Command line: /data/home/root/SPAdes-3.10.1-Linux/bin/rnaspades.py --cov-cutoff auto -o /data/home/pitagoras/public_html/gigas/transcriptome/rnaSpades/spadesRNA/output --dataset /data/home/pitagoras/public_html/gigas/transcriptome/fastqs.yaml System information: SPAdes version: 3.10.1 Python version: 2.7.5 OS: Linux-3.10.0-862.3.2.el7.x86_64-x86_64-with-centos-7.5.1804-Core Output dir: /data/home/pitagoras/public_html/gigas/transcriptome/rnaSpades/spadesRNA/output 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: [55] 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/spadesRNA/output/tmp Threads: 16 Memory limit (in Gb): 220 ======= SPAdes pipeline started. Log can be found here: /data/home/pitagoras/public_html/gigas/transcriptome/rnaSpades/spadesRNA/output/spades.log ===== Read error correction started. == Running read error correction tool: /data/home/root/SPAdes-3.10.1-Linux/bin/hammer /data/home/pitagoras/public_html/gigas/transcriptome/rnaSpades/spadesRNA/output/corrected/configs/config.info 0:00:00.000 4M / 4M INFO General (main.cpp : 83) Starting BayesHammer, built from N/A, git revision N/A 0:00:00.000 4M / 4M INFO General (main.cpp : 84) Loading config from /data/home/pitagoras/public_html/gigas/transcriptome/rnaSpades/spadesRNA/output/corrected/configs/config.info 0:00:00.003 4M / 4M INFO General (memory_limit.hpp : 47) Memory limit set to 220 Gb 0:00:00.003 4M / 4M INFO General (main.cpp : 93) Trying to determine PHRED offset 0:00:00.005 4M / 4M INFO General (main.cpp : 99) Determined value is 33 0:00:00.005 4M / 4M INFO General (hammer_tools.cpp : 36) Hamming graph threshold tau=1, k=21, subkmer positions = [ 0 10 ] 0:00:00.005 4M / 4M INFO General (main.cpp : 120) Size of aux. kmer data 24 bytes === ITERATION 0 begins === 0:00:00.017 4M / 4M INFO K-mer Index Building (kmer_index_builder.hpp : 428) Building kmer index 0:00:00.017 4M / 4M INFO K-mer Splitting (kmer_data.cpp : 91) Splitting kmer instances into 256 buckets. This might take a while. 0:00:00.017 4M / 4M INFO General (file_limit.hpp : 30) Open file limit set to 64000 0:00:00.017 4M / 4M INFO General (kmer_index_builder.hpp : 108) Memory available for splitting buffers: 4.58325 Gb 0:00:00.017 4M / 4M INFO General (kmer_index_builder.hpp : 116) Using cell size of 262144 0:00:00.096 8G / 8G INFO K-mer Splitting (kmer_data.cpp : 98) Processing /data2/process/RnaPira/trim/Ova_R2.t.fastq 0:00:13.977 8G / 8G INFO K-mer Splitting (kmer_data.cpp : 108) Processed 1140113 reads 0:00:28.898 8G / 8G INFO K-mer Splitting (kmer_data.cpp : 108) Processed 2322446 reads 0:00:47.989 8G / 8G INFO K-mer Splitting (kmer_data.cpp : 108) Processed 3599362 reads 0:01:03.910 8G / 8G INFO K-mer Splitting (kmer_data.cpp : 108) Processed 4678611 reads 0:01:16.855 8G / 8G INFO K-mer Splitting (kmer_data.cpp : 108) Processed 5622317 reads 0:01:31.192 8G / 8G INFO K-mer Splitting (kmer_data.cpp : 108) Processed 6777491 reads 0:01:49.491 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 108) Processed 8391438 reads 0:02:17.788 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 108) Processed 10875213 reads 0:02:42.824 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 108) Processed 13540046 reads 0:03:20.499 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 108) Processed 16816205 reads 0:06:03.119 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 98) Processing /data2/process/RnaPira/trim/Cerebro-femea_R2.t.fastq 0:07:57.041 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 108) Processed 34113000 reads 0:10:47.829 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 98) Processing /data2/process/RnaPira/trim/Cerebro-macho_R2.t.fastq 0:14:02.275 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 98) Processing /data2/process/RnaPira/trim/Pulmao-femea_R2.t.fastq 0:16:19.796 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 98) Processing /data2/process/RnaPira/trim/Pulmao-macho_R2.t.fastq 0:19:09.328 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 108) Processed 67971974 reads 0:22:55.209 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 98) Processing /data2/process/RnaPira/trim/Hipofise-femea_R2.t.fastq 0:26:14.116 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 98) Processing /data2/process/RnaPira/trim/Rim-femea_R2.t.fastq 0:28:17.123 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 98) Processing /data2/process/RnaPira/trim/Hipofise-macho_R2.t.fastq 0:31:10.785 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 98) Processing /data2/process/RnaPira/trim/Rim-macho_R2.t.fastq 0:36:39.845 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 98) Processing /data2/process/RnaPira/trim/Musculo-femea_R2.t.fastq 0:40:45.216 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 98) Processing /data2/process/RnaPira/trim/Testiculo_R2.t.fastq 0:42:56.697 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 98) Processing /data2/process/RnaPira/trim/Ova_R1.t.fastq 0:44:00.808 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 108) Processed 135084816 reads 0:48:00.272 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 98) Processing /data2/process/RnaPira/trim/Cerebro-femea_R1.t.fastq 0:50:54.418 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 98) Processing /data2/process/RnaPira/trim/Cerebro-macho_R1.t.fastq 0:54:16.780 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 98) Processing /data2/process/RnaPira/trim/Pulmao-femea_R1.t.fastq 0:55:55.454 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 98) Processing /data2/process/RnaPira/trim/Pulmao-macho_R1.t.fastq 0:59:27.386 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 98) Processing /data2/process/RnaPira/trim/Hipofise-femea_R1.t.fastq 1:01:29.905 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 98) Processing /data2/process/RnaPira/trim/Rim-femea_R1.t.fastq 1:03:12.625 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 98) Processing /data2/process/RnaPira/trim/Hipofise-macho_R1.t.fastq 1:05:12.188 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 98) Processing /data2/process/RnaPira/trim/Rim-macho_R1.t.fastq 1:07:36.270 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 98) Processing /data2/process/RnaPira/trim/Musculo-femea_R1.t.fastq 1:09:15.080 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 98) Processing /data2/process/RnaPira/trim/Testiculo_R1.t.fastq 1:11:16.335 8G / 9G INFO K-mer Splitting (kmer_data.cpp : 113) Total 262072356 reads processed 1:11:17.070 64M / 9G INFO General (kmer_index_builder.hpp : 252) Starting k-mer counting. 1:20:40.932 64M / 9G INFO General (kmer_index_builder.hpp : 258) K-mer counting done. There are 853373588 kmers in total. 1:20:40.932 64M / 9G INFO General (kmer_index_builder.hpp : 260) Merging temporary buckets. 1:24:56.640 64M / 9G INFO K-mer Index Building (kmer_index_builder.hpp : 437) Building perfect hash indices 1:25:57.792 320M / 21G INFO General (kmer_index_builder.hpp : 276) Merging final buckets. 1:29:44.452 320M / 21G INFO K-mer Index Building (kmer_index_builder.hpp : 483) Index built. Total 278813288 bytes occupied (2.61375 bits per kmer). 1:29:44.497 320M / 21G INFO K-mer Counting (kmer_data.cpp : 359) Arranging kmers in hash map order 1:30:44.932 13G / 21G INFO General (main.cpp : 155) Clustering Hamming graph. 1:54:07.663 13G / 21G INFO General (main.cpp : 162) Extracting clusters 2:04:09.111 13G / 37G INFO General (main.cpp : 174) Clustering done. Total clusters: 471670243 2:04:09.908 6G / 37G INFO K-mer Counting (kmer_data.cpp : 381) Collecting K-mer information, this takes a while. 2:04:21.842 25G / 37G INFO K-mer Counting (kmer_data.cpp : 387) Processing /data2/process/RnaPira/trim/Ova_R2.t.fastq 2:08:29.860 25G / 37G INFO K-mer Counting (kmer_data.cpp : 387) Processing /data2/process/RnaPira/trim/Cerebro-femea_R2.t.fastq 2:10:20.517 25G / 37G INFO K-mer Counting (kmer_data.cpp : 387) Processing /data2/process/RnaPira/trim/Cerebro-macho_R2.t.fastq 2:12:08.918 25G / 37G INFO K-mer Counting (kmer_data.cpp : 387) Processing /data2/process/RnaPira/trim/Pulmao-femea_R2.t.fastq 2:13:09.949 25G / 37G INFO K-mer Counting (kmer_data.cpp : 387) Processing /data2/process/RnaPira/trim/Pulmao-macho_R2.t.fastq 2:15:11.848 25G / 37G INFO K-mer Counting (kmer_data.cpp : 387) Processing /data2/process/RnaPira/trim/Hipofise-femea_R2.t.fastq 2:16:35.487 25G / 37G INFO K-mer Counting (kmer_data.cpp : 387) Processing /data2/process/RnaPira/trim/Rim-femea_R2.t.fastq 2:17:43.494 25G / 37G INFO K-mer Counting (kmer_data.cpp : 387) Processing /data2/process/RnaPira/trim/Hipofise-macho_R2.t.fastq 2:18:54.223 25G / 37G INFO K-mer Counting (kmer_data.cpp : 387) Processing /data2/process/RnaPira/trim/Rim-macho_R2.t.fastq 2:20:29.215 25G / 37G INFO K-mer Counting (kmer_data.cpp : 387) Processing /data2/process/RnaPira/trim/Musculo-femea_R2.t.fastq 2:21:51.038 25G / 37G INFO K-mer Counting (kmer_data.cpp : 387) Processing /data2/process/RnaPira/trim/Testiculo_R2.t.fastq 2:23:06.325 25G / 37G INFO K-mer Counting (kmer_data.cpp : 387) Processing /data2/process/RnaPira/trim/Ova_R1.t.fastq 2:27:21.590 25G / 37G INFO K-mer Counting (kmer_data.cpp : 387) Processing /data2/process/RnaPira/trim/Cerebro-femea_R1.t.fastq 2:29:19.748 25G / 37G INFO K-mer Counting (kmer_data.cpp : 387) Processing /data2/process/RnaPira/trim/Cerebro-macho_R1.t.fastq 2:31:08.905 25G / 37G INFO K-mer Counting (kmer_data.cpp : 387) Processing /data2/process/RnaPira/trim/Pulmao-femea_R1.t.fastq 2:32:11.191 25G / 37G INFO K-mer Counting (kmer_data.cpp : 387) Processing /data2/process/RnaPira/trim/Pulmao-macho_R1.t.fastq 2:34:22.025 25G / 37G INFO K-mer Counting (kmer_data.cpp : 387) Processing /data2/process/RnaPira/trim/Hipofise-femea_R1.t.fastq 2:35:48.960 25G / 37G INFO K-mer Counting (kmer_data.cpp : 387) Processing /data2/process/RnaPira/trim/Rim-femea_R1.t.fastq 2:37:02.305 25G / 37G INFO K-mer Counting (kmer_data.cpp : 387) Processing /data2/process/RnaPira/trim/Hipofise-macho_R1.t.fastq 2:38:20.580 25G / 37G INFO K-mer Counting (kmer_data.cpp : 387) Processing /data2/process/RnaPira/trim/Rim-macho_R1.t.fastq 2:39:52.956 25G / 37G INFO K-mer Counting (kmer_data.cpp : 387) Processing /data2/process/RnaPira/trim/Musculo-femea_R1.t.fastq 2:41:23.814 25G / 37G INFO K-mer Counting (kmer_data.cpp : 387) Processing /data2/process/RnaPira/trim/Testiculo_R1.t.fastq 2:42:41.907 25G / 37G INFO K-mer Counting (kmer_data.cpp : 394) Collection done, postprocessing. 2:42:45.031 25G / 37G INFO K-mer Counting (kmer_data.cpp : 408) There are 853373588 kmers in total. Among them 453841768 (53.1821%) are singletons. 2:42:45.031 25G / 37G INFO General (main.cpp : 180) Subclustering Hamming graph 3:00:39.837 25G / 37G INFO Hamming Subclustering (kmer_cluster.cpp : 649) Subclustering done. Total 14834 non-read kmers were generated. 