Command line: /home/administrator/SPAdes-3.13.0-Linux/bin/spades.py --meta -k 21,41,71,101,127 -m 230 -t 32 -o /DATA/markop/CPB_metaSpades/output -1 /DATA/markop/CPB_metaSpades/input/unmerged_1.fq -2 /DATA/markop/CPB_metaSpades/input/unmerged_2.fq -s /DATA/markop/CPB_metaSpades/input/merged.fq System information: SPAdes version: 3.13.0 Python version: 2.7.15 OS: Linux-4.13.0-41-generic-x86_64-with-debian-stretch-sid Output dir: /DATA/markop/CPB_metaSpades/output Mode: read error correction and assembling Debug mode is turned OFF Dataset parameters: Metagenomic mode Reads: Library number: 1, library type: paired-end orientation: fr left reads: ['/DATA/markop/CPB_metaSpades/input/unmerged_1.fq'] right reads: ['/DATA/markop/CPB_metaSpades/input/unmerged_2.fq'] interlaced reads: not specified single reads: ['/DATA/markop/CPB_metaSpades/input/merged.fq'] merged reads: not specified Read error correction parameters: Iterations: 1 PHRED offset will be auto-detected Corrected reads will be compressed Assembly parameters: k: [21, 41, 71, 101, 127] Repeat resolution is enabled Mismatch careful mode is turned OFF MismatchCorrector will be SKIPPED Coverage cutoff is turned OFF Other parameters: Dir for temp files: /DATA/markop/CPB_metaSpades/output/tmp Threads: 32 Memory limit (in Gb): 230 ======= SPAdes pipeline started. Log can be found here: /DATA/markop/CPB_metaSpades/output/spades.log ===== Read error correction started. == Running read error correction tool: /home/administrator/SPAdes-3.13.0-Linux/bin/spades-hammer /DATA/markop/CPB_metaSpades/output/corrected/configs/config.info 0:00:00.000 4M / 4M INFO General (main.cpp : 75) Starting BayesHammer, built from refs/heads/spades_3.13.0, git revision 8ea46659e9b2aca35444a808db550ac333006f8b 0:00:00.000 4M / 4M INFO General (main.cpp : 76) Loading config from /DATA/markop/CPB_metaSpades/output/corrected/configs/config.info 0:00:00.001 4M / 4M INFO General (main.cpp : 78) Maximum # of threads to use (adjusted due to OMP capabilities): 32 0:00:00.001 4M / 4M INFO General (memory_limit.cpp : 49) Memory limit set to 230 Gb 0:00:00.001 4M / 4M INFO General (main.cpp : 86) Trying to determine PHRED offset 0:00:00.002 4M / 4M INFO General (main.cpp : 92) Determined value is 33 0:00:00.002 4M / 4M INFO General (hammer_tools.cpp : 36) Hamming graph threshold tau=1, k=21, subkmer positions = [ 0 10 ] 0:00:00.002 4M / 4M INFO General (main.cpp : 113) Size of aux. kmer data 24 bytes === ITERATION 0 begins === 0:00:00.002 4M / 4M INFO K-mer Counting (kmer_data.cpp : 280) Estimating k-mer count 0:00:00.357 516M / 516M INFO K-mer Counting (kmer_data.cpp : 285) Processing /DATA/markop/CPB_metaSpades/input/unmerged_1.fq 0:10:52.896 640M / 640M INFO K-mer Counting (kmer_data.cpp : 294) Processed 135321241 reads 0:10:52.896 640M / 640M INFO K-mer Counting (kmer_data.cpp : 285) Processing /DATA/markop/CPB_metaSpades/input/unmerged_2.fq 0:21:16.796 640M / 640M INFO K-mer Counting (kmer_data.cpp : 294) Processed 270642482 reads 0:21:16.797 640M / 640M INFO K-mer Counting (kmer_data.cpp : 285) Processing /DATA/markop/CPB_metaSpades/input/merged.fq 1:21:39.897 644M / 648M INFO K-mer Counting (kmer_data.cpp : 294) Processed 833145089 reads 1:21:39.897 644M / 648M INFO K-mer Counting (kmer_data.cpp : 299) Total 833145089 reads processed 1:21:42.995 644M / 648M INFO K-mer Counting (kmer_data.cpp : 306) Estimated 5536627456 distinct kmers 1:21:43.028 132M / 648M INFO K-mer Counting (kmer_data.cpp : 311) Filtering singleton k-mers 42 8 0 nslots: 17179869184 bits per slot: 8 range: 0000040000000000 1:21:43.028 20G / 20G INFO K-mer Counting (kmer_data.cpp : 317) Processing /DATA/markop/CPB_metaSpades/input/unmerged_1.fq 3:35:39.885 20G / 20G INFO K-mer Counting (kmer_data.cpp : 326) Processed 135321241 reads 3:35:39.885 20G / 20G INFO K-mer Counting (kmer_data.cpp : 317) Processing /DATA/markop/CPB_metaSpades/input/unmerged_2.fq 5:19:27.930 20G / 20G INFO K-mer Counting (kmer_data.cpp : 326) Processed 270642482 reads 5:19:27.930 20G / 20G INFO K-mer Counting (kmer_data.cpp : 317) Processing /DATA/markop/CPB_metaSpades/input/merged.fq 23:01:29.626 20G / 20G INFO K-mer Counting (kmer_data.cpp : 326) Processed 833145089 reads 23:01:29.626 20G / 20G INFO K-mer Counting (kmer_data.cpp : 331) Total 833145089 reads processed 23:01:29.686 20G / 20G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 23:01:29.686 20G / 20G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 512 files using 32 threads. This might take a while. 23:01:29.687 20G / 20G INFO General (file_limit.hpp : 32) Open file limit set to 10000 23:01:29.687 20G / 20G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.18331 Gb 23:01:29.687 20G / 20G INFO General (kmer_splitters.hpp : 97) Using cell size of 131072 23:01:29.811 38G / 38G INFO K-mer Splitting (kmer_data.cpp : 97) Processing /DATA/markop/CPB_metaSpades/input/unmerged_1.fq 23:02:11.417 38G / 38G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 6886928 reads 23:03:13.120 38G / 38G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 14453232 reads 23:04:22.934 38G / 38G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 22335640 reads 23:05:27.908 38G / 38G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 30039291 reads 23:06:34.280 38G / 38G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 37323794 reads 23:07:42.614 38G / 38G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 44905083 reads 23:08:50.710 38G / 38G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 52824642 reads 23:10:02.256 38G / 38G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 60678220 reads 23:11:07.680 38G / 38G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 68460414 reads 23:12:16.978 38G / 38G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 76009455 reads 23:13:04.491 38G / 38G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 80542103 reads 23:14:05.077 38G / 38G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 88311649 reads 23:20:50.814 38G / 38G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 135321241 reads 23:20:50.814 38G / 38G INFO K-mer Splitting (kmer_data.cpp : 97) Processing /DATA/markop/CPB_metaSpades/input/unmerged_2.fq 23:40:53.864 38G / 38G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 270642482 reads 23:40:53.864 38G / 38G INFO K-mer Splitting (kmer_data.cpp : 97) Processing /DATA/markop/CPB_metaSpades/input/merged.fq 24:42:25.612 38G / 38G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 540135745 reads 25:47:06.454 38G / 39G INFO K-mer Splitting (kmer_data.cpp : 112) Total 833145089 reads processed 25:47:08.077 20G / 39G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 26:40:38.728 20G / 39G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 3120000706 kmers in total. 26:40:38.729 20G / 39G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 26:41:02.440 20G / 39G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 26:43:10.220 21G / 39G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 26:47:26.435 21G / 39G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 1446784560 bytes occupied (3.7097 bits per kmer). 26:47:28.840 1G / 39G INFO K-mer Counting (kmer_data.cpp : 356) Arranging kmers in hash map order 26:49:53.105 48G / 48G INFO General (main.cpp : 148) Clustering Hamming graph. 28:02:01.240 48G / 48G INFO General (main.cpp : 155) Extracting clusters 28:47:48.122 48G / 129G INFO General (main.cpp : 167) Clustering done. Total clusters: 1532504054 28:47:50.197 24G / 129G INFO K-mer Counting (kmer_data.cpp : 376) Collecting K-mer information, this takes a while. 28:48:29.227 94G / 129G INFO K-mer Counting (kmer_data.cpp : 382) Processing /DATA/markop/CPB_metaSpades/input/unmerged_1.fq 29:10:47.912 94G / 129G INFO K-mer Counting (kmer_data.cpp : 382) Processing /DATA/markop/CPB_metaSpades/input/unmerged_2.fq 29:29:21.484 94G / 129G INFO K-mer Counting (kmer_data.cpp : 382) Processing /DATA/markop/CPB_metaSpades/input/merged.fq 32:36:57.339 94G / 129G INFO K-mer Counting (kmer_data.cpp : 389) Collection done, postprocessing. 32:37:16.092 94G / 129G INFO K-mer Counting (kmer_data.cpp : 403) There are 3120000706 kmers in total. Among them 3041950 (0.0974984%) are singletons. 32:37:16.092 94G / 129G INFO General (main.cpp : 173) Subclustering Hamming graph 35:14:41.443 94G / 129G INFO Hamming Subclustering (kmer_cluster.cpp : 649) Subclustering done. Total 359281 non-read kmers were generated. 35:14:41.443 94G / 129G INFO Hamming Subclustering (kmer_cluster.cpp : 650) Subclustering statistics: 35:14:41.449 94G / 129G INFO Hamming Subclustering (kmer_cluster.cpp : 651) Total singleton hamming clusters: 1191444616. Among them 1184615962 (99.4269%) are good 35:14:41.449 94G / 129G INFO Hamming Subclustering (kmer_cluster.cpp : 652) Total singleton subclusters: 518460250. Among them 518442934 (99.9967%) are good 35:14:41.449 94G / 129G INFO Hamming Subclustering (kmer_cluster.cpp : 653) Total non-singleton subcluster centers: 272307007. Among them 270571702 (99.3627%) are good 35:14:41.449 94G / 129G INFO Hamming Subclustering (kmer_cluster.cpp : 654) Average size of non-trivial subcluster: 7.08571 kmers 35:14:41.449 94G / 129G INFO Hamming Subclustering (kmer_cluster.cpp : 655) Average number of sub-clusters per non-singleton cluster: 2.31856 35:14:41.449 94G / 129G INFO Hamming Subclustering (kmer_cluster.cpp : 656) Total solid k-mers: 1973630598 35:14:41.450 94G / 129G INFO Hamming Subclustering (kmer_cluster.cpp : 657) Substitution probabilities: [4,4]((0.875603,0.0291038,0.043367,0.0519263),(0.051958,0.835411,0.0284625,0.0841685),(0.0830735,0.0281767,0.836087,0.0526624),(0.0512449,0.0429051,0.028877,0.876973)) 35:14:43.418 94G / 129G INFO General (main.cpp : 178) Finished clustering. 35:14:43.424 94G / 129G INFO General (main.cpp : 197) Starting solid k-mers expansion in 32 threads. 36:42:13.437 94G / 129G INFO General (main.cpp : 218) Solid k-mers iteration 0 produced 763959153 new k-mers. 38:07:06.720 94G / 129G INFO General (main.cpp : 218) Solid k-mers iteration 1 produced 41154402 new k-mers. 39:31:49.536 94G / 129G INFO General (main.cpp : 218) Solid k-mers iteration 2 produced 6499177 new k-mers. 40:56:26.918 94G / 129G INFO General (main.cpp : 218) Solid k-mers iteration 3 produced 1137087 new k-mers. 42:21:08.920 94G / 129G INFO General (main.cpp : 218) Solid k-mers iteration 4 produced 211594 new k-mers. 43:45:43.820 94G / 129G INFO General (main.cpp : 218) Solid k-mers iteration 5 produced 42244 new k-mers. 45:10:18.248 94G / 129G INFO General (main.cpp : 218) Solid k-mers iteration 6 produced 10903 new k-mers. 46:35:08.228 94G / 129G INFO General (main.cpp : 218) Solid k-mers iteration 7 produced 1877 new k-mers. 47:59:55.424 94G / 129G INFO General (main.cpp : 218) Solid k-mers iteration 8 produced 265 new k-mers. 49:24:51.296 94G / 129G INFO General (main.cpp : 218) Solid k-mers iteration 9 produced 51 new k-mers. 50:49:43.040 94G / 129G INFO General (main.cpp : 218) Solid k-mers iteration 10 produced 0 new k-mers. 50:49:43.040 94G / 129G INFO General (main.cpp : 222) Solid k-mers finalized 50:49:43.048 94G / 129G INFO General (hammer_tools.cpp : 220) Starting read correction in 32 threads. 50:49:43.048 94G / 129G INFO General (hammer_tools.cpp : 233) Correcting pair of reads: /DATA/markop/CPB_metaSpades/input/unmerged_1.fq and /DATA/markop/CPB_metaSpades/input/unmerged_2.fq 50:50:03.349 97G / 129G INFO General (hammer_tools.cpp : 168) Prepared batch 0 of 3200000 reads. 50:50:22.216 98G / 129G INFO General (hammer_tools.cpp : 175) Processed batch 0 50:50:28.083 98G / 129G INFO General (hammer_tools.cpp : 185) Written batch 0 50:51:09.378 98G / 129G INFO General (hammer_tools.cpp : 168) Prepared batch 1 of 3200000 reads. 50:51:27.236 98G / 129G INFO General (hammer_tools.cpp : 175) Processed batch 1 50:51:33.572 98G / 129G INFO General (hammer_tools.cpp : 185) Written batch 1 50:52:14.496 98G / 129G INFO General (hammer_tools.cpp : 168) Prepared batch 2 of 3200000 reads. 50:52:33.396 98G / 129G INFO General (hammer_tools.cpp : 175) Processed batch 2 50:52:40.541 98G / 129G INFO General (hammer_tools.cpp : 185) Written batch 2 50:53:21.505 98G / 129G INFO General (hammer_tools.cpp : 168) Prepared batch 3 of 3200000 reads. 50:53:40.139 98G / 129G INFO General (hammer_tools.cpp : 175) Processed batch 3 50:53:46.364 98G / 129G INFO General (hammer_tools.cpp : 185) Written batch 3 50:54:28.838 98G / 129G INFO General (hammer_tools.cpp : 168) Prepared batch 4 of 3200000 reads. 50:54:47.792 98G / 129G INFO General (hammer_tools.cpp : 175) Processed batch 4 50:54:54.052 98G / 129G INFO General (hammer_tools.cpp : 185) Written batch 4 50:55:34.207 98G / 129G INFO General (hammer_tools.cpp : 168) Prepared batch 5 of 3200000 reads. 50:55:52.871 98G / 129G INFO General (hammer_tools.cpp : 175) Processed batch 5 50:55:59.817 98G / 129G INFO General (hammer_tools.cpp : 185) Written batch 5 50:56:41.705 98G / 129G INFO General (hammer_tools.cpp : 168) Prepared batch 6 of 3200000 reads. 50:57:00.074 98G / 129G INFO General (hammer_tools.cpp : 175) Processed batch 6 50:57:06.367 98G / 129G INFO General (hammer_tools.cpp : 185) Written batch 6 50:57:48.069 98G / 129G INFO General (hammer_tools.cpp : 168) Prepared batch 7 of 3200000 reads. 50:58:07.128 98G / 129G INFO General (hammer_tools.cpp : 175) Processed batch 7 50:58:13.269 98G / 129G INFO General (hammer_tools.cpp : 185) Written batch 7 50:58:52.791 98G / 129G INFO General (hammer_tools.cpp : 168) Prepared batch 8 of 3200000 reads. 50:59:11.550 98G / 129G INFO General (hammer_tools.cpp : 175) Processed batch 8 50:59:18.660 98G / 129G INFO General (hammer_tools.cpp : 185) Written batch 8 51:00:00.687 98G / 129G INFO General (hammer_tools.cpp : 168) Prepared batch 9 of 3200000 reads. 51:00:19.154 98G / 129G INFO General (hammer_tools.cpp : 175) Processed batch 9 51:00:25.410 98G / 129G INFO General (hammer_tools.cpp : 185) Written batch 9 51:01:07.420 98G / 129G INFO General (hammer_tools.cpp : 168) Prepared batch 10 of 3200000 reads. 51:01:26.156 98G / 129G INFO General (hammer_tools.cpp : 175) Processed batch 10 51:01:32.287 98G / 129G INFO General (hammer_tools.cpp : 185) Written batch 10 51:02:12.014 98G / 129G INFO General (hammer_tools.cpp : 168) Prepared batch 11 of 3200000 reads. 51:02:30.620 98G / 129G INFO General (hammer_tools.cpp : 175) Processed batch 11 51:02:37.882 98G / 129G INFO General (hammer_tools.cpp : 185) Written batch 11 51:03:19.375 98G / 129G INFO General (hammer_tools.cpp : 168) Prepared batch 12 of 3200000 reads. 51:03:37.594 98G / 129G INFO General (hammer_tools.cpp : 175) Processed batch 12 51:03:44.021 98G / 129G INFO General (hammer_tools.cpp : 185) Written batch 12 51:04:26.269 98G / 129G INFO General (hammer_tools.cpp : 168) Prepared batch 13 of 3200000 reads. 51:04:44.784 98G / 129G INFO General (hammer_tools.cpp : 175) Processed batch 13 51:04:51.009 98G / 129G INFO General (hammer_tools.cpp : 185) Written batch 13 51:05:31.579 98G / 129G INFO General (hammer_tools.cpp : 168) Prepared batch 14 of 3200000 reads. 51:05:50.322 98G / 129G INFO General (hammer_tools.cpp : 175) Processed batch 14 51:05:57.847 98G / 129G INFO General (hammer_tools.cpp : 185) Written batch 14 51:06:39.753 98G / 129G INFO General (hammer_tools.cpp : 168) Prepared batch 15 of 3200000 reads. 51:06:58.305 98G / 129G INFO General (hammer_tools.cpp : 175) Processed batch 15 51:07:04.828 98G / 129G INFO General (hammer_tools.cpp : 185) Written batch 15 51:07:48.024 98G / 129G INFO General (hammer_tools.cpp : 168) Prepared batch 16 of 3200000 reads. 51:08:06.884 98G / 129G INFO General (hammer_tools.cpp : 175) Processed batch 16 51:08:13.196 98G / 129G INFO General (hammer_tools.cpp : 185) Written batch 16 51:08:53.342 98G / 129G INFO General (hammer_tools.cpp : 168) Prepared batch 17 of 3200000 reads. 51:09:11.916 98G / 129G INFO General (hammer_tools.cpp : 175) Processed batch 17 51:09:18.803 98G / 129G INFO General (hammer_tools.cpp : 185) Written batch 17 51:10:00.182 98G / 129G INFO General (hammer_tools.cpp : 168) Prepared batch 18 of 3200000 reads. 51:10:18.464 98G / 129G INFO General (hammer_tools.cpp : 175) Processed batch 18 51:10:24.589 98G / 129G INFO General (hammer_tools.cpp : 185) Written batch 18 51:11:08.720 98G / 129G INFO General (hammer_tools.cpp : 168) Prepared batch 19 of 3200000 reads. 51:11:27.563 98G / 129G INFO General (hammer_tools.cpp : 175) Processed batch 19 51:11:34.099 98G / 129G INFO General (hammer_tools.cpp : 185) Written batch 19 51:12:15.723 98G / 129G INFO General (hammer_tools.cpp : 168) Prepared batch 20 of 3200000 reads. 51:12:34.460 98G / 129G INFO General (hammer_tools.cpp : 175) Processed batch 20 51:12:40.545 98G / 129G INFO General (hammer_tools.cpp : 185) Written batch 20 51:13:21.725 98G / 129G INFO General (hammer_tools.cpp : 168) Prepared batch 21 of 3200000 reads. 51:13:40.916 98G / 129G INFO General (hammer_tools.cpp : 175) Processed batch 21 51:13:47.007 98G / 129G INFO General (hammer_tools.cpp : 185) Written batch 21 51:14:31.003 98G / 129G INFO General (hammer_tools.cpp : 168) Prepared batch 22 of 3200000 reads. 51:14:49.882 98G / 129G INFO General (hammer_tools.cpp : 175) Processed batch 22 51:14:56.461 98G / 129G INFO General (hammer_tools.cpp : 185) Written batch 22 51:15:40.041 98G / 129G INFO General (hammer_tools.cpp : 168) Prepared batch 23 of 3200000 reads. 51:15:57.992 98G / 129G INFO General (hammer_tools.cpp : 175) Processed batch 23 51:16:04.131 98G / 129G INFO General (hammer_tools.cpp : 185) Written batch 23 51:16:47.324 98G / 129G INFO General (hammer_tools.cpp : 168) Prepared batch 24 of 3200000 reads. 51:17:05.765 98G / 129G INFO General (hammer_tools.cpp : 175) Processed batch 24 51:17:11.736 98G / 129G INFO General (hammer_tools.cpp : 185) Written batch 24 51:17:55.060 98G / 129G INFO General (hammer_tools.cpp : 168) Prepared batch 25 of 3200000 reads. 51:18:14.105 98G / 129G INFO General (hammer_tools.cpp : 175) Processed batch 25 51:18:21.042 98G / 129G INFO General (hammer_tools.cpp : 185) Written batch 25 51:19:03.235 98G / 129G INFO General (hammer_tools.cpp : 168) Prepared batch 26 of 3200000 reads. 51:19:21.500 98G / 129G INFO General (hammer_tools.cpp : 175) Processed batch 26 51:19:27.621 98G / 129G INFO General (hammer_tools.cpp : 185) Written batch 26 51:20:07.278 98G / 129G INFO General (hammer_tools.cpp : 168) Prepared batch 27 of 3200000 reads. 51:20:25.742 98G / 129G INFO General (hammer_tools.cpp : 175) Processed batch 27 51:20:31.852 98G / 129G INFO General (hammer_tools.cpp : 185) Written batch 27 51:21:16.180 98G / 129G INFO General (hammer_tools.cpp : 168) Prepared batch 28 of 3200000 reads. 51:21:36.957 98G / 129G INFO General (hammer_tools.cpp : 175) Processed batch 28 51:21:44.340 98G / 129G INFO General (hammer_tools.cpp : 185) Written batch 28 51:22:29.358 98G / 129G INFO General (hammer_tools.cpp : 168) Prepared batch 29 of 3200000 reads. 51:22:47.224 98G / 129G INFO General (hammer_tools.cpp : 175) Processed batch 29 51:22:53.287 98G / 129G INFO General (hammer_tools.cpp : 185) Written batch 29 51:23:35.062 98G / 129G INFO General (hammer_tools.cpp : 168) Prepared batch 30 of 3200000 reads. 51:23:54.250 98G / 129G INFO General (hammer_tools.cpp : 175) Processed batch 30 51:24:00.530 98G / 129G INFO General (hammer_tools.cpp : 185) Written batch 30 51:24:43.207 98G / 129G INFO General (hammer_tools.cpp : 168) Prepared batch 31 of 3200000 reads. 51:25:01.815 98G / 129G INFO General (hammer_tools.cpp : 175) Processed batch 31 51:25:08.380 98G / 129G INFO General (hammer_tools.cpp : 185) Written batch 31 51:25:51.489 98G / 129G INFO General (hammer_tools.cpp : 168) Prepared batch 32 of 3200000 reads. 51:26:09.736 98G / 129G INFO General (hammer_tools.cpp : 175) Processed batch 32 51:26:15.919 98G / 129G INFO General (hammer_tools.cpp : 185) Written batch 32 51:26:57.692 98G / 129G INFO General (hammer_tools.cpp : 168) Prepared batch 33 of 3200000 reads. 51:27:16.127 98G / 129G INFO General (hammer_tools.cpp : 175) Processed batch 33 51:27:22.642 98G / 129G INFO General (hammer_tools.cpp : 185) Written batch 33 51:28:05.164 98G / 129G INFO General (hammer_tools.cpp : 168) Prepared batch 34 of 3200000 reads. 51:28:23.463 98G / 129G INFO General (hammer_tools.cpp : 175) Processed batch 34 51:28:29.875 98G / 129G INFO General (hammer_tools.cpp : 185) Written batch 34 51:29:12.884 98G / 129G INFO General (hammer_tools.cpp : 168) Prepared batch 35 of 3200000 reads. 51:29:31.241 98G / 129G INFO General (hammer_tools.cpp : 175) Processed batch 35 51:29:37.439 98G / 129G INFO General (hammer_tools.cpp : 185) Written batch 35 51:30:20.534 98G / 129G INFO General (hammer_tools.cpp : 168) Prepared batch 36 of 3200000 reads. 51:30:39.210 98G / 129G INFO General (hammer_tools.cpp : 175) Processed batch 36 51:30:46.066 98G / 129G INFO General (hammer_tools.cpp : 185) Written batch 36 51:31:27.669 98G / 129G INFO General (hammer_tools.cpp : 168) Prepared batch 37 of 3200000 reads. 51:31:46.302 98G / 129G INFO General (hammer_tools.cpp : 175) Processed batch 37 51:31:52.534 98G / 129G INFO General (hammer_tools.cpp : 185) Written batch 37 51:32:35.492 98G / 129G INFO General (hammer_tools.cpp : 168) Prepared batch 38 of 3200000 reads. 51:32:54.932 98G / 129G INFO General (hammer_tools.cpp : 175) Processed batch 38 51:33:01.115 98G / 129G INFO General (hammer_tools.cpp : 185) Written batch 38 51:33:45.186 98G / 129G INFO General (hammer_tools.cpp : 168) Prepared batch 39 of 3200000 reads. 51:34:03.756 98G / 129G INFO General (hammer_tools.cpp : 175) Processed batch 39 51:34:10.632 98G / 129G INFO General (hammer_tools.cpp : 185) Written batch 39 51:34:52.043 98G / 129G INFO General (hammer_tools.cpp : 168) Prepared batch 40 of 3200000 reads. 51:35:10.396 98G / 129G INFO General (hammer_tools.cpp : 175) Processed batch 40 51:35:16.421 98G / 129G INFO General (hammer_tools.cpp : 185) Written batch 40 51:36:00.297 98G / 129G INFO General (hammer_tools.cpp : 168) Prepared batch 41 of 3200000 reads. 51:36:18.716 98G / 129G INFO General (hammer_tools.cpp : 175) Processed batch 41 51:36:25.018 98G / 129G INFO General (hammer_tools.cpp : 185) Written batch 41 51:36:32.972 98G / 129G INFO General (hammer_tools.cpp : 168) Prepared batch 42 of 921241 reads. 51:36:38.740 98G / 129G INFO General (hammer_tools.cpp : 175) Processed batch 42 51:36:40.572 98G / 129G INFO General (hammer_tools.cpp : 185) Written batch 42 51:36:43.629 94G / 129G INFO General (hammer_tools.cpp : 264) Correcting single reads: /DATA/markop/CPB_metaSpades/input/merged.fq 51:37:06.719 96G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 0 of 3200000 reads. 51:37:19.232 97G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 0 51:37:24.031 97G / 129G INFO General (hammer_tools.cpp : 136) Written batch 0 51:37:36.113 98G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 1 of 3200000 reads. 51:37:48.160 98G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 1 51:37:52.898 98G / 129G INFO General (hammer_tools.cpp : 136) Written batch 1 51:38:02.947 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 2 of 3200000 reads. 51:38:15.362 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 2 51:38:21.490 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 2 51:38:57.694 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 3 of 3200000 reads. 51:39:09.747 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 3 51:39:14.544 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 3 51:39:25.256 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 4 of 3200000 reads. 51:39:37.879 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 4 51:39:42.798 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 4 51:40:06.249 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 5 of 3200000 reads. 51:40:18.616 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 5 51:40:23.438 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 5 51:40:46.114 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 6 of 3200000 reads. 51:40:58.286 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 6 51:41:03.576 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 6 51:41:20.793 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 7 of 3200000 reads. 51:41:33.010 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 7 51:41:38.036 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 7 51:41:47.988 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 8 of 3200000 reads. 51:42:00.261 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 8 51:42:05.627 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 8 51:42:37.988 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 9 of 3200000 reads. 51:42:50.164 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 9 51:42:55.870 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 9 51:43:06.925 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 10 of 3200000 reads. 51:43:19.053 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 10 51:43:23.942 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 10 51:43:46.927 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 11 of 3200000 reads. 51:43:59.338 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 11 51:44:05.373 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 11 51:44:29.685 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 12 of 3200000 reads. 51:44:42.408 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 12 51:44:47.197 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 12 51:44:56.710 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 13 of 3200000 reads. 51:45:09.069 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 13 51:45:14.200 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 13 51:45:38.293 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 14 of 3200000 reads. 51:45:50.863 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 14 51:45:55.720 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 14 51:46:06.412 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 15 of 3200000 reads. 51:46:18.732 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 15 51:46:23.499 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 15 51:46:33.299 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 16 of 3200000 reads. 51:46:48.275 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 16 51:46:54.248 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 16 51:47:24.289 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 17 of 3200000 reads. 51:47:36.698 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 17 51:47:41.515 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 17 51:47:52.376 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 18 of 3200000 reads. 51:48:05.152 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 18 51:48:11.529 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 18 51:48:34.904 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 19 of 3200000 reads. 51:48:47.192 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 19 51:48:52.012 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 19 51:49:15.433 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 20 of 3200000 reads. 51:49:27.814 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 20 51:49:32.664 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 20 51:49:43.449 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 21 of 3200000 reads. 51:49:56.458 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 21 51:50:01.921 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 21 51:50:28.117 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 22 of 3200000 reads. 51:50:40.601 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 22 51:50:45.453 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 22 51:50:56.196 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 23 of 3200000 reads. 51:51:08.493 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 23 51:51:13.750 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 23 51:51:37.352 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 24 of 3200000 reads. 51:51:49.612 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 24 51:51:54.457 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 24 51:52:04.982 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 25 of 3200000 reads. 51:52:17.831 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 25 51:52:24.029 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 25 51:52:47.068 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 26 of 3200000 reads. 51:52:59.350 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 26 51:53:04.146 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 26 51:53:28.084 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 27 of 3200000 reads. 51:53:41.430 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 27 51:53:46.306 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 27 51:54:11.139 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 28 of 3200000 reads. 51:54:23.326 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 28 51:54:28.163 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 28 51:54:38.247 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 29 of 3200000 reads. 51:54:50.569 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 29 51:54:56.129 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 29 51:55:22.160 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 30 of 3200000 reads. 51:55:34.501 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 30 51:55:39.487 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 30 51:56:02.917 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 31 of 3200000 reads. 51:56:14.912 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 31 51:56:19.844 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 31 51:56:32.131 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 32 of 3200000 reads. 51:56:44.622 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 32 51:56:50.599 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 32 51:57:00.554 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 33 of 3200000 reads. 51:57:12.744 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 33 51:57:17.885 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 33 51:57:56.302 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 34 of 3200000 reads. 51:58:09.819 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 34 51:58:15.344 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 34 51:58:39.569 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 35 of 3200000 reads. 51:58:51.482 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 35 51:58:56.566 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 35 51:59:21.508 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 36 of 3200000 reads. 51:59:34.183 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 36 51:59:39.394 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 36 51:59:49.800 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 37 of 3200000 reads. 52:00:02.251 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 37 52:00:07.379 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 37 52:00:33.086 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 38 of 3200000 reads. 52:00:45.242 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 38 52:00:50.171 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 38 52:01:01.471 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 39 of 3200000 reads. 