Command line: /home/psgendb/BIRCHDEV/bin-linux-x86_64/spades.py -1 /local/genbank/workspace/reads.uncorr/20090202_7_R1.fq -2 /local/genbank/workspace/reads.uncorr/20090202_7_R2.fq -1 /local/genbank/workspace/reads.uncorr/20090202_8_R1.fq -2 /local/genbank/workspace/reads.uncorr/20090202_8_R2.fq -1 /local/genbank/workspace/reads.uncorr/AB2kb_R1.fq -2 /local/genbank/workspace/reads.uncorr/AB2kb_R2.fq -1 /local/genbank/workspace/reads.uncorr/AB4kb_R1.fq -2 /local/genbank/workspace/reads.uncorr/AB4kb_R2.fq -1 /local/genbank/workspace/reads.uncorr/Algae6.2GB_6_R1.fq -2 /local/genbank/workspace/reads.uncorr/Algae6.2GB_6_R2.fq -1 /local/genbank/workspace/reads.uncorr/Algae6.2GB_7_R1.fq -2 /local/genbank/workspace/reads.uncorr/Algae6.2GB_7_R2.fq -1 /local/genbank/workspace/reads.uncorr/Algae6.2GB_8_R1.fq -2 /local/genbank/workspace/reads.uncorr/Algae6.2GB_8_R2.fq -1 /local/genbank/workspace/reads.uncorr/Algae7.2GB_6_R1.fq -2 /local/genbank/workspace/reads.uncorr/Algae7.2GB_6_R2.fq -1 /local/genbank/workspace/reads.uncorr/Algae7.2GB_7_R1.fq -2 /local/genbank/workspace/reads.uncorr/Algae7.2GB_7_R2.fq -1 /local/genbank/workspace/reads.uncorr/Algae7.2GB_8_R1.fq -2 /local/genbank/workspace/reads.uncorr/Algae7.2GB_8_R2.fq -s /local/genbank/workspace/reads.uncorr/2008-09allU.fq -s /local/genbank/workspace/reads.uncorr/3-6.2-7.2allU.fq -s /local/genbank/workspace/reads.uncorr/AGRFallU.fq -s /local/genbank/workspace/reads.uncorr/454all.fq -m 204 -t 32 -o /local/genbank/workspace/reads.uncorr.spades1 System information: SPAdes version: 3.13.0 Python version: 2.7.5 OS: Linux-3.10.0-1160.25.1.el7.x86_64-x86_64-with-redhat-7.9-Maipo Output dir: /local/genbank/workspace/reads.uncorr.spades1 Mode: read error correction and assembling Debug mode is turned OFF Dataset parameters: Multi-cell mode (you should set '--sc' flag if input data was obtained with MDA (single-cell) technology or --meta flag if processing metagenomic dataset) Reads: Library number: 1, library type: paired-end orientation: fr left reads: ['/local/genbank/workspace/reads.uncorr/20090202_7_R1.fq', '/local/genbank/workspace/reads.uncorr/20090202_8_R1.fq', '/local/genbank/workspace/reads.uncorr/AB2kb_R1.fq', '/local/genbank/workspace/reads.uncorr/AB4kb_R1.fq', '/local/genbank/workspace/reads.uncorr/Algae6.2GB_6_R1.fq', '/local/genbank/workspace/reads.uncorr/Algae6.2GB_7_R1.fq', '/local/genbank/workspace/reads.uncorr/Algae6.2GB_8_R1.fq', '/local/genbank/workspace/reads.uncorr/Algae7.2GB_6_R1.fq', '/local/genbank/workspace/reads.uncorr/Algae7.2GB_7_R1.fq', '/local/genbank/workspace/reads.uncorr/Algae7.2GB_8_R1.fq'] right reads: ['/local/genbank/workspace/reads.uncorr/20090202_7_R2.fq', '/local/genbank/workspace/reads.uncorr/20090202_8_R2.fq', '/local/genbank/workspace/reads.uncorr/AB2kb_R2.fq', '/local/genbank/workspace/reads.uncorr/AB4kb_R2.fq', '/local/genbank/workspace/reads.uncorr/Algae6.2GB_6_R2.fq', '/local/genbank/workspace/reads.uncorr/Algae6.2GB_7_R2.fq', '/local/genbank/workspace/reads.uncorr/Algae6.2GB_8_R2.fq', '/local/genbank/workspace/reads.uncorr/Algae7.2GB_6_R2.fq', '/local/genbank/workspace/reads.uncorr/Algae7.2GB_7_R2.fq', '/local/genbank/workspace/reads.uncorr/Algae7.2GB_8_R2.fq'] interlaced reads: not specified single reads: ['/local/genbank/workspace/reads.uncorr/2008-09allU.fq', '/local/genbank/workspace/reads.uncorr/3-6.2-7.2allU.fq', '/local/genbank/workspace/reads.uncorr/AGRFallU.fq', '/local/genbank/workspace/reads.uncorr/454all.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: automatic selection based on read length 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: /local/genbank/workspace/reads.uncorr.spades1/tmp Threads: 32 Memory limit (in Gb): 204 ======= SPAdes pipeline started. Log can be found here: /local/genbank/workspace/reads.uncorr.spades1/spades.log ===== Read error correction started. == Running read error correction tool: /home/psgendb/BIRCHDEV/pkg/SPAdes-3.13.0/linux-x86_64/bin/spades-hammer /local/genbank/workspace/reads.uncorr.spades1/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 0:00:00.001 4M / 4M INFO General (main.cpp : 76) Loading config from /local/genbank/workspace/reads.uncorr.spades1/corrected/configs/config.info 0:00:00.003 4M / 4M INFO General (main.cpp : 78) Maximum # of threads to use (adjusted due to OMP capabilities): 32 0:00:00.003 4M / 4M INFO General (memory_limit.cpp : 49) Memory limit set to 204 Gb 0:00:00.003 4M / 4M INFO General (main.cpp : 86) Trying to determine PHRED offset 0:00:00.004 4M / 4M INFO General (main.cpp : 92) Determined value is 33 0:00:00.004 4M / 4M INFO General (hammer_tools.cpp : 36) Hamming graph threshold tau=1, k=21, subkmer positions = [ 0 10 ] 0:00:00.004 4M / 4M INFO General (main.cpp : 113) Size of aux. kmer data 24 bytes === ITERATION 0 begins === 0:00:00.011 4M / 4M INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:00:00.011 4M / 4M INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 512 files using 32 threads. This might take a while. 0:00:00.014 4M / 4M INFO General (file_limit.hpp : 32) Open file limit set to 4096 0:00:00.014 4M / 4M INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.12496 Gb 0:00:00.014 4M / 4M INFO General (kmer_splitters.hpp : 97) Using cell size of 131072 0:00:01.682 17G / 17G INFO K-mer Splitting (kmer_data.cpp : 97) Processing /local/genbank/workspace/reads.uncorr/20090202_7_R1.fq 0:00:38.205 17G / 18G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 3151308 reads 0:00:38.205 17G / 18G INFO K-mer Splitting (kmer_data.cpp : 97) Processing /local/genbank/workspace/reads.uncorr/20090202_8_R1.fq 0:01:18.571 17G / 18G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 6710753 reads 0:01:18.571 17G / 18G INFO K-mer Splitting (kmer_data.cpp : 97) Processing /local/genbank/workspace/reads.uncorr/AB2kb_R1.fq 0:03:23.327 17G / 18G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 17393955 reads 0:05:11.666 17G / 18G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 27623982 reads 0:07:00.440 17G / 18G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 38279537 reads 0:07:04.262 17G / 18G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 38328668 reads 0:07:04.262 17G / 18G INFO K-mer Splitting (kmer_data.cpp : 97) Processing /local/genbank/workspace/reads.uncorr/AB4kb_R1.fq 0:08:19.309 17G / 18G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 44730544 reads 0:09:37.403 17G / 18G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 51348102 reads 0:10:11.007 17G / 18G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 53557260 reads 0:10:11.007 17G / 18G INFO K-mer Splitting (kmer_data.cpp : 97) Processing /local/genbank/workspace/reads.uncorr/Algae6.2GB_6_R1.fq 0:11:20.819 17G / 18G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 60126475 reads 0:11:20.819 17G / 18G INFO K-mer Splitting (kmer_data.cpp : 97) Processing /local/genbank/workspace/reads.uncorr/Algae6.2GB_7_R1.fq 0:12:37.702 17G / 18G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 67613068 reads 0:12:37.702 17G / 18G INFO K-mer Splitting (kmer_data.cpp : 97) Processing /local/genbank/workspace/reads.uncorr/Algae6.2GB_8_R1.fq 0:13:59.543 17G / 18G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 75902544 reads 0:13:59.543 17G / 18G INFO K-mer Splitting (kmer_data.cpp : 97) Processing /local/genbank/workspace/reads.uncorr/Algae7.2GB_6_R1.fq 0:15:44.226 17G / 18G INFO K-mer Splitting (kmer_data.cpp : 97) Processing /local/genbank/workspace/reads.uncorr/Algae7.2GB_7_R1.fq 0:17:20.268 17G / 18G INFO K-mer Splitting (kmer_data.cpp : 97) Processing /local/genbank/workspace/reads.uncorr/Algae7.2GB_8_R1.fq 0:18:55.313 17G / 18G INFO K-mer Splitting (kmer_data.cpp : 97) Processing /local/genbank/workspace/reads.uncorr/20090202_7_R2.fq 0:19:33.384 17G / 18G INFO K-mer Splitting (kmer_data.cpp : 97) Processing /local/genbank/workspace/reads.uncorr/20090202_8_R2.fq 0:20:15.530 17G / 18G INFO K-mer Splitting (kmer_data.cpp : 97) Processing /local/genbank/workspace/reads.uncorr/AB2kb_R2.fq 0:25:54.232 17G / 18G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 144589789 reads 0:25:54.232 17G / 18G INFO K-mer Splitting (kmer_data.cpp : 97) Processing /local/genbank/workspace/reads.uncorr/AB4kb_R2.fq 0:29:05.627 17G / 18G INFO K-mer Splitting (kmer_data.cpp : 97) Processing /local/genbank/workspace/reads.uncorr/Algae6.2GB_6_R2.fq 0:30:13.388 17G / 18G INFO K-mer Splitting (kmer_data.cpp : 97) Processing /local/genbank/workspace/reads.uncorr/Algae6.2GB_7_R2.fq 0:31:26.406 17G / 18G INFO K-mer Splitting (kmer_data.cpp : 97) Processing /local/genbank/workspace/reads.uncorr/Algae6.2GB_8_R2.fq 0:32:50.228 17G / 18G INFO K-mer Splitting (kmer_data.cpp : 97) Processing /local/genbank/workspace/reads.uncorr/Algae7.2GB_6_R2.fq 0:34:33.056 17G / 18G INFO K-mer Splitting (kmer_data.cpp : 97) Processing /local/genbank/workspace/reads.uncorr/Algae7.2GB_7_R2.fq 0:36:05.910 17G / 18G INFO K-mer Splitting (kmer_data.cpp : 97) Processing /local/genbank/workspace/reads.uncorr/Algae7.2GB_8_R2.fq 0:37:39.018 17G / 18G INFO K-mer Splitting (kmer_data.cpp : 97) Processing /local/genbank/workspace/reads.uncorr/2008-09allU.fq 0:43:30.433 17G / 18G INFO K-mer Splitting (kmer_data.cpp : 97) Processing /local/genbank/workspace/reads.uncorr/3-6.2-7.2allU.fq 0:47:25.186 17G / 18G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 275125352 reads 0:51:31.105 17G / 18G INFO K-mer Splitting (kmer_data.cpp : 97) Processing /local/genbank/workspace/reads.uncorr/AGRFallU.fq 0:53:21.342 17G / 18G INFO K-mer Splitting (kmer_data.cpp : 97) Processing /local/genbank/workspace/reads.uncorr/454all.fq 0:54:42.117 17G / 18G INFO K-mer Splitting (kmer_data.cpp : 112) Total 312091251 reads processed 0:54:49.482 128M / 18G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 1:00:29.046 128M / 18G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 3520096154 kmers in total. 1:00:29.046 128M / 18G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 1:05:59.659 128M / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 1:10:32.353 1G / 18G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 1:14:41.182 1G / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 1632302388 bytes occupied (3.70968 bits per kmer). 1:14:41.204 1G / 18G INFO K-mer Counting (kmer_data.cpp : 356) Arranging kmers in hash map order 1:21:42.598 54G / 54G INFO General (main.cpp : 148) Clustering Hamming graph. 2:34:40.977 54G / 54G INFO General (main.cpp : 155) Extracting clusters 4:21:14.587 54G / 146G INFO General (main.cpp : 167) Clustering done. Total clusters: 1726882156 4:21:25.552 28G / 146G INFO K-mer Counting (kmer_data.cpp : 376) Collecting K-mer information, this takes a while. 4:23:44.892 106G / 146G INFO K-mer Counting (kmer_data.cpp : 382) Processing /local/genbank/workspace/reads.uncorr/20090202_7_R1.fq 4:24:19.197 106G / 146G INFO K-mer Counting (kmer_data.cpp : 382) Processing /local/genbank/workspace/reads.uncorr/20090202_8_R1.fq 4:24:36.416 106G / 146G INFO K-mer Counting (kmer_data.cpp : 382) Processing /local/genbank/workspace/reads.uncorr/AB2kb_R1.fq 4:28:14.521 106G / 146G INFO K-mer Counting (kmer_data.cpp : 382) Processing /local/genbank/workspace/reads.uncorr/AB4kb_R1.fq 4:30:01.365 106G / 146G INFO K-mer Counting (kmer_data.cpp : 382) Processing /local/genbank/workspace/reads.uncorr/Algae6.2GB_6_R1.fq 4:30:34.879 106G / 146G INFO K-mer Counting (kmer_data.cpp : 382) Processing /local/genbank/workspace/reads.uncorr/Algae6.2GB_7_R1.fq 4:31:12.239 106G / 146G INFO K-mer Counting (kmer_data.cpp : 382) Processing /local/genbank/workspace/reads.uncorr/Algae6.2GB_8_R1.fq 4:31:54.413 106G / 146G INFO K-mer Counting (kmer_data.cpp : 382) Processing /local/genbank/workspace/reads.uncorr/Algae7.2GB_6_R1.fq 4:32:50.064 106G / 146G INFO K-mer Counting (kmer_data.cpp : 382) Processing /local/genbank/workspace/reads.uncorr/Algae7.2GB_7_R1.fq 4:33:37.724 106G / 146G INFO K-mer Counting (kmer_data.cpp : 382) Processing /local/genbank/workspace/reads.uncorr/Algae7.2GB_8_R1.fq 4:34:28.474 106G / 146G INFO K-mer Counting (kmer_data.cpp : 382) Processing /local/genbank/workspace/reads.uncorr/20090202_7_R2.fq 4:34:44.417 106G / 146G INFO K-mer Counting (kmer_data.cpp : 382) Processing /local/genbank/workspace/reads.uncorr/20090202_8_R2.fq 4:35:01.384 106G / 146G INFO K-mer Counting (kmer_data.cpp : 382) Processing /local/genbank/workspace/reads.uncorr/AB2kb_R2.fq 4:38:32.743 106G / 146G INFO K-mer Counting (kmer_data.cpp : 382) Processing /local/genbank/workspace/reads.uncorr/AB4kb_R2.fq 4:40:14.311 106G / 146G INFO K-mer Counting (kmer_data.cpp : 382) Processing /local/genbank/workspace/reads.uncorr/Algae6.2GB_6_R2.fq 4:40:46.898 106G / 146G INFO K-mer Counting (kmer_data.cpp : 382) Processing /local/genbank/workspace/reads.uncorr/Algae6.2GB_7_R2.fq 4:41:22.966 106G / 146G INFO K-mer Counting (kmer_data.cpp : 382) Processing /local/genbank/workspace/reads.uncorr/Algae6.2GB_8_R2.fq 4:42:04.179 106G / 146G INFO K-mer Counting (kmer_data.cpp : 382) Processing /local/genbank/workspace/reads.uncorr/Algae7.2GB_6_R2.fq 4:42:59.494 106G / 146G INFO K-mer Counting (kmer_data.cpp : 382) Processing /local/genbank/workspace/reads.uncorr/Algae7.2GB_7_R2.fq 4:43:47.410 106G / 146G INFO K-mer Counting (kmer_data.cpp : 382) Processing /local/genbank/workspace/reads.uncorr/Algae7.2GB_8_R2.fq 4:44:37.467 106G / 146G INFO K-mer Counting (kmer_data.cpp : 382) Processing /local/genbank/workspace/reads.uncorr/2008-09allU.fq 4:48:16.414 106G / 146G INFO K-mer Counting (kmer_data.cpp : 382) Processing /local/genbank/workspace/reads.uncorr/3-6.2-7.2allU.fq 4:52:22.770 106G / 146G INFO K-mer Counting (kmer_data.cpp : 382) Processing /local/genbank/workspace/reads.uncorr/AGRFallU.fq 4:53:30.299 106G / 146G INFO K-mer Counting (kmer_data.cpp : 382) Processing /local/genbank/workspace/reads.uncorr/454all.fq 4:54:46.751 106G / 146G INFO K-mer Counting (kmer_data.cpp : 389) Collection done, postprocessing. 4:56:05.788 106G / 146G INFO K-mer Counting (kmer_data.cpp : 403) There are 3520096154 kmers in total. Among them 2112743216 (60.0195%) are singletons. 4:56:05.788 106G / 146G INFO General (main.cpp : 173) Subclustering Hamming graph 16:49:54.403 106G / 146G INFO Hamming Subclustering (kmer_cluster.cpp : 649) Subclustering done. Total 601149 non-read kmers were generated. 16:49:54.404 106G / 146G INFO Hamming Subclustering (kmer_cluster.cpp : 650) Subclustering statistics: 16:49:54.404 106G / 146G INFO Hamming Subclustering (kmer_cluster.cpp : 651) Total singleton hamming clusters: 1298926146. Among them 607354426 (46.7582%) are good 16:49:54.404 106G / 146G INFO Hamming Subclustering (kmer_cluster.cpp : 652) Total singleton subclusters: 24295747. Among them 24100760 (99.1974%) are good 16:49:54.404 106G / 146G INFO Hamming Subclustering (kmer_cluster.cpp : 653) Total non-singleton subcluster centers: 515697295. Among them 273671350 (53.0682%) are good 16:49:54.404 106G / 146G INFO Hamming Subclustering (kmer_cluster.cpp : 654) Average size of non-trivial subcluster: 4.30851 kmers 16:49:54.404 106G / 146G INFO Hamming Subclustering (kmer_cluster.cpp : 655) Average number of sub-clusters per non-singleton cluster: 1.2618 16:49:54.404 106G / 146G INFO Hamming Subclustering (kmer_cluster.cpp : 656) Total solid k-mers: 905126536 16:49:54.404 106G / 146G INFO Hamming Subclustering (kmer_cluster.cpp : 657) Substitution probabilities: [4,4]((0.896302,0.0567139,0.0320626,0.0149212),(0.0250673,0.927078,0.0292194,0.0186356),(0.0179616,0.0286109,0.927579,0.025848),(0.0144787,0.031526,0.0557573,0.898238)) 16:50:03.231 106G / 146G INFO General (main.cpp : 178) Finished clustering. 16:50:03.231 106G / 146G INFO General (main.cpp : 197) Starting solid k-mers expansion in 32 threads. 17:16:38.197 106G / 146G INFO General (main.cpp : 218) Solid k-mers iteration 0 produced 230558361 new k-mers. 17:41:57.103 106G / 146G INFO General (main.cpp : 218) Solid k-mers iteration 1 produced 15824305 new k-mers. 18:10:39.413 106G / 146G INFO General (main.cpp : 218) Solid k-mers iteration 2 produced 749561 new k-mers. 18:39:11.017 106G / 146G INFO General (main.cpp : 218) Solid k-mers iteration 3 produced 45709 new k-mers. 19:07:57.249 106G / 146G INFO General (main.cpp : 218) Solid k-mers iteration 4 produced 2825 new k-mers. 19:36:28.519 106G / 146G INFO General (main.cpp : 218) Solid k-mers iteration 5 produced 131 new k-mers. 20:05:05.655 106G / 146G INFO General (main.cpp : 218) Solid k-mers iteration 6 produced 20 new k-mers. 20:29:32.391 106G / 146G INFO General (main.cpp : 218) Solid k-mers iteration 7 produced 0 new k-mers. 20:29:32.391 106G / 146G INFO General (main.cpp : 222) Solid k-mers finalized 20:29:32.391 106G / 146G INFO General (hammer_tools.cpp : 220) Starting read correction in 32 threads. 20:29:32.391 106G / 146G INFO General (hammer_tools.cpp : 233) Correcting pair of reads: /local/genbank/workspace/reads.uncorr/20090202_7_R1.fq and /local/genbank/workspace/reads.uncorr/20090202_7_R2.fq 20:29:48.915 108G / 146G INFO General (hammer_tools.cpp : 168) Prepared batch 0 of 3151308 reads. 20:30:06.749 108G / 146G INFO General (hammer_tools.cpp : 175) Processed batch 0 20:30:27.770 108G / 146G INFO General (hammer_tools.cpp : 185) Written batch 0 20:30:37.812 106G / 146G INFO General (hammer_tools.cpp : 233) Correcting pair of reads: /local/genbank/workspace/reads.uncorr/20090202_8_R1.fq and /local/genbank/workspace/reads.uncorr/20090202_8_R2.fq 20:31:06.640 108G / 146G INFO General (hammer_tools.cpp : 168) Prepared batch 0 of 3200000 reads. 20:31:31.094 108G / 146G INFO General (hammer_tools.cpp : 175) Processed batch 0 20:31:53.029 108G / 146G INFO General (hammer_tools.cpp : 185) Written batch 0 20:31:55.952 108G / 146G INFO General (hammer_tools.cpp : 168) Prepared batch 1 of 359445 reads. 20:32:00.518 108G / 146G INFO General (hammer_tools.cpp : 175) Processed batch 1 20:32:01.977 108G / 146G INFO General (hammer_tools.cpp : 185) Written batch 1 20:32:13.880 106G / 146G INFO General (hammer_tools.cpp : 233) Correcting pair of reads: /local/genbank/workspace/reads.uncorr/AB2kb_R1.fq and /local/genbank/workspace/reads.uncorr/AB2kb_R2.fq 20:32:48.314 108G / 146G INFO General (hammer_tools.cpp : 168) Prepared batch 0 of 3200000 reads. 20:33:15.791 109G / 146G INFO General (hammer_tools.cpp : 175) Processed batch 0 20:33:40.577 109G / 146G INFO General (hammer_tools.cpp : 185) Written batch 0 20:34:14.354 110G / 146G INFO General (hammer_tools.cpp : 168) Prepared batch 1 of 3200000 reads. 20:34:40.786 110G / 146G INFO General (hammer_tools.cpp : 175) Processed batch 1 20:35:07.884 110G / 146G INFO General (hammer_tools.cpp : 185) Written batch 1 20:35:41.677 110G / 146G INFO General (hammer_tools.cpp : 168) Prepared batch 2 of 3200000 reads. 20:36:08.454 110G / 146G INFO General (hammer_tools.cpp : 175) Processed batch 2 20:36:38.279 110G / 146G INFO General (hammer_tools.cpp : 185) Written batch 2 20:37:10.706 110G / 146G INFO General (hammer_tools.cpp : 168) Prepared batch 3 of 3200000 reads. 20:37:34.686 110G / 146G INFO General (hammer_tools.cpp : 175) Processed batch 3 20:37:56.088 110G / 146G INFO General (hammer_tools.cpp : 185) Written batch 3 20:38:28.754 110G / 146G INFO General (hammer_tools.cpp : 168) Prepared batch 4 of 3200000 reads. 20:38:52.614 110G / 146G INFO General (hammer_tools.cpp : 175) Processed batch 4 20:39:18.716 110G / 146G INFO General (hammer_tools.cpp : 185) Written batch 4 20:39:50.604 110G / 146G INFO General (hammer_tools.cpp : 168) Prepared batch 5 of 3200000 reads. 20:40:13.314 110G / 146G INFO General (hammer_tools.cpp : 175) Processed batch 5 20:40:39.867 110G / 146G INFO General (hammer_tools.cpp : 185) Written batch 5 20:41:10.278 110G / 146G INFO General (hammer_tools.cpp : 168) Prepared batch 6 of 3200000 reads. 20:41:31.866 110G / 146G INFO General (hammer_tools.cpp : 175) Processed batch 6 20:42:01.002 110G / 146G INFO General (hammer_tools.cpp : 185) Written batch 6 20:42:30.633 110G / 146G INFO General (hammer_tools.cpp : 168) Prepared batch 7 of 3200000 reads. 20:42:54.118 110G / 146G INFO General (hammer_tools.cpp : 175) Processed batch 7 20:43:23.348 110G / 146G INFO General (hammer_tools.cpp : 185) Written batch 7 20:43:52.909 110G / 146G INFO General (hammer_tools.cpp : 168) Prepared batch 8 of 3200000 reads. 20:44:16.380 110G / 146G INFO General (hammer_tools.cpp : 175) Processed batch 8 20:44:45.085 110G / 146G INFO General (hammer_tools.cpp : 185) Written batch 8 20:45:12.142 110G / 146G INFO General (hammer_tools.cpp : 168) Prepared batch 9 of 2817915 reads. 20:45:40.441 110G / 146G INFO General (hammer_tools.cpp : 175) Processed batch 9 20:46:08.257 110G / 146G INFO General (hammer_tools.cpp : 185) Written batch 9 20:46:19.007 106G / 146G INFO General (hammer_tools.cpp : 233) Correcting pair of reads: /local/genbank/workspace/reads.uncorr/AB4kb_R1.fq and /local/genbank/workspace/reads.uncorr/AB4kb_R2.fq 20:46:54.209 108G / 146G INFO General (hammer_tools.cpp : 168) Prepared batch 0 of 3200000 reads. 20:47:28.398 109G / 146G INFO General (hammer_tools.cpp : 175) Processed batch 0 20:47:53.593 109G / 146G INFO General (hammer_tools.cpp : 185) Written batch 0 20:48:27.310 109G / 146G INFO General (hammer_tools.cpp : 168) Prepared batch 1 of 3200000 reads. 20:48:57.564 109G / 146G INFO General (hammer_tools.cpp : 175) Processed batch 1 20:49:24.408 109G / 146G INFO General (hammer_tools.cpp : 185) Written batch 1 20:49:56.187 110G / 146G INFO General (hammer_tools.cpp : 168) Prepared batch 2 of 3200000 reads. 20:50:22.681 110G / 146G INFO General (hammer_tools.cpp : 175) Processed batch 2 20:50:52.353 110G / 146G INFO General (hammer_tools.cpp : 185) Written batch 2 20:51:24.826 110G / 146G INFO General (hammer_tools.cpp : 168) Prepared batch 3 of 3200000 reads. 20:51:49.320 110G / 146G INFO General (hammer_tools.cpp : 175) Processed batch 3 20:52:00.531 110G / 146G INFO General (hammer_tools.cpp : 185) Written batch 3 20:52:15.600 110G / 146G INFO General (hammer_tools.cpp : 168) Prepared batch 4 of 2428592 reads. 20:52:31.709 110G / 146G INFO General (hammer_tools.cpp : 175) Processed batch 4 20:52:43.990 110G / 146G INFO General (hammer_tools.cpp : 185) Written batch 4 20:53:02.350 106G / 146G INFO General (hammer_tools.cpp : 233) Correcting pair of reads: /local/genbank/workspace/reads.uncorr/Algae6.2GB_6_R1.fq and /local/genbank/workspace/reads.uncorr/Algae6.2GB_6_R2.fq 20:53:31.299 108G / 146G INFO General (hammer_tools.cpp : 168) Prepared batch 0 of 3200000 reads. 20:54:04.411 108G / 146G INFO General (hammer_tools.cpp : 175) Processed batch 0 20:54:25.861 108G / 146G INFO General (hammer_tools.cpp : 185) Written batch 0 20:54:53.108 109G / 146G INFO General (hammer_tools.cpp : 168) Prepared batch 1 of 3200000 reads. 20:55:21.982 109G / 146G INFO General (hammer_tools.cpp : 175) Processed batch 1 20:55:38.046 109G / 146G INFO General (hammer_tools.cpp : 185) Written batch 1 20:55:39.388 109G / 146G INFO General (hammer_tools.cpp : 168) Prepared batch 2 of 169215 reads. 