triggered 4320534 times 1:50:30.069 11G / 36G INFO General (simplification.cpp : 349) Running Dead end clipper 1:50:31.710 11G / 36G INFO General (simplification.cpp : 351) Triggered 66473 times 1:50:31.710 11G / 36G INFO General (simplification.cpp : 349) Running Bulge remover 1:51:57.701 11G / 36G INFO General (simplification.cpp : 351) Triggered 121068 times 1:51:57.701 11G / 36G INFO General (simplification.cpp : 456) PROCEDURE == Tip clipper and bulge removal cycle, iteration 1.1 1:51:57.701 11G / 36G INFO General (simplification.cpp : 349) Running Tip clipper 1:51:58.012 11G / 36G INFO General (simplification.cpp : 351) Triggered 3168 times 1:51:58.012 11G / 36G INFO General (simplification.cpp : 349) Running Dead end clipper 1:51:58.198 11G / 36G INFO General (simplification.cpp : 351) Triggered 47 times 1:51:58.198 11G / 36G INFO General (simplification.cpp : 349) Running Bulge remover 1:51:58.259 11G / 36G INFO General (simplification.cpp : 351) Triggered 91 times 1:51:58.259 11G / 36G INFO General (simplification.cpp : 456) PROCEDURE == Tip clipper and bulge removal cycle, iteration 1.2 1:51:58.260 11G / 36G INFO General (simplification.cpp : 349) Running Tip clipper 1:51:58.261 11G / 36G INFO General (simplification.cpp : 351) Triggered 16 times 1:51:58.261 11G / 36G INFO General (simplification.cpp : 349) Running Dead end clipper 1:51:58.262 11G / 36G INFO General (simplification.cpp : 351) Triggered 0 times 1:51:58.262 11G / 36G INFO General (simplification.cpp : 349) Running Bulge remover 1:51:58.262 11G / 36G INFO General (simplification.cpp : 351) Triggered 0 times 1:51:58.263 11G / 36G INFO General (simplification.cpp : 456) PROCEDURE == Tip clipper and bulge removal cycle, iteration 1.3 1:51:58.263 11G / 36G INFO General (simplification.cpp : 349) Running Tip clipper 1:51:58.263 11G / 36G INFO General (simplification.cpp : 351) Triggered 0 times 1:51:58.263 11G / 36G INFO General (simplification.cpp : 349) Running Dead end clipper 1:51:58.263 11G / 36G INFO General (simplification.cpp : 351) Triggered 0 times 1:51:58.264 11G / 36G INFO General (simplification.cpp : 349) Running Bulge remover 1:51:58.264 11G / 36G INFO General (simplification.cpp : 351) Triggered 0 times 1:51:58.264 11G / 36G INFO General (simplification.cpp : 460) PROCEDURE == Erroneous connection, iteration 1 1:51:58.264 11G / 36G INFO General (simplification.cpp : 349) Running Low coverage edge remover 1:52:25.590 11G / 36G INFO General (simplification.cpp : 351) Triggered 305004 times 1:52:25.961 11G / 36G INFO General (graph_simplification.hpp : 617) Creating parallel br instance 1:52:25.961 11G / 36G INFO General (simplification.cpp : 456) PROCEDURE == Tip clipper and bulge removal cycle, iteration 2.0 1:52:25.961 11G / 36G INFO General (simplification.cpp : 349) Running Tip clipper 1:52:29.698 11G / 36G INFO General (simplification.cpp : 351) Triggered 75005 times 1:52:29.698 11G / 36G INFO General (simplification.cpp : 349) Running Dead end clipper 1:52:30.760 11G / 36G INFO General (simplification.cpp : 351) Triggered 42 times 1:52:30.760 11G / 36G INFO General (simplification.cpp : 349) Running Bulge remover 1:53:32.108 11G / 36G INFO General (simplification.cpp : 351) Triggered 54896 times 1:53:32.108 11G / 36G INFO General (simplification.cpp : 456) PROCEDURE == Tip clipper and bulge removal cycle, iteration 2.1 1:53:32.108 11G / 36G INFO General (simplification.cpp : 349) Running Tip clipper 1:53:32.169 11G / 36G INFO General (simplification.cpp : 351) Triggered 282 times 1:53:32.169 11G / 36G INFO General (simplification.cpp : 349) Running Dead end clipper 1:53:32.210 11G / 36G INFO General (simplification.cpp : 351) Triggered 0 times 1:53:32.210 11G / 36G INFO General (simplification.cpp : 349) Running Bulge remover 1:53:32.238 11G / 36G INFO General (simplification.cpp : 351) Triggered 20 times 1:53:32.238 11G / 36G INFO General (simplification.cpp : 456) PROCEDURE == Tip clipper and bulge removal cycle, iteration 2.2 1:53:32.238 11G / 36G INFO General (simplification.cpp : 349) Running Tip clipper 1:53:32.239 11G / 36G INFO General (simplification.cpp : 351) Triggered 1 times 1:53:32.239 11G / 36G INFO General (simplification.cpp : 349) Running Dead end clipper 1:53:32.239 11G / 36G INFO General (simplification.cpp : 351) Triggered 0 times 1:53:32.240 11G / 36G INFO General (simplification.cpp : 349) Running Bulge remover 1:53:32.240 11G / 36G INFO General (simplification.cpp : 351) Triggered 0 times 1:53:32.240 11G / 36G INFO General (simplification.cpp : 456) PROCEDURE == Tip clipper and bulge removal cycle, iteration 2.3 1:53:32.240 11G / 36G INFO General (simplification.cpp : 349) Running Tip clipper 1:53:32.241 11G / 36G INFO General (simplification.cpp : 351) Triggered 0 times 1:53:32.241 11G / 36G INFO General (simplification.cpp : 349) Running Dead end clipper 1:53:32.241 11G / 36G INFO General (simplification.cpp : 351) Triggered 0 times 1:53:32.241 11G / 36G INFO General (simplification.cpp : 349) Running Bulge remover 1:53:32.241 11G / 36G INFO General (simplification.cpp : 351) Triggered 0 times 1:53:32.242 11G / 36G INFO General (simplification.cpp : 460) PROCEDURE == Erroneous connection, iteration 2 1:53:32.242 11G / 36G INFO General (simplification.cpp : 349) Running Low coverage edge remover 1:53:34.396 11G / 36G INFO General (simplification.cpp : 351) Triggered 25456 times 1:53:34.447 11G / 36G INFO General (graph_simplification.hpp : 617) Creating parallel