Command line: /home/psgendb/BIRCHDEV/bin-linux-x86_64/spades.py -1 /local/genbank/workspace/reads.all3/20090202_7_R1.fq -2 /local/genbank/workspace/reads.all3/20090202_7_R2.fq -1 /local/genbank/workspace/reads.all3/20090202_8_R1.fq -2 /local/genbank/workspace/reads.all3/20090202_8_R2.fq -1 /local/genbank/workspace/reads.all3/AB2kb_R1.fq -2 /local/genbank/workspace/reads.all3/AB2kb_R2.fq -1 /local/genbank/workspace/reads.all3/AB4kb_R1.fq -2 /local/genbank/workspace/reads.all3/AB4kb_R2.fq -1 /local/genbank/workspace/reads.all3/Algae6.2_6_R1.fq -2 /local/genbank/workspace/reads.all3/Algae6.2_6_R2.fq -1 /local/genbank/workspace/reads.all3/Algae6.2_7_R1.fq -2 /local/genbank/workspace/reads.all3/Algae6.2_7_R2.fq -1 /local/genbank/workspace/reads.all3/Algae6.2_8_R1.fq -2 /local/genbank/workspace/reads.all3/Algae6.2_8_R2.fq -1 /local/genbank/workspace/reads.all3/Algae7.2GB_6_R1.fq -2 /local/genbank/workspace/reads.all3/Algae7.2GB_6_R2.fq -1 /local/genbank/workspace/reads.all3/Algae7.2GB_7_R1.fq -2 /local/genbank/workspace/reads.all3/Algae7.2GB_7_R2.fq -1 /local/genbank/workspace/reads.all3/Algae7.2GB_8_R1.fq -2 /local/genbank/workspace/reads.all3/Algae7.2GB_8_R2.fq -s /local/genbank/workspace/reads.all3/2008-09allU.fq -s /local/genbank/workspace/reads.all3/3-6.2-7.2GBallU.fq -s /local/genbank/workspace/reads.all3/AGRFUall.fq -s /local/genbank/workspace/reads.all3/454U.fq --only-assembler -m 130 -t 32 -o /local/genbank/workspace/reads.all3.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.all3.spades1 Mode: ONLY assembling (without read error correction) 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.all3/20090202_7_R1.fq', '/local/genbank/workspace/reads.all3/20090202_8_R1.fq', '/local/genbank/workspace/reads.all3/AB2kb_R1.fq', '/local/genbank/workspace/reads.all3/AB4kb_R1.fq', '/local/genbank/workspace/reads.all3/Algae6.2_6_R1.fq', '/local/genbank/workspace/reads.all3/Algae6.2_7_R1.fq', '/local/genbank/workspace/reads.all3/Algae6.2_8_R1.fq', '/local/genbank/workspace/reads.all3/Algae7.2GB_6_R1.fq', '/local/genbank/workspace/reads.all3/Algae7.2GB_7_R1.fq', '/local/genbank/workspace/reads.all3/Algae7.2GB_8_R1.fq'] right reads: ['/local/genbank/workspace/reads.all3/20090202_7_R2.fq', '/local/genbank/workspace/reads.all3/20090202_8_R2.fq', '/local/genbank/workspace/reads.all3/AB2kb_R2.fq', '/local/genbank/workspace/reads.all3/AB4kb_R2.fq', '/local/genbank/workspace/reads.all3/Algae6.2_6_R2.fq', '/local/genbank/workspace/reads.all3/Algae6.2_7_R2.fq', '/local/genbank/workspace/reads.all3/Algae6.2_8_R2.fq', '/local/genbank/workspace/reads.all3/Algae7.2GB_6_R2.fq', '/local/genbank/workspace/reads.all3/Algae7.2GB_7_R2.fq', '/local/genbank/workspace/reads.all3/Algae7.2GB_8_R2.fq'] interlaced reads: not specified single reads: ['/local/genbank/workspace/reads.all3/2008-09allU.fq', '/local/genbank/workspace/reads.all3/3-6.2-7.2GBallU.fq', '/local/genbank/workspace/reads.all3/AGRFUall.fq', '/local/genbank/workspace/reads.all3/454U.fq'] merged reads: not specified 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.all3.spades1/tmp Threads: 32 Memory limit (in Gb): 130 ======= SPAdes pipeline started. Log can be found here: /local/genbank/workspace/reads.all3.spades1/spades.log ===== Assembling started. == Running assembler: K21 0:00:00.000 4M / 4M INFO General (main.cpp : 74) Loaded config from /local/genbank/workspace/reads.all3.spades1/K21/configs/config.info 0:00:00.000 4M / 4M INFO General (memory_limit.cpp : 49) Memory limit set to 130 Gb 0:00:00.000 4M / 4M INFO General (main.cpp : 87) Starting SPAdes, built from refs/heads/spades_3.13.0, git revision 8ea46659e9b2aca35444a808db550ac333006f8b 0:00:00.000 4M / 4M INFO General (main.cpp : 88) Maximum k-mer length: 128 0:00:00.000 4M / 4M INFO General (main.cpp : 89) Assembling dataset (/local/genbank/workspace/reads.all3.spades1/dataset.info) with K=21 0:00:00.000 4M / 4M INFO General (main.cpp : 90) Maximum # of threads to use (adjusted due to OMP capabilities): 32 0:00:00.000 4M / 4M INFO General (launch.hpp : 51) SPAdes started 0:00:00.000 