52:01:14.032 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 39 52:01:19.471 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 39 52:01:43.193 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 40 of 3200000 reads. 52:01:55.184 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 40 52:02:00.114 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 40 52:02:10.260 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 41 of 3200000 reads. 52:02:22.456 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 41 52:02:29.453 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 41 52:02:54.042 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 42 of 3200000 reads. 52:03:06.168 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 42 52:03:11.056 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 42 52:03:35.175 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 43 of 3200000 reads. 52:03:47.549 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 43 52:03:52.441 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 43 52:04:06.040 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 44 of 3200000 reads. 52:04:18.730 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 44 52:04:23.618 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 44 52:04:34.144 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 45 of 3200000 reads. 52:04:46.317 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 45 52:04:51.348 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 45 52:05:28.137 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 46 of 3200000 reads. 52:05:40.364 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 46 52:05:46.026 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 46 52:05:57.618 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 47 of 3200000 reads. 52:06:09.698 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 47 52:06:14.984 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 47 52:06:37.822 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 48 of 3200000 reads. 52:06:50.985 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 48 52:06:57.215 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 48 52:07:20.944 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 49 of 3200000 reads. 52:07:32.949 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 49 52:07:38.092 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 49 52:07:48.628 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 50 of 3200000 reads. 52:08:01.220 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 50 52:08:07.269 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 50 52:08:35.323 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 51 of 3200000 reads. 52:08:47.489 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 51 52:08:52.443 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 51 52:09:18.201 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 52 of 3200000 reads. 52:09:30.407 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 52 52:09:35.374 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 52 52:09:45.909 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 53 of 3200000 reads. 52:09:58.387 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 53 52:10:03.999 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 53 52:10:28.033 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 54 of 3200000 reads. 52:10:40.402 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 54 52:10:45.351 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 54 52:11:10.284 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 55 of 3200000 reads. 52:11:22.324 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 55 52:11:28.210 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 55 52:11:39.942 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 56 of 3200000 reads. 52:11:52.244 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 56 52:11:57.127 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 56 52:12:07.130 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 57 of 3200000 reads. 52:12:19.443 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 57 52:12:24.498 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 57 52:13:02.443 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 58 of 3200000 reads. 52:13:14.560 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 58 52:13:19.424 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 58 52:13:44.094 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 59 of 3200000 reads. 52:13:56.586 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 59 52:14:01.525 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 59 52:14:11.749 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 60 of 3200000 reads. 52:14:23.914 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 60 52:14:29.523 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 60 52:14:54.244 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 61 of 3200000 reads. 52:15:06.796 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 61 52:15:12.221 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 61 52:15:22.976 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 62 of 3200000 reads. 52:15:35.133 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 62 52:15:41.655 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 62 52:16:04.960 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 63 of 3200000 reads. 52:16:17.100 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 63 52:16:21.999 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 63 52:16:34.649 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 64 of 3200000 reads. 52:16:47.384 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 64 52:16:53.158 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 64 52:17:04.006 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 65 of 3200000 reads. 52:17:16.228 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 65 52:17:21.808 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 65 52:17:51.532 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 66 of 3200000 reads. 52:18:03.870 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 66 52:18:08.821 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 66 52:18:20.928 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 67 of 3200000 reads. 52:18:33.360 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 67 52:18:38.625 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 67 52:19:01.678 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 68 of 3200000 reads. 52:19:13.986 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 68 52:19:18.943 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 68 52:19:44.038 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 69 of 3200000 reads. 52:19:56.546 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 69 52:20:02.177 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 69 52:20:21.668 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 70 of 3200000 reads. 52:20:33.923 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 70 52:20:38.811 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 70 52:20:49.132 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 71 of 3200000 reads. 52:21:01.585 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 71 52:21:07.343 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 71 52:21:33.769 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 72 of 3200000 reads. 52:21:45.980 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 72 52:21:50.840 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 72 52:22:15.146 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 73 of 3200000 reads. 52:22:27.338 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 73 52:22:32.238 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 73 52:22:42.780 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 74 of 3200000 reads. 52:22:55.333 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 74 52:23:01.001 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 74 52:23:25.670 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 75 of 3200000 reads. 52:23:38.060 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 75 52:23:42.984 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 75 52:23:54.294 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 76 of 3200000 reads. 52:24:06.761 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 76 52:24:12.756 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 76 52:24:36.614 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 77 of 3200000 reads. 52:24:48.782 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 77 52:24:53.801 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 77 52:25:17.940 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 78 of 3200000 reads. 52:25:30.593 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 78 52:25:36.741 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 78 52:25:48.056 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 79 of 3200000 reads. 52:25:59.960 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 79 52:26:05.333 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 79 52:26:29.268 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 80 of 3200000 reads. 52:26:41.530 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 80 52:26:46.465 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 80 52:27:12.334 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 81 of 3200000 reads. 52:27:24.480 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 81 52:27:29.373 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 81 52:27:45.407 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 82 of 3200000 reads. 52:27:58.193 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 82 52:28:03.177 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 82 52:28:13.755 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 83 of 3200000 reads. 52:28:26.399 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 83 52:28:32.293 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 83 52:29:05.237 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 84 of 3200000 reads. 52:29:19.591 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 84 52:29:24.525 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 84 52:29:50.113 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 85 of 3200000 reads. 52:30:02.621 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 85 52:30:08.747 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 85 52:30:18.690 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 86 of 3200000 reads. 52:30:30.646 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 86 52:30:36.437 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 86 52:31:01.709 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 87 of 3200000 reads. 52:31:14.388 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 87 52:31:19.362 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 87 52:31:45.138 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 88 of 3200000 reads. 52:31:57.118 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 88 52:32:02.037 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 88 52:32:13.231 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 89 of 3200000 reads. 52:32:25.403 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 89 52:32:30.387 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 89 52:32:41.186 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 90 of 3200000 reads. 52:32:53.435 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 90 52:32:59.966 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 90 52:33:35.614 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 91 of 3200000 reads. 52:33:47.685 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 91 52:33:52.732 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 91 52:34:03.906 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 92 of 3200000 reads. 52:34:16.103 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 92 52:34:22.527 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 92 52:34:46.520 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 93 of 3200000 reads. 52:34:58.776 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 93 52:35:03.814 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 93 52:35:13.887 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 94 of 3200000 reads. 52:35:26.286 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 94 52:35:32.626 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 94 52:35:59.283 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 95 of 3200000 reads. 52:36:11.539 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 95 52:36:16.519 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 95 52:36:27.570 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 96 of 3200000 reads. 52:36:39.878 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 96 52:36:45.298 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 96 52:37:09.743 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 97 of 3200000 reads. 52:37:22.114 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 97 52:37:27.375 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 97 52:37:53.028 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 98 of 3200000 reads. 52:38:05.251 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 98 52:38:10.229 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 98 52:38:20.845 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 99 of 3200000 reads. 52:38:33.048 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 99 52:38:39.466 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 99 52:39:03.735 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 100 of 3200000 reads. 52:39:15.971 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 100 52:39:20.950 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 100 52:39:32.107 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 101 of 3200000 reads. 52:39:44.364 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 101 52:39:49.456 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 101 52:40:00.565 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 102 of 3200000 reads. 52:40:12.565 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 102 52:40:17.551 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 102 52:40:57.298 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 103 of 3200000 reads. 52:41:10.031 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 103 52:41:15.039 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 103 52:41:26.089 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 104 of 3200000 reads. 52:41:38.419 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 104 52:41:44.151 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 104 52:42:10.871 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 105 of 3200000 reads. 52:42:23.266 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 105 52:42:28.240 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 105 52:42:55.214 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 106 of 3200000 reads. 52:43:07.786 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 106 52:43:13.333 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 106 52:43:24.580 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 107 of 3200000 reads. 52:43:38.297 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 107 52:43:43.243 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 107 52:43:53.761 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 108 of 3200000 reads. 52:44:05.965 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 108 52:44:12.386 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 108 52:44:50.859 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 109 of 3200000 reads. 52:45:02.917 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 109 52:45:07.894 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 109 52:45:33.391 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 110 of 3200000 reads. 52:45:46.441 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 110 52:45:51.363 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 110 52:46:03.505 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 111 of 3200000 reads. 52:46:15.474 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 111 52:46:20.464 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 111 52:46:30.744 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 112 of 3200000 reads. 52:46:43.201 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 112 52:46:49.278 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 112 52:47:26.801 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 113 of 3200000 reads. 52:47:39.354 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 113 52:47:44.792 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 113 52:48:09.813 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 114 of 3200000 reads. 52:48:22.425 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 114 52:48:27.375 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 114 52:48:39.473 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 115 of 3200000 reads. 52:48:51.741 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 115 52:48:58.467 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 115 52:49:22.311 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 116 of 3200000 reads. 52:49:34.190 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 116 52:49:39.059 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 116 52:50:04.161 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 117 of 3200000 reads. 52:50:16.400 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 117 52:50:21.435 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 117 52:50:36.414 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 118 of 3200000 reads. 52:50:48.474 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 118 52:50:53.428 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 118 52:51:03.826 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 119 of 3200000 reads. 52:51:15.695 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 119 52:51:20.773 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 119 52:52:01.765 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 120 of 3200000 reads. 52:52:14.278 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 120 52:52:19.622 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 120 52:52:45.162 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 121 of 3200000 reads. 52:52:57.703 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 121 52:53:02.684 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 121 52:53:28.591 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 122 of 3200000 reads. 52:53:41.463 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 122 52:53:47.374 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 122 52:53:57.599 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 123 of 3200000 reads. 52:54:09.721 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 123 52:54:15.392 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 123 52:54:44.034 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 124 of 3200000 reads. 52:54:56.687 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 124 52:55:02.238 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 124 52:55:27.931 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 125 of 3200000 reads. 52:55:40.264 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 125 52:55:45.175 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 125 52:56:09.619 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 126 of 3200000 reads. 52:56:22.321 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 126 52:56:27.256 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 126 52:56:37.984 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 127 of 3200000 reads. 52:56:50.581 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 127 52:56:56.615 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 127 52:57:27.401 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 128 of 3200000 reads. 52:57:40.102 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 128 52:57:44.986 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 128 52:58:12.362 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 129 of 3200000 reads. 52:58:24.650 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 129 52:58:30.056 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 129 52:58:41.062 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 130 of 3200000 reads. 52:58:53.152 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 130 52:58:58.211 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 130 52:59:24.892 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 131 of 3200000 reads. 52:59:37.905 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 131 52:59:44.191 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 131 52:59:55.574 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 132 of 3200000 reads. 53:00:07.947 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 132 53:00:13.357 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 132 53:00:39.858 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 133 of 3200000 reads. 53:00:52.712 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 133 53:00:57.757 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 133 53:01:09.001 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 134 of 3200000 reads. 53:01:21.115 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 134 53:01:26.855 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 134 53:01:53.741 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 135 of 3200000 reads. 53:02:05.914 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 135 53:02:10.834 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 135 53:02:22.424 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 136 of 3200000 reads. 53:02:34.839 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 136 53:02:40.114 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 136 53:02:51.106 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 137 of 3200000 reads. 53:03:03.604 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 137 53:03:09.343 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 137 53:03:47.122 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 138 of 3200000 reads. 53:03:59.295 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 138 53:04:05.575 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 138 53:04:31.800 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 139 of 3200000 reads. 53:04:44.045 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 139 53:04:49.024 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 139 53:05:01.997 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 140 of 3200000 reads. 53:05:14.577 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 140 53:05:19.570 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 140 53:05:30.085 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 141 of 3200000 reads. 53:05:42.367 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 141 53:05:47.761 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 141 53:06:26.829 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 142 of 3200000 reads. 53:06:38.760 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 142 53:06:43.801 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 142 53:07:03.688 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 143 of 3200000 reads. 53:07:16.233 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 143 53:07:21.467 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 143 53:07:32.344 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 144 of 3200000 reads. 53:07:44.678 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 144 53:07:50.134 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 144 53:08:19.267 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 145 of 3200000 reads. 53:08:31.396 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 145 53:08:37.439 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 145 53:09:04.720 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 146 of 3200000 reads. 53:09:16.859 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 146 53:09:21.837 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 146 53:09:34.294 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 147 of 3200000 reads. 53:09:46.710 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 147 53:09:51.765 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 147 53:10:02.667 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 148 of 3200000 reads. 53:10:15.044 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 148 53:10:20.279 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 148 53:11:03.218 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 149 of 3200000 reads. 53:11:15.909 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 149 53:11:21.013 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 149 53:11:31.531 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 150 of 3200000 reads. 53:11:44.188 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 150 53:11:49.938 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 150 53:12:18.181 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 151 of 3200000 reads. 53:12:30.742 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 151 53:12:35.696 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 151 53:13:01.791 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 152 of 3200000 reads. 53:13:14.012 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 152 53:13:20.136 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 152 53:13:48.085 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 153 of 3200000 reads. 53:14:00.910 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 153 53:14:05.927 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 153 53:14:16.218 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 154 of 3200000 reads. 53:14:28.489 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 154 53:14:34.537 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 154 53:15:02.196 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 155 of 3200000 reads. 53:15:14.596 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 155 53:15:19.613 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 155 53:15:46.769 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 156 of 3200000 reads. 53:15:59.087 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 156 53:16:04.191 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 156 53:16:30.597 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 157 of 3200000 reads. 53:16:43.322 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 157 53:16:48.364 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 157 53:16:59.762 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 158 of 3200000 reads. 53:17:12.307 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 158 53:17:17.816 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 158 53:17:43.067 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 159 of 3200000 reads. 53:17:55.333 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 159 53:18:00.897 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 159 53:18:16.480 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 160 of 3200000 reads. 53:18:31.023 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 160 53:18:36.039 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 160 53:18:46.675 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 161 of 3200000 reads. 53:18:58.815 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 161 53:19:06.092 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 161 53:19:37.413 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 162 of 3200000 reads. 53:19:49.300 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 162 53:19:54.200 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 162 53:20:05.544 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 163 of 3200000 reads. 53:20:18.010 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 163 53:20:23.495 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 163 53:20:50.314 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 164 of 3200000 reads. 53:21:02.793 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 164 53:21:07.731 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 164 53:21:34.254 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 165 of 3200000 reads. 53:21:46.977 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 165 53:21:51.885 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 165 53:22:04.029 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 166 of 3200000 reads. 53:22:16.565 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 166 53:22:22.200 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 166 53:22:46.986 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 167 of 3200000 reads. 53:22:59.089 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 167 53:23:04.048 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 167 53:23:15.591 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 168 of 3200000 reads. 53:23:28.254 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 168 53:23:34.416 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 168 53:24:00.445 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 169 of 3200000 reads. 53:24:12.456 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 169 53:24:17.455 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 169 53:24:44.548 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 170 of 3200000 reads. 53:24:57.708 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 170 53:25:03.625 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 170 53:25:31.349 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 171 of 3200000 reads. 53:25:43.753 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 171 53:25:48.667 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 171 53:26:14.259 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 172 of 3200000 reads. 53:26:26.765 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 172 53:26:31.699 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 172 53:26:44.284 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 173 of 3200000 reads. 53:26:56.358 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 173 53:27:02.156 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 173 53:27:27.392 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 174 of 3200000 reads. 53:27:39.571 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 174 53:27:44.594 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 174 53:27:52.873 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 175 of 2502607 reads. 53:28:02.869 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 175 53:28:08.260 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 175 53:28:10.415 94G / 129G INFO General (hammer_tools.cpp : 274) Correction done. Changed 68218099 bases in 28721685 reads. 53:28:10.415 94G / 129G INFO General (hammer_tools.cpp : 275) Failed to correct 799344 bases out of 189800670900. 