Command line: /data/home/root/SPAdes-3.10.1-Linux/bin/spades.py --cov-cutoff auto -k 43 --rna -o /data/home/pitagoras/public_html/gigas/transcriptome/rnaSpades/output43 --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/output43 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: [43] 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/output43/tmp Threads: 16 Memory limit (in Gb): 220 ======= SPAdes pipeline started. Log can be found here: /data/home/pitagoras/public_html/gigas/transcriptome/rnaSpades/output43/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/output43/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 0:00:00.001 4M / 4M INFO General (main.cpp : 84) Loading config from /data/home/pitagoras/public_html/gigas/transcriptome/rnaSpades/output43/corrected/configs/config.info 0:00:00.004 4M / 4M INFO General (memory_limit.hpp : 47) Memory limit set to 220 Gb 0:00:00.004 4M / 4M INFO General (main.cpp : 93) Trying to determine PHRED offset 0:00:00.224 4M / 4M INFO General (main.cpp : 99) Determined value is 33 0:00:00.225 4M / 4M INFO General (hammer_tools.cpp : 36) Hamming graph threshold tau=1, k=21, subkmer positions = [ 0 10 ] 0:00:00.225 4M / 4M INFO General (main.cpp : 120) Size of aux. kmer data 24 bytes === ITERATION 0 begins === 0:00:00.230 4M / 4M INFO K-mer Index Building (kmer_index_builder.hpp : 428) Building kmer index 0:00:00.230 4M / 4M INFO K-mer Splitting (kmer_data.cpp : 91) Splitting kmer instances into 256 buckets. This might take a while. 0:00:00.230 4M / 4M INFO General (file_limit.hpp : 30) Open file limit set to 64000 0:00:00.230 4M / 4M INFO General (kmer_index_builder.hpp : 108) Memory available for splitting buffers: 4.58325 Gb 0:00:00.230 4M / 4M INFO General (kmer_index_builder.hpp : 116) Using cell size of 262144 0:00:00.319 8G / 8G INFO K-mer Splitting (kmer_data.cpp : 98) Processing /data2/process/RnaPira/trim/Ova_R2.t.fastq 0:00:13.467 8G / 8G INFO K-mer Splitting (kmer_data.cpp : 108) Processed 1077967 reads 0:00:27.461 8G / 8G INFO K-mer Splitting (kmer_data.cpp : 108) Processed 2202723 reads 0:00:43.467 8G / 8G INFO K-mer Splitting (kmer_data.cpp : 108) Processed 3243679 reads 0:01:01.032 8G / 8G INFO K-mer Splitting (kmer_data.cpp : 108) Processed 4381678 reads 0:01:17.584 8G / 8G INFO K-mer Splitting (kmer_data.cpp : 108) Processed 5534306 reads 0:01:37.226 8G / 8G INFO K-mer Splitting (kmer_data.cpp : 108) Processed 6719783 reads 0:01:55.285 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 108) Processed 8249773 reads 0:02:22.006 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 108) Processed 10901081 reads 0:02:49.448 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 108) Processed 13545124 reads 0:03:35.458 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 108) Processed 16842429 reads 0:06:19.661 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 98) Processing /data2/process/RnaPira/trim/Cerebro-femea_R2.t.fastq 0:07:50.795 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 108) Processed 34008113 reads 0:10:15.282 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 98) Processing /data2/process/RnaPira/trim/Cerebro-macho_R2.t.fastq 0:14:22.147 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 98) Processing /data2/process/RnaPira/trim/Pulmao-femea_R2.t.fastq 0:16:58.291 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 98) Processing /data2/process/RnaPira/trim/Pulmao-macho_R2.t.fastq 0:18:38.937 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 108) Processed 67271841 reads 0:21:38.622 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 98) Processing /data2/process/RnaPira/trim/Hipofise-femea_R2.t.fastq 0:24:24.028 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 98) Processing /data2/process/RnaPira/trim/Rim-femea_R2.t.fastq 0:27:03.066 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 98) Processing /data2/process/RnaPira/trim/Hipofise-macho_R2.t.fastq 0:29:23.462 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 98) Processing /data2/process/RnaPira/trim/Rim-macho_R2.t.fastq 0:34:11.609 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 98) Processing /data2/process/RnaPira/trim/Musculo-femea_R2.t.fastq 0:36:38.519 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 98) Processing /data2/process/RnaPira/trim/Testiculo_R2.t.fastq 0:38:40.594 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 98) Processing /data2/process/RnaPira/trim/Ova_R1.t.fastq 0:39:39.691 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 108) Processed 135157585 reads 0:45:00.954 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 98) Processing /data2/process/RnaPira/trim/Cerebro-femea_R1.t.fastq 0:49:18.636 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 98) Processing /data2/process/RnaPira/trim/Cerebro-macho_R1.t.fastq 0:53:22.932 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 98) Processing /data2/process/RnaPira/trim/Pulmao-femea_R1.t.fastq 0:55:28.555 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 98) Processing /data2/process/RnaPira/trim/Pulmao-macho_R1.t.fastq 0:59:46.073 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 98) Processing /data2/process/RnaPira/trim/Hipofise-femea_R1.t.fastq 1:02:14.357 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 98) Processing /data2/process/RnaPira/trim/Rim-femea_R1.t.fastq 1:04:24.707 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 98) Processing /data2/process/RnaPira/trim/Hipofise-macho_R1.t.fastq 1:06:45.955 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 98) Processing /data2/process/RnaPira/trim/Rim-macho_R1.t.fastq 1:09:50.746 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 98) Processing /data2/process/RnaPira/trim/Musculo-femea_R1.t.fastq 1:11:51.056 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 98) Processing /data2/process/RnaPira/trim/Testiculo_R1.t.fastq 1:14:50.937 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 113) Total 262072356 reads processed 1:14:51.575 64M / 9G INFO General (kmer_index_builder.hpp : 252) Starting k-mer counting. 1:59:27.584 64M / 9G INFO General (kmer_index_builder.hpp : 258) K-mer counting done. There are 853373588 kmers in total. 1:59:27.584 64M / 9G INFO General (kmer_index_builder.hpp : 260) Merging temporary buckets. 2:03:30.275 64M / 9G INFO K-mer Index Building (kmer_index_builder.hpp : 437) Building perfect hash indices 2:04:55.236 320M / 21G INFO General (kmer_index_builder.hpp : 276) Merging final buckets. 2:10:44.448 320M / 21G INFO K-mer Index Building (kmer_index_builder.hpp : 483) Index built. Total 278813288 bytes occupied (2.61375 bits per kmer). 2:10:44.530 320M / 21G INFO K-mer Counting (kmer_data.cpp : 359) Arranging kmers in hash map order 2:11:59.204 13G / 21G INFO General (main.cpp : 155) Clustering Hamming graph. 3:05:02.453 13G / 21G INFO General (main.cpp : 162) Extracting clusters 3:22:46.689 13G / 37G INFO General (main.cpp : 174) Clustering done. Total clusters: 471665368 3:22:48.672 6G / 37G INFO K-mer Counting (kmer_data.cpp : 381) Collecting K-mer information, this takes a while. 3:23:04.145 25G / 37G INFO K-mer Counting (kmer_data.cpp : 387) Processing /data2/process/RnaPira/trim/Ova_R2.t.fastq 3:30:58.745 25G / 37G INFO K-mer Counting (kmer_data.cpp : 387) Processing /data2/process/RnaPira/trim/Cerebro-femea_R2.t.fastq 3:34:25.973 25G / 37G INFO K-mer Counting (kmer_data.cpp : 387) Processing /data2/process/RnaPira/trim/Cerebro-macho_R2.t.fastq 3:37:39.020 25G / 37G INFO K-mer Counting (kmer_data.cpp : 387) Processing /data2/process/RnaPira/trim/Pulmao-femea_R2.t.fastq 3:39:30.515 25G / 37G INFO K-mer Counting (kmer_data.cpp : 387) Processing /data2/process/RnaPira/trim/Pulmao-macho_R2.t.fastq 3:43:36.425 25G / 37G INFO K-mer Counting (kmer_data.cpp : 387) Processing /data2/process/RnaPira/trim/Hipofise-femea_R2.t.fastq 3:46:16.948 25G / 37G INFO K-mer Counting (kmer_data.cpp : 387) Processing /data2/process/RnaPira/trim/Rim-femea_R2.t.fastq 3:48:24.251 25G / 37G INFO K-mer Counting (kmer_data.cpp : 387) Processing /data2/process/RnaPira/trim/Hipofise-macho_R2.t.fastq 3:50:19.071 25G / 37G INFO K-mer Counting (kmer_data.cpp : 387) Processing /data2/process/RnaPira/trim/Rim-macho_R2.t.fastq 3:52:36.483 25G / 37G INFO K-mer Counting (kmer_data.cpp : 387) Processing /data2/process/RnaPira/trim/Musculo-femea_R2.t.fastq 3:55:26.003 25G / 37G INFO K-mer Counting (kmer_data.cpp : 387) Processing /data2/process/RnaPira/trim/Testiculo_R2.t.fastq 3:57:12.865 25G / 37G INFO K-mer Counting (kmer_data.cpp : 387) Processing /data2/process/RnaPira/trim/Ova_R1.t.fastq 4:05:02.323 25G / 37G INFO K-mer Counting (kmer_data.cpp : 387) Processing /data2/process/RnaPira/trim/Cerebro-femea_R1.t.fastq 4:08:44.052 25G / 37G INFO K-mer Counting (kmer_data.cpp : 387) Processing /data2/process/RnaPira/trim/Cerebro-macho_R1.t.fastq 4:12:08.754 25G / 37G INFO K-mer Counting (kmer_data.cpp : 387) Processing /data2/process/RnaPira/trim/Pulmao-femea_R1.t.fastq 4:14:07.363 25G / 37G INFO K-mer Counting (kmer_data.cpp : 387) Processing /data2/process/RnaPira/trim/Pulmao-macho_R1.t.fastq 4:18:30.363 25G / 37G INFO K-mer Counting (kmer_data.cpp : 387) Processing /data2/process/RnaPira/trim/Hipofise-femea_R1.t.fastq 4:21:21.615 25G / 37G INFO K-mer Counting (kmer_data.cpp : 387) Processing /data2/process/RnaPira/trim/Rim-femea_R1.t.fastq 4:23:38.628 25G / 37G INFO K-mer Counting (kmer_data.cpp : 387) Processing /data2/process/RnaPira/trim/Hipofise-macho_R1.t.fastq 4:25:47.226 25G / 37G INFO K-mer Counting (kmer_data.cpp : 387) Processing /data2/process/RnaPira/trim/Rim-macho_R1.t.fastq 4:28:20.888 25G / 37G INFO K-mer Counting (kmer_data.cpp : 387) Processing /data2/process/RnaPira/trim/Musculo-femea_R1.t.fastq 4:31:29.730 25G / 37G INFO K-mer Counting (kmer_data.cpp : 387) Processing /data2/process/RnaPira/trim/Testiculo_R1.t.fastq 4:33:25.550 25G / 37G INFO K-mer Counting (kmer_data.cpp : 394) Collection done, postprocessing. 4:33:31.270 25G / 37G INFO K-mer Counting (kmer_data.cpp : 408) There are 853373588 kmers in total. Among them 453841768 (53.1821%) are singletons. 4:33:31.270 25G / 37G INFO General (main.cpp : 180) Subclustering Hamming graph 5:01:52.712 25G / 37G INFO Hamming Subclustering (kmer_cluster.cpp : 649) Subclustering done. Total 14726 non-read kmers were generated. 5:01:52.713 25G / 37G INFO Hamming Subclustering (kmer_cluster.cpp : 650) Subclustering statistics: 5:01:52.713 25G / 37G INFO Hamming Subclustering (kmer_cluster.cpp : 651) Total singleton hamming clusters: 373380008. Among them 197436218 (52.8781%) are good 5:01:52.713 25G / 37G INFO Hamming Subclustering (kmer_cluster.cpp : 652) Total singleton subclusters: 4428051. Among them 4415790 (99.7231%) are good 5:01:52.714 25G / 37G INFO Hamming Subclustering (kmer_cluster.cpp : 653) Total non-singleton subcluster centers: 106087649. Among them 76147241 (71.7777%) are good 5:01:52.714 25G / 37G INFO Hamming Subclustering (kmer_cluster.cpp : 654) Average size of non-trivial subcluster: 4.52497 kmers 5:01:52.714 25G / 37G INFO Hamming Subclustering (kmer_cluster.cpp : 655) Average number of sub-clusters per non-singleton cluster: 1.12444 5:01:52.714 25G / 37G INFO Hamming Subclustering (kmer_cluster.cpp : 656) Total solid k-mers: 277999249 5:01:52.715 25G / 37G INFO Hamming Subclustering (kmer_cluster.cpp : 657) Substitution probabilities: [4,4]((0.935094,0.0147492,0.015711,0.0344461),(0.023118,0.922604,0.0103254,0.0439527),(0.0426235,0.00995293,0.923141,0.0242823),(0.0332816,0.0150218,0.0143518,0.937345)) 5:01:54.089 25G / 37G INFO General (main.cpp : 185) Finished clustering. 