20:55:41.692 109G / 146G INFO General (hammer_tools.cpp : 175) Processed batch 2 20:55:43.338 109G / 146G INFO General (hammer_tools.cpp : 185) Written batch 2 20:55:58.259 106G / 146G INFO General (hammer_tools.cpp : 233) Correcting pair of reads: /local/genbank/workspace/reads.uncorr/Algae6.2GB_7_R1.fq and /local/genbank/workspace/reads.uncorr/Algae6.2GB_7_R2.fq 20:56:27.126 108G / 146G INFO General (hammer_tools.cpp : 168) Prepared batch 0 of 3200000 reads. 20:56:55.548 108G / 146G INFO General (hammer_tools.cpp : 175) Processed batch 0 20:57:17.415 108G / 146G INFO General (hammer_tools.cpp : 185) Written batch 0 20:57:44.821 109G / 146G INFO General (hammer_tools.cpp : 168) Prepared batch 1 of 3200000 reads. 20:58:10.237 109G / 146G INFO General (hammer_tools.cpp : 175) Processed batch 1 20:58:24.844 109G / 146G INFO General (hammer_tools.cpp : 185) Written batch 1 20:58:34.077 109G / 146G INFO General (hammer_tools.cpp : 168) Prepared batch 2 of 1086593 reads. 20:58:40.466 109G / 146G INFO General (hammer_tools.cpp : 175) Processed batch 2 20:58:50.742 109G / 146G INFO General (hammer_tools.cpp : 185) Written batch 2 20:59:02.780 106G / 146G INFO General (hammer_tools.cpp : 233) Correcting pair of reads: /local/genbank/workspace/reads.uncorr/Algae6.2GB_8_R1.fq and /local/genbank/workspace/reads.uncorr/Algae6.2GB_8_R2.fq 20:59:31.901 108G / 146G INFO General (hammer_tools.cpp : 168) Prepared batch 0 of 3200000 reads. 20:59:54.974 108G / 146G INFO General (hammer_tools.cpp : 175) Processed batch 0 21:00:17.093 108G / 146G INFO General (hammer_tools.cpp : 185) Written batch 0 21:00:44.703 109G / 146G INFO General (hammer_tools.cpp : 168) Prepared batch 1 of 3200000 reads. 21:01:03.779 109G / 146G INFO General (hammer_tools.cpp : 175) Processed batch 1 21:01:18.022 109G / 146G INFO General (hammer_tools.cpp : 185) Written batch 1 21:01:32.395 109G / 146G INFO General (hammer_tools.cpp : 168) Prepared batch 2 of 1889476 reads. 21:01:41.894 109G / 146G INFO General (hammer_tools.cpp : 175) Processed batch 2 21:01:54.001 109G / 146G INFO General (hammer_tools.cpp : 185) Written batch 2 21:02:09.125 106G / 146G INFO General (hammer_tools.cpp : 233) Correcting pair of reads: /local/genbank/workspace/reads.uncorr/Algae7.2GB_6_R1.fq and /local/genbank/workspace/reads.uncorr/Algae7.2GB_6_R2.fq 21:02:38.525 108G / 146G INFO General (hammer_tools.cpp : 168) Prepared batch 0 of 3200000 reads. 21:02:59.236 108G / 146G INFO General (hammer_tools.cpp : 175) Processed batch 0 21:03:21.148 108G / 146G INFO General (hammer_tools.cpp : 185) Written batch 0 21:03:49.230 109G / 146G INFO General (hammer_tools.cpp : 168) Prepared batch 1 of 3200000 reads. 21:04:06.757 109G / 146G INFO General (hammer_tools.cpp : 175) Processed batch 1 21:04:20.959 109G / 146G INFO General (hammer_tools.cpp : 185) Written batch 1 21:04:46.073 109G / 146G INFO General (hammer_tools.cpp : 168) Prepared batch 2 of 3200000 reads. 21:05:03.276 109G / 146G INFO General (hammer_tools.cpp : 175) Processed batch 2 21:05:27.500 109G / 146G INFO General (hammer_tools.cpp : 185) Written batch 2 21:05:37.143 109G / 146G INFO General (hammer_tools.cpp : 168) Prepared batch 3 of 1223032 reads. 21:05:46.526 109G / 146G INFO General (hammer_tools.cpp : 175) Processed batch 3 21:05:51.700 109G / 146G INFO General (hammer_tools.cpp : 185) Written batch 3 21:06:03.123 106G / 146G INFO General (hammer_tools.cpp : 233) Correcting pair of reads: /local/genbank/workspace/reads.uncorr/Algae7.2GB_7_R1.fq and /local/genbank/workspace/reads.uncorr/Algae7.2GB_7_R2.fq 21:06:32.777 108G / 146G INFO General (hammer_tools.cpp : 168) Prepared batch 0 of 3200000 reads. 21:06:52.991 108G / 146G INFO General (hammer_tools.cpp : 175) Processed batch 0 21:07:15.034 108G / 146G INFO General (hammer_tools.cpp : 185) Written batch 0 21:07:41.713 109G / 146G INFO General (hammer_tools.cpp : 168) Prepared batch 1 of 3200000 reads. 21:08:02.728 109G / 146G INFO General (hammer_tools.cpp : 175) Processed batch 1 21:08:16.626 109G / 146G INFO General (hammer_tools.cpp : 185) Written batch 1 21:08:43.479 109G / 146G INFO General (hammer_tools.cpp : 168) Prepared batch 2 of 3170621 reads. 21:09:01.324 109G / 146G INFO General (hammer_tools.cpp : 175) Processed batch 2 21:09:15.800 109G / 146G INFO General (hammer_tools.cpp : 185) Written batch 2 21:09:33.429 106G / 146G INFO General (hammer_tools.cpp : 233) Correcting pair of reads: /local/genbank/workspace/reads.uncorr/Algae7.2GB_8_R1.fq and /local/genbank/workspace/reads.uncorr/Algae7.2GB_8_R2.fq 21:10:02.749 108G / 146G INFO General (hammer_tools.cpp : 168) Prepared batch 0 of 3200000 reads. 21:10:21.166 108G / 146G INFO General (hammer_tools.cpp : 175) Processed batch 0 21:10:42.981 108G / 146G INFO General (hammer_tools.cpp : 185) Written batch 0 21:11:09.318 109G / 146G INFO General (hammer_tools.cpp : 168) Prepared batch 1 of 3200000 reads. 21:11:28.195 109G / 146G INFO General (hammer_tools.cpp : 175) Processed batch 1 21:11:44.375 109G / 146G INFO General (hammer_tools.cpp : 185) Written batch 1 21:12:09.666 109G / 146G INFO General (hammer_tools.cpp : 168) Prepared batch 2 of 3200000 reads. 21:12:29.153 109G / 146G INFO General (hammer_tools.cpp : 175) Processed batch 2 21:12:43.773 109G / 146G INFO General (hammer_tools.cpp : 185) Written batch 2 21:12:46.563 109G / 146G INFO General (hammer_tools.cpp : 168) Prepared batch 3 of 364924 reads. 21:12:49.119 109G / 146G INFO General (hammer_tools.cpp : 175) Processed batch 3 21:12:50.722 109G / 146G INFO General (hammer_tools.cpp : 185) Written batch 3 21:13:02.179 106G / 146G INFO General (hammer_tools.cpp : 264) Correcting single reads: /local/genbank/workspace/reads.uncorr/2008-09allU.fq 21:13:16.727 107G / 146G INFO General (hammer_tools.cpp : 127) Prepared batch 0 of 3200000 reads. 21:13:32.172 107G / 146G INFO General (hammer_tools.cpp : 132) Processed batch 0 21:13:39.855 107G / 146G INFO General (hammer_tools.cpp : 136) Written batch 0 21:13:53.353 108G / 146G INFO General (hammer_tools.cpp : 127) Prepared batch 1 of 3200000 reads. 21:14:08.206 108G / 146G INFO General (hammer_tools.cpp : 132) Processed batch 1 21:14:15.969 108G / 146G INFO General (hammer_tools.cpp : 136) Written batch 1 21:14:29.370 108G / 146G INFO General (hammer_tools.cpp : 127) Prepared batch 2 of 3200000 reads. 21:14:40.911 108G / 146G INFO General (hammer_tools.cpp : 132) Processed batch 2 21:14:49.468 108G / 146G INFO General (hammer_tools.cpp : 136) Written batch 2 21:15:01.800 108G / 146G INFO General (hammer_tools.cpp : 127) Prepared batch 3 of 3200000 reads. 21:15:19.569 108G / 146G INFO General (hammer_tools.cpp : 132) Processed batch 3 21:15:29.304 108G / 146G INFO General (hammer_tools.cpp : 136) Written batch 3 21:15:42.334 108G / 146G INFO General (hammer_tools.cpp : 127) Prepared batch 4 of 3200000 reads. 21:15:57.554 108G / 146G INFO General (hammer_tools.cpp : 132) Processed batch 4 21:16:08.254 108G / 146G INFO General (hammer_tools.cpp : 136) Written batch 4 21:16:20.430 108G / 146G INFO General (hammer_tools.cpp : 127) Prepared batch 5 of 3200000 reads. 21:16:36.821 108G / 146G INFO General (hammer_tools.cpp : 132) Processed batch 5 21:16:46.633 108G / 146G INFO General (hammer_tools.cpp : 136) Written batch 5 21:16:59.616 108G / 146G INFO General (hammer_tools.cpp : 127) Prepared batch 6 of 3200000 reads. 21:17:11.783 108G / 146G INFO General (hammer_tools.cpp : 132) Processed batch 6 21:17:25.547 108G / 146G INFO General (hammer_tools.cpp : 136) Written batch 6 21:17:37.750 108G / 146G INFO General (hammer_tools.cpp : 127) Prepared batch 7 of 3200000 reads. 21:17:51.603 108G / 146G INFO General (hammer_tools.cpp : 132) Processed batch 7 21:17:59.099 108G / 146G INFO General (hammer_tools.cpp : 136) Written batch 7 21:18:11.958 108G / 146G INFO General (hammer_tools.cpp : 127) Prepared batch 8 of 3200000 reads. 21:18:22.903 108G / 146G INFO General (hammer_tools.cpp : 132) Processed batch 8 21:18:35.431 108G / 146G INFO General (hammer_tools.cpp : 136) Written batch 8 21:18:47.582 108G / 146G INFO General (hammer_tools.cpp : 127) Prepared batch 9 of 3200000 reads. 21:19:01.146 108G / 146G INFO General (hammer_tools.cpp : 132) Processed batch 9 21:19:10.958 108G / 146G INFO General (hammer_tools.cpp : 136) Written batch 9 21:19:22.698 108G / 146G INFO General (hammer_tools.cpp : 127) Prepared batch 10 of 3200000 reads. 21:19:32.040 108G / 146G INFO General (hammer_tools.cpp : 132) Processed batch 10 21:19:48.433 108G / 146G INFO General (hammer_tools.cpp : 136) Written batch 10 21:19:53.410 108G / 146G INFO General (hammer_tools.cpp : 127) Prepared batch 11 of 1360456 reads. 21:19:58.795 108G / 146G INFO General (hammer_tools.cpp : 132) Processed batch 11 21:20:01.997 108G / 146G INFO General (hammer_tools.cpp : 136) Written batch 11 21:20:10.390 106G / 146G INFO General (hammer_tools.cpp : 264) Correcting single reads: /local/genbank/workspace/reads.uncorr/3-6.2-7.2allU.fq 21:20:24.318 107G / 146G INFO General (hammer_tools.cpp : 127) Prepared batch 0 of 3200000 reads. 21:20:34.263 107G / 146G INFO General (hammer_tools.cpp : 132) Processed batch 0 21:20:41.593 107G / 146G INFO General (hammer_tools.cpp : 136) Written batch 0 21:20:55.921 108G / 146G INFO General (hammer_tools.cpp : 127) Prepared batch 1 of 3200000 reads. 21:21:03.196 108G / 146G INFO General (hammer_tools.cpp : 132) Processed batch 1 21:21:10.419 108G / 146G INFO General (hammer_tools.cpp : 136) Written batch 1 21:21:22.522 108G / 146G INFO General (hammer_tools.cpp : 127) Prepared batch 2 of 3200000 reads. 21:21:34.015 108G / 146G INFO General (hammer_tools.cpp : 132) Processed batch 2 21:21:42.123 108G / 146G INFO General (hammer_tools.cpp : 136) Written batch 2 21:21:54.077 108G / 146G INFO General (hammer_tools.cpp : 127) Prepared batch 3 of 3200000 reads. 21:22:02.776 108G / 146G INFO General (hammer_tools.cpp : 132) Processed batch 3 21:22:20.068 108G / 146G INFO General (hammer_tools.cpp : 136) Written batch 3 21:22:33.096 108G / 146G INFO General (hammer_tools.cpp : 127) Prepared batch 4 of 3200000 reads. 21:22:41.061 108G / 146G INFO General (hammer_tools.cpp : 132) Processed batch 4 21:22:48.295 108G / 146G INFO General (hammer_tools.cpp : 136) Written batch 4 21:23:00.350 108G / 146G INFO General (hammer_tools.cpp : 127) Prepared batch 5 of 3200000 reads. 21:23:10.945 108G / 146G INFO General (hammer_tools.cpp : 132) Processed batch 5 21:23:18.119 108G / 146G INFO General (hammer_tools.cpp : 136) Written batch 5 21:23:30.025 108G / 146G INFO General (hammer_tools.cpp : 127) Prepared batch 6 of 3200000 reads. 21:23:38.425 108G / 146G INFO General (hammer_tools.cpp : 132) Processed batch 6 21:23:48.304 108G / 146G INFO General (hammer_tools.cpp : 136) Written batch 6 21:24:00.956 108G / 146G INFO General (hammer_tools.cpp : 127) Prepared batch 7 of 3200000 reads. 21:24:08.728 108G / 146G INFO General (hammer_tools.cpp : 132) Processed batch 7 21:24:25.533 108G / 146G INFO General (hammer_tools.cpp : 136) Written batch 7 21:24:37.195 108G / 146G INFO General (hammer_tools.cpp : 127) Prepared batch 8 of 3200000 reads. 21:24:49.169 108G / 146G INFO General (hammer_tools.cpp : 132) Processed batch 8 21:25:02.204 108G / 146G INFO General (hammer_tools.cpp : 136) Written batch 8 21:25:13.486 108G / 146G INFO General (hammer_tools.cpp : 127) Prepared batch 9 of 3200000 reads. 21:25:26.633 108G / 146G INFO General (hammer_tools.cpp : 132) Processed batch 9 21:25:35.252 108G / 146G INFO General (hammer_tools.cpp : 136) Written batch 9 21:25:46.517 108G / 146G INFO General (hammer_tools.cpp : 127) Prepared batch 10 of 3200000 reads. 21:26:00.029 108G / 146G INFO General (hammer_tools.cpp : 132) Processed batch 10 21:26:07.179 108G / 146G INFO General (hammer_tools.cpp : 136) Written batch 10 21:26:18.436 108G / 146G INFO General (hammer_tools.cpp : 127) Prepared batch 11 of 3200000 reads. 21:26:30.021 108G / 146G INFO General (hammer_tools.cpp : 132) Processed batch 11 21:26:37.483 108G / 146G INFO General (hammer_tools.cpp : 136) Written batch 11 21:26:49.683 108G / 146G INFO General (hammer_tools.cpp : 127) Prepared batch 12 of 3200000 reads. 21:26:58.047 108G / 146G INFO General (hammer_tools.cpp : 132) Processed batch 12 21:27:05.178 108G / 146G INFO General (hammer_tools.cpp : 136) Written batch 12 21:27:16.880 108G / 146G INFO General (hammer_tools.cpp : 127) Prepared batch 13 of 3200000 reads. 21:27:26.341 108G / 146G INFO General (hammer_tools.cpp : 132) Processed batch 13 21:27:33.436 108G / 146G INFO General (hammer_tools.cpp : 136) Written batch 13 21:27:45.172 108G / 146G INFO General (hammer_tools.cpp : 127) Prepared batch 14 of 3200000 reads. 21:27:54.651 108G / 146G INFO General (hammer_tools.cpp : 132) Processed batch 14 21:28:08.243 108G / 146G INFO General (hammer_tools.cpp : 136) Written batch 14 21:28:20.785 108G / 146G INFO General (hammer_tools.cpp : 127) Prepared batch 15 of 3200000 reads. 21:28:29.130 108G / 146G INFO General (hammer_tools.cpp : 132) Processed batch 15 21:28:36.579 108G / 146G INFO General (hammer_tools.cpp : 136) Written batch 15 21:28:36.632 108G / 146G INFO General (hammer_tools.cpp : 127) Prepared batch 16 of 14954 reads. 21:28:36.745 108G / 146G INFO General (hammer_tools.cpp : 132) Processed batch 16 21:28:36.783 108G / 146G INFO General (hammer_tools.cpp : 136) Written batch 16 21:28:46.399 106G / 146G INFO General (hammer_tools.cpp : 264) Correcting single reads: /local/genbank/workspace/reads.uncorr/AGRFallU.fq 21:29:02.794 107G / 146G INFO General (hammer_tools.cpp : 127) Prepared batch 0 of 3200000 reads. 21:29:16.358 108G / 146G INFO General (hammer_tools.cpp : 132) Processed batch 0 21:29:21.198 108G / 146G INFO General (hammer_tools.cpp : 136) Written batch 0 21:29:31.187 108G / 146G INFO General (hammer_tools.cpp : 127) Prepared batch 1 of 3200000 reads. 21:29:42.782 108G / 146G INFO General (hammer_tools.cpp : 132) Processed batch 1 21:29:50.847 108G / 146G INFO General (hammer_tools.cpp : 136) Written batch 1 21:30:05.090 108G / 146G INFO General (hammer_tools.cpp : 127) Prepared batch 2 of 3200000 reads. 21:30:19.354 108G / 146G INFO General (hammer_tools.cpp : 132) Processed batch 2 21:30:27.304 108G / 146G INFO General (hammer_tools.cpp : 136) Written batch 2 21:30:27.615 108G / 146G INFO General (hammer_tools.cpp : 127) Prepared batch 3 of 71062 reads. 21:30:28.325 108G / 146G INFO General (hammer_tools.cpp : 132) Processed batch 3 21:30:28.517 108G / 146G INFO General (hammer_tools.cpp : 136) Written batch 3 21:30:39.570 106G / 146G INFO General (hammer_tools.cpp : 264) Correcting single reads: /local/genbank/workspace/reads.uncorr/454all.fq 21:31:20.649 108G / 146G INFO General (hammer_tools.cpp : 127) Prepared batch 0 of 2122537 reads. 21:33:20.592 109G / 146G INFO General (hammer_tools.cpp : 132) Processed batch 0 21:33:36.366 109G / 146G INFO General (hammer_tools.cpp : 136) Written batch 0 21:33:47.362 106G / 146G INFO General (hammer_tools.cpp : 274) Correction done. Changed 67445872 bases in 48766493 reads. 21:33:47.362 106G / 146G INFO General (hammer_tools.cpp : 275) Failed to correct 17508456 bases out of 24190562862. 21:34:28.286 128M / 146G INFO General (main.cpp : 255) Saving corrected dataset description to /local/genbank/workspace/reads.uncorr.spades1/corrected/corrected.yaml 21:34:28.301 128M / 146G INFO General (main.cpp : 262) All done. Exiting. == Compressing corrected reads (with pigz) == Dataset description file was created: /local/genbank/workspace/reads.uncorr.spades1/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 /local/genbank/workspace/reads.uncorr.spades1/K21/configs/config.info 0:00:00.001 4M / 4M INFO General (memory_limit.cpp : 49) Memory limit set to 204 Gb 0:00:00.001 4M / 4M INFO General (main.cpp : 87) Starting SPAdes, built from refs/heads/spades_3.13.0, git revision 8ea46659e9b2aca35444a808db550ac333006f8b 0:00:00.001 4M / 4M INFO General (main.cpp : 88) Maximum k-mer length: 128 0:00:00.001 4M / 4M INFO General (main.cpp : 89) Assembling dataset (/local/genbank/workspace/reads.uncorr.spades1/dataset.info) with K=21 0:00:00.001 4M / 4M INFO General (main.cpp : 90) Maximum # of threads to use (adjusted due to OMP capabilities): 32 0:00:00.001 4M / 4M INFO General (launch.hpp : 51) SPAdes started 0:00:00.001 4M / 4M INFO General (launch.hpp : 58) Starting from stage: construction 0:00:00.001 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 0:00:00.009 4M / 4M INFO General (read_converter.hpp : 77) Converting reads to binary format for library #0 (takes a while) 0:00:00.009 4M / 4M INFO General (read_converter.hpp : 78) Converting paired reads 0:00:00.607 76M / 76M INFO General (binary_converter.hpp : 93) 16384 reads processed 0:00:00.981 84M / 84M INFO General (binary_converter.hpp : 93) 32768 reads processed 0:00:01.729 104M / 104M INFO General (binary_converter.hpp : 93) 65536 reads processed 0:00:03.225 136M / 136M INFO General (binary_converter.hpp : 93) 131072 reads processed 0:00:06.226 208M / 208M INFO General (binary_converter.hpp : 93) 262144 reads processed 0:00:12.242 348M / 348M INFO General (binary_converter.hpp : 93) 524288 reads processed 0:00:28.039 564M / 564M INFO General (binary_converter.hpp : 93) 1048576 reads processed 0:00:56.717 616M / 616M INFO General (binary_converter.hpp : 93) 2097152 reads processed 0:01:54.041 620M / 620M INFO General (binary_converter.hpp : 93) 4194304 reads processed 0:04:03.330 872M / 876M INFO General (binary_converter.hpp : 93) 8388608 reads processed 0:08:42.205 956M / 956M INFO General (binary_converter.hpp : 93) 16777216 reads processed 0:18:07.806 916M / 956M INFO General (binary_converter.hpp : 93) 33554432 reads processed 0:36:16.016 696M / 956M INFO General (binary_converter.hpp : 93) 67108864 reads processed 0:56:14.821 636M / 956M INFO General (binary_converter.hpp : 117) 105822607 reads written 0:56:17.895 8M / 956M INFO General (read_converter.hpp : 87) Converting single reads 0:56:18.433 140M / 956M INFO General (binary_converter.hpp : 93) 16384 reads processed 0:56:18.616 144M / 956M INFO General (binary_converter.hpp : 93) 32768 reads processed 0:56:19.005 152M / 956M INFO General (binary_converter.hpp : 93) 65536 reads processed 0:56:19.772 168M / 956M INFO General (binary_converter.hpp : 93) 131072 reads processed 0:56:21.239 204M / 956M INFO General (binary_converter.hpp : 93) 262144 reads processed 0:56:24.215 276M / 956M INFO General (binary_converter.hpp : 93) 524288 reads processed 0:56:30.180 416M / 956M INFO General (binary_converter.hpp : 93) 1048576 reads processed 0:56:41.923 704M / 956M INFO General (binary_converter.hpp : 93) 2097152 reads processed 0:57:05.042 1G / 1G INFO General (binary_converter.hpp : 93) 4194304 reads processed 0:58:00.826 1G / 1G INFO General (binary_converter.hpp : 93) 8388608 reads processed 0:59:53.100 1G / 1G INFO General (binary_converter.hpp : 93) 16777216 reads processed 1:03:37.713 1G / 1G INFO General (binary_converter.hpp : 93) 33554432 reads processed 1:11:04.619 1G / 1G INFO General (binary_converter.hpp : 93) 67108864 reads processed 1:20:11.467 3G / 3G INFO General (binary_converter.hpp : 117) 99317237 reads written 1:20:18.999 16M / 3G INFO General (read_converter.hpp : 95) Converting merged reads 1:20:19.341 144M / 3G INFO General (binary_converter.hpp : 117) 0 reads written 1:20:19.527 8M / 3G INFO General (construction.cpp : 111) Max read length 700 1:20:19.527 8M / 3G INFO General (construction.cpp : 117) Average read length 77.5334 1:20:19.527 8M / 3G INFO General (stage.cpp : 101) PROCEDURE == k+1-mer counting 1:20:19.531 8M / 3G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 1024 files using 32 threads. This might take a while. 1:20:19.536 8M / 3G INFO General (file_limit.hpp : 32) Open file limit set to 4096 1:20:19.536 8M / 3G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.12492 Gb 1:20:19.536 8M / 3G INFO General (kmer_splitters.hpp : 97) Using cell size of 65536 1:20:53.851 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 22699149 reads 1:21:21.253 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 45531155 reads 1:21:51.421 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 72960596 reads 1:22:23.599 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 101922482 reads 1:22:54.963 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 130819211 reads 1:23:17.539 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 148301006 reads 1:23:36.339 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 160564696 reads 1:23:56.346 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 174573455 reads 1:24:22.176 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 190469228 reads 1:24:33.493 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 194124470 reads 1:25:18.005 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 212187155 reads 1:25:58.172 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 243732429 reads 1:26:31.721 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 271043019 reads 1:27:04.177 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 298032524 reads 1:32:41.401 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 557138643 reads 1:33:59.240 17G / 18G INFO General (kmer_splitters.hpp : 295) Adding contigs from previous K 1:34:04.234 132M / 18G INFO General (kmer_splitters.hpp : 308) Used 621924902 reads 1:34:04.234 132M / 18G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 1:36:45.955 132M / 18G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 1130980114 kmers in total. 1:36:45.956 132M / 18G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 1:39:08.394 128M / 18G INFO General (stage.cpp : 101) PROCEDURE == Extension index construction 1:39:08.396 128M / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 1:39:08.396 128M / 18G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 512 files using 32 threads. This might take a while. 1:39:08.404 128M / 18G INFO General (file_limit.hpp : 32) Open file limit set to 4096 1:39:08.404 128M / 18G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.1237 Gb 1:39:08.404 128M / 18G INFO General (kmer_splitters.hpp : 97) Using cell size of 131072 1:39:19.999 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 4735301 kmers 1:39:27.022 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 14283773 kmers 1:39:36.555 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 39965224 kmers 1:39:43.561 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 47907590 kmers 1:39:55.301 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 75302333 kmers 1:40:01.890 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 83221491 kmers 1:40:13.948 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 110645789 kmers 1:40:19.833 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 118545191 kmers 1:40:31.355 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 145994915 kmers 1:40:37.402 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 153931351 kmers 1:40:48.760 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 181334091 kmers 1:40:55.117 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 189241469 kmers 1:41:06.141 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 216680838 kmers 1:41:11.710 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 224593941 kmers 1:41:22.985 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 252019846 kmers 1:41:28.863 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 259943819 kmers 1:41:40.557 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 287364222 kmers 1:41:46.358 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 295300745 kmers 1:41:58.449 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 322698300 kmers 1:43:51.785 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 542705435 kmers 1:47:41.977 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 1100252940 kmers 1:47:57.573 17G / 18G INFO General (kmer_splitters.hpp : 385) Used 1130982162 kmers. 