53:28:21.017 148M / 129G INFO General (main.cpp : 255) Saving corrected dataset description to /DATA/markop/CPB_metaSpades/output/corrected/corrected.yaml 53:28:21.025 148M / 129G INFO General (main.cpp : 262) All done. Exiting. == Compressing corrected reads (with pigz) == Dataset description file was created: /DATA/markop/CPB_metaSpades/output/corrected/corrected.yaml ===== Read error correction finished. ===== Assembling started. == Running assembler: K21 0:00:00.000 4M / 4M INFO General (main.cpp : 74) Loaded config from /DATA/markop/CPB_metaSpades/output/K21/configs/config.info 0:00:00.000 4M / 4M INFO General (main.cpp : 74) Loaded config from /DATA/markop/CPB_metaSpades/output/K21/configs/mda_mode.info 0:00:00.000 4M / 4M INFO General (main.cpp : 74) Loaded config from /DATA/markop/CPB_metaSpades/output/K21/configs/meta_mode.info 0:00:00.000 4M / 4M INFO General (memory_limit.cpp : 49) Memory limit set to 230 Gb 0:00:00.000 4M / 4M INFO General (main.cpp : 87) Starting SPAdes, built from refs/heads/spades_3.13.0, git revision 8ea46659e9b2aca35444a808db550ac333006f8b 0:00:00.000 4M / 4M INFO General (main.cpp : 88) Maximum k-mer length: 128 0:00:00.000 4M / 4M INFO General (main.cpp : 89) Assembling dataset (/DATA/markop/CPB_metaSpades/output/dataset.info) with K=21 0:00:00.000 4M / 4M INFO General (main.cpp : 90) Maximum # of threads to use (adjusted due to OMP capabilities): 32 0:00:00.000 4M / 4M INFO General (launch.hpp : 51) SPAdes started 0:00:00.000 4M / 4M INFO General (launch.hpp : 58) Starting from stage: construction 0:00:00.000 4M / 4M INFO General (launch.hpp : 65) Two-step RR enabled: 0 0:00:00.001 4M / 4M INFO StageManager (stage.cpp : 132) STAGE == de Bruijn graph construction 0:00:00.002 4M / 4M INFO General (read_converter.hpp : 77) Converting reads to binary format for library #0 (takes a while) 0:00:00.002 4M / 4M INFO General (read_converter.hpp : 78) Converting paired reads 0:00:00.237 80M / 80M INFO General (binary_converter.hpp : 93) 16384 reads processed 0:00:00.388 96M / 96M INFO General (binary_converter.hpp : 93) 32768 reads processed 0:00:00.682 124M / 124M INFO General (binary_converter.hpp : 93) 65536 reads processed 0:00:01.280 180M / 180M INFO General (binary_converter.hpp : 93) 131072 reads processed 0:00:02.587 292M / 292M INFO General (binary_converter.hpp : 93) 262144 reads processed 0:00:04.975 516M / 516M INFO General (binary_converter.hpp : 93) 524288 reads processed 0:00:12.392 864M / 864M INFO General (binary_converter.hpp : 93) 1048576 reads processed 0:00:24.556 868M / 868M INFO General (binary_converter.hpp : 93) 2097152 reads processed 0:00:50.579 868M / 868M INFO General (binary_converter.hpp : 93) 4194304 reads processed 0:01:42.941 880M / 880M INFO General (binary_converter.hpp : 93) 8388608 reads processed 0:03:28.271 884M / 884M INFO General (binary_converter.hpp : 93) 16777216 reads processed 0:06:58.300 888M / 888M INFO General (binary_converter.hpp : 93) 33554432 reads processed 0:14:04.956 884M / 888M INFO General (binary_converter.hpp : 93) 67108864 reads processed 0:27:18.614 876M / 892M INFO General (binary_converter.hpp : 117) 129219073 reads written 0:27:19.792 8M / 892M INFO General (read_converter.hpp : 87) Converting single reads 0:27:20.021 140M / 892M INFO General (binary_converter.hpp : 93) 16384 reads processed 0:27:20.100 144M / 892M INFO General (binary_converter.hpp : 93) 32768 reads processed 0:27:20.256 156M / 892M INFO General (binary_converter.hpp : 93) 65536 reads processed 0:27:20.568 184M / 892M INFO General (binary_converter.hpp : 93) 131072 reads processed 0:27:21.189 232M / 892M INFO General (binary_converter.hpp : 93) 262144 reads processed 0:27:22.437 336M / 892M INFO General (binary_converter.hpp : 93) 524288 reads processed 0:27:24.917 540M / 892M INFO General (binary_converter.hpp : 93) 1048576 reads processed 0:27:30.982 948M / 948M INFO General (binary_converter.hpp : 93) 2097152 reads processed 0:27:40.916 1G / 1G INFO General (binary_converter.hpp : 93) 4194304 reads processed 0:28:10.643 2G / 2G INFO General (binary_converter.hpp : 93) 8388608 reads processed 0:29:22.860 3G / 3G INFO General (binary_converter.hpp : 93) 16777216 reads processed 0:31:48.702 3G / 3G INFO General (binary_converter.hpp : 93) 33554432 reads processed 0:36:48.011 3G / 3G INFO General (binary_converter.hpp : 93) 67108864 reads processed 0:46:52.539 3G / 3G INFO General (binary_converter.hpp : 93) 134217728 reads processed 1:06:57.549 3G / 3G INFO General (binary_converter.hpp : 93) 268435456 reads processed 1:46:25.941 3G / 3G INFO General (binary_converter.hpp : 93) 536870912 reads processed 1:51:14.544 3G / 3G INFO General (binary_converter.hpp : 117) 568147731 reads written 1:51:17.278 16M / 3G INFO General (read_converter.hpp : 95) Converting merged reads 1:51:17.384 144M / 3G INFO General (binary_converter.hpp : 117) 0 reads written 1:51:17.393 16M / 3G INFO General (construction.cpp : 111) Max read length 391 1:51:17.393 16M / 3G INFO General (construction.cpp : 117) Average read length 229.3 1:51:17.393 16M / 3G INFO General (stage.cpp : 101) PROCEDURE == k+1-mer counting 1:51:17.399 16M / 3G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 1024 files using 32 threads. This might take a while. 1:51:17.406 12M / 3G INFO General (file_limit.hpp : 32) Open file limit set to 10000 1:51:17.406 12M / 3G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.39571 Gb 1:51:17.407 12M / 3G INFO General (kmer_splitters.hpp : 97) Using cell size of 65536 1:51:41.990 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 23060198 reads 1:52:04.730 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 38860813 reads 1:52:27.188 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 54500365 reads 1:52:49.588 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 69799795 reads 1:53:11.221 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 84751366 reads 1:53:33.172 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 100157733 reads 1:53:54.852 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 115491813 reads 1:54:16.502 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 130776909 reads 1:54:39.241 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 146182226 reads 1:55:02.265 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 161718785 reads 1:55:22.854 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 176177207 reads 1:55:45.325 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 191941724 reads 1:56:07.366 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 207313175 reads 1:57:51.572 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 280389552 reads 2:04:09.993 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 542854058 reads 2:17:01.002 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 1080412228 reads 2:24:17.575 17G / 18G INFO General (kmer_splitters.hpp : 295) Adding contigs from previous K 2:24:19.087 132M / 18G INFO General (kmer_splitters.hpp : 308) Used 1653171754 reads 2:24:19.087 132M / 18G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 2:26:24.301 132M / 18G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 2045839657 kmers in total. 2:26:24.301 132M / 18G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 2:26:53.532 128M / 18G INFO General (stage.cpp : 101) PROCEDURE == Extension index construction 2:26:53.532 128M / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 2:26:53.532 128M / 18G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 512 files using 32 threads. This might take a while. 2:26:53.532 128M / 18G INFO General (file_limit.hpp : 32) Open file limit set to 10000 2:26:53.532 128M / 18G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.39453 Gb 2:26:53.532 128M / 18G INFO General (kmer_splitters.hpp : 97) Using cell size of 131072 2:26:54.111 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 4305316 kmers 2:26:54.655 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 8922913 kmers 2:26:55.173 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 14054761 kmers 2:26:55.738 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 20071655 kmers 2:26:56.425 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 28522850 kmers 2:26:58.328 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 68079738 kmers 2:26:58.850 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 72685210 kmers 2:26:59.419 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 77793004 kmers 2:27:00.002 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 83773103 kmers 2:27:01.247 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 92053406 kmers 2:27:03.235 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 132002095 kmers 2:27:03.839 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 136608580 kmers 2:27:04.405 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 141717446 kmers 2:27:05.004 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 147697234 kmers 2:27:05.669 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 155979364 kmers 2:27:07.595 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 195932484 kmers 2:27:08.187 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 200538003 kmers 2:27:08.762 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 205645244 kmers 2:27:13.206 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 269582468 kmers 2:27:32.225 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 539559427 kmers 2:28:10.065 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 1090993447 kmers 2:29:16.937 17G / 18G INFO General (kmer_splitters.hpp : 385) Used 2045844777 kmers. 2:29:17.236 128M / 18G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 2:29:52.135 128M / 18G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 1976321898 kmers in total. 2:29:52.136 128M / 18G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 2:30:07.090 128M / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 2:31:23.993 1G / 18G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 2:34:51.529 1G / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 916465000 bytes occupied (3.70978 bits per kmer). 2:34:53.100 2G / 18G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 99) Building k-mer extensions from k+1-mers 2:36:40.899 2G / 18G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 103) Building k-mer extensions from k+1-mers finished. 2:36:40.902 2G / 18G INFO General (stage.cpp : 101) PROCEDURE == Early tip clipping 2:36:40.902 2G / 18G INFO General (construction.cpp : 253) Early tip clipper length bound set as (RL - K) 2:36:40.902 2G / 18G INFO Early tip clipping (early_simplification.hpp : 181) Early tip clipping 2:41:16.092 2G / 18G INFO Early tip clipping (early_simplification.hpp : 184) 229648019 22-mers were removed by early tip clipper 2:41:16.092 2G / 18G INFO General (stage.cpp : 101) PROCEDURE == Condensing graph 2:41:16.117 2G / 18G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 355) Extracting unbranching paths 2:43:54.012 11G / 19G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 374) Extracting unbranching paths finished. 171315498 sequences extracted 2:45:10.300 11G / 19G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 310) Collecting perfect loops 2:45:53.048 11G / 19G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 343) Collecting perfect loops finished. 2835 loops collected 2:47:09.997 47G / 61G INFO General (stage.cpp : 101) PROCEDURE == Filling coverage indices (PHM) 2:47:09.997 47G / 61G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 2:47:09.997 47G / 61G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 2:48:13.017 48G / 61G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 948693702 bytes occupied (3.70975 bits per kmer). 2:48:18.208 55G / 61G INFO General (construction.cpp : 388) Collecting k-mer coverage information from reads, this takes a while. 3:41:11.074 55G / 61G INFO General (construction.cpp : 508) Filling coverage and flanking coverage from PHM 3:41:27.535 55G / 61G INFO General (construction.cpp : 464) Processed 32000000 edges 3:41:38.107 55G / 61G INFO General (construction.cpp : 464) Processed 64000000 edges 3:41:48.304 55G / 61G INFO General (construction.cpp : 464) Processed 96000000 edges 3:41:58.557 55G / 61G INFO General (construction.cpp : 464) Processed 128000000 edges 3:42:09.166 55G / 61G INFO General (construction.cpp : 464) Processed 160000000 edges 3:42:19.184 55G / 61G INFO General (construction.cpp : 464) Processed 192000000 edges 3:42:29.652 55G / 61G INFO General (construction.cpp : 464) Processed 224000000 edges 3:42:39.920 55G / 61G INFO General (construction.cpp : 464) Processed 256000000 edges 3:42:50.202 55G / 61G INFO General (construction.cpp : 464) Processed 288000000 edges 3:43:00.856 55G / 61G INFO General (construction.cpp : 464) Processed 320000000 edges 3:43:07.900 55G / 61G INFO General (construction.cpp : 464) Processed 342601160 edges 3:43:14.890 44G / 61G INFO StageManager (stage.cpp : 132) STAGE == Raw Simplification 3:43:14.896 44G / 61G INFO General (simplification.cpp : 128) PROCEDURE == InitialCleaning 3:43:14.897 44G / 61G INFO General (graph_simplification.hpp : 662) Flanking coverage based disconnection disabled 3:43:14.897 44G / 61G INFO Simplification (parallel_processing.hpp : 165) Running Self conjugate edge remover 3:43:25.569 44G / 61G INFO Simplification (parallel_processing.hpp : 167) Self conjugate edge remover triggered 0 times 3:43:25.569 44G / 61G INFO Simplification (parallel_processing.hpp : 165) Running Initial tip clipper 3:43:44.900 44G / 61G INFO Simplification (parallel_processing.hpp : 167) Initial tip clipper triggered 185693 times 3:43:44.900 44G / 61G INFO Simplification (parallel_processing.hpp : 165) Running Initial ec remover 3:58:28.242 46G / 61G INFO Simplification (parallel_processing.hpp : 167) Initial ec remover triggered 16564542 times 3:58:28.242 46G / 61G INFO Simplification (parallel_processing.hpp : 165) Running Initial isolated edge remover 3:58:42.648 46G / 61G INFO Simplification (parallel_processing.hpp : 167) Initial isolated edge remover triggered 363151 times 3:58:58.872 46G / 61G INFO StageManager (stage.cpp : 132) STAGE == Simplification 3:58:58.872 46G / 61G INFO General (simplification.cpp : 357) Graph simplification started 3:58:58.872 46G / 61G INFO General (graph_simplification.hpp : 634) Creating parallel br instance 3:58:58.872 46G / 61G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 1 3:58:58.872 46G / 61G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 3:59:15.269 46G / 61G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 240409 times 3:59:15.269 46G / 61G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 6:32:23.841 48G / 61G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 11534116 times 6:32:23.841 48G / 61G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 6:32:48.282 48G / 61G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 6:32:48.282 48G / 61G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 2 6:32:48.282 48G / 61G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 6:33:30.357 48G / 61G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 44381 times 6:33:30.357 48G / 61G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 6:33:45.544 48G / 61G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 1592 times 6:33:45.544 48G / 61G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 6:34:30.581 48G / 61G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 722588 times 6:34:30.581 48G / 61G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 3 6:34:30.581 48G / 61G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 6:34:33.063 48G / 61G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 13014 times 6:34:33.064 48G / 61G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 6:37:38.374 48G / 61G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 107553 times 6:37:38.374 48G / 61G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 6:42:11.413 48G / 61G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 4531017 times 6:42:11.413 48G / 61G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 4 6:42:11.413 48G / 61G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 6:42:22.682 48G / 61G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 15269 times 6:42:22.682 48G / 61G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 7:57:19.647 48G / 61G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 466881 times 7:57:19.647 48G / 61G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 7:57:31.911 48G / 61G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 91 times 7:57:31.912 48G / 61G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 5 7:57:31.913 48G / 61G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 7:57:37.084 48G / 61G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 171 times 7:57:37.084 48G / 61G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 7:57:37.395 48G / 61G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 13 times 7:57:37.395 48G / 61G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 7:57:37.395 48G / 61G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 7:57:37.395 48G / 61G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 6 7:57:37.395 48G / 61G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 7:57:37.395 48G / 61G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 7:57:37.395 48G / 61G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 7:57:37.395 48G / 61G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 7:57:37.395 48G / 61G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 7:57:37.395 48G / 61G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 7:57:37.395 48G / 61G INFO StageManager (stage.cpp : 132) STAGE == Simplification Cleanup 7:57:37.395 48G / 61G INFO General (simplification.cpp : 196) PROCEDURE == Post simplification 7:57:37.395 48G / 61G INFO General (graph_simplification.hpp : 634) Creating parallel br instance 7:57:37.395 48G / 61G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover 8:25:38.648 47G / 61G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 6922330 times 8:25:38.648 47G / 61G INFO Simplification (parallel_processing.hpp : 165) Running Disconnecting edges with relatively low coverage 8:42:09.388 47G / 61G INFO Simplification (parallel_processing.hpp : 167) Disconnecting edges with relatively low coverage triggered 3160427 times 8:42:09.388 47G / 61G INFO Simplification (parallel_processing.hpp : 165) Running Complex tip clipper 8:43:02.339 47G / 61G INFO Simplification (parallel_processing.hpp : 167) Complex tip clipper triggered 839872 times 8:43:02.339 47G / 61G INFO Simplification (parallel_processing.hpp : 165) Running Complex bulge remover 8:46:35.670 47G / 61G INFO Simplification (parallel_processing.hpp : 167) Complex bulge remover triggered 36389 times 8:46:35.670 47G / 61G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 8:47:18.484 47G / 61G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 1616922 times 8:47:18.484 47G / 61G INFO Simplification (parallel_processing.hpp : 165) Running Final tip clipper 8:47:24.823 47G / 61G INFO Simplification (parallel_processing.hpp : 167) Final tip clipper triggered 443 times 8:47:24.823 47G / 61G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 9:25:13.739 47G / 61G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 359752 times 9:25:13.739 47G / 61G INFO Simplification (parallel_processing.hpp : 165) Running Thorn remover (meta) 9:25:24.628 47G / 61G INFO Simplification (parallel_processing.hpp : 167) Thorn remover (meta) triggered 0 times 9:25:24.628 47G / 61G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover 9:30:37.171 47G / 61G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 154623 times 9:30:37.171 47G / 61G INFO Simplification (parallel_processing.hpp : 165) Running Disconnecting edges with relatively low coverage 9:41:34.716 47G / 61G INFO Simplification (parallel_processing.hpp : 167) Disconnecting edges with relatively low coverage triggered 125519 times 9:41:34.716 47G / 61G INFO Simplification (parallel_processing.hpp : 165) Running Complex tip clipper 9:41:47.231 47G / 61G INFO Simplification (parallel_processing.hpp : 167) Complex tip clipper triggered 69179 times 9:41:47.231 47G / 61G INFO Simplification (parallel_processing.hpp : 165) Running Complex bulge remover 9:44:50.325 47G / 61G INFO Simplification (parallel_processing.hpp : 167) Complex bulge remover triggered 2701 times 9:44:50.325 47G / 61G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 9:45:00.613 47G / 61G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 88471 times 9:45:00.613 47G / 61G INFO Simplification (parallel_processing.hpp : 165) Running Final tip clipper 9:45:07.081 47G / 61G INFO Simplification (parallel_processing.hpp : 167) Final tip clipper triggered 23 times 9:45:07.081 47G / 61G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 10:17:26.900 47G / 61G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 20161 times 10:17:26.900 47G / 61G INFO Simplification (parallel_processing.hpp : 165) Running Thorn remover (meta) 10:17:36.956 47G / 61G INFO Simplification (parallel_processing.hpp : 167) Thorn remover (meta) triggered 2 times 10:17:36.956 47G / 61G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover 10:21:47.386 47G / 61G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 11428 times 10:21:47.386 47G / 61G INFO Simplification (parallel_processing.hpp : 165) Running Disconnecting edges with relatively low coverage 10:23:23.100 47G / 61G INFO Simplification (parallel_processing.hpp : 167) Disconnecting edges with relatively low coverage triggered 3975 times 10:23:23.100 47G / 61G INFO Simplification (parallel_processing.hpp : 165) Running Complex tip clipper 10:23:26.943 47G / 61G INFO Simplification (parallel_processing.hpp : 167) Complex tip clipper triggered 1143 times 10:23:26.943 47G / 61G INFO Simplification (parallel_processing.hpp : 165) Running Complex bulge remover 10:26:34.477 47G / 61G INFO Simplification (parallel_processing.hpp : 167) Complex bulge remover triggered 222 times 10:26:34.478 47G / 61G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 10:26:34.918 47G / 61G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 3204 times 10:26:34.918 47G / 61G INFO Simplification (parallel_processing.hpp : 165) Running Final tip clipper 10:26:35.140 47G / 61G INFO Simplification (parallel_processing.hpp : 167) Final tip clipper triggered 0 times 10:26:35.140 47G / 61G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 10:26:43.157 47G / 61G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 868 times 10:26:43.157 47G / 61G INFO Simplification (parallel_processing.hpp : 165) Running Thorn remover (meta) 10:26:43.315 47G / 61G INFO Simplification (parallel_processing.hpp : 167) Thorn remover (meta) triggered 0 times 10:26:43.315 47G / 61G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover 10:30:46.345 47G / 61G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 305 times 10:30:46.345 47G / 61G INFO Simplification (parallel_processing.hpp : 165) Running Disconnecting edges with relatively low coverage 10:30:48.538 47G / 61G INFO Simplification (parallel_processing.hpp : 167) Disconnecting edges with relatively low coverage triggered 182 times 10:30:48.538 47G / 61G INFO Simplification (parallel_processing.hpp : 165) Running Complex tip clipper 10:30:52.461 47G / 61G INFO Simplification (parallel_processing.hpp : 167) Complex tip clipper triggered 46 times 10:30:52.462 47G / 61G INFO Simplification (parallel_processing.hpp : 165) Running Complex bulge remover 10:33:58.877 47G / 61G INFO Simplification (parallel_processing.hpp : 167) Complex bulge remover triggered 6 times 10:33:58.877 47G / 61G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 10:33:58.901 47G / 61G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 132 times 10:33:58.901 47G / 61G INFO Simplification (parallel_processing.hpp : 165) Running Final tip clipper 10:33:58.908 47G / 61G INFO Simplification (parallel_processing.hpp : 167) Final tip clipper triggered 0 times 10:33:58.908 47G / 61G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 10:33:59.294 47G / 61G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 33 times 10:33:59.294 47G / 61G INFO Simplification (parallel_processing.hpp : 165) Running Thorn remover (meta) 10:33:59.298 47G / 61G INFO Simplification (parallel_processing.hpp : 167) Thorn remover (meta) triggered 0 times 10:33:59.298 47G / 61G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover 10:38:08.272 47G / 61G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 12 times 10:38:08.272 47G / 61G INFO Simplification (parallel_processing.hpp : 165) Running Disconnecting edges with relatively low coverage 10:38:08.364 47G / 61G INFO Simplification (parallel_processing.hpp : 167) Disconnecting edges with relatively low coverage triggered 12 times 10:38:08.364 47G / 61G INFO Simplification (parallel_processing.hpp : 165) Running Complex tip clipper 10:38:12.116 47G / 61G INFO Simplification (parallel_processing.hpp : 167) Complex tip clipper triggered 6 times 10:38:12.116 47G / 61G INFO Simplification (parallel_processing.hpp : 165) Running Complex bulge remover 10:41:15.611 47G / 61G INFO Simplification (parallel_processing.hpp : 167) Complex bulge remover triggered 0 times 10:41:15.611 47G / 61G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 10:41:15.613 47G / 61G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 6 times 10:41:15.613 47G / 61G INFO Simplification (parallel_processing.hpp : 165) Running Final tip clipper 10:41:15.613 47G / 61G INFO Simplification (parallel_processing.hpp : 167) Final tip clipper triggered 0 times 10:41:15.613 47G / 61G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 10:41:15.659 47G / 61G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 1 times 10:41:15.659 47G / 61G INFO Simplification (parallel_processing.hpp : 165) Running Thorn remover (meta) 10:41:15.659 47G / 61G INFO Simplification (parallel_processing.hpp : 167) Thorn remover (meta) triggered 0 times 10:41:15.659 47G / 61G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover 10:45:19.813 47G / 61G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 1 times 10:45:19.813 47G / 61G INFO Simplification (parallel_processing.hpp : 165) Running Disconnecting edges with relatively low coverage 10:45:19.820 47G / 61G INFO Simplification (parallel_processing.hpp : 167) Disconnecting edges with relatively low coverage triggered 0 times 10:45:19.820 47G / 61G INFO Simplification (parallel_processing.hpp : 165) Running Complex tip clipper 10:45:23.339 47G / 61G INFO Simplification (parallel_processing.hpp : 167) Complex tip clipper triggered 0 times 10:45:23.341 47G / 61G INFO Simplification (parallel_processing.hpp : 165) Running Complex bulge remover 10:48:26.032 47G / 61G INFO Simplification (parallel_processing.hpp : 167) Complex bulge remover triggered 0 times 10:48:26.032 47G / 61G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 10:48:26.032 47G / 61G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 10:48:26.032 47G / 61G INFO Simplification (parallel_processing.hpp : 165) Running Final tip clipper 10:48:26.032 47G / 61G INFO Simplification (parallel_processing.hpp : 167) Final tip clipper triggered 0 times 10:48:26.032 47G / 61G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 10:48:26.034 47G / 61G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 10:48:26.034 47G / 61G INFO Simplification (parallel_processing.hpp : 165) Running Thorn remover (meta) 10:48:26.034 47G / 61G INFO Simplification (parallel_processing.hpp : 167) Thorn remover (meta) triggered 0 times 10:48:26.034 47G / 61G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover 10:52:31.324 47G / 61G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 0 times 10:52:31.324 47G / 61G INFO Simplification (parallel_processing.hpp : 165) Running Disconnecting edges with relatively low coverage 10:52:31.324 47G / 61G INFO Simplification (parallel_processing.hpp : 167) Disconnecting edges with relatively low coverage triggered 0 times 10:52:31.324 47G / 61G INFO Simplification (parallel_processing.hpp : 165) Running Complex tip clipper 10:52:34.875 47G / 61G INFO Simplification (parallel_processing.hpp : 167) Complex tip clipper triggered 0 times 10:52:34.875 47G / 61G INFO Simplification (parallel_processing.hpp : 165) Running Complex bulge remover 10:55:38.550 47G / 61G INFO Simplification (parallel_processing.hpp : 167) Complex bulge remover triggered 0 times 10:55:38.550 47G / 61G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 10:55:38.550 47G / 61G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 10:55:38.550 47G / 61G INFO Simplification (parallel_processing.hpp : 165) Running Final tip clipper 10:55:38.550 47G / 61G INFO Simplification (parallel_processing.hpp : 167) Final tip clipper triggered 0 times 10:55:38.550 47G / 61G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 10:55:38.550 47G / 61G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 10:55:38.550 47G / 61G INFO Simplification (parallel_processing.hpp : 165) Running Thorn remover (meta) 10:55:38.550 47G / 61G INFO Simplification (parallel_processing.hpp : 167) Thorn remover (meta) triggered 0 times 10:55:38.550 47G / 61G INFO General (simplification.cpp : 326) Running Hidden EC remover (meta) 10:55:45.083 47G / 61G INFO General (simplification.cpp : 330) Disrupting self-conjugate edges 10:59:27.001 47G / 61G INFO Simplification (parallel_processing.hpp : 165) Running Removing isolated edges 10:59:32.923 47G / 61G INFO Simplification (parallel_processing.hpp : 167) Removing isolated edges triggered 31778 times 10:59:32.923 47G / 61G INFO General (simplification.cpp : 470) Counting average coverage 11:00:37.448 47G / 61G INFO General (simplification.cpp : 476) Average coverage = 189.154 11:00:37.448 47G / 61G INFO StageManager (stage.cpp : 132) STAGE == Contig Output 11:00:37.450 47G / 61G INFO General (contig_output_stage.cpp : 40) Writing GFA to /DATA/markop/CPB_metaSpades/output//K21/assembly_graph_with_scaffolds.gfa 11:05:21.809 47G / 61G INFO General (contig_output.hpp : 22) Outputting contigs to /DATA/markop/CPB_metaSpades/output//K21/before_rr.fasta 11:10:08.032 47G / 61G INFO General (contig_output_stage.cpp : 51) Outputting FastG graph to /DATA/markop/CPB_metaSpades/output//K21/assembly_graph.fastg 11:24:16.886 47G / 61G INFO General (contig_output.hpp : 22) Outputting contigs to /DATA/markop/CPB_metaSpades/output//K21/simplified_contigs.fasta 11:28:50.920 47G / 61G INFO General (contig_output.hpp : 22) Outputting contigs to /DATA/markop/CPB_metaSpades/output//K21/final_contigs.fasta 11:33:23.821 47G / 61G INFO StageManager (stage.cpp : 132) STAGE == Contig Output 11:33:23.821 47G / 61G INFO General (contig_output_stage.cpp : 40) Writing GFA to /DATA/markop/CPB_metaSpades/output//K21/assembly_graph_with_scaffolds.gfa 11:38:24.040 47G / 61G INFO General (contig_output.hpp : 22) Outputting contigs to /DATA/markop/CPB_metaSpades/output//K21/before_rr.fasta 11:43:16.536 47G / 61G INFO General (contig_output_stage.cpp : 51) Outputting FastG graph to /DATA/markop/CPB_metaSpades/output//K21/assembly_graph.fastg 11:57:57.132 47G / 61G INFO General (contig_output.hpp : 22) Outputting contigs to /DATA/markop/CPB_metaSpades/output//K21/simplified_contigs.fasta 12:02:28.771 47G / 61G INFO General (contig_output.hpp : 22) Outputting contigs to /DATA/markop/CPB_metaSpades/output//K21/final_contigs.fasta 12:07:06.222 47G / 61G INFO General (launch.hpp : 149) SPAdes finished 12:11:43.469 132M / 61G INFO General (main.cpp : 109) Assembling time: 12 hours 11 minutes 43 seconds Max read length detected as 391 == Running assembler: K41 0:00:00.000 4M / 4M INFO General (main.cpp : 74) Loaded config from /DATA/markop/CPB_metaSpades/output/K41/configs/config.info 0:00:00.000 4M / 4M INFO General (main.cpp : 74) Loaded config from /DATA/markop/CPB_metaSpades/output/K41/configs/mda_mode.info 0:00:00.000 4M / 4M INFO General (main.cpp : 74) Loaded config from /DATA/markop/CPB_metaSpades/output/K41/configs/meta_mode.info 0:00:00.000 4M / 4M INFO General (memory_limit.cpp : 49) Memory limit set to 230 Gb 0:00:00.000 4M / 4M INFO General (main.cpp : 87) Starting SPAdes, built from refs/heads/spades_3.13.0, git revision 8ea46659e9b2aca35444a808db550ac333006f8b 0:00:00.000 4M / 4M INFO General (main.cpp : 88) Maximum k-mer length: 128 0:00:00.000 4M / 4M INFO General (main.cpp : 89) Assembling dataset (/DATA/markop/CPB_metaSpades/output/dataset.info) with K=41 0:00:00.000 4M / 4M INFO General (main.cpp : 90) Maximum # of threads to use (adjusted due to OMP capabilities): 32 0:00:00.000 4M / 4M INFO General (launch.hpp : 51) SPAdes started 0:00:00.000 4M / 4M INFO General (launch.hpp : 58) Starting from stage: construction 0:00:00.000 4M / 4M INFO General (launch.hpp : 65) Two-step RR enabled: 0 0:00:00.000 4M / 4M INFO StageManager (stage.cpp : 132) STAGE == de Bruijn graph construction 0:00:00.001 4M / 4M INFO General (read_converter.hpp : 59) Binary reads detected 0:00:00.003 4M / 4M INFO General (construction.cpp : 111) Max read length 391 0:00:00.003 4M / 4M INFO General (construction.cpp : 117) Average read length 229.3 0:00:00.003 4M / 4M INFO General (stage.cpp : 101) PROCEDURE == k+1-mer counting 0:00:00.003 4M / 4M INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 1024 files using 32 threads. This might take a while. 