5:01:54.090 25G / 37G INFO General (main.cpp : 204) Starting solid k-mers expansion in 16 threads. 5:28:13.987 25G / 37G INFO General (main.cpp : 225) Solid k-mers iteration 0 produced 26913403 new k-mers. 5:53:20.881 25G / 37G INFO General (main.cpp : 225) Solid k-mers iteration 1 produced 2197164 new k-mers. 6:17:42.590 25G / 37G INFO General (main.cpp : 225) Solid k-mers iteration 2 produced 176769 new k-mers. 6:42:05.570 25G / 37G INFO General (main.cpp : 225) Solid k-mers iteration 3 produced 20818 new k-mers. 7:06:28.572 25G / 37G INFO General (main.cpp : 225) Solid k-mers iteration 4 produced 3344 new k-mers. 7:30:54.612 25G / 37G INFO General (main.cpp : 225) Solid k-mers iteration 5 produced 631 new k-mers. 7:55:14.322 25G / 37G INFO General (main.cpp : 225) Solid k-mers iteration 6 produced 116 new k-mers. 8:19:40.685 25G / 37G INFO General (main.cpp : 225) Solid k-mers iteration 7 produced 49 new k-mers. 8:44:07.772 25G / 37G INFO General (main.cpp : 225) Solid k-mers iteration 8 produced 15 new k-mers. 9:08:08.590 25G / 37G INFO General (main.cpp : 225) Solid k-mers iteration 9 produced 29 new k-mers. 9:32:06.119 25G / 37G INFO General (main.cpp : 225) Solid k-mers iteration 10 produced 0 new k-mers. 9:32:06.119 25G / 37G INFO General (main.cpp : 229) Solid k-mers finalized 9:32:06.119 25G / 37G INFO General (hammer_tools.cpp : 211) Starting read correction in 16 threads. 9:32:06.119 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 9:32:11.890 26G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 0 of 1600000 reads. 9:32:28.060 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 0 9:32:32.188 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 0 9:32:37.554 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 1 of 1600000 reads. 9:32:52.314 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 1 9:32:56.505 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 1 9:33:01.866 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 2 of 1600000 reads. 9:33:18.332 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 2 9:33:22.969 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 2 9:33:27.173 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 3 of 1600000 reads. 9:33:45.056 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 3 9:33:50.445 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 3 9:33:54.932 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 4 of 1600000 reads. 9:34:12.017 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 4 9:34:16.868 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 4 9:34:21.219 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 5 of 1600000 reads. 9:34:38.395 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 5 9:34:46.761 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 5 9:34:51.001 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 6 of 1600000 reads. 9:35:07.917 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 6 9:35:16.817 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 6 9:35:20.578 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 7 of 1600000 reads. 9:35:38.305 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 7 9:35:48.593 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 7 9:35:52.787 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 8 of 1600000 reads. 9:36:09.320 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 8 9:36:19.128 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 8 9:36:23.365 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 9 of 1600000 reads. 9:36:40.336 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 9 9:36:49.512 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 9 9:36:53.553 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 10 of 1600000 reads. 9:37:10.315 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 10 9:37:20.001 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 10 9:37:23.699 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 11 of 1600000 reads. 9:37:37.990 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 11 9:37:51.373 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 11 9:37:55.705 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 12 of 1600000 reads. 9:38:12.038 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 12 9:38:22.115 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 12 9:38:26.236 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 13 of 1600000 reads. 9:38:42.990 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 13 9:38:52.137 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 13 9:38:56.198 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 14 of 1600000 reads. 9:39:11.257 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 14 9:39:23.206 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 14 9:39:27.164 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 15 of 1600000 reads. 9:39:40.932 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 15 9:39:53.356 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 15 9:39:57.672 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 16 of 1600000 reads. 9:40:15.018 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 16 9:40:24.632 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 16 9:40:28.821 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 17 of 1600000 reads. 9:40:45.499 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 17 9:40:55.507 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 17 9:40:57.932 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 18 of 811697 reads. 9:41:06.557 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 18 9:41:08.812 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 18 9:41:30.706 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 9:41:36.062 26G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 0 of 1600000 reads. 9:41:51.870 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 0 9:41:55.724 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 0 9:42:00.682 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 1 of 1600000 reads. 9:42:19.417 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 1 9:42:39.466 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 1 9:42:44.466 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 2 of 1600000 reads. 9:43:01.326 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 2 9:43:06.808 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 2 9:43:11.688 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 3 of 1600000 reads. 9:43:27.910 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 3 9:43:38.933 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 3 9:43:43.305 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 4 of 1600000 reads. 9:43:56.942 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 4 9:44:09.747 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 4 9:44:13.899 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 5 of 1600000 reads. 9:44:30.932 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 5 9:44:39.925 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 5 9:44:44.375 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 6 of 1600000 reads. 9:44:58.016 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 6 9:45:11.708 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 6 9:45:16.463 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 7 of 1600000 reads. 9:45:32.233 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 7 9:45:40.903 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 7 9:45:43.034 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 8 of 811070 reads. 9:45:50.446 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 8 9:45:52.864 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 8 9:46:27.853 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 9:46:34.936 26G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 0 of 1600000 reads. 9:46:50.827 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 0 9:46:55.785 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 0 9:47:01.215 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 1 of 1600000 reads. 9:47:16.957 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 1 9:47:43.289 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 1 9:47:47.608 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 2 of 1600000 reads. 9:48:04.832 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 2 9:48:09.379 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 2 9:48:13.647 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 3 of 1600000 reads. 9:48:28.692 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 3 9:48:42.037 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 3 9:48:46.220 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 4 of 1600000 reads. 9:48:59.899 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 4 9:49:10.784 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 4 9:49:14.995 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 5 of 1600000 reads. 9:49:31.317 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 5 9:49:40.294 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 5 9:49:45.101 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 6 of 1600000 reads. 9:50:02.329 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 6 9:50:11.279 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 6 9:50:13.337 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 7 of 700384 reads. 9:50:21.035 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 7 9:50:22.839 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 7 9:50:47.939 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 9:50:55.139 26G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 0 of 1600000 reads. 9:51:09.893 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 0 9:51:13.993 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 0 9:51:19.350 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 1 of 1600000 reads. 9:51:35.410 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 1 9:51:43.735 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 1 9:51:48.322 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 2 of 1600000 reads. 9:52:03.310 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 2 9:52:15.452 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 2 9:52:19.607 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 3 of 1600000 reads. 9:52:35.254 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 3 9:52:46.490 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 3 9:52:47.691 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 4 of 442334 reads. 9:52:52.307 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 4 9:52:53.624 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 4 9:53:19.282 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 9:53:26.559 26G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 0 of 1600000 reads. 