3:00:39.837 25G / 37G INFO Hamming Subclustering (kmer_cluster.cpp : 650) Subclustering statistics: 3:00:39.837 25G / 37G INFO Hamming Subclustering (kmer_cluster.cpp : 651) Total singleton hamming clusters: 373381924. Among them 197437564 (52.8782%) are good 3:00:39.837 25G / 37G INFO Hamming Subclustering (kmer_cluster.cpp : 652) Total singleton subclusters: 4428133. Among them 4415954 (99.725%) are good 3:00:39.837 25G / 37G INFO Hamming Subclustering (kmer_cluster.cpp : 653) Total non-singleton subcluster centers: 106092210. Among them 76151289 (71.7784%) are good 3:00:39.837 25G / 37G INFO Hamming Subclustering (kmer_cluster.cpp : 654) Average size of non-trivial subcluster: 4.52475 kmers 3:00:39.837 25G / 37G INFO Hamming Subclustering (kmer_cluster.cpp : 655) Average number of sub-clusters per non-singleton cluster: 1.12445 3:00:39.837 25G / 37G INFO Hamming Subclustering (kmer_cluster.cpp : 656) Total solid k-mers: 278004807 3:00:39.837 25G / 37G INFO Hamming Subclustering (kmer_cluster.cpp : 657) Substitution probabilities: [4,4]((0.935122,0.0147418,0.0157084,0.0344276),(0.0231286,0.922587,0.010334,0.0439505),(0.0426327,0.0099529,0.923122,0.0242923),(0.033283,0.0150149,0.0143597,0.937342)) 3:00:40.489 25G / 37G INFO General (main.cpp : 185) Finished clustering. 3:00:40.489 25G / 37G INFO General (main.cpp : 204) Starting solid k-mers expansion in 16 threads. 3:13:14.877 25G / 37G INFO General (main.cpp : 225) Solid k-mers iteration 0 produced 26925431 new k-mers. 3:25:35.049 25G / 37G INFO General (main.cpp : 225) Solid k-mers iteration 1 produced 2197462 new k-mers. 3:37:50.449 25G / 37G INFO General (main.cpp : 225) Solid k-mers iteration 2 produced 175829 new k-mers. 3:50:46.407 25G / 37G INFO General (main.cpp : 225) Solid k-mers iteration 3 produced 22218 new k-mers. 4:02:31.379 25G / 37G INFO General (main.cpp : 225) Solid k-mers iteration 4 produced 3328 new k-mers. 4:14:29.299 25G / 37G INFO General (main.cpp : 225) Solid k-mers iteration 5 produced 700 new k-mers. 4:26:43.863 25G / 37G INFO General (main.cpp : 225) Solid k-mers iteration 6 produced 114 new k-mers. 4:39:02.219 25G / 37G INFO General (main.cpp : 225) Solid k-mers iteration 7 produced 60 new k-mers. 4:51:34.134 25G / 37G INFO General (main.cpp : 225) Solid k-mers iteration 8 produced 16 new k-mers. 5:03:50.241 25G / 37G INFO General (main.cpp : 225) Solid k-mers iteration 9 produced 29 new k-mers. 5:15:44.815 25G / 37G INFO General (main.cpp : 225) Solid k-mers iteration 10 produced 0 new k-mers. 5:15:44.815 25G / 37G INFO General (main.cpp : 229) Solid k-mers finalized 5:15:44.815 25G / 37G INFO General (hammer_tools.cpp : 211) Starting read correction in 16 threads. 5:15:44.815 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 5:15:48.772 26G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 0 of 1600000 reads. 5:15:58.323 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 0 5:16:00.645 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 0 5:16:03.725 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 1 of 1600000 reads. 5:16:13.300 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 1 5:16:15.739 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 1 5:16:18.454 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 2 of 1600000 reads. 5:16:28.073 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 2 5:16:30.622 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 2 5:16:33.246 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 3 of 1600000 reads. 5:16:43.035 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 3 5:17:02.584 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 3 5:17:05.341 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 4 of 1600000 reads. 5:17:15.517 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 4 5:17:17.862 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 4 5:17:20.389 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 5 of 1600000 reads. 5:17:30.205 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 5 5:17:32.796 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 5 5:17:35.346 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 6 of 1600000 reads. 5:17:45.331 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 6 5:17:54.292 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 6 5:17:56.757 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 7 of 1600000 reads. 5:18:06.495 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 7 5:18:17.739 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 7 5:18:20.233 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 8 of 1600000 reads. 5:18:30.182 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 8 5:18:33.024 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 8 5:18:35.546 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 9 of 1600000 reads. 5:18:45.344 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 9 5:18:55.084 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 9 5:18:57.551 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 10 of 1600000 reads. 5:19:07.205 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 10 5:19:18.292 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 10 5:19:20.848 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 11 of 1600000 reads. 5:19:30.473 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 11 5:19:33.011 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 11 5:19:35.548 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 12 of 1600000 reads. 5:19:45.477 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 12 5:20:00.277 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 12 5:20:02.693 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 13 of 1600000 reads. 5:20:12.386 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 13 5:20:18.637 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 13 5:20:21.496 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 14 of 1600000 reads. 5:20:31.457 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 14 5:20:33.867 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 14 5:20:36.462 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 15 of 1600000 reads. 5:20:46.168 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 15 5:20:59.766 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 15 5:21:02.224 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 16 of 1600000 reads. 5:21:12.039 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 16 5:21:18.737 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 16 5:21:21.130 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 17 of 1600000 reads. 5:21:31.064 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 17 5:21:33.503 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 17 5:21:34.832 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 18 of 811697 reads. 5:21:39.709 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 18 5:21:54.285 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 18 5:22:08.958 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 5:22:12.133 26G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 0 of 1600000 reads. 5:22:21.906 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 0 5:22:24.432 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 0 5:22:27.455 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 1 of 1600000 reads. 5:22:37.238 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 1 5:22:39.653 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 1 5:22:42.468 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 2 of 1600000 reads. 5:22:52.247 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 2 5:23:13.806 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 2 5:23:16.229 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 3 of 1600000 reads. 5:23:25.811 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 3 5:23:31.014 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 3 5:23:33.754 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 4 of 1600000 reads. 5:23:45.597 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 4 5:23:48.011 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 4 5:23:50.747 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 5 of 1600000 reads. 5:24:01.888 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 5 5:24:11.946 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 5 5:24:14.664 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 6 of 1600000 reads. 5:24:26.844 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 6 5:24:35.322 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 6 5:24:38.085 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 7 of 1600000 reads. 5:24:50.044 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 7 5:24:52.479 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 7 5:24:53.859 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 8 of 811070 reads. 5:24:59.531 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 8 5:25:11.457 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 8 5:25:26.441 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 5:25:29.653 26G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 0 of 1600000 reads. 5:25:39.259 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 0 5:25:41.495 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 0 5:25:44.252 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 1 of 1600000 reads. 5:25:53.659 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 1 5:26:10.260 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 1 5:26:12.906 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 2 of 1600000 reads. 5:26:23.014 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 2 5:26:25.115 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 2 5:26:27.679 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 3 of 1600000 reads. 5:26:37.712 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 3 5:26:39.906 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 3 5:26:42.306 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 4 of 1600000 reads. 5:26:51.819 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 4 5:26:54.375 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 4 5:26:56.805 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 5 of 1600000 reads. 5:27:06.992 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 5 5:27:14.342 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 5 5:27:16.753 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 6 of 1600000 reads. 5:27:26.698 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 6 5:27:39.101 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 6 5:27:40.141 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 7 of 700384 reads. 5:27:44.652 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 7 5:27:45.597 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 7 5:28:07.866 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 5:28:11.575 26G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 0 of 1600000 reads. 5:28:21.450 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 0 5:28:23.791 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 0 5:28:26.901 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 1 of 1600000 reads. 