0:00:00.004 4M / 4M INFO General (file_limit.hpp : 32) Open file limit set to 10000 0:00:00.004 4M / 4M INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.39579 Gb 0:00:00.004 4M / 4M INFO General (kmer_splitters.hpp : 97) Using cell size of 32768 0:00:14.888 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 16293987 reads 0:00:27.830 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 24540202 reads 0:00:41.425 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 32625211 reads 0:00:54.640 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 40833963 reads 0:01:08.459 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 49092129 reads 0:01:21.292 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 57098839 reads 0:01:35.852 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 65450358 reads 0:01:49.476 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 73639915 reads 0:02:00.566 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 80421720 reads 0:02:14.301 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 88742707 reads 0:02:28.068 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 96938140 reads 0:02:40.831 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 104812314 reads 0:03:33.144 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 136384116 reads 0:07:12.600 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 269591402 reads 0:14:43.093 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 543849052 reads 0:29:30.658 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 1079698136 reads 0:39:59.314 17G / 18G INFO General (kmer_splitters.hpp : 295) Adding contigs from previous K 0:48:25.158 132M / 18G INFO General (kmer_splitters.hpp : 308) Used 1653171754 reads 0:48:25.158 132M / 18G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 1:29:37.310 132M / 18G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 2949512921 kmers in total. 1:29:37.311 132M / 18G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 1:30:26.763 128M / 18G INFO General (stage.cpp : 101) PROCEDURE == Extension index construction 1:30:26.769 128M / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 1:30:26.769 128M / 18G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 512 files using 32 threads. This might take a while. 1:30:26.769 128M / 18G INFO General (file_limit.hpp : 32) Open file limit set to 10000 1:30:26.769 128M / 18G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.39453 Gb 1:30:26.769 128M / 18G INFO General (kmer_splitters.hpp : 97) Using cell size of 65536 1:30:27.386 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 5359330 kmers 1:30:28.050 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 11046516 kmers 1:30:28.803 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 17028244 kmers 1:30:29.482 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 22961657 kmers 1:30:30.150 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 28750468 kmers 1:30:30.825 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 34741732 kmers 1:30:31.511 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 41368877 kmers 1:30:32.173 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 47501198 kmers 1:30:32.946 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 53857576 kmers 1:30:33.872 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 60210724 kmers 1:30:34.550 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 66153150 kmers 1:30:35.232 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 72141995 kmers 1:30:35.945 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 78346001 kmers 1:30:36.635 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 84403574 kmers 1:30:37.421 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 90421604 kmers 1:30:38.281 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 97516787 kmers 1:30:39.211 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 103204193 kmers 1:30:43.716 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 139675929 kmers 1:30:58.070 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 268710320 kmers 1:31:54.481 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 539143445 kmers 1:33:35.829 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 1074092382 kmers 1:37:02.143 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 2148740858 kmers 1:39:33.127 17G / 18G INFO General (kmer_splitters.hpp : 385) Used 2949528281 kmers. 1:39:33.403 128M / 18G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 1:44:04.028 128M / 18G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 2915367632 kmers in total. 1:44:04.028 128M / 18G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 1:48:00.924 128M / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 1:50:01.625 1G / 18G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 1:56:17.323 1G / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 1351920592 bytes occupied (3.70978 bits per kmer). 1:56:19.727 4G / 18G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 99) Building k-mer extensions from k+1-mers 1:59:11.278 4G / 18G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 103) Building k-mer extensions from k+1-mers finished. 1:59:11.283 4G / 18G INFO General (stage.cpp : 101) PROCEDURE == Early tip clipping 1:59:11.283 4G / 18G INFO General (construction.cpp : 253) Early tip clipper length bound set as (RL - K) 1:59:11.284 4G / 18G INFO Early tip clipping (early_simplification.hpp : 181) Early tip clipping 2:06:03.213 4G / 18G INFO Early tip clipping (early_simplification.hpp : 184) 330223819 42-mers were removed by early tip clipper 2:06:03.213 4G / 18G INFO General (stage.cpp : 101) PROCEDURE == Condensing graph 2:06:03.246 4G / 18G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 355) Extracting unbranching paths 2:10:00.703 10G / 18G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 374) Extracting unbranching paths finished. 103911528 sequences extracted 2:11:42.093 10G / 18G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 310) Collecting perfect loops 2:12:49.042 10G / 18G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 343) Collecting perfect loops finished. 2864 loops collected 2:13:40.207 33G / 42G INFO General (stage.cpp : 101) PROCEDURE == Filling coverage indices (PHM) 2:13:40.207 33G / 42G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 2:13:40.207 33G / 42G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 2:15:18.630 34G / 42G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 1367723606 bytes occupied (3.70969 bits per kmer). 2:15:25.224 45G / 45G INFO General (construction.cpp : 388) Collecting k-mer coverage information from reads, this takes a while. 3:06:46.954 45G / 45G INFO General (construction.cpp : 508) Filling coverage and flanking coverage from PHM 3:07:16.918 45G / 45G INFO General (construction.cpp : 464) Processed 32000000 edges 3:07:41.295 45G / 45G INFO General (construction.cpp : 464) Processed 64000000 edges 3:08:05.632 45G / 45G INFO General (construction.cpp : 464) Processed 96000000 edges 3:08:29.949 45G / 45G INFO General (construction.cpp : 464) Processed 128000000 edges 3:08:54.247 45G / 45G INFO General (construction.cpp : 464) Processed 160000000 edges 3:09:18.533 45G / 45G INFO General (construction.cpp : 464) Processed 192000000 edges 3:09:30.925 45G / 45G INFO General (construction.cpp : 464) Processed 207817849 edges 3:09:44.712 29G / 45G INFO StageManager (stage.cpp : 132) STAGE == Raw Simplification 3:09:44.718 29G / 45G INFO General (simplification.cpp : 128) PROCEDURE == InitialCleaning 3:09:44.719 29G / 45G INFO General (graph_simplification.hpp : 662) Flanking coverage based disconnection disabled 3:09:44.719 29G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Self conjugate edge remover 3:09:51.352 29G / 45G INFO Simplification (parallel_processing.hpp : 167) Self conjugate edge remover triggered 429 times 3:09:51.352 29G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Initial tip clipper 3:10:10.893 29G / 45G INFO Simplification (parallel_processing.hpp : 167) Initial tip clipper triggered 415433 times 3:10:10.893 29G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Initial ec remover 3:20:12.151 30G / 45G INFO Simplification (parallel_processing.hpp : 167) Initial ec remover triggered 10537302 times 3:20:12.151 30G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Initial isolated edge remover 3:20:44.064 30G / 45G INFO Simplification (parallel_processing.hpp : 167) Initial isolated edge remover triggered 2511683 times 3:20:52.955 30G / 45G INFO StageManager (stage.cpp : 132) STAGE == Simplification 3:20:52.955 30G / 45G INFO General (simplification.cpp : 357) Graph simplification started 3:20:52.955 30G / 45G INFO General (graph_simplification.hpp : 634) Creating parallel br instance 3:20:52.955 30G / 45G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 1 3:20:52.955 30G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 3:21:06.625 30G / 45G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 344169 times 3:21:06.625 30G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 4:21:50.355 31G / 45G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 11150066 times 4:21:50.355 31G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 4:21:58.652 31G / 45G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 379 times 4:21:58.652 31G / 45G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 2 4:21:58.652 31G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 4:22:27.177 31G / 45G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 63769 times 4:22:27.177 31G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 4:22:29.911 31G / 45G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 2500 times 4:22:29.911 31G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 4:22:52.292 31G / 45G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 298264 times 4:22:52.292 31G / 45G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 3 4:22:52.292 31G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 4:22:53.641 31G / 45G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 9335 times 4:22:53.641 31G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 4:23:57.108 31G / 45G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 59208 times 4:23:57.108 31G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 4:25:52.255 31G / 45G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 1497180 times 4:25:52.255 31G / 45G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 4 4:25:52.255 31G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 4:25:57.886 31G / 45G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 19645 times 4:25:57.886 31G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 4:41:04.623 31G / 45G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 309436 times 4:41:04.623 31G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 4:41:10.221 31G / 45G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 96 times 4:41:10.221 31G / 45G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 5 4:41:10.222 31G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 4:41:13.571 31G / 45G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 561 times 4:41:13.571 31G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 4:41:13.706 31G / 45G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 39 times 4:41:13.706 31G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 4:41:13.706 31G / 45G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 4:41:13.706 31G / 45G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 6 4:41:13.706 31G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 4:41:13.706 31G / 45G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 1 times 4:41:13.706 31G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 4:41:13.706 31G / 45G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 4:41:13.706 31G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 4:41:13.706 31G / 45G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 4:41:13.706 31G / 45G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 7 4:41:13.706 31G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 4:41:13.706 31G / 45G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 4:41:13.706 31G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 4:41:13.706 31G / 45G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 4:41:13.706 31G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 4:41:13.706 31G / 45G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 4:41:13.707 31G / 45G INFO StageManager (stage.cpp : 132) STAGE == Simplification Cleanup 4:41:13.707 31G / 45G INFO General (simplification.cpp : 196) PROCEDURE == Post simplification 4:41:13.707 31G / 45G INFO General (graph_simplification.hpp : 634) Creating parallel br instance 4:41:13.707 31G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover 4:51:21.864 30G / 45G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 2606848 times 4:51:21.864 30G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Disconnecting edges with relatively low coverage 4:59:45.014 30G / 45G INFO Simplification (parallel_processing.hpp : 167) Disconnecting edges with relatively low coverage triggered 1575117 times 4:59:45.014 30G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Complex tip clipper 5:00:11.821 30G / 45G INFO Simplification (parallel_processing.hpp : 167) Complex tip clipper triggered 434812 times 5:00:11.821 30G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Complex bulge remover 5:01:54.180 30G / 45G INFO Simplification (parallel_processing.hpp : 167) Complex bulge remover triggered 107703 times 5:01:54.180 30G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 5:02:19.368 30G / 45G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 823150 times 5:02:19.368 30G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Final tip clipper 5:02:22.549 30G / 45G INFO Simplification (parallel_processing.hpp : 167) Final tip clipper triggered 675 times 5:02:22.549 30G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 5:08:28.372 30G / 45G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 190368 times 5:08:28.372 30G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Thorn remover (meta) 5:08:39.652 30G / 45G INFO Simplification (parallel_processing.hpp : 167) Thorn remover (meta) triggered 13 times 5:08:39.652 30G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover 5:10:23.192 30G / 45G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 75481 times 5:10:23.192 30G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Disconnecting edges with relatively low coverage 5:16:58.623 30G / 45G INFO Simplification (parallel_processing.hpp : 167) Disconnecting edges with relatively low coverage triggered 195233 times 5:16:58.623 30G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Complex tip clipper 5:17:06.017 30G / 45G INFO Simplification (parallel_processing.hpp : 167) Complex tip clipper triggered 38173 times 5:17:06.017 30G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Complex bulge remover 5:18:21.305 30G / 45G INFO Simplification (parallel_processing.hpp : 167) Complex bulge remover triggered 4589 times 5:18:21.305 30G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 5:18:31.742 30G / 45G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 167694 times 5:18:31.742 30G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Final tip clipper 5:18:34.591 30G / 45G INFO Simplification (parallel_processing.hpp : 167) Final tip clipper triggered 195 times 5:18:34.591 30G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 5:22:29.783 30G / 45G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 29334 times 5:22:29.783 30G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Thorn remover (meta) 5:22:40.688 30G / 45G INFO Simplification (parallel_processing.hpp : 167) Thorn remover (meta) triggered 2 times 5:22:40.689 30G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover 5:23:52.158 30G / 45G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 12991 times 5:23:52.158 30G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Disconnecting edges with relatively low coverage 5:25:39.919 30G / 45G INFO Simplification (parallel_processing.hpp : 167) Disconnecting edges with relatively low coverage triggered 5755 times 5:25:39.919 30G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Complex tip clipper 5:25:42.328 30G / 45G INFO Simplification (parallel_processing.hpp : 167) Complex tip clipper triggered 1644 times 5:25:42.328 30G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Complex bulge remover 5:26:50.942 30G / 45G INFO Simplification (parallel_processing.hpp : 167) Complex bulge remover triggered 785 times 5:26:50.942 30G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 5:26:51.625 30G / 45G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 4833 times 5:26:51.625 30G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Final tip clipper 5:26:51.990 30G / 45G INFO Simplification (parallel_processing.hpp : 167) Final tip clipper triggered 6 times 5:26:51.990 30G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 5:26:57.635 30G / 45G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 1492 times 5:26:57.635 30G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Thorn remover (meta) 5:26:57.903 30G / 45G INFO Simplification (parallel_processing.hpp : 167) Thorn remover (meta) triggered 0 times 5:26:57.903 30G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover 5:28:07.534 30G / 45G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 619 times 5:28:07.534 30G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Disconnecting edges with relatively low coverage 5:28:11.001 30G / 45G INFO Simplification (parallel_processing.hpp : 167) Disconnecting edges with relatively low coverage triggered 269 times 5:28:11.001 30G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Complex tip clipper 5:28:13.471 30G / 45G INFO Simplification (parallel_processing.hpp : 167) Complex tip clipper triggered 43 times 5:28:13.471 30G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Complex bulge remover 5:29:19.484 30G / 45G INFO Simplification (parallel_processing.hpp : 167) Complex bulge remover triggered 33 times 5:29:19.485 30G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 5:29:19.523 30G / 45G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 215 times 5:29:19.523 30G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Final tip clipper 5:29:19.538 30G / 45G INFO Simplification (parallel_processing.hpp : 167) Final tip clipper triggered 1 times 5:29:19.538 30G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 5:29:19.979 30G / 45G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 57 times 5:29:19.979 30G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Thorn remover (meta) 5:29:19.985 30G / 45G INFO Simplification (parallel_processing.hpp : 167) Thorn remover (meta) triggered 0 times 5:29:19.986 30G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover 5:30:27.842 30G / 45G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 31 times 5:30:27.842 30G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Disconnecting edges with relatively low coverage 5:30:27.932 30G / 45G INFO Simplification (parallel_processing.hpp : 167) Disconnecting edges with relatively low coverage triggered 18 times 5:30:27.932 30G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Complex tip clipper 5:30:30.193 30G / 45G INFO Simplification (parallel_processing.hpp : 167) Complex tip clipper triggered 5 times 5:30:30.193 30G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Complex bulge remover 5:31:36.751 30G / 45G INFO Simplification (parallel_processing.hpp : 167) Complex bulge remover triggered 3 times 5:31:36.751 30G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 5:31:36.754 30G / 45G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 12 times 5:31:36.755 30G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Final tip clipper 5:31:36.756 30G / 45G INFO Simplification (parallel_processing.hpp : 167) Final tip clipper triggered 0 times 5:31:36.756 30G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 5:31:36.788 30G / 45G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 6 times 5:31:36.788 30G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Thorn remover (meta) 5:31:36.788 30G / 45G INFO Simplification (parallel_processing.hpp : 167) Thorn remover (meta) triggered 0 times 5:31:36.788 30G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover 5:32:43.750 30G / 45G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 1 times 5:32:43.750 30G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Disconnecting edges with relatively low coverage 5:32:43.761 30G / 45G INFO Simplification (parallel_processing.hpp : 167) Disconnecting edges with relatively low coverage triggered 0 times 5:32:43.761 30G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Complex tip clipper 5:32:45.970 30G / 45G INFO Simplification (parallel_processing.hpp : 167) Complex tip clipper triggered 0 times 5:32:45.970 30G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Complex bulge remover 5:33:52.586 30G / 45G INFO Simplification (parallel_processing.hpp : 167) Complex bulge remover triggered 0 times 5:33:52.586 30G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 5:33:52.586 30G / 45G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 5:33:52.586 30G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Final tip clipper 5:33:52.586 30G / 45G INFO Simplification (parallel_processing.hpp : 167) Final tip clipper triggered 0 times 5:33:52.586 30G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 5:33:52.588 30G / 45G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 1 times 5:33:52.588 30G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Thorn remover (meta) 5:33:52.588 30G / 45G INFO Simplification (parallel_processing.hpp : 167) Thorn remover (meta) triggered 0 times 5:33:52.588 30G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover 5:35:00.131 30G / 45G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 0 times 5:35:00.131 30G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Disconnecting edges with relatively low coverage 5:35:00.131 30G / 45G INFO Simplification (parallel_processing.hpp : 167) Disconnecting edges with relatively low coverage triggered 0 times 5:35:00.131 30G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Complex tip clipper 5:35:02.373 30G / 45G INFO Simplification (parallel_processing.hpp : 167) Complex tip clipper triggered 0 times 5:35:02.373 30G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Complex bulge remover 5:36:08.466 30G / 45G INFO Simplification (parallel_processing.hpp : 167) Complex bulge remover triggered 0 times 5:36:08.466 30G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 5:36:08.467 30G / 45G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 5:36:08.467 30G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Final tip clipper 5:36:08.467 30G / 45G INFO Simplification (parallel_processing.hpp : 167) Final tip clipper triggered 0 times 5:36:08.468 30G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 5:36:08.468 30G / 45G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 5:36:08.468 30G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Thorn remover (meta) 5:36:08.469 30G / 45G INFO Simplification (parallel_processing.hpp : 167) Thorn remover (meta) triggered 0 times 5:36:08.469 30G / 45G INFO General (simplification.cpp : 326) Running Hidden EC remover (meta) 5:36:11.734 30G / 45G INFO General (simplification.cpp : 330) Disrupting self-conjugate edges 5:37:39.593 30G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Removing isolated edges 5:37:43.037 30G / 45G INFO Simplification (parallel_processing.hpp : 167) Removing isolated edges triggered 35463 times 5:37:43.038 30G / 45G INFO General (simplification.cpp : 470) Counting average coverage 5:38:06.951 30G / 45G INFO General (simplification.cpp : 476) Average coverage = 132.33 5:38:06.951 30G / 45G INFO StageManager (stage.cpp : 132) STAGE == Contig Output 5:38:06.957 30G / 45G INFO General (contig_output_stage.cpp : 40) Writing GFA to /DATA/markop/CPB_metaSpades/output//K41/assembly_graph_with_scaffolds.gfa 5:40:01.984 30G / 45G INFO General (contig_output.hpp : 22) Outputting contigs to /DATA/markop/CPB_metaSpades/output//K41/before_rr.fasta 5:41:41.771 30G / 45G INFO General (contig_output_stage.cpp : 51) Outputting FastG graph to /DATA/markop/CPB_metaSpades/output//K41/assembly_graph.fastg 5:47:14.978 30G / 45G INFO General (contig_output.hpp : 22) Outputting contigs to /DATA/markop/CPB_metaSpades/output//K41/simplified_contigs.fasta 5:49:00.009 30G / 45G INFO General (contig_output.hpp : 22) Outputting contigs to /DATA/markop/CPB_metaSpades/output//K41/final_contigs.fasta 5:50:41.375 30G / 45G INFO StageManager (stage.cpp : 132) STAGE == Contig Output 5:50:41.375 30G / 45G INFO General (contig_output_stage.cpp : 40) Writing GFA to /DATA/markop/CPB_metaSpades/output//K41/assembly_graph_with_scaffolds.gfa 5:52:13.938 30G / 45G INFO General (contig_output.hpp : 22) Outputting contigs to /DATA/markop/CPB_metaSpades/output//K41/before_rr.fasta 5:53:54.465 30G / 45G INFO General (contig_output_stage.cpp : 51) Outputting FastG graph to /DATA/markop/CPB_metaSpades/output//K41/assembly_graph.fastg 5:59:13.326 30G / 45G INFO General (contig_output.hpp : 22) Outputting contigs to /DATA/markop/CPB_metaSpades/output//K41/simplified_contigs.fasta 6:00:55.344 30G / 45G INFO General (contig_output.hpp : 22) Outputting contigs to /DATA/markop/CPB_metaSpades/output//K41/final_contigs.fasta 6:02:38.383 30G / 45G INFO General (launch.hpp : 149) SPAdes finished 6:04:42.273 140M / 45G INFO General (main.cpp : 109) Assembling time: 6 hours 4 minutes 42 seconds == Running assembler: K71 0:00:00.000 4M / 4M INFO General (main.cpp : 74) Loaded config from /DATA/markop/CPB_metaSpades/output/K71/configs/config.info 0:00:00.000 4M / 4M INFO General (main.cpp : 74) Loaded config from /DATA/markop/CPB_metaSpades/output/K71/configs/mda_mode.info 0:00:00.000 4M / 4M INFO General (main.cpp : 74) Loaded config from /DATA/markop/CPB_metaSpades/output/K71/configs/meta_mode.info 0:00:00.000 4M / 4M INFO General (memory_limit.cpp : 49) Memory limit set to 230 Gb 0:00:00.000 4M / 4M INFO General (main.cpp : 87) Starting SPAdes, built from refs/heads/spades_3.13.0, git revision 8ea46659e9b2aca35444a808db550ac333006f8b 0:00:00.000 4M / 4M INFO General (main.cpp : 88) Maximum k-mer length: 128 0:00:00.000 4M / 4M INFO General (main.cpp : 89) Assembling dataset (/DATA/markop/CPB_metaSpades/output/dataset.info) with K=71 0:00:00.000 4M / 4M INFO General (main.cpp : 90) Maximum # of threads to use (adjusted due to OMP capabilities): 32 0:00:00.000 4M / 4M INFO General (launch.hpp : 51) SPAdes started 0:00:00.000 4M / 4M INFO General (launch.hpp : 58) Starting from stage: construction 0:00:00.000 4M / 4M INFO General (launch.hpp : 65) Two-step RR enabled: 0 0:00:00.000 4M / 4M INFO General (launch.hpp : 76) Will need read mapping, kmer mapper will be attached 0:00:00.000 4M / 4M INFO StageManager (stage.cpp : 132) STAGE == de Bruijn graph construction 0:00:00.008 4M / 4M INFO General (read_converter.hpp : 59) Binary reads detected 0:00:00.011 4M / 4M INFO General (construction.cpp : 111) Max read length 391 0:00:00.011 4M / 4M INFO General (construction.cpp : 117) Average read length 229.3 0:00:00.011 4M / 4M INFO General (stage.cpp : 101) PROCEDURE == k+1-mer counting 0:00:00.011 4M / 4M INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 1024 files using 32 threads. This might take a while. 0:00:00.012 4M / 4M INFO General (file_limit.hpp : 32) Open file limit set to 10000 0:00:00.012 4M / 4M INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.39579 Gb 0:00:00.012 4M / 4M INFO General (kmer_splitters.hpp : 97) Using cell size of 21845 0:00:12.755 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 15207297 reads 0:00:22.042 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 21278852 reads 0:00:32.468 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 27307485 reads 0:00:42.414 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 33368915 reads 0:00:53.024 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 39309976 reads 0:01:03.036 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 45387241 reads 0:01:13.673 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 51595562 reads 0:01:23.042 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 57268238 reads 0:01:33.422 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 63443181 reads 0:01:43.883 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 69517639 reads 0:01:53.477 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 75265631 reads 0:02:02.118 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 80838718 reads 0:03:30.489 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 135552843 reads 0:07:09.234 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 272905024 reads 0:14:19.384 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 537123187 reads 0:32:41.110 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 1074107474 reads 0:53:26.068 17G / 18G INFO General (kmer_splitters.hpp : 295) Adding contigs from previous K 1:02:49.854 132M / 18G INFO General (kmer_splitters.hpp : 308) Used 1653171754 reads 1:02:49.854 132M / 18G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 2:12:42.967 132M / 18G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 3590364827 kmers in total. 