9:53:41.185 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 0 9:53:44.866 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 0 9:53:50.485 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 1 of 1600000 reads. 9:54:05.389 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 1 9:54:09.882 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 1 9:54:13.958 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 2 of 1600000 reads. 9:54:29.352 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 2 9:54:33.450 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 2 9:54:37.371 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 3 of 1600000 reads. 9:54:53.349 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 3 9:54:58.216 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 3 9:55:03.301 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 4 of 1600000 reads. 9:55:20.355 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 4 9:55:27.944 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 4 9:55:32.482 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 5 of 1600000 reads. 9:55:47.765 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 5 9:56:01.451 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 5 9:56:05.450 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 6 of 1600000 reads. 9:56:18.000 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 6 9:56:28.657 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 6 9:56:32.093 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 7 of 1600000 reads. 9:56:46.443 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 7 9:56:59.053 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 7 9:57:03.169 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 8 of 1600000 reads. 9:57:20.943 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 8 9:57:29.692 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 8 9:57:34.273 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 9 of 1600000 reads. 9:57:50.810 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 9 9:58:00.839 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 9 9:58:01.622 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 10 of 228975 reads. 9:58:04.173 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 10 9:58:04.832 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 10 9:58:28.978 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 9:58:34.684 26G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 0 of 1600000 reads. 9:58:47.330 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 0 9:58:52.535 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 0 9:58:58.055 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 1 of 1600000 reads. 9:59:12.207 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 1 9:59:16.250 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 1 9:59:20.520 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 2 of 1600000 reads. 9:59:36.560 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 2 9:59:41.359 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 2 9:59:45.893 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 3 of 1600000 reads. 10:00:01.810 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 3 10:00:06.570 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 3 10:00:10.884 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 4 of 1600000 reads. 10:00:24.533 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 4 10:00:41.143 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 4 10:00:45.733 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 5 of 1600000 reads. 10:01:00.125 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 5 10:01:05.188 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 5 10:01:07.807 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 6 of 862876 reads. 10:01:16.993 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 6 10:01:19.341 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 6 10:01:52.633 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 10:01:57.903 26G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 0 of 1600000 reads. 10:02:12.550 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 0 10:02:17.202 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 0 10:02:21.848 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 1 of 1600000 reads. 10:02:36.788 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 1 10:02:41.023 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 1 10:02:46.299 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 2 of 1600000 reads. 10:03:00.941 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 2 10:03:05.706 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 2 10:03:10.880 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 3 of 1600000 reads. 10:03:28.078 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 3 10:03:32.523 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 3 10:03:36.463 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 4 of 1600000 reads. 10:03:53.556 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 4 10:03:57.806 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 4 10:03:59.180 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 5 of 531717 reads. 10:04:04.151 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 5 10:04:05.376 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 5 10:04:26.260 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 10:04:32.890 26G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 0 of 1600000 reads. 10:04:44.715 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 0 10:04:48.436 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 0 10:04:52.907 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 1 of 1600000 reads. 10:05:09.063 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 1 10:05:14.136 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 1 10:05:18.687 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 2 of 1600000 reads. 10:05:33.774 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 2 10:05:38.995 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 2 10:05:43.339 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 3 of 1600000 reads. 10:05:57.921 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 3 10:06:02.525 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 3 10:06:04.669 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 4 of 678859 reads. 10:06:11.691 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 4 10:06:13.333 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 4 10:06:37.384 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 10:06:42.199 26G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 0 of 1600000 reads. 10:06:57.372 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 0 10:07:02.018 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 0 10:07:07.061 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 1 of 1600000 reads. 10:07:22.665 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 1 10:07:26.798 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 1 10:07:31.143 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 2 of 1600000 reads. 10:07:44.029 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 2 10:07:58.479 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 2 10:08:02.476 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 3 of 1600000 reads. 10:08:18.346 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 3 10:08:22.525 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 3 10:08:26.567 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 4 of 1600000 reads. 10:08:42.722 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 4 10:08:47.381 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 4 10:08:50.049 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 5 of 880546 reads. 10:08:57.497 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 5 10:08:59.488 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 5 10:09:35.146 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 10:09:40.364 26G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 0 of 1600000 reads. 10:09:54.887 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 0 10:09:59.458 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 0 10:10:04.456 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 1 of 1600000 reads. 10:10:17.348 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 1 10:10:22.331 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 1 10:10:28.196 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 2 of 1600000 reads. 10:10:41.081 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 2 10:10:52.316 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 2 10:10:56.332 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 3 of 1600000 reads. 10:11:10.781 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 3 10:11:20.175 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 3 10:11:24.509 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 4 of 1600000 reads. 10:11:39.469 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 4 10:11:49.539 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 4 10:11:53.629 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 5 of 1600000 reads. 10:12:08.094 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 5 10:12:17.176 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 5 10:12:20.998 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 6 of 1600000 reads. 10:12:33.822 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 6 10:12:44.284 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 6 10:12:45.381 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 7 of 359991 reads. 10:12:49.293 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 7 10:12:50.223 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 7 10:13:13.230 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 10:13:18.927 26G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 0 of 1600000 reads. 10:13:33.108 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 0 10:13:37.260 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 0 10:13:43.160 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 1 of 1600000 reads. 10:13:59.683 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 1 10:14:03.761 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 1 10:14:07.884 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 2 of 1600000 reads. 10:14:21.133 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 2 10:14:29.297 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 2 10:14:33.178 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 3 of 1527729 reads. 10:14:45.575 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 3 10:14:51.147 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 3 10:15:13.145 25G / 37G INFO General (hammer_tools.cpp : 270) Correction done. Changed 15372900 bases in 10325507 reads. 10:15:13.145 25G / 37G INFO General (hammer_tools.cpp : 271) Failed to correct 20826 bases out of 19020763726. 