1:48:02.166 128M / 18G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 1:51:24.480 128M / 18G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 1109963021 kmers in total. 1:51:24.480 128M / 18G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 1:53:19.353 128M / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 1:54:56.818 708M / 18G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 1:56:31.676 708M / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 514710736 bytes occupied (3.70975 bits per kmer). 1:56:33.973 1G / 18G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 99) Building k-mer extensions from k+1-mers 1:57:34.984 1G / 18G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 103) Building k-mer extensions from k+1-mers finished. 1:57:34.995 1G / 18G INFO General (stage.cpp : 101) PROCEDURE == Early tip clipping 1:57:34.995 1G / 18G INFO General (construction.cpp : 253) Early tip clipper length bound set as (RL - K) 1:57:34.995 1G / 18G INFO Early tip clipping (early_simplification.hpp : 181) Early tip clipping 2:00:00.121 1G / 18G INFO Early tip clipping (early_simplification.hpp : 184) 199373355 22-mers were removed by early tip clipper 2:00:00.121 1G / 18G INFO General (stage.cpp : 101) PROCEDURE == Condensing graph 2:00:00.364 1G / 18G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 355) Extracting unbranching paths 2:01:29.278 4G / 18G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 374) Extracting unbranching paths finished. 60353493 sequences extracted 2:02:09.912 4G / 18G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 310) Collecting perfect loops 2:02:32.918 4G / 18G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 343) Collecting perfect loops finished. 604 loops collected 2:03:43.310 17G / 23G INFO General (stage.cpp : 101) PROCEDURE == Filling coverage indices (PHM) 2:03:43.310 17G / 23G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 2:03:43.310 17G / 23G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 2:04:27.830 18G / 23G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 524480334 bytes occupied (3.70992 bits per kmer). 2:04:32.837 22G / 23G INFO General (construction.cpp : 388) Collecting k-mer coverage information from reads, this takes a while. 2:13:12.130 22G / 23G INFO General (construction.cpp : 508) Filling coverage and flanking coverage from PHM 2:13:32.509 22G / 23G INFO General (construction.cpp : 464) Processed 32000000 edges 2:13:46.794 22G / 23G INFO General (construction.cpp : 464) Processed 64000000 edges 2:14:01.360 22G / 23G INFO General (construction.cpp : 464) Processed 96000000 edges 2:14:12.324 22G / 23G INFO General (construction.cpp : 464) Processed 120675653 edges 2:14:25.327 16G / 23G INFO StageManager (stage.cpp : 132) STAGE == EC Threshold Finding 2:14:33.189 16G / 23G INFO General (kmer_coverage_model.cpp : 181) Kmer coverage valley at: 277 2:14:33.467 16G / 23G INFO General (kmer_coverage_model.cpp : 201) K-mer histogram maximum: 279 2:14:33.468 16G / 23G INFO General (kmer_coverage_model.cpp : 237) Estimated median coverage: 280. Coverage mad: 2.9652 2:14:33.633 16G / 23G INFO General (kmer_coverage_model.cpp : 259) Fitting coverage model 2:14:35.683 16G / 23G INFO General (kmer_coverage_model.cpp : 295) ... iteration 2 2:14:40.090 16G / 23G INFO General (kmer_coverage_model.cpp : 295) ... iteration 4 2:14:51.030 16G / 23G INFO General (kmer_coverage_model.cpp : 295) ... iteration 8 2:15:20.164 16G / 23G INFO General (kmer_coverage_model.cpp : 295) ... iteration 16 2:16:10.908 16G / 23G INFO General (kmer_coverage_model.cpp : 295) ... iteration 32 2:17:18.213 16G / 23G INFO General (kmer_coverage_model.cpp : 295) ... iteration 64 2:19:24.705 16G / 23G INFO General (kmer_coverage_model.cpp : 295) ... iteration 128 2:22:49.489 16G / 23G INFO General (kmer_coverage_model.cpp : 295) ... iteration 256 2:23:19.776 16G / 23G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 33.0415. Fitted coverage std. dev: 21.719 2:23:19.778 16G / 23G WARN General (kmer_coverage_model.cpp : 327) Valley value was estimated improperly, reset to 2 2:23:19.804 16G / 23G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 0.986443 2:23:19.804 16G / 23G WARN General (kmer_coverage_model.cpp : 366) Failed to determine erroneous kmer threshold. Threshold set to: 2 2:23:19.804 16G / 23G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 661832992 2:23:19.807 16G / 23G INFO General (genomic_info_filler.cpp : 114) Failed to estimate mean coverage 2:23:19.807 16G / 23G INFO General (genomic_info_filler.cpp : 127) EC coverage threshold value was calculated as 2 2:23:19.807 16G / 23G INFO General (genomic_info_filler.cpp : 128) Trusted kmer low bound: 0 2:23:19.807 16G / 23G INFO StageManager (stage.cpp : 132) STAGE == Raw Simplification 2:23:19.807 16G / 23G INFO General (simplification.cpp : 128) PROCEDURE == InitialCleaning 2:23:19.844 16G / 23G INFO General (simplification.cpp : 68) Most init cleaning disabled since detected mean 0 was less than activation coverage 10 2:23:19.844 16G / 23G INFO Simplification (parallel_processing.hpp : 165) Running Self conjugate edge remover 2:23:26.090 16G / 23G INFO Simplification (parallel_processing.hpp : 167) Self conjugate edge remover triggered 0 times 2:23:26.090 16G / 23G INFO StageManager (stage.cpp : 132) STAGE == Simplification 2:23:26.091 16G / 23G INFO General (simplification.cpp : 357) Graph simplification started 2:23:26.091 16G / 23G INFO General (graph_simplification.hpp : 634) Creating parallel br instance 2:23:26.091 16G / 23G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 1 2:23:26.091 16G / 23G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 2:24:03.659 16G / 23G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 669987 times 2:24:03.659 16G / 23G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 3:05:01.164 17G / 23G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 2222893 times 3:05:01.164 17G / 23G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 3:06:17.336 17G / 23G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 3:06:17.336 17G / 23G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 2 3:06:17.336 17G / 23G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 3:06:38.291 17G / 23G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 72996 times 3:06:38.291 17G / 23G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 3:06:45.233 17G / 23G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 1225 times 3:06:45.233 17G / 23G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 3:06:45.233 17G / 23G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 3:06:45.233 17G / 23G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 3 3:06:45.233 17G / 23G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 3:06:45.243 17G / 23G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 38 times 3:06:45.243 17G / 23G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 3:06:45.245 17G / 23G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 3:06:45.245 17G / 23G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 3:06:45.245 17G / 23G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 3:06:45.245 17G / 23G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 4 3:06:45.245 17G / 23G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 3:06:45.245 17G / 23G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 3:06:45.245 17G / 23G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 3:06:45.245 17G / 23G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 3:06:45.245 17G / 23G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 3:06:45.245 17G / 23G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 3:06:45.245 17G / 23G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 5 3:06:45.245 17G / 23G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 3:06:45.245 17G / 23G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 3:06:45.245 17G / 23G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 3:06:45.245 17G / 23G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 3:06:45.245 17G / 23G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 3:33:04.470 17G / 23G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 10032342 times 3:33:04.470 17G / 23G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 6 3:33:04.470 17G / 23G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 3:33:40.317 17G / 23G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 197490 times 3:33:40.317 17G / 23G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 3:46:57.810 17G / 23G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 401268 times 3:46:57.810 17G / 23G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 3:50:12.339 17G / 23G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 1144112 times 3:50:12.339 17G / 23G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 7 3:50:12.339 17G / 23G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 3:50:19.444 17G / 23G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 13898 times 3:50:19.444 17G / 23G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 3:52:20.038 17G / 23G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 56851 times 3:52:20.039 17G / 23G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 3:53:37.091 17G / 23G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 403383 times 3:53:37.091 17G / 23G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 8 3:53:37.091 17G / 23G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 3:53:39.700 17G / 23G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 8452 times 3:53:39.700 17G / 23G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 3:54:27.689 17G / 23G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 20565 times 3:54:27.690 17G / 23G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 3:55:14.554 17G / 23G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 301428 times 3:55:14.554 17G / 23G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 9 3:55:14.554 17G / 23G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 3:55:16.441 17G / 23G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 7415 times 3:55:16.441 17G / 23G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 3:55:50.200 17G / 23G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 14506 times 3:55:50.200 17G / 23G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 3:56:32.056 17G / 23G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 261820 times 3:56:32.056 17G / 23G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 10 3:56:32.056 17G / 23G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 3:56:33.796 17G / 23G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 6622 times 3:56:33.796 17G / 23G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 3:57:00.676 17G / 23G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 12770 times 3:57:00.676 17G / 23G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 4:02:15.166 17G / 23G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 1896084 times 4:02:15.166 17G / 23G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 11 4:02:15.166 17G / 23G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 4:02:22.123 17G / 23G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 32189 times 4:02:22.123 17G / 23G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 4:09:59.688 17G / 23G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 104282 times 4:09:59.688 17G / 23G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 4:10:07.340 17G / 23G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 86 times 4:10:07.340 17G / 23G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 12 4:10:07.340 17G / 23G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 4:10:08.599 17G / 23G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 138 times 4:10:08.599 17G / 23G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 4:10:08.776 17G / 23G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 3 times 4:10:08.777 17G / 23G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 4:10:08.777 17G / 23G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 4:10:08.777 17G / 23G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 13 4:10:08.777 17G / 23G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 4:10:08.777 17G / 23G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 4:10:08.777 17G / 23G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 4:10:08.777 17G / 23G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 4:10:08.777 17G / 23G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 4:10:08.777 17G / 23G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 4:10:08.777 17G / 23G INFO StageManager (stage.cpp : 132) STAGE == Simplification Cleanup 4:10:08.777 17G / 23G INFO General (simplification.cpp : 196) PROCEDURE == Post simplification 4:10:08.777 17G / 23G INFO General (graph_simplification.hpp : 453) Disconnection of relatively low covered edges disabled 4:10:08.777 17G / 23G INFO General (graph_simplification.hpp : 489) Complex tip clipping disabled 4:10:08.777 17G / 23G INFO General (graph_simplification.hpp : 634) Creating parallel br instance 4:10:08.777 17G / 23G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 4:10:11.202 17G / 23G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 20 times 4:10:11.202 17G / 23G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 4:15:34.812 17G / 23G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 284 times 4:15:34.812 17G / 23G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 4:15:37.200 17G / 23G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 3 times 4:15:37.200 17G / 23G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 4:20:59.903 17G / 23G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 3 times 4:20:59.904 17G / 23G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 4:20:59.904 17G / 23G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 4:20:59.904 17G / 23G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 4:20:59.904 17G / 23G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 4:20:59.904 17G / 23G INFO General (simplification.cpp : 330) Disrupting self-conjugate edges 4:22:18.686 17G / 23G INFO Simplification (parallel_processing.hpp : 165) Running Removing isolated edges 4:22:37.589 17G / 23G INFO Simplification (parallel_processing.hpp : 167) Removing isolated edges triggered 1016134 times 4:22:37.589 17G / 23G INFO General (simplification.cpp : 470) Counting average coverage 4:23:00.782 17G / 23G INFO General (simplification.cpp : 476) Average coverage = 34.5409 4:23:00.782 17G / 23G INFO StageManager (stage.cpp : 132) STAGE == Contig Output 4:23:00.782 17G / 23G INFO General (contig_output_stage.cpp : 40) Writing GFA to /local/genbank/workspace/reads.uncorr.spades1//K21/assembly_graph_with_scaffolds.gfa 4:25:42.865 17G / 23G INFO General (contig_output.hpp : 22) Outputting contigs to /local/genbank/workspace/reads.uncorr.spades1//K21/before_rr.fasta 4:29:08.368 17G / 23G INFO General (contig_output_stage.cpp : 51) Outputting FastG graph to /local/genbank/workspace/reads.uncorr.spades1//K21/assembly_graph.fastg 4:38:35.521 17G / 23G INFO General (contig_output.hpp : 22) Outputting contigs to /local/genbank/workspace/reads.uncorr.spades1//K21/simplified_contigs.fasta 4:41:56.030 17G / 23G INFO General (contig_output.hpp : 22) Outputting contigs to /local/genbank/workspace/reads.uncorr.spades1//K21/final_contigs.fasta 4:45:20.802 17G / 23G INFO StageManager (stage.cpp : 132) STAGE == Contig Output 4:45:20.802 17G / 23G INFO General (contig_output_stage.cpp : 40) Writing GFA to /local/genbank/workspace/reads.uncorr.spades1//K21/assembly_graph_with_scaffolds.gfa 4:47:51.016 17G / 23G INFO General (contig_output.hpp : 22) Outputting contigs to /local/genbank/workspace/reads.uncorr.spades1//K21/before_rr.fasta 4:51:11.418 17G / 23G INFO General (contig_output_stage.cpp : 51) Outputting FastG graph to /local/genbank/workspace/reads.uncorr.spades1//K21/assembly_graph.fastg 5:00:43.076 17G / 23G INFO General (contig_output.hpp : 22) Outputting contigs to /local/genbank/workspace/reads.uncorr.spades1//K21/simplified_contigs.fasta 5:04:26.838 17G / 23G INFO General (contig_output.hpp : 22) Outputting contigs to /local/genbank/workspace/reads.uncorr.spades1//K21/final_contigs.fasta 5:08:01.414 17G / 23G INFO General (launch.hpp : 149) SPAdes finished 5:11:07.525 128M / 23G INFO General (main.cpp : 109) Assembling time: 5 hours 11 minutes 7 seconds Max read length detected as 700 Default k-mer sizes were set to [21, 33, 55, 77, 99, 127] because estimated read length (700) is equal to or greater than 250 == Running assembler: K33 0:00:00.000 4M / 4M INFO General (main.cpp : 74) Loaded config from /local/genbank/workspace/reads.uncorr.spades1/K33/configs/config.info 0:00:00.001 4M / 4M INFO General (memory_limit.cpp : 49) Memory limit set to 204 Gb 0:00:00.001 4M / 4M INFO General (main.cpp : 87) Starting SPAdes, built from refs/heads/spades_3.13.0, git revision 8ea46659e9b2aca35444a808db550ac333006f8b 0:00:00.001 4M / 4M INFO General (main.cpp : 88) Maximum k-mer length: 128 0:00:00.001 4M / 4M INFO General (main.cpp : 89) Assembling dataset (/local/genbank/workspace/reads.uncorr.spades1/dataset.info) with K=33 0:00:00.001 4M / 4M INFO General (main.cpp : 90) Maximum # of threads to use (adjusted due to OMP capabilities): 32 0:00:00.001 4M / 4M INFO General (launch.hpp : 51) SPAdes started 0:00:00.001 4M / 4M INFO General (launch.hpp : 58) Starting from stage: construction 0:00:00.001 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 0:00:00.012 4M / 4M INFO General (read_converter.hpp : 59) Binary reads detected 0:00:00.237 4M / 4M INFO General (construction.cpp : 111) Max read length 700 0:00:00.237 4M / 4M INFO General (construction.cpp : 117) Average read length 77.5334 0:00:00.237 4M / 4M INFO General (stage.cpp : 101) PROCEDURE == k+1-mer counting 0:00:00.242 4M / 4M INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 1024 files using 32 threads. This might take a while. 0:00:00.256 4M / 4M INFO General (file_limit.hpp : 32) Open file limit set to 4096 0:00:00.256 4M / 4M INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.12496 Gb 0:00:00.256 4M / 4M INFO General (kmer_splitters.hpp : 97) Using cell size of 32768 0:01:15.642 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 17721688 reads 0:02:40.869 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 35480210 reads 0:03:29.573 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 55337407 reads 0:04:08.491 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 76529441 reads 0:04:46.783 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 99281704 reads 0:05:26.490 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 123053047 reads 0:05:58.269 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 139916184 reads 0:06:22.620 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 151612472 reads 0:06:43.564 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 160410215 reads 0:07:06.703 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 170569082 reads 0:07:44.133 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 185884671 reads 0:08:05.350 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 191677021 reads 0:08:26.817 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 194798523 reads 0:12:28.509 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 287787351 reads 0:22:31.538 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 545407871 reads 0:26:31.181 17G / 18G INFO General (kmer_splitters.hpp : 295) Adding contigs from previous K 0:33:37.099 132M / 18G INFO General (kmer_splitters.hpp : 308) Used 621924902 reads 0:33:37.099 132M / 18G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:39:24.436 132M / 18G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 1264610216 kmers in total. 0:39:24.436 132M / 18G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:43:28.031 128M / 18G INFO General (stage.cpp : 101) PROCEDURE == Extension index construction 0:43:28.033 128M / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:43:28.034 128M / 18G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 512 files using 32 threads. This might take a while. 0:43:28.037 128M / 18G INFO General (file_limit.hpp : 32) Open file limit set to 4096 0:43:28.037 128M / 18G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.1237 Gb 0:43:28.037 128M / 18G INFO General (kmer_splitters.hpp : 97) Using cell size of 65536 0:43:37.385 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 7423317 kmers 0:43:43.855 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 15481651 kmers 0:43:50.947 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 23774487 kmers 0:43:58.235 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 33121318 kmers 0:44:06.987 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 46869920 kmers 0:44:13.357 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 54914131 kmers 0:44:20.230 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 63199609 kmers 0:44:27.200 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 72555953 kmers 0:44:36.668 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 86381240 kmers 0:44:43.026 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 94424090 kmers 0:44:50.087 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 102713952 kmers 0:44:56.942 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 112066310 kmers 0:45:06.246 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 125899228 kmers 0:45:11.564 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 133944106 kmers 0:45:17.481 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 142231134 kmers 0:45:23.439 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 151578845 kmers 0:45:31.113 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 165409138 kmers 0:45:36.370 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 173439510 kmers 0:46:37.218 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 270127661 kmers 0:49:22.934 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 537436447 kmers 0:54:59.796 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 1074344961 kmers 0:56:58.310 17G / 18G INFO General (kmer_splitters.hpp : 385) Used 1264614312 kmers. 0:57:02.954 128M / 18G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 1:00:34.041 128M / 18G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 1258602684 kmers in total. 