2:12:42.967 132M / 18G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 2:18:01.505 128M / 18G INFO General (stage.cpp : 101) PROCEDURE == Extension index construction 2:18:01.511 128M / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 2:18:01.511 128M / 18G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 512 files using 32 threads. This might take a while. 2:18:01.512 128M / 18G INFO General (file_limit.hpp : 32) Open file limit set to 10000 2:18:01.512 128M / 18G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.39453 Gb 2:18:01.512 128M / 18G INFO General (kmer_splitters.hpp : 97) Using cell size of 43690 2:18:02.098 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 3614726 kmers 2:18:02.681 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 7378981 kmers 2:18:03.196 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 11183311 kmers 2:18:03.795 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 14969735 kmers 2:18:04.412 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 19025172 kmers 2:18:05.090 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 22921320 kmers 2:18:05.697 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 26974987 kmers 2:18:06.363 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 30768015 kmers 2:18:07.437 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 34688653 kmers 2:18:08.981 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 38532352 kmers 2:18:10.750 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 42609769 kmers 2:18:12.513 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 46893943 kmers 2:18:14.488 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 51170187 kmers 2:18:16.206 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 55296215 kmers 2:18:18.192 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 59213498 kmers 2:18:20.313 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 63291984 kmers 2:18:22.561 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 67609739 kmers 2:18:50.082 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 135146701 kmers 2:19:39.706 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 271312352 kmers 2:21:21.698 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 540486341 kmers 2:24:43.257 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 1077410505 kmers 2:31:19.331 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 2150852268 kmers 2:52:28.639 17G / 18G INFO General (kmer_splitters.hpp : 385) Used 3590393499 kmers. 2:52:28.838 128M / 18G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 3:07:28.575 128M / 18G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 3577643922 kmers in total. 3:07:28.576 128M / 18G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 3:15:14.743 128M / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 3:18:32.613 1G / 18G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 3:32:37.209 1G / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 1659000600 bytes occupied (3.70971 bits per kmer). 3:32:40.248 5G / 18G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 99) Building k-mer extensions from k+1-mers 3:53:11.070 5G / 18G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 103) Building k-mer extensions from k+1-mers finished. 3:53:11.077 5G / 18G INFO General (stage.cpp : 101) PROCEDURE == Condensing graph 3:53:11.142 5G / 18G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 355) Extracting unbranching paths 3:58:34.619 11G / 18G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 374) Extracting unbranching paths finished. 90760601 sequences extracted 4:00:58.940 11G / 18G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 310) Collecting perfect loops 4:03:49.230 11G / 18G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 343) Collecting perfect loops finished. 172 loops collected 4:04:44.874 32G / 41G INFO General (stage.cpp : 101) PROCEDURE == Filling coverage indices (PHM) 4:04:44.880 32G / 41G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 4:04:44.880 32G / 41G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 4:13:53.100 34G / 41G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 1664941782 bytes occupied (3.7098 bits per kmer). 4:14:01.597 47G / 47G INFO General (construction.cpp : 388) Collecting k-mer coverage information from reads, this takes a while. 4:59:18.625 47G / 47G INFO General (construction.cpp : 508) Filling coverage and flanking coverage from PHM 5:00:03.404 47G / 47G INFO General (construction.cpp : 464) Processed 32000000 edges 5:00:43.110 47G / 47G INFO General (construction.cpp : 464) Processed 64000000 edges 5:01:23.014 47G / 47G INFO General (construction.cpp : 464) Processed 96000000 edges 5:02:03.140 47G / 47G INFO General (construction.cpp : 464) Processed 128000000 edges 5:02:43.322 47G / 47G INFO General (construction.cpp : 464) Processed 160000000 edges 5:03:10.275 47G / 47G INFO General (construction.cpp : 464) Processed 181518961 edges 5:03:29.970 27G / 47G INFO StageManager (stage.cpp : 132) STAGE == Gap Closer 5:03:29.976 27G / 47G INFO General (graph_pack.hpp : 101) Index refill 5:03:29.976 27G / 47G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 5:03:29.976 27G / 47G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 512 files using 32 threads. This might take a while. 5:03:29.977 27G / 47G INFO General (file_limit.hpp : 32) Open file limit set to 10000 5:03:29.977 27G / 47G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.10779 Gb 5:03:29.977 27G / 47G INFO General (kmer_splitters.hpp : 97) Using cell size of 43690 5:03:55.292 45G / 47G INFO General (edge_index_builders.hpp : 77) Processed 32003376 edges 5:04:17.221 45G / 47G INFO General (edge_index_builders.hpp : 77) Processed 63999718 edges 5:04:46.370 45G / 47G INFO General (edge_index_builders.hpp : 77) Processed 96020239 edges 5:06:58.769 45G / 47G INFO General (edge_index_builders.hpp : 77) Processed 128047309 edges 5:09:06.625 45G / 47G INFO General (edge_index_builders.hpp : 77) Processed 160043632 edges 5:10:33.681 45G / 47G INFO General (edge_index_builders.hpp : 77) Processed 181519121 edges 5:10:33.681 45G / 47G INFO General (edge_index_builders.hpp : 82) Used 181519121 sequences. 5:10:34.952 27G / 47G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 5:21:46.655 27G / 47G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 3590364827 kmers in total. 5:21:46.656 27G / 47G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 5:32:21.481 27G / 47G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 5:35:21.204 29G / 47G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 5:44:20.456 29G / 47G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 1664888054 bytes occupied (3.70968 bits per kmer). 5:45:12.659 109G / 109G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while. 5:47:25.927 109G / 109G INFO General (edge_index.hpp : 92) Index refilled 5:47:26.220 109G / 109G INFO General (gap_closer.cpp : 159) Preparing shift maps 5:50:31.887 113G / 113G INFO General (gap_closer.cpp : 119) Processing paired reads (takes a while) 5:53:07.273 114G / 114G INFO General (gap_closer.cpp : 138) Used 129219073 paired reads 5:53:07.273 114G / 114G INFO General (gap_closer.cpp : 140) Merging paired indices 5:53:42.128 110G / 114G INFO GapCloser (gap_closer.cpp : 346) Closing short gaps 6:03:48.008 110G / 118G INFO GapCloser (gap_closer.cpp : 380) Closing short gaps complete: filled 112713 gaps after checking 994271 candidates 6:05:22.433 109G / 118G INFO StageManager (stage.cpp : 132) STAGE == Raw Simplification 6:05:28.293 27G / 118G INFO General (simplification.cpp : 128) PROCEDURE == InitialCleaning 6:05:28.295 27G / 118G INFO General (graph_simplification.hpp : 662) Flanking coverage based disconnection disabled 6:05:28.295 27G / 118G INFO Simplification (parallel_processing.hpp : 165) Running Self conjugate edge remover 6:05:35.550 27G / 118G INFO Simplification (parallel_processing.hpp : 167) Self conjugate edge remover triggered 183 times 6:05:35.550 27G / 118G INFO Simplification (parallel_processing.hpp : 165) Running Initial tip clipper 6:12:26.114 28G / 118G INFO Simplification (parallel_processing.hpp : 167) Initial tip clipper triggered 15402076 times 6:12:26.114 28G / 118G INFO Simplification (parallel_processing.hpp : 165) Running Initial ec remover 6:16:58.280 28G / 118G INFO Simplification (parallel_processing.hpp : 167) Initial ec remover triggered 4147418 times 6:16:58.280 28G / 118G INFO Simplification (parallel_processing.hpp : 165) Running Initial isolated edge remover 6:18:02.890 28G / 118G INFO Simplification (parallel_processing.hpp : 167) Initial isolated edge remover triggered 5463077 times 6:18:10.648 28G / 118G INFO StageManager (stage.cpp : 132) STAGE == Simplification 6:18:10.648 28G / 118G INFO General (simplification.cpp : 357) Graph simplification started 6:18:10.648 28G / 118G INFO General (graph_simplification.hpp : 634) Creating parallel br instance 6:18:10.648 28G / 118G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 1 6:18:10.648 28G / 118G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 6:18:42.970 28G / 118G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 1264098 times 6:18:42.970 28G / 118G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 8:21:50.763 112G / 118G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 7039138 times 8:21:50.763 112G / 118G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 8:21:55.237 112G / 118G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 185 times 8:21:55.237 112G / 118G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 2 8:21:55.237 112G / 118G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 8:22:09.571 112G / 118G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 40908 times 8:22:09.571 112G / 118G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 8:22:14.244 112G / 118G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 1767 times 8:22:14.244 112G / 118G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 8:22:21.151 112G / 118G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 107521 times 8:22:21.151 112G / 118G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 3 8:22:21.151 112G / 118G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 8:22:21.602 112G / 118G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 5565 times 8:22:21.602 112G / 118G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 8:23:20.743 113G / 118G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 27925 times 8:23:20.743 113G / 118G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 8:24:10.658 113G / 118G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 705547 times 8:24:10.658 113G / 118G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 4 8:24:10.658 113G / 118G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 8:24:15.080 113G / 118G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 23351 times 8:24:15.081 113G / 118G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 8:34:27.333 115G / 118G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 190061 times 8:34:27.333 115G / 118G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 8:34:30.849 115G / 118G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 35 times 8:34:30.849 115G / 118G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 5 8:34:30.849 115G / 118G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 8:34:32.553 115G / 118G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 757 times 8:34:32.553 115G / 118G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 8:34:32.811 115G / 118G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 48 times 8:34:32.811 115G / 118G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 8:34:32.811 115G / 118G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 8:34:32.811 115G / 118G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 6 8:34:32.811 115G / 118G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 8:34:32.811 115G / 118G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 1 times 8:34:32.811 115G / 118G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 8:34:32.811 115G / 118G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 8:34:32.811 115G / 118G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 8:34:32.811 115G / 118G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 8:34:32.811 115G / 118G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 7 8:34:32.811 115G / 118G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 8:34:32.811 115G / 118G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 8:34:32.811 115G / 118G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 8:34:32.811 115G / 118G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 8:34:32.811 115G / 118G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 8:34:32.811 115G / 118G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 8:34:32.812 115G / 118G INFO StageManager (stage.cpp : 132) STAGE == Gap Closer 8:34:32.812 115G / 118G INFO General (graph_pack.hpp : 101) Index refill 8:34:32.812 115G / 118G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 8:34:32.812 115G / 118G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 512 files using 32 threads. This might take a while. 8:34:32.812 115G / 118G INFO General (file_limit.hpp : 32) Open file limit set to 10000 8:34:32.812 115G / 118G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 1.19157 Gb 8:34:32.812 115G / 118G INFO General (kmer_splitters.hpp : 97) Using cell size of 43690 8:34:55.225 133G / 134G INFO General (edge_index_builders.hpp : 77) Processed 14696826 edges 8:35:52.374 133G / 134G INFO General (edge_index_builders.hpp : 77) Processed 29353942 edges 8:36:36.005 133G / 134G INFO General (edge_index_builders.hpp : 77) Processed 36139634 edges 8:36:36.005 133G / 134G INFO General (edge_index_builders.hpp : 82) Used 36139634 sequences. 8:36:37.760 115G / 134G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 8:39:31.413 115G / 134G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 1661224144 kmers in total. 8:39:31.413 115G / 134G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 8:42:41.596 115G / 134G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 8:43:54.503 116G / 134G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 8:49:06.554 116G / 134G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 770339136 bytes occupied (3.70974 bits per kmer). 8:49:37.707 153G / 153G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while. 8:50:37.790 153G / 153G INFO General (edge_index.hpp : 92) Index refilled 8:50:37.792 153G / 153G INFO General (gap_closer.cpp : 159) Preparing shift maps 8:51:11.521 153G / 153G INFO General (gap_closer.cpp : 119) Processing paired reads (takes a while) 8:59:29.141 153G / 153G INFO General (gap_closer.cpp : 138) Used 129219073 paired reads 8:59:29.141 153G / 153G INFO General (gap_closer.cpp : 140) Merging paired indices 8:59:31.876 153G / 153G INFO GapCloser (gap_closer.cpp : 346) Closing short gaps 9:01:08.096 153G / 154G INFO GapCloser (gap_closer.cpp : 380) Closing short gaps complete: filled 1530 gaps after checking 54313 candidates 9:01:18.932 153G / 154G INFO StageManager (stage.cpp : 132) STAGE == Simplification Cleanup 9:01:18.932 153G / 154G INFO General (simplification.cpp : 196) PROCEDURE == Post simplification 9:01:18.932 153G / 154G INFO General (graph_simplification.hpp : 634) Creating parallel br instance 9:01:18.932 153G / 154G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover 9:19:18.187 153G / 154G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 1140437 times 9:19:18.187 153G / 154G INFO Simplification (parallel_processing.hpp : 165) Running Disconnecting edges with relatively low coverage 9:40:14.036 153G / 154G INFO Simplification (parallel_processing.hpp : 167) Disconnecting edges with relatively low coverage triggered 1417969 times 9:40:14.036 153G / 154G INFO Simplification (parallel_processing.hpp : 165) Running Complex tip clipper 9:42:19.557 153G / 154G INFO Simplification (parallel_processing.hpp : 167) Complex tip clipper triggered 236384 times 9:42:19.557 153G / 154G INFO Simplification (parallel_processing.hpp : 165) Running Complex bulge remover 9:58:49.390 157G / 157G INFO Simplification (parallel_processing.hpp : 167) Complex bulge remover triggered 156575 times 9:58:49.390 157G / 157G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 10:04:44.734 157G / 157G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 840488 times 10:04:44.734 157G / 157G INFO Simplification (parallel_processing.hpp : 165) Running Final tip clipper 10:04:52.546 157G / 157G INFO Simplification (parallel_processing.hpp : 167) Final tip clipper triggered 3106 times 10:04:52.546 157G / 157G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 10:13:15.738 159G / 159G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 140291 times 10:13:15.738 159G / 159G INFO Simplification (parallel_processing.hpp : 165) Running Thorn remover (meta) 10:13:31.839 159G / 159G INFO Simplification (parallel_processing.hpp : 167) Thorn remover (meta) triggered 20 times 10:13:31.839 159G / 159G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover 10:14:34.948 159G / 159G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 34950 times 10:14:34.949 159G / 159G INFO Simplification (parallel_processing.hpp : 165) Running Disconnecting edges with relatively low coverage 10:21:08.397 158G / 159G INFO Simplification (parallel_processing.hpp : 167) Disconnecting edges with relatively low coverage triggered 221397 times 10:21:08.397 158G / 159G INFO Simplification (parallel_processing.hpp : 165) Running Complex tip clipper 10:21:27.282 158G / 159G INFO Simplification (parallel_processing.hpp : 167) Complex tip clipper triggered 22468 times 10:21:27.282 158G / 159G INFO Simplification (parallel_processing.hpp : 165) Running Complex bulge remover 10:22:51.643 159G / 159G INFO Simplification (parallel_processing.hpp : 167) Complex bulge remover triggered 7831 times 10:22:51.643 159G / 159G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 10:24:45.704 159G / 159G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 200654 times 10:24:45.704 159G / 159G INFO Simplification (parallel_processing.hpp : 165) Running Final tip clipper 10:24:50.533 159G / 159G INFO Simplification (parallel_processing.hpp : 167) Final tip clipper triggered 997 times 10:24:50.533 159G / 159G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 10:26:50.232 159G / 159G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 23558 times 10:26:50.232 159G / 159G INFO Simplification (parallel_processing.hpp : 165) Running Thorn remover (meta) 10:27:01.194 159G / 159G INFO Simplification (parallel_processing.hpp : 167) Thorn remover (meta) triggered 0 times 10:27:01.194 159G / 159G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover 10:27:26.981 159G / 159G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 5916 times 10:27:26.981 159G / 159G INFO Simplification (parallel_processing.hpp : 165) Running Disconnecting edges with relatively low coverage 10:28:16.637 159G / 159G INFO Simplification (parallel_processing.hpp : 167) Disconnecting edges with relatively low coverage triggered 6156 times 10:28:16.637 159G / 159G INFO Simplification (parallel_processing.hpp : 165) Running Complex tip clipper 10:28:20.389 159G / 159G INFO Simplification (parallel_processing.hpp : 167) Complex tip clipper triggered 1623 times 10:28:20.389 159G / 159G INFO Simplification (parallel_processing.hpp : 165) Running Complex bulge remover 10:29:03.508 159G / 159G INFO Simplification (parallel_processing.hpp : 167) Complex bulge remover triggered 1414 times 10:29:03.508 159G / 159G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 10:29:08.019 159G / 159G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 5895 times 10:29:08.019 159G / 159G INFO Simplification (parallel_processing.hpp : 165) Running Final tip clipper 10:29:08.392 159G / 159G INFO Simplification (parallel_processing.hpp : 167) Final tip clipper triggered 25 times 10:29:08.392 159G / 159G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 10:29:13.309 159G / 159G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 968 times 10:29:13.309 159G / 159G INFO Simplification (parallel_processing.hpp : 165) Running Thorn remover (meta) 10:29:13.508 159G / 159G INFO Simplification (parallel_processing.hpp : 167) Thorn remover (meta) triggered 0 times 10:29:13.508 159G / 159G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover 10:29:33.352 159G / 159G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 309 times 10:29:33.352 159G / 159G INFO Simplification (parallel_processing.hpp : 165) Running Disconnecting edges with relatively low coverage 10:29:35.292 159G / 159G INFO Simplification (parallel_processing.hpp : 167) Disconnecting edges with relatively low coverage triggered 265 times 10:29:35.292 159G / 159G INFO Simplification (parallel_processing.hpp : 165) Running Complex tip clipper 10:29:36.348 159G / 159G INFO Simplification (parallel_processing.hpp : 167) Complex tip clipper triggered 53 times 10:29:36.348 159G / 159G INFO Simplification (parallel_processing.hpp : 165) Running Complex bulge remover 10:30:08.365 159G / 159G INFO Simplification (parallel_processing.hpp : 167) Complex bulge remover triggered 58 times 10:30:08.365 159G / 159G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 10:30:08.568 159G / 159G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 229 times 10:30:08.569 159G / 159G INFO Simplification (parallel_processing.hpp : 165) Running Final tip clipper 10:30:08.577 159G / 159G INFO Simplification (parallel_processing.hpp : 167) Final tip clipper triggered 0 times 10:30:08.577 159G / 159G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 10:30:08.896 159G / 159G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 51 times 10:30:08.896 159G / 159G INFO Simplification (parallel_processing.hpp : 165) Running Thorn remover (meta) 10:30:08.915 159G / 159G INFO Simplification (parallel_processing.hpp : 167) Thorn remover (meta) triggered 0 times 10:30:08.916 159G / 159G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover 10:30:27.952 159G / 159G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 14 times 10:30:27.952 159G / 159G INFO Simplification (parallel_processing.hpp : 165) Running Disconnecting edges with relatively low coverage 10:30:28.038 159G / 159G INFO Simplification (parallel_processing.hpp : 167) Disconnecting edges with relatively low coverage triggered 14 times 10:30:28.038 159G / 159G INFO Simplification (parallel_processing.hpp : 165) Running Complex tip clipper 10:30:29.351 159G / 159G INFO Simplification (parallel_processing.hpp : 167) Complex tip clipper triggered 5 times 10:30:29.352 159G / 159G INFO Simplification (parallel_processing.hpp : 165) Running Complex bulge remover 10:31:01.015 159G / 159G INFO Simplification (parallel_processing.hpp : 167) Complex bulge remover triggered 4 times 10:31:01.015 159G / 159G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 10:31:01.039 159G / 159G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 12 times 10:31:01.039 159G / 159G INFO Simplification (parallel_processing.hpp : 165) Running Final tip clipper 10:31:01.040 159G / 159G INFO Simplification (parallel_processing.hpp : 167) Final tip clipper triggered 0 times 10:31:01.040 159G / 159G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 10:31:01.058 159G / 159G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 2 times 10:31:01.058 159G / 159G INFO Simplification (parallel_processing.hpp : 165) Running Thorn remover (meta) 10:31:01.058 159G / 159G INFO Simplification (parallel_processing.hpp : 167) Thorn remover (meta) triggered 0 times 10:31:01.058 159G / 159G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover 10:31:19.135 159G / 159G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 1 times 10:31:19.137 159G / 159G INFO Simplification (parallel_processing.hpp : 165) Running Disconnecting edges with relatively low coverage 10:31:19.150 159G / 159G INFO Simplification (parallel_processing.hpp : 167) Disconnecting edges with relatively low coverage triggered 3 times 10:31:19.150 159G / 159G INFO Simplification (parallel_processing.hpp : 165) Running Complex tip clipper 10:31:20.180 159G / 159G INFO Simplification (parallel_processing.hpp : 167) Complex tip clipper triggered 0 times 10:31:20.180 159G / 159G INFO Simplification (parallel_processing.hpp : 165) Running Complex bulge remover 10:31:52.468 159G / 159G INFO Simplification (parallel_processing.hpp : 167) Complex bulge remover triggered 1 times 10:31:52.468 159G / 159G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 10:31:52.472 159G / 159G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 2 times 10:31:52.472 159G / 159G INFO Simplification (parallel_processing.hpp : 165) Running Final tip clipper 10:31:52.472 159G / 159G INFO Simplification (parallel_processing.hpp : 167) Final tip clipper triggered 0 times 10:31:52.472 159G / 159G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 10:31:52.472 159G / 159G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 10:31:52.472 159G / 159G INFO Simplification (parallel_processing.hpp : 165) Running Thorn remover (meta) 10:31:52.472 159G / 159G INFO Simplification (parallel_processing.hpp : 167) Thorn remover (meta) triggered 0 times 10:31:52.472 159G / 159G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover 10:32:10.448 159G / 159G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 1 times 10:32:10.449 159G / 159G INFO Simplification (parallel_processing.hpp : 165) Running Disconnecting edges with relatively low coverage 10:32:10.451 159G / 159G INFO Simplification (parallel_processing.hpp : 167) Disconnecting edges with relatively low coverage triggered 0 times 10:32:10.451 159G / 159G INFO Simplification (parallel_processing.hpp : 165) Running Complex tip clipper 10:32:11.448 159G / 159G INFO Simplification (parallel_processing.hpp : 167) Complex tip clipper triggered 0 times 10:32:11.448 159G / 159G INFO Simplification (parallel_processing.hpp : 165) Running Complex bulge remover 10:32:43.631 159G / 159G INFO Simplification (parallel_processing.hpp : 167) Complex bulge remover triggered 1 times 10:32:43.631 159G / 159G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 10:32:43.631 159G / 159G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 10:32:43.631 159G / 159G INFO Simplification (parallel_processing.hpp : 165) Running Final tip clipper 10:32:43.631 159G / 159G INFO Simplification (parallel_processing.hpp : 167) Final tip clipper triggered 0 times 10:32:43.631 159G / 159G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 10:32:43.633 159G / 159G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 1 times 10:32:43.633 159G / 159G INFO Simplification (parallel_processing.hpp : 165) Running Thorn remover (meta) 10:32:43.633 159G / 159G INFO Simplification (parallel_processing.hpp : 167) Thorn remover (meta) triggered 0 times 10:32:43.633 159G / 159G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover 10:33:02.181 159G / 159G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 0 times 10:33:02.181 159G / 159G INFO Simplification (parallel_processing.hpp : 165) Running Disconnecting edges with relatively low coverage 10:33:02.194 159G / 159G INFO Simplification (parallel_processing.hpp : 167) Disconnecting edges with relatively low coverage triggered 1 times 10:33:02.195 159G / 159G INFO Simplification (parallel_processing.hpp : 165) Running Complex tip clipper 10:33:03.219 159G / 159G INFO Simplification (parallel_processing.hpp : 167) Complex tip clipper triggered 0 times 10:33:03.219 159G / 159G INFO Simplification (parallel_processing.hpp : 165) Running Complex bulge remover 10:33:34.770 159G / 159G INFO Simplification (parallel_processing.hpp : 167) Complex bulge remover triggered 0 times 10:33:34.770 159G / 159G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 10:33:34.770 159G / 159G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 10:33:34.770 159G / 159G INFO Simplification (parallel_processing.hpp : 165) Running Final tip clipper 10:33:34.770 159G / 159G INFO Simplification (parallel_processing.hpp : 167) Final tip clipper triggered 0 times 10:33:34.770 159G / 159G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 10:33:34.770 159G / 159G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 10:33:34.770 159G / 159G INFO Simplification (parallel_processing.hpp : 165) Running Thorn remover (meta) 10:33:34.770 159G / 159G INFO Simplification (parallel_processing.hpp : 167) Thorn remover (meta) triggered 0 times 10:33:34.770 159G / 159G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover 10:33:54.634 159G / 159G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 0 times 10:33:54.634 159G / 159G INFO Simplification (parallel_processing.hpp : 165) Running Disconnecting edges with relatively low coverage 10:33:54.634 159G / 159G INFO Simplification (parallel_processing.hpp : 167) Disconnecting edges with relatively low coverage triggered 0 times 10:33:54.634 159G / 159G INFO Simplification (parallel_processing.hpp : 165) Running Complex tip clipper 10:33:55.676 159G / 159G INFO Simplification (parallel_processing.hpp : 167) Complex tip clipper triggered 0 times 10:33:55.676 159G / 159G INFO Simplification (parallel_processing.hpp : 165) Running Complex bulge remover 10:34:27.580 159G / 159G INFO Simplification (parallel_processing.hpp : 167) Complex bulge remover triggered 0 times 10:34:27.580 159G / 159G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 10:34:27.580 159G / 159G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 10:34:27.580 159G / 159G INFO Simplification (parallel_processing.hpp : 165) Running Final tip clipper 10:34:27.580 159G / 159G INFO Simplification (parallel_processing.hpp : 167) Final tip clipper triggered 0 times 10:34:27.580 159G / 159G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 10:34:27.580 159G / 159G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 10:34:27.580 159G / 159G INFO Simplification (parallel_processing.hpp : 165) Running Thorn remover (meta) 10:34:27.580 159G / 159G INFO Simplification (parallel_processing.hpp : 167) Thorn remover (meta) triggered 0 times 10:34:27.580 159G / 159G INFO General (simplification.cpp : 326) Running Hidden EC remover (meta) 10:34:29.808 159G / 159G INFO General (simplification.cpp : 330) Disrupting self-conjugate edges 10:34:56.093 159G / 159G INFO Simplification (parallel_processing.hpp : 165) Running Removing isolated edges 10:35:12.695 159G / 159G INFO Simplification (parallel_processing.hpp : 167) Removing isolated edges triggered 33356 times 10:35:12.695 159G / 159G INFO General (simplification.cpp : 470) Counting average coverage 10:35:24.557 159G / 159G INFO General (simplification.cpp : 476) Average coverage = 92.2438 10:35:24.557 159G / 159G INFO StageManager (stage.cpp : 132) STAGE == Contig Output 10:35:24.563 159G / 159G INFO General (contig_output_stage.cpp : 40) Writing GFA to /DATA/markop/CPB_metaSpades/output//K71/assembly_graph_with_scaffolds.gfa 10:36:18.591 159G / 159G INFO General (contig_output.hpp : 22) Outputting contigs to /DATA/markop/CPB_metaSpades/output//K71/before_rr.fasta 10:37:28.892 159G / 159G INFO General (contig_output_stage.cpp : 51) Outputting FastG graph to /DATA/markop/CPB_metaSpades/output//K71/assembly_graph.fastg 10:40:48.693 159G / 159G INFO General (contig_output.hpp : 22) Outputting contigs to /DATA/markop/CPB_metaSpades/output//K71/simplified_contigs.fasta 10:41:50.636 159G / 159G INFO General (contig_output.hpp : 22) Outputting contigs to /DATA/markop/CPB_metaSpades/output//K71/final_contigs.fasta 10:42:52.747 159G / 159G INFO StageManager (stage.cpp : 132) STAGE == Contig Output 10:42:52.747 159G / 159G INFO General (contig_output_stage.cpp : 40) Writing GFA to /DATA/markop/CPB_metaSpades/output//K71/assembly_graph_with_scaffolds.gfa 10:43:49.494 159G / 159G INFO General (contig_output.hpp : 22) Outputting contigs to /DATA/markop/CPB_metaSpades/output//K71/before_rr.fasta 10:44:51.895 159G / 159G INFO General (contig_output_stage.cpp : 51) Outputting FastG graph to /DATA/markop/CPB_metaSpades/output//K71/assembly_graph.fastg 10:48:07.760 159G / 159G INFO General (contig_output.hpp : 22) Outputting contigs to /DATA/markop/CPB_metaSpades/output//K71/simplified_contigs.fasta 10:49:15.426 159G / 159G INFO General (contig_output.hpp : 22) Outputting contigs to /DATA/markop/CPB_metaSpades/output//K71/final_contigs.fasta 10:50:21.401 159G / 159G INFO General (launch.hpp : 149) SPAdes finished 11:23:17.949 136M / 159G INFO General (main.cpp : 109) Assembling time: 11 hours 23 minutes 17 seconds == Running assembler: K101 0:00:00.000 4M / 4M INFO General (main.cpp : 74) Loaded config from /DATA/markop/CPB_metaSpades/output/K101/configs/config.info 0:00:00.000 4M / 4M INFO General (main.cpp : 74) Loaded config from /DATA/markop/CPB_metaSpades/output/K101/configs/mda_mode.info 0:00:00.000 4M / 4M INFO General (main.cpp : 74) Loaded config from /DATA/markop/CPB_metaSpades/output/K101/configs/meta_mode.info 0:00:00.000 4M / 4M INFO General (memory_limit.cpp : 49) Memory limit set to 230 Gb 0:00:00.000 4M / 4M INFO General (main.cpp : 87) Starting SPAdes, built from refs/heads/spades_3.13.0, git revision 8ea46659e9b2aca35444a808db550ac333006f8b 0:00:00.000 4M / 4M INFO General (main.cpp : 88) Maximum k-mer length: 128 0:00:00.000 4M / 4M INFO General (main.cpp : 89) Assembling dataset (/DATA/markop/CPB_metaSpades/output/dataset.info) with K=101 0:00:00.000 4M / 4M INFO General (main.cpp : 90) Maximum # of threads to use (adjusted due to OMP capabilities): 32 0:00:00.000 4M / 4M INFO General (launch.hpp : 51) SPAdes started 0:00:00.000 4M / 4M INFO General (launch.hpp : 58) Starting from stage: construction 0:00:00.000 4M / 4M INFO General (launch.hpp : 65) Two-step RR enabled: 0 0:00:00.000 4M / 4M INFO General (launch.hpp : 76) Will need read mapping, kmer mapper will be attached 0:00:00.000 4M / 4M INFO StageManager (stage.cpp : 132) STAGE == de Bruijn graph construction 0:00:00.001 4M / 4M INFO General (read_converter.hpp : 59) Binary reads detected 0:00:00.122 4M / 4M INFO General (construction.cpp : 111) Max read length 391 0:00:00.122 4M / 4M INFO General (construction.cpp : 117) Average read length 229.3 0:00:00.122 4M / 4M INFO General (stage.cpp : 101) PROCEDURE == k+1-mer counting 0:00:00.122 4M / 4M INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 1024 files using 32 threads. This might take a while. 