10:15:20.597 64M / 37G INFO General (main.cpp : 262) Saving corrected dataset description to /data/home/pitagoras/public_html/gigas/transcriptome/rnaSpades/output43/corrected/corrected.yaml 10:15:20.720 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/output43/corrected/corrected.yaml ===== Read error correction finished. ===== Assembling started. == Running assembler: K43 0:00:00.000 4M / 4M INFO General (main.cpp : 75) Loading config from /data/home/pitagoras/public_html/gigas/transcriptome/rnaSpades/output43/K43/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/output43/K43/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/output43/K43/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/output43/dataset.info) with K=43 0:00:00.000 4M / 4M INFO General (launch.hpp : 51) SPAdes started 0:00:00.000 4M / 4M INFO General (launch.hpp : 58) Starting from stage: construction 0:00:00.000 4M / 4M INFO General (launch.hpp : 61) Two-step RR enabled: 0 0:00:00.003 4M / 4M INFO General (launch.hpp : 79) Will need read mapping, kmer mapper will be attached 0:00:00.003 4M / 4M INFO StageManager (stage.cpp : 126) STAGE == Construction 0:00:00.037 4M / 4M INFO General (read_converter.hpp : 84) Converting reads to binary format for library #0 (takes a while) 0:00:00.037 4M / 4M INFO General (read_converter.hpp : 85) Converting paired reads 0:00:00.356 80M / 80M INFO General (binary_converter.hpp : 139) 16384 reads processed 0:00:00.470 88M / 88M INFO General (binary_converter.hpp : 139) 32768 reads processed 0:00:00.754 108M / 108M INFO General (binary_converter.hpp : 139) 65536 reads processed 0:00:01.283 148M / 148M INFO General (binary_converter.hpp : 139) 131072 reads processed 0:00:02.314 228M / 228M INFO General (binary_converter.hpp : 139) 262144 reads processed 0:00:04.363 392M / 392M INFO General (binary_converter.hpp : 139) 524288 reads processed 0:00:10.028 640M / 640M INFO General (binary_converter.hpp : 139) 1048576 reads processed 0:00:19.257 640M / 640M INFO General (binary_converter.hpp : 139) 2097152 reads processed 0:00:37.077 640M / 640M INFO General (binary_converter.hpp : 139) 4194304 reads processed 0:01:14.053 640M / 640M INFO General (binary_converter.hpp : 139) 8388608 reads processed 0:02:31.331 644M / 644M INFO General (binary_converter.hpp : 139) 16777216 reads processed 0:05:10.555 648M / 648M INFO General (binary_converter.hpp : 139) 33554432 reads processed 0:10:37.291 656M / 656M INFO General (binary_converter.hpp : 139) 67108864 reads processed 0:17:17.014 656M / 660M INFO General (binary_converter.hpp : 159) 127432190 reads written 0:17:18.205 8M / 660M INFO General (read_converter.hpp : 94) Converting single reads 0:17:20.443 140M / 660M INFO General (binary_converter.hpp : 139) 16384 reads processed 0:17:20.493 144M / 660M INFO General (binary_converter.hpp : 139) 32768 reads processed 0:17:20.594 152M / 660M INFO General (binary_converter.hpp : 139) 65536 reads processed 0:17:20.793 172M / 660M INFO General (binary_converter.hpp : 139) 131072 reads processed 0:17:21.175 212M / 660M INFO General (binary_converter.hpp : 139) 262144 reads processed 0:17:21.837 292M / 660M INFO General (binary_converter.hpp : 139) 524288 reads processed 0:17:23.142 448M / 660M INFO General (binary_converter.hpp : 139) 1048576 reads processed 0:17:25.747 764M / 764M INFO General (binary_converter.hpp : 139) 2097152 reads processed 0:17:30.738 1G / 1G INFO General (binary_converter.hpp : 159) 3534013 reads written 0:17:35.753 4M / 1G INFO General (graph_construction.hpp : 120) Constructing DeBruijn graph for k=43 0:17:35.794 4M / 1G INFO General (kmer_splitters.hpp : 129) Splitting kmer instances into 256 buckets. This might take a while. 0:17:35.794 4M / 1G INFO General (file_limit.hpp : 30) Open file limit set to 64000 0:17:35.794 4M / 1G INFO General (kmer_index_builder.hpp : 108) Memory available for splitting buffers: 4.58325 Gb 0:17:35.795 4M / 1G INFO General (kmer_index_builder.hpp : 116) Using cell size of 131072 0:17:47.390 8G / 8G INFO General (kmer_splitters.hpp : 153) Processed 2509323 reads 0:17:59.225 8G / 8G INFO General (kmer_splitters.hpp : 153) Processed 5863897 reads 0:18:11.731 8G / 8G INFO General (kmer_splitters.hpp : 153) Processed 8073094 reads 0:18:26.948 8G / 8G INFO General (kmer_splitters.hpp : 153) Processed 11632886 reads 0:18:38.571 8G / 8G INFO General (kmer_splitters.hpp : 153) Processed 14311565 reads 0:18:52.334 8G / 8G INFO General (kmer_splitters.hpp : 153) Processed 16794268 reads 0:19:03.122 8G / 8G INFO General (kmer_splitters.hpp : 153) Processed 19508031 reads 0:19:13.163 8G / 8G INFO General (kmer_splitters.hpp : 153) Processed 21981959 reads 0:19:25.476 8G / 8G INFO General (kmer_splitters.hpp : 153) Processed 25382917 reads 0:19:35.244 8G / 8G INFO General (kmer_splitters.hpp : 153) Processed 27459979 reads 0:20:04.960 8G / 9G INFO General (kmer_splitters.hpp : 153) Processed 42376671 reads 0:21:20.396 8G / 9G INFO General (kmer_splitters.hpp : 153) Processed 70322629 reads 0:24:57.099 8G / 9G INFO General (kmer_splitters.hpp : 153) Processed 138528903 reads 0:35:01.589 8G / 9G INFO General (kmer_splitters.hpp : 153) Processed 269762699 reads 1:02:10.524 8G / 9G INFO General (kmer_splitters.hpp : 159) Adding contigs from previous K 1:02:11.088 64M / 9G INFO General (kmer_splitters.hpp : 172) Used 516796786 reads. Maximum read length 76 1:02:11.089 64M / 9G INFO General (kmer_splitters.hpp : 173) Average read length 73.1885 1:02:11.089 64M / 9G INFO General (kmer_index_builder.hpp : 252) Starting k-mer counting. 1:11:41.045 64M / 9G INFO General (kmer_index_builder.hpp : 258) K-mer counting done. There are 244456153 kmers in total. 1:11:41.045 64M / 9G INFO General (kmer_index_builder.hpp : 260) Merging temporary buckets. 1:13:26.391 64M / 9G INFO K-mer Index Building (kmer_index_builder.hpp : 428) Building kmer index 1:13:26.391 64M / 9G INFO General (kmer_splitters.hpp : 285) Splitting kmer instances into 256 buckets. This might take a while. 1:13:26.391 64M / 9G INFO General (file_limit.hpp : 30) Open file limit set to 64000 1:13:26.391 64M / 9G INFO General (kmer_index_builder.hpp : 108) Memory available for splitting buffers: 4.58203 Gb 1:13:26.391 64M / 9G INFO General (kmer_index_builder.hpp : 116) Using cell size of 131072 1:16:07.992 8G / 9G INFO General (kmer_splitters.hpp : 304) Processed 244456153 kmers 1:16:07.992 8G / 9G INFO General (kmer_splitters.hpp : 309) Used 244456153 kmers. 1:16:09.212 64M / 9G INFO General (kmer_index_builder.hpp : 252) Starting k-mer counting. 1:17:47.770 64M / 9G INFO General (kmer_index_builder.hpp : 258) K-mer counting done. There are 246507635 kmers in total. 1:17:47.771 64M / 9G INFO General (kmer_index_builder.hpp : 260) Merging temporary buckets. 1:19:52.388 64M / 9G INFO K-mer Index Building (kmer_index_builder.hpp : 437) Building perfect hash indices 1:20:02.303 192M / 9G INFO General (kmer_index_builder.hpp : 276) Merging final buckets. 1:20:55.004 192M / 9G INFO K-mer Index Building (kmer_index_builder.hpp : 483) Index built. Total 80538784 bytes occupied (2.61375 bits per kmer). 1:20:55.280 428M / 9G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 85) Building k-mer extensions from k+1-mers 1:21:19.534 428M / 9G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 89) Building k-mer extensions from k+1-mers finished. 1:21:19.559 428M / 9G INFO General (graph_construction.hpp : 136) Condensing graph 1:21:19.559 428M / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 340) Extracting unbranching paths 1:24:00.493 4G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths finished. 34286036 sequences extracted 1:24:24.659 3G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 313) Collecting perfect loops 1:26:22.384 3G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 329) Collecting perfect loops finished. 24 loops collected 1:26:42.043 8G / 10G INFO General (graph_construction.hpp : 141) Building index with from graph 1:26:42.055 8G / 10G INFO K-mer Index Building (kmer_index_builder.hpp : 428) Building kmer index 1:26:42.055 8G / 10G INFO General (kmer_splitters.hpp : 214) Splitting kmer instances into 16 buckets. This might take a while. 1:26:42.055 8G / 10G INFO General (file_limit.hpp : 30) Open file limit set to 64000 1:26:42.055 8G / 10G INFO General (kmer_index_builder.hpp : 108) Memory available for splitting buffers: 70.5378 Gb 1:26:42.055 8G / 10G INFO General (kmer_index_builder.hpp : 116) Using cell size of 2097152 1:26:58.412 8G / 10G INFO General (kmer_splitters.hpp : 225) Processed 4072732 edges 1:27:13.118 8G / 10G INFO General (kmer_splitters.hpp : 225) Processed 8147602 edges 1:27:27.750 8G / 10G INFO General (kmer_splitters.hpp : 225) Processed 12217519 edges 1:27:42.433 8G / 10G INFO General (kmer_splitters.hpp : 225) Processed 16282217 edges 1:27:56.943 8G / 10G INFO General (kmer_splitters.hpp : 225) Processed 20354498 edges 1:28:11.405 8G / 10G INFO General (kmer_splitters.hpp : 225) Processed 24423585 edges 1:28:25.769 8G / 10G INFO General (kmer_splitters.hpp : 225) Processed 28483216 edges 1:28:40.256 8G / 10G INFO General (kmer_splitters.hpp : 225) Processed 32541492 edges 1:28:46.519 8G / 10G INFO General (kmer_splitters.hpp : 225) Processed 34286068 edges 1:28:46.519 8G / 10G INFO General (kmer_splitters.hpp : 230) Used 34286068 sequences. 1:28:46.610 8G / 10G INFO General (kmer_index_builder.hpp : 252) Starting k-mer counting. 1:30:34.143 8G / 10G INFO General (kmer_index_builder.hpp : 258) K-mer counting done. There are 244456153 kmers in total. 1:30:34.143 8G / 10G INFO General (kmer_index_builder.hpp : 260) Merging temporary buckets. 1:31:51.561 8G / 10G INFO K-mer Index Building (kmer_index_builder.hpp : 437) Building perfect hash indices 1:33:32.823 8G / 10G INFO General (kmer_index_builder.hpp : 276) Merging final buckets. 1:34:24.380 8G / 10G INFO K-mer Index Building (kmer_index_builder.hpp : 483) Index built. Total 79868544 bytes occupied (2.61375 bits per kmer). 1:34:27.624 13G / 13G INFO General (edge_index_builders.hpp : 27) Collecting k-mer coverage information from graph, this takes a while. 1:34:43.892 13G / 13G INFO General (edge_index.hpp : 91) Index refilled 1:34:45.326 13G / 13G INFO General (graph_construction.hpp : 173) Filling coverage index 1:34:45.326 13G / 13G INFO General (edge_index_builders.hpp : 105) Collecting k-mer coverage information from reads, this takes a while. 