4M / 4M INFO General (launch.hpp : 58) Starting from stage: construction 0:00:00.000 4M / 4M INFO General (launch.hpp : 65) Two-step RR enabled: 0 0:00:00.000 4M / 4M INFO StageManager (stage.cpp : 132) STAGE == de Bruijn graph construction 0:00:00.005 4M / 4M INFO General (read_converter.hpp : 77) Converting reads to binary format for library #0 (takes a while) 0:00:00.005 4M / 4M INFO General (read_converter.hpp : 78) Converting paired reads 0:00:00.276 76M / 76M INFO General (binary_converter.hpp : 93) 16384 reads processed 0:00:00.426 84M / 84M INFO General (binary_converter.hpp : 93) 32768 reads processed 0:00:00.726 104M / 104M INFO General (binary_converter.hpp : 93) 65536 reads processed 0:00:01.325 136M / 136M INFO General (binary_converter.hpp : 93) 131072 reads processed 0:00:02.532 208M / 208M INFO General (binary_converter.hpp : 93) 262144 reads processed 0:00:04.935 344M / 344M INFO General (binary_converter.hpp : 93) 524288 reads processed 0:00:12.215 564M / 564M INFO General (binary_converter.hpp : 93) 1048576 reads processed 0:00:25.043 596M / 596M INFO General (binary_converter.hpp : 93) 2097152 reads processed 0:00:52.898 844M / 848M INFO General (binary_converter.hpp : 93) 4194304 reads processed 0:01:54.493 868M / 880M INFO General (binary_converter.hpp : 93) 8388608 reads processed 0:03:57.827 940M / 952M INFO General (binary_converter.hpp : 93) 16777216 reads processed 0:08:08.182 868M / 952M INFO General (binary_converter.hpp : 93) 33554432 reads processed 0:15:57.424 668M / 952M INFO General (binary_converter.hpp : 93) 67108864 reads processed 0:18:59.169 516M / 952M INFO General (binary_converter.hpp : 117) 80455197 reads written 0:19:00.362 8M / 952M INFO General (read_converter.hpp : 87) Converting single reads 0:19:00.623 136M / 952M INFO General (binary_converter.hpp : 93) 16384 reads processed 0:19:00.695 140M / 952M INFO General (binary_converter.hpp : 93) 32768 reads processed 0:19:00.841 148M / 952M INFO General (binary_converter.hpp : 93) 65536 reads processed 0:19:01.133 168M / 952M INFO General (binary_converter.hpp : 93) 131072 reads processed 0:19:01.719 204M / 952M INFO General (binary_converter.hpp : 93) 262144 reads processed 0:19:02.893 272M / 952M INFO General (binary_converter.hpp : 93) 524288 reads processed 0:19:05.239 412M / 952M INFO General (binary_converter.hpp : 93) 1048576 reads processed 0:19:09.752 700M / 952M INFO General (binary_converter.hpp : 93) 2097152 reads processed 0:19:18.602 1G / 1G INFO General (binary_converter.hpp : 93) 4194304 reads processed 0:19:41.503 1G / 1G INFO General (binary_converter.hpp : 93) 8388608 reads processed 0:20:27.623 1G / 1G INFO General (binary_converter.hpp : 93) 16777216 reads processed 0:22:00.792 1G / 1G INFO General (binary_converter.hpp : 93) 33554432 reads processed 0:24:07.393 2G / 3G INFO General (binary_converter.hpp : 117) 48800134 reads written 0:24:11.472 12M / 3G INFO General (read_converter.hpp : 95) Converting merged reads 0:24:11.690 140M / 3G INFO General (binary_converter.hpp : 117) 0 reads written 0:24:13.877 8M / 3G INFO General (construction.cpp : 111) Max read length 700 0:24:13.877 8M / 3G INFO General (construction.cpp : 117) Average read length 80.6457 0:24:13.877 8M / 3G INFO General (stage.cpp : 101) PROCEDURE == k+1-mer counting 0:24:13.880 8M / 3G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 1024 files using 32 threads. This might take a while. 0:24:13.882 8M / 3G INFO General (file_limit.hpp : 32) Open file limit set to 4096 0:24:13.882 8M / 3G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 1.35409 Gb 0:24:13.882 8M / 3G INFO General (kmer_splitters.hpp : 97) Using cell size of 65536 0:24:31.096 17G / 17G INFO General (kmer_splitters.hpp : 289) Processed 10601247 reads 0:24:45.090 17G / 17G INFO General (kmer_splitters.hpp : 289) Processed 21424968 reads 0:24:57.763 17G / 17G INFO General (kmer_splitters.hpp : 289) Processed 32206986 reads 0:25:12.402 17G / 17G INFO General (kmer_splitters.hpp : 289) Processed 45734457 reads 0:25:29.807 17G / 17G INFO