0:00:00.124 4M / 4M INFO General (file_limit.hpp : 32) Open file limit set to 10000 0:00:00.124 4M / 4M INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.39579 Gb 0:00:00.124 4M / 4M INFO General (kmer_splitters.hpp : 97) Using cell size of 16384 0:00:14.909 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 15118831 reads 0:00:33.335 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 20591011 reads 0:00:47.938 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 26067004 reads 0:01:07.061 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 31560368 reads 0:01:20.256 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 36863364 reads 0:01:33.879 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 42381438 reads 0:01:43.091 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 47730744 reads 0:01:55.983 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 53055567 reads 0:02:08.827 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 58228556 reads 0:02:22.534 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 63770533 reads 0:02:31.333 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 68881734 reads 0:02:40.063 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 74255829 reads 0:04:22.557 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 136970261 reads 0:07:58.851 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 271528096 reads 0:24:08.848 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 540003898 reads 1:04:00.395 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 1077258199 reads 1:23:20.640 17G / 18G INFO General (kmer_splitters.hpp : 295) Adding contigs from previous K 1:32:44.565 132M / 18G INFO General (kmer_splitters.hpp : 308) Used 1653171754 reads 1:32:44.566 132M / 18G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 3:03:47.764 132M / 18G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 3774429990 kmers in total. 3:03:47.764 132M / 18G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 3:14:10.281 128M / 18G INFO General (stage.cpp : 101) PROCEDURE == Extension index construction 3:14:10.281 128M / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 3:14:10.281 128M / 18G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 512 files using 32 threads. This might take a while. 3:14:10.281 128M / 18G INFO General (file_limit.hpp : 32) Open file limit set to 10000 3:14:10.281 128M / 18G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.39453 Gb 3:14:10.281 128M / 18G INFO General (kmer_splitters.hpp : 97) Using cell size of 32768 3:14:10.783 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 2765081 kmers 3:14:11.236 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 5565196 kmers 3:14:11.723 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 8482599 kmers 3:14:12.247 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 11379103 kmers 3:14:12.936 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 14185777 kmers 3:14:13.777 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 17110568 kmers 3:14:14.819 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 20142587 kmers 3:14:16.511 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 23051793 kmers 3:14:18.705 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 26091060 kmers 3:14:21.466 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 29014597 kmers 3:14:24.337 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 31832339 kmers 3:14:26.501 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 34759173 kmers 3:14:28.075 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 37644994 kmers 3:14:29.547 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 40563380 kmers 3:14:31.465 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 43589298 kmers 3:14:33.065 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 46713845 kmers 3:14:45.828 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 68232287 kmers 3:15:21.984 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 135060613 kmers 3:16:34.325 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 270677633 kmers 3:18:55.224 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 536903490 kmers 3:23:50.081 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 1075764187 kmers 3:35:32.432 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 2149230595 kmers 4:26:08.832 17G / 18G INFO General (kmer_splitters.hpp : 385) Used 3774469926 kmers. 4:26:09.054 128M / 18G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 5:00:29.652 128M / 18G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 3772357944 kmers in total. 5:00:29.652 128M / 18G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 5:08:27.682 128M / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 5:12:36.876 1G / 18G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 5:26:24.454 1G / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 1749268740 bytes occupied (3.70966 bits per kmer). 5:26:28.828 5G / 18G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 99) Building k-mer extensions from k+1-mers 6:29:47.033 5G / 18G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 103) Building k-mer extensions from k+1-mers finished. 6:29:47.038 5G / 18G INFO General (stage.cpp : 101) PROCEDURE == Condensing graph 6:29:47.144 5G / 18G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 355) Extracting unbranching paths 6:37:00.190 11G / 18G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 374) Extracting unbranching paths finished. 73106921 sequences extracted 6:40:16.132 11G / 18G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 310) Collecting perfect loops 6:44:22.043 11G / 18G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 343) Collecting perfect loops finished. 130 loops collected 6:45:25.227 29G / 36G INFO General (stage.cpp : 101) PROCEDURE == Filling coverage indices (PHM) 6:45:25.227 29G / 36G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 6:45:25.227 29G / 36G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 6:59:30.956 31G / 36G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 1750271336 bytes occupied (3.70974 bits per kmer). 6:59:40.890 45G / 45G INFO General (construction.cpp : 388) Collecting k-mer coverage information from reads, this takes a while. 7:46:13.955 45G / 45G INFO General (construction.cpp : 508) Filling coverage and flanking coverage from PHM 7:47:21.699 45G / 45G INFO General (construction.cpp : 464) Processed 32000000 edges 7:48:26.174 45G / 45G INFO General (construction.cpp : 464) Processed 64000000 edges 7:49:32.308 45G / 45G INFO General (construction.cpp : 464) Processed 96000000 edges 7:50:35.664 45G / 45G INFO General (construction.cpp : 464) Processed 128000000 edges 7:51:12.469 45G / 45G INFO General (construction.cpp : 464) Processed 146213612 edges 7:51:48.653 23G / 45G INFO StageManager (stage.cpp : 132) STAGE == Gap Closer 7:51:48.653 23G / 45G INFO General (graph_pack.hpp : 101) Index refill 7:51:48.653 23G / 45G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 7:51:48.653 23G / 45G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 512 files using 32 threads. This might take a while. 7:51:48.654 23G / 45G INFO General (file_limit.hpp : 32) Open file limit set to 10000 7:51:48.654 23G / 45G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.14608 Gb 7:51:48.654 23G / 45G INFO General (kmer_splitters.hpp : 97) Using cell size of 32768 7:52:15.299 41G / 45G INFO General (edge_index_builders.hpp : 77) Processed 18794221 edges 7:52:39.473 41G / 45G INFO General (edge_index_builders.hpp : 77) Processed 37606340 edges 7:53:18.342 41G / 45G INFO General (edge_index_builders.hpp : 77) Processed 56422731 edges 7:55:04.980 41G / 45G INFO General (edge_index_builders.hpp : 77) Processed 75194331 edges 7:56:49.566 41G / 45G INFO General (edge_index_builders.hpp : 77) Processed 94007507 edges 7:58:35.755 41G / 45G INFO General (edge_index_builders.hpp : 77) Processed 112812535 edges 8:00:23.216 41G / 45G INFO General (edge_index_builders.hpp : 77) Processed 131610693 edges 8:01:46.008 41G / 45G INFO General (edge_index_builders.hpp : 77) Processed 146213836 edges 8:01:46.008 41G / 45G INFO General (edge_index_builders.hpp : 82) Used 146213836 sequences. 8:01:47.395 23G / 45G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 8:14:54.157 23G / 45G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 3774429990 kmers in total. 8:14:54.157 23G / 45G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 8:28:29.162 23G / 45G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 8:32:41.253 25G / 45G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 8:48:33.646 25G / 45G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 1750231774 bytes occupied (3.70966 bits per kmer). 8:49:36.200 110G / 110G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while. 8:52:25.957 110G / 110G INFO General (edge_index.hpp : 92) Index refilled 8:52:26.230 110G / 110G INFO General (gap_closer.cpp : 159) Preparing shift maps 8:55:32.122 115G / 115G INFO General (gap_closer.cpp : 119) Processing paired reads (takes a while) 8:57:23.876 116G / 116G INFO General (gap_closer.cpp : 138) Used 129219073 paired reads 8:57:23.876 116G / 116G INFO General (gap_closer.cpp : 140) Merging paired indices 8:58:08.057 110G / 116G INFO GapCloser (gap_closer.cpp : 346) Closing short gaps 9:06:26.095 110G / 117G INFO GapCloser (gap_closer.cpp : 380) Closing short gaps complete: filled 117317 gaps after checking 1105008 candidates 9:08:12.721 110G / 117G INFO StageManager (stage.cpp : 132) STAGE == Raw Simplification 9:08:18.819 24G / 117G INFO General (simplification.cpp : 128) PROCEDURE == InitialCleaning 9:08:18.822 24G / 117G INFO General (graph_simplification.hpp : 662) Flanking coverage based disconnection disabled 9:08:18.822 24G / 117G INFO Simplification (parallel_processing.hpp : 165) Running Self conjugate edge remover 9:08:27.265 24G / 117G INFO Simplification (parallel_processing.hpp : 167) Self conjugate edge remover triggered 36 times 9:08:27.265 24G / 117G INFO Simplification (parallel_processing.hpp : 165) Running Initial tip clipper 9:15:45.848 24G / 117G INFO Simplification (parallel_processing.hpp : 167) Initial tip clipper triggered 13592223 times 9:15:45.848 24G / 117G INFO Simplification (parallel_processing.hpp : 165) Running Initial ec remover 9:18:50.992 24G / 117G INFO Simplification (parallel_processing.hpp : 167) Initial ec remover triggered 2403702 times 9:18:50.992 24G / 117G INFO Simplification (parallel_processing.hpp : 165) Running Initial isolated edge remover 9:20:46.067 24G / 117G INFO Simplification (parallel_processing.hpp : 167) Initial isolated edge remover triggered 9080535 times 9:20:53.044 24G / 117G INFO StageManager (stage.cpp : 132) STAGE == Simplification 9:20:53.044 24G / 117G INFO General (simplification.cpp : 357) Graph simplification started 9:20:53.045 24G / 117G INFO General (graph_simplification.hpp : 634) Creating parallel br instance 9:20:53.045 24G / 117G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 1 9:20:53.045 24G / 117G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 9:21:46.334 24G / 117G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 1814615 times 9:21:46.334 24G / 117G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 11:34:49.685 114G / 117G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 4586458 times 11:34:49.685 114G / 117G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 11:34:53.407 114G / 117G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 119 times 11:34:53.407 114G / 117G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 2 11:34:53.407 114G / 117G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 11:35:02.154 114G / 117G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 25922 times 11:35:02.154 114G / 117G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 11:35:10.144 114G / 117G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 1352 times 11:35:10.144 114G / 117G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 11:35:14.941 114G / 117G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 64519 times 11:35:14.941 114G / 117G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 3 11:35:14.941 114G / 117G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 11:35:15.375 114G / 117G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 3836 times 11:35:15.375 114G / 117G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 11:36:17.990 114G / 117G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 19425 times 11:36:17.990 114G / 117G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 11:37:06.572 114G / 117G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 487195 times 11:37:06.572 114G / 117G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 4 11:37:06.572 114G / 117G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 11:37:11.584 114G / 117G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 25446 times 11:37:11.584 114G / 117G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 11:47:01.619 117G / 117G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 144200 times 11:47:01.619 117G / 117G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 11:47:05.952 117G / 117G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 24 times 11:47:05.952 117G / 117G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 5 11:47:05.952 117G / 117G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 11:47:07.542 117G / 117G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 973 times 11:47:07.542 117G / 117G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 11:47:08.084 117G / 117G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 64 times 11:47:08.084 117G / 117G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 11:47:08.084 117G / 117G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 11:47:08.084 117G / 117G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 6 11:47:08.084 117G / 117G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 11:47:08.085 117G / 117G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 11:47:08.085 117G / 117G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 11:47:08.085 117G / 117G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 11:47:08.085 117G / 117G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 11:47:08.085 117G / 117G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 11:47:08.086 117G / 117G INFO StageManager (stage.cpp : 132) STAGE == Gap Closer 11:47:08.086 117G / 117G INFO General (graph_pack.hpp : 101) Index refill 11:47:08.087 117G / 117G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 11:47:08.087 117G / 117G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 512 files using 32 threads. This might take a while. 11:47:08.087 117G / 117G INFO General (file_limit.hpp : 32) Open file limit set to 10000 11:47:08.087 117G / 117G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 1.16866 Gb 11:47:08.087 117G / 117G INFO General (kmer_splitters.hpp : 97) Using cell size of 32768 11:47:32.764 135G / 136G INFO General (edge_index_builders.hpp : 77) Processed 6449115 edges 11:48:49.570 135G / 136G INFO General (edge_index_builders.hpp : 77) Processed 12889683 edges 11:50:41.821 135G / 136G INFO General (edge_index_builders.hpp : 77) Processed 19344547 edges 11:51:41.783 135G / 136G INFO General (edge_index_builders.hpp : 77) Processed 22944845 edges 11:51:41.783 135G / 136G INFO General (edge_index_builders.hpp : 82) Used 22944845 sequences. 11:51:43.025 117G / 136G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 11:57:59.597 117G / 136G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 1834528053 kmers in total. 11:57:59.598 117G / 136G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 12:04:12.996 117G / 136G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 12:06:06.868 118G / 136G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 12:13:48.451 118G / 136G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 850691774 bytes occupied (3.70969 bits per kmer). 12:14:23.885 159G / 159G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while. 12:15:42.557 159G / 159G INFO General (edge_index.hpp : 92) Index refilled 12:15:42.558 159G / 159G INFO General (gap_closer.cpp : 159) Preparing shift maps 12:16:03.761 159G / 159G INFO General (gap_closer.cpp : 119) Processing paired reads (takes a while) 12:22:40.366 159G / 159G INFO General (gap_closer.cpp : 138) Used 129219073 paired reads 12:22:40.366 159G / 159G INFO General (gap_closer.cpp : 140) Merging paired indices 12:22:42.967 159G / 159G INFO GapCloser (gap_closer.cpp : 346) Closing short gaps 12:24:08.848 159G / 160G INFO GapCloser (gap_closer.cpp : 380) Closing short gaps complete: filled 540 gaps after checking 33654 candidates 12:24:15.527 159G / 160G INFO StageManager (stage.cpp : 132) STAGE == Simplification Cleanup 12:24:15.527 159G / 160G INFO General (simplification.cpp : 196) PROCEDURE == Post simplification 12:24:15.527 159G / 160G INFO General (graph_simplification.hpp : 634) Creating parallel br instance 12:24:15.527 159G / 160G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover 12:38:27.581 159G / 160G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 497563 times 12:38:27.581 159G / 160G INFO Simplification (parallel_processing.hpp : 165) Running Disconnecting edges with relatively low coverage 13:00:53.105 159G / 160G INFO Simplification (parallel_processing.hpp : 167) Disconnecting edges with relatively low coverage triggered 1063287 times 13:00:53.105 159G / 160G INFO Simplification (parallel_processing.hpp : 165) Running Complex tip clipper 13:02:44.375 159G / 160G INFO Simplification (parallel_processing.hpp : 167) Complex tip clipper triggered 117633 times 13:02:44.375 159G / 160G INFO Simplification (parallel_processing.hpp : 165) Running Complex bulge remover 13:26:37.777 165G / 165G INFO Simplification (parallel_processing.hpp : 167) Complex bulge remover triggered 131921 times 13:26:37.777 165G / 165G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 13:35:16.336 165G / 165G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 634776 times 13:35:16.336 165G / 165G INFO Simplification (parallel_processing.hpp : 165) Running Final tip clipper 13:35:41.552 165G / 165G INFO Simplification (parallel_processing.hpp : 167) Final tip clipper triggered 6552 times 13:35:41.552 165G / 165G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 13:43:49.848 167G / 167G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 86219 times 13:43:49.848 167G / 167G INFO Simplification (parallel_processing.hpp : 165) Running Thorn remover (meta) 13:44:05.565 167G / 167G INFO Simplification (parallel_processing.hpp : 167) Thorn remover (meta) triggered 15 times 13:44:05.565 167G / 167G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover 13:45:02.324 167G / 167G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 17507 times 13:45:02.324 167G / 167G INFO Simplification (parallel_processing.hpp : 165) Running Disconnecting edges with relatively low coverage 13:49:36.243 167G / 167G INFO Simplification (parallel_processing.hpp : 167) Disconnecting edges with relatively low coverage triggered 100845 times 13:49:36.243 167G / 167G INFO Simplification (parallel_processing.hpp : 165) Running Complex tip clipper 13:49:52.293 167G / 167G INFO Simplification (parallel_processing.hpp : 167) Complex tip clipper triggered 10065 times 13:49:52.293 167G / 167G INFO Simplification (parallel_processing.hpp : 165) Running Complex bulge remover 13:51:27.108 168G / 168G INFO Simplification (parallel_processing.hpp : 167) Complex bulge remover triggered 6286 times 13:51:27.108 168G / 168G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 13:53:08.365 167G / 168G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 90567 times 13:53:08.365 167G / 168G INFO Simplification (parallel_processing.hpp : 165) Running Final tip clipper 13:53:16.646 167G / 168G INFO Simplification (parallel_processing.hpp : 167) Final tip clipper triggered 1345 times 13:53:16.646 167G / 168G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 13:54:34.889 168G / 168G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 9962 times 13:54:34.889 168G / 168G INFO Simplification (parallel_processing.hpp : 165) Running Thorn remover (meta) 13:54:46.714 168G / 168G INFO Simplification (parallel_processing.hpp : 167) Thorn remover (meta) triggered 1 times 13:54:46.714 168G / 168G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover 13:55:05.664 168G / 168G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 2774 times 13:55:05.664 168G / 168G INFO Simplification (parallel_processing.hpp : 165) Running Disconnecting edges with relatively low coverage 13:55:28.416 168G / 168G INFO Simplification (parallel_processing.hpp : 167) Disconnecting edges with relatively low coverage triggered 2094 times 13:55:28.416 168G / 168G INFO Simplification (parallel_processing.hpp : 165) Running Complex tip clipper 13:55:31.424 168G / 168G INFO Simplification (parallel_processing.hpp : 167) Complex tip clipper triggered 655 times 13:55:31.425 168G / 168G INFO Simplification (parallel_processing.hpp : 165) Running Complex bulge remover 13:56:05.894 168G / 168G INFO Simplification (parallel_processing.hpp : 167) Complex bulge remover triggered 791 times 13:56:05.894 168G / 168G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 13:56:08.760 168G / 168G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 2070 times 13:56:08.760 168G / 168G INFO Simplification (parallel_processing.hpp : 165) Running Final tip clipper 13:56:09.010 168G / 168G INFO Simplification (parallel_processing.hpp : 167) Final tip clipper triggered 16 times 13:56:09.010 168G / 168G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 13:56:11.944 168G / 168G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 430 times 13:56:11.944 168G / 168G INFO Simplification (parallel_processing.hpp : 165) Running Thorn remover (meta) 13:56:12.117 168G / 168G INFO Simplification (parallel_processing.hpp : 167) Thorn remover (meta) triggered 0 times 13:56:12.117 168G / 168G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover 13:56:23.782 168G / 168G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 119 times 13:56:23.782 168G / 168G INFO Simplification (parallel_processing.hpp : 165) Running Disconnecting edges with relatively low coverage 13:56:24.444 168G / 168G INFO Simplification (parallel_processing.hpp : 167) Disconnecting edges with relatively low coverage triggered 96 times 13:56:24.444 168G / 168G INFO Simplification (parallel_processing.hpp : 165) Running Complex tip clipper 13:56:25.436 168G / 168G INFO Simplification (parallel_processing.hpp : 167) Complex tip clipper triggered 14 times 13:56:25.437 168G / 168G INFO Simplification (parallel_processing.hpp : 165) Running Complex bulge remover 13:56:50.656 168G / 168G INFO Simplification (parallel_processing.hpp : 167) Complex bulge remover triggered 18 times 13:56:50.656 168G / 168G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 13:56:50.754 168G / 168G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 82 times 13:56:50.754 168G / 168G INFO Simplification (parallel_processing.hpp : 165) Running Final tip clipper 13:56:50.760 168G / 168G INFO Simplification (parallel_processing.hpp : 167) Final tip clipper triggered 0 times 13:56:50.760 168G / 168G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 13:56:50.882 168G / 168G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 16 times 13:56:50.882 168G / 168G INFO Simplification (parallel_processing.hpp : 165) Running Thorn remover (meta) 13:56:50.884 168G / 168G INFO Simplification (parallel_processing.hpp : 167) Thorn remover (meta) triggered 0 times 13:56:50.884 168G / 168G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover 13:57:02.875 168G / 168G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 7 times 13:57:02.875 168G / 168G INFO Simplification (parallel_processing.hpp : 165) Running Disconnecting edges with relatively low coverage 13:57:02.904 168G / 168G INFO Simplification (parallel_processing.hpp : 167) Disconnecting edges with relatively low coverage triggered 5 times 13:57:02.904 168G / 168G INFO Simplification (parallel_processing.hpp : 165) Running Complex tip clipper 13:57:03.731 168G / 168G INFO Simplification (parallel_processing.hpp : 167) Complex tip clipper triggered 3 times 13:57:03.732 168G / 168G INFO Simplification (parallel_processing.hpp : 165) Running Complex bulge remover 13:57:28.481 168G / 168G INFO Simplification (parallel_processing.hpp : 167) Complex bulge remover triggered 3 times 13:57:28.481 168G / 168G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 13:57:28.485 168G / 168G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 2 times 13:57:28.485 168G / 168G INFO Simplification (parallel_processing.hpp : 165) Running Final tip clipper 13:57:28.486 168G / 168G INFO Simplification (parallel_processing.hpp : 167) Final tip clipper triggered 0 times 13:57:28.486 168G / 168G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 13:57:28.493 168G / 168G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 1 times 13:57:28.493 168G / 168G INFO Simplification (parallel_processing.hpp : 165) Running Thorn remover (meta) 13:57:28.493 168G / 168G INFO Simplification (parallel_processing.hpp : 167) Thorn remover (meta) triggered 0 times 13:57:28.493 168G / 168G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover 13:57:40.482 168G / 168G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 6 times 13:57:40.483 168G / 168G INFO Simplification (parallel_processing.hpp : 165) Running Disconnecting edges with relatively low coverage 13:57:40.488 168G / 168G INFO Simplification (parallel_processing.hpp : 167) Disconnecting edges with relatively low coverage triggered 1 times 13:57:40.489 168G / 168G INFO Simplification (parallel_processing.hpp : 165) Running Complex tip clipper 13:57:41.336 168G / 168G INFO Simplification (parallel_processing.hpp : 167) Complex tip clipper triggered 0 times 13:57:41.336 168G / 168G INFO Simplification (parallel_processing.hpp : 165) Running Complex bulge remover 13:58:06.440 168G / 168G INFO Simplification (parallel_processing.hpp : 167) Complex bulge remover triggered 0 times 13:58:06.440 168G / 168G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 13:58:06.443 168G / 168G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 1 times 13:58:06.444 168G / 168G INFO Simplification (parallel_processing.hpp : 165) Running Final tip clipper 13:58:06.444 168G / 168G INFO Simplification (parallel_processing.hpp : 167) Final tip clipper triggered 0 times 13:58:06.444 168G / 168G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 13:58:06.456 168G / 168G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 1 times 13:58:06.456 168G / 168G INFO Simplification (parallel_processing.hpp : 165) Running Thorn remover (meta) 13:58:06.456 168G / 168G INFO Simplification (parallel_processing.hpp : 167) Thorn remover (meta) triggered 0 times 13:58:06.456 168G / 168G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover 13:58:18.872 168G / 168G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 0 times 13:58:18.872 168G / 168G INFO Simplification (parallel_processing.hpp : 165) Running Disconnecting edges with relatively low coverage 13:58:18.874 168G / 168G INFO Simplification (parallel_processing.hpp : 167) Disconnecting edges with relatively low coverage triggered 0 times 13:58:18.874 168G / 168G INFO Simplification (parallel_processing.hpp : 165) Running Complex tip clipper 13:58:19.714 168G / 168G INFO Simplification (parallel_processing.hpp : 167) Complex tip clipper triggered 0 times 13:58:19.714 168G / 168G INFO Simplification (parallel_processing.hpp : 165) Running Complex bulge remover 13:58:44.168 168G / 168G INFO Simplification (parallel_processing.hpp : 167) Complex bulge remover triggered 0 times 13:58:44.168 168G / 168G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 13:58:44.168 168G / 168G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 13:58:44.168 168G / 168G INFO Simplification (parallel_processing.hpp : 165) Running Final tip clipper 13:58:44.168 168G / 168G INFO Simplification (parallel_processing.hpp : 167) Final tip clipper triggered 0 times 13:58:44.168 168G / 168G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 13:58:44.168 168G / 168G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 13:58:44.168 168G / 168G INFO Simplification (parallel_processing.hpp : 165) Running Thorn remover (meta) 13:58:44.168 168G / 168G INFO Simplification (parallel_processing.hpp : 167) Thorn remover (meta) triggered 0 times 13:58:44.168 168G / 168G INFO General (simplification.cpp : 326) Running Hidden EC remover (meta) 13:58:46.315 168G / 168G INFO General (simplification.cpp : 330) Disrupting self-conjugate edges 13:59:13.340 168G / 168G INFO Simplification (parallel_processing.hpp : 165) Running Removing isolated edges 13:59:25.289 168G / 168G INFO Simplification (parallel_processing.hpp : 167) Removing isolated edges triggered 17378 times 13:59:25.293 168G / 168G INFO General (simplification.cpp : 470) Counting average coverage 13:59:32.085 168G / 168G INFO General (simplification.cpp : 476) Average coverage = 65.1735 13:59:32.085 168G / 168G INFO StageManager (stage.cpp : 132) STAGE == Contig Output 13:59:32.091 168G / 168G INFO General (contig_output_stage.cpp : 40) Writing GFA to /DATA/markop/CPB_metaSpades/output//K101/assembly_graph_with_scaffolds.gfa 14:00:29.384 168G / 168G INFO General (contig_output.hpp : 22) Outputting contigs to /DATA/markop/CPB_metaSpades/output//K101/before_rr.fasta 14:01:35.659 168G / 168G INFO General (contig_output_stage.cpp : 51) Outputting FastG graph to /DATA/markop/CPB_metaSpades/output//K101/assembly_graph.fastg 14:05:11.186 168G / 168G INFO General (contig_output.hpp : 22) Outputting contigs to /DATA/markop/CPB_metaSpades/output//K101/simplified_contigs.fasta 14:06:19.370 168G / 168G INFO General (contig_output.hpp : 22) Outputting contigs to /DATA/markop/CPB_metaSpades/output//K101/final_contigs.fasta 14:07:25.813 168G / 168G INFO StageManager (stage.cpp : 132) STAGE == Contig Output 14:07:25.813 168G / 168G INFO General (contig_output_stage.cpp : 40) Writing GFA to /DATA/markop/CPB_metaSpades/output//K101/assembly_graph_with_scaffolds.gfa 14:08:28.770 168G / 168G INFO General (contig_output.hpp : 22) Outputting contigs to /DATA/markop/CPB_metaSpades/output//K101/before_rr.fasta 14:09:39.488 168G / 168G INFO General (contig_output_stage.cpp : 51) Outputting FastG graph to /DATA/markop/CPB_metaSpades/output//K101/assembly_graph.fastg 14:13:21.159 168G / 168G INFO General (contig_output.hpp : 22) Outputting contigs to /DATA/markop/CPB_metaSpades/output//K101/simplified_contigs.fasta 14:14:34.578 168G / 168G INFO General (contig_output.hpp : 22) Outputting contigs to /DATA/markop/CPB_metaSpades/output//K101/final_contigs.fasta 14:15:45.185 168G / 168G INFO General (launch.hpp : 149) SPAdes finished 14:55:07.072 136M / 168G INFO General (main.cpp : 109) Assembling time: 14 hours 55 minutes 7 seconds == Running assembler: K127 0:00:00.000 4M / 4M INFO General (main.cpp : 74) Loaded config from /DATA/markop/CPB_metaSpades/output/K127/configs/config.info 0:00:00.000 4M / 4M INFO General (main.cpp : 74) Loaded config from /DATA/markop/CPB_metaSpades/output/K127/configs/mda_mode.info 0:00:00.000 4M / 4M INFO General (main.cpp : 74) Loaded config from /DATA/markop/CPB_metaSpades/output/K127/configs/meta_mode.info 0:00:00.000 4M / 4M INFO General (memory_limit.cpp : 49) Memory limit set to 230 Gb 0:00:00.000 4M / 4M INFO General (main.cpp : 87) Starting SPAdes, built from refs/heads/spades_3.13.0, git revision 8ea46659e9b2aca35444a808db550ac333006f8b 0:00:00.000 4M / 4M INFO General (main.cpp : 88) Maximum k-mer length: 128 0:00:00.000 4M / 4M INFO General (main.cpp : 89) Assembling dataset (/DATA/markop/CPB_metaSpades/output/dataset.info) with K=127 0:00:00.000 4M / 4M INFO General (main.cpp : 90) Maximum # of threads to use (adjusted due to OMP capabilities): 32 0:00:00.000 4M / 4M INFO General (launch.hpp : 51) SPAdes started 0:00:00.000 4M / 4M INFO General (launch.hpp : 58) Starting from stage: construction 0:00:00.000 4M / 4M INFO General (launch.hpp : 65) Two-step RR enabled: 1 0:00:00.000 4M / 4M INFO General (launch.hpp : 76) Will need read mapping, kmer mapper will be attached 0:00:00.000 4M / 4M INFO StageManager (stage.cpp : 132) STAGE == de Bruijn graph construction 0:00:00.010 4M / 4M INFO General (read_converter.hpp : 59) Binary reads detected 0:00:00.131 4M / 4M INFO General (construction.cpp : 111) Max read length 391 0:00:00.131 4M / 4M INFO General (construction.cpp : 117) Average read length 229.3 0:00:00.131 4M / 4M INFO General (stage.cpp : 101) PROCEDURE == k+1-mer counting 0:00:00.131 4M / 4M INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 1024 files using 32 threads. This might take a while. 