1:44:14.116 13G / 13G INFO General (graph_construction.hpp : 175) Filling coverage and flanking coverage from index 1:45:34.937 13G / 13G INFO General (construction.cpp : 30) Figured out: read length = 76 1:45:34.955 13G / 13G INFO StageManager (stage.cpp : 126) STAGE == EC Threshold Finding 1:45:53.553 13G / 13G INFO ThresholdFinder (ec_threshold_finder.hpp : 114) Bucket size: 14 1:45:53.554 13G / 13G INFO General (genomic_info_filler.cpp : 104) Average edge coverage: 32.3927 1:45:53.554 13G / 13G INFO General (genomic_info_filler.cpp : 105) Graph threshold: 373 1:48:50.569 17G / 38G INFO General (genomic_info_filler.cpp : 147) EC coverage threshold value was calculated as 32.3927 1:48:50.569 17G / 38G INFO General (genomic_info_filler.cpp : 148) Trusted kmer low bound: 0 1:48:50.569 17G / 38G INFO StageManager (stage.cpp : 126) STAGE == Gap Closer 1:48:50.614 17G / 38G INFO General (gap_closer.cpp : 159) Preparing shift maps 1:49:19.125 19G / 38G INFO General (gap_closer.cpp : 119) Processing paired reads (takes a while) 1:53:25.447 20G / 38G INFO General (gap_closer.cpp : 138) Used 127432190 paired reads 1:53:25.447 20G / 38G INFO General (gap_closer.cpp : 140) Merging paired indices 1:53:46.149 17G / 38G INFO GapCloser (gap_closer.cpp : 347) Closing short gaps 1:55:19.256 17G / 38G INFO GapCloser (gap_closer.cpp : 381) Closing short gaps complete: filled 319875 gaps after checking 950630 candidates 1:56:24.245 17G / 38G INFO StageManager (stage.cpp : 126) STAGE == Simplification 1:56:25.071 11G / 38G INFO General (simplification.cpp : 420) Graph simplification started 1:56:25.071 11G / 38G INFO General (simplification.cpp : 76) PROCEDURE == InitialCleaning 1:56:25.071 11G / 38G INFO General (simplification.cpp : 64) Removing short polyAT 1:57:32.272 11G / 38G INFO General (parallel_simplification_al: 806) Parallel compression 1:57:34.892 11G / 38G INFO General (parallel_simplification_al: 815) Launching post-compression to compress loops 1:57:36.068 11G / 38G INFO General (graph_simplification.hpp : 645) Flanking coverage based disconnection disabled 1:57:36.068 11G / 38G INFO General (simplification.cpp : 349) Running Self conjugate edge remover 1:57:37.753 11G / 38G INFO General (simplification.cpp : 351) Triggered 0 times 1:57:37.753 11G / 38G INFO General (simplification.cpp : 349) Running Short PolyA/T Edges 1:57:39.474 11G / 38G INFO General (simplification.cpp : 351) Triggered 0 times 1:57:39.475 11G / 38G INFO General (simplification.cpp : 349) Running AT Tips 1:58:24.700 11G / 38G INFO General (simplification.cpp : 351) Triggered 2502813 times 1:58:24.701 11G / 38G INFO General (graph_simplification.hpp : 666) Removing loops and rc loops with erroneous connections 1:59:20.726 11G / 38G INFO ECLoopRemover (erroneous_connection_remov: 441) Loops: accurately removed/deadend removed/other: 3/91/9 1:59:20.726 11G / 38G INFO ECLoopRemover (erroneous_connection_remov: 442) RC loops: accurately removed/deadend removed/other: 5/377/2976 1:59:22.083 11G / 38G INFO General (graph_simplification.hpp : 617) Creating parallel br instance 1:59:22.083 11G / 38G INFO General (simplification.cpp : 456) PROCEDURE == Tip clipper and bulge removal cycle, iteration 1.0 1:59:22.083 11G / 38G INFO General (simplification.cpp : 349) Running Tip clipper 2:01:14.830 11G / 38G INFO General (simplification.cpp : 351) Triggered 4412666 times 2:01:14.830 11G / 38G INFO General (simplification.cpp : 349) Running Dead end clipper 2:01:16.596 11G / 38G INFO General (simplification.cpp : 351) Triggered 72304 times 2:01:16.596 11G / 38G INFO General (simplification.cpp : 349) Running Bulge remover 2:02:38.012 12G / 38G INFO General (simplification.cpp : 351) Triggered 133206 times 2:02:38.012 12G / 38G INFO General (simplification.cpp : 456) PROCEDURE == Tip clipper and bulge removal cycle, iteration 1.1 2:02:38.012 12G / 38G INFO General (simplification.cpp : 349) Running Tip clipper 2:02:38.311 12G / 38G INFO General (simplification.cpp : 351) Triggered 3131 times 2:02:38.311 12G / 38G INFO General (simplification.cpp : 349) Running Dead end clipper 2:02:38.490 12G / 38G INFO General (simplification.cpp : 351) Triggered 36 times 2:02:38.490 12G / 38G INFO General (simplification.cpp : 349) Running Bulge remover 2:02:38.575 12G / 38G INFO General (simplification.cpp : 351) Triggered 96 times 2:02:38.575 12G / 38G INFO General (simplification.cpp : 456) PROCEDURE == Tip clipper and bulge removal cycle, iteration 1.2 2:02:38.575 12G / 38G INFO General (simplification.cpp : 349) Running Tip clipper 2:02:38.576 12G / 38G INFO General (simplification.cpp : 351) Triggered 11 times 2:02:38.576 12G / 38G INFO General (simplification.cpp : 349) Running Dead end clipper 2:02:38.577 12G / 38G INFO General (simplification.cpp : 351) Triggered 1 times 2:02:38.577 12G / 38G INFO General (simplification.cpp : 349) Running Bulge remover 2:02:38.577 12G / 38G INFO General (simplification.cpp : 351) Triggered 0 times 2:02:38.577 12G / 38G INFO General (simplification.cpp : 456) PROCEDURE == Tip clipper and bulge removal cycle, iteration 1.3 2:02:38.577 12G / 38G INFO General (simplification.cpp : 349) Running Tip clipper 2:02:38.577 12G / 38G INFO General (simplification.cpp : 351) Triggered 0 times 2:02:38.577 12G / 38G INFO General (simplification.cpp : 349) Running Dead end clipper 2:02:38.577 12G / 38G INFO General (simplification.cpp : 351) Triggered 0 times 2:02:38.577 12G / 38G INFO General (simplification.cpp : 349) Running Bulge remover 2:02:38.577 12G / 38G INFO General (simplification.cpp : 351) Triggered 0 times 2:02:38.577 12G / 38G INFO General (simplification.cpp : 460) PROCEDURE == Erroneous connection, iteration 1 2:02:38.577 12G / 38G INFO General (simplification.cpp : 349) Running Low coverage edge remover 2:03:02.115 12G / 38G INFO General (simplification.cpp : 351) Triggered 373550 times 2:03:02.433 12G / 38G INFO General (graph_simplification.hpp : 617) Creating parallel br instance 2:03:02.433 12G / 38G INFO General (simplification.cpp : 456) PROCEDURE == Tip clipper and bulge removal cycle, iteration 2.0 2:03:02.433 12G / 38G INFO General (simplification.cpp : 349) Running Tip clipper 2:03:05.340 12G / 38G INFO General (simplification.cpp : 351) Triggered 80907 times 2:03:05.340 12G / 38G INFO General (simplification.cpp : 349) Running Dead end clipper 2:03:06.166 12G / 38G INFO General (simplification.cpp : 351) Triggered 68 times 2:03:06.166 12G / 38G INFO General (simplification.cpp : 349) Running Bulge remover 2:04:08.900 12G / 38G INFO General (simplification.cpp : 351) Triggered 62397 times 2:04:08.900 12G / 38G INFO General (simplification.cpp : 456) PROCEDURE == Tip clipper and bulge removal cycle, iteration 2.1 2:04:08.901 12G / 38G INFO General (simplification.cpp : 349) Running Tip clipper 2:04:08.976 12G / 38G INFO General (simplification.cpp : 351) Triggered 331 times 2:04:08.976 12G / 38G INFO General (simplification.cpp : 349) Running Dead end clipper 2:04:09.025 12G / 38G INFO General (simplification.cpp : 351) Triggered 0 times 2:04:09.025 12G / 38G INFO General (simplification.cpp : 349) Running Bulge remover 2:04:09.054 12G / 38G INFO General (simplification.cpp : 351) Triggered 30 times 2:04:09.054 12G / 38G INFO General (simplification.cpp : 456) PROCEDURE == Tip clipper and bulge removal cycle, iteration 2.2 2:04:09.054 12G / 38G INFO General (simplification.cpp : 349) Running Tip clipper 2:04:09.054 12G / 38G INFO General (simplification.cpp : 351) Triggered 0 times 2:04:09.054 12G / 38G INFO General (simplification.cpp : 349) Running Dead end clipper 2:04:09.054 12G / 38G INFO General (simplification.cpp : 351) Triggered 0 times 2:04:09.054 12G / 38G INFO General (simplification.cpp : 349) Running Bulge remover 2:04:09.054 12G / 38G INFO General (simplification.cpp : 351) Triggered 0 times 2:04:09.054 12G / 38G INFO General (simplification.cpp : 460) PROCEDURE == Erroneous connection, iteration 2 2:04:09.054 12G / 38G INFO General (simplification.cpp : 349) Running Low coverage edge remover 2:04:11.733 12G / 38G INFO General (simplification.cpp : 351) Triggered 30381 times 2:04:11.792 12G / 38G INFO General (graph_simplification.hpp : 617) Creating parallel br instance 2:04:11.792 12G / 38G INFO General (simplification.cpp : 456) PROCEDURE == Tip clipper and bulge removal cycle, iteration 3.0 2:04:11.792 12G / 38G INFO General (simplification.cpp : 349) Running Tip clipper 2:04:13.237 12G / 38G INFO General (simplification.cpp : 351) Triggered 3211 times 2:04:13.237 12G / 38G INFO General (simplification.cpp : 349) Running Dead end clipper 2:04:14.162 12G / 38G INFO General (simplification.cpp : 351) Triggered 3 times 2:04:14.162 12G / 38G INFO General (simplification.cpp : 349) Running Bulge remover 2:04:19.377 12G / 38G INFO General (simplification.cpp : 351) Triggered 5502 times 2:04:19.377 12G / 38G INFO General (simplification.cpp : 456) PROCEDURE == Tip clipper and bulge removal cycle, iteration 3.1 2:04:19.378 12G / 38G INFO General (simplification.cpp : 349) Running Tip clipper 2:04:19.396 12G / 38G INFO General (simplification.cpp : 351) Triggered 41 times 2:04:19.396 12G / 38G INFO General (simplification.cpp : 349) Running Dead end clipper 2:04:19.412 12G / 38G INFO General (simplification.cpp : 351) Triggered 0 times 2:04:19.412 12G / 38G INFO General (simplification.cpp : 349) Running Bulge remover 2:04:19.417 12G / 38G INFO General (simplification.cpp : 351) Triggered 3 times 2:04:19.417 12G / 38G INFO General (simplification.cpp : 456) PROCEDURE == Tip clipper and bulge removal cycle, iteration 3.2 2:04:19.417 12G / 38G INFO General (simplification.cpp : 349) Running Tip clipper 2:04:19.417 12G / 38G INFO General (simplification.cpp : 351) Triggered 0 times 2:04:19.418 12G / 38G INFO General (simplification.cpp : 349) Running Dead end clipper 2:04:19.418 12G / 38G INFO General (simplification.cpp : 351) Triggered 0 times 2:04:19.418 12G / 38G INFO General (simplification.cpp : 349) Running Bulge remover 2:04:19.418 12G / 38G INFO General (simplification.cpp : 351) Triggered 0 times 2:04:19.419 12G / 38G INFO General (simplification.cpp : 460) PROCEDURE == Erroneous connection, iteration 3 2:04:19.419 12G / 38G INFO General (simplification.cpp : 349) Running Low coverage edge remover 2:04:20.153 12G / 38G INFO General (simplification.cpp : 351) Triggered 10063 times 2:04:20.175 12G / 38G INFO General (graph_simplification.hpp : 617) Creating parallel br instance 2:04:20.175 12G / 38G INFO General (simplification.cpp : 456) PROCEDURE == Tip clipper and bulge removal cycle, iteration 4.0 2:04:20.175 12G / 38G INFO General (simplification.cpp : 349) Running Tip clipper 2:04:21.167 12G / 38G INFO General (simplification.cpp : 351) Triggered 550 times 2:04:21.167 12G / 38G INFO General (simplification.cpp : 349) Running Dead end clipper 2:04:22.087 12G / 38G INFO General (simplification.cpp : 351) Triggered 0 times 2:04:22.088 12G / 38G INFO General (simplification.cpp : 349) Running Bulge remover 2:04:24.158 12G / 38G INFO General (simplification.cpp : 351) Triggered 1612 times 2:04:24.158 12G / 38G INFO General (simplification.cpp : 456) PROCEDURE == Tip clipper and bulge removal cycle, iteration 4.1 2:04:24.159 12G / 38G INFO General (simplification.cpp : 349) Running Tip clipper 2:04:24.164 12G / 38G INFO General (simplification.cpp : 351) Triggered 5 times 2:04:24.164 12G / 38G INFO General (simplification.cpp : 349) Running Dead end clipper 2:04:24.168 12G / 38G INFO General (simplification.cpp : 351) Triggered 0 times 2:04:24.168 12G / 38G INFO General (simplification.cpp : 349) Running Bulge remover 2:04:24.171 12G / 38G INFO General (simplification.cpp : 351) Triggered 1 times 2:04:24.171 12G / 38G INFO General (simplification.cpp : 456) PROCEDURE == Tip clipper and bulge removal cycle, iteration 4.2 2:04:24.171 12G / 38G INFO General (simplification.cpp : 349) Running Tip clipper 2:04:24.171 12G / 38G INFO General (simplification.cpp : 351) Triggered 0 times 2:04:24.171 12G / 38G INFO General (simplification.cpp : 349) Running Dead end clipper 2:04:24.171 12G / 38G INFO General (simplification.cpp : 351) Triggered 