5:28:37.313 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 1 5:28:47.635 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 1 5:28:50.575 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 2 of 1600000 reads. 5:29:01.355 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 2 5:29:03.713 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 2 5:29:06.469 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 3 of 1600000 reads. 5:29:17.353 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 3 5:29:24.959 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 3 5:29:25.720 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 4 of 442334 reads. 5:29:28.635 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 4 5:29:29.278 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 4 5:29:48.145 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 5:29:51.830 26G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 0 of 1600000 reads. 5:30:02.160 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 0 5:30:04.451 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 0 5:30:07.560 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 1 of 1600000 reads. 5:30:17.563 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 1 5:30:22.939 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 1 5:30:25.875 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 2 of 1600000 reads. 5:30:35.994 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 2 5:30:38.336 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 2 5:30:41.086 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 3 of 1600000 reads. 5:30:53.023 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 3 5:31:02.064 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 3 5:31:04.785 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 4 of 1600000 reads. 5:31:15.890 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 4 5:31:25.458 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 4 5:31:28.177 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 5 of 1600000 reads. 5:31:38.094 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 5 5:31:40.671 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 5 5:31:43.442 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 6 of 1600000 reads. 5:31:53.180 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 6 5:32:02.200 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 6 5:32:04.607 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 7 of 1600000 reads. 5:32:12.826 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 7 5:32:15.272 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 7 5:32:17.844 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 8 of 1600000 reads. 5:32:26.683 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 8 5:32:33.327 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 8 5:32:35.718 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 9 of 1600000 reads. 5:32:44.962 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 9 5:32:58.474 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 9 5:32:58.839 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 10 of 228975 reads. 5:33:00.851 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 10 5:33:01.229 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 10 5:33:21.338 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 5:33:24.598 26G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 0 of 1600000 reads. 5:33:35.951 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 0 5:33:38.150 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 0 5:33:40.978 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 1 of 1600000 reads. 5:33:50.425 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 1 5:34:04.725 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 1 5:34:07.269 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 2 of 1600000 reads. 5:34:16.327 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 2 5:34:18.915 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 2 5:34:21.355 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 3 of 1600000 reads. 5:34:30.416 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 3 5:34:40.492 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 3 5:34:42.886 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 4 of 1600000 reads. 5:34:52.121 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 4 5:35:03.201 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 4 5:35:05.595 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 5 of 1600000 reads. 5:35:14.618 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 5 5:35:17.016 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 5 5:35:18.306 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 6 of 862876 reads. 5:35:23.203 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 6 5:35:43.002 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 6 5:35:57.310 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 5:36:00.676 26G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 0 of 1600000 reads. 5:36:09.959 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 0 5:36:12.198 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 0 5:36:15.231 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 1 of 1600000 reads. 5:36:24.648 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 1 5:36:26.789 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 1 5:36:29.340 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 2 of 1600000 reads. 5:36:38.784 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 2 5:36:41.181 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 2 5:36:43.636 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 3 of 1600000 reads. 5:36:52.979 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 3 5:37:09.195 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 3 5:37:12.121 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 4 of 1600000 reads. 5:37:23.021 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 4 5:37:25.348 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 4 5:37:26.250 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 5 of 531717 reads. 5:37:30.092 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 5 5:37:30.957 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 5 5:37:52.341 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 5:37:56.048 26G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 0 of 1600000 reads. 5:38:05.819 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 0 5:38:08.328 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 0 5:38:11.499 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 1 of 1600000 reads. 5:38:21.605 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 1 5:38:28.992 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 1 5:38:31.924 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 2 of 1600000 reads. 5:38:41.431 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 2 5:38:44.020 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 2 5:38:46.801 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 3 of 1600000 reads. 5:38:59.400 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 3 5:39:07.846 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 3 5:39:09.018 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 4 of 678859 reads. 5:39:13.925 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 4 5:39:15.221 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 4 5:39:33.724 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 5:39:37.480 26G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 0 of 1600000 reads. 5:39:47.419 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 0 5:39:49.970 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 0 5:39:53.160 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 1 of 1600000 reads. 5:40:04.145 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 1 5:40:17.538 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 1 5:40:20.495 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 2 of 1600000 reads. 5:40:30.049 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 2 5:40:32.361 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 2 5:40:35.387 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 3 of 1600000 reads. 5:40:44.953 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 3 5:40:51.135 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 3 5:40:53.872 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 4 of 1600000 reads. 5:41:03.880 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 4 5:41:06.346 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 4 5:41:07.948 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 5 of 880546 reads. 5:41:13.308 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 5 5:41:22.923 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 5 5:41:38.383 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 5:41:41.869 26G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 0 of 1600000 reads. 5:41:50.263 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 0 5:41:52.452 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 0 5:41:55.319 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 1 of 1600000 reads. 5:42:03.603 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 1 5:42:05.894 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 1 5:42:08.694 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 2 of 1600000 reads. 5:42:17.045 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 2 5:42:23.521 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 2 5:42:25.996 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 3 of 1600000 reads. 5:42:34.409 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 3 5:42:36.694 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 3 5:42:39.638 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 4 of 1600000 reads. 5:42:47.594 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 4 5:42:56.437 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 4 5:42:58.868 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 5 of 1600000 reads. 5:43:07.321 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 5 5:43:20.058 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 5 5:43:22.513 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 6 of 1600000 reads. 5:43:30.874 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 6 5:43:33.539 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 6 5:43:34.093 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 7 of 359991 reads. 5:43:36.107 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 7 5:43:36.619 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 7 5:44:00.481 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 5:44:03.743 26G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 0 of 1600000 reads. 5:44:12.650 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 0 5:44:15.383 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 0 5:44:18.189 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 1 of 1600000 reads. 