br instance 1:53:34.447 11G / 36G INFO General (simplification.cpp : 456) PROCEDURE == Tip clipper and bulge removal cycle, iteration 3.0 1:53:34.447 11G / 36G INFO General (simplification.cpp : 349) Running Tip clipper 1:53:35.668 11G / 36G INFO General (simplification.cpp : 351) Triggered 2996 times 1:53:35.668 11G / 36G INFO General (simplification.cpp : 349) Running Dead end clipper 1:53:36.626 11G / 36G INFO General (simplification.cpp : 351) Triggered 0 times 1:53:36.626 11G / 36G INFO General (simplification.cpp : 349) Running Bulge remover 1:53:41.200 11G / 36G INFO General (simplification.cpp : 351) Triggered 4454 times 1:53:41.200 11G / 36G INFO General (simplification.cpp : 456) PROCEDURE == Tip clipper and bulge removal cycle, iteration 3.1 1:53:41.200 11G / 36G INFO General (simplification.cpp : 349) Running Tip clipper 1:53:41.214 11G / 36G INFO General (simplification.cpp : 351) Triggered 19 times 1:53:41.214 11G / 36G INFO General (simplification.cpp : 349) Running Dead end clipper 1:53:41.226 11G / 36G INFO General (simplification.cpp : 351) Triggered 0 times 1:53:41.226 11G / 36G INFO General (simplification.cpp : 349) Running Bulge remover 1:53:41.227 11G / 36G INFO General (simplification.cpp : 351) Triggered 1 times 1:53:41.227 11G / 36G INFO General (simplification.cpp : 456) PROCEDURE == Tip clipper and bulge removal cycle, iteration 3.2 1:53:41.227 11G / 36G INFO General (simplification.cpp : 349) Running Tip clipper 1:53:41.227 11G / 36G INFO General (simplification.cpp : 351) Triggered 0 times 1:53:41.228 11G / 36G INFO General (simplification.cpp : 349) Running Dead end clipper 1:53:41.228 11G / 36G INFO General (simplification.cpp : 351) Triggered 0 times 1:53:41.228 11G / 36G INFO General (simplification.cpp : 349) Running Bulge remover 1:53:41.228 11G / 36G INFO General (simplification.cpp : 351) Triggered 0 times 1:53:41.228 11G / 36G INFO General (simplification.cpp : 460) PROCEDURE == Erroneous connection, iteration 3 1:53:41.228 11G / 36G INFO General (simplification.cpp : 349) Running Low coverage edge remover 1:53:41.885 11G / 36G INFO General (simplification.cpp : 351) Triggered 8564 times 1:53:41.905 11G / 36G INFO General (graph_simplification.hpp : 617) Creating parallel br instance 1:53:41.905 11G / 36G INFO General (simplification.cpp : 456) PROCEDURE == Tip clipper and bulge removal cycle, iteration 4.0 1:53:41.905 11G / 36G INFO General (simplification.cpp : 349) Running Tip clipper 1:53:43.237 11G / 36G INFO General (simplification.cpp : 351) Triggered 509 times 1:53:43.237 11G / 36G INFO General (simplification.cpp : 349) Running Dead end clipper 1:53:44.250 11G / 36G INFO General (simplification.cpp : 351) Triggered 0 times 1:53:44.251 11G / 36G INFO General (simplification.cpp : 349) Running Bulge remover 1:53:46.328 11G / 36G INFO General (simplification.cpp : 351) Triggered 1333 times 1:53:46.328 11G / 36G INFO General (simplification.cpp : 456) PROCEDURE == Tip clipper and bulge removal cycle, iteration 4.1 1:53:46.328 11G / 36G INFO General (simplification.cpp : 349) Running Tip clipper 1:53:46.334 11G / 36G INFO General (simplification.cpp : 351) Triggered 4 times 1:53:46.334 11G / 36G INFO General (simplification.cpp : 349) Running Dead end clipper 1:53:46.340 11G / 36G INFO General (simplification.cpp : 351) Triggered 0 times 1:53:46.340 11G / 36G INFO General (simplification.cpp : 349) Running Bulge remover 1:53:46.340 11G / 36G INFO General (simplification.cpp : 351) Triggered 0 times 1:53:46.340 11G / 36G INFO General (simplification.cpp : 456) PROCEDURE == Tip clipper and bulge removal cycle, iteration 4.2 1:53:46.340 11G / 36G INFO General (simplification.cpp : 349) Running Tip clipper 1:53:46.340 11G / 36G INFO General (simplification.cpp : 351) Triggered 0 times 1:53:46.340 11G / 36G INFO General (simplification.cpp : 349) Running Dead end clipper 1:53:46.340 11G / 36G INFO General (simplification.cpp : 351) Triggered 0 times 1:53:46.340 11G / 36G INFO General (simplification.cpp : 349) Running Bulge remover 1:53:46.340 11G / 36G INFO General (simplification.cpp : 351) Triggered 0 times 1:53:46.340 11G / 36G INFO General (simplification.cpp : 460) PROCEDURE == Erroneous connection, iteration 4 1:53:46.340 11G / 36G INFO General (simplification.cpp : 349) Running Low coverage edge remover 1:53:46.655 11G / 36G INFO General (simplification.cpp : 351) Triggered 4381 times 1:53:46.666 11G / 36G INFO General (graph_simplification.hpp : 617) Creating parallel br instance 1:53:46.666 11G / 36G INFO General (simplification.cpp : 456) PROCEDURE == Tip clipper and bulge removal cycle, iteration 5.0 1:53:46.666 11G / 36G INFO General (simplification.cpp : 349) Running Tip clipper 1:53:47.679 11G / 36G INFO General (simplification.cpp : 351) Triggered 147 times 1:53:47.679 11G / 36G INFO General (simplification.cpp : 349) Running Dead end clipper 1:53:48.645 11G / 36G INFO General (simplification.cpp : 351) Triggered 0 times 1:53:48.645 11G / 36G INFO General (simplification.cpp : 349) Running Bulge remover 1:53:50.257 11G / 36G INFO General (simplification.cpp : 351) Triggered 611 times 1:53:50.257 11G / 36G INFO General (simplification.cpp : 456) PROCEDURE == Tip clipper and bulge removal cycle, iteration 5.1 1:53:50.257 11G / 36G INFO General (simplification.cpp : 349) Running Tip clipper 1:53:50.261 11G / 36G INFO General (simplification.cpp : 351) Triggered 1 times 1:53:50.261 11G / 36G INFO General (simplification.cpp : 