0 times 2:04:24.171 12G / 38G INFO General (simplification.cpp : 349) Running Bulge remover 2:04:24.171 12G / 38G INFO General (simplification.cpp : 351) Triggered 0 times 2:04:24.171 12G / 38G INFO General (simplification.cpp : 460) PROCEDURE == Erroneous connection, iteration 4 2:04:24.171 12G / 38G INFO General (simplification.cpp : 349) Running Low coverage edge remover 2:04:24.526 12G / 38G INFO General (simplification.cpp : 351) Triggered 5135 times 2:04:24.537 12G / 38G INFO General (graph_simplification.hpp : 617) Creating parallel br instance 2:04:24.537 12G / 38G INFO General (simplification.cpp : 456) PROCEDURE == Tip clipper and bulge removal cycle, iteration 5.0 2:04:24.537 12G / 38G INFO General (simplification.cpp : 349) Running Tip clipper 2:04:25.648 12G / 38G INFO General (simplification.cpp : 351) Triggered 163 times 2:04:25.648 12G / 38G INFO General (simplification.cpp : 349) Running Dead end clipper 2:04:26.517 12G / 38G INFO General (simplification.cpp : 351) Triggered 0 times 2:04:26.517 12G / 38G INFO General (simplification.cpp : 349) Running Bulge remover 2:04:28.019 12G / 38G INFO General (simplification.cpp : 351) Triggered 743 times 2:04:28.019 12G / 38G INFO General (simplification.cpp : 456) PROCEDURE == Tip clipper and bulge removal cycle, iteration 5.1 2:04:28.019 12G / 38G INFO General (simplification.cpp : 349) Running Tip clipper 2:04:28.022 12G / 38G INFO General (simplification.cpp : 351) Triggered 1 times 2:04:28.022 12G / 38G INFO General (simplification.cpp : 349) Running Dead end clipper 2:04:28.024 12G / 38G INFO General (simplification.cpp : 351) Triggered 0 times 2:04:28.024 12G / 38G INFO General (simplification.cpp : 349) Running Bulge remover 2:04:28.024 12G / 38G INFO General (simplification.cpp : 351) Triggered 0 times 2:04:28.024 12G / 38G INFO General (simplification.cpp : 456) PROCEDURE == Tip clipper and bulge removal cycle, iteration 5.2 2:04:28.024 12G / 38G INFO General (simplification.cpp : 349) Running Tip clipper 2:04:28.024 12G / 38G INFO General (simplification.cpp : 351) Triggered 0 times 2:04:28.024 12G / 38G INFO General (simplification.cpp : 349) Running Dead end clipper 2:04:28.024 12G / 38G INFO General (simplification.cpp : 351) Triggered 0 times 2:04:28.024 12G / 38G INFO General (simplification.cpp : 349) Running Bulge remover 2:04:28.024 12G / 38G INFO General (simplification.cpp : 351) Triggered 0 times 2:04:28.024 12G / 38G INFO General (simplification.cpp : 460) PROCEDURE == Erroneous connection, iteration 5 2:04:28.024 12G / 38G INFO General (simplification.cpp : 349) Running Low coverage edge remover 2:04:28.226 12G / 38G INFO General (simplification.cpp : 351) Triggered 3149 times 2:04:28.233 12G / 38G INFO General (graph_simplification.hpp : 617) Creating parallel br instance 2:04:28.233 12G / 38G INFO General (simplification.cpp : 456) PROCEDURE == Tip clipper and bulge removal cycle, iteration 6.0 2:04:28.233 12G / 38G INFO General (simplification.cpp : 349) Running Tip clipper 2:04:29.138 12G / 38G INFO General (simplification.cpp : 351) Triggered 76 times 2:04:29.138 12G / 38G INFO General (simplification.cpp : 349) Running Dead end clipper 2:04:30.025 12G / 38G INFO General (simplification.cpp : 351) Triggered 0 times 2:04:30.026 12G / 38G INFO General (simplification.cpp : 349) Running Bulge remover 2:04:31.246 12G / 38G INFO General (simplification.cpp : 351) Triggered 387 times 2:04:31.247 12G / 38G INFO General (simplification.cpp : 456) PROCEDURE == Tip clipper and bulge removal cycle, iteration 6.1 2:04:31.247 12G / 38G INFO General (simplification.cpp : 349) Running Tip clipper 2:04:31.249 12G / 38G INFO General (simplification.cpp : 351) Triggered 0 times 2:04:31.249 12G / 38G INFO General (simplification.cpp : 349) Running Dead end clipper 2:04:31.251 12G / 38G INFO General (simplification.cpp : 351) Triggered 0 times 2:04:31.251 12G / 38G INFO General (simplification.cpp : 349) Running Bulge remover 2:04:31.251 12G / 38G INFO General (simplification.cpp : 351) Triggered 0 times 2:04:31.253 12G / 38G INFO General (simplification.cpp : 460) PROCEDURE == Erroneous connection, iteration 6 2:04:31.253 12G / 38G INFO General (simplification.cpp : 349) Running Low coverage edge remover 2:04:31.388 12G / 38G INFO General (simplification.cpp : 351) Triggered 2170 times 2:04:31.393 12G / 38G INFO General (graph_simplification.hpp : 617) Creating parallel br instance 2:04:31.393 12G / 38G INFO General (simplification.cpp : 456) PROCEDURE == Tip clipper and bulge removal cycle, iteration 7.0 2:04:31.393 12G / 38G INFO General (simplification.cpp : 349) Running Tip clipper 2:04:32.266 12G / 38G INFO General (simplification.cpp : 351) Triggered 34 times 2:04:32.267 12G / 38G INFO General (simplification.cpp : 349) Running Dead end clipper 2:04:33.134 12G / 38G INFO General (simplification.cpp : 351) Triggered 0 times 2:04:33.134 12G / 38G INFO General (simplification.cpp : 349) Running Bulge remover 2:04:34.285 12G / 38G INFO General (simplification.cpp : 351) Triggered 279 times 2:04:34.286 12G / 38G INFO General (simplification.cpp : 456) PROCEDURE == Tip clipper and bulge removal cycle, iteration 7.1 2:04:34.286 12G / 38G INFO General (simplification.cpp : 349) Running Tip clipper 2:04:34.288 12G / 38G INFO General (simplification.cpp : 351) Triggered 0 times 2:04:34.288 12G / 38G INFO General (simplification.cpp : 349) Running Dead end clipper 2:04:34.288 12G / 38G INFO General (simplification.cpp : 351) Triggered 0 times 2:04:34.288 12G / 38G INFO General (simplification.cpp : 349) Running Bulge remover 2:04:34.289 12G / 38G INFO General (simplification.cpp : 351) Triggered 0 times 2:04:34.289 12G / 38G INFO General (simplification.cpp : 460) PROCEDURE == Erroneous connection, iteration 7 2:04:34.289 12G / 38G INFO General (simplification.cpp : 349) Running Low coverage edge remover 2:04:34.386 12G / 38G INFO General (simplification.cpp : 351) Triggered 1600 times 2:04:34.390 12G / 38G INFO General (graph_simplification.hpp : 617) Creating parallel br instance 2:04:34.390 12G / 38G INFO General (simplification.cpp : 456) PROCEDURE == Tip clipper and bulge removal cycle, iteration 8.0 2:04:34.390 12G / 38G INFO General (simplification.cpp : 349) Running Tip clipper 2:04:35.259 12G / 38G INFO General (simplification.cpp : 351) Triggered 28 times 2:04:35.259 12G / 38G INFO General (simplification.cpp : 349) Running Dead end clipper 2:04:36.119 12G / 38G INFO General (simplification.cpp : 351) Triggered 0 times 2:04:36.120 12G / 38G INFO General (simplification.cpp : 349) Running Bulge remover 2:04:37.294 12G / 38G INFO General (simplification.cpp : 351) Triggered 183 times 2:04:37.294 12G / 38G INFO General (simplification.cpp : 456) PROCEDURE == Tip clipper and bulge removal cycle, iteration 8.1 2:04:37.294 12G / 38G INFO General (simplification.cpp : 349) Running Tip clipper 2:04:37.296 12G / 38G INFO General (simplification.cpp : 351) Triggered 0 times 2:04:37.296 12G / 38G INFO General (simplification.cpp : 349) Running Dead end clipper 2:04:37.297 12G / 38G INFO General (simplification.cpp : 351) Triggered 0 times 2:04:37.297 12G / 38G INFO General (simplification.cpp : 349) Running Bulge remover 2:04:37.299 12G / 38G INFO General (simplification.cpp : 351) Triggered 0 times 2:04:37.299 12G / 38G INFO General (simplification.cpp : 460) PROCEDURE == Erroneous connection, iteration 8 2:04:37.299 12G / 38G INFO General (simplification.cpp : 349) Running Low coverage edge remover 2:04:37.377 12G / 38G INFO General (simplification.cpp : 351) Triggered 1252 times 2:04:37.379 12G / 38G INFO General (graph_simplification.hpp : 617) Creating parallel br instance 2:04:37.379 12G / 38G INFO General (simplification.cpp : 456) PROCEDURE == Tip clipper and bulge removal cycle, iteration 9.0 2:04:37.379 12G / 38G INFO General (simplification.cpp : 349) Running Tip clipper 2:04:38.287 12G / 38G INFO General (simplification.cpp : 351) Triggered 25 times 2:04:38.288 12G / 38G INFO General (simplification.cpp : 349) Running Dead end clipper 2:04:39.151 12G / 38G INFO General (simplification.cpp : 351) Triggered 0 times 2:04:39.152 12G / 38G INFO General (simplification.cpp : 349) Running Bulge remover 2:04:40.422 12G / 38G INFO General (simplification.cpp : 351) Triggered 110 times 2:04:40.422 12G / 38G INFO General (simplification.cpp : 456) PROCEDURE == Tip clipper and bulge removal cycle, iteration 9.1 2:04:40.422 12G / 38G INFO General (simplification.cpp : 349) Running Tip clipper 2:04:40.423 12G / 38G INFO General (simplification.cpp : 351) Triggered 0 times 2:04:40.424 12G / 38G INFO General (simplification.cpp : 349) Running Dead end clipper 2:04:40.424 12G / 38G INFO General (simplification.cpp : 351) Triggered 0 times 2:04:40.424 12G / 38G INFO General (simplification.cpp : 349) Running Bulge remover 2:04:40.427 12G / 38G INFO General (simplification.cpp : 351) Triggered 0 times 2:04:40.427 12G / 38G INFO General (simplification.cpp : 460) PROCEDURE == Erroneous connection, iteration 9 2:04:40.427 12G / 38G INFO General (simplification.cpp : 349) Running Low coverage edge remover 2:04:40.489 12G / 38G INFO General (simplification.cpp : 351) Triggered 1027 times 2:04:40.491 12G / 38G INFO General (graph_simplification.hpp : 617) Creating parallel br instance 2:04:40.491 12G / 38G INFO General (simplification.cpp : 456) PROCEDURE == Tip clipper and bulge removal cycle, iteration 10.0 2:04:40.491 12G / 38G INFO General (simplification.cpp : 349) Running Tip clipper 2:04:41.408 12G / 38G INFO General (simplification.cpp : 351) Triggered 10 times 2:04:41.408 12G / 38G INFO General (simplification.cpp : 349) Running Dead end clipper 2:04:42.278 12G / 38G INFO General (simplification.cpp : 351) Triggered 0 times 2:04:42.278 12G / 38G INFO General (simplification.cpp : 349) Running Bulge remover 2:04:43.258 12G / 38G INFO General (simplification.cpp : 351) Triggered 69 times 2:04:43.259 12G / 38G INFO General (simplification.cpp : 456) PROCEDURE == Tip clipper and bulge removal cycle, iteration 10.1 2:04:43.259 12G / 38G INFO General (simplification.cpp : 349) Running Tip clipper 2:04:43.260 12G / 38G INFO General (simplification.cpp : 351) Triggered 0 times 2:04:43.260 12G / 38G INFO General (simplification.cpp : 349) Running Dead end clipper 2:04:43.260 12G / 38G INFO General (simplification.cpp : 351) Triggered 0 times 2:04:43.260 12G / 38G INFO General (simplification.cpp : 349) Running Bulge remover 2:04:43.261 12G / 38G INFO General (simplification.cpp : 351) Triggered 0 times 2:04:43.261 12G / 38G INFO General (simplification.cpp : 460) PROCEDURE == Erroneous connection, iteration 10 2:04:43.261 12G / 38G INFO General (simplification.cpp : 349) Running Low coverage edge remover 2:04:43.317 12G / 38G INFO General (simplification.cpp : 351) Triggered 932 times 2:04:43.319 12G / 38G INFO General (graph_simplification.hpp : 617) Creating parallel br instance 2:04:43.319 12G / 38G INFO General (simplification.cpp : 456) PROCEDURE == Tip clipper and bulge removal cycle, iteration 11.0 2:04:43.319 12G / 38G INFO General (simplification.cpp : 349) Running Tip clipper 2:04:44.220 12G / 38G INFO General (simplification.cpp : 351) Triggered 12 times 2:04:44.221 12G / 38G