General (kmer_splitters.hpp : 289) Processed 63814278 reads 0:25:41.462 17G / 17G INFO General (kmer_splitters.hpp : 289) Processed 73443147 reads 0:25:50.146 17G / 17G INFO General (kmer_splitters.hpp : 289) Processed 78998923 reads 0:25:58.479 17G / 17G INFO General (kmer_splitters.hpp : 289) Processed 84402488 reads 0:26:09.602 17G / 17G INFO General (kmer_splitters.hpp : 289) Processed 92572111 reads 0:26:14.078 17G / 17G INFO General (kmer_splitters.hpp : 289) Processed 93662144 reads 0:26:33.276 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 98992799 reads 0:26:54.070 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 116778066 reads 0:27:18.234 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 136796419 reads 0:30:33.895 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 272177961 reads 0:33:25.997 17G / 18G INFO General (kmer_splitters.hpp : 295) Adding contigs from previous K 0:33:29.114 132M / 18G INFO General (kmer_splitters.hpp : 308) Used 419421056 reads 0:33:29.114 132M / 18G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:35:05.057 132M / 18G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 913442405 kmers in total. 0:35:05.058 132M / 18G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:36:24.511 128M / 18G INFO General (stage.cpp : 101) PROCEDURE == Extension index construction 0:36:24.513 128M / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:36:24.513 128M / 18G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 512 files using 32 threads. This might take a while. 0:36:24.515 128M / 18G INFO General (file_limit.hpp : 32) Open file limit set to 4096 0:36:24.515 128M / 18G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 1.35286 Gb 0:36:24.515 128M / 18G INFO General (kmer_splitters.hpp : 97) Using cell size of 131072 0:36:30.201 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 4910630 kmers 0:36:37.099 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 33321137 kmers 0:36:43.980 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 61864794 kmers 0:36:50.878 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 90404061 kmers 0:36:57.898 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 118958044 kmers 0:37:04.826 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 147502295 kmers 0:37:11.888 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 176050668 kmers 0:37:18.925 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 204589391 kmers 0:37:26.049 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 233129894 kmers 0:37:32.981 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 261665737 kmers 0:37:40.184 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 290209551 kmers 0:37:47.158 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 318746623 kmers 0:37:54.106 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 347292121 kmers 0:38:01.088 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 375835576 kmers 0:38:07.991 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 404383785 kmers 0:38:14.981 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 432930083 kmers 0:38:21.869 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 461471794 kmers 0:38:28.824 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 490006940 kmers 0:38:35.739 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 518561339 kmers 0:38:42.928 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 547106890 kmers 0:40:12.232 17G / 18G INFO General (kmer_splitters.hpp : 385) Used 913443429 kmers. 0:40:16.047 128M / 18G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:41:27.928 128M / 18G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 898427045 kmers in total. 0:41:27.929 128M / 18G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:42:44.264 128M / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:43:46.810 580M / 18G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 0:44:57.160 580M / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 416610960 bytes occupied (3.70969 bits per kmer). 