349) Running Dead end clipper 1:53:50.263 11G / 36G INFO General (simplification.cpp : 351) Triggered 0 times 1:53:50.263 11G / 36G INFO General (simplification.cpp : 349) Running Bulge remover 1:53:50.263 11G / 36G INFO General (simplification.cpp : 351) Triggered 0 times 1:53:50.264 11G / 36G INFO General (simplification.cpp : 456) PROCEDURE == Tip clipper and bulge removal cycle, iteration 5.2 1:53:50.264 11G / 36G INFO General (simplification.cpp : 349) Running Tip clipper 1:53:50.264 11G / 36G INFO General (simplification.cpp : 351) Triggered 0 times 1:53:50.264 11G / 36G INFO General (simplification.cpp : 349) Running Dead end clipper 1:53:50.265 11G / 36G INFO General (simplification.cpp : 351) Triggered 0 times 1:53:50.265 11G / 36G INFO General (simplification.cpp : 349) Running Bulge remover 1:53:50.265 11G / 36G INFO General (simplification.cpp : 351) Triggered 0 times 1:53:50.265 11G / 36G INFO General (simplification.cpp : 460) PROCEDURE == Erroneous connection, iteration 5 1:53:50.265 11G / 36G INFO General (simplification.cpp : 349) Running Low coverage edge remover 1:53:50.467 11G / 36G INFO General (simplification.cpp : 351) Triggered 2766 times 1:53:50.474 11G / 36G INFO General (graph_simplification.hpp : 617) Creating parallel br instance 1:53:50.474 11G / 36G INFO General (simplification.cpp : 456) PROCEDURE == Tip clipper and bulge removal cycle, iteration 6.0 1:53:50.474 11G / 36G INFO General (simplification.cpp : 349) Running Tip clipper 1:53:51.564 11G / 36G INFO General (simplification.cpp : 351) Triggered 83 times 1:53:51.564 11G / 36G INFO General (simplification.cpp : 349) Running Dead end clipper 1:53:52.757 11G / 36G INFO General (simplification.cpp : 351) Triggered 0 times 1:53:52.758 11G / 36G INFO General (simplification.cpp : 349) Running Bulge remover 1:53:54.187 11G / 36G INFO General (simplification.cpp : 351) Triggered 333 times 1:53:54.188 11G / 36G INFO General (simplification.cpp : 456) PROCEDURE == Tip clipper and bulge removal cycle, iteration 6.1 1:53:54.188 11G / 36G INFO General (simplification.cpp : 349) Running Tip clipper 1:53:54.191 11G / 36G INFO General (simplification.cpp : 351) Triggered 0 times 1:53:54.191 11G / 36G INFO General (simplification.cpp : 349) Running Dead end clipper 1:53:54.193 11G / 36G INFO General (simplification.cpp : 351) Triggered 0 times 1:53:54.193 11G / 36G INFO General (simplification.cpp : 349) Running Bulge remover 1:53:54.193 11G / 36G INFO General (simplification.cpp : 351) Triggered 0 times 1:53:54.193 11G / 36G INFO General (simplification.cpp : 460) PROCEDURE == Erroneous connection, iteration 6 1:53:54.194 11G / 36G INFO General (simplification.cpp : 349) Running Low coverage edge remover 1:53:54.370 11G / 36G INFO General (simplification.cpp : 351) Triggered 1881 times 1:53:54.376 11G / 36G INFO General (graph_simplification.hpp : 617) Creating parallel br instance 1:53:54.376 11G / 36G INFO General (simplification.cpp : 456) PROCEDURE == Tip clipper and bulge removal cycle, iteration 7.0 1:53:54.376 11G / 36G INFO General (simplification.cpp : 349) Running Tip clipper 1:53:55.747 11G / 36G INFO General (simplification.cpp : 351) Triggered 30 times 1:53:55.747 11G / 36G INFO General (simplification.cpp : 349) Running Dead end clipper 1:53:56.947 11G / 36G INFO General (simplification.cpp : 351) Triggered 0 times 1:53:56.947 11G / 36G INFO General (simplification.cpp : 349) Running Bulge remover 1:53:58.149 11G / 36G INFO General (simplification.cpp : 351) Triggered 215 times 1:53:58.149 11G / 36G INFO General (simplification.cpp : 456) PROCEDURE == Tip clipper and bulge removal cycle, iteration 7.1 1:53:58.149 11G / 36G INFO General (simplification.cpp : 349) Running Tip clipper 1:53:58.151 11G / 36G INFO General (simplification.cpp : 351) Triggered 0 times 1:53:58.151 11G / 36G INFO General (simplification.cpp : 349) Running Dead end clipper 1:53:58.152 11G / 36G INFO General (simplification.cpp : 351) Triggered 0 times 1:53:58.152 11G / 36G INFO General (simplification.cpp : 349) Running Bulge remover 1:53:58.152 11G / 36G INFO General (simplification.cpp : 351) Triggered 0 times 1:53:58.152 11G / 36G INFO General (simplification.cpp : 460) PROCEDURE == Erroneous connection, iteration 7 1:53:58.152 11G / 36G INFO General (simplification.cpp : 349) Running Low coverage edge remover 1:53:58.243 11G / 36G INFO General (simplification.cpp : 351) Triggered 1387 times 1:53:58.247 11G / 36G INFO General (graph_simplification.hpp : 617) Creating parallel br instance 1:53:58.247 11G / 36G INFO General (simplification.cpp : 456) PROCEDURE == Tip clipper and bulge removal cycle, iteration 8.0 1:53:58.247 11G / 36G INFO General (simplification.cpp : 349) Running Tip clipper 1:53:59.205 11G / 36G INFO General (simplification.cpp : 351) Triggered 25 times 1:53:59.205 11G / 36G INFO General (simplification.cpp : 349) Running Dead end clipper 1:54:00.184 11G / 36G INFO General (simplification.cpp : 351) Triggered 0 times 1:54:00.184 11G / 36G INFO General (simplification.cpp : 349) Running Bulge remover 1:54:01.360 11G / 36G INFO General (simplification.cpp : 351) Triggered 147 times 1:54:01.360 11G / 36G INFO General (simplification.cpp : 456) PROCEDURE == Tip clipper and bulge removal cycle, iteration 8.1 1:54:01.360 11G / 36G INFO General (simplification.cpp : 349) Running Tip clipper 1:54:01.361 11G / 36G INFO General (simplification.cpp : 351) Triggered 0 times 1:54:01.361 11G / 36G INFO General (simplification.cpp : 349) Running Dead end clipper 1:54:01.362 11G / 36G INFO General (simplification.cpp : 351) Triggered 0 times 1:54:01.362 11G / 36G INFO General (simplification.cpp : 349) Running Bulge remover 1:54:01.362 11G / 36G INFO General (simplification.cpp : 351) Triggered 0 times 1:54:01.362 11G / 36G INFO General (simplification.cpp : 460) PROCEDURE == Erroneous connection, iteration 8 1:54:01.362 11G / 36G INFO General (simplification.cpp : 349) Running Low coverage edge remover 1:54:01.435 11G / 36G INFO General (simplification.cpp : 351) Triggered 1161 times 1:54:01.438 11G / 36G INFO General (graph_simplification.hpp : 617) Creating parallel br instance 1:54:01.438 11G / 36G INFO General (simplification.cpp : 456) PROCEDURE == Tip clipper and bulge removal cycle, iteration 9.0 1:54:01.438 11G / 36G INFO General (simplification.cpp : 349) Running Tip clipper 1:54:02.407 11G / 36G INFO General (simplification.cpp : 351) Triggered 19 times 1:54:02.407 11G / 36G INFO General (simplification.cpp : 349) Running Dead end clipper 1:54:03.458 11G / 36G INFO General (simplification.cpp : 351) Triggered 0 times 1:54:03.459 11G / 36G INFO General (simplification.cpp : 349) Running Bulge remover 1:54:04.632 11G / 36G INFO General (simplification.cpp : 351) Triggered 95 times 1:54:04.633 11G / 36G INFO General (simplification.cpp : 456) PROCEDURE == Tip clipper and bulge removal cycle, iteration 9.1 1:54:04.633 11G / 36G INFO General (simplification.cpp : 349) Running Tip clipper 1:54:04.634 11G / 36G INFO General (simplification.cpp : 351) Triggered 0 times 1:54:04.634 11G / 36G INFO General (simplification.cpp : 349) Running Dead end clipper 1:54:04.635 11G / 36G INFO General (simplification.cpp : 351) Triggered 0 times 1:54:04.635 11G / 36G INFO General (simplification.cpp : 349) Running Bulge remover 1:54:04.635 11G / 36G INFO General (simplification.cpp : 351) Triggered 0 times 1:54:04.636 11G / 36G INFO General (simplification.cpp : 460) PROCEDURE == Erroneous connection, iteration 9 1:54:04.636 11G / 36G INFO General (simplification.cpp : 349) Running Low coverage edge remover 1:54:04.703 11G / 36G INFO General (simplification.cpp : 351) Triggered 944 times 1:54:04.705 11G / 36G INFO General (graph_simplification.hpp : 617) Creating parallel br instance 1:54:04.705 11G / 36G INFO General (simplification.cpp : 456) PROCEDURE == Tip clipper and bulge removal cycle, iteration 10.0 1:54:04.705 11G / 36G INFO General (simplification.cpp : 349) Running Tip clipper 1:54:05.786 11G / 36G INFO General (simplification.cpp : 351) Triggered 10 times 1:54:05.787 11G / 36G INFO General (simplification.cpp : 349) Running Dead end clipper 1:54:06.831 11G / 36G INFO General (simplification.cpp : 351) Triggered 0 times 1:54:06.831 11G / 36G INFO General (simplification.cpp : 349) Running Bulge remover 1:54:07.919 11G / 36G INFO General (simplification.cpp : 351) Triggered 69 times 1:54:07.919 11G / 36G INFO General (simplification.cpp : 456) PROCEDURE == Tip clipper and bulge removal cycle, iteration 10.1 1:54:07.919 11G / 36G INFO General (simplification.cpp : 349) Running Tip clipper 1:54:07.920 11G / 36G INFO General (simplification.cpp : 351) Triggered 0 times 1:54:07.920 11G / 36G INFO General (simplification.cpp : 349) Running Dead end clipper 1:54:07.920 11G / 36G INFO General (simplification.cpp : 351) Triggered 0 times 1:54:07.920 11G / 36G INFO General (simplification.cpp : 349) Running Bulge remover 1:54:07.920 11G / 36G INFO General (simplification.cpp : 351) Triggered 0 times 1:54:07.920 11G / 36G INFO General (simplification.cpp : 460) PROCEDURE == Erroneous connection, iteration 10 1:54:07.920 11G / 36G INFO General (simplification.cpp : 349) Running Low coverage edge remover 1:54:07.974 11G / 36G INFO General (simplification.cpp : 351) Triggered 800 times 1:54:07.976 11G / 36G INFO General (graph_simplification.hpp : 617) Creating parallel br instance 1:54:07.976 11G / 36G INFO General (simplification.cpp : 456) PROCEDURE == Tip clipper and bulge removal cycle, iteration 11.0 1:54:07.976 11G / 36G INFO General (simplification.cpp : 349) Running Tip clipper 1:54:09.060 11G / 36G INFO General (simplification.cpp : 351) Triggered 7 times 1:54:09.061 11G / 36G INFO General (simplification.cpp : 349) Running Dead end clipper 1:54:10.117 11G / 36G INFO General (simplification.cpp : 351) Triggered 0 times 1:54:10.117 11G / 36G INFO General (simplification.cpp : 349) Running Bulge remover 1:54:11.255 11G / 36G INFO General (simplification.cpp : 351) Triggered 61 times 1:54:11.256 11G / 36G INFO General (simplification.cpp : 456) PROCEDURE == Tip clipper and bulge removal cycle, iteration 11.1 1:54:11.256 11G / 36G INFO General (simplification.cpp : 349) Running Tip clipper 1:54:11.257 11G / 36G INFO General (simplification.cpp : 351) Triggered 1 times 1:54:11.257 11G / 36G INFO General (simplification.cpp : 349) Running Dead end clipper 1:54:11.257 11G / 36G INFO General (simplification.cpp : 351) Triggered 0 times 1:54:11.257 11G / 36G INFO General (simplification.cpp : 349) Running Bulge remover 1:54:11.258 11G / 36G INFO General (simplification.cpp : 351) Triggered 0 times 1:54:11.258 11G / 36G INFO General (simplification.cpp : 456) PROCEDURE == Tip clipper and bulge removal cycle, iteration 11.2 1:54:11.258 11G / 36G INFO General (simplification.cpp : 349) Running Tip clipper 1:54:11.259 11G / 36G INFO General (simplification.cpp : 351) Triggered 0 times 1:54:11.259 