5:44:27.797 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 1 5:44:40.092 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 1 5:44:43.097 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 2 of 1600000 reads. 5:44:51.542 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 2 5:44:53.917 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 2 5:44:56.288 27G / 37G INFO General (hammer_tools.cpp : 166) Prepared batch 3 of 1527729 reads. 5:45:05.135 27G / 37G INFO General (hammer_tools.cpp : 175) Processed batch 3 5:45:13.280 27G / 37G INFO General (hammer_tools.cpp : 185) Written batch 3 5:45:32.328 25G / 37G INFO General (hammer_tools.cpp : 270) Correction done. Changed 15370727 bases in 10323514 reads. 5:45:32.328 25G / 37G INFO General (hammer_tools.cpp : 271) Failed to correct 20496 bases out of 19020763726. 5:45:36.729 64M / 37G INFO General (main.cpp : 262) Saving corrected dataset description to /data/home/pitagoras/public_html/gigas/transcriptome/rnaSpades/spadesRNA/output/corrected/corrected.yaml 5:45:36.820 64M / 37G INFO General (main.cpp : 269) All done. Exiting. == Compressing corrected reads (with gzip) == Dataset description file was created: /data/home/pitagoras/public_html/gigas/transcriptome/rnaSpades/spadesRNA/output/corrected/corrected.yaml ===== Read error correction finished. ===== Assembling started. == Running assembler: K55 0:00:00.000 4M / 4M INFO General (main.cpp : 75) Loading config from /data/home/pitagoras/public_html/gigas/transcriptome/rnaSpades/spadesRNA/output/K55/configs/config.info 0:00:00.000 4M / 4M INFO General (main.cpp : 75) Loading config from /data/home/pitagoras/public_html/gigas/transcriptome/rnaSpades/spadesRNA/output/K55/configs/mda_mode.info 0:00:00.000 4M / 4M INFO General (main.cpp : 75) Loading config from /data/home/pitagoras/public_html/gigas/transcriptome/rnaSpades/spadesRNA/output/K55/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/spadesRNA/output/dataset.info) with K=55 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 0:00:00.707 4M / 4M INFO General (launch.hpp : 79) Will need read mapping, kmer mapper will be attached 0:00:00.707 4M / 4M INFO StageManager (stage.cpp : 126) STAGE == Construction 0:00:00.738 4M / 4M INFO General (read_converter.hpp : 84) Converting reads to binary format for library #0 (takes a while) 0:00:00.738 4M / 4M INFO General (read_converter.hpp : 85) Converting paired reads 0:00:01.027 80M / 80M INFO General (binary_converter.hpp : 139) 16384 reads processed 0:00:01.113 88M / 88M INFO General (binary_converter.hpp : 139) 32768 reads processed 0:00:01.261 108M / 108M INFO General (binary_converter.hpp : 139) 65536 reads processed 0:00:01.558 148M / 148M INFO General (binary_converter.hpp : 139) 131072 reads processed 0:00:02.150 228M / 228M INFO General (binary_converter.hpp : 139) 262144 reads processed 0:00:03.368 392M / 392M INFO General (binary_converter.hpp : 139) 524288 reads processed 0:00:06.690 640M / 640M INFO General (binary_converter.hpp : 139) 1048576 reads processed 0:00:12.596 640M / 640M INFO General (binary_converter.hpp : 139) 2097152 reads processed 0:00:23.723 640M / 640M INFO General (binary_converter.hpp : 139) 4194304 reads processed 0:00:49.007 640M / 640M INFO General (binary_converter.hpp : 139) 8388608 reads processed 0:01:35.936 644M / 644M INFO General (binary_converter.hpp : 139) 16777216 reads processed 0:03:14.233 648M / 648M INFO General (binary_converter.hpp : 139) 33554432 reads processed 0:06:35.862 656M / 656M INFO General (binary_converter.hpp : 139) 67108864 reads processed 0:12:53.630 656M / 660M INFO General (binary_converter.hpp : 159) 127432598 reads written 0:12:54.636 8M / 660M INFO General (read_converter.hpp : 94) Converting single reads 0:12:54.857 140M / 660M INFO General (binary_converter.hpp : 139) 16384 reads processed 0:12:54.893 144M / 660M INFO General (binary_converter.hpp : 139) 32768 reads processed 0:12:54.968 152M / 660M INFO General (binary_converter.hpp : 139) 65536 reads processed 0:12:55.119 172M / 660M INFO General (binary_converter.hpp : 139) 131072 reads processed 0:12:55.419 212M / 660M INFO General (binary_converter.hpp : 139) 262144 reads processed 0:12:56.021 292M / 660M INFO General (binary_converter.hpp : 139) 524288 reads processed 0:12:57.224 448M / 660M INFO General (binary_converter.hpp : 139) 1048576 reads processed 0:12:59.564 764M / 764M INFO General (binary_converter.hpp : 139) 2097152 reads processed 0:13:04.306 1G / 1G INFO General (binary_converter.hpp : 159) 3533641 reads written 0:13:10.425 4M / 1G INFO General (graph_construction.hpp : 120) Constructing DeBruijn graph for k=55 0:13:10.537 4M / 1G INFO General (kmer_splitters.hpp : 129) Splitting kmer instances into 256 buckets. This might take a while. 0:13:10.537 4M / 1G INFO General (file_limit.hpp : 30) Open file limit set to 64000 0:13:10.537 4M / 1G INFO General (kmer_index_builder.hpp : 108) Memory available for splitting buffers: 4.58325 Gb 0:13:10.537 4M / 1G INFO General (kmer_index_builder.hpp : 116) Using cell size of 131072 0:13:18.773 8G / 8G INFO General (kmer_splitters.hpp : 153) Processed 4224021 reads 0:13:26.039 8G / 8G INFO General (kmer_splitters.hpp : 153) Processed 8773383 reads 0:13:33.925 8G / 8G INFO General (kmer_splitters.hpp : 153) Processed 13869960 reads 0:13:41.237 8G / 8G INFO General (kmer_splitters.hpp : 153) Processed 18105848 reads 0:13:48.350 8G / 8G INFO General (kmer_splitters.hpp : 153) Processed 22187876 reads 0:13:55.929 8G / 8G INFO General (kmer_splitters.hpp : 153) Processed 26781230 reads 0:14:06.901 8G / 9G INFO General (kmer_splitters.hpp : 153) Processed 36019295 reads 0:14:21.462 8G / 9G INFO General (kmer_splitters.hpp : 153) Processed 53283315 reads 0:14:31.754 8G / 9G INFO General (kmer_splitters.hpp : 153) Processed 62300081 reads 0:14:40.272 8G / 9G INFO General (kmer_splitters.hpp : 153) Processed 68146973 reads 0:14:48.862 8G / 9G INFO General (kmer_splitters.hpp : 153) Processed 73849264 reads 0:14:56.593 8G / 9G INFO General (kmer_splitters.hpp : 153) Processed 78681518 reads 0:16:21.033 8G / 9G INFO General (kmer_splitters.hpp : 153) Processed 141460009 reads 0:21:22.274 8G / 9G INFO General (kmer_splitters.hpp : 153) Processed 273372097 reads 0:30:18.474 8G / 9G INFO General (kmer_splitters.hpp : 159) Adding contigs from previous K 0:30:19.068 64M / 9G INFO General (kmer_splitters.hpp : 172) Used 516797674 reads. Maximum read length 76 0:30:19.068 64M / 9G INFO General (kmer_splitters.hpp : 173) Average read length 73.1885 0:30:19.068 64M / 9G INFO General (kmer_index_builder.hpp : 252) Starting k-mer counting. 0:31:46.140 64M / 9G INFO General (kmer_index_builder.hpp : 258) K-mer counting done. There are 205681856 kmers in total. 0:31:46.140 64M / 9G INFO General (kmer_index_builder.hpp : 260) Merging temporary buckets. 0:32:54.240 64M / 9G INFO K-mer Index Building (kmer_index_builder.hpp : 428) Building kmer index 0:32:54.240 64M / 9G INFO General (kmer_splitters.hpp : 285) Splitting kmer instances into 256 buckets. This might take a while. 0:32:54.241 64M / 9G INFO General (file_limit.hpp : 30) Open file limit set to 64000 0:32:54.241 64M / 9G INFO General (kmer_index_builder.hpp : 108) Memory available for splitting buffers: 4.58203 Gb 0:32:54.241 64M / 9G INFO General (kmer_index_builder.hpp : 116) Using cell size of 131072 0:34:19.454 8G / 9G INFO General (kmer_splitters.hpp : 304) Processed 205681856 kmers 0:34:19.455 8G / 9G INFO General (kmer_splitters.hpp : 309) Used 205681856 kmers. 0:34:20.461 64M / 9G INFO General (kmer_index_builder.hpp : 252) Starting k-mer counting. 0:35:22.902 64M / 9G INFO General (kmer_index_builder.hpp : 258) K-mer counting done. There are 209893438 kmers in total. 0:35:22.902 64M / 9G INFO General (kmer_index_builder.hpp : 260) Merging temporary buckets. 0:36:32.229 64M / 9G INFO K-mer Index Building (kmer_index_builder.hpp : 437) Building perfect hash indices 0:36:41.185 128M / 9G INFO General (kmer_index_builder.hpp : 276) Merging final buckets. 0:37:26.899 128M / 9G INFO K-mer Index Building (kmer_index_builder.hpp : 483) Index built. Total 68576248 bytes occupied (2.61375 bits per kmer). 0:37:27.136 332M / 9G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 85) Building k-mer extensions from k+1-mers 0:37:49.157 332M / 9G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 89) Building k-mer extensions from k+1-mers finished. 0:37:49.167 332M / 9G INFO General (graph_construction.hpp : 136) Condensing graph 0:37:49.167 332M / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 340) Extracting unbranching paths 0:40:37.700 3G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths finished. 31500294 sequences extracted 0:40:54.900 3G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 313) Collecting perfect loops 0:41:45.387 3G / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 329) Collecting perfect loops finished. 14 loops collected 0:42:03.585 8G / 10G INFO General (graph_construction.hpp : 141) Building index with from graph 0:42:03.614 8G / 10G INFO K-mer Index Building (kmer_index_builder.hpp : 428) Building kmer index 0:42:03.614 8G / 10G INFO General (kmer_splitters.hpp : 214) Splitting kmer instances into 16 buckets. This might take a while. 0:42:03.614 8G / 10G INFO General (file_limit.hpp : 30) Open file limit set to 64000 0:42:03.614 8G / 10G INFO General (kmer_index_builder.hpp : 108) Memory available for splitting buffers: 70.6042 Gb 0:42:03.614 8G / 10G INFO General (kmer_index_builder.hpp : 116) Using cell size of 2097152 0:42:19.665 8G / 10G INFO General (kmer_splitters.hpp : 225) Processed 4528802 edges 0:42:36.168 8G / 10G INFO General (kmer_splitters.hpp : 225) Processed 9061378 edges 0:42:51.881 8G / 10G INFO General (kmer_splitters.hpp : 225) Processed 13588979 edges 0:43:07.185 8G / 10G INFO General (kmer_splitters.hpp : 225) Processed 18123300 edges 0:43:22.815 8G / 10G INFO General (kmer_splitters.hpp : 225) Processed 22652190 edges 0:43:37.695 8G / 10G INFO General (kmer_splitters.hpp : 225) Processed 27192266 edges 0:43:52.193 8G / 10G INFO General (kmer_splitters.hpp : 225) Processed 31500314 edges 0:43:52.194 8G / 10G INFO General (kmer_splitters.hpp : 230) Used 31500314 sequences. 0:43:52.269 8G / 10G INFO General (kmer_index_builder.hpp : 252) Starting k-mer counting. 0:45:23.010 8G / 10G INFO General (kmer_index_builder.hpp : 258) K-mer counting done. There are 205681856 kmers in total. 0:45:23.010 8G / 10G INFO General (kmer_index_builder.hpp : 260) Merging temporary buckets. 0:46:28.297 8G / 10G INFO K-mer Index Building (kmer_index_builder.hpp : 437) Building perfect hash indices 0:47:50.980 8G / 10G INFO General (kmer_index_builder.hpp : 276) Merging final buckets. 0:48:35.172 8G / 10G INFO K-mer Index Building (kmer_index_builder.hpp : 483) Index built. Total 67200232 bytes occupied (2.61375 bits per kmer). 0:48:38.033 12G / 12G INFO General (edge_index_builders.hpp : 27) Collecting k-mer coverage information from graph, this takes a while. 