1:00:34.041 128M / 18G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 1:04:28.474 128M / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 1:06:20.473 704M / 18G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 1:09:21.674 704M / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 583625208 bytes occupied (3.70967 bits per kmer). 1:09:24.957 1G / 18G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 99) Building k-mer extensions from k+1-mers 1:10:49.450 1G / 18G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 103) Building k-mer extensions from k+1-mers finished. 1:10:49.460 1G / 18G INFO General (stage.cpp : 101) PROCEDURE == Early tip clipping 1:10:49.460 1G / 18G INFO General (construction.cpp : 253) Early tip clipper length bound set as (RL - K) 1:10:49.460 1G / 18G INFO Early tip clipping (early_simplification.hpp : 181) Early tip clipping 1:14:08.169 1G / 18G INFO Early tip clipping (early_simplification.hpp : 184) 323733993 34-mers were removed by early tip clipper 1:14:08.169 1G / 18G INFO General (stage.cpp : 101) PROCEDURE == Condensing graph 1:14:08.379 1G / 18G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 355) Extracting unbranching paths 1:15:51.279 3G / 18G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 374) Extracting unbranching paths finished. 31349555 sequences extracted 1:16:44.252 3G / 18G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 310) Collecting perfect loops 1:17:12.600 3G / 18G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 343) Collecting perfect loops finished. 988 loops collected 1:18:00.630 10G / 18G INFO General (stage.cpp : 101) PROCEDURE == Filling coverage indices (PHM) 1:18:00.630 10G / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 1:18:00.630 10G / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 1:19:06.237 11G / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 586433448 bytes occupied (3.70981 bits per kmer). 1:19:12.684 16G / 18G INFO General (construction.cpp : 388) Collecting k-mer coverage information from reads, this takes a while. 1:26:33.711 16G / 18G INFO General (construction.cpp : 508) Filling coverage and flanking coverage from PHM 1:27:06.525 16G / 18G INFO General (construction.cpp : 464) Processed 32000000 edges 1:27:34.809 16G / 18G INFO General (construction.cpp : 464) Processed 62688351 edges 1:27:51.406 9G / 18G INFO StageManager (stage.cpp : 132) STAGE == EC Threshold Finding 1:27:55.688 9G / 18G INFO General (kmer_coverage_model.cpp : 181) Kmer coverage valley at: 251 1:27:55.800 9G / 18G INFO General (kmer_coverage_model.cpp : 201) K-mer histogram maximum: 252 1:27:55.800 9G / 18G WARN General (kmer_coverage_model.cpp : 218) Too many erroneous kmers, the estimates might be unreliable 1:27:55.800 9G / 18G INFO General (kmer_coverage_model.cpp : 237) Estimated median coverage: 252. Coverage mad: 52.6271 1:27:55.919 9G / 18G INFO General (kmer_coverage_model.cpp : 259) Fitting coverage model 1:27:57.439 9G / 18G INFO General (kmer_coverage_model.cpp : 295) ... iteration 2 1:28:00.175 9G / 18G INFO General (kmer_coverage_model.cpp : 295) ... iteration 4 1:28:06.603 9G / 18G INFO General (kmer_coverage_model.cpp : 295) ... iteration 8 1:28:22.604 9G / 18G INFO General (kmer_coverage_model.cpp : 295) ... iteration 16 1:28:53.755 9G / 18G INFO General (kmer_coverage_model.cpp : 295) ... iteration 32 1:29:36.746 9G / 18G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 23.0487. Fitted coverage std. dev: 9.82197 1:29:36.746 9G / 18G WARN General (kmer_coverage_model.cpp : 327) Valley value was estimated improperly, reset to 12 1:29:36.772 9G / 18G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 0.632851 1:29:36.772 9G / 18G WARN General (kmer_coverage_model.cpp : 366) Failed to determine erroneous kmer threshold. Threshold set to: 12 1:29:36.772 9G / 18G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 270396602 1:29:36.773 9G / 18G INFO General (genomic_info_filler.cpp : 114) Failed to estimate mean coverage 1:29:36.773 9G / 18G INFO General (genomic_info_filler.cpp : 127) EC coverage threshold value was calculated as 12 1:29:36.773 9G / 18G INFO General (genomic_info_filler.cpp : 128) Trusted kmer low bound: 0 1:29:36.773 9G / 18G INFO StageManager (stage.cpp : 132) STAGE == Raw Simplification 1:29:36.773 9G / 18G INFO General (simplification.cpp : 128) PROCEDURE == InitialCleaning 1:29:36.775 9G / 18G INFO General (simplification.cpp : 68) Most init cleaning disabled since detected mean 0 was less than activation coverage 10 1:29:36.775 9G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Self conjugate edge remover 1:29:41.301 9G / 18G INFO Simplification (parallel_processing.hpp : 167) Self conjugate edge remover triggered 791 times 1:29:41.301 9G / 18G INFO StageManager (stage.cpp : 132) STAGE == Simplification 1:29:41.301 9G / 18G INFO General (simplification.cpp : 357) Graph simplification started 1:29:41.301 9G / 18G INFO General (graph_simplification.hpp : 634) Creating parallel br instance 1:29:41.301 9G / 18G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 1 1:29:41.301 9G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 1:30:50.238 9G / 18G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 1175463 times 1:30:50.238 9G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 1:50:42.180 10G / 18G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 1621510 times 1:50:42.180 10G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 2:03:20.685 10G / 18G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 4282014 times 2:03:20.685 10G / 18G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 2 2:03:20.685 10G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 2:03:48.116 10G / 18G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 185033 times 2:03:48.116 10G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 2:09:48.479 10G / 18G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 218647 times 2:09:48.479 10G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 2:13:42.329 10G / 18G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 1461552 times 2:13:42.329 10G / 18G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 3 2:13:42.329 10G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 2:13:59.029 10G / 18G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 35981 times 2:13:59.029 10G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 2:17:00.807 10G / 18G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 98116 times 2:17:00.807 10G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 2:18:56.547 10G / 18G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 508569 times 2:18:56.548 10G / 18G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 4 2:18:56.548 10G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 2:18:59.743 10G / 18G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 10527 times 2:18:59.743 10G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 2:19:57.644 10G / 18G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 37754 times 2:19:57.644 10G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 2:20:37.660 10G / 18G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 240866 times 2:20:37.660 10G / 18G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 5 2:20:37.660 10G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 2:20:38.965 10G / 18G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 4329 times 2:20:38.965 10G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 2:21:07.399 10G / 18G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 19131 times 2:21:07.400 10G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 2:21:49.180 10G / 18G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 150377 times 2:21:49.180 10G / 18G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 6 2:21:49.180 10G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 2:21:50.644 10G / 18G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 2320 times 2:21:50.644 10G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 2:22:12.421 10G / 18G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 12717 times 2:22:12.421 10G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 2:22:25.199 10G / 18G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 71079 times 2:22:25.199 10G / 18G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 7 2:22:25.199 10G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 2:22:25.726 10G / 18G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 964 times 2:22:25.726 10G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 2:22:35.619 10G / 18G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 6400 times 2:22:35.619 10G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 2:22:41.094 10G / 18G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 50481 times 2:22:41.094 10G / 18G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 8 2:22:41.094 10G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 2:22:41.269 10G / 18G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 551 times 2:22:41.269 10G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 2:22:46.559 10G / 18G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 4322 times 2:22:46.559 10G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 2:22:50.580 10G / 18G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 39154 times 2:22:50.580 10G / 18G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 9 2:22:50.580 10G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 2:22:50.706 10G / 18G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 384 times 2:22:50.706 10G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 2:22:57.017 10G / 18G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 3118 times 2:22:57.017 10G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 2:23:00.340 10G / 18G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 32208 times 2:23:00.340 10G / 18G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 10 2:23:00.340 10G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 2:23:00.441 10G / 18G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 237 times 2:23:00.441 10G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 2:23:05.605 10G / 18G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 2542 times 2:23:05.605 10G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 2:23:08.736 10G / 18G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 30276 times 2:23:08.736 10G / 18G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 11 2:23:08.736 10G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 2:23:10.347 10G / 18G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 1997 times 2:23:10.347 10G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 2:23:28.604 10G / 18G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 4832 times 2:23:28.605 10G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 2:23:31.029 9G / 18G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 11 times 2:23:31.030 9G / 18G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 12 2:23:31.030 9G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 2:23:31.141 9G / 18G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 3 times 2:23:31.141 9G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 2:23:31.160 9G / 18G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 2:23:31.160 9G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 2:23:31.161 9G / 18G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 2:23:31.161 9G / 18G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 13 2:23:31.161 9G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 2:23:31.161 9G / 18G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 2:23:31.161 9G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 2:23:31.161 9G / 18G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 2:23:31.161 9G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 2:23:31.161 9G / 18G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 2:23:31.161 9G / 18G INFO StageManager (stage.cpp : 132) STAGE == Simplification Cleanup 2:23:31.161 9G / 18G INFO General (simplification.cpp : 196) PROCEDURE == Post simplification 2:23:31.161 9G / 18G INFO General (graph_simplification.hpp : 453) Disconnection of relatively low covered edges disabled 2:23:31.161 9G / 18G INFO General (graph_simplification.hpp : 489) Complex tip clipping disabled 2:23:31.161 9G / 18G INFO General (graph_simplification.hpp : 634) Creating parallel br instance 2:23:31.161 9G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 2:23:32.626 9G / 18G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 2:23:32.626 9G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 2:23:46.701 9G / 18G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 20 times 2:23:46.701 9G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 2:23:48.623 9G / 18G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 2:23:48.623 9G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 2:24:02.706 9G / 18G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 2:24:02.707 9G / 18G INFO General (simplification.cpp : 330) Disrupting self-conjugate edges 2:24:20.632 9G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Removing isolated edges 2:25:17.830 7G / 18G INFO Simplification (parallel_processing.hpp : 167) Removing isolated edges triggered 3277784 times 2:25:17.830 7G / 18G INFO General (simplification.cpp : 470) Counting average coverage 2:25:22.049 7G / 18G INFO General (simplification.cpp : 476) Average coverage = 33.5719 2:25:22.049 7G / 18G INFO StageManager (stage.cpp : 132) STAGE == Contig Output 2:25:22.049 7G / 18G INFO General (contig_output_stage.cpp : 40) Writing GFA to /local/genbank/workspace/reads.uncorr.spades1//K33/assembly_graph_with_scaffolds.gfa 2:25:47.678 7G / 18G INFO General (contig_output.hpp : 22) Outputting contigs to /local/genbank/workspace/reads.uncorr.spades1//K33/before_rr.fasta 2:26:23.884 7G / 18G INFO General (contig_output_stage.cpp : 51) Outputting FastG graph to /local/genbank/workspace/reads.uncorr.spades1//K33/assembly_graph.fastg 2:28:02.635 7G / 18G INFO General (contig_output.hpp : 22) Outputting contigs to /local/genbank/workspace/reads.uncorr.spades1//K33/simplified_contigs.fasta 2:28:35.718 7G / 18G INFO General (contig_output.hpp : 22) Outputting contigs to /local/genbank/workspace/reads.uncorr.spades1//K33/final_contigs.fasta 2:29:08.165 7G / 18G INFO StageManager (stage.cpp : 132) STAGE == Contig Output 2:29:08.165 7G / 18G INFO General (contig_output_stage.cpp : 40) Writing GFA to /local/genbank/workspace/reads.uncorr.spades1//K33/assembly_graph_with_scaffolds.gfa 2:29:31.154 7G / 18G INFO General (contig_output.hpp : 22) Outputting contigs to /local/genbank/workspace/reads.uncorr.spades1//K33/before_rr.fasta 2:30:04.403 7G / 18G INFO General (contig_output_stage.cpp : 51) Outputting FastG graph to /local/genbank/workspace/reads.uncorr.spades1//K33/assembly_graph.fastg 2:31:05.047 7G / 18G INFO General (contig_output.hpp : 22) Outputting contigs to /local/genbank/workspace/reads.uncorr.spades1//K33/simplified_contigs.fasta 2:31:27.128 7G / 18G INFO General (contig_output.hpp : 22) Outputting contigs to /local/genbank/workspace/reads.uncorr.spades1//K33/final_contigs.fasta 2:31:48.204 7G / 18G INFO General (launch.hpp : 149) SPAdes finished 2:32:11.791 132M / 18G INFO General (main.cpp : 109) Assembling time: 2 hours 32 minutes 11 seconds == Running assembler: K55 0:00:00.000 4M / 4M INFO General (main.cpp : 74) Loaded config from /local/genbank/workspace/reads.uncorr.spades1/K55/configs/config.info 0:00:00.001 4M / 4M INFO General (memory_limit.cpp : 49) Memory limit set to 204 Gb 0:00:00.001 4M / 4M INFO General (main.cpp : 87) Starting SPAdes, built from refs/heads/spades_3.13.0, git revision 8ea46659e9b2aca35444a808db550ac333006f8b 0:00:00.001 4M / 4M INFO General (main.cpp : 88) Maximum k-mer length: 128 0:00:00.001 4M / 4M INFO General (main.cpp : 89) Assembling dataset (/local/genbank/workspace/reads.uncorr.spades1/dataset.info) with K=55 0:00:00.001 4M / 4M INFO General (main.cpp : 90) Maximum # of threads to use (adjusted due to OMP capabilities): 32 0:00:00.001 4M / 4M INFO General (launch.hpp : 51) SPAdes started 0:00:00.001 4M / 4M INFO General (launch.hpp : 58) Starting from stage: construction 0:00:00.001 4M / 4M INFO General (launch.hpp : 65) Two-step RR enabled: 0 0:00:00.001 4M / 4M INFO General (launch.hpp : 76) Will need read mapping, kmer mapper will be attached 0:00:00.001 4M / 4M INFO StageManager (stage.cpp : 132) STAGE == de Bruijn graph construction 0:00:00.009 4M / 4M INFO General (read_converter.hpp : 59) Binary reads detected 0:00:00.243 4M / 4M INFO General (construction.cpp : 111) Max read length 700 0:00:00.243 4M / 4M INFO General (construction.cpp : 117) Average read length 77.5334 0:00:00.243 4M / 4M INFO General (stage.cpp : 101) PROCEDURE == k+1-mer counting 0:00:00.245 4M / 4M INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 1024 files using 32 threads. This might take a while. 0:00:00.248 4M / 4M INFO General (file_limit.hpp : 32) Open file limit set to 4096 0:00:00.248 4M / 4M INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.12496 Gb 0:00:00.248 4M / 4M INFO General (kmer_splitters.hpp : 97) Using cell size of 32768 0:00:54.212 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 61554675 reads 0:01:40.023 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 138375765 reads 0:02:06.197 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 171041524 reads 0:02:55.700 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 195576208 reads 0:04:03.071 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 230850666 reads 0:05:07.301 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 278378531 reads 0:06:07.871 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 325252361 reads 0:07:10.728 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 365384434 reads 0:08:01.285 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 395183096 reads 0:09:02.566 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 447999477 reads 0:09:57.933 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 525261074 reads 0:10:51.928 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 598809398 reads 0:11:21.231 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 621924902 reads 0:11:21.231 17G / 18G INFO General (kmer_splitters.hpp : 295) Adding contigs from previous K 0:15:47.442 132M / 18G INFO General (kmer_splitters.hpp : 308) Used 621924902 reads 0:15:47.442 132M / 18G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:19:17.526 132M / 18G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 1181779085 kmers in total. 0:19:17.526 132M / 18G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:22:56.320 128M / 18G INFO General (stage.cpp : 101) PROCEDURE == Extension index construction 0:22:56.323 128M / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:22:56.323 128M / 18G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 512 files using 32 threads. This might take a while. 0:22:56.326 128M / 18G INFO General (file_limit.hpp : 32) Open file limit set to 4096 0:22:56.326 128M / 18G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.1237 Gb 0:22:56.326 128M / 18G INFO General (kmer_splitters.hpp : 97) Using cell size of 65536 0:23:05.005 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 7471464 kmers 0:23:10.949 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 16747922 kmers 0:23:16.779 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 26201339 kmers 0:23:22.429 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 34728113 kmers 0:23:28.982 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 44363306 kmers 0:23:34.995 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 53624727 kmers 0:23:40.810 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 63085609 kmers 0:23:46.286 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 71620066 kmers 0:23:52.261 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 81291933 kmers 0:23:58.260 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 90550985 kmers 0:24:04.281 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 100003769 kmers 0:24:09.988 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 108546496 kmers 0:24:16.009 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 118224073 kmers 0:24:22.094 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 127484281 kmers 0:24:28.576 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 136947460 kmers 0:24:34.021 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 145485298 kmers 0:24:40.006 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 155154691 kmers 0:24:46.211 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 164428524 kmers 0:26:02.202 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 275215221 kmers 0:29:16.178 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 543189766 kmers 0:36:15.377 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 1078430328 kmers 0:37:30.093 17G / 18G INFO General (kmer_splitters.hpp : 385) Used 1181783181 kmers. 0:37:35.959 128M / 18G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:41:26.198 128M / 18G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 1193171744 kmers in total. 0:41:26.199 128M / 18G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:45:12.028 128M / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:47:00.680 704M / 18G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 0:49:53.004 704M / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 553284672 bytes occupied (3.70967 bits per kmer). 0:49:54.702 1G / 18G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 99) Building k-mer extensions from k+1-mers 0:51:04.455 1G / 18G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 103) Building k-mer extensions from k+1-mers finished. 0:51:04.479 1G / 18G INFO General (stage.cpp : 101) PROCEDURE == Condensing graph 0:51:04.700 1G / 18G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 355) Extracting unbranching paths 0:52:57.479 5G / 18G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 374) Extracting unbranching paths finished. 57796351 sequences extracted 0:53:55.004 5G / 18G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 310) Collecting perfect loops 0:54:20.944 5G / 18G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 343) Collecting perfect loops finished. 130 loops collected 0:55:43.528 20G / 26G INFO General (stage.cpp : 101) PROCEDURE == Filling coverage indices (PHM) 0:55:43.528 20G / 26G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:55:43.528 20G / 26G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:56:35.942 21G / 26G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 548025840 bytes occupied (3.70984 bits per kmer). 0:56:42.824 25G / 26G INFO General (construction.cpp : 388) Collecting k-mer coverage information from reads, this takes a while. 