INFO General (simplification.cpp : 349) Running Dead end clipper 2:04:45.111 12G / 38G INFO General (simplification.cpp : 351) Triggered 0 times 2:04:45.112 12G / 38G INFO General (simplification.cpp : 349) Running Bulge remover 2:04:46.067 12G / 38G INFO General (simplification.cpp : 351) Triggered 61 times 2:04:46.068 12G / 38G INFO General (simplification.cpp : 456) PROCEDURE == Tip clipper and bulge removal cycle, iteration 11.1 2:04:46.068 12G / 38G INFO General (simplification.cpp : 349) Running Tip clipper 2:04:46.070 12G / 38G INFO General (simplification.cpp : 351) Triggered 0 times 2:04:46.070 12G / 38G INFO General (simplification.cpp : 349) Running Dead end clipper 2:04:46.070 12G / 38G INFO General (simplification.cpp : 351) Triggered 0 times 2:04:46.070 12G / 38G INFO General (simplification.cpp : 349) Running Bulge remover 2:04:46.070 12G / 38G INFO General (simplification.cpp : 351) Triggered 0 times 2:04:46.070 12G / 38G INFO General (simplification.cpp : 460) PROCEDURE == Erroneous connection, iteration 11 2:04:46.070 12G / 38G INFO General (simplification.cpp : 349) Running Low coverage edge remover 2:04:46.070 12G / 38G INFO General (simplification.cpp : 351) Triggered 0 times 2:04:46.071 12G / 38G INFO General (simplification.cpp : 162) PROCEDURE == Post simplification 2:04:46.071 12G / 38G INFO General (graph_simplification.hpp : 446) Disconnection of relatively low covered edges disabled 2:04:46.071 12G / 38G INFO General (graph_simplification.hpp : 476) Complex tip clipping disabled 2:04:46.071 12G / 38G INFO General (graph_simplification.hpp : 617) Creating parallel br instance 2:04:46.071 12G / 38G INFO General (graph_simplification.hpp : 617) Creating parallel br instance 2:04:46.071 12G / 38G INFO General (simplification.cpp : 294) Iteration 0 2:04:46.071 12G / 38G INFO General (simplification.cpp : 349) Running Relative coverage component remover 2:04:47.212 12G / 38G INFO General (simplification.cpp : 351) Triggered 908 times 2:04:47.212 12G / 38G INFO General (simplification.cpp : 349) Running Relative coverage component remover 2:04:48.419 12G / 38G INFO General (simplification.cpp : 351) Triggered 6849 times 2:04:48.419 12G / 38G INFO General (simplification.cpp : 349) Running Complex bulge remover 2:05:03.233 12G / 38G INFO General (simplification.cpp : 351) Triggered 127 times 2:05:03.233 12G / 38G INFO General (simplification.cpp : 349) Running Tip clipper 2:05:04.308 12G / 38G INFO General (simplification.cpp : 351) Triggered 18 times 2:05:04.309 12G / 38G INFO General (simplification.cpp : 349) Running Final tip clipper 2:05:05.680 12G / 38G INFO General (simplification.cpp : 351) Triggered 11022 times 2:05:05.680 12G / 38G INFO General (simplification.cpp : 349) Running Bulge remover 2:05:06.726 12G / 38G INFO General (simplification.cpp : 351) Triggered 225 times 2:05:06.727 12G / 38G INFO General (simplification.cpp : 349) Running Final bulge remover 2:05:07.602 12G / 38G INFO General (simplification.cpp : 351) Triggered 0 times 2:05:07.602 12G / 38G INFO General (simplification.cpp : 349) Running AT Tips 2:05:08.650 12G / 38G INFO General (simplification.cpp : 351) Triggered 2530 times 2:05:08.650 12G / 38G INFO General (simplification.cpp : 294) Iteration 1 2:05:08.650 12G / 38G INFO General (simplification.cpp : 349) Running Relative coverage component remover 2:05:08.679 12G / 38G INFO General (simplification.cpp : 351) Triggered 18 times 2:05:08.679 12G / 38G INFO General (simplification.cpp : 349) Running Relative coverage component remover 2:05:09.523 12G / 38G INFO General (simplification.cpp : 351) Triggered 43 times 2:05:09.523 12G / 38G INFO General (simplification.cpp : 349) Running Complex bulge remover 2:05:24.017 12G / 38G INFO General (simplification.cpp : 351) Triggered 6 times 2:05:24.017 12G / 38G INFO General (simplification.cpp : 349) Running Tip clipper 2:05:24.041 12G / 38G INFO General (simplification.cpp : 351) Triggered 0 times 2:05:24.041 12G / 38G INFO General (simplification.cpp : 349) Running Final tip clipper 2:05:24.043 12G / 38G INFO General (simplification.cpp : 351) Triggered 10 times 2:05:24.043 12G / 38G INFO General (simplification.cpp : 349) Running Bulge remover 2:05:24.076 12G / 38G INFO General (simplification.cpp : 351) Triggered 7 times 2:05:24.076 12G / 38G INFO General (simplification.cpp : 349) Running Final bulge remover 2:05:24.078 12G / 38G INFO General (simplification.cpp : 351) Triggered 0 times 2:05:24.078 12G / 38G INFO General (simplification.cpp : 349) Running AT Tips 2:05:24.079 12G / 38G INFO General (simplification.cpp : 351) Triggered 0 times 2:05:24.079 12G / 38G INFO General (simplification.cpp : 294) Iteration 2 2:05:24.079 12G / 38G INFO General (simplification.cpp : 349) Running Relative coverage component remover 2:05:24.080 12G / 38G INFO General (simplification.cpp : 351) Triggered 1 times 2:05:24.080 12G / 38G INFO General (simplification.cpp : 349) Running Relative coverage component remover 2:05:25.218 12G / 38G INFO General (simplification.cpp : 351) Triggered 0 times 2:05:25.220 12G / 38G INFO General (simplification.cpp : 349) Running Complex bulge remover 2:05:39.191 12G / 38G INFO General (simplification.cpp : 351) Triggered 0 times 2:05:39.191 12G / 38G INFO General (simplification.cpp : 349) Running Tip clipper 2:05:39.191 12G / 38G INFO General (simplification.cpp : 351) Triggered 0 times 2:05:39.191 12G / 38G INFO General (simplification.cpp : 349) Running Final tip clipper 2:05:39.191 12G / 38G INFO General (simplification.cpp : 351) Triggered 0 times 2:05:39.191 12G / 38G INFO General (simplification.cpp : 349) Running Bulge remover 2:05:39.192 12G / 38G INFO General (simplification.cpp : 351) Triggered 0 times 2:05:39.192 12G / 38G INFO General (simplification.cpp : 349) Running Final bulge remover 2:05:39.192 12G / 38G INFO General (simplification.cpp : 351) Triggered 0 times 2:05:39.192 12G / 38G INFO General (simplification.cpp : 349) Running AT Tips 2:05:39.192 12G / 38G INFO General (simplification.cpp : 351) Triggered 0 times 2:05:39.192 12G / 38G INFO General (simplification.cpp : 294) Iteration 3 2:05:39.192 12G / 38G INFO General (simplification.cpp : 349) Running Relative coverage component remover 2:05:39.192 12G / 38G INFO General (simplification.cpp : 351) Triggered 0 times 2:05:39.192 12G / 38G INFO General (simplification.cpp : 349) Running Relative coverage component remover 2:05:40.166 12G / 38G INFO General (simplification.cpp : 351) Triggered 0 times 2:05:40.167 12G / 38G INFO General (simplification.cpp : 349) Running Complex bulge remover 2:05:54.254 12G / 38G INFO General (simplification.cpp : 351) Triggered 0 times 2:05:54.254 12G / 38G INFO General (simplification.cpp : 349) Running Tip clipper 2:05:54.254 12G / 38G INFO General (simplification.cpp : 351) Triggered 0 times 2:05:54.254 12G / 38G INFO General (simplification.cpp : 349) Running Final tip clipper 2:05:54.254 12G / 38G INFO General (simplification.cpp : 351) Triggered 0 times 2:05:54.254 12G / 38G INFO General (simplification.cpp : 349) Running Bulge remover 2:05:54.256 12G / 38G INFO General (simplification.cpp : 351) Triggered 0 times 2:05:54.257 12G / 38G INFO General (simplification.cpp : 349) Running Final bulge remover 2:05:54.257 12G / 38G INFO General (simplification.cpp : 351) Triggered 0 times 2:05:54.257 12G / 38G INFO General (simplification.cpp : 349) Running AT Tips 2:05:54.257 12G / 38G INFO General (simplification.cpp : 351) Triggered 0 times 2:05:54.258 12G / 38G INFO General (simplification.cpp : 326) Disrupting self-conjugate edges 2:05:59.246 12G / 38G INFO StageManager (stage.cpp : 126) STAGE == Gap Closer 2:05:59.246 12G / 38G INFO General (graph_pack.hpp : 96) Index refill 2:05:59.257 12G / 38G INFO K-mer Index Building (kmer_index_builder.hpp : 428) Building kmer index 2:05:59.257 12G / 38G INFO General (kmer_splitters.hpp : 214) Splitting kmer instances into 16 buckets. This might take a while. 2:05:59.257 12G / 38G INFO General (file_limit.hpp : 30) Open file limit set to 64000 2:05:59.257 12G / 38G INFO General (kmer_index_builder.hpp : 108) Memory available for splitting buffers: 69.2747 Gb 2:05:59.257 12G / 38G INFO General (kmer_index_builder.hpp : 116) Using cell size of 2097152 2:06:13.835 12G / 38G INFO General (kmer_splitters.hpp : 225) Processed 949285 edges 2:06:28.319 12G / 38G INFO General (kmer_splitters.hpp : 225) Processed 1901392 edges 2:06:42.901 12G / 38G INFO General (kmer_splitters.hpp : 225) Processed 2851468 edges 2:06:57.419 12G / 38G INFO General (kmer_splitters.hpp : 225) Processed 3796811 edges 2:07:12.418 12G / 38G INFO General (kmer_splitters.hpp : 225) Processed 4737608 edges 2:07:12.908 12G / 38G INFO General (kmer_splitters.hpp : 225) Processed 4758943 edges 2:07:12.908 12G / 38G INFO General (kmer_splitters.hpp : 230) Used 4758943 sequences. 2:07:13.001 12G / 38G INFO General (kmer_index_builder.hpp : 252) Starting k-mer counting. 2:08:23.831 12G / 38G INFO General (kmer_index_builder.hpp : 258) K-mer counting done. There are 165010850 kmers in total. 2:08:23.831 12G / 38G INFO General (kmer_index_builder.hpp : 260) Merging temporary buckets. 2:09:20.589 12G / 38G INFO K-mer Index Building (kmer_index_builder.hpp : 437) Building perfect hash indices 2:10:28.666 12G / 38G INFO General (kmer_index_builder.hpp : 276) Merging final buckets. 2:11:08.916 12G / 38G INFO K-mer Index Building (kmer_index_builder.hpp : 483) Index built. Total 53912288 bytes occupied (2.61376 bits per kmer). 2:11:11.351 15G / 38G INFO General (edge_index_builders.hpp : 27) Collecting k-mer coverage information from graph, this takes a while. 