0:48:51.638 12G / 12G INFO General (edge_index.hpp : 91) Index refilled 0:48:53.602 12G / 12G INFO General (graph_construction.hpp : 173) Filling coverage index 0:48:53.602 12G / 12G INFO General (edge_index_builders.hpp : 105) Collecting k-mer coverage information from reads, this takes a while. 0:55:17.989 12G / 12G INFO General (graph_construction.hpp : 175) Filling coverage and flanking coverage from index 0:56:22.119 12G / 12G INFO General (construction.cpp : 30) Figured out: read length = 76 0:56:22.137 12G / 12G INFO StageManager (stage.cpp : 126) STAGE == EC Threshold Finding 0:56:37.687 12G / 12G INFO ThresholdFinder (ec_threshold_finder.hpp : 114) Bucket size: 12 0:56:37.687 12G / 12G INFO General (genomic_info_filler.cpp : 104) Average edge coverage: 24.118 0:56:37.687 12G / 12G INFO General (genomic_info_filler.cpp : 105) Graph threshold: 354 0:58:20.344 14G / 27G INFO General (genomic_info_filler.cpp : 147) EC coverage threshold value was calculated as 24.118 0:58:20.344 14G / 27G INFO General (genomic_info_filler.cpp : 148) Trusted kmer low bound: 0 0:58:20.344 14G / 27G INFO StageManager (stage.cpp : 126) STAGE == Gap Closer 0:58:20.364 14G / 27G INFO General (gap_closer.cpp : 159) Preparing shift maps 0:58:50.263 16G / 27G INFO General (gap_closer.cpp : 119) Processing paired reads (takes a while) 1:02:05.285 19G / 27G INFO General (gap_closer.cpp : 138) Used 127432598 paired reads 1:02:05.285 19G / 27G INFO General (gap_closer.cpp : 140) Merging paired indices 1:02:32.441 15G / 27G INFO GapCloser (gap_closer.cpp : 347) Closing short gaps 1:03:57.879 15G / 27G INFO GapCloser (gap_closer.cpp : 381) Closing short gaps complete: filled 519486 gaps after checking 1378041 candidates 1:05:14.026 14G / 27G INFO StageManager (stage.cpp : 126) STAGE == Simplification 1:05:14.702 10G / 27G INFO General (simplification.cpp : 420) Graph simplification started 1:05:14.702 10G / 27G INFO General (simplification.cpp : 76) PROCEDURE == InitialCleaning 1:05:14.702 10G / 27G INFO General (simplification.cpp : 64) Removing short polyAT 1:06:12.663 10G / 27G INFO General (parallel_simplification_al: 806) Parallel compression 1:06:15.329 10G / 27G INFO General (parallel_simplification_al: 815) Launching post-compression to compress loops 1:06:16.801 10G / 27G INFO General (graph_simplification.hpp : 645) Flanking coverage based disconnection disabled 1:06:16.801 10G / 27G INFO General (simplification.cpp : 349) Running Self conjugate edge remover 1:06:18.586 10G / 27G INFO General (simplification.cpp : 351) Triggered 1 times 1:06:18.586 10G / 27G INFO General (simplification.cpp : 349) Running Short PolyA/T Edges 1:06:20.402 10G / 27G INFO General (simplification.cpp : 351) Triggered 0 times 1:06:20.402 10G / 27G INFO General (simplification.cpp : 349) Running AT Tips 1:07:03.755 10G / 27G INFO General (simplification.cpp : 351) Triggered 2385374 times 1:07:03.755 10G / 27G INFO General (graph_simplification.hpp : 666) Removing loops and rc loops with erroneous connections 1:07:47.887 10G / 27G INFO ECLoopRemover (erroneous_connection_remov: 441) Loops: accurately removed/deadend removed/other: 4/78/2 1:07:47.887 10G / 27G INFO ECLoopRemover (erroneous_connection_remov: 442) RC loops: accurately removed/deadend removed/other: 12/125/1848 1:07:48.940 10G / 27G INFO General (graph_simplification.hpp : 617) Creating parallel br instance 1:07:48.940 10G / 27G INFO General (simplification.cpp : 456) PROCEDURE == Tip clipper and bulge removal cycle, iteration 1.0 1:07:48.940 10G / 27G INFO General (simplification.cpp : 349) Running Tip clipper 1:09:03.933 10G / 27G INFO General (simplification.cpp : 351) Triggered 3573688 times 1:09:03.933 10G / 27G INFO General (simplification.cpp : 349) Running Dead end clipper 1:09:05.449 10G / 27G INFO General (simplification.cpp : 351) Triggered 29475 times 1:09:05.449 10G / 27G INFO General (simplification.cpp : 349) Running Bulge remover 1:09:52.780 10G / 27G INFO General (simplification.cpp : 351) Triggered 63513 times 1:09:52.780 10G / 27G INFO General (simplification.cpp : 456) PROCEDURE == Tip clipper and bulge removal cycle, iteration 1.1 1:09:52.780 10G / 27G INFO General (simplification.cpp : 349) Running Tip clipper 1:09:52.915 10G / 27G INFO General (simplification.cpp : 351) Triggered 2643 times 1:09:52.915 10G / 27G INFO General (simplification.cpp : 349) Running Dead end clipper 1:09:52.981 10G / 27G INFO General (simplification.cpp : 351) Triggered 4 times 1:09:52.981 10G / 27G INFO General (simplification.cpp : 349) Running Bulge remover 1:09:53.023 10G / 27G INFO General (simplification.cpp : 351) Triggered 63 times 1:09:53.023 10G / 27G INFO General (simplification.cpp : 456) PROCEDURE == Tip clipper and bulge removal cycle, iteration 1.2 1:09:53.023 10G / 27G INFO General (simplification.cpp : 349) Running Tip clipper 1:09:53.024 10G / 27G INFO General (simplification.cpp : 351) Triggered 3 times 1:09:53.024 10G / 27G INFO General (simplification.cpp : 349) Running Dead end clipper 1:09:53.024 10G / 27G INFO General (simplification.cpp : 351) Triggered 0 times 1:09:53.024 10G / 27G INFO General (simplification.cpp : 349) Running Bulge remover 1:09:53.024 10G / 27G INFO General (simplification.cpp : 351) Triggered 0 times 1:09:53.024 10G / 27G INFO General (simplification.cpp : 456) PROCEDURE == Tip clipper and bulge removal cycle, iteration 1.3 1:09:53.024 10G / 27G INFO General (simplification.cpp : 349) Running Tip clipper 1:09:53.024 10G / 27G INFO General (simplification.cpp : 351) Triggered 0 times 1:09:53.024 10G / 27G INFO General (simplification.cpp : 349) Running Dead end clipper 1:09:53.024 10G / 27G INFO General (simplification.cpp : 351) Triggered 0 times 1:09:53.024 10G / 27G INFO General (simplification.cpp : 349) Running Bulge remover 1:09:53.024 10G / 27G INFO General (simplification.cpp : 351) Triggered 0 times 1:09:53.024 10G / 27G INFO General (simplification.cpp : 460) PROCEDURE == Erroneous connection, iteration 1 1:09:53.024 10G / 27G INFO General (simplification.cpp : 349) Running Low coverage edge remover 1:09:58.689 10G / 27G INFO General (simplification.cpp : 351) Triggered 88630 times 1:09:58.790 10G / 27G INFO General (graph_simplification.hpp : 617) Creating parallel br instance 1:09:58.790 10G / 27G INFO General (simplification.cpp : 456) PROCEDURE == Tip clipper and bulge removal cycle, iteration 2.0 1:09:58.790 10G / 27G INFO General (simplification.cpp : 349) Running Tip clipper 1:10:00.936 10G / 27G INFO General (simplification.cpp : 351) Triggered 40253 times 1:10:00.936 10G / 27G INFO General (simplification.cpp : 349) Running Dead end clipper 1:10:02.084 10G / 27G INFO General (simplification.cpp : 351) Triggered 10 times 1:10:02.084 10G / 27G INFO General (simplification.cpp : 349) Running Bulge remover 1:10:17.719 10G / 27G INFO General (simplification.cpp : 351) Triggered 18842 times 1:10:17.719 10G / 27G INFO General (simplification.cpp : 456) PROCEDURE == Tip clipper and bulge removal cycle, iteration 2.1 1:10:17.719 10G / 27G INFO General (simplification.cpp : 349) Running Tip clipper 1:10:17.732 10G / 27G INFO General (simplification.cpp : 351) Triggered 90 times 1:10:17.733 10G / 27G INFO General (simplification.cpp : 349) Running Dead end clipper 1:10:17.741 10G / 27G INFO General (simplification.cpp : 351) Triggered 0 times 1:10:17.741 10G / 27G INFO General (simplification.cpp : 349) Running Bulge remover 1:10:17.743 10G / 27G INFO General (simplification.cpp : 351) Triggered 3 times 1:10:17.743 10G / 27G INFO General (simplification.cpp : 456) PROCEDURE == Tip clipper and bulge removal cycle, iteration 2.2 1:10:17.743 10G / 27G INFO General (simplification.cpp : 349) Running Tip clipper 1:10:17.743 10G / 27G INFO General (simplification.cpp : 351) Triggered 0 times 1:10:17.743 10G / 27G INFO General (simplification.cpp : 349) Running Dead end clipper 1:10:17.743 10G / 27G INFO General (simplification.cpp : 351) Triggered 0 times 1:10:17.743 10G / 27G INFO General (simplification.cpp : 349) Running Bulge remover 1:10:17.743 10G / 27G INFO General (simplification.cpp : 351) Triggered 0 times 1:10:17.743 10G / 27G INFO General (simplification.cpp : 460) PROCEDURE == Erroneous connection, iteration 2 1:10:17.743 10G / 27G INFO General (simplification.cpp : 349) Running Low coverage edge remover 1:10:18.177 10G / 27G INFO General (simplification.cpp : 351) Triggered 8991 times 1:10:18.190 10G / 27G INFO General (graph_simplification.hpp : 617) Creating parallel br instance 1:10:18.190 10G / 27G INFO General (simplification.cpp : 456) PROCEDURE == Tip clipper and bulge removal cycle, iteration 3.0 1:10:18.190 10G / 27G INFO General (simplification.cpp : 349) Running Tip clipper 1:10:19.504 10G / 27G INFO General (simplification.cpp : 351) Triggered 2004 times 1:10:19.504 10G / 27G INFO General (simplification.cpp : 349) Running Dead end clipper 1:10:20.670 10G / 27G INFO General (simplification.cpp : 351) Triggered 1 times 1:10:20.670 10G / 27G INFO General (simplification.cpp : 349) Running Bulge remover 1:10:22.506 10G / 27G INFO General (simplification.cpp : 351) Triggered 1255 times 1:10:22.506 10G / 27G INFO General (simplification.cpp : 456) PROCEDURE == Tip clipper and bulge removal cycle, iteration 3.1 1:10:22.506 10G / 27G INFO General (simplification.cpp : 349) Running Tip clipper 1:10:22.510 10G / 27G INFO General (simplification.cpp : 351) Triggered 5 times 1:10:22.510 10G / 27G INFO General (simplification.cpp : 349) Running Dead end clipper 1:10:22.512 10G / 27G INFO General (simplification.cpp : 351) Triggered 0 times 1:10:22.512 10G / 27G INFO General (simplification.cpp : 349) Running Bulge remover 1:10:22.513 10G / 27G INFO General (simplification.cpp : 351) Triggered 1 times 1:10:22.513 10G / 27G INFO General (simplification.cpp : 456) PROCEDURE == Tip clipper and bulge removal cycle, iteration 3.2 1:10:22.513 10G / 27G INFO General (simplification.cpp : 349) Running Tip clipper 1:10:22.513 10G / 27G INFO General (simplification.cpp : 351) Triggered 0 times 1:10:22.513 10G / 27G INFO General (simplification.cpp : 349) Running Dead end clipper 1:10:22.513 10G / 27G INFO General (simplification.cpp : 351) Triggered 0 times 1:10:22.513 10G / 27G INFO General (simplification.cpp : 349) Running Bulge remover 1:10:22.513 10G / 27G INFO General (simplification.cpp : 351) Triggered 0 times 1:10:22.513 10G / 27G INFO General (simplification.cpp : 460) PROCEDURE == Erroneous connection, iteration 3 1:10:22.513 10G / 27G INFO General (simplification.cpp : 349) Running Low coverage edge remover 1:10:22.681 10G / 27G INFO General (simplification.cpp : 351) Triggered 3704 times 1:10:22.687 10G / 27G INFO General (graph_simplification.hpp : 617) Creating parallel br instance 1:10:22.687 10G / 27G INFO General (simplification.cpp : 456) PROCEDURE == Tip clipper and bulge removal cycle, iteration 4.0 1:10:22.687 10G / 27G INFO General (simplification.cpp : 349) Running Tip clipper 1:10:23.897 10G / 27G INFO General (simplification.cpp : 351) Triggered 