0:00:00.132 4M / 4M INFO General (file_limit.hpp : 32) Open file limit set to 10000 0:00:00.132 4M / 4M INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.39579 Gb 0:00:00.132 4M / 4M INFO General (kmer_splitters.hpp : 97) Using cell size of 16384 0:00:19.355 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 17140129 reads 0:00:32.356 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 23520925 reads 0:00:42.792 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 29992420 reads 0:01:05.448 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 36236148 reads 0:01:31.203 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 42736415 reads 0:01:54.644 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 49210758 reads 0:02:19.202 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 55280562 reads 0:02:43.190 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 61718196 reads 0:03:09.718 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 67983612 reads 0:03:35.152 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 74290861 reads 0:03:55.816 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 79477653 reads 0:04:21.658 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 85889932 reads 0:07:44.464 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 136387847 reads 0:16:18.721 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 272811252 reads 0:33:45.474 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 542509926 reads 1:08:45.923 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 1079247014 reads 1:21:49.474 17G / 18G INFO General (kmer_splitters.hpp : 295) Adding contigs from previous K 1:35:19.890 132M / 18G INFO General (kmer_splitters.hpp : 308) Used 1653171754 reads 1:35:19.890 132M / 18G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 2:50:27.610 132M / 18G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 3723768626 kmers in total. 2:50:27.610 132M / 18G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 2:58:57.713 128M / 18G INFO General (stage.cpp : 101) PROCEDURE == Extension index construction 2:58:57.713 128M / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 2:58:57.713 128M / 18G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 512 files using 32 threads. This might take a while. 2:58:57.714 128M / 18G INFO General (file_limit.hpp : 32) Open file limit set to 10000 2:58:57.714 128M / 18G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.39453 Gb 2:58:57.714 128M / 18G INFO General (kmer_splitters.hpp : 97) Using cell size of 32768 2:58:59.144 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 2813582 kmers 2:59:00.693 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 5658767 kmers 2:59:01.990 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 8543596 kmers 2:59:03.466 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 11428796 kmers 2:59:04.820 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 14295951 kmers 2:59:06.007 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 17246063 kmers 2:59:07.153 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 20211545 kmers 2:59:08.451 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 23106226 kmers 2:59:09.734 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 26080313 kmers 2:59:11.298 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 28985625 kmers 2:59:12.732 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 31852746 kmers 2:59:14.062 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 34766489 kmers 2:59:15.613 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 37655712 kmers 2:59:16.912 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 40603664 kmers 2:59:18.264 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 43598434 kmers 2:59:19.540 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 46764703 kmers 2:59:29.607 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 68246622 kmers 3:00:00.616 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 136575717 kmers 3:01:03.097 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 270415046 kmers 3:03:08.227 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 539831168 kmers 3:07:14.860 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 1076348452 kmers 3:15:37.760 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 2147682876 kmers 3:51:26.844 17G / 18G INFO General (kmer_splitters.hpp : 385) Used 3723808562 kmers. 3:51:27.068 132M / 18G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 4:20:33.020 132M / 18G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 3727975608 kmers in total. 4:20:33.020 132M / 18G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 4:29:45.914 132M / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 4:34:03.384 1G / 18G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 4:49:25.116 1G / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 1728709048 bytes occupied (3.7097 bits per kmer). 4:49:29.463 5G / 18G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 99) Building k-mer extensions from k+1-mers 5:48:08.182 5G / 18G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 103) Building k-mer extensions from k+1-mers finished. 5:48:08.185 5G / 18G INFO General (stage.cpp : 101) PROCEDURE == Condensing graph 5:48:08.268 5G / 18G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 355) Extracting unbranching paths 5:55:08.429 10G / 18G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 374) Extracting unbranching paths finished. 62724298 sequences extracted 5:58:18.912 10G / 18G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 310) Collecting perfect loops 6:00:15.946 10G / 18G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 343) Collecting perfect loops finished. 83 loops collected 6:01:08.228 26G / 32G INFO General (stage.cpp : 101) PROCEDURE == Filling coverage indices (PHM) 6:01:08.228 26G / 32G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 6:01:08.228 26G / 32G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 6:12:29.104 28G / 32G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 1726776208 bytes occupied (3.70974 bits per kmer). 6:12:37.935 42G / 42G INFO General (construction.cpp : 388) Collecting k-mer coverage information from reads, this takes a while. 6:50:36.759 42G / 42G INFO General (construction.cpp : 508) Filling coverage and flanking coverage from PHM 6:51:53.248 42G / 42G INFO General (construction.cpp : 464) Processed 32000000 edges 6:53:06.132 42G / 42G INFO General (construction.cpp : 464) Processed 64000000 edges 6:54:19.427 42G / 42G INFO General (construction.cpp : 464) Processed 96000000 edges 6:55:25.275 42G / 42G INFO General (construction.cpp : 464) Processed 125448625 edges 6:55:57.272 21G / 42G INFO StageManager (stage.cpp : 132) STAGE == Gap Closer 6:55:57.272 21G / 42G INFO General (graph_pack.hpp : 101) Index refill 6:55:57.272 21G / 42G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 6:55:57.272 21G / 42G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 512 files using 32 threads. This might take a while. 6:55:57.272 21G / 42G INFO General (file_limit.hpp : 32) Open file limit set to 10000 6:55:57.272 21G / 42G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.17192 Gb 6:55:57.272 21G / 42G INFO General (kmer_splitters.hpp : 97) Using cell size of 32768 6:56:23.508 39G / 42G INFO General (edge_index_builders.hpp : 77) Processed 16516156 edges 6:56:45.900 39G / 42G INFO General (edge_index_builders.hpp : 77) Processed 33031257 edges 6:57:33.309 39G / 42G INFO General (edge_index_builders.hpp : 77) Processed 49554183 edges 6:59:27.249 39G / 42G INFO General (edge_index_builders.hpp : 77) Processed 66062702 edges 7:01:21.952 39G / 42G INFO General (edge_index_builders.hpp : 77) Processed 82572204 edges 7:03:17.488 39G / 42G INFO General (edge_index_builders.hpp : 77) Processed 99091671 edges 7:05:15.023 39G / 42G INFO General (edge_index_builders.hpp : 77) Processed 115606911 edges 7:06:24.648 39G / 42G INFO General (edge_index_builders.hpp : 77) Processed 125448849 edges 7:06:24.648 39G / 42G INFO General (edge_index_builders.hpp : 82) Used 125448849 sequences. 7:06:26.069 21G / 42G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 7:20:32.511 21G / 42G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 3723768626 kmers in total. 7:20:32.511 21G / 42G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 7:35:17.329 21G / 42G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 7:39:14.384 23G / 42G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 7:57:25.403 23G / 42G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 1726729784 bytes occupied (3.70964 bits per kmer). 7:58:20.946 106G / 106G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while. 8:01:02.538 106G / 106G INFO General (edge_index.hpp : 92) Index refilled 8:01:02.806 106G / 106G INFO General (gap_closer.cpp : 159) Preparing shift maps 8:04:04.701 112G / 112G INFO General (gap_closer.cpp : 119) Processing paired reads (takes a while) 8:05:38.441 113G / 113G INFO General (gap_closer.cpp : 138) Used 129219073 paired reads 8:05:38.441 113G / 113G INFO General (gap_closer.cpp : 140) Merging paired indices 8:06:32.098 107G / 113G INFO GapCloser (gap_closer.cpp : 346) Closing short gaps 8:14:42.555 107G / 113G INFO GapCloser (gap_closer.cpp : 380) Closing short gaps complete: filled 114077 gaps after checking 1027187 candidates 8:16:27.980 106G / 113G INFO StageManager (stage.cpp : 132) STAGE == Raw Simplification 8:16:33.842 21G / 113G INFO General (simplification.cpp : 128) PROCEDURE == InitialCleaning 8:16:33.844 21G / 113G INFO Simplification (parallel_processing.hpp : 165) Running Self conjugate edge remover 8:16:41.096 21G / 113G INFO Simplification (parallel_processing.hpp : 167) Self conjugate edge remover triggered 10 times 8:16:41.097 21G / 113G INFO Simplification (parallel_processing.hpp : 165) Running Initial tip clipper 8:21:28.031 22G / 113G INFO Simplification (parallel_processing.hpp : 167) Initial tip clipper triggered 8157417 times 8:21:28.031 22G / 113G INFO Simplification (parallel_processing.hpp : 165) Running Initial ec remover 8:21:47.635 22G / 113G INFO Simplification (parallel_processing.hpp : 167) Initial ec remover triggered 195523 times 8:21:47.635 22G / 113G INFO Simplification (parallel_processing.hpp : 165) Running Disconnecting edges with low flanking coverage 8:22:05.130 22G / 113G INFO Simplification (parallel_processing.hpp : 167) Disconnecting edges with low flanking coverage triggered 186440 times 8:22:05.130 22G / 113G INFO Simplification (parallel_processing.hpp : 165) Running Initial isolated edge remover 8:24:15.351 22G / 113G INFO Simplification (parallel_processing.hpp : 167) Initial isolated edge remover triggered 11847392 times 8:24:17.598 22G / 113G INFO StageManager (stage.cpp : 132) STAGE == Preliminary Simplification 8:24:17.598 22G / 113G INFO General (simplification.cpp : 357) Graph simplification started 8:24:17.598 22G / 113G INFO General (graph_simplification.hpp : 634) Creating parallel br instance 8:24:17.598 22G / 113G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 1 8:24:17.598 22G / 113G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 8:26:53.656 22G / 113G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 5320234 times 8:26:53.656 22G / 113G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 9:26:29.134 64G / 113G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 1893493 times 9:26:29.134 64G / 113G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 9:26:36.061 64G / 113G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 54 times 9:26:36.061 64G / 113G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 2 9:26:36.061 64G / 113G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 9:26:45.974 64G / 113G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 34567 times 9:26:45.974 64G / 113G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 9:26:53.923 64G / 113G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 1488 times 9:26:53.923 64G / 113G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 9:28:52.821 64G / 113G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 1120709 times 9:28:52.821 64G / 113G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 3 9:28:52.821 64G / 113G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 9:29:02.674 64G / 113G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 94794 times 9:29:02.674 64G / 113G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 9:39:45.261 69G / 113G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 196075 times 9:39:45.261 69G / 113G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 9:40:40.598 69G / 113G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 479037 times 9:40:40.598 69G / 113G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 4 9:40:40.598 69G / 113G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 9:40:46.196 69G / 113G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 30005 times 9:40:46.196 69G / 113G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 9:48:51.023 72G / 113G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 113577 times 9:48:51.024 72G / 113G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 9:48:55.109 72G / 113G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 35 times 9:48:55.109 72G / 113G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 5 9:48:55.109 72G / 113G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 9:48:56.133 72G / 113G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 1141 times 9:48:56.133 72G / 113G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 9:48:56.619 72G / 113G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 52 times 9:48:56.619 72G / 113G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 9:48:56.619 72G / 113G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 9:48:56.619 72G / 113G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 6 9:48:56.619 72G / 113G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 9:48:56.620 72G / 113G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 9:48:56.620 72G / 113G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 9:48:56.620 72G / 113G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 9:48:56.620 72G / 113G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 9:48:56.620 72G / 113G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 9:48:56.621 72G / 113G INFO StageManager (stage.cpp : 132) STAGE == Gap Closer 9:48:56.621 72G / 113G INFO General (graph_pack.hpp : 101) Index refill 9:48:56.621 72G / 113G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 9:48:56.621 72G / 113G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 512 files using 32 threads. This might take a while. 9:48:56.621 72G / 113G INFO General (file_limit.hpp : 32) Open file limit set to 10000 9:48:56.621 72G / 113G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 1.64299 Gb 9:48:56.621 72G / 113G INFO General (kmer_splitters.hpp : 97) Using cell size of 32768 9:49:23.713 89G / 113G INFO General (edge_index_builders.hpp : 77) Processed 5911248 edges 9:49:53.322 89G / 113G INFO General (edge_index_builders.hpp : 77) Processed 11822813 edges 9:52:24.377 89G / 113G INFO General (edge_index_builders.hpp : 77) Processed 17728132 edges 9:54:48.976 89G / 113G INFO General (edge_index_builders.hpp : 77) Processed 23517314 edges 9:55:19.288 89G / 113G INFO General (edge_index_builders.hpp : 77) Processed 24653805 edges 9:55:19.289 89G / 113G INFO General (edge_index_builders.hpp : 82) Used 24653805 sequences. 9:55:20.532 72G / 113G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 10:04:27.100 72G / 113G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 2180784948 kmers in total. 10:04:27.100 72G / 113G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 10:11:36.884 72G / 113G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 10:13:58.974 73G / 113G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 10:21:31.124 73G / 113G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 1011243968 bytes occupied (3.70965 bits per kmer). 10:22:18.564 122G / 122G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while. 10:23:50.386 122G / 122G INFO General (edge_index.hpp : 92) Index refilled 10:23:50.388 122G / 122G INFO General (gap_closer.cpp : 159) Preparing shift maps 10:24:16.261 122G / 122G INFO General (gap_closer.cpp : 119) Processing paired reads (takes a while) 10:27:02.437 122G / 122G INFO General (gap_closer.cpp : 138) Used 129219073 paired reads 10:27:02.438 122G / 122G INFO General (gap_closer.cpp : 140) Merging paired indices 10:27:04.758 122G / 122G INFO GapCloser (gap_closer.cpp : 346) Closing short gaps 10:28:23.402 122G / 123G INFO GapCloser (gap_closer.cpp : 380) Closing short gaps complete: filled 1054 gaps after checking 31581 candidates 10:28:32.467 122G / 123G INFO StageManager (stage.cpp : 132) STAGE == Preliminary Paired Information Counting 10:33:30.144 131G / 131G INFO General (graph_pack.hpp : 109) Normalizing k-mer map. Total 697722884 kmers to process 10:54:32.629 131G / 152G INFO General (graph_pack.hpp : 111) Normalizing done 10:54:32.629 131G / 152G INFO General (pair_info_count.cpp : 320) Min edge length for estimation: 900 10:54:32.629 131G / 152G INFO General (pair_info_count.cpp : 331) Estimating insert size for library #0 10:54:32.629 131G / 152G INFO General (pair_info_count.cpp : 190) Estimating insert size (takes a while) 10:54:33.036 132G / 152G INFO General (pair_info_count.cpp : 39) Selecting usual mapper 10:54:44.052 132G / 152G INFO General (sequence_mapper_notifier.h: 80) Processed 200000 reads 10:54:44.115 132G / 152G INFO General (sequence_mapper_notifier.h: 80) Processed 400000 reads 10:54:44.163 132G / 152G INFO General (sequence_mapper_notifier.h: 80) Processed 600000 reads 10:54:44.221 132G / 152G INFO General (sequence_mapper_notifier.h: 80) Processed 800000 reads 10:54:44.255 132G / 152G INFO General (sequence_mapper_notifier.h: 80) Processed 1000000 reads 10:54:44.290 132G / 152G INFO General (sequence_mapper_notifier.h: 80) Processed 1200000 reads 10:54:44.516 132G / 152G INFO General (sequence_mapper_notifier.h: 80) Processed 2200000 reads 10:54:44.992 132G / 152G INFO General (sequence_mapper_notifier.h: 80) Processed 4200000 reads 10:54:53.230 132G / 152G INFO General (sequence_mapper_notifier.h: 80) Processed 8400000 reads 10:55:02.302 132G / 152G INFO General (sequence_mapper_notifier.h: 80) Processed 16800000 reads 10:55:26.070 132G / 152G INFO General (sequence_mapper_notifier.h: 80) Processed 33600000 reads 10:56:07.638 132G / 152G INFO General (sequence_mapper_notifier.h: 80) Processed 67200000 reads 10:57:32.336 132G / 152G INFO General (sequence_mapper_notifier.h: 98) Total 129219073 reads processed 10:57:34.629 132G / 152G INFO General (pair_info_count.cpp : 209) Edge pairs: 256407501 10:57:34.629 132G / 152G INFO General (pair_info_count.cpp : 213) 16622995 paired reads (12.8642% of all) aligned to long edges 10:57:34.670 131G / 152G INFO General (pair_info_count.cpp : 354) Insert size = 400.101, deviation = 55.5732, left quantile = 341, right quantile = 458, read length = 391 10:57:34.670 131G / 152G WARN General (pair_info_count.cpp : 358) Estimated mean insert size 400.101 is very small compared to read length 391 10:57:35.156 132G / 152G INFO General (pair_info_count.cpp : 371) Filtering data for library #0 10:57:35.157 132G / 152G INFO General (pair_info_count.cpp : 39) Selecting usual mapper 10:57:44.845 132G / 152G INFO General (sequence_mapper_notifier.h: 80) Processed 200000 reads 10:57:44.854 132G / 152G INFO General (sequence_mapper_notifier.h: 80) Processed 400000 reads 10:57:44.856 132G / 152G INFO General (sequence_mapper_notifier.h: 80) Processed 600000 reads 10:57:44.885 132G / 152G INFO General (sequence_mapper_notifier.h: 80) Processed 800000 reads 10:57:44.890 132G / 152G INFO General (sequence_mapper_notifier.h: 80) Processed 1000000 reads 10:57:44.900 132G / 152G INFO General (sequence_mapper_notifier.h: 80) Processed 1200000 reads 10:57:45.024 132G / 152G INFO General (sequence_mapper_notifier.h: 80) Processed 2200000 reads 10:57:45.762 132G / 152G INFO General (sequence_mapper_notifier.h: 80) Processed 4200000 reads 10:57:53.857 132G / 152G INFO General (sequence_mapper_notifier.h: 80) Processed 8400000 reads 10:58:03.994 132G / 152G INFO General (sequence_mapper_notifier.h: 80) Processed 16800000 reads 10:58:31.277 132G / 152G INFO General (sequence_mapper_notifier.h: 80) Processed 33600000 reads 10:59:25.534 132G / 152G INFO General (sequence_mapper_notifier.h: 80) Processed 67200000 reads 11:01:05.838 132G / 152G INFO General (sequence_mapper_notifier.h: 98) Total 129219073 reads processed 11:01:05.839 132G / 152G INFO General (pair_info_count.cpp : 383) Mapping library #0 11:01:05.839 132G / 152G INFO General (pair_info_count.cpp : 385) Mapping paired reads (takes a while) 11:01:05.839 132G / 152G INFO General (pair_info_count.cpp : 289) Left insert size quantile 341, right insert size quantile 458, filtering threshold 1, rounding threshold 0 11:01:05.860 132G / 152G INFO General (pair_info_count.cpp : 39) Selecting usual mapper 11:01:19.118 133G / 152G INFO General (sequence_mapper_notifier.h: 80) Processed 200000 reads 11:01:19.418 133G / 152G INFO General (sequence_mapper_notifier.h: 80) Processed 400000 reads 11:01:19.457 133G / 152G INFO General (sequence_mapper_notifier.h: 80) Processed 600000 reads 11:01:19.479 133G / 152G INFO General (sequence_mapper_notifier.h: 80) Processed 800000 reads 11:01:19.480 133G / 152G INFO General (sequence_mapper_notifier.h: 80) Processed 1000000 reads 11:01:19.496 133G / 152G INFO General (sequence_mapper_notifier.h: 80) Processed 1200000 reads 11:01:19.576 133G / 152G INFO General (sequence_mapper_notifier.h: 80) Processed 2200000 reads 11:01:19.979 133G / 152G INFO General (sequence_mapper_notifier.h: 80) Processed 4200000 reads 11:01:30.665 134G / 152G INFO General (sequence_mapper_notifier.h: 80) Processed 8400000 reads 11:01:42.001 134G / 152G INFO General (sequence_mapper_notifier.h: 80) Processed 16800000 reads 11:02:17.085 136G / 152G INFO General (sequence_mapper_notifier.h: 80) Processed 33600000 reads 11:03:16.116 139G / 152G INFO General (sequence_mapper_notifier.h: 80) Processed 67200000 reads 11:05:15.515 142G / 152G INFO General (sequence_mapper_notifier.h: 98) Total 129219073 reads processed 11:05:24.573 141G / 152G INFO StageManager (stage.cpp : 132) STAGE == Preliminary Distance Estimation 11:05:24.579 141G / 152G INFO General (distance_estimation.cpp : 173) Processing library #0 11:05:24.579 141G / 152G INFO General (distance_estimation.cpp : 149) Weight Filter Done 11:05:24.580 141G / 152G INFO DistanceEstimator (distance_estimation.hpp : 116) Using SIMPLE distance estimator 12:24:22.743 151G / 155G INFO General (distance_estimation.cpp : 34) Filtering info 12:24:22.743 151G / 155G INFO General (pair_info_filters.hpp : 242) Start filtering; index size: 559067957 12:29:18.703 158G / 163G INFO General (pair_info_filters.hpp : 263) Done filtering 12:29:18.994 150G / 163G INFO General (distance_estimation.cpp : 156) Refining clustered pair information 12:30:24.820 150G / 163G INFO General (distance_estimation.cpp : 158) The refining of clustered pair information has been finished 12:30:24.820 150G / 163G INFO General (distance_estimation.cpp : 160) Improving paired information 13:06:11.337 160G / 182G INFO PairInfoImprover (pair_info_improver.hpp : 103) Paired info stats: missing = 159026392; contradictional = 0 14:21:04.044 166G / 219G INFO PairInfoImprover (pair_info_improver.hpp : 103) Paired info stats: missing = 105034138; contradictional = 0 14:21:04.044 166G / 219G INFO General (distance_estimation.cpp : 103) Filling scaffolding index 14:21:04.045 166G / 219G INFO DistanceEstimator (distance_estimation.hpp : 116) Using SMOOTHING distance estimator 15:25:01.695 167G / 219G INFO General (distance_estimation.cpp : 34) Filtering info 15:25:01.695 167G / 219G INFO General (pair_info_filters.hpp : 242) Start filtering; index size: 45641509 15:25:33.097 169G / 219G INFO General (pair_info_filters.hpp : 263) Done filtering 15:25:33.178 167G / 219G INFO General (distance_estimation.cpp : 182) Clearing raw paired index 15:27:03.233 157G / 219G INFO StageManager (stage.cpp : 132) STAGE == Preliminary Repeat Resolving 15:27:03.233 157G / 219G INFO General (repeat_resolving.cpp : 56) Setting up preliminary path extend settings 15:27:03.233 157G / 219G INFO General (repeat_resolving.cpp : 69) Using Path-Extend repeat resolving 15:27:03.234 157G / 219G INFO General (launcher.cpp : 477) ExSPAnder repeat resolving tool started : Error in malloc(): out of memory. Requested: 512, active: 176018161664 == Error == system call for: "['/home/administrator/SPAdes-3.13.0-Linux/bin/spades-core', '/DATA/markop/CPB_metaSpades/output/K127/configs/config.info', '/DATA/markop/CPB_metaSpades/output/K127/configs/mda_mode.info', '/DATA/markop/CPB_metaSpades/output/K127/configs/meta_mode.info']" finished abnormally, err code: -6 ======= SPAdes pipeline finished abnormally and WITH WARNINGS! === Error correction and assembling warnings: * 10:57:34.670 131G / 152G WARN General (pair_info_count.cpp : 358) Estimated mean insert size 400.101 is very small compared to read length 391 ======= Warnings saved to /DATA/markop/CPB_metaSpades/output/warnings.log === ERRORs: * system call for: "['/home/administrator/SPAdes-3.13.0-Linux/bin/spades-core', '/DATA/markop/CPB_metaSpades/output/K127/configs/config.info', '/DATA/markop/CPB_metaSpades/output/K127/configs/mda_mode.info', '/DATA/markop/CPB_metaSpades/output/K127/configs/meta_mode.info']" finished abnormally, err code: -6 In case you have troubles running SPAdes, you can write to spades.support@cab.spbu.ru or report an issue on our GitHub repository github.com/ablab/spades Please provide us with params.txt and spades.log files from the output directory. ======= SPAdes pipeline continued. Log can be found here: /DATA/markop/CPB_metaSpades/output/spades.log Restored from Command line: /home/administrator/SPAdes-3.13.0-Linux/bin/spades.py --meta -k 21,41,71,101,127 -m 230 -t 32 -o /DATA/markop/CPB_metaSpades/output -1 /DATA/markop/CPB_metaSpades/input/unmerged_1.fq -2 /DATA/markop/CPB_metaSpades/input/unmerged_2.fq -s /DATA/markop/CPB_metaSpades/input/merged.fq Command line: /home/administrator/SPAdes-3.13.0-Linux/bin/spades.py --meta -k 21,41,71,101,127 -m 230 -t 32 -o /DATA/markop/CPB_metaSpades/output -1 /DATA/markop/CPB_metaSpades/input/unmerged_1.fq -2 /DATA/markop/CPB_metaSpades/input/unmerged_2.fq -s /DATA/markop/CPB_metaSpades/input/merged.fq System information: SPAdes version: 3.13.0 Python version: 2.7.15 OS: Linux-4.13.0-41-generic-x86_64-with-debian-stretch-sid Output dir: /DATA/markop/CPB_metaSpades/output Mode: read error correction and assembling Debug mode is turned OFF Dataset parameters: Metagenomic mode Reads: Library number: 1, library type: paired-end orientation: fr left reads: ['/DATA/markop/CPB_metaSpades/input/unmerged_1.fq'] right reads: ['/DATA/markop/CPB_metaSpades/input/unmerged_2.fq'] interlaced reads: not specified single reads: ['/DATA/markop/CPB_metaSpades/input/merged.fq'] merged reads: not specified Read error correction parameters: Iterations: 1 PHRED offset will be auto-detected Corrected reads will be compressed Assembly parameters: k: [21, 41, 71, 101, 127] Repeat resolution is enabled Mismatch careful mode is turned OFF MismatchCorrector will be SKIPPED Coverage cutoff is turned OFF Other parameters: Dir for temp files: /DATA/markop/CPB_metaSpades/output/tmp Threads: 32 Memory limit (in Gb): 230 ===== Skipping Read error correction (already processed). ===== Assembling started. == Skipping assembler: K21 (already processed) Max read length detected as 391 == Skipping assembler: K41 (already processed) == Skipping assembler: K71 (already processed) == Skipping assembler: K101 (already processed) == Running assembler: K127 0:00:00.000 4M / 4M INFO General (main.cpp : 74) Loaded config from /DATA/markop/CPB_metaSpades/output/K127/configs/config.info 0:00:00.000 4M / 4M INFO General (main.cpp : 74) Loaded config from /DATA/markop/CPB_metaSpades/output/K127/configs/mda_mode.info 0:00:00.000 4M / 4M INFO General (main.cpp : 74) Loaded config from /DATA/markop/CPB_metaSpades/output/K127/configs/meta_mode.info 0:00:00.000 4M / 4M INFO General (memory_limit.cpp : 49) Memory limit set to 230 Gb 0:00:00.000 4M / 4M INFO General (main.cpp : 87) Starting SPAdes, built from refs/heads/spades_3.13.0, git revision 8ea46659e9b2aca35444a808db550ac333006f8b 0:00:00.000 4M / 4M INFO General (main.cpp : 88) Maximum k-mer length: 128 0:00:00.000 4M / 4M INFO General (main.cpp : 89) Assembling dataset (/DATA/markop/CPB_metaSpades/output/dataset.info) with K=127 0:00:00.000 4M / 4M INFO General (main.cpp : 90) Maximum # of threads to use (adjusted due to OMP capabilities): 32 0:00:00.000 4M / 4M INFO General (launch.hpp : 51) SPAdes started 0:00:00.000 4M / 4M INFO General (launch.hpp : 58) Starting from stage: construction 0:00:00.000 4M / 4M INFO General (launch.hpp : 65) Two-step RR enabled: 1 0:00:00.000 4M / 4M INFO General (launch.hpp : 76) Will need read mapping, kmer mapper will be attached 0:00:00.000 4M / 4M INFO StageManager (stage.cpp : 132) STAGE == de Bruijn graph construction 0:00:00.010 4M / 4M INFO General (read_converter.hpp : 59) Binary reads detected 0:00:00.411 4M / 4M INFO General (construction.cpp : 111) Max read length 391 0:00:00.411 4M / 4M INFO General (construction.cpp : 117) Average read length 229.3 0:00:00.411 4M / 4M INFO General (stage.cpp : 101) PROCEDURE == k+1-mer counting 0:00:00.413 4M / 4M INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 1024 files using 32 threads. This might take a while. 