2:11:21.013 15G / 38G INFO General (edge_index.hpp : 91) Index refilled 2:11:21.031 15G / 38G INFO General (gap_closer.cpp : 159) Preparing shift maps 2:11:32.621 16G / 38G INFO General (gap_closer.cpp : 119) Processing paired reads (takes a while) 2:13:33.564 17G / 38G INFO General (gap_closer.cpp : 138) Used 127432190 paired reads 2:13:33.564 17G / 38G INFO General (gap_closer.cpp : 140) Merging paired indices 2:13:55.494 16G / 38G INFO GapCloser (gap_closer.cpp : 347) Closing short gaps 2:14:14.887 16G / 38G INFO GapCloser (gap_closer.cpp : 381) Closing short gaps complete: filled 40586 gaps after checking 1017446 candidates 2:14:55.779 15G / 38G INFO StageManager (stage.cpp : 126) STAGE == Simplification Cleanup 2:14:55.779 15G / 38G INFO General (simplification.cpp : 561) Counting average coverage 2:14:57.734 15G / 38G INFO General (simplification.cpp : 566) Average coverage = 43.6046 2:14:57.734 15G / 38G INFO StageManager (stage.cpp : 126) STAGE == Mismatch Correction 2:14:57.734 15G / 38G INFO General (graph_pack.hpp : 105) Normalizing k-mer map. Total 17694922 kmers to process 2:15:14.098 15G / 38G INFO General (graph_pack.hpp : 107) Normalizing done 2:20:28.066 16G / 38G INFO General (mismatch_shall_not_pass.hp: 187) Finished collecting potential mismatches positions 2:20:45.124 15G / 38G INFO General (mismatch_shall_not_pass.hp: 284) All edges processed 2:20:46.036 15G / 38G INFO General (mismatch_correction.cpp : 26) Corrected 676 nucleotides 2:20:46.044 15G / 38G INFO StageManager (stage.cpp : 126) STAGE == Contig Output 2:20:46.045 15G / 38G INFO General (contig_output.hpp : 478) Outputting contigs to /data/home/pitagoras/public_html/gigas/transcriptome/rnaSpades/output43//K43/pre_pe_before_rr.fasta 2:21:10.871 15G / 38G INFO General (contig_output.hpp : 518) Outputting graph to /data/home/pitagoras/public_html/gigas/transcriptome/rnaSpades/output43//K43/pre_pe_assembly_graph.fastg 2:22:02.356 15G / 38G INFO General (contig_output.hpp : 478) Outputting contigs to /data/home/pitagoras/public_html/gigas/transcriptome/rnaSpades/output43//K43/pre_pe_simplified_contigs.fasta 2:22:28.841 15G / 38G INFO General (contig_output.hpp : 478) Outputting contigs to /data/home/pitagoras/public_html/gigas/transcriptome/rnaSpades/output43//K43/pre_pe_final_contigs.fasta 2:22:54.092 15G / 38G INFO StageManager (stage.cpp : 126) STAGE == Paired Information Counting 2:23:12.383 16G / 38G INFO General (graph_pack.hpp : 105) Normalizing k-mer map. Total 17718884 kmers to process 2:23:25.568 16G / 38G INFO General (graph_pack.hpp : 107) Normalizing done 2:23:27.703 16G / 38G INFO General (pair_info_count.cpp : 300) Min edge length for estimation: 212 2:23:27.703 16G / 38G INFO General (pair_info_count.cpp : 311) Estimating insert size for library #0 2:23:27.703 16G / 38G INFO General (pair_info_count.cpp : 116) Estimating insert size (takes a while) 2:23:27.885 16G / 38G INFO General (short_read_mapper.hpp : 88) Selecting usual mapper 2:23:30.461 16G / 38G INFO General (sequence_mapper_notifier.h: 82) Processed 200000 reads 2:23:30.493 16G / 38G INFO General (sequence_mapper_notifier.h: 82) Processed 400000 reads 2:23:30.524 16G / 38G INFO General (sequence_mapper_notifier.h: 82) Processed 600000 reads 2:23:30.555 16G / 38G INFO General (sequence_mapper_notifier.h: 82) Processed 800000 reads 2:23:30.587 16G / 38G INFO General (sequence_mapper_notifier.h: 82) Processed 1000000 reads 2:23:30.618 16G / 38G INFO General (sequence_mapper_notifier.h: 82) Processed 1200000 reads 2:23:30.803 16G / 38G INFO General (sequence_mapper_notifier.h: 82) Processed 2200000 reads 2:23:32.968 16G / 38G INFO General (sequence_mapper_notifier.h: 82) Processed 4200000 reads 2:23:35.991 16G / 38G INFO General (sequence_mapper_notifier.h: 82) Processed 8400000 reads 2:23:42.384 16G / 38G INFO General (sequence_mapper_notifier.h: 82) Processed 16800000 reads 2:23:55.746 16G / 38G INFO General (sequence_mapper_notifier.h: 82) Processed 33600000 reads 2:24:23.816 16G / 38G INFO General (sequence_mapper_notifier.h: 82) Processed 67200000 reads 2:25:20.878 16G / 38G INFO General (sequence_mapper_notifier.h: 100) Total 127432190 reads processed 2:25:22.250 16G / 38G INFO General (pair_info_count.cpp : 134) Edge pairs: 67108864 (rough upper limit) 2:25:22.250 16G / 38G INFO General (pair_info_count.cpp : 138) 68904820 paired reads (54.0718% of all) aligned to long edges 2:25:22.291 16G / 38G INFO General (pair_info_count.cpp : 334) Insert size = 155.853, deviation = 45.0329, left quantile = 110, right quantile = 215, read length = 76 2:25:22.291 16G / 38G INFO General (pair_info_count.cpp : 363) Mapping library #0 2:25:22.291 16G / 38G INFO General (pair_info_count.cpp : 365) Mapping paired reads (takes a while) 2:25:22.291 16G / 38G INFO General (pair_info_count.cpp : 204) Left insert size quantile 110, right insert size quantile 215, filtering threshold 0, rounding threshold 0 2:25:22.305 16G / 38G INFO General (short_read_mapper.hpp : 88) Selecting usual mapper 2:25:25.232 16G / 38G INFO General (sequence_mapper_notifier.h: 82) Processed 200000 reads 2:25:25.239 16G / 38G INFO General (sequence_mapper_notifier.h: 82) Processed 400000 reads 2:25:25.254 16G / 38G INFO General (sequence_mapper_notifier.h: 82) Processed 600000 reads 2:25:25.255 16G / 38G INFO General (sequence_mapper_notifier.h: 82) Processed 800000 reads 2:25:25.262 16G / 38G INFO General (sequence_mapper_notifier.h: 82) Processed 1000000 reads 2:25:25.309 16G / 38G INFO General (sequence_mapper_notifier.h: 82) Processed 1200000 reads 2:25:25.375 16G / 38G INFO General (sequence_mapper_notifier.h: 82) Processed 2200000 reads 2:25:28.024 16G / 38G INFO General (sequence_mapper_notifier.h: 82) Processed 4200000 reads 2:25:31.291 16G / 38G INFO General (sequence_mapper_notifier.h: 82) Processed 8400000 reads 2:25:39.113 16G / 38G INFO General (sequence_mapper_notifier.h: 82) Processed 16800000 reads 2:25:53.098 16G / 38G INFO General (sequence_mapper_notifier.h: 82) Processed 33600000 reads 2:26:39.459 16G / 38G INFO General (sequence_mapper_notifier.h: 82) Processed 67200000 reads 2:27:55.003 17G / 38G INFO General (sequence_mapper_notifier.h: 100) Total 127432190 reads processed 2:27:56.059 17G / 38G INFO StageManager (stage.cpp : 126) STAGE == Distance Estimation 2:27:56.059 17G / 38G INFO General (distance_estimation.cpp : 224) Processing library #0 2:27:56.059 17G / 38G INFO General (distance_estimation.cpp : 130) Weight Filter Done 2:27:56.059 17G / 38G INFO DistanceEstimator (distance_estimation.hpp : 176) Using SIMPLE distance estimator 2:28:14.538 17G / 38G INFO General (distance_estimation.cpp : 35) Filtering info 2:28:14.538 17G / 38G INFO General (pair_info_filters.hpp : 242) Start filtering; index size: 6516675 2:28:20.788 17G / 38G INFO General (pair_info_filters.hpp : 263) Done filtering 2:28:20.805 17G / 38G INFO General (distance_estimation.cpp : 172) Refining clustered pair information 2:28:21.387 17G / 38G INFO General (distance_estimation.cpp : 174) The refining of clustered pair information has been finished 2:28:21.387 17G / 38G INFO General (distance_estimation.cpp : 176) Improving paired information 2:28:32.237 17G / 38G INFO PairInfoImprover (pair_info_improver.hpp : 103) Paired info stats: missing = 168400; contradictional = 80 2:28:42.609 17G / 38G INFO PairInfoImprover (pair_info_improver.hpp : 103) Paired info stats: missing = 84670; contradictional = 0 2:28:42.609 17G / 38G INFO StageManager (stage.cpp : 126) STAGE == Repeat Resolving 2:28:42.610 17G / 38G INFO General (repeat_resolving.cpp : 68) Using Path-Extend repeat resolving 2:28:55.201 17G / 38G INFO General (launcher.cpp : 399) ExSPAnder repeat resolving tool started 2:29:22.058 26G / 38G INFO General (launcher.cpp : 357) Creating main extenders, unique edge length = 2000 2:29:26.317 27G / 38G INFO General (extenders_logic.cpp : 415) Using 1 paired-end library 2:29:26.317 27G / 38G INFO General (extenders_logic.cpp : 416) Using 1 paired-end scaffolding library 2:29:26.317 27G / 38G INFO General (extenders_logic.cpp : 417) Using 0 single read libraries 2:29:26.317 27G / 38G INFO General (launcher.cpp : 385) Total number of extenders is 4 2:29:26.318 27G / 38G INFO PathExtender (path_extender.hpp :1031) Processed 0 paths from 2338454 (0%) 2:29:26.356 27G / 38G INFO PathExtender (path_extender.hpp :1029) Processed 128 paths from 2338454 (0%) 2:29:26.383 27G / 38G INFO PathExtender (path_extender.hpp :1029) Processed 256 paths from 2338454 (0%) 2:29:26.431 27G / 38G INFO PathExtender (path_extender.hpp :1029) Processed 512 paths from 2338454 (0%) 2:29:26.515 27G / 38G INFO PathExtender (path_extender.hpp :1029) Processed 1024 paths from 2338454 (0%) 2:29:26.686 27G / 38G INFO PathExtender (path_extender.hpp :1029) Processed 2048 paths from 2338454 (0%) 2:29:27.072 27G / 38G INFO PathExtender (path_extender.hpp :1029) Processed 4096 paths from 2338454 (0%) 2:29:27.816 27G / 38G INFO PathExtender (path_extender.hpp :1029) Processed 8192 paths from 2338454 (0%) 2:29:29.071 27G / 38G INFO PathExtender (path_extender.hpp :1029) Processed 16384 paths from 2338454 (0%) 2:29:31.241 27G / 38G INFO PathExtender (path_extender.hpp :1029) Processed 32768 paths from 2338454 (1%) 2:29:34.494 27G / 38G INFO PathExtender (path_extender.hpp :1029) Processed 65536 paths from 2338454 (2%) 2:29:39.518 27G / 38G INFO PathExtender (path_extender.hpp :1029) Processed 131072 paths from 2338454 (5%) 2:29:44.864 28G / 38G INFO PathExtender (path_extender.hpp :1031) Processed 233846 paths from 2338454 (10%) 2:29:45.564 28G / 38G INFO PathExtender (path_extender.hpp :1029) Processed 262144 paths from 2338454 (11%) 2:29:51.343 29G / 38G INFO PathExtender (path_extender.hpp :1031) Processed 467692 paths from 2338454 (20%) 2:29:53.965 29G / 38G INFO PathExtender (path_extender.hpp :1029) Processed 524288 paths from 2338454 (22%) 2:29:58.732 29G / 38G INFO PathExtender (path_extender.hpp :1031) Processed 701538 paths from 2338454 (30%) 2:30:03.939 30G / 38G INFO PathExtender (path_extender.hpp :1031) Processed 935384 paths from 2338454 (40%) 2:30:06.472 31G / 38G INFO PathExtender (path_extender.hpp :1029) Processed 1048576 paths from 2338454 (44%) 2:30:09.186 31G / 38G INFO PathExtender (path_extender.hpp :1031) Processed 1169230 paths from 2338454 (50%) 2:30:14.651 32G / 38G INFO PathExtender (path_extender.hpp :1031) Processed 1403076 paths from 2338454 (60%) 2:30:19.987 33G / 38G INFO PathExtender (path_extender.hpp :1031) Processed 1636922 paths from 2338454 (70%) 2:30:24.640 34G / 38G INFO PathExtender (path_extender.hpp :1031) Processed 1870768 paths from 2338454 (80%) 2:30:28.236 35G / 38G INFO PathExtender (path_extender.hpp :1029) Processed 2097152 paths from 2338454 (89%) 2:30:28.348 35G / 38G INFO PathExtender (path_extender.hpp :1031) Processed 2104614 paths from 2338454 (90%) 2:47:44.811 36G / 38G INFO General (launcher.cpp : 248) Traversing tandem repeats 2:48:09.715 36G / 38G INFO General (launcher.cpp : 258) Traversed 13 loops 2:48:09.715 36G / 38G INFO General (launcher.cpp : 391) Closing gaps in paths 2:48:12.551 37G / 38G INFO General (launcher.cpp : 395) Gap closing completed 3:15:09.587 46G / 46G INFO General (launcher.cpp : 445) ExSPAnder repeat resolving tool finished 3:15:28.984 35G / 46G INFO StageManager (stage.cpp : 126) STAGE == Contig Output 3:15:28.984 35G / 46G INFO General (contig_output.hpp : 478) Outputting contigs to /data/home/pitagoras/public_html/gigas/transcriptome/rnaSpades/output43//K43/before_rr.fasta 3:15:55.947 35G / 46G INFO General (contig_output.hpp : 518) Outputting graph to /data/home/pitagoras/public_html/gigas/transcriptome/rnaSpades/output43//K43/assembly_graph.fastg 3:17:14.772 35G / 46G INFO PathExtendIO (bidirectional_path_output.: 31) Writing contigs to /data/home/pitagoras/public_html/gigas/transcriptome/rnaSpades/output43//K43/transcripts 3:17:27.070 35G / 46G INFO General (contig_output.hpp : 509) Outputting graph to /data/home/pitagoras/public_html/gigas/transcriptome/rnaSpades/output43//K43/assembly_graph.gfa 3:17:54.488 35G / 46G INFO General (launch.hpp : 136) SPAdes finished 3:18:37.202 17G / 46G INFO General (main.cpp : 109) Assembling time: 3 hours 18 minutes 37 seconds ===== Assembling finished. Used k-mer sizes: 43 * Corrected reads are in /data/home/pitagoras/public_html/gigas/transcriptome/rnaSpades/output43/corrected/ * Assembled transcripts are in /data/home/pitagoras/public_html/gigas/transcriptome/rnaSpades/output43/transcripts.fasta * Paths in the assembly graph corresponding to the transcripts are in /data/home/pitagoras/public_html/gigas/transcriptome/rnaSpades/output43/transcripts.paths ======= SPAdes pipeline finished. SPAdes log can be found here: /data/home/pitagoras/public_html/gigas/transcriptome/rnaSpades/output43/spades.log Thank you for using SPAdes!