1:00:52.969 25G / 26G INFO General (construction.cpp : 508) Filling coverage and flanking coverage from PHM 1:01:20.941 25G / 26G INFO General (construction.cpp : 464) Processed 32000000 edges 1:01:41.536 25G / 26G INFO General (construction.cpp : 464) Processed 64000000 edges 1:02:01.857 25G / 26G INFO General (construction.cpp : 464) Processed 96000000 edges 1:02:14.155 25G / 26G INFO General (construction.cpp : 464) Processed 115590728 edges 1:02:29.318 19G / 26G INFO StageManager (stage.cpp : 132) STAGE == EC Threshold Finding 1:02:30.263 19G / 26G INFO General (kmer_coverage_model.cpp : 181) Kmer coverage valley at: 212 1:02:30.281 19G / 26G INFO General (kmer_coverage_model.cpp : 201) K-mer histogram maximum: 213 1:02:30.281 19G / 26G WARN General (kmer_coverage_model.cpp : 218) Too many erroneous kmers, the estimates might be unreliable 1:02:30.281 19G / 26G INFO General (kmer_coverage_model.cpp : 237) Estimated median coverage: 213. Coverage mad: 48.3837 1:02:30.305 19G / 26G INFO General (kmer_coverage_model.cpp : 259) Fitting coverage model 1:02:31.900 19G / 26G INFO General (kmer_coverage_model.cpp : 295) ... iteration 2 1:02:35.356 19G / 26G INFO General (kmer_coverage_model.cpp : 295) ... iteration 4 1:02:38.761 19G / 26G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 386.521. Fitted coverage std. dev: 36.9019 1:02:38.808 19G / 26G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 1 1:02:38.808 19G / 26G WARN General (kmer_coverage_model.cpp : 366) Failed to determine erroneous kmer threshold. Threshold set to: 212 1:02:38.808 19G / 26G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 837906 1:02:38.809 19G / 26G INFO General (genomic_info_filler.cpp : 114) Failed to estimate mean coverage 1:02:38.809 19G / 26G INFO General (genomic_info_filler.cpp : 127) EC coverage threshold value was calculated as 212 1:02:38.809 19G / 26G INFO General (genomic_info_filler.cpp : 128) Trusted kmer low bound: 0 1:02:38.809 19G / 26G INFO StageManager (stage.cpp : 132) STAGE == Gap Closer 1:02:38.809 19G / 26G INFO General (graph_pack.hpp : 101) Index refill 1:02:38.814 19G / 26G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 1:02:38.814 19G / 26G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 512 files using 32 threads. This might take a while. 1:02:38.822 19G / 26G INFO General (file_limit.hpp : 32) Open file limit set to 4096 1:02:38.822 19G / 26G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 1.92651 Gb 1:02:38.822 19G / 26G INFO General (kmer_splitters.hpp : 97) Using cell size of 65536 1:05:32.606 36G / 37G INFO General (edge_index_builders.hpp : 77) Processed 87970420 edges 1:06:25.501 36G / 37G INFO General (edge_index_builders.hpp : 77) Processed 115590760 edges 1:06:25.501 36G / 37G INFO General (edge_index_builders.hpp : 82) Used 115590760 sequences. 1:06:32.663 19G / 37G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 1:09:25.416 19G / 37G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 1181779085 kmers in total. 1:09:25.416 19G / 37G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 1:13:08.710 19G / 37G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 1:15:29.892 19G / 37G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 1:18:21.831 19G / 37G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 548011766 bytes occupied (3.70974 bits per kmer). 1:19:09.197 46G / 46G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while. 1:20:05.547 46G / 46G INFO General (edge_index.hpp : 92) Index refilled 1:20:05.584 46G / 46G INFO General (gap_closer.cpp : 159) Preparing shift maps 1:23:46.342 53G / 53G INFO General (gap_closer.cpp : 119) Processing paired reads (takes a while) 1:25:03.691 54G / 54G INFO General (gap_closer.cpp : 138) Used 105822607 paired reads 1:25:03.691 54G / 54G INFO General (gap_closer.cpp : 140) Merging paired indices 1:27:09.368 46G / 54G INFO GapCloser (gap_closer.cpp : 346) Closing short gaps 1:39:58.577 46G / 54G INFO GapCloser (gap_closer.cpp : 380) Closing short gaps complete: filled 62443 gaps after checking 942466 candidates 1:41:20.435 46G / 54G INFO StageManager (stage.cpp : 132) STAGE == Raw Simplification 1:41:31.747 19G / 54G INFO General (simplification.cpp : 128) PROCEDURE == InitialCleaning 1:41:31.747 19G / 54G INFO General (simplification.cpp : 68) Most init cleaning disabled since detected mean 0 was less than activation coverage 10 1:41:31.747 19G / 54G INFO Simplification (parallel_processing.hpp : 165) Running Self conjugate edge remover 1:41:44.083 19G / 54G INFO Simplification (parallel_processing.hpp : 167) Self conjugate edge remover triggered 441 times 1:41:44.083 19G / 54G INFO StageManager (stage.cpp : 132) STAGE == Simplification 1:41:44.083 19G / 54G INFO General (simplification.cpp : 357) Graph simplification started 1:41:44.083 19G / 54G INFO General (graph_simplification.hpp : 634) Creating parallel br instance 1:41:44.083 19G / 54G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 1 1:41:44.083 19G / 54G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 2:00:04.741 20G / 54G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 21166908 times 2:00:04.741 20G / 54G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 2:16:53.563 23G / 54G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 846595 times 2:16:53.563 23G / 54G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 2:18:46.543 23G / 54G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 636434 times 2:18:46.543 23G / 54G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 2 2:18:46.543 23G / 54G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 2:18:59.624 23G / 54G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 115129 times 2:18:59.624 23G / 54G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 2:19:51.120 23G / 54G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 24345 times 2:19:51.120 23G / 54G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 2:19:53.829 23G / 54G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 14817 times 2:19:53.829 23G / 54G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 3 2:19:53.829 23G / 54G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 2:19:53.915 23G / 54G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 180 times 2:19:53.916 23G / 54G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 2:20:00.353 23G / 54G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 2677 times 2:20:00.354 23G / 54G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 2:20:00.992 23G / 54G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 3989 times 2:20:00.992 23G / 54G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 4 2:20:00.992 23G / 54G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 2:20:01.017 23G / 54G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 51 times 2:20:01.017 23G / 54G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 2:20:02.478 23G / 54G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 730 times 2:20:02.478 23G / 54G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 2:20:02.773 23G / 54G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 1899 times 2:20:02.773 23G / 54G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 5 2:20:02.773 23G / 54G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 2:20:02.785 23G / 54G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 28 times 2:20:02.785 23G / 54G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 2:20:03.684 23G / 54G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 365 times 2:20:03.684 23G / 54G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 2:20:03.849 23G / 54G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 1116 times 2:20:03.849 23G / 54G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 6 2:20:03.849 23G / 54G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 2:20:03.857 23G / 54G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 24 times 2:20:03.857 23G / 54G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 2:20:04.324 23G / 54G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 214 times 2:20:04.324 23G / 54G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 2:20:04.423 23G / 54G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 701 times 2:20:04.423 23G / 54G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 7 2:20:04.423 23G / 54G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 2:20:04.428 23G / 54G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 14 times 2:20:04.428 23G / 54G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 2:20:04.775 23G / 54G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 125 times 2:20:04.775 23G / 54G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 2:20:04.847 23G / 54G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 502 times 2:20:04.847 23G / 54G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 8 2:20:04.847 23G / 54G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 2:20:04.850 23G / 54G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 9 times 2:20:04.850 23G / 54G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 2:20:05.013 23G / 54G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 84 times 2:20:05.013 23G / 54G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 2:20:05.063 23G / 54G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 367 times 2:20:05.063 23G / 54G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 9 2:20:05.063 23G / 54G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 2:20:05.066 23G / 54G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 12 times 2:20:05.066 23G / 54G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 2:20:05.138 23G / 54G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 60 times 2:20:05.138 23G / 54G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 2:20:05.174 23G / 54G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 264 times 2:20:05.174 23G / 54G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 10 2:20:05.174 23G / 54G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 2:20:05.176 23G / 54G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 4 times 2:20:05.176 23G / 54G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 2:20:05.234 23G / 54G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 41 times 2:20:05.234 23G / 54G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 2:20:05.269 23G / 54G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 231 times 2:20:05.269 23G / 54G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 11 2:20:05.269 23G / 54G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 2:20:11.214 23G / 54G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 1721 times 2:20:11.214 23G / 54G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 2:20:16.623 23G / 54G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 80 times 2:20:16.623 23G / 54G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 2:20:21.000 23G / 54G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 4 times 2:20:21.000 23G / 54G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 12 2:20:21.000 23G / 54G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 2:20:21.001 23G / 54G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 2:20:21.001 23G / 54G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 2:20:21.001 23G / 54G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 2:20:21.001 23G / 54G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 2:20:21.001 23G / 54G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 2:20:21.001 23G / 54G INFO StageManager (stage.cpp : 132) STAGE == Gap Closer 2:20:21.001 23G / 54G INFO General (graph_pack.hpp : 101) Index refill 2:20:21.026 23G / 54G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 2:20:21.026 23G / 54G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 512 files using 32 threads. This might take a while. 2:20:21.031 23G / 54G INFO General (file_limit.hpp : 32) Open file limit set to 4096 2:20:21.031 23G / 54G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 1.87687 Gb 2:20:21.031 23G / 54G INFO General (kmer_splitters.hpp : 97) Using cell size of 65536 2:22:30.205 41G / 54G INFO General (edge_index_builders.hpp : 77) Processed 25942789 edges 2:22:30.205 41G / 54G INFO General (edge_index_builders.hpp : 82) Used 25942789 sequences. 2:22:36.545 23G / 54G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 2:24:18.024 23G / 54G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 680625261 kmers in total. 2:24:18.025 23G / 54G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 2:26:27.013 23G / 54G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 2:27:21.613 24G / 54G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 2:29:03.794 24G / 54G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 315615568 bytes occupied (3.70971 bits per kmer). 2:29:32.667 39G / 54G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while. 2:30:10.979 39G / 54G INFO General (edge_index.hpp : 92) Index refilled 2:30:11.013 39G / 54G INFO General (gap_closer.cpp : 159) Preparing shift maps 2:31:36.757 43G / 54G INFO General (gap_closer.cpp : 119) Processing paired reads (takes a while) 2:34:13.685 45G / 54G INFO General (gap_closer.cpp : 138) Used 105822607 paired reads 2:34:13.686 45G / 54G INFO General (gap_closer.cpp : 140) Merging paired indices 2:36:11.898 39G / 54G INFO GapCloser (gap_closer.cpp : 346) Closing short gaps 2:39:55.223 39G / 54G INFO GapCloser (gap_closer.cpp : 380) Closing short gaps complete: filled 25362 gaps after checking 1199283 candidates 2:43:21.284 39G / 54G INFO StageManager (stage.cpp : 132) STAGE == Simplification Cleanup 2:43:21.284 39G / 54G INFO General (simplification.cpp : 196) PROCEDURE == Post simplification 2:43:21.284 39G / 54G INFO General (graph_simplification.hpp : 453) Disconnection of relatively low covered edges disabled 2:43:21.284 39G / 54G INFO General (graph_simplification.hpp : 489) Complex tip clipping disabled 2:43:21.285 39G / 54G INFO General (graph_simplification.hpp : 634) Creating parallel br instance 2:43:21.285 39G / 54G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 2:43:27.865 39G / 54G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 2:43:27.866 39G / 54G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 2:43:33.549 39G / 54G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 2:43:33.549 39G / 54G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 2:43:38.827 39G / 54G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 2:43:38.827 39G / 54G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 2:43:43.635 39G / 54G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 2:43:43.635 39G / 54G INFO General (simplification.cpp : 330) Disrupting self-conjugate edges 2:44:54.722 39G / 54G INFO Simplification (parallel_processing.hpp : 165) Running Removing isolated edges 3:07:04.784 28G / 54G INFO Simplification (parallel_processing.hpp : 167) Removing isolated edges triggered 12793615 times 3:07:04.785 28G / 54G INFO General (simplification.cpp : 470) Counting average coverage 3:07:06.080 28G / 54G INFO General (simplification.cpp : 476) Average coverage = 15.6489 3:07:06.080 28G / 54G WARN General (simplification.cpp : 479) The determined erroneous connection coverage threshold may be determined improperly 3:07:06.080 28G / 54G INFO StageManager (stage.cpp : 132) STAGE == Contig Output 3:07:06.080 28G / 54G INFO General (contig_output_stage.cpp : 40) Writing GFA to /local/genbank/workspace/reads.uncorr.spades1//K55/assembly_graph_with_scaffolds.gfa 3:07:19.432 28G / 54G INFO General (contig_output.hpp : 22) Outputting contigs to /local/genbank/workspace/reads.uncorr.spades1//K55/before_rr.fasta 3:07:35.693 28G / 54G INFO General (contig_output_stage.cpp : 51) Outputting FastG graph to /local/genbank/workspace/reads.uncorr.spades1//K55/assembly_graph.fastg 3:08:20.965 28G / 54G INFO General (contig_output.hpp : 22) Outputting contigs to /local/genbank/workspace/reads.uncorr.spades1//K55/simplified_contigs.fasta 3:08:36.660 28G / 54G INFO General (contig_output.hpp : 22) Outputting contigs to /local/genbank/workspace/reads.uncorr.spades1//K55/final_contigs.fasta 3:08:53.903 28G / 54G INFO StageManager (stage.cpp : 132) STAGE == Contig Output 3:08:53.903 28G / 54G INFO General (contig_output_stage.cpp : 40) Writing GFA to /local/genbank/workspace/reads.uncorr.spades1//K55/assembly_graph_with_scaffolds.gfa 3:09:05.693 28G / 54G INFO General (contig_output.hpp : 22) Outputting contigs to /local/genbank/workspace/reads.uncorr.spades1//K55/before_rr.fasta 3:09:22.301 28G / 54G INFO General (contig_output_stage.cpp : 51) Outputting FastG graph to /local/genbank/workspace/reads.uncorr.spades1//K55/assembly_graph.fastg 3:10:14.306 28G / 54G INFO General (contig_output.hpp : 22) Outputting contigs to /local/genbank/workspace/reads.uncorr.spades1//K55/simplified_contigs.fasta 3:10:32.265 28G / 54G INFO General (contig_output.hpp : 22) Outputting contigs to /local/genbank/workspace/reads.uncorr.spades1//K55/final_contigs.fasta 3:10:48.787 28G / 54G INFO General (launch.hpp : 149) SPAdes finished 3:15:08.306 140M / 54G INFO General (main.cpp : 109) Assembling time: 3 hours 15 minutes 8 seconds == Running assembler: K77 0:00:00.000 4M / 4M INFO General (main.cpp : 74) Loaded config from /local/genbank/workspace/reads.uncorr.spades1/K77/configs/config.info 0:00:00.001 4M / 4M INFO General (memory_limit.cpp : 49) Memory limit set to 204 Gb 0:00:00.001 4M / 4M INFO General (main.cpp : 87) Starting SPAdes, built from refs/heads/spades_3.13.0, git revision 8ea46659e9b2aca35444a808db550ac333006f8b 0:00:00.001 4M / 4M INFO General (main.cpp : 88) Maximum k-mer length: 128 0:00:00.001 4M / 4M INFO General (main.cpp : 89) Assembling dataset (/local/genbank/workspace/reads.uncorr.spades1/dataset.info) with K=77 0:00:00.001 4M / 4M INFO General (main.cpp : 90) Maximum # of threads to use (adjusted due to OMP capabilities): 32 0:00:00.001 4M / 4M INFO General (launch.hpp : 51) SPAdes started 0:00:00.001 4M / 4M INFO General (launch.hpp : 58) Starting from stage: construction 0:00:00.001 4M / 4M INFO General (launch.hpp : 65) Two-step RR enabled: 0 0:00:00.001 4M / 4M INFO General (launch.hpp : 76) Will need read mapping, kmer mapper will be attached 0:00:00.001 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 0:00:00.086 4M / 4M INFO General (construction.cpp : 111) Max read length 700 0:00:00.086 4M / 4M INFO General (construction.cpp : 117) Average read length 77.5334 0:00:00.086 4M / 4M INFO General (stage.cpp : 101) PROCEDURE == k+1-mer counting 0:00:00.088 4M / 4M INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 1024 files using 32 threads. This might take a while. 0:00:00.092 4M / 4M INFO General (file_limit.hpp : 32) Open file limit set to 4096 0:00:00.092 4M / 4M INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.12496 Gb 0:00:00.092 4M / 4M INFO General (kmer_splitters.hpp : 97) Using cell size of 21845 0:01:20.564 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 197455513 reads 0:02:47.066 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 294850139 reads 0:04:11.937 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 381765748 reads 0:04:55.949 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 621924902 reads 0:04:55.949 17G / 18G INFO General (kmer_splitters.hpp : 295) Adding contigs from previous K 0:10:30.571 132M / 18G INFO General (kmer_splitters.hpp : 308) Used 621924902 reads 0:10:30.571 132M / 18G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:13:35.866 132M / 18G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 784002483 kmers in total. 0:13:35.866 132M / 18G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:17:13.309 128M / 18G INFO General (stage.cpp : 101) PROCEDURE == Extension index construction 0:17:13.311 128M / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:17:13.311 128M / 18G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 512 files using 32 threads. This might take a while. 0:17:13.314 128M / 18G INFO General (file_limit.hpp : 32) Open file limit set to 4096 0:17:13.314 128M / 18G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.1237 Gb 0:17:13.314 128M / 18G INFO General (kmer_splitters.hpp : 97) Using cell size of 43690 0:17:20.759 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 5457491 kmers 0:17:26.637 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 11413316 kmers 0:17:32.079 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 17345988 kmers 0:17:37.642 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 23108133 kmers 0:17:43.563 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 29938963 kmers 0:17:49.268 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 35892041 kmers 0:17:55.015 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 41822946 kmers 0:18:00.578 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 47587096 kmers 0:18:06.591 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 54454532 kmers 0:18:12.359 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 60411481 kmers 0:18:18.171 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 66345314 kmers 0:18:23.730 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 72111303 kmers 0:18:29.727 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 78947433 kmers 0:18:35.491 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 84901011 kmers 0:18:41.854 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 90833380 kmers 0:18:47.245 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 96605384 kmers 0:18:53.405 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 103451649 kmers 0:19:28.091 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 139836134 kmers 0:21:36.578 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 274942458 kmers 0:25:44.662 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 537587864 kmers 0:29:33.945 17G / 18G INFO General (kmer_splitters.hpp : 385) Used 784006579 kmers. 0:29:38.162 132M / 18G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:32:53.860 132M / 18G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 796633857 kmers in total. 0:32:53.861 132M / 18G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:36:42.234 132M / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:38:12.098 516M / 18G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 0:41:04.826 516M / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 369409064 bytes occupied (3.7097 bits per kmer). 0:41:06.481 1G / 18G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 99) Building k-mer extensions from k+1-mers 0:41:51.974 1G / 18G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 103) Building k-mer extensions from k+1-mers finished. 0:41:51.979 1G / 18G INFO General (stage.cpp : 101) PROCEDURE == Condensing graph 0:41:52.184 1G / 18G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 355) Extracting unbranching paths 0:43:02.084 3G / 18G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 374) Extracting unbranching paths finished. 28578843 sequences extracted 0:43:38.967 3G / 18G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 310) Collecting perfect loops 0:43:56.292 3G / 18G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 343) Collecting perfect loops finished. 56 loops collected 0:44:50.194 11G / 18G INFO General (stage.cpp : 101) PROCEDURE == Filling coverage indices (PHM) 0:44:50.195 11G / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:44:50.195 11G / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:45:35.097 11G / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 363572542 bytes occupied (3.70991 bits per kmer). 