11G / 36G INFO General (simplification.cpp : 349) Running Dead end clipper 1:54:11.259 11G / 36G INFO General (simplification.cpp : 351) Triggered 0 times 1:54:11.259 11G / 36G INFO General (simplification.cpp : 349) Running Bulge remover 1:54:11.259 11G / 36G INFO General (simplification.cpp : 351) Triggered 0 times 1:54:11.260 11G / 36G INFO General (simplification.cpp : 460) PROCEDURE == Erroneous connection, iteration 11 1:54:11.260 11G / 36G INFO General (simplification.cpp : 349) Running Low coverage edge remover 1:54:11.260 11G / 36G INFO General (simplification.cpp : 351) Triggered 0 times 1:54:11.260 11G / 36G INFO General (simplification.cpp : 162) PROCEDURE == Post simplification 1:54:11.261 11G / 36G INFO General (graph_simplification.hpp : 446) Disconnection of relatively low covered edges disabled 1:54:11.261 11G / 36G INFO General (graph_simplification.hpp : 476) Complex tip clipping disabled 1:54:11.261 11G / 36G INFO General (graph_simplification.hpp : 617) Creating parallel br instance 1:54:11.261 11G / 36G INFO General (graph_simplification.hpp : 617) Creating parallel br instance 1:54:11.262 11G / 36G INFO General (simplification.cpp : 294) Iteration 0 1:54:11.262 11G / 36G INFO General (simplification.cpp : 349) Running Relative coverage component remover 1:54:12.499 11G / 36G INFO General (simplification.cpp : 351) Triggered 698 times 1:54:12.499 11G / 36G INFO General (simplification.cpp : 349) Running Relative coverage component remover 1:54:14.015 11G / 36G INFO General (simplification.cpp : 351) Triggered 6336 times 1:54:14.015 11G / 36G INFO General (simplification.cpp : 349) Running Complex bulge remover 1:54:31.534 11G / 36G INFO General (simplification.cpp : 351) Triggered 106 times 1:54:31.534 11G / 36G INFO General (simplification.cpp : 349) Running Tip clipper 1:54:32.834 11G / 36G INFO General (simplification.cpp : 351) Triggered 14 times 1:54:32.835 11G / 36G INFO General (simplification.cpp : 349) Running Final tip clipper 1:54:34.463 11G / 36G INFO General (simplification.cpp : 351) Triggered 10548 times 1:54:34.463 11G / 36G INFO General (simplification.cpp : 349) Running Bulge remover 1:54:35.840 11G / 36G INFO General (simplification.cpp : 351) Triggered 197 times 1:54:35.840 11G / 36G INFO General (simplification.cpp : 349) Running Final bulge remover 1:54:36.945 11G / 36G INFO General (simplification.cpp : 351) Triggered 0 times 1:54:36.945 11G / 36G INFO General (simplification.cpp : 349) Running AT Tips 1:54:38.326 11G / 36G INFO General (simplification.cpp : 351) Triggered 2339 times 1:54:38.326 11G / 36G INFO General (simplification.cpp : 294) Iteration 1 1:54:38.326 11G / 36G INFO General (simplification.cpp : 349) Running Relative coverage component remover 1:54:38.361 11G / 36G INFO General (simplification.cpp : 351) Triggered 26 times 1:54:38.361 11G / 36G INFO General (simplification.cpp : 349) Running Relative coverage component remover 1:54:39.430 11G / 36G INFO General (simplification.cpp : 351) Triggered 41 times 1:54:39.430 11G / 36G INFO General (simplification.cpp : 349) Running Complex bulge remover 1:54:57.056 11G / 36G INFO General (simplification.cpp : 351) Triggered 8 times 1:54:57.056 11G / 36G INFO General (simplification.cpp : 349) Running Tip clipper 1:54:57.077 11G / 36G INFO General (simplification.cpp : 351) Triggered 0 times 1:54:57.077 11G / 36G INFO General (simplification.cpp : 349) Running Final tip clipper 1:54:57.079 11G / 36G INFO General (simplification.cpp : 351) Triggered 8 times 1:54:57.079 11G / 36G INFO General (simplification.cpp : 349) Running Bulge remover 1:54:57.088 11G / 36G INFO General (simplification.cpp : 351) Triggered 4 times 1:54:57.088 11G / 36G INFO General (simplification.cpp : 349) Running Final bulge remover 1:54:57.090 11G / 36G INFO General (simplification.cpp : 351) Triggered 0 times 1:54:57.090 11G / 36G INFO General (simplification.cpp : 349) Running AT Tips 1:54:57.093 11G / 36G INFO General (simplification.cpp : 351) Triggered 0 times 1:54:57.093 11G / 36G INFO General (simplification.cpp : 294) Iteration 2 1:54:57.093 11G / 36G INFO General (simplification.cpp : 349) Running Relative coverage component remover 1:54:57.093 11G / 36G INFO General (simplification.cpp : 351) Triggered 0 times 1:54:57.094 11G / 36G INFO General (simplification.cpp : 349) Running Relative coverage component remover 1:54:58.314 11G / 36G INFO General (simplification.cpp : 351) Triggered 1 times 1:54:58.315 11G / 36G INFO General (simplification.cpp : 349) Running Complex bulge remover 1:55:16.189 11G / 36G INFO General (simplification.cpp : 351) Triggered 0 times 1:55:16.189 11G / 36G INFO General (simplification.cpp : 349) Running Tip clipper 1:55:16.189 11G / 36G INFO General (simplification.cpp : 351) Triggered 0 times 1:55:16.189 11G / 36G INFO General (simplification.cpp : 349) Running Final tip clipper 1:55:16.189 11G / 36G INFO General (simplification.cpp : 351) Triggered 1 times 1:55:16.189 11G / 36G INFO General (simplification.cpp : 349) Running Bulge remover 1:55:16.189 11G / 36G INFO General (simplification.cpp : 351) Triggered 0 times 1:55:16.189 11G / 36G INFO General (simplification.cpp : 349) Running Final bulge remover 1:55:16.190 11G / 36G INFO General (simplification.cpp : 351) Triggered 0 times 1:55:16.190 11G / 36G INFO General (simplification.cpp : 349) Running AT Tips 1:55:16.190 11G / 36G INFO General (simplification.cpp : 351) Triggered 0 times 1:55:16.190 11G / 36G