396 times 1:10:23.897 10G / 27G INFO General (simplification.cpp : 349) Running Dead end clipper 1:10:25.308 10G / 27G INFO General (simplification.cpp : 351) Triggered 0 times 1:10:25.308 10G / 27G INFO General (simplification.cpp : 349) Running Bulge remover 1:10:26.732 10G / 27G INFO General (simplification.cpp : 351) Triggered 409 times 1:10:26.732 10G / 27G INFO General (simplification.cpp : 456) PROCEDURE == Tip clipper and bulge removal cycle, iteration 4.1 1:10:26.732 10G / 27G INFO General (simplification.cpp : 349) Running Tip clipper 1:10:26.733 10G / 27G INFO General (simplification.cpp : 351) Triggered 1 times 1:10:26.733 10G / 27G INFO General (simplification.cpp : 349) Running Dead end clipper 1:10:26.734 10G / 27G INFO General (simplification.cpp : 351) Triggered 0 times 1:10:26.734 10G / 27G INFO General (simplification.cpp : 349) Running Bulge remover 1:10:26.734 10G / 27G INFO General (simplification.cpp : 351) Triggered 0 times 1:10:26.734 10G / 27G INFO General (simplification.cpp : 456) PROCEDURE == Tip clipper and bulge removal cycle, iteration 4.2 1:10:26.734 10G / 27G INFO General (simplification.cpp : 349) Running Tip clipper 1:10:26.734 10G / 27G INFO General (simplification.cpp : 351) Triggered 0 times 1:10:26.734 10G / 27G INFO General (simplification.cpp : 349) Running Dead end clipper 1:10:26.734 10G / 27G INFO General (simplification.cpp : 351) Triggered 0 times 1:10:26.734 10G / 27G INFO General (simplification.cpp : 349) Running Bulge remover 1:10:26.734 10G / 27G INFO General (simplification.cpp : 351) Triggered 0 times 1:10:26.734 10G / 27G INFO General (simplification.cpp : 460) PROCEDURE == Erroneous connection, iteration 4 1:10:26.734 10G / 27G INFO General (simplification.cpp : 349) Running Low coverage edge remover 1:10:26.823 10G / 27G INFO General (simplification.cpp : 351) Triggered 1947 times 1:10:26.826 10G / 27G INFO General (graph_simplification.hpp : 617) Creating parallel br instance 1:10:26.826 10G / 27G INFO General (simplification.cpp : 456) PROCEDURE == Tip clipper and bulge removal cycle, iteration 5.0 1:10:26.826 10G / 27G INFO General (simplification.cpp : 349) Running Tip clipper 1:10:27.952 10G / 27G INFO General (simplification.cpp : 351) Triggered 137 times 1:10:27.952 10G / 27G INFO General (simplification.cpp : 349) Running Dead end clipper 1:10:29.089 10G / 27G INFO General (simplification.cpp : 351) Triggered 0 times 1:10:29.089 10G / 27G INFO General (simplification.cpp : 349) Running Bulge remover 1:10:30.337 10G / 27G INFO General (simplification.cpp : 351) Triggered 192 times 1:10:30.337 10G / 27G INFO General (simplification.cpp : 456) PROCEDURE == Tip clipper and bulge removal cycle, iteration 5.1 1:10:30.337 10G / 27G INFO General (simplification.cpp : 349) Running Tip clipper 1:10:30.337 10G / 27G INFO General (simplification.cpp : 351) Triggered 0 times 1:10:30.337 10G / 27G INFO General (simplification.cpp : 349) Running Dead end clipper 1:10:30.338 10G / 27G INFO General (simplification.cpp : 351) Triggered 0 times 1:10:30.338 10G / 27G INFO General (simplification.cpp : 349) Running Bulge remover 1:10:30.338 10G / 27G INFO General (simplification.cpp : 351) Triggered 0 times 1:10:30.338 10G / 27G INFO General (simplification.cpp : 460) PROCEDURE == Erroneous connection, iteration 5 1:10:30.338 10G / 27G INFO General (simplification.cpp : 349) Running Low coverage edge remover 1:10:30.400 10G / 27G INFO General (simplification.cpp : 351) Triggered 1295 times 1:10:30.402 10G / 27G INFO General (graph_simplification.hpp : 617) Creating parallel br instance 1:10:30.402 10G / 27G INFO General (simplification.cpp : 456) PROCEDURE == Tip clipper and bulge removal cycle, iteration 6.0 1:10:30.402 10G / 27G INFO General (simplification.cpp : 349) Running Tip clipper 1:10:31.592 10G / 27G INFO General (simplification.cpp : 351) Triggered 56 times 1:10:31.593 10G / 27G INFO General (simplification.cpp : 349) Running Dead end clipper 1:10:32.947 10G / 27G INFO General (simplification.cpp : 351) Triggered 0 times 1:10:32.947 10G / 27G INFO General (simplification.cpp : 349) Running Bulge remover 1:10:34.130 10G / 27G INFO General (simplification.cpp : 351) Triggered 108 times 1:10:34.130 10G / 27G INFO General (simplification.cpp : 456) PROCEDURE == Tip clipper and bulge removal cycle, iteration 6.1 1:10:34.131 10G / 27G INFO General (simplification.cpp : 349) Running Tip clipper 1:10:34.131 10G / 27G INFO General (simplification.cpp : 351) Triggered 0 times 1:10:34.132 10G / 27G INFO General (simplification.cpp : 349) Running Dead end clipper 1:10:34.132 10G / 27G INFO General (simplification.cpp : 351) Triggered 0 times 1:10:34.132 10G / 27G INFO General (simplification.cpp : 349) Running Bulge remover 1:10:34.132 10G / 27G INFO General (simplification.cpp : 351) Triggered 0 times 1:10:34.132 10G / 27G INFO General (simplification.cpp : 460) PROCEDURE == Erroneous connection, iteration 6 1:10:34.132 10G / 27G INFO General (simplification.cpp : 349) Running Low coverage edge remover 1:10:34.174 10G / 27G INFO General (simplification.cpp : 351) Triggered 904 times 1:10:34.176 10G / 27G INFO General (graph_simplification.hpp : 617) Creating parallel br instance 1:10:34.176 10G / 27G INFO General (simplification.cpp : 456) PROCEDURE == Tip clipper and bulge removal cycle, iteration 7.0 1:10:34.176 10G / 27G INFO General (simplification.cpp : 349) Running Tip clipper 1:10:35.353 10G / 27G INFO General (simplification.cpp : 351) Triggered 28 times 1:10:35.353 10G / 27G INFO General (simplification.cpp : 349) Running Dead end clipper 1:10:36.502 10G / 27G INFO General (simplification.cpp : 351) Triggered 1 times 1:10:36.502 10G / 27G INFO General (simplification.cpp : 349) Running Bulge remover 1:10:37.627 10G / 27G INFO General (simplification.cpp : 351) Triggered 73 times 1:10:37.627 10G / 27G INFO General (simplification.cpp : 456) PROCEDURE == Tip clipper and bulge removal cycle, iteration 7.1 1:10:37.627 10G / 27G INFO General (simplification.cpp : 349) Running Tip clipper 1:10:37.627 10G / 27G INFO General (simplification.cpp : 351) Triggered 0 times 1:10:37.627 10G / 27G INFO General (simplification.cpp : 349) Running Dead end clipper 1:10:37.628 10G / 27G INFO General (simplification.cpp : 351) Triggered 0 times 1:10:37.628 10G / 27G INFO General (simplification.cpp : 349) Running Bulge remover 1:10:37.628 10G / 27G INFO General (simplification.cpp : 351) Triggered 0 times 1:10:37.628 10G / 27G INFO General (simplification.cpp : 460) PROCEDURE == Erroneous connection, iteration 7 1:10:37.628 10G / 27G INFO General (simplification.cpp : 349) Running Low coverage edge remover 1:10:37.660 10G / 27G INFO General (simplification.cpp : 351) Triggered 709 times 1:10:37.661 10G / 27G INFO General (graph_simplification.hpp : 617) Creating parallel br instance 1:10:37.661 10G / 27G INFO General (simplification.cpp : 456) PROCEDURE == Tip clipper and bulge removal cycle, iteration 8.0 1:10:37.661 10G / 27G INFO General (simplification.cpp : 349) Running Tip clipper 1:10:38.799 10G / 27G INFO General (simplification.cpp : 351) Triggered 25 times 1:10:38.799 10G / 27G INFO General (simplification.cpp : 349) Running Dead end clipper 1:10:39.930 10G / 27G INFO General (simplification.cpp : 351) Triggered 0 times 1:10:39.930 10G / 27G INFO General (simplification.cpp : 349) Running Bulge remover 1:10:41.031 10G / 27G INFO General (simplification.cpp : 351) Triggered 39 times 1:10:41.031 10G / 27G INFO General (simplification.cpp : 456) PROCEDURE == Tip clipper and bulge removal cycle, iteration 8.1 1:10:41.031 10G / 27G INFO General (simplification.cpp : 349) Running Tip clipper 1:10:41.032 10G / 27G INFO General (simplification.cpp : 351) Triggered 0 times 1:10:41.032 10G / 27G INFO General (simplification.cpp : 349) Running Dead end clipper 1:10:41.032 10G / 27G INFO General (simplification.cpp : 351) Triggered 0 times 1:10:41.032 10G / 27G INFO General (simplification.cpp : 349) Running Bulge remover 1:10:41.032 10G / 27G INFO General (simplification.cpp : 351) Triggered 0 times 1:10:41.032 10G / 27G INFO General (simplification.cpp : 460) PROCEDURE == Erroneous connection, iteration 8 1:10:41.032 10G / 27G INFO General (simplification.cpp : 349) Running Low coverage edge remover 1:10:41.057 10G / 27G INFO General (simplification.cpp : 351) Triggered 576 times 1:10:41.058 10G / 27G INFO General (graph_simplification.hpp : 617) Creating parallel br instance 1:10:41.058 10G / 27G INFO General (simplification.cpp : 456) PROCEDURE == Tip clipper and bulge removal cycle, iteration 9.0 1:10:41.058 10G / 27G INFO General (simplification.cpp : 349) Running Tip clipper 1:10:42.150 10G / 27G INFO General (simplification.cpp : 351) Triggered 15 times 1:10:42.150 10G / 27G INFO General (simplification.cpp : 349) Running Dead end clipper 1:10:43.287 10G / 27G INFO General (simplification.cpp : 351) Triggered 0 times 1:10:43.287 10G / 27G INFO General (simplification.cpp : 349) Running Bulge remover 1:10:44.398 10G / 27G INFO General (simplification.cpp : 351) Triggered 37 times 1:10:44.398 10G / 27G INFO General (simplification.cpp : 456) PROCEDURE == Tip clipper and bulge removal cycle, iteration 9.1 1:10:44.398 10G / 27G INFO General (simplification.cpp : 349) Running Tip clipper 1:10:44.398 10G / 27G INFO General (simplification.cpp : 351) Triggered 0 times 1:10:44.398 10G / 27G INFO General (simplification.cpp : 349) Running Dead end clipper 1:10:44.398 10G / 27G INFO General (simplification.cpp : 351) Triggered 0 times 1:10:44.398 10G / 27G INFO General (simplification.cpp : 349) Running Bulge remover 1:10:44.398 10G / 27G INFO General (simplification.cpp : 351) Triggered 0 times 1:10:44.398 10G / 27G INFO General (simplification.cpp : 460) PROCEDURE == Erroneous connection, iteration 9 1:10:44.398 10G / 27G INFO General (simplification.cpp : 349) Running Low coverage edge remover 1:10:44.420 10G / 27G INFO General (simplification.cpp : 351) Triggered 447 times 1:10:44.420 10G / 27G INFO General (graph_simplification.hpp : 617) Creating parallel br instance 1:10:44.420 10G / 27G INFO General (simplification.cpp : 456) PROCEDURE == Tip clipper and bulge removal cycle, iteration 10.0 1:10:44.420 10G / 27G INFO General (simplification.cpp : 349) Running Tip clipper 1:10:45.563 10G / 27G INFO General (simplification.cpp : 351) Triggered 14 times 1:10:45.564 10G / 27G INFO General (simplification.cpp : 349) Running Dead end clipper 1:10:46.707 10G / 27G INFO General (simplification.cpp : 351) Triggered 0 times 1:10:46.707 10G / 27G INFO General (simplification.cpp : 349) Running Bulge remover 1:10:47.788 10G / 27G INFO General (simplification.cpp : 351) Triggered 19 times 1:10:47.789 10G / 27G INFO General (simplification.cpp : 456) PROCEDURE == Tip clipper and bulge removal cycle, iteration 10.1 1:10:47.789 10G / 27G INFO General (simplification.cpp : 349) Running Tip clipper 1:10:47.789 10G / 27G INFO General (simplification.cpp : 351) Triggered 0 times 1:10:47.789 10G / 27G INFO General (simplification.cpp : 