0:45:38.968 14G / 18G INFO General (construction.cpp : 388) Collecting k-mer coverage information from reads, this takes a while. 0:46:58.439 14G / 18G INFO General (construction.cpp : 508) Filling coverage and flanking coverage from PHM 0:47:31.096 14G / 18G INFO General (construction.cpp : 464) Processed 32000000 edges 0:47:51.958 14G / 18G INFO General (construction.cpp : 464) Processed 57157332 edges 0:48:05.636 10G / 18G INFO StageManager (stage.cpp : 132) STAGE == EC Threshold Finding 0:48:05.677 10G / 18G INFO General (kmer_coverage_model.cpp : 181) Kmer coverage valley at: 127 0:48:05.679 10G / 18G INFO General (kmer_coverage_model.cpp : 201) K-mer histogram maximum: 129 0:48:05.679 10G / 18G INFO General (kmer_coverage_model.cpp : 237) Estimated median coverage: 130. Coverage mad: 2.9652 0:48:05.681 10G / 18G INFO General (kmer_coverage_model.cpp : 259) Fitting coverage model 0:48:06.531 10G / 18G INFO General (kmer_coverage_model.cpp : 295) ... iteration 2 0:48:08.369 10G / 18G INFO General (kmer_coverage_model.cpp : 295) ... iteration 4 0:48:10.101 10G / 18G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 124.013. Fitted coverage std. dev: 7.64354 0:48:10.125 10G / 18G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 0.995756 0:48:10.125 10G / 18G WARN General (kmer_coverage_model.cpp : 366) Failed to determine erroneous kmer threshold. Threshold set to: 127 0:48:10.126 10G / 18G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 172541 0:48:10.126 10G / 18G INFO General (genomic_info_filler.cpp : 114) Failed to estimate mean coverage 0:48:10.126 10G / 18G INFO General (genomic_info_filler.cpp : 127) EC coverage threshold value was calculated as 127 0:48:10.126 10G / 18G INFO General (genomic_info_filler.cpp : 128) Trusted kmer low bound: 0 0:48:10.126 10G / 18G INFO StageManager (stage.cpp : 132) STAGE == Gap Closer 0:48:10.126 10G / 18G INFO General (graph_pack.hpp : 101) Index refill 0:48:10.132 10G / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:48:10.132 10G / 18G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 512 files using 32 threads. This might take a while. 0:48:10.135 10G / 18G INFO General (file_limit.hpp : 32) Open file limit set to 4096 0:48:10.135 10G / 18G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.0177 Gb 0:48:10.135 10G / 18G INFO General (kmer_splitters.hpp : 97) Using cell size of 43690 0:51:08.073 27G / 28G INFO General (edge_index_builders.hpp : 77) Processed 45502674 edges 0:51:53.681 27G / 28G INFO General (edge_index_builders.hpp : 77) Processed 57157364 edges 0:51:53.681 27G / 28G INFO General (edge_index_builders.hpp : 82) Used 57157364 sequences. 0:52:01.066 10G / 28G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:54:47.326 10G / 28G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 784002483 kmers in total. 0:54:47.326 10G / 28G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:58:30.465 10G / 28G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:59:57.014 10G / 28G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 1:02:46.616 10G / 28G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 363557206 bytes occupied (3.70976 bits per kmer). 1:03:12.971 28G / 28G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while. 1:03:53.187 28G / 28G INFO General (edge_index.hpp : 92) Index refilled 1:03:53.214 28G / 28G INFO General (gap_closer.cpp : 159) Preparing shift maps 1:06:31.878 33G / 33G INFO General (gap_closer.cpp : 119) Processing paired reads (takes a while) 1:06:57.110 34G / 34G INFO General (gap_closer.cpp : 138) Used 105822607 paired reads 1:06:57.110 34G / 34G INFO General (gap_closer.cpp : 140) Merging paired indices 1:08:26.319 28G / 34G INFO GapCloser (gap_closer.cpp : 346) Closing short gaps 1:14:58.286 28G / 34G INFO GapCloser (gap_closer.cpp : 380) Closing short gaps complete: filled 47059 gaps after checking 669381 candidates 1:15:53.506 28G / 34G INFO StageManager (stage.cpp : 132) STAGE == Raw Simplification 1:16:00.533 10G / 34G INFO General (simplification.cpp : 128) PROCEDURE == InitialCleaning 1:16:00.533 10G / 34G INFO General (simplification.cpp : 68) Most init cleaning disabled since detected mean 0 was less than activation coverage 10 1:16:00.533 10G / 34G INFO Simplification (parallel_processing.hpp : 165) Running Self conjugate edge remover 1:16:06.717 10G / 34G INFO Simplification (parallel_processing.hpp : 167) Self conjugate edge remover triggered 96 times 1:16:06.717 10G / 34G INFO StageManager (stage.cpp : 132) STAGE == Simplification 1:16:06.717 10G / 34G INFO General (simplification.cpp : 357) Graph simplification started 1:16:06.717 10G / 34G INFO General (graph_simplification.hpp : 634) Creating parallel br instance 1:16:06.717 10G / 34G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 1 1:16:06.718 10G / 34G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 1:23:50.946 10G / 34G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 7055304 times 1:23:50.946 10G / 34G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 1:34:46.778 15G / 34G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 474880 times 1:34:46.779 15G / 34G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 1:35:08.527 15G / 34G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 82851 times 1:35:08.527 15G / 34G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 2 1:35:08.527 15G / 34G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 1:35:13.024 15G / 34G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 23064 times 1:35:13.025 15G / 34G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 1:35:27.072 15G / 34G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 3186 times 1:35:27.073 15G / 34G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 1:35:27.548 15G / 34G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 1696 times 1:35:27.548 15G / 34G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 3 1:35:27.548 15G / 34G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 1:35:27.585 15G / 34G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 78 times 1:35:27.585 15G / 34G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 1:35:28.617 15G / 34G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 280 times 1:35:28.617 15G / 34G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 1:35:28.732 15G / 34G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 583 times 1:35:28.732 15G / 34G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 4 1:35:28.732 15G / 34G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 1:35:28.736 15G / 34G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 25 times 1:35:28.736 15G / 34G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 1:35:29.008 15G / 34G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 84 times 1:35:29.009 15G / 34G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 1:35:29.071 15G / 34G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 293 times 1:35:29.071 15G / 34G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 5 1:35:29.071 15G / 34G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 1:35:29.073 15G / 34G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 15 times 1:35:29.073 15G / 34G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 1:35:29.218 15G / 34G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 28 times 1:35:29.218 15G / 34G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 1:35:29.250 15G / 34G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 182 times 1:35:29.250 15G / 34G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 6 1:35:29.250 15G / 34G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 1:35:29.251 15G / 34G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 10 times 1:35:29.252 15G / 34G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 1:35:29.367 15G / 34G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 22 times 1:35:29.367 15G / 34G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 1:35:29.394 15G / 34G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 107 times 1:35:29.394 15G / 34G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 7 1:35:29.394 15G / 34G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 1:35:29.395 15G / 34G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 7 times 1:35:29.395 15G / 34G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 1:35:29.450 15G / 34G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 14 times 1:35:29.450 15G / 34G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 1:35:29.466 15G / 34G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 88 times 1:35:29.467 15G / 34G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 8 1:35:29.467 15G / 34G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 1:35:29.468 15G / 34G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 8 times 1:35:29.468 15G / 34G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 1:35:29.545 15G / 34G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 11 times 1:35:29.545 15G / 34G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 1:35:29.557 15G / 34G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 66 times 1:35:29.557 15G / 34G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 9 1:35:29.557 15G / 34G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 1:35:29.558 15G / 34G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 7 times 1:35:29.558 15G / 34G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 1:35:29.576 15G / 34G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 5 times 1:35:29.576 15G / 34G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 1:35:29.585 15G / 34G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 52 times 1:35:29.585 15G / 34G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 10 1:35:29.585 15G / 34G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 1:35:29.585 15G / 34G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 5 times 1:35:29.585 15G / 34G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 1:35:29.606 15G / 34G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 8 times 1:35:29.606 15G / 34G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 1:35:29.612 15G / 34G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 39 times 1:35:29.612 15G / 34G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 11 1:35:29.612 15G / 34G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 1:35:36.298 15G / 34G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 971 times 1:35:36.298 15G / 34G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 1:35:40.681 15G / 34G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 29 times 1:35:40.681 15G / 34G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 1:35:44.958 15G / 34G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 2 times 1:35:44.958 15G / 34G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 12 1:35:44.958 15G / 34G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 1:35:44.959 15G / 34G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 1:35:44.959 15G / 34G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 1:35:44.959 15G / 34G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 1:35:44.959 15G / 34G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 1:35:44.959 15G / 34G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 1:35:44.960 15G / 34G INFO StageManager (stage.cpp : 132) STAGE == Gap Closer 1:35:44.960 15G / 34G INFO General (graph_pack.hpp : 101) Index refill 1:35:44.970 15G / 34G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 1:35:44.970 15G / 34G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 512 files using 32 threads. This might take a while. 1:35:44.978 15G / 34G INFO General (file_limit.hpp : 32) Open file limit set to 4096 1:35:44.979 15G / 34G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 1.96041 Gb 1:35:44.979 15G / 34G INFO General (kmer_splitters.hpp : 97) Using cell size of 43690 1:38:39.256 33G / 34G INFO General (edge_index_builders.hpp : 77) Processed 26338438 edges 1:38:39.256 33G / 34G INFO General (edge_index_builders.hpp : 82) Used 26338438 sequences. 1:38:46.732 15G / 34G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 1:41:00.573 15G / 34G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 612774272 kmers in total. 1:41:00.573 15G / 34G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 1:43:57.683 15G / 34G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 1:45:10.333 16G / 34G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 1:47:25.021 16G / 34G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 284173572 bytes occupied (3.70999 bits per kmer). 1:47:50.175 29G / 34G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while. 1:48:17.217 29G / 34G INFO General (edge_index.hpp : 92) Index refilled 1:48:17.245 29G / 34G INFO General (gap_closer.cpp : 159) Preparing shift maps 1:49:55.805 33G / 34G INFO General (gap_closer.cpp : 119) Processing paired reads (takes a while) 1:50:36.352 35G / 35G INFO General (gap_closer.cpp : 138) Used 105822607 paired reads 1:50:36.352 35G / 35G INFO General (gap_closer.cpp : 140) Merging paired indices 1:53:06.265 30G / 35G INFO GapCloser (gap_closer.cpp : 346) Closing short gaps 1:57:16.363 30G / 35G INFO GapCloser (gap_closer.cpp : 380) Closing short gaps complete: filled 6846 gaps after checking 1512457 candidates 1:58:54.040 29G / 35G INFO StageManager (stage.cpp : 132) STAGE == Simplification Cleanup 1:58:54.040 29G / 35G INFO General (simplification.cpp : 196) PROCEDURE == Post simplification 1:58:54.040 29G / 35G INFO General (graph_simplification.hpp : 453) Disconnection of relatively low covered edges disabled 1:58:54.040 29G / 35G INFO General (graph_simplification.hpp : 489) Complex tip clipping disabled 1:58:54.040 29G / 35G INFO General (graph_simplification.hpp : 634) Creating parallel br instance 1:58:54.040 29G / 35G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 1:58:58.616 29G / 35G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 1:58:58.617 29G / 35G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 1:59:02.699 29G / 35G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 1:59:02.700 29G / 35G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 1:59:07.004 29G / 35G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 1:59:07.004 29G / 35G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 1:59:10.766 29G / 35G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 1:59:10.766 29G / 35G INFO General (simplification.cpp : 330) Disrupting self-conjugate edges 2:00:13.946 29G / 35G INFO Simplification (parallel_processing.hpp : 165) Running Removing isolated edges 2:20:27.115 24G / 35G INFO Simplification (parallel_processing.hpp : 167) Removing isolated edges triggered 13051246 times 2:20:27.120 24G / 35G INFO General (simplification.cpp : 470) Counting average coverage 2:20:27.851 24G / 35G INFO General (simplification.cpp : 476) Average coverage = 3.99102 2:20:27.851 24G / 35G WARN General (simplification.cpp : 479) The determined erroneous connection coverage threshold may be determined improperly 2:20:27.851 24G / 35G INFO StageManager (stage.cpp : 132) STAGE == Contig Output 2:20:27.851 24G / 35G INFO General (contig_output_stage.cpp : 40) Writing GFA to /local/genbank/workspace/reads.uncorr.spades1//K77/assembly_graph_with_scaffolds.gfa 2:20:40.680 24G / 35G INFO General (contig_output.hpp : 22) Outputting contigs to /local/genbank/workspace/reads.uncorr.spades1//K77/before_rr.fasta 2:20:56.082 24G / 35G INFO General (contig_output_stage.cpp : 51) Outputting FastG graph to /local/genbank/workspace/reads.uncorr.spades1//K77/assembly_graph.fastg 2:21:25.964 24G / 35G INFO General (contig_output.hpp : 22) Outputting contigs to /local/genbank/workspace/reads.uncorr.spades1//K77/simplified_contigs.fasta 2:21:36.448 24G / 35G INFO General (contig_output.hpp : 22) Outputting contigs to /local/genbank/workspace/reads.uncorr.spades1//K77/final_contigs.fasta 2:21:46.970 24G / 35G INFO StageManager (stage.cpp : 132) STAGE == Contig Output 2:21:46.970 24G / 35G INFO General (contig_output_stage.cpp : 40) Writing GFA to /local/genbank/workspace/reads.uncorr.spades1//K77/assembly_graph_with_scaffolds.gfa 2:21:57.113 24G / 35G INFO General (contig_output.hpp : 22) Outputting contigs to /local/genbank/workspace/reads.uncorr.spades1//K77/before_rr.fasta 2:22:07.799 24G / 35G INFO General (contig_output_stage.cpp : 51) Outputting FastG graph to /local/genbank/workspace/reads.uncorr.spades1//K77/assembly_graph.fastg 2:22:37.603 24G / 35G INFO General (contig_output.hpp : 22) Outputting contigs to /local/genbank/workspace/reads.uncorr.spades1//K77/simplified_contigs.fasta 2:22:48.671 24G / 35G INFO General (contig_output.hpp : 22) Outputting contigs to /local/genbank/workspace/reads.uncorr.spades1//K77/final_contigs.fasta 2:22:59.456 24G / 35G INFO General (launch.hpp : 149) SPAdes finished 2:25:48.688 140M / 35G INFO General (main.cpp : 109) Assembling time: 2 hours 25 minutes 48 seconds == Running assembler: K99 0:00:00.000 4M / 4M INFO General (main.cpp : 74) Loaded config from /local/genbank/workspace/reads.uncorr.spades1/K99/configs/config.info 0:00:00.001 4M / 4M INFO General (memory_limit.cpp : 49) Memory limit set to 204 Gb 0:00:00.001 4M / 4M INFO General (main.cpp : 87) Starting SPAdes, built from refs/heads/spades_3.13.0, git revision 8ea46659e9b2aca35444a808db550ac333006f8b 0:00:00.001 4M / 4M INFO General (main.cpp : 88) Maximum k-mer length: 128 0:00:00.001 4M / 4M INFO General (main.cpp : 89) Assembling dataset (/local/genbank/workspace/reads.uncorr.spades1/dataset.info) with K=99 0:00:00.001 4M / 4M INFO General (main.cpp : 90) Maximum # of threads to use (adjusted due to OMP capabilities): 32 0:00:00.001 4M / 4M INFO General (launch.hpp : 51) SPAdes started 0:00:00.001 4M / 4M INFO General (launch.hpp : 58) Starting from stage: construction 0:00:00.001 4M / 4M INFO General (launch.hpp : 65) Two-step RR enabled: 0 0:00:00.001 4M / 4M INFO General (launch.hpp : 76) Will need read mapping, kmer mapper will be attached 0:00:00.001 4M / 4M INFO StageManager (stage.cpp : 132) STAGE == de Bruijn graph construction 0:00:00.006 4M / 4M INFO General (read_converter.hpp : 59) Binary reads detected 0:00:00.087 4M / 4M INFO General (construction.cpp : 111) Max read length 700 0:00:00.087 4M / 4M INFO General (construction.cpp : 117) Average read length 77.5334 0:00:00.087 4M / 4M INFO General (stage.cpp : 101) PROCEDURE == k+1-mer counting 0:00:00.090 4M / 4M INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 1024 files using 32 threads. This might take a while. 0:00:00.092 4M / 4M INFO General (file_limit.hpp : 32) Open file limit set to 4096 0:00:00.092 4M / 4M INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.12496 Gb 0:00:00.092 4M / 4M INFO General (kmer_splitters.hpp : 97) Using cell size of 16384 0:01:29.934 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 197448563 reads 0:02:31.676 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 621924902 reads 0:02:31.676 17G / 18G INFO General (kmer_splitters.hpp : 295) Adding contigs from previous K 0:08:45.386 132M / 18G INFO General (kmer_splitters.hpp : 308) Used 621924902 reads 0:08:45.386 132M / 18G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:11:18.774 132M / 18G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 484900009 kmers in total. 0:11:18.774 132M / 18G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:14:18.449 128M / 18G INFO General (stage.cpp : 101) PROCEDURE == Extension index construction 0:14:18.452 128M / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:14:18.452 128M / 18G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 512 files using 32 threads. This might take a while. 0:14:18.455 128M / 18G INFO General (file_limit.hpp : 32) Open file limit set to 4096 0:14:18.455 128M / 18G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.1237 Gb 0:14:18.455 128M / 18G INFO General (kmer_splitters.hpp : 97) Using cell size of 32768 0:14:25.772 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 4161149 kmers 0:14:31.398 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 8556077 kmers 0:14:36.809 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 13125520 kmers 0:14:43.446 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 19279939 kmers 0:14:48.900 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 23680618 kmers 0:14:54.633 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 28257030 kmers 0:15:01.339 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 34426922 kmers 0:15:06.754 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 38822778 kmers 0:15:12.347 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 43390201 kmers 0:15:19.028 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 49580455 kmers 0:15:24.503 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 53981701 kmers 0:15:30.131 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 58552614 kmers 0:15:37.048 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 64736688 kmers 0:15:43.258 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 69140133 kmers 0:15:48.689 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 73713229 kmers 0:15:55.604 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 79885570 kmers 0:16:01.108 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 84284680 kmers 0:17:00.710 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 134323104 kmers 0:19:41.183 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 270695082 kmers 0:23:57.027 17G / 18G INFO General (kmer_splitters.hpp : 385) Used 484903081 kmers. 0:24:00.871 132M / 18G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:26:30.681 132M / 18G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 496924072 kmers in total. 0:26:30.681 132M / 18G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:29:37.504 132M / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:30:39.321 328M / 18G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 0:33:33.707 328M / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 230438056 bytes occupied (3.70983 bits per kmer). 0:33:34.739 804M / 18G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 99) Building k-mer extensions from k+1-mers 0:34:04.582 804M / 18G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 103) Building k-mer extensions from k+1-mers finished. 0:34:04.589 804M / 18G INFO General (stage.cpp : 101) PROCEDURE == Condensing graph 0:34:04.810 804M / 18G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 355) Extracting unbranching paths 0:34:48.689 2G / 18G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 374) Extracting unbranching paths finished. 15812798 sequences extracted 0:35:15.985 2G / 18G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 310) Collecting perfect loops 0:35:26.931 2G / 18G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 343) Collecting perfect loops finished. 