INFO General (simplification.cpp : 294) Iteration 3 1:55:16.190 11G / 36G INFO General (simplification.cpp : 349) Running Relative coverage component remover 1:55:16.190 11G / 36G INFO General (simplification.cpp : 351) Triggered 0 times 1:55:16.190 11G / 36G INFO General (simplification.cpp : 349) Running Relative coverage component remover 1:55:17.162 11G / 36G INFO General (simplification.cpp : 351) Triggered 0 times 1:55:17.162 11G / 36G INFO General (simplification.cpp : 349) Running Complex bulge remover 1:55:35.906 11G / 36G INFO General (simplification.cpp : 351) Triggered 0 times 1:55:35.906 11G / 36G INFO General (simplification.cpp : 349) Running Tip clipper 1:55:35.906 11G / 36G INFO General (simplification.cpp : 351) Triggered 0 times 1:55:35.906 11G / 36G INFO General (simplification.cpp : 349) Running Final tip clipper 1:55:35.906 11G / 36G INFO General (simplification.cpp : 351) Triggered 0 times 1:55:35.906 11G / 36G INFO General (simplification.cpp : 349) Running Bulge remover 1:55:35.906 11G / 36G INFO General (simplification.cpp : 351) Triggered 0 times 1:55:35.906 11G / 36G INFO General (simplification.cpp : 349) Running Final bulge remover 1:55:35.906 11G / 36G INFO General (simplification.cpp : 351) Triggered 0 times 1:55:35.906 11G / 36G INFO General (simplification.cpp : 349) Running AT Tips 1:55:35.906 11G / 36G INFO General (simplification.cpp : 351) Triggered 0 times 1:55:35.906 11G / 36G INFO General (simplification.cpp : 326) Disrupting self-conjugate edges 1:55:40.898 11G / 36G INFO StageManager (stage.cpp : 126) STAGE == Gap Closer 1:55:40.899 11G / 36G INFO General (graph_pack.hpp : 96) Index refill 1:55:40.910 11G / 36G INFO K-mer Index Building (kmer_index_builder.hpp : 428) Building kmer index 1:55:40.910 11G / 36G INFO General (kmer_splitters.hpp : 214) Splitting kmer instances into 16 buckets. This might take a while. 1:55:40.911 11G / 36G INFO General (file_limit.hpp : 30) Open file limit set to 64000 1:55:40.911 11G / 36G INFO General (kmer_index_builder.hpp : 108) Memory available for splitting buffers: 69.3724 Gb 1:55:40.911 11G / 36G INFO General (kmer_index_builder.hpp : 116) Using cell size of 2097152 1:55:55.167 12G / 36G INFO General (kmer_splitters.hpp : 225) Processed 1021311 edges 1:56:09.316 12G / 36G INFO General (kmer_splitters.hpp : 225) Processed 2037886 edges 1:56:23.851 12G / 36G INFO General (kmer_splitters.hpp : 225) Processed 3063938 edges 1:56:38.399 12G / 36G INFO General (kmer_splitters.hpp : 225) Processed 4070356 edges 1:56:54.494 12G / 36G INFO General (kmer_splitters.hpp : 225) Processed 5082375 edges 1:56:55.454 12G / 36G INFO General (kmer_splitters.hpp : 225) Processed 5132693 edges 1:56:55.454 12G / 36G INFO General (kmer_splitters.hpp : 230) Used 5132693 sequences. 1:56:55.539 11G / 36G INFO General (kmer_index_builder.hpp : 252) Starting k-mer counting. 1:58:07.837 11G / 36G INFO General (kmer_index_builder.hpp : 258) K-mer counting done. There are 165697426 kmers in total. 1:58:07.837 11G / 36G INFO General (kmer_index_builder.hpp : 260) Merging temporary buckets. 1:59:02.022 11G / 36G INFO K-mer Index Building (kmer_index_builder.hpp : 437) Building perfect hash indices 2:00:09.240 11G / 36G INFO General (kmer_index_builder.hpp : 276) Merging final buckets. 2:00:46.571 11G / 36G INFO K-mer Index Building (kmer_index_builder.hpp : 483) Index built. Total 54136592 bytes occupied (2.61376 bits per kmer). 2:00:48.922 15G / 36G INFO General (edge_index_builders.hpp : 27) Collecting k-mer coverage information from graph, this takes a while. 2:00:58.883 15G / 36G INFO General (edge_index.hpp : 91) Index refilled 2:00:58.902 15G / 36G INFO General (gap_closer.cpp : 159) Preparing shift maps 2:01:10.009 16G / 36G INFO General (gap_closer.cpp : 119) Processing paired reads (takes a while) 2:02:52.099 17G / 36G INFO General (gap_closer.cpp : 138) Used 127434831 paired reads 2:02:52.100 17G / 36G INFO General (gap_closer.cpp : 140) Merging paired indices 2:03:13.151 15G / 36G INFO GapCloser (gap_closer.cpp : 347) Closing short gaps 2:03:33.528 15G / 36G INFO GapCloser (gap_closer.cpp : 381) Closing short gaps complete: filled 47235 gaps after checking 1086855 candidates 2:04:16.723 15G / 36G INFO StageManager (stage.cpp : 126) STAGE == Simplification Cleanup 2:04:16.723 15G / 36G INFO General (simplification.cpp : 561) Counting average coverage 2:04:20.237 15G / 36G INFO General (simplification.cpp : 566) Average coverage = 40.6562 2:04:20.237 15G / 36G INFO StageManager (stage.cpp : 126) STAGE == Mismatch Correction 2:04:20.237 15G / 36G INFO General (graph_pack.hpp : 105) Normalizing k-mer map. Total 16592729 kmers to process 2:04:32.812 15G / 36G INFO General (graph_pack.hpp : 107) Normalizing done 2:09:42.011 15G / 36G INFO General (mismatch_shall_not_pass.hp: 187) Finished collecting potential mismatches positions 2:09:59.372 15G / 36G INFO General (mismatch_shall_not_pass.hp: 284) All edges processed 2:10:00.298 15G / 36G INFO General (mismatch_correction.cpp : 26) Corrected 550 nucleotides 2:10:00.305 15G / 36G INFO StageManager (stage.cpp : 126) STAGE == Contig Output 2:10:00.305 15G / 36G INFO General (contig_output.hpp : 478) Outputting contigs to /data/home/pitagoras/public_html/gigas/transcriptome/rnaSpades/output45//K45/pre_pe_before_rr.fasta 2:10:30.409 15G / 36G INFO General (contig_output.hpp : 518) Outputting graph to /data/home/pitagoras/public_html/gigas/transcriptome/rnaSpades/output45//K45/pre_pe_assembly_graph.fastg 