0:00:00.415 4M / 4M INFO General (file_limit.hpp : 32) Open file limit set to 10000 0:00:00.415 4M / 4M INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.39579 Gb 0:00:00.415 4M / 4M INFO General (kmer_splitters.hpp : 97) Using cell size of 16384 0:00:16.171 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 17140129 reads 0:00:33.963 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 23520925 reads 0:00:45.933 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 29992420 reads 0:01:08.688 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 36236148 reads 0:01:29.973 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 42736415 reads 0:01:52.069 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 49210758 reads 0:02:12.453 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 55280562 reads 0:02:31.583 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 61718196 reads 0:02:52.866 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 67983612 reads 0:03:14.486 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 74290861 reads 0:03:32.109 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 79477653 reads 0:03:57.737 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 85889932 reads 0:06:53.632 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 136387847 reads 0:14:48.730 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 272811252 reads 0:31:05.513 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 542509926 reads 1:10:43.150 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 1079247014 reads 1:26:33.502 17G / 18G INFO General (kmer_splitters.hpp : 295) Adding contigs from previous K 1:36:50.770 132M / 18G INFO General (kmer_splitters.hpp : 308) Used 1653171754 reads 1:36:50.770 132M / 18G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 2:49:49.105 132M / 18G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 3723768626 kmers in total. 2:49:49.105 132M / 18G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 2:57:41.301 128M / 18G INFO General (stage.cpp : 101) PROCEDURE == Extension index construction 2:57:41.306 128M / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 2:57:41.307 128M / 18G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 512 files using 32 threads. This might take a while. 2:57:41.307 128M / 18G INFO General (file_limit.hpp : 32) Open file limit set to 10000 2:57:41.307 128M / 18G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.39453 Gb 2:57:41.307 128M / 18G INFO General (kmer_splitters.hpp : 97) Using cell size of 32768 2:57:41.863 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 2813582 kmers 2:57:42.373 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 5658767 kmers 2:57:42.995 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 8543596 kmers 2:57:43.498 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 11428796 kmers 2:57:44.017 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 14295951 kmers 2:57:44.621 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 17246063 kmers 2:57:45.177 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 20211545 kmers 2:57:45.820 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 23106226 kmers 2:57:47.085 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 26080313 kmers 2:57:48.723 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 28985625 kmers 2:57:50.230 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 31852746 kmers 2:57:51.608 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 34766489 kmers 2:57:53.029 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 37655712 kmers 2:57:54.593 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 40603664 kmers 2:57:56.083 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 43598434 kmers 2:57:57.749 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 46764703 kmers 2:58:07.602 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 68246622 kmers 2:58:38.739 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 136575717 kmers 2:59:41.970 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 270415046 kmers 3:01:48.382 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 539831168 kmers 3:05:54.823 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 1076348452 kmers 3:14:17.275 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 2147682876 kmers 3:47:47.724 17G / 18G INFO General (kmer_splitters.hpp : 385) Used 3723808562 kmers. 3:47:47.946 132M / 18G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 4:07:13.238 132M / 18G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 3727975608 kmers in total. 4:07:13.238 132M / 18G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 4:20:43.042 132M / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 4:24:02.109 1G / 18G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 4:41:09.349 1G / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 1728709048 bytes occupied (3.7097 bits per kmer). 4:41:12.375 5G / 18G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 99) Building k-mer extensions from k+1-mers 5:14:06.780 5G / 18G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 103) Building k-mer extensions from k+1-mers finished. 5:14:06.785 5G / 18G INFO General (stage.cpp : 101) PROCEDURE == Condensing graph 5:14:06.854 5G / 18G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 355) Extracting unbranching paths 5:19:44.948 10G / 18G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 374) Extracting unbranching paths finished. 62724298 sequences extracted 5:22:16.340 10G / 18G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 310) Collecting perfect loops 5:23:53.027 10G / 18G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 343) Collecting perfect loops finished. 83 loops collected 5:24:36.126 26G / 33G INFO General (stage.cpp : 101) PROCEDURE == Filling coverage indices (PHM) 5:24:36.127 26G / 33G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 5:24:36.127 26G / 33G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 5:36:21.318 28G / 33G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 1726776208 bytes occupied (3.70974 bits per kmer). 5:36:29.817 42G / 42G INFO General (construction.cpp : 388) Collecting k-mer coverage information from reads, this takes a while. 6:08:12.786 42G / 42G INFO General (construction.cpp : 508) Filling coverage and flanking coverage from PHM 6:09:18.445 42G / 42G INFO General (construction.cpp : 464) Processed 32000000 edges 6:10:18.220 42G / 42G INFO General (construction.cpp : 464) Processed 64000000 edges 6:11:19.100 42G / 42G INFO General (construction.cpp : 464) Processed 96000000 edges 6:12:14.336 42G / 42G INFO General (construction.cpp : 464) Processed 125448625 edges 6:12:42.058 21G / 42G INFO StageManager (stage.cpp : 132) STAGE == Gap Closer 6:12:42.064 21G / 42G INFO General (graph_pack.hpp : 101) Index refill 6:12:42.064 21G / 42G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 6:12:42.064 21G / 42G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 512 files using 32 threads. This might take a while. 6:12:42.065 21G / 42G INFO General (file_limit.hpp : 32) Open file limit set to 10000 6:12:42.065 21G / 42G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.17167 Gb 6:12:42.065 21G / 42G INFO General (kmer_splitters.hpp : 97) Using cell size of 32768 6:13:05.693 39G / 42G INFO General (edge_index_builders.hpp : 77) Processed 16516156 edges 6:13:26.192 39G / 42G INFO General (edge_index_builders.hpp : 77) Processed 33031257 edges 6:14:09.528 39G / 42G INFO General (edge_index_builders.hpp : 77) Processed 49554183 edges 6:16:10.754 39G / 42G INFO General (edge_index_builders.hpp : 77) Processed 66062702 edges 6:18:11.754 39G / 42G INFO General (edge_index_builders.hpp : 77) Processed 82572204 edges 6:20:13.857 39G / 42G INFO General (edge_index_builders.hpp : 77) Processed 99091671 edges 6:22:16.907 39G / 42G INFO General (edge_index_builders.hpp : 77) Processed 115606911 edges 6:23:30.768 39G / 42G INFO General (edge_index_builders.hpp : 77) Processed 125448849 edges 6:23:30.768 39G / 42G INFO General (edge_index_builders.hpp : 82) Used 125448849 sequences. 6:23:32.071 21G / 42G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 6:38:14.245 21G / 42G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 3723768626 kmers in total. 6:38:14.246 21G / 42G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 6:53:46.899 21G / 42G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 6:57:08.465 23G / 42G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 7:12:49.726 23G / 42G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 1726729784 bytes occupied (3.70964 bits per kmer). 7:13:44.644 106G / 106G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while. 7:16:05.733 106G / 106G INFO General (edge_index.hpp : 92) Index refilled 7:16:05.753 106G / 106G INFO General (gap_closer.cpp : 159) Preparing shift maps 7:18:37.277 112G / 112G INFO General (gap_closer.cpp : 119) Processing paired reads (takes a while) 7:19:35.016 113G / 113G INFO General (gap_closer.cpp : 138) Used 129219073 paired reads 7:19:35.016 113G / 113G INFO General (gap_closer.cpp : 140) Merging paired indices 7:20:19.133 107G / 113G INFO GapCloser (gap_closer.cpp : 346) Closing short gaps 7:27:07.055 107G / 113G INFO GapCloser (gap_closer.cpp : 380) Closing short gaps complete: filled 114077 gaps after checking 1027187 candidates 7:28:37.704 106G / 113G INFO StageManager (stage.cpp : 132) STAGE == Raw Simplification 7:28:44.351 21G / 113G INFO General (simplification.cpp : 128) PROCEDURE == InitialCleaning 7:28:44.352 21G / 113G INFO Simplification (parallel_processing.hpp : 165) Running Self conjugate edge remover 7:28:49.760 21G / 113G INFO Simplification (parallel_processing.hpp : 167) Self conjugate edge remover triggered 10 times 7:28:49.761 21G / 113G INFO Simplification (parallel_processing.hpp : 165) Running Initial tip clipper 7:32:46.105 22G / 113G INFO Simplification (parallel_processing.hpp : 167) Initial tip clipper triggered 8157417 times 7:32:46.105 22G / 113G INFO Simplification (parallel_processing.hpp : 165) Running Initial ec remover 7:33:02.064 22G / 113G INFO Simplification (parallel_processing.hpp : 167) Initial ec remover triggered 195523 times 7:33:02.064 22G / 113G INFO Simplification (parallel_processing.hpp : 165) Running Disconnecting edges with low flanking coverage 7:33:16.785 22G / 113G INFO Simplification (parallel_processing.hpp : 167) Disconnecting edges with low flanking coverage triggered 186440 times 7:33:16.785 22G / 113G INFO Simplification (parallel_processing.hpp : 165) Running Initial isolated edge remover 7:35:13.676 22G / 113G INFO Simplification (parallel_processing.hpp : 167) Initial isolated edge remover triggered 11847392 times 7:35:15.601 22G / 113G INFO StageManager (stage.cpp : 132) STAGE == Preliminary Simplification 7:35:15.601 22G / 113G INFO General (simplification.cpp : 357) Graph simplification started 7:35:15.601 22G / 113G INFO General (graph_simplification.hpp : 634) Creating parallel br instance 7:35:15.601 22G / 113G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 1 7:35:15.601 22G / 113G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 7:37:35.758 22G / 113G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 5320234 times 7:37:35.758 22G / 113G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 8:26:16.739 64G / 113G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 1893493 times 8:26:16.739 64G / 113G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 8:26:23.141 64G / 113G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 54 times 8:26:23.141 64G / 113G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 2 8:26:23.141 64G / 113G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 8:26:30.575 64G / 113G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 34567 times 8:26:30.575 64G / 113G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 8:26:37.662 64G / 113G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 1488 times 8:26:37.662 64G / 113G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 8:28:19.670 64G / 113G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 1120709 times 8:28:19.670 64G / 113G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 3 8:28:19.670 64G / 113G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 8:28:27.651 64G / 113G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 94794 times 8:28:27.651 64G / 113G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 8:37:09.455 69G / 113G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 196075 times 8:37:09.455 69G / 113G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 8:37:58.513 69G / 113G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 479037 times 8:37:58.513 69G / 113G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 4 8:37:58.513 69G / 113G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 8:38:03.432 69G / 113G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 30005 times 8:38:03.432 69G / 113G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 8:44:55.239 72G / 113G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 113577 times 8:44:55.239 72G / 113G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 8:44:59.277 72G / 113G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 35 times 8:44:59.278 72G / 113G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 5 8:44:59.278 72G / 113G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 8:45:00.320 72G / 113G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 1141 times 8:45:00.320 72G / 113G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 8:45:00.687 72G / 113G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 52 times 8:45:00.687 72G / 113G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 8:45:00.687 72G / 113G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 8:45:00.687 72G / 113G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 6 8:45:00.687 72G / 113G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 8:45:00.688 72G / 113G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 8:45:00.688 72G / 113G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 8:45:00.688 72G / 113G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 8:45:00.688 72G / 113G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 8:45:00.688 72G / 113G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 8:45:00.689 72G / 113G INFO StageManager (stage.cpp : 132) STAGE == Gap Closer 8:45:00.689 72G / 113G INFO General (graph_pack.hpp : 101) Index refill 8:45:00.689 72G / 113G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 8:45:00.689 72G / 113G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 512 files using 32 threads. This might take a while. 8:45:00.689 72G / 113G INFO General (file_limit.hpp : 32) Open file limit set to 10000 8:45:00.689 72G / 113G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 1.64303 Gb 8:45:00.689 72G / 113G INFO General (kmer_splitters.hpp : 97) Using cell size of 32768 8:45:21.936 89G / 113G INFO General (edge_index_builders.hpp : 77) Processed 5911248 edges 8:45:43.458 89G / 113G INFO General (edge_index_builders.hpp : 77) Processed 11822813 edges 8:47:15.263 89G / 113G INFO General (edge_index_builders.hpp : 77) Processed 17728132 edges 8:48:48.948 89G / 113G INFO General (edge_index_builders.hpp : 77) Processed 23517314 edges 8:49:06.031 89G / 113G INFO General (edge_index_builders.hpp : 77) Processed 24653805 edges 8:49:06.046 89G / 113G INFO General (edge_index_builders.hpp : 82) Used 24653805 sequences. 8:49:07.367 72G / 113G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 8:55:02.976 72G / 113G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 2180784948 kmers in total. 8:55:02.976 72G / 113G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 9:01:04.559 72G / 113G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 9:03:01.833 73G / 113G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 9:11:39.976 73G / 113G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 1011243968 bytes occupied (3.70965 bits per kmer). 9:12:20.652 122G / 122G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while. 9:13:40.141 122G / 122G INFO General (edge_index.hpp : 92) Index refilled 9:13:40.150 122G / 122G INFO General (gap_closer.cpp : 159) Preparing shift maps 9:14:10.041 122G / 122G INFO General (gap_closer.cpp : 119) Processing paired reads (takes a while) 9:16:26.289 122G / 122G INFO General (gap_closer.cpp : 138) Used 129219073 paired reads 9:16:26.289 122G / 122G INFO General (gap_closer.cpp : 140) Merging paired indices 9:16:28.627 122G / 122G INFO GapCloser (gap_closer.cpp : 346) Closing short gaps 9:17:40.922 122G / 123G INFO GapCloser (gap_closer.cpp : 380) Closing short gaps complete: filled 1054 gaps after checking 31581 candidates 9:17:47.286 122G / 123G INFO StageManager (stage.cpp : 132) STAGE == Preliminary Paired Information Counting 9:22:52.639 131G / 131G INFO General (graph_pack.hpp : 109) Normalizing k-mer map. Total 697722884 kmers to process 9:40:13.108 131G / 152G INFO General (graph_pack.hpp : 111) Normalizing done 9:40:13.108 131G / 152G INFO General (pair_info_count.cpp : 320) Min edge length for estimation: 900 9:40:13.108 131G / 152G INFO General (pair_info_count.cpp : 331) Estimating insert size for library #0 9:40:13.108 131G / 152G INFO General (pair_info_count.cpp : 190) Estimating insert size (takes a while) 9:40:13.672 132G / 152G INFO General (pair_info_count.cpp : 39) Selecting usual mapper 9:40:23.328 132G / 152G INFO General (sequence_mapper_notifier.h: 80) Processed 200000 reads 9:40:23.384 132G / 152G INFO General (sequence_mapper_notifier.h: 80) Processed 400000 reads 9:40:23.457 132G / 152G INFO General (sequence_mapper_notifier.h: 80) Processed 600000 reads 9:40:23.520 132G / 152G INFO General (sequence_mapper_notifier.h: 80) Processed 800000 reads 9:40:23.583 132G / 152G INFO General (sequence_mapper_notifier.h: 80) Processed 1000000 reads 9:40:23.646 132G / 152G INFO General (sequence_mapper_notifier.h: 80) Processed 1200000 reads 9:40:23.926 132G / 152G INFO General (sequence_mapper_notifier.h: 80) Processed 2200000 reads 9:40:24.413 132G / 152G INFO General (sequence_mapper_notifier.h: 80) Processed 4200000 reads 9:40:30.775 132G / 152G INFO General (sequence_mapper_notifier.h: 80) Processed 8400000 reads 9:40:38.455 132G / 152G INFO General (sequence_mapper_notifier.h: 80) Processed 16800000 reads 9:40:58.460 132G / 152G INFO General (sequence_mapper_notifier.h: 80) Processed 33600000 reads 9:41:35.421 132G / 152G INFO General (sequence_mapper_notifier.h: 80) Processed 67200000 reads 9:42:43.247 132G / 152G INFO General (sequence_mapper_notifier.h: 98) Total 129219073 reads processed 9:42:44.856 132G / 152G INFO General (pair_info_count.cpp : 209) Edge pairs: 256407501 9:42:44.856 132G / 152G INFO General (pair_info_count.cpp : 213) 16622995 paired reads (12.8642% of all) aligned to long edges 9:42:44.900 131G / 152G INFO General (pair_info_count.cpp : 354) Insert size = 400.101, deviation = 55.5732, left quantile = 341, right quantile = 458, read length = 391 9:42:44.900 131G / 152G WARN General (pair_info_count.cpp : 358) Estimated mean insert size 400.101 is very small compared to read length 391 9:42:45.311 132G / 152G INFO General (pair_info_count.cpp : 371) Filtering data for library #0 9:42:45.312 132G / 152G INFO General (pair_info_count.cpp : 39) Selecting usual mapper 9:42:53.069 132G / 152G INFO General (sequence_mapper_notifier.h: 80) Processed 200000 reads 9:42:53.076 132G / 152G INFO General (sequence_mapper_notifier.h: 80) Processed 400000 reads 9:42:53.077 132G / 152G INFO General (sequence_mapper_notifier.h: 80) Processed 600000 reads 9:42:53.084 132G / 152G INFO General (sequence_mapper_notifier.h: 80) Processed 800000 reads 9:42:53.099 132G / 152G INFO General (sequence_mapper_notifier.h: 80) Processed 1000000 reads 9:42:53.100 132G / 152G INFO General (sequence_mapper_notifier.h: 80) Processed 1200000 reads 9:42:53.152 132G / 152G INFO General (sequence_mapper_notifier.h: 80) Processed 2200000 reads 9:42:53.755 132G / 152G INFO General (sequence_mapper_notifier.h: 80) Processed 4200000 reads 9:43:00.361 132G / 152G INFO General (sequence_mapper_notifier.h: 80) Processed 8400000 reads 9:43:09.260 132G / 152G INFO General (sequence_mapper_notifier.h: 80) Processed 16800000 reads 9:43:29.340 132G / 152G INFO General (sequence_mapper_notifier.h: 80) Processed 33600000 reads 9:44:08.221 132G / 152G INFO General (sequence_mapper_notifier.h: 80) Processed 67200000 reads 9:45:27.674 132G / 152G INFO General (sequence_mapper_notifier.h: 98) Total 129219073 reads processed 9:45:27.674 132G / 152G INFO General (pair_info_count.cpp : 383) Mapping library #0 9:45:27.675 132G / 152G INFO General (pair_info_count.cpp : 385) Mapping paired reads (takes a while) 9:45:27.675 132G / 152G INFO General (pair_info_count.cpp : 289) Left insert size quantile 341, right insert size quantile 458, filtering threshold 1, rounding threshold 0 9:45:27.701 132G / 152G INFO General (pair_info_count.cpp : 39) Selecting usual mapper 9:45:39.337 133G / 152G INFO General (sequence_mapper_notifier.h: 80) Processed 200000 reads 9:45:39.338 133G / 152G INFO General (sequence_mapper_notifier.h: 80) Processed 400000 reads 9:45:39.339 133G / 152G INFO General (sequence_mapper_notifier.h: 80) Processed 600000 reads 9:45:39.341 133G / 152G INFO General (sequence_mapper_notifier.h: 80) Processed 800000 reads 9:45:39.341 133G / 152G INFO General (sequence_mapper_notifier.h: 80) Processed 1000000 reads 9:45:39.345 133G / 152G INFO General (sequence_mapper_notifier.h: 80) Processed 1200000 reads 9:45:39.365 133G / 152G INFO General (sequence_mapper_notifier.h: 80) Processed 2200000 reads 9:45:39.631 133G / 152G INFO General (sequence_mapper_notifier.h: 80) Processed 4200000 reads 9:45:48.241 134G / 152G INFO General (sequence_mapper_notifier.h: 80) Processed 8400000 reads 9:45:57.634 134G / 152G INFO General (sequence_mapper_notifier.h: 80) Processed 16800000 reads 9:46:27.608 136G / 152G INFO General (sequence_mapper_notifier.h: 80) Processed 33600000 reads 9:47:16.383 139G / 152G INFO General (sequence_mapper_notifier.h: 80) Processed 67200000 reads 9:48:52.178 142G / 152G INFO General (sequence_mapper_notifier.h: 98) Total 129219073 reads processed 9:48:58.559 141G / 152G INFO StageManager (stage.cpp : 132) STAGE == Preliminary Distance Estimation 9:48:58.565 141G / 152G INFO General (distance_estimation.cpp : 173) Processing library #0 9:48:58.565 141G / 152G INFO General (distance_estimation.cpp : 149) Weight Filter Done 9:48:58.566 141G / 152G INFO DistanceEstimator (distance_estimation.hpp : 116) Using SIMPLE distance estimator 10:58:34.418 151G / 155G INFO General (distance_estimation.cpp : 34) Filtering info 10:58:34.418 151G / 155G INFO General (pair_info_filters.hpp : 242) Start filtering; index size: 559067957 11:03:17.736 158G / 163G INFO General (pair_info_filters.hpp : 263) Done filtering 11:03:18.050 150G / 163G INFO General (distance_estimation.cpp : 156) Refining clustered pair information 11:04:17.393 150G / 163G INFO General (distance_estimation.cpp : 158) The refining of clustered pair information has been finished 11:04:17.393 150G / 163G INFO General (distance_estimation.cpp : 160) Improving paired information 11:39:23.480 160G / 182G INFO PairInfoImprover (pair_info_improver.hpp : 103) Paired info stats: missing = 159026392; contradictional = 0 12:53:40.161 166G / 219G INFO PairInfoImprover (pair_info_improver.hpp : 103) Paired info stats: missing = 105034138; contradictional = 0 12:53:40.161 166G / 219G INFO General (distance_estimation.cpp : 103) Filling scaffolding index 12:53:40.161 166G / 219G INFO DistanceEstimator (distance_estimation.hpp : 116) Using SMOOTHING distance estimator 13:57:47.635 167G / 219G INFO General (distance_estimation.cpp : 34) Filtering info 13:57:47.635 167G / 219G INFO General (pair_info_filters.hpp : 242) Start filtering; index size: 45641509 13:58:17.828 169G / 219G INFO General (pair_info_filters.hpp : 263) Done filtering 13:58:17.909 167G / 219G INFO General (distance_estimation.cpp : 182) Clearing raw paired index 13:59:45.978 157G / 219G INFO StageManager (stage.cpp : 132) STAGE == Preliminary Repeat Resolving 13:59:45.978 157G / 219G INFO General (repeat_resolving.cpp : 56) Setting up preliminary path extend settings 13:59:45.978 157G / 219G INFO General (repeat_resolving.cpp : 69) Using Path-Extend repeat resolving 13:59:45.978 157G / 219G INFO General (launcher.cpp : 477) ExSPAnder repeat resolving tool started : Error in malloc(): out of memory. Requested: 512, active: 176198516736 == Error == system call for: "['/home/administrator/SPAdes-3.13.0-Linux/bin/spades-core', '/DATA/markop/CPB_metaSpades/output/K127/configs/config.info', '/DATA/markop/CPB_metaSpades/output/K127/configs/mda_mode.info', '/DATA/markop/CPB_metaSpades/output/K127/configs/meta_mode.info']" finished abnormally, err code: -6 ======= SPAdes pipeline finished abnormally and WITH WARNINGS! === Error correction and assembling warnings: * 9:42:44.900 131G / 152G WARN General (pair_info_count.cpp : 358) Estimated mean insert size 400.101 is very small compared to read length 391 ======= Warnings saved to /DATA/markop/CPB_metaSpades/output/warnings.log === ERRORs: * system call for: "['/home/administrator/SPAdes-3.13.0-Linux/bin/spades-core', '/DATA/markop/CPB_metaSpades/output/K127/configs/config.info', '/DATA/markop/CPB_metaSpades/output/K127/configs/mda_mode.info', '/DATA/markop/CPB_metaSpades/output/K127/configs/meta_mode.info']" finished abnormally, err code: -6 In case you have troubles running SPAdes, you can write to spades.support@cab.spbu.ru or report an issue on our GitHub repository github.com/ablab/spades Please provide us with params.txt and spades.log files from the output directory. ======= SPAdes pipeline continued. Log can be found here: /DATA/markop/CPB_metaSpades/output/spades.log Restored from Command line: /home/administrator/SPAdes-3.13.0-Linux/bin/spades.py --meta -k 21,41,71,101 -m 230 -t 32 -o /DATA/markop/CPB_metaSpades/output -1 /DATA/markop/CPB_metaSpades/input/unmerged_1.fq -2 /DATA/markop/CPB_metaSpades/input/unmerged_2.fq -s /DATA/markop/CPB_metaSpades/input/merged.fq Command line: /home/administrator/SPAdes-3.13.0-Linux/bin/spades.py --meta -k 21,41,71,101 -m 230 -t 32 -o /DATA/markop/CPB_metaSpades/output -1 /DATA/markop/CPB_metaSpades/input/unmerged_1.fq -2 /DATA/markop/CPB_metaSpades/input/unmerged_2.fq -s /DATA/markop/CPB_metaSpades/input/merged.fq System information: SPAdes version: 3.13.0 Python version: 2.7.15 OS: Linux-4.13.0-41-generic-x86_64-with-debian-stretch-sid Output dir: /DATA/markop/CPB_metaSpades/output Mode: read error correction and assembling Debug mode is turned OFF Dataset parameters: Metagenomic mode Reads: Library number: 1, library type: paired-end orientation: fr left reads: ['/DATA/markop/CPB_metaSpades/input/unmerged_1.fq'] right reads: ['/DATA/markop/CPB_metaSpades/input/unmerged_2.fq'] interlaced reads: not specified single reads: ['/DATA/markop/CPB_metaSpades/input/merged.fq'] merged reads: not specified Read error correction parameters: Iterations: 1 PHRED offset will be auto-detected Corrected reads will be compressed Assembly parameters: k: [21, 41, 71, 101] Repeat resolution is enabled Mismatch careful mode is turned OFF MismatchCorrector will be SKIPPED Coverage cutoff is turned OFF Other parameters: Dir for temp files: /DATA/markop/CPB_metaSpades/output/tmp Threads: 32 Memory limit (in Gb): 230 ===== Skipping Read error correction (already processed). ===== Assembling started. == Skipping assembler: K21 (already processed) Max read length detected as 391 == Skipping assembler: K41 (already processed) == Skipping assembler: K71 (already processed) == Skipping assembler: K101 (already processed) ===== Assembling finished. Used k-mer sizes: 21, 41, 71, 101 * Corrected reads are in /DATA/markop/CPB_metaSpades/output/corrected/ * Assembled contigs are in /DATA/markop/CPB_metaSpades/output/contigs.fasta * Assembly graph is in /DATA/markop/CPB_metaSpades/output/assembly_graph.fastg * Assembly graph in GFA format is in /DATA/markop/CPB_metaSpades/output/assembly_graph_with_scaffolds.gfa ======= SPAdes pipeline finished WITH WARNINGS! === Error correction and assembling warnings: * 10:57:34.670 131G / 152G WARN General (pair_info_count.cpp : 358) Estimated mean insert size 400.101 is very small compared to read length 391 ======= Warnings saved to /DATA/markop/CPB_metaSpades/output/warnings.log SPAdes log can be found here: /DATA/markop/CPB_metaSpades/output/spades.log Thank you for using SPAdes!