18 loops collected 0:36:06.135 7G / 18G INFO General (stage.cpp : 101) PROCEDURE == Filling coverage indices (PHM) 0:36:06.135 7G / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:36:06.135 7G / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:36:30.501 7G / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 224865604 bytes occupied (3.70989 bits per kmer). 0:36:33.575 9G / 18G INFO General (construction.cpp : 388) Collecting k-mer coverage information from reads, this takes a while. 0:37:11.039 9G / 18G INFO General (construction.cpp : 508) Filling coverage and flanking coverage from PHM 0:37:47.165 9G / 18G INFO General (construction.cpp : 464) Processed 31625588 edges 0:38:00.182 6G / 18G INFO StageManager (stage.cpp : 132) STAGE == EC Threshold Finding 0:38:00.190 6G / 18G INFO General (kmer_coverage_model.cpp : 181) Kmer coverage valley at: 78 0:38:00.190 6G / 18G INFO General (kmer_coverage_model.cpp : 201) K-mer histogram maximum: 80 0:38:00.191 6G / 18G INFO General (kmer_coverage_model.cpp : 237) Estimated median coverage: 81. Coverage mad: 2.9652 0:38:00.191 6G / 18G INFO General (kmer_coverage_model.cpp : 259) Fitting coverage model 0:38:00.448 6G / 18G INFO General (kmer_coverage_model.cpp : 295) ... iteration 2 0:38:00.924 6G / 18G INFO General (kmer_coverage_model.cpp : 295) ... iteration 4 0:38:01.778 6G / 18G INFO General (kmer_coverage_model.cpp : 295) ... iteration 8 0:38:03.400 6G / 18G INFO General (kmer_coverage_model.cpp : 295) ... iteration 16 0:38:07.541 6G / 18G INFO General (kmer_coverage_model.cpp : 295) ... iteration 32 0:38:19.855 6G / 18G INFO General (kmer_coverage_model.cpp : 295) ... iteration 64 0:38:23.669 6G / 18G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 17.1808. Fitted coverage std. dev: 2.40312 0:38:23.669 6G / 18G WARN General (kmer_coverage_model.cpp : 327) Valley value was estimated improperly, reset to 7 0:38:23.698 6G / 18G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 1 0:38:23.698 6G / 18G WARN General (kmer_coverage_model.cpp : 366) Failed to determine erroneous kmer threshold. Threshold set to: 7 0:38:23.698 6G / 18G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 19873661 0:38:23.698 6G / 18G INFO General (genomic_info_filler.cpp : 114) Failed to estimate mean coverage 0:38:23.698 6G / 18G INFO General (genomic_info_filler.cpp : 127) EC coverage threshold value was calculated as 7 0:38:23.698 6G / 18G INFO General (genomic_info_filler.cpp : 128) Trusted kmer low bound: 0 0:38:23.698 6G / 18G INFO StageManager (stage.cpp : 132) STAGE == Gap Closer 0:38:23.698 6G / 18G INFO General (graph_pack.hpp : 101) Index refill 0:38:23.705 6G / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:38:23.705 6G / 18G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 512 files using 32 threads. This might take a while. 0:38:23.707 6G / 18G INFO General (file_limit.hpp : 32) Open file limit set to 4096 0:38:23.707 6G / 18G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.05835 Gb 0:38:23.707 6G / 18G INFO General (kmer_splitters.hpp : 97) Using cell size of 32768 0:41:24.635 24G / 25G INFO General (edge_index_builders.hpp : 77) Processed 30908312 edges 0:41:32.256 24G / 25G INFO General (edge_index_builders.hpp : 77) Processed 31625620 edges 0:41:32.256 24G / 25G INFO General (edge_index_builders.hpp : 82) Used 31625620 sequences. 0:41:39.915 6G / 25G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:44:01.992 6G / 25G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 484900009 kmers in total. 0:44:01.992 6G / 25G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:47:02.246 6G / 25G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:48:04.130 6G / 25G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 0:50:51.428 6G / 25G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 224861016 bytes occupied (3.70981 bits per kmer). 0:51:07.808 17G / 25G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while. 0:51:31.521 17G / 25G INFO General (edge_index.hpp : 92) Index refilled 0:51:31.548 17G / 25G INFO General (gap_closer.cpp : 159) Preparing shift maps 0:52:58.609 21G / 25G INFO General (gap_closer.cpp : 119) Processing paired reads (takes a while) 0:53:11.490 22G / 25G INFO General (gap_closer.cpp : 138) Used 105822607 paired reads 0:53:11.490 22G / 25G INFO General (gap_closer.cpp : 140) Merging paired indices 0:54:07.367 17G / 25G INFO GapCloser (gap_closer.cpp : 346) Closing short gaps 0:57:45.546 17G / 25G INFO GapCloser (gap_closer.cpp : 380) Closing short gaps complete: filled 23174 gaps after checking 434952 candidates 0:58:20.828 17G / 25G INFO StageManager (stage.cpp : 132) STAGE == Raw Simplification 0:58:25.249 6G / 25G INFO General (simplification.cpp : 128) PROCEDURE == InitialCleaning 0:58:25.249 6G / 25G INFO General (simplification.cpp : 68) Most init cleaning disabled since detected mean 0 was less than activation coverage 10 0:58:25.250 6G / 25G INFO Simplification (parallel_processing.hpp : 165) Running Self conjugate edge remover 0:58:29.358 6G / 25G INFO Simplification (parallel_processing.hpp : 167) Self conjugate edge remover triggered 7 times 0:58:29.358 6G / 25G INFO StageManager (stage.cpp : 132) STAGE == Simplification 0:58:29.358 6G / 25G INFO General (simplification.cpp : 357) Graph simplification started 0:58:29.358 6G / 25G INFO General (graph_simplification.hpp : 634) Creating parallel br instance 0:58:29.359 6G / 25G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 1 0:58:29.359 6G / 25G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 1:00:19.433 6G / 25G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 1255195 times 1:00:19.433 6G / 25G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 1:08:00.466 11G / 25G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 298719 times 1:08:00.466 11G / 25G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 1:08:05.536 11G / 25G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 1455 times 1:08:05.536 11G / 25G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 2 1:08:05.536 11G / 25G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 1:08:06.789 11G / 25G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 6097 times 1:08:06.789 11G / 25G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 1:08:08.995 11G / 25G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 1253 times 1:08:08.995 11G / 25G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 1:08:10.988 11G / 25G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 13275 times 1:08:10.988 11G / 25G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 3 1:08:10.988 11G / 25G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 1:08:11.178 11G / 25G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 1766 times 1:08:11.178 11G / 25G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 1:08:18.440 11G / 25G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 4894 times 1:08:18.440 11G / 25G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 1:08:18.796 11G / 25G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 1625 times 1:08:18.796 11G / 25G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 4 1:08:18.796 11G / 25G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 1:08:18.835 11G / 25G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 162 times 1:08:18.835 11G / 25G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 1:08:19.811 11G / 25G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 612 times 1:08:19.811 11G / 25G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 1:08:19.908 11G / 25G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 709 times 1:08:19.908 11G / 25G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 5 1:08:19.908 11G / 25G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 1:08:19.913 11G / 25G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 20 times 1:08:19.913 11G / 25G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 1:08:20.215 11G / 25G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 210 times 1:08:20.215 11G / 25G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 1:08:20.348 11G / 25G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 542 times 1:08:20.348 11G / 25G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 6 1:08:20.348 11G / 25G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 1:08:20.352 11G / 25G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 21 times 1:08:20.352 11G / 25G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 1:08:20.575 11G / 25G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 175 times 1:08:20.575 11G / 25G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 1:08:20.629 11G / 25G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 288 times 1:08:20.629 11G / 25G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 7 1:08:20.629 11G / 25G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 1:08:20.631 11G / 25G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 7 times 1:08:20.631 11G / 25G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 1:08:20.739 11G / 25G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 66 times 1:08:20.739 11G / 25G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 1:08:20.763 11G / 25G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 180 times 1:08:20.763 11G / 25G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 8 1:08:20.763 11G / 25G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 1:08:20.764 11G / 25G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 5 times 1:08:20.764 11G / 25G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 1:08:20.841 11G / 25G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 57 times 1:08:20.841 11G / 25G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 1:08:20.862 11G / 25G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 126 times 1:08:20.862 11G / 25G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 9 1:08:20.862 11G / 25G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 1:08:20.863 11G / 25G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 2 times 1:08:20.863 11G / 25G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 1:08:20.883 11G / 25G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 19 times 1:08:20.883 11G / 25G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 1:08:20.900 11G / 25G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 105 times 1:08:20.900 11G / 25G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 10 1:08:20.900 11G / 25G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 1:08:20.901 11G / 25G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 2 times 1:08:20.901 11G / 25G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 1:08:20.923 11G / 25G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 19 times 1:08:20.923 11G / 25G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 1:08:20.932 11G / 25G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 81 times 1:08:20.932 11G / 25G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 11 1:08:20.932 11G / 25G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 1:08:23.691 11G / 25G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 113 times 1:08:23.691 11G / 25G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 1:08:26.110 11G / 25G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 30 times 1:08:26.110 11G / 25G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 1:08:28.444 11G / 25G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 1 times 1:08:28.444 11G / 25G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 12 1:08:28.444 11G / 25G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 1:08:28.444 11G / 25G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 1:08:28.444 11G / 25G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 1:08:28.444 11G / 25G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 1:08:28.444 11G / 25G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 1:08:28.444 11G / 25G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 1:08:28.445 11G / 25G INFO StageManager (stage.cpp : 132) STAGE == Gap Closer 1:08:28.445 11G / 25G INFO General (graph_pack.hpp : 101) Index refill 1:08:28.455 11G / 25G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 1:08:28.455 11G / 25G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 512 files using 32 threads. This might take a while. 1:08:28.457 11G / 25G INFO General (file_limit.hpp : 32) Open file limit set to 4096 1:08:28.457 11G / 25G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.00749 Gb 1:08:28.457 11G / 25G INFO General (kmer_splitters.hpp : 97) Using cell size of 32768 1:10:50.061 28G / 29G INFO General (edge_index_builders.hpp : 77) Processed 24671109 edges 1:10:50.062 28G / 29G INFO General (edge_index_builders.hpp : 82) Used 24671109 sequences. 1:10:56.519 11G / 29G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 1:12:51.369 11G / 29G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 385734298 kmers in total. 1:12:51.369 11G / 29G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 1:15:15.143 11G / 29G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 1:15:57.453 11G / 29G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 1:17:52.019 11G / 29G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 178873936 bytes occupied (3.70979 bits per kmer). 1:18:09.186 20G / 29G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while. 1:18:29.059 20G / 29G INFO General (edge_index.hpp : 92) Index refilled 1:18:29.085 20G / 29G INFO General (gap_closer.cpp : 159) Preparing shift maps 1:19:44.425 23G / 29G INFO General (gap_closer.cpp : 119) Processing paired reads (takes a while) 1:20:00.264 24G / 29G INFO General (gap_closer.cpp : 138) Used 105822607 paired reads 1:20:00.264 24G / 29G INFO General (gap_closer.cpp : 140) Merging paired indices 1:21:06.719 20G / 29G INFO GapCloser (gap_closer.cpp : 346) Closing short gaps 1:24:37.406 20G / 29G INFO GapCloser (gap_closer.cpp : 380) Closing short gaps complete: filled 464 gaps after checking 774613 candidates 1:25:02.109 20G / 29G INFO StageManager (stage.cpp : 132) STAGE == Simplification Cleanup 1:25:02.109 20G / 29G INFO General (simplification.cpp : 196) PROCEDURE == Post simplification 1:25:02.109 20G / 29G INFO General (graph_simplification.hpp : 453) Disconnection of relatively low covered edges disabled 1:25:02.109 20G / 29G INFO General (graph_simplification.hpp : 489) Complex tip clipping disabled 1:25:02.109 20G / 29G INFO General (graph_simplification.hpp : 634) Creating parallel br instance 1:25:02.109 20G / 29G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 1:25:06.344 20G / 29G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 1 times 1:25:06.344 20G / 29G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 1:25:09.760 20G / 29G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 1:25:09.760 20G / 29G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 1:25:14.089 20G / 29G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 1:25:14.089 20G / 29G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 1:25:17.563 20G / 29G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 1:25:17.563 20G / 29G INFO General (simplification.cpp : 330) Disrupting self-conjugate edges 1:26:11.003 20G / 29G INFO Simplification (parallel_processing.hpp : 165) Running Removing isolated edges 1:34:35.665 17G / 29G INFO Simplification (parallel_processing.hpp : 167) Removing isolated edges triggered 12230196 times 1:34:35.666 17G / 29G INFO General (simplification.cpp : 470) Counting average coverage 1:34:37.160 17G / 29G INFO General (simplification.cpp : 476) Average coverage = 1.54699 1:34:37.160 17G / 29G WARN General (simplification.cpp : 479) The determined erroneous connection coverage threshold may be determined improperly 1:34:37.160 17G / 29G INFO StageManager (stage.cpp : 132) STAGE == Contig Output 1:34:37.160 17G / 29G INFO General (contig_output_stage.cpp : 40) Writing GFA to /local/genbank/workspace/reads.uncorr.spades1//K99/assembly_graph_with_scaffolds.gfa 1:34:49.346 17G / 29G INFO General (contig_output.hpp : 22) Outputting contigs to /local/genbank/workspace/reads.uncorr.spades1//K99/before_rr.fasta 1:35:05.136 17G / 29G INFO General (contig_output_stage.cpp : 51) Outputting FastG graph to /local/genbank/workspace/reads.uncorr.spades1//K99/assembly_graph.fastg 1:35:52.397 17G / 29G INFO General (contig_output.hpp : 22) Outputting contigs to /local/genbank/workspace/reads.uncorr.spades1//K99/simplified_contigs.fasta 1:36:08.628 17G / 29G INFO General (contig_output.hpp : 22) Outputting contigs to /local/genbank/workspace/reads.uncorr.spades1//K99/final_contigs.fasta 1:36:24.622 17G / 29G INFO StageManager (stage.cpp : 132) STAGE == Contig Output 1:36:24.622 17G / 29G INFO General (contig_output_stage.cpp : 40) Writing GFA to /local/genbank/workspace/reads.uncorr.spades1//K99/assembly_graph_with_scaffolds.gfa 1:36:34.810 17G / 29G INFO General (contig_output.hpp : 22) Outputting contigs to /local/genbank/workspace/reads.uncorr.spades1//K99/before_rr.fasta 1:36:51.354 17G / 29G INFO General (contig_output_stage.cpp : 51) Outputting FastG graph to /local/genbank/workspace/reads.uncorr.spades1//K99/assembly_graph.fastg 1:37:37.811 17G / 29G INFO General (contig_output.hpp : 22) Outputting contigs to /local/genbank/workspace/reads.uncorr.spades1//K99/simplified_contigs.fasta 1:37:53.877 17G / 29G INFO General (contig_output.hpp : 22) Outputting contigs to /local/genbank/workspace/reads.uncorr.spades1//K99/final_contigs.fasta 1:38:09.140 17G / 29G INFO General (launch.hpp : 149) SPAdes finished 1:40:38.164 132M / 29G INFO General (main.cpp : 109) Assembling time: 1 hours 40 minutes 38 seconds == Running assembler: K127 0:00:00.000 4M / 4M INFO General (main.cpp : 74) Loaded config from /local/genbank/workspace/reads.uncorr.spades1/K127/configs/config.info 0:00:00.001 4M / 4M INFO General (memory_limit.cpp : 49) Memory limit set to 204 Gb 0:00:00.001 4M / 4M INFO General (main.cpp : 87) Starting SPAdes, built from refs/heads/spades_3.13.0, git revision 8ea46659e9b2aca35444a808db550ac333006f8b 0:00:00.001 4M / 4M INFO General (main.cpp : 88) Maximum k-mer length: 128 0:00:00.001 4M / 4M INFO General (main.cpp : 89) Assembling dataset (/local/genbank/workspace/reads.uncorr.spades1/dataset.info) with K=127 0:00:00.001 4M / 4M INFO General (main.cpp : 90) Maximum # of threads to use (adjusted due to OMP capabilities): 32 0:00:00.001 4M / 4M INFO General (launch.hpp : 51) SPAdes started 0:00:00.001 4M / 4M INFO General (launch.hpp : 58) Starting from stage: construction 0:00:00.001 4M / 4M INFO General (launch.hpp : 65) Two-step RR enabled: 0 0:00:00.001 4M / 4M INFO General (launch.hpp : 76) Will need read mapping, kmer mapper will be attached 0:00:00.001 4M / 4M INFO StageManager (stage.cpp : 132) STAGE == de Bruijn graph construction 0:00:00.007 4M / 4M INFO General (read_converter.hpp : 59) Binary reads detected 0:00:00.085 4M / 4M INFO General (construction.cpp : 111) Max read length 700 0:00:00.085 4M / 4M INFO General (construction.cpp : 117) Average read length 77.5334 0:00:00.085 4M / 4M INFO General (stage.cpp : 101) PROCEDURE == k+1-mer counting 0:00:00.089 4M / 4M INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 1024 files using 32 threads. This might take a while. 0:00:00.092 4M / 4M INFO General (file_limit.hpp : 32) Open file limit set to 4096 0:00:00.092 4M / 4M INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.12496 Gb 0:00:00.092 4M / 4M INFO General (kmer_splitters.hpp : 97) Using cell size of 16384 0:01:31.106 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 197832789 reads 0:02:11.332 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 621924902 reads 0:02:11.332 17G / 18G INFO General (kmer_splitters.hpp : 295) Adding contigs from previous K 0:08:34.897 132M / 18G INFO General (kmer_splitters.hpp : 308) Used 621924902 reads 0:08:34.897 132M / 18G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:11:03.532 132M / 18G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 468205614 kmers in total. 0:11:03.532 132M / 18G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:13:58.258 128M / 18G INFO General (stage.cpp : 101) PROCEDURE == Extension index construction 0:13:58.263 128M / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:13:58.263 128M / 18G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 512 files using 32 threads. This might take a while. 0:13:58.266 128M / 18G INFO General (file_limit.hpp : 32) Open file limit set to 4096 0:13:58.266 128M / 18G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.1237 Gb 0:13:58.266 128M / 18G INFO General (kmer_splitters.hpp : 97) Using cell size of 32768 0:14:06.599 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 4039457 kmers 0:14:12.405 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 8820416 kmers 0:14:17.663 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 13247865 kmers 0:14:23.702 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 18652643 kmers 0:14:29.124 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 23429935 kmers 0:14:34.761 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 27862498 kmers 0:14:40.537 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 33284343 kmers 0:14:46.239 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 38066354 kmers 0:14:51.699 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 42499389 kmers 0:14:57.812 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 47911992 kmers 0:15:03.384 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 52688663 kmers 0:15:08.956 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 57117125 kmers 0:15:15.022 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 62539939 kmers 0:15:21.526 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 67314898 kmers 0:15:26.733 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 71742530 kmers 0:15:33.073 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 77173294 kmers 0:15:39.214 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 81947860 kmers 0:16:43.068 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 135707194 kmers 0:19:25.066 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 272176226 kmers 0:23:17.331 17G / 18G INFO General (kmer_splitters.hpp : 385) Used 468208686 kmers. 0:23:21.565 132M / 18G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:26:37.386 132M / 18G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 468304023 kmers in total. 0:26:37.386 132M / 18G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:29:32.389 132M / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:30:32.208 332M / 18G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 0:32:55.377 332M / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 217168216 bytes occupied (3.70987 bits per kmer). 0:32:56.181 780M / 18G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 99) Building k-mer extensions from k+1-mers 0:33:24.583 780M / 18G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 103) Building k-mer extensions from k+1-mers finished. 