2:11:33.519 15G / 36G INFO General (contig_output.hpp : 478) Outputting contigs to /data/home/pitagoras/public_html/gigas/transcriptome/rnaSpades/output45//K45/pre_pe_simplified_contigs.fasta 2:12:01.515 15G / 36G INFO General (contig_output.hpp : 478) Outputting contigs to /data/home/pitagoras/public_html/gigas/transcriptome/rnaSpades/output45//K45/pre_pe_final_contigs.fasta 2:12:28.876 15G / 36G INFO StageManager (stage.cpp : 126) STAGE == Paired Information Counting 2:12:49.015 16G / 36G INFO General (graph_pack.hpp : 105) Normalizing k-mer map. Total 16613057 kmers to process 2:13:02.017 16G / 36G INFO General (graph_pack.hpp : 107) Normalizing done 2:13:04.248 16G / 36G INFO General (pair_info_count.cpp : 300) Min edge length for estimation: 191 2:13:04.248 16G / 36G INFO General (pair_info_count.cpp : 311) Estimating insert size for library #0 2:13:04.248 16G / 36G INFO General (pair_info_count.cpp : 116) Estimating insert size (takes a while) 2:13:04.443 16G / 36G INFO General (short_read_mapper.hpp : 88) Selecting usual mapper 2:13:06.893 16G / 36G INFO General (sequence_mapper_notifier.h: 82) Processed 200000 reads 2:13:06.924 16G / 36G INFO General (sequence_mapper_notifier.h: 82) Processed 400000 reads 2:13:06.962 16G / 36G INFO General (sequence_mapper_notifier.h: 82) Processed 600000 reads 2:13:06.994 16G / 36G INFO General (sequence_mapper_notifier.h: 82) Processed 800000 reads 2:13:07.026 16G / 36G INFO General (sequence_mapper_notifier.h: 82) Processed 1000000 reads 2:13:07.068 16G / 36G INFO General (sequence_mapper_notifier.h: 82) Processed 1200000 reads 2:13:07.240 16G / 36G INFO General (sequence_mapper_notifier.h: 82) Processed 2200000 reads 2:13:09.432 16G / 36G INFO General (sequence_mapper_notifier.h: 82) Processed 4200000 reads 2:13:12.610 16G / 36G INFO General (sequence_mapper_notifier.h: 82) Processed 8400000 reads 2:13:19.777 16G / 36G INFO General (sequence_mapper_notifier.h: 82) Processed 16800000 reads 2:13:32.547 16G / 36G INFO General (sequence_mapper_notifier.h: 82) Processed 33600000 reads 2:14:04.178 16G / 36G INFO General (sequence_mapper_notifier.h: 82) Processed 67200000 reads 2:15:07.912 16G / 36G INFO General (sequence_mapper_notifier.h: 100) Total 127434831 reads processed 2:15:09.499 16G / 36G INFO General (pair_info_count.cpp : 134) Edge pairs: 67108864 (rough upper limit) 2:15:09.499 16G / 36G INFO General (pair_info_count.cpp : 138) 70354380 paired reads (55.2081% of all) aligned to long edges 2:15:09.536 16G / 36G INFO General (pair_info_count.cpp : 334) Insert size = 155.772, deviation = 44.9157, left quantile = 110, right quantile = 214, read length = 76 2:15:09.536 16G / 36G INFO General (pair_info_count.cpp : 363) Mapping library #0 2:15:09.536 16G / 36G INFO General (pair_info_count.cpp : 365) Mapping paired reads (takes a while) 2:15:09.536 16G / 36G INFO General (pair_info_count.cpp : 204) Left insert size quantile 110, right insert size quantile 214, filtering threshold 0, rounding threshold 0 2:15:09.552 16G / 36G INFO General (short_read_mapper.hpp : 88) Selecting usual mapper 2:15:12.750 16G / 36G INFO General (sequence_mapper_notifier.h: 82) Processed 200000 reads 2:15:12.774 16G / 36G INFO General (sequence_mapper_notifier.h: 82) Processed 400000 reads 2:15:12.840 16G / 36G INFO General (sequence_mapper_notifier.h: 82) Processed 600000 reads 2:15:12.886 16G / 36G INFO General (sequence_mapper_notifier.h: 82) Processed 800000 reads 2:15:12.891 16G / 36G INFO General (sequence_mapper_notifier.h: 82) Processed 1000000 reads 2:15:12.918 16G / 36G INFO General (sequence_mapper_notifier.h: 82) Processed 1200000 reads 2:15:12.987 16G / 36G INFO General (sequence_mapper_notifier.h: 82) Processed 2200000 reads 2:15:15.974 16G / 36G INFO General (sequence_mapper_notifier.h: 82) Processed 4200000 reads 2:15:19.389 16G / 36G INFO General (sequence_mapper_notifier.h: 82) Processed 8400000 reads 2:15:28.115 16G / 36G INFO General (sequence_mapper_notifier.h: 82) Processed 16800000 reads 2:15:42.122 16G / 36G INFO General (sequence_mapper_notifier.h: 82) Processed 33600000 reads 2:16:23.836 16G / 36G INFO General (sequence_mapper_notifier.h: 82) Processed 67200000 reads 2:17:35.269 16G / 36G INFO General (sequence_mapper_notifier.h: 100) Total 127434831 reads processed 2:17:36.263 16G / 36G INFO StageManager (stage.cpp : 126) STAGE == Distance Estimation 2:17:36.263 16G / 36G INFO General (distance_estimation.cpp : 224) Processing library #0 2:17:36.263 16G / 36G INFO General (distance_estimation.cpp : 130) Weight Filter Done 2:17:36.263 16G / 36G INFO DistanceEstimator (distance_estimation.hpp : 176) Using SIMPLE distance estimator 2:17:49.123 16G / 36G INFO General (distance_estimation.cpp : 35) Filtering info 2:17:49.123 16G / 36G INFO General (pair_info_filters.hpp : 242) Start filtering; index size: 6404296 2:17:56.052 17G / 36G INFO General (pair_info_filters.hpp : 263) Done filtering 2:17:56.069 16G / 36G INFO General (distance_estimation.cpp : 172) Refining clustered pair information 2:17:56.610 16G / 36G INFO General (distance_estimation.cpp : 174) The refining of clustered pair information has been finished 2:17:56.610 16G / 36G INFO General (distance_estimation.cpp : 176) Improving paired information 2:18:06.478 16G / 36G INFO PairInfoImprover (pair_info_improver.hpp : 103) Paired info stats: missing = 119037; contradictional = 76 2:18:15.382 16G / 36G INFO PairInfoImprover (pair_info_improver.hpp : 103) Paired info stats: missing = 61978; contradictional = 0 2:18:15.382 16G / 36G INFO StageManager (stage.cpp : 126) STAGE == Repeat Resolving 2:18:15.382 16G / 36G INFO General (repeat_resolving.cpp : 68) Using Path-Extend repeat resolving 2:18:33.189 17G / 36G INFO General (launcher.cpp : 399) ExSPAnder repeat resolving tool started 2:19:09.184 27G / 36G INFO General (launcher.cpp : 357) Creating main extenders, unique edge length = 2000 2:19:14.590 27G / 36G INFO General (extenders_logic.cpp : 415) Using 1 paired-end library 2:19:14.590 27G / 36G INFO General (extenders_logic.cpp : 416) Using 1 paired-end scaffolding library 2:19:14.590 27G / 36G INFO General (extenders_logic.cpp : 417) Using 0 single read libraries 2:19:14.590 27G / 36G INFO General (launcher.cpp : 385) Total number of extenders is 4 2:19:14.590 27G / 36G INFO PathExtender (path_extender.hpp :1031) Processed 0 paths from 2518747 (0%) 2:19:14.637 27G / 36G INFO PathExtender (path_extender.hpp :1029) Processed 128 paths from 2518747 (0%) 2:19:14.666 27G / 36G INFO PathExtender (path_extender.hpp :1029) Processed 256 paths from 2518747 (0%) 2:19:14.726 27G / 36G INFO PathExtender (path_extender.hpp :1029) Processed 512 paths from 2518747 (0%) 2:19:14.836 27G / 36G INFO PathExtender (path_extender.hpp :1029) Processed 1024 paths from 2518747 (0%) 2:19:15.042 27G / 36G INFO PathExtender (path_extender.hpp :1029) Processed 2048 paths from 2518747 (0%) 2:19:15.465 27G / 36G INFO PathExtender (path_extender.hpp :1029) Processed 4096 paths from 2518747 (0%) 2:19:16.295 27G / 36G INFO PathExtender (path_extender.hpp :1029) Processed 8192 paths from 2518747 (0%) 2:19:17.859 27G / 36G INFO PathExtender (path_extender.hpp :1029) Processed 16384 paths from 2518747 (0%) 2:19:20.412 27G / 36G INFO PathExtender (path_extender.hpp :1029) Processed 32768 paths from 2518747 (1%) 2:19:24.263 27G / 36G INFO PathExtender (path_extender.hpp :1029) Processed 65536 paths from 2518747 (2%) 2:19:30.053 28G / 36G INFO PathExtender (path_extender.hpp :1029) Processed 131072 paths from 2518747 (5%) 2:19:36.124 28G / 36G INFO PathExtender (path_extender.hpp :1031) Processed 251875 paths from 2518747 (10%) 2:19:36.413 28G / 36G INFO PathExtender (path_extender.hpp :1029) Processed 262144 paths from 2518747 (10%) 2:19:45.448 29G / 36G INFO PathExtender (path_extender.hpp :1031) Processed 503750 paths from 2518747 (20%) 2:19:46.435 29G / 36G INFO PathExtender (path_extender.hpp :1029) Processed 524288 paths from 2518747 (20%) 2:19:53.099 30G / 36G INFO PathExtender (path_extender.hpp :1031) Processed 755625 paths from 2518747 (30%) 2:19:59.301 31G / 36G INFO PathExtender (path_extender.hpp :1031) Processed 1007500 paths from 2518747 (40%) 2:20:00.273 31G / 36G INFO PathExtender (path_extender.hpp :1029) Processed 1048576 paths from 2518747 (41%) 2:20:05.238 32G / 36G INFO PathExtender (path_extender.hpp :1031) Processed 1259375 paths from 2518747 (50%) 2:20:11.227 33G / 36G INFO PathExtender (path_extender.hpp :1031) Processed 1511250 paths from 2518747 (60%) 2:20:16.795 34G / 36G INFO PathExtender (path_extender.hpp :1031) Processed 1763125 paths from 2518747 (70%) 2:20:22.158 35G / 36G INFO PathExtender (path_extender.hpp :1031) Processed 2015000 paths from 2518747 (80%) 2:20:23.701 35G / 36G INFO PathExtender (path_extender.hpp :1029) Processed 2097152 paths from 2518747 (83%) 2:20:27.194 36G / 36G INFO PathExtender (path_extender.hpp :1031) Processed 2266875 paths from 2518747 (90%) 2:41:45.506 37G / 37G INFO General (launcher.cpp : 248) Traversing tandem repeats 2:42:12.040 37G / 37G INFO General (launcher.cpp : 258) Traversed 14 loops 2:42:12.040 37G / 37G INFO General (launcher.cpp : 391) Closing gaps in paths 2:42:14.938 39G / 39G INFO General (launcher.cpp : 395) Gap closing completed 3:16:11.181 48G / 48G INFO General (launcher.cpp : 445) ExSPAnder repeat resolving tool finished 3:16:31.627 36G / 48G INFO StageManager (stage.cpp : 126) STAGE == Contig Output 3:16:31.627 36G / 48G INFO General (contig_output.hpp : 478) Outputting contigs to /data/home/pitagoras/public_html/gigas/transcriptome/rnaSpades/output45//K45/before_rr.fasta 3:16:58.338 36G / 48G INFO General (contig_output.hpp : 518) Outputting graph to /data/home/pitagoras/public_html/gigas/transcriptome/rnaSpades/output45//K45/assembly_graph.fastg 3:18:15.046 36G / 48G INFO PathExtendIO (bidirectional_path_output.: 31) Writing contigs to /data/home/pitagoras/public_html/gigas/transcriptome/rnaSpades/output45//K45/transcripts 3:18:28.286 36G / 48G INFO General (contig_output.hpp : 509) Outputting graph to /data/home/pitagoras/public_html/gigas/transcriptome/rnaSpades/output45//K45/assembly_graph.gfa 3:18:57.182 36G / 48G INFO General (launch.hpp : 136) SPAdes finished 3:19:33.215 19G / 48G INFO General (main.cpp : 109) Assembling time: 3 hours 19 minutes 33 seconds ===== Assembling finished. Used k-mer sizes: 45 * Corrected reads are in /data/home/pitagoras/public_html/gigas/transcriptome/rnaSpades/output45/corrected/ * Assembled transcripts are in /data/home/pitagoras/public_html/gigas/transcriptome/rnaSpades/output45/transcripts.fasta * Paths in the assembly graph corresponding to the transcripts are in /data/home/pitagoras/public_html/gigas/transcriptome/rnaSpades/output45/transcripts.paths ======= SPAdes pipeline finished. SPAdes log can be found here: /data/home/pitagoras/public_html/gigas/transcriptome/rnaSpades/output45/spades.log Thank you for using SPAdes!