349) Running Dead end clipper 1:10:47.789 10G / 27G INFO General (simplification.cpp : 351) Triggered 0 times 1:10:47.789 10G / 27G INFO General (simplification.cpp : 349) Running Bulge remover 1:10:47.789 10G / 27G INFO General (simplification.cpp : 351) Triggered 0 times 1:10:47.789 10G / 27G INFO General (simplification.cpp : 460) PROCEDURE == Erroneous connection, iteration 10 1:10:47.789 10G / 27G INFO General (simplification.cpp : 349) Running Low coverage edge remover 1:10:47.807 10G / 27G INFO General (simplification.cpp : 351) Triggered 386 times 1:10:47.807 10G / 27G INFO General (graph_simplification.hpp : 617) Creating parallel br instance 1:10:47.807 10G / 27G INFO General (simplification.cpp : 456) PROCEDURE == Tip clipper and bulge removal cycle, iteration 11.0 1:10:47.807 10G / 27G INFO General (simplification.cpp : 349) Running Tip clipper 1:10:48.951 10G / 27G INFO General (simplification.cpp : 351) Triggered 8 times 1:10:48.951 10G / 27G INFO General (simplification.cpp : 349) Running Dead end clipper 1:10:50.093 10G / 27G INFO General (simplification.cpp : 351) Triggered 0 times 1:10:50.093 10G / 27G INFO General (simplification.cpp : 349) Running Bulge remover 1:10:51.175 10G / 27G INFO General (simplification.cpp : 351) Triggered 11 times 1:10:51.175 10G / 27G INFO General (simplification.cpp : 456) PROCEDURE == Tip clipper and bulge removal cycle, iteration 11.1 1:10:51.175 10G / 27G INFO General (simplification.cpp : 349) Running Tip clipper 1:10:51.175 10G / 27G INFO General (simplification.cpp : 351) Triggered 0 times 1:10:51.175 10G / 27G INFO General (simplification.cpp : 349) Running Dead end clipper 1:10:51.175 10G / 27G INFO General (simplification.cpp : 351) Triggered 0 times 1:10:51.175 10G / 27G INFO General (simplification.cpp : 349) Running Bulge remover 1:10:51.176 10G / 27G INFO General (simplification.cpp : 351) Triggered 0 times 1:10:51.176 10G / 27G INFO General (simplification.cpp : 460) PROCEDURE == Erroneous connection, iteration 11 1:10:51.176 10G / 27G INFO General (simplification.cpp : 349) Running Low coverage edge remover 1:10:51.176 10G / 27G INFO General (simplification.cpp : 351) Triggered 0 times 1:10:51.176 10G / 27G INFO General (simplification.cpp : 162) PROCEDURE == Post simplification 1:10:51.176 10G / 27G INFO General (graph_simplification.hpp : 446) Disconnection of relatively low covered edges disabled 1:10:51.176 10G / 27G INFO General (graph_simplification.hpp : 476) Complex tip clipping disabled 1:10:51.176 10G / 27G INFO General (graph_simplification.hpp : 617) Creating parallel br instance 1:10:51.176 10G / 27G INFO General (graph_simplification.hpp : 617) Creating parallel br instance 1:10:51.176 10G / 27G INFO General (simplification.cpp : 294) Iteration 0 1:10:51.176 10G / 27G INFO General (simplification.cpp : 349) Running Relative coverage component remover 1:10:52.672 10G / 27G INFO General (simplification.cpp : 351) Triggered 302 times 1:10:52.672 10G / 27G INFO General (simplification.cpp : 349) Running Relative coverage component remover 1:10:53.910 10G / 27G INFO General (simplification.cpp : 351) Triggered 4296 times 1:10:53.910 10G / 27G INFO General (simplification.cpp : 349) Running Complex bulge remover 1:11:19.840 10G / 27G INFO General (simplification.cpp : 351) Triggered 67 times 1:11:19.840 10G / 27G INFO General (simplification.cpp : 349) Running Tip clipper 1:11:21.296 10G / 27G INFO General (simplification.cpp : 351) Triggered 16 times 1:11:21.296 10G / 27G INFO General (simplification.cpp : 349) Running Final tip clipper 1:11:22.719 10G / 27G INFO General (simplification.cpp : 351) Triggered 7891 times 1:11:22.719 10G / 27G INFO General (simplification.cpp : 349) Running Bulge remover 1:11:23.861 10G / 27G INFO General (simplification.cpp : 351) Triggered 116 times 1:11:23.861 10G / 27G INFO General (simplification.cpp : 349) Running Final bulge remover 1:11:24.924 10G / 27G INFO General (simplification.cpp : 351) Triggered 0 times 1:11:24.924 10G / 27G INFO General (simplification.cpp : 349) Running AT Tips 1:11:26.323 10G / 27G INFO General (simplification.cpp : 351) Triggered 1908 times 1:11:26.323 10G / 27G INFO General (simplification.cpp : 294) Iteration 1 1:11:26.323 10G / 27G INFO General (simplification.cpp : 349) Running Relative coverage component remover 1:11:26.338 10G / 27G INFO General (simplification.cpp : 351) Triggered 6 times 1:11:26.338 10G / 27G INFO General (simplification.cpp : 349) Running Relative coverage component remover 1:11:27.405 10G / 27G INFO General (simplification.cpp : 351) Triggered 16 times 1:11:27.405 10G / 27G INFO General (simplification.cpp : 349) Running Complex bulge remover 1:11:52.569 10G / 27G INFO General (simplification.cpp : 351) Triggered 3 times 1:11:52.569 10G / 27G INFO General (simplification.cpp : 349) Running Tip clipper 1:11:52.591 10G / 27G INFO General (simplification.cpp : 351) Triggered 0 times 1:11:52.591 10G / 27G INFO General (simplification.cpp : 349) Running Final tip clipper 1:11:52.591 10G / 27G INFO General (simplification.cpp : 351) Triggered 3 times 1:11:52.591 10G / 27G INFO General (simplification.cpp : 349) Running Bulge remover 1:11:52.595 10G / 27G INFO General (simplification.cpp : 351) Triggered 0 times 1:11:52.595 10G / 27G INFO General (simplification.cpp : 349) Running Final bulge remover 1:11:52.595 10G / 27G INFO General (simplification.cpp : 351) Triggered 0 times 1:11:52.595 10G / 27G INFO General (simplification.cpp : 349) Running AT Tips 1:11:52.595 10G / 27G INFO General (simplification.cpp : 351) Triggered 0 times 1:11:52.595 10G / 27G INFO General (simplification.cpp : 294) Iteration 2 1:11:52.595 10G / 27G INFO General (simplification.cpp : 349) Running Relative coverage component remover 1:11:52.595 10G / 27G INFO General (simplification.cpp : 351) Triggered 0 times 1:11:52.595 10G / 27G INFO General (simplification.cpp : 349) Running Relative coverage component remover 1:11:54.029 10G / 27G INFO General (simplification.cpp : 351) Triggered 0 times 1:11:54.029 10G / 27G INFO General (simplification.cpp : 349) Running Complex bulge remover 1:12:20.442 10G / 27G INFO General (simplification.cpp : 351) Triggered 0 times 1:12:20.442 10G / 27G INFO General (simplification.cpp : 349) Running Tip clipper 1:12:20.442 10G / 27G INFO General (simplification.cpp : 351) Triggered 0 times 1:12:20.442 10G / 27G INFO General (simplification.cpp : 349) Running Final tip clipper 1:12:20.442 10G / 27G INFO General (simplification.cpp : 351) Triggered 0 times 1:12:20.442 10G / 27G INFO General (simplification.cpp : 349) Running Bulge remover 1:12:20.444 10G / 27G INFO General (simplification.cpp : 351) Triggered 0 times 1:12:20.444 10G / 27G INFO General (simplification.cpp : 349) Running Final bulge remover 1:12:20.444 10G / 27G INFO General (simplification.cpp : 351) Triggered 0 times 1:12:20.444 10G / 27G INFO General (simplification.cpp : 349) Running AT Tips 1:12:20.444 10G / 27G INFO General (simplification.cpp : 351) Triggered 0 times 1:12:20.444 10G / 27G INFO General (simplification.cpp : 326) Disrupting self-conjugate edges 1:12:27.848 10G / 27G INFO StageManager (stage.cpp : 126) STAGE == Gap Closer 1:12:27.848 10G / 27G INFO General (graph_pack.hpp : 96) Index refill 1:12:27.859 10G / 27G INFO K-mer Index Building (kmer_index_builder.hpp : 428) Building kmer index 1:12:27.859 10G / 27G INFO General (kmer_splitters.hpp : 214) Splitting kmer instances into 16 buckets. This might take a while. 1:12:27.859 10G / 27G INFO General (file_limit.hpp : 30) Open file limit set to 64000 1:12:27.859 10G / 27G INFO General (kmer_index_builder.hpp : 108) Memory available for splitting buffers: 69.8281 Gb 1:12:27.859 10G / 27G INFO General (kmer_index_builder.hpp : 116) Using cell size of 2097152 1:12:43.018 11G / 27G INFO General (kmer_splitters.hpp : 225) Processed 1535404 edges 1:12:58.401 11G / 27G INFO General (kmer_splitters.hpp : 225) Processed 3059684 edges 1:13:13.477 11G / 27G INFO General (kmer_splitters.hpp : 225) Processed 4572336 edges 1:13:28.438 11G / 27G INFO General (kmer_splitters.hpp : 225) Processed 6083172 edges 1:13:43.362 11G / 27G INFO General (kmer_splitters.hpp : 225) Processed 7589043 edges 1:13:44.314 11G / 27G INFO General (kmer_splitters.hpp : 225) Processed 7663447 edges 1:13:44.314 11G / 27G INFO General (kmer_splitters.hpp : 230) Used 7663447 sequences. 1:13:44.414 10G / 27G INFO General (kmer_index_builder.hpp : 252) Starting k-mer counting. 1:14:56.279 10G / 27G INFO General (kmer_index_builder.hpp : 258) K-mer counting done. There are 163332403 kmers in total. 1:14:56.279 10G / 27G INFO General (kmer_index_builder.hpp : 260) Merging temporary buckets. 1:15:48.782 10G / 27G INFO K-mer Index Building (kmer_index_builder.hpp : 437) Building perfect hash indices 1:16:53.873 10G / 27G INFO General (kmer_index_builder.hpp : 276) Merging final buckets. 1:17:31.225 10G / 27G INFO K-mer Index Building (kmer_index_builder.hpp : 483) Index built. Total 53363880 bytes occupied (2.61376 bits per kmer). 1:17:33.590 14G / 27G INFO General (edge_index_builders.hpp : 27) Collecting k-mer coverage information from graph, this takes a while. 1:17:43.798 14G / 27G INFO General (edge_index.hpp : 91) Index refilled 1:17:43.815 14G / 27G INFO General (gap_closer.cpp : 159) Preparing shift maps 1:17:58.967 15G / 27G INFO General (gap_closer.cpp : 119) Processing paired reads (takes a while) 1:19:28.256 16G / 27G INFO General (gap_closer.cpp : 138) Used 127432598 paired reads 1:19:28.256 16G / 27G INFO General (gap_closer.cpp : 140) Merging paired indices 1:19:58.936 14G / 27G INFO GapCloser (gap_closer.cpp : 347) Closing short gaps 1:20:27.967 14G / 27G INFO GapCloser (gap_closer.cpp : 381) Closing short gaps complete: filled 97726 gaps after checking 1570100 candidates 1:21:30.796 14G / 27G INFO StageManager (stage.cpp : 126) STAGE == Simplification Cleanup 1:21:30.796 14G / 27G INFO General (simplification.cpp : 561) Counting average coverage 1:21:33.262 14G / 27G INFO General (simplification.cpp : 566) Average coverage = 27.2228 1:21:33.262 14G / 27G INFO StageManager (stage.cpp : 126) STAGE == Mismatch Correction 1:21:33.262 14G / 27G INFO General (graph_pack.hpp : 105) Normalizing k-mer map. Total 9400584 kmers to process 1:21:39.879 14G / 27G INFO General (graph_pack.hpp : 107) Normalizing done 1:25:39.879 14G / 27G INFO General (mismatch_shall_not_pass.hp: 187) Finished collecting potential mismatches positions 1:25:55.906 14G / 27G INFO General (mismatch_shall_not_pass.hp: 284) All edges processed 1:25:56.918 14G / 27G INFO General (mismatch_correction.cpp : 26) Corrected 193 nucleotides 1:25:56.927 14G / 27G INFO StageManager (stage.cpp : 126) STAGE == Contig Output 1:25:56.927 14G / 27G INFO General (contig_output.hpp : 478) Outputting contigs to /data/home/pitagoras/public_html/gigas/transcriptome/rnaSpades/spadesRNA/output//K55/pre_pe_before_rr.fasta 1:26:34.020 14G / 27G INFO General (contig_output.hpp : 518) Outputting graph to /data/home/pitagoras/public_html/gigas/transcriptome/rnaSpades/spadesRNA/output//K55/pre_pe_assembly_graph.fastg 1:27:53.109 14G / 27G INFO General (contig_output.hpp : 478) Outputting contigs to /data/home/pitagoras/public_html/gigas/transcriptome/rnaSpades/spadesRNA/output//K55/pre_pe_simplified_contigs.fasta 1:28:30.380 14G / 27G INFO General (contig_output.hpp : 478) Outputting contigs to /data/home/pitagoras/public_html/gigas/transcriptome/rnaSpades/spadesRNA/output//K55/pre_pe_final_contigs.fasta 1:29:06.753 14G / 27G INFO StageManager (stage.cpp : 126) STAGE == Paired Information Counting 1:29:37.269 15G / 27G INFO General (graph_pack.hpp : 105) Normalizing k-mer map. Total 9412108 kmers to process 1:29:43.923 15G / 27G INFO General (graph_pack.hpp : 107) Normalizing done 1:29:45.918 15G / 27G INFO General (pair_info_count.cpp : 300) Min edge length for estimation: 105 1:29:45.918 15G / 27G INFO General (pair_info_count.cpp : 311) Estimating insert size for library #0 1:29:45.918 15G / 27G INFO General (pair_info_count.cpp : 116) Estimating insert size (takes a while) 1:29:46.108 15G / 27G INFO General (short_read_mapper.hpp : 88) Selecting usual mapper 1:29:48.184 15G / 27G INFO General (sequence_mapper_notifier.h: 82) Processed 200000 reads 1:29:48.216 15G / 27G INFO General (sequence_mapper_notifier.h: 82) Processed 400000 reads 1:29:48.248 15G / 27G INFO General (sequence_mapper_notifier.h: 82) Processed 600000 reads 1:29:48.280 15G / 27G INFO General (sequence_mapper_notifier.h: 82) Processed 800000 reads 1:29:48.311 15G / 27G INFO General (sequence_mapper_notifier.h: 82) Processed 1000000 reads 1:29:48.344 15G / 27G INFO General (sequence_mapper_notifier.h: 82) Processed 1200000 reads 1:29:48.513 15G / 27G INFO General (sequence_mapper_notifier.h: 82) Processed 2200000 reads 1:29:50.259 15G / 27G INFO General (sequence_mapper_notifier.h: 82) Processed 4200000 reads 1:29:52.361 15G / 27G INFO General (sequence_mapper_notifier.h: 82) Processed 8400000 reads 1:29:57.350 15G / 27G INFO General (sequence_mapper_notifier.h: 82) Processed 16800000 reads 1:30:07.549 15G / 27G INFO General (sequence_mapper_notifier.h: 82) Processed 33600000 reads 1:30:27.960 15G / 27G INFO General (sequence_mapper_notifier.h: 82) Processed 67200000 reads 1:31:10.092 15G / 27G INFO General (sequence_mapper_notifier.h: 100) Total 127432598 reads processed 1:31:11.477 15G / 27G INFO General (pair_info_count.cpp : 134) Edge pairs: 67108864 (rough upper limit) 1:31:11.477 15G / 27G INFO General (pair_info_count.cpp : 138) 75970702 paired reads (59.6164% of all) aligned to long edges 1:31:11.516 15G / 27G INFO General (pair_info_count.cpp : 334) Insert size = 155.592, deviation = 44.6017, left quantile = 110, right quantile = 214, read length = 76 1:31:11.516 15G / 27G INFO General (pair_info_count.cpp : 363) Mapping library #0 1:31:11.516 15G / 27G INFO General (pair_info_count.cpp : 365) Mapping paired reads (takes a while) 1:31:11.516 15G / 27G INFO General (pair_info_count.cpp : 204) Left insert size quantile 110, right insert size quantile 214, filtering threshold 0, rounding threshold 0 1:31:11.530 15G / 27G INFO General (short_read_mapper.hpp : 88) Selecting usual mapper 1:31:13.827 15G / 27G INFO General (sequence_mapper_notifier.h: 82) Processed 200000 reads 1:31:13.827 15G / 27G INFO General (sequence_mapper_notifier.h: 82) Processed 400000 reads 1:31:13.851 15G / 27G INFO General (sequence_mapper_notifier.h: 82) Processed 600000 reads 1:31:13.883 15G / 27G INFO General (sequence_mapper_notifier.h: 82) Processed 800000 reads 1:31:13.930 15G / 27G INFO General (sequence_mapper_notifier.h: 82) Processed 1000000 reads 1:31:13.941 15G / 27G INFO General (sequence_mapper_notifier.h: 82) Processed 1200000 reads 1:31:14.043 15G / 27G INFO General (sequence_mapper_notifier.h: 82) Processed 2200000 reads 1:31:15.953 15G / 27G INFO General (sequence_mapper_notifier.h: 82) Processed 4200000 reads 1:31:18.362 15G / 27G INFO General (sequence_mapper_notifier.h: 82) Processed 8400000 reads 1:31:24.114 15G / 27G INFO General (sequence_mapper_notifier.h: 82) Processed 16800000 reads 1:31:35.016 15G / 27G INFO General (sequence_mapper_notifier.h: 82) Processed 33600000 reads 1:31:59.308 15G / 27G INFO General (sequence_mapper_notifier.h: 82) Processed 67200000 reads 1:32:47.972 15G / 27G INFO General (sequence_mapper_notifier.h: 100) Total 127432598 reads processed 1:32:49.611 15G / 27G INFO StageManager (stage.cpp : 126) STAGE == Distance Estimation 1:32:49.611 15G / 27G INFO General (distance_estimation.cpp : 224) Processing library #0 1:32:49.611 15G / 27G INFO General (distance_estimation.cpp : 130) Weight Filter Done 1:32:49.611 15G / 27G INFO DistanceEstimator (distance_estimation.hpp : 176) Using SIMPLE distance estimator 1:32:54.619 15G / 27G INFO General (distance_estimation.cpp : 35) Filtering info 1:32:54.619 15G / 27G INFO General (pair_info_filters.hpp : 242) Start filtering; index size: 7628797 1:33:04.695 15G / 27G INFO General (pair_info_filters.hpp : 263) Done filtering 1:33:04.721 15G / 27G INFO General (distance_estimation.cpp : 172) Refining clustered pair information 1:33:05.216 15G / 27G INFO General (distance_estimation.cpp : 174) The refining of clustered pair information has been finished 1:33:05.216 15G / 27G INFO General (distance_estimation.cpp : 176) Improving paired information 1:33:15.950 15G / 27G INFO PairInfoImprover (pair_info_improver.hpp : 103) Paired info stats: missing = 9436; contradictional = 8 1:33:24.042 15G / 27G INFO PairInfoImprover (pair_info_improver.hpp : 103) Paired info stats: missing = 1713; contradictional = 12 1:33:24.042 15G / 27G INFO StageManager (stage.cpp : 126) STAGE == Repeat Resolving 1:33:24.042 15G / 27G INFO General (repeat_resolving.cpp : 68) Using Path-Extend repeat resolving 1:33:44.034 16G / 27G INFO General (launcher.cpp : 399) ExSPAnder repeat resolving tool started 1:34:29.290 31G / 31G INFO General (launcher.cpp : 357) Creating main extenders, unique edge length = 2000 1:34:35.480 31G / 31G INFO General (extenders_logic.cpp : 415) Using 1 paired-end library 1:34:35.480 31G / 31G INFO General (extenders_logic.cpp : 416) Using 1 paired-end scaffolding library 1:34:35.480 31G / 31G INFO General (extenders_logic.cpp : 417) Using 0 single read libraries 1:34:35.480 31G / 31G INFO General (launcher.cpp : 385) Total number of extenders is 4 1:34:35.480 31G / 31G INFO PathExtender (path_extender.hpp :1031) Processed 0 paths from 3733773 (0%) 1:34:35.532 31G / 31G INFO PathExtender (path_extender.hpp :1029) Processed 128 paths from 3733773 (0%) 1:34:35.559 31G / 31G INFO PathExtender (path_extender.hpp :1029) Processed 256 paths from 3733773 (0%) 1:34:35.611 31G / 31G INFO PathExtender (path_extender.hpp :1029) Processed 512 paths from 3733773 (0%) 1:34:35.696 31G / 31G INFO PathExtender (path_extender.hpp :1029) Processed 1024 paths from 3733773 (0%) 1:34:35.872 31G / 31G INFO PathExtender (path_extender.hpp :1029) Processed 2048 paths from 3733773 (0%) 1:34:36.203 31G / 31G INFO PathExtender (path_extender.hpp :1029) Processed 4096 paths from 3733773 (0%) 1:34:36.856 31G / 31G INFO PathExtender (path_extender.hpp :1029) Processed 8192 paths from 3733773 (0%) 1:34:37.983 31G / 31G INFO PathExtender (path_extender.hpp :1029) Processed 16384 paths from 3733773 (0%) 1:34:39.842 31G / 31G INFO PathExtender (path_extender.hpp :1029) Processed 32768 paths from 3733773 (0%) 1:34:42.570 31G / 31G INFO PathExtender (path_extender.hpp :1029) Processed 65536 paths from 3733773 (1%) 1:34:46.722 32G / 32G INFO PathExtender (path_extender.hpp :1029) Processed 131072 paths from 3733773 (3%) 1:34:51.202 32G / 32G INFO PathExtender (path_extender.hpp :1029) Processed 262144 paths from 3733773 (7%) 1:34:54.060 32G / 32G INFO PathExtender (path_extender.hpp :1031) Processed 373378 paths from 3733773 (10%) 1:34:58.901 33G / 33G INFO PathExtender (path_extender.hpp :1029) Processed 524288 paths from 3733773 (14%) 1:35:05.091 34G / 34G INFO PathExtender (path_extender.hpp :1031) Processed 746756 paths from 3733773 (20%) 1:35:11.133 35G / 35G INFO PathExtender (path_extender.hpp :1029) Processed 1048576 paths from 3733773 (28%) 1:35:12.448 35G / 35G INFO PathExtender (path_extender.hpp :1031) Processed 1120134 paths from 3733773 (30%) 1:35:19.365 37G / 37G INFO PathExtender (path_extender.hpp :1031) Processed 1493512 paths from 3733773 (40%) 1:35:26.358 38G / 38G INFO PathExtender (path_extender.hpp :1031) Processed 1866890 paths from 3733773 (50%) 1:35:30.604 39G / 39G INFO PathExtender (path_extender.hpp :1029) Processed 2097152 paths from 3733773 (56%) 1:35:33.228 40G / 40G INFO PathExtender (path_extender.hpp :1031) Processed 2240268 paths from 3733773 (60%) 1:35:40.232 41G / 41G INFO PathExtender (path_extender.hpp :1031) Processed 2613646 paths from 3733773 (70%) 1:35:47.068 43G / 43G INFO PathExtender (path_extender.hpp :1031) Processed 2987024 paths from 3733773 (80%) 1:35:54.011 44G / 44G INFO PathExtender (path_extender.hpp :1031) Processed 3360402 paths from 3733773 (90%) 3:30:11.901 46G / 46G INFO General (launcher.cpp : 248) Traversing tandem repeats 3:30:50.732 46G / 47G INFO General (launcher.cpp : 258) Traversed 2 loops 3:30:50.732 46G / 47G INFO General (launcher.cpp : 391) Closing gaps in paths 3:30:53.617 47G / 47G INFO General (launcher.cpp : 395) Gap closing completed 5:54:55.908 62G / 62G INFO General (launcher.cpp : 445) ExSPAnder repeat resolving tool finished 5:55:31.642 44G / 62G INFO StageManager (stage.cpp : 126) STAGE == Contig Output 5:55:31.642 44G / 62G INFO General (contig_output.hpp : 478) Outputting contigs to /data/home/pitagoras/public_html/gigas/transcriptome/rnaSpades/spadesRNA/output//K55/before_rr.fasta 5:56:09.512 44G / 62G INFO General (contig_output.hpp : 518) Outputting graph to /data/home/pitagoras/public_html/gigas/transcriptome/rnaSpades/spadesRNA/output//K55/assembly_graph.fastg 5:58:06.171 45G / 62G INFO PathExtendIO (bidirectional_path_output.: 31) Writing contigs to /data/home/pitagoras/public_html/gigas/transcriptome/rnaSpades/spadesRNA/output//K55/transcripts 5:58:21.042 45G / 62G INFO General (contig_output.hpp : 509) Outputting graph to /data/home/pitagoras/public_html/gigas/transcriptome/rnaSpades/spadesRNA/output//K55/assembly_graph.gfa 5:59:04.666 44G / 62G INFO General (launch.hpp : 136) SPAdes finished 5:59:53.483 28G / 62G INFO General (main.cpp : 109) Assembling time: 5 hours 59 minutes 53 seconds ===== Assembling finished. Used k-mer sizes: 55 * Corrected reads are in /data/home/pitagoras/public_html/gigas/transcriptome/rnaSpades/spadesRNA/output/corrected/ * Assembled transcripts are in /data/home/pitagoras/public_html/gigas/transcriptome/rnaSpades/spadesRNA/output/transcripts.fasta * Paths in the assembly graph corresponding to the transcripts are in /data/home/pitagoras/public_html/gigas/transcriptome/rnaSpades/spadesRNA/output/transcripts.paths ======= SPAdes pipeline finished. SPAdes log can be found here: /data/home/pitagoras/public_html/gigas/transcriptome/rnaSpades/spadesRNA/output/spades.log Thank you for using SPAdes!