0:33:24.592 780M / 18G INFO General (stage.cpp : 101) PROCEDURE == Condensing graph 0:33:24.795 780M / 18G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 355) Extracting unbranching paths 0:34:03.229 1G / 18G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 374) Extracting unbranching paths finished. 2944802 sequences extracted 0:34:26.661 1G / 18G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 310) Collecting perfect loops 0:34:37.044 1G / 18G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 343) Collecting perfect loops finished. 22 loops collected 0:34:44.093 1G / 18G INFO General (stage.cpp : 101) PROCEDURE == Filling coverage indices (PHM) 0:34:44.093 1G / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:34:44.093 1G / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:35:10.467 2G / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 217123912 bytes occupied (3.70989 bits per kmer). 0:35:13.412 3G / 18G INFO General (construction.cpp : 388) Collecting k-mer coverage information from reads, this takes a while. 0:35:46.826 3G / 18G INFO General (construction.cpp : 508) Filling coverage and flanking coverage from PHM 0:36:19.488 3G / 18G INFO General (construction.cpp : 464) Processed 5889638 edges 0:36:33.258 1G / 18G INFO StageManager (stage.cpp : 132) STAGE == EC Threshold Finding 0:36:33.265 1G / 18G INFO General (kmer_coverage_model.cpp : 181) Kmer coverage valley at: 58 0:36:33.265 1G / 18G INFO General (kmer_coverage_model.cpp : 201) K-mer histogram maximum: 60 0:36:33.265 1G / 18G INFO General (kmer_coverage_model.cpp : 237) Estimated median coverage: 61. Coverage mad: 2.9652 0:36:33.265 1G / 18G INFO General (kmer_coverage_model.cpp : 259) Fitting coverage model 0:36:33.464 1G / 18G INFO General (kmer_coverage_model.cpp : 295) ... iteration 2 0:36:33.731 1G / 18G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 76.1403. Fitted coverage std. dev: 3.47774 0:36:33.743 1G / 18G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 1 0:36:33.743 1G / 18G WARN General (kmer_coverage_model.cpp : 366) Failed to determine erroneous kmer threshold. Threshold set to: 58 0:36:33.743 1G / 18G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 16417 0:36:33.744 1G / 18G INFO General (genomic_info_filler.cpp : 114) Failed to estimate mean coverage 0:36:33.744 1G / 18G INFO General (genomic_info_filler.cpp : 127) EC coverage threshold value was calculated as 58 0:36:33.744 1G / 18G INFO General (genomic_info_filler.cpp : 128) Trusted kmer low bound: 0 0:36:33.744 1G / 18G INFO StageManager (stage.cpp : 132) STAGE == Gap Closer 0:36:33.744 1G / 18G INFO General (graph_pack.hpp : 101) Index refill 0:36:33.749 1G / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:36:33.749 1G / 18G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 512 files using 32 threads. This might take a while. 0:36:33.754 1G / 18G INFO General (file_limit.hpp : 32) Open file limit set to 4096 0:36:33.754 1G / 18G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.11267 Gb 0:36:33.754 1G / 18G INFO General (kmer_splitters.hpp : 97) Using cell size of 32768 0:39:18.962 18G / 19G INFO General (edge_index_builders.hpp : 77) Processed 5889638 edges 0:39:18.962 18G / 19G INFO General (edge_index_builders.hpp : 82) Used 5889638 sequences. 0:39:26.850 1G / 19G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:41:42.573 1G / 19G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 468205614 kmers in total. 0:41:42.573 1G / 19G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:44:37.692 1G / 19G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:45:33.939 1G / 19G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 0:47:51.139 1G / 19G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 217121208 bytes occupied (3.70984 bits per kmer). 0:48:01.899 11G / 19G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while. 0:48:20.626 11G / 19G INFO General (edge_index.hpp : 92) Index refilled 0:48:20.650 11G / 19G INFO General (gap_closer.cpp : 159) Preparing shift maps 0:48:28.309 12G / 19G INFO General (gap_closer.cpp : 119) Processing paired reads (takes a while) 0:48:35.120 12G / 19G INFO General (gap_closer.cpp : 138) Used 105822607 paired reads 0:48:35.120 12G / 19G INFO General (gap_closer.cpp : 140) Merging paired indices 0:48:37.583 11G / 19G INFO GapCloser (gap_closer.cpp : 346) Closing short gaps 0:48:55.870 11G / 19G INFO GapCloser (gap_closer.cpp : 380) Closing short gaps complete: filled 0 gaps after checking 0 candidates 0:48:56.410 11G / 19G INFO StageManager (stage.cpp : 132) STAGE == Raw Simplification 0:48:58.342 1G / 19G INFO General (simplification.cpp : 128) PROCEDURE == InitialCleaning 0:48:58.343 1G / 19G INFO General (simplification.cpp : 68) Most init cleaning disabled since detected mean 0 was less than activation coverage 10 0:48:58.343 1G / 19G INFO Simplification (parallel_processing.hpp : 165) Running Self conjugate edge remover 0:48:58.839 1G / 19G INFO Simplification (parallel_processing.hpp : 167) Self conjugate edge remover triggered 1 times 0:48:58.839 1G / 19G INFO StageManager (stage.cpp : 132) STAGE == Simplification 0:48:58.839 1G / 19G INFO General (simplification.cpp : 357) Graph simplification started 0:48:58.840 1G / 19G INFO General (graph_simplification.hpp : 634) Creating parallel br instance 0:48:58.841 1G / 19G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 1 0:48:58.842 1G / 19G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:50:00.722 1G / 19G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 1062759 times 0:50:00.722 1G / 19G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:54:40.361 4G / 19G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 166411 times 0:54:40.362 4G / 19G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:54:43.837 4G / 19G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 13409 times 0:54:43.838 4G / 19G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 2 0:54:43.838 4G / 19G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:54:46.405 4G / 19G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 5713 times 0:54:46.405 4G / 19G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:54:47.437 4G / 19G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 454 times 0:54:47.437 4G / 19G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:54:47.497 4G / 19G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 190 times 0:54:47.497 4G / 19G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 3 0:54:47.497 4G / 19G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:54:47.499 4G / 19G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 9 times 0:54:47.499 4G / 19G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:54:47.558 4G / 19G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 34 times 0:54:47.558 4G / 19G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:54:47.568 4G / 19G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 54 times 0:54:47.568 4G / 19G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 4 0:54:47.568 4G / 19G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:54:47.568 4G / 19G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:54:47.568 4G / 19G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:54:47.572 4G / 19G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 2 times 0:54:47.572 4G / 19G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:54:47.577 4G / 19G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 31 times 0:54:47.577 4G / 19G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 5 0:54:47.577 4G / 19G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:54:47.577 4G / 19G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 1 times 0:54:47.577 4G / 19G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:54:47.580 4G / 19G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 2 times 0:54:47.580 4G / 19G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:54:47.582 4G / 19G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 11 times 0:54:47.582 4G / 19G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 6 0:54:47.582 4G / 19G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:54:47.582 4G / 19G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:54:47.582 4G / 19G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:54:47.582 4G / 19G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:54:47.582 4G / 19G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:54:47.583 4G / 19G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 12 times 0:54:47.583 4G / 19G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 7 0:54:47.583 4G / 19G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:54:47.584 4G / 19G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:54:47.584 4G / 19G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:54:47.589 4G / 19G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 3 times 0:54:47.589 4G / 19G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:54:47.590 4G / 19G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 8 times 0:54:47.590 4G / 19G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 8 0:54:47.590 4G / 19G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:54:47.590 4G / 19G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:54:47.590 4G / 19G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:54:47.590 4G / 19G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:54:47.590 4G / 19G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:54:47.591 4G / 19G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 4 times 0:54:47.591 4G / 19G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 9 0:54:47.591 4G / 19G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:54:47.591 4G / 19G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:54:47.591 4G / 19G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:54:47.591 4G / 19G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:54:47.591 4G / 19G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:54:47.592 4G / 19G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 5 times 0:54:47.592 4G / 19G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 10 0:54:47.592 4G / 19G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:54:47.592 4G / 19G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:54:47.592 4G / 19G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:54:47.593 4G / 19G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 1 times 0:54:47.593 4G / 19G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:54:47.596 4G / 19G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 4 times 0:54:47.597 4G / 19G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 11 0:54:47.597 4G / 19G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:54:47.751 4G / 19G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 8 times 0:54:47.751 4G / 19G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:54:47.876 4G / 19G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:54:47.876 4G / 19G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:54:48.001 4G / 19G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:54:48.001 4G / 19G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 12 0:54:48.001 4G / 19G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:54:48.001 4G / 19G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:54:48.001 4G / 19G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:54:48.001 4G / 19G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:54:48.001 4G / 19G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:54:48.001 4G / 19G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:54:48.001 4G / 19G INFO StageManager (stage.cpp : 132) STAGE == Gap Closer 0:54:48.001 4G / 19G INFO General (graph_pack.hpp : 101) Index refill 0:54:48.013 4G / 19G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:54:48.013 4G / 19G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 512 files using 32 threads. This might take a while. 0:54:48.015 4G / 19G INFO General (file_limit.hpp : 32) Open file limit set to 4096 0:54:48.015 4G / 19G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.07833 Gb 0:54:48.015 4G / 19G INFO General (kmer_splitters.hpp : 97) Using cell size of 32768 0:57:00.986 22G / 22G INFO General (edge_index_builders.hpp : 77) Processed 564997 edges 0:57:00.987 22G / 22G INFO General (edge_index_builders.hpp : 82) Used 564997 sequences. 0:57:07.159 4G / 22G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:58:54.872 4G / 22G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 369889907 kmers in total. 0:58:54.872 4G / 22G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 1:01:12.296 4G / 22G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 1:01:58.483 4G / 22G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 1:03:48.757 4G / 22G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 171530818 bytes occupied (3.70988 bits per kmer). 1:03:59.365 12G / 22G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while. 1:04:13.242 12G / 22G INFO General (edge_index.hpp : 92) Index refilled 1:04:13.271 12G / 22G INFO General (gap_closer.cpp : 159) Preparing shift maps 1:04:15.108 13G / 22G INFO General (gap_closer.cpp : 119) Processing paired reads (takes a while) 1:04:20.468 13G / 22G INFO General (gap_closer.cpp : 138) Used 105822607 paired reads 1:04:20.468 13G / 22G INFO General (gap_closer.cpp : 140) Merging paired indices 1:04:21.018 12G / 22G INFO GapCloser (gap_closer.cpp : 346) Closing short gaps 1:04:22.758 12G / 22G INFO GapCloser (gap_closer.cpp : 380) Closing short gaps complete: filled 0 gaps after checking 0 candidates 1:04:22.888 12G / 22G INFO StageManager (stage.cpp : 132) STAGE == Simplification Cleanup 1:04:22.889 12G / 22G INFO General (simplification.cpp : 196) PROCEDURE == Post simplification 1:04:22.889 12G / 22G INFO General (graph_simplification.hpp : 453) Disconnection of relatively low covered edges disabled 1:04:22.889 12G / 22G INFO General (graph_simplification.hpp : 489) Complex tip clipping disabled 1:04:22.889 12G / 22G INFO General (graph_simplification.hpp : 634) Creating parallel br instance 1:04:22.889 12G / 22G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 1:04:23.118 12G / 22G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 1:04:23.118 12G / 22G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 1:04:23.239 12G / 22G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 1:04:23.239 12G / 22G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 1:04:23.369 12G / 22G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 1:04:23.369 12G / 22G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 1:04:23.488 12G / 22G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 1:04:23.488 12G / 22G INFO General (simplification.cpp : 330) Disrupting self-conjugate edges 1:04:24.451 12G / 22G INFO Simplification (parallel_processing.hpp : 165) Running Removing isolated edges 1:07:10.416 12G / 22G INFO Simplification (parallel_processing.hpp : 167) Removing isolated edges triggered 183899 times 1:07:10.416 12G / 22G INFO General (simplification.cpp : 470) Counting average coverage 1:07:11.605 12G / 22G INFO General (simplification.cpp : 476) Average coverage = 1.30069 1:07:11.605 12G / 22G WARN General (simplification.cpp : 479) The determined erroneous connection coverage threshold may be determined improperly 1:07:11.605 12G / 22G INFO StageManager (stage.cpp : 132) STAGE == Mismatch Correction 1:07:11.605 12G / 22G INFO General (graph_pack.hpp : 109) Normalizing k-mer map. Total 44485668 kmers to process 1:09:00.677 12G / 22G INFO General (graph_pack.hpp : 111) Normalizing done 1:38:17.623 46G / 46G INFO General (mismatch_shall_not_pass.hp: 189) Finished collecting potential mismatches positions 1:44:44.051 13G / 46G INFO General (mismatch_shall_not_pass.hp: 290) All edges processed 1:44:50.264 12G / 46G INFO General (mismatch_correction.cpp : 27) Corrected 94 nucleotides 1:44:50.270 12G / 46G INFO StageManager (stage.cpp : 132) STAGE == Contig Output 1:44:50.270 12G / 46G INFO General (contig_output_stage.cpp : 40) Writing GFA to /local/genbank/workspace/reads.uncorr.spades1//K127/assembly_graph_with_scaffolds.gfa 1:45:03.527 12G / 46G INFO General (contig_output.hpp : 22) Outputting contigs to /local/genbank/workspace/reads.uncorr.spades1//K127/before_rr.fasta 1:45:18.941 12G / 46G INFO General (contig_output_stage.cpp : 51) Outputting FastG graph to /local/genbank/workspace/reads.uncorr.spades1//K127/assembly_graph.fastg 1:46:03.789 12G / 46G INFO General (contig_output.hpp : 22) Outputting contigs to /local/genbank/workspace/reads.uncorr.spades1//K127/simplified_contigs.fasta 1:46:19.150 12G / 46G INFO General (contig_output.hpp : 22) Outputting contigs to /local/genbank/workspace/reads.uncorr.spades1//K127/intermediate_contigs.fasta 1:46:34.393 12G / 46G INFO StageManager (stage.cpp : 132) STAGE == Paired Information Counting 1:46:35.888 12G / 46G INFO General (graph_pack.hpp : 109) Normalizing k-mer map. Total 44505508 kmers to process 1:48:31.715 12G / 46G INFO General (graph_pack.hpp : 111) Normalizing done 1:48:32.210 12G / 46G INFO General (pair_info_count.cpp : 320) Min edge length for estimation: 5214 1:48:32.210 12G / 46G INFO General (pair_info_count.cpp : 331) Estimating insert size for library #0 1:48:32.210 12G / 46G INFO General (pair_info_count.cpp : 190) Estimating insert size (takes a while) 1:48:33.625 13G / 46G INFO General (pair_info_count.cpp : 39) Selecting usual mapper 1:48:41.036 13G / 46G INFO General (sequence_mapper_notifier.h: 80) Processed 200000 reads 1:48:41.231 13G / 46G INFO General (sequence_mapper_notifier.h: 80) Processed 400000 reads 1:48:41.300 13G / 46G INFO General (sequence_mapper_notifier.h: 80) Processed 600000 reads 1:48:41.388 13G / 46G INFO General (sequence_mapper_notifier.h: 80) Processed 800000 reads 1:48:41.498 13G / 46G INFO General (sequence_mapper_notifier.h: 80) Processed 1000000 reads 1:48:41.605 13G / 46G INFO General (sequence_mapper_notifier.h: 80) Processed 1200000 reads 1:48:42.575 13G / 46G INFO General (sequence_mapper_notifier.h: 80) Processed 2200000 reads 1:48:43.973 13G / 46G INFO General (sequence_mapper_notifier.h: 80) Processed 4200000 reads 1:48:47.540 13G / 46G INFO General (sequence_mapper_notifier.h: 80) Processed 8400000 reads 1:48:58.480 13G / 46G INFO General (sequence_mapper_notifier.h: 80) Processed 16800000 reads 1:49:17.907 13G / 46G INFO General (sequence_mapper_notifier.h: 80) Processed 33600000 reads 1:50:00.229 13G / 46G INFO General (sequence_mapper_notifier.h: 80) Processed 67200000 reads 1:50:48.557 13G / 46G INFO General (sequence_mapper_notifier.h: 98) Total 105822607 reads processed 1:50:49.727 13G / 46G INFO General (pair_info_count.cpp : 209) Edge pairs: 67108864 (rough upper limit) 1:50:49.728 13G / 46G INFO General (pair_info_count.cpp : 213) 0 paired reads (0% of all) aligned to long edges 1:50:49.926 12G / 46G WARN General (pair_info_count.cpp : 339) Unable to estimate insert size for paired library #0 1:50:49.926 12G / 46G WARN General (pair_info_count.cpp : 345) None of paired reads aligned properly. Please, check orientation of your read pairs. 1:50:49.926 12G / 46G INFO StageManager (stage.cpp : 132) STAGE == Distance Estimation 1:50:49.926 12G / 46G INFO General (distance_estimation.cpp : 182) Clearing raw paired index 1:50:49.926 12G / 46G INFO StageManager (stage.cpp : 132) STAGE == Repeat Resolving 1:50:49.926 12G / 46G WARN General (repeat_resolving.cpp : 63) Insert size was not estimated for any of the paired libraries, repeat resolution module will not run. 1:50:49.926 12G / 46G INFO StageManager (stage.cpp : 132) STAGE == Contig Output 1:50:49.926 12G / 46G INFO General (contig_output_stage.cpp : 40) Writing GFA to /local/genbank/workspace/reads.uncorr.spades1//K127/assembly_graph_with_scaffolds.gfa 1:51:03.019 12G / 46G INFO General (contig_output.hpp : 22) Outputting contigs to /local/genbank/workspace/reads.uncorr.spades1//K127/before_rr.fasta 1:51:18.633 12G / 46G INFO General (contig_output_stage.cpp : 51) Outputting FastG graph to /local/genbank/workspace/reads.uncorr.spades1//K127/assembly_graph.fastg 1:52:05.322 12G / 46G INFO General (contig_output.hpp : 22) Outputting contigs to /local/genbank/workspace/reads.uncorr.spades1//K127/simplified_contigs.fasta 1:52:21.117 12G / 46G INFO General (contig_output.hpp : 22) Outputting contigs to /local/genbank/workspace/reads.uncorr.spades1//K127/final_contigs.fasta 1:52:36.572 12G / 46G INFO General (launch.hpp : 149) SPAdes finished 1:53:51.892 132M / 46G INFO General (main.cpp : 109) Assembling time: 1 hours 53 minutes 51 seconds ===== Assembling finished. Used k-mer sizes: 21, 33, 55, 77, 99, 127 * Corrected reads are in /local/genbank/workspace/reads.uncorr.spades1/corrected/ * Assembled contigs are in /local/genbank/workspace/reads.uncorr.spades1/contigs.fasta * Assembly graph is in /local/genbank/workspace/reads.uncorr.spades1/assembly_graph.fastg * Assembly graph in GFA format is in /local/genbank/workspace/reads.uncorr.spades1/assembly_graph_with_scaffolds.gfa ======= SPAdes pipeline finished WITH WARNINGS! === Error correction and assembling warnings: * 2:23:19.778 16G / 23G WARN General (kmer_coverage_model.cpp : 327) Valley value was estimated improperly, reset to 2 * 2:23:19.804 16G / 23G WARN General (kmer_coverage_model.cpp : 366) Failed to determine erroneous kmer threshold. Threshold set to: 2 * 1:27:55.800 9G / 18G WARN General (kmer_coverage_model.cpp : 218) Too many erroneous kmers, the estimates might be unreliable * 1:29:36.746 9G / 18G WARN General (kmer_coverage_model.cpp : 327) Valley value was estimated improperly, reset to 12 * 1:29:36.772 9G / 18G WARN General (kmer_coverage_model.cpp : 366) Failed to determine erroneous kmer threshold. Threshold set to: 12 * 1:02:38.808 19G / 26G WARN General (kmer_coverage_model.cpp : 366) Failed to determine erroneous kmer threshold. Threshold set to: 212 * 3:07:06.080 28G / 54G WARN General (simplification.cpp : 479) The determined erroneous connection coverage threshold may be determined improperly * 0:48:10.125 10G / 18G WARN General (kmer_coverage_model.cpp : 366) Failed to determine erroneous kmer threshold. Threshold set to: 127 * 0:38:23.669 6G / 18G WARN General (kmer_coverage_model.cpp : 327) Valley value was estimated improperly, reset to 7 * 0:38:23.698 6G / 18G WARN General (kmer_coverage_model.cpp : 366) Failed to determine erroneous kmer threshold. Threshold set to: 7 * 0:36:33.743 1G / 18G WARN General (kmer_coverage_model.cpp : 366) Failed to determine erroneous kmer threshold. Threshold set to: 58 * 1:50:49.926 12G / 46G WARN General (pair_info_count.cpp : 339) Unable to estimate insert size for paired library #0 * 1:50:49.926 12G / 46G WARN General (pair_info_count.cpp : 345) None of paired reads aligned properly. Please, check orientation of your read pairs. * 1:50:49.926 12G / 46G WARN General (repeat_resolving.cpp : 63) Insert size was not estimated for any of the paired libraries, repeat resolution module will not run. ======= Warnings saved to /local/genbank/workspace/reads.uncorr.spades1/warnings.log SPAdes log can be found here: /local/genbank/workspace/reads.uncorr.spades1/spades.log Thank you for using SPAdes!