0:44:58.264 1G / 18G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 99) Building k-mer extensions from k+1-mers 0:45:46.245 1G / 18G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 103) Building k-mer extensions from k+1-mers finished. 0:45:46.249 1G / 18G INFO General (stage.cpp : 101) PROCEDURE == Early tip clipping 0:45:46.249 1G / 18G INFO General (construction.cpp : 253) Early tip clipper length bound set as (RL - K) 0:45:46.249 1G / 18G INFO Early tip clipping (early_simplification.hpp : 181) Early tip clipping 0:47:38.867 1G / 18G INFO Early tip clipping (early_simplification.hpp : 184) 198521692 22-mers were removed by early tip clipper 0:47:38.867 1G / 18G INFO General (stage.cpp : 101) PROCEDURE == Condensing graph 0:47:39.041 1G / 18G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 355) Extracting unbranching paths 0:48:45.245 3G / 18G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 374) Extracting unbranching paths finished. 45119188 sequences extracted 0:49:15.712 3G / 18G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 310) Collecting perfect loops 0:49:34.104 3G / 18G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 343) Collecting perfect loops finished. 570 loops collected 0:50:05.712 13G / 18G INFO General (stage.cpp : 101) PROCEDURE == Filling coverage indices (PHM) 0:50:05.713 13G / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:50:05.713 13G / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:50:41.591 13G / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 423591744 bytes occupied (3.70985 bits per kmer). 0:50:43.122 17G / 18G INFO General (construction.cpp : 388) Collecting k-mer coverage information from reads, this takes a while. 0:55:55.779 17G / 18G INFO General (construction.cpp : 508) Filling coverage and flanking coverage from PHM 0:56:11.085 17G / 18G INFO General (construction.cpp : 464) Processed 32000000 edges 0:56:23.959 17G / 18G INFO General (construction.cpp : 464) Processed 64000000 edges 0:56:34.318 17G / 18G INFO General (construction.cpp : 464) Processed 90217856 edges 0:56:39.243 12G / 18G INFO StageManager (stage.cpp : 132) STAGE == EC Threshold Finding 0:56:45.703 12G / 18G INFO General (kmer_coverage_model.cpp : 181) Kmer coverage valley at: 228 0:56:45.813 12G / 18G INFO General (kmer_coverage_model.cpp : 201) K-mer histogram maximum: 230 0:56:45.813 12G / 18G INFO General (kmer_coverage_model.cpp : 237) Estimated median coverage: 231. Coverage mad: 2.9652 0:56:45.947 12G / 18G INFO General (kmer_coverage_model.cpp : 259) Fitting coverage model 0:56:47.137 12G / 18G INFO General (kmer_coverage_model.cpp : 295) ... iteration 2 0:56:49.453 12G / 18G INFO General (kmer_coverage_model.cpp : 295) ... iteration 4 0:56:57.151 12G / 18G INFO General (kmer_coverage_model.cpp : 295) ... iteration 8 0:57:14.786 12G / 18G INFO General (kmer_coverage_model.cpp : 295) ... iteration 16 0:57:45.118 12G / 18G INFO General (kmer_coverage_model.cpp : 295) ... iteration 32 0:58:32.180 12G / 18G INFO General (kmer_coverage_model.cpp : 295) ... iteration 64 0:59:09.918 12G / 18G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 16.9538. Fitted coverage std. dev: 6.87466 0:59:09.918 12G / 18G WARN General (kmer_coverage_model.cpp : 327) Valley value was estimated improperly, reset to 9 0:59:09.934 12G / 18G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 0.664956 0:59:09.934 12G / 18G WARN General (kmer_coverage_model.cpp : 366) Failed to determine erroneous kmer threshold. Threshold set to: 9 0:59:09.934 12G / 18G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 252330322 0:59:09.937 12G / 18G INFO General (genomic_info_filler.cpp : 114) Failed to estimate mean coverage 0:59:09.937 12G / 18G INFO General (genomic_info_filler.cpp : 127) EC coverage threshold value was calculated as 9 0:59:09.937 12G / 18G INFO General (genomic_info_filler.cpp : 128) Trusted kmer low bound: 0 0:59:09.937 12G / 18G INFO StageManager (stage.cpp : 132) STAGE == Raw Simplification 0:59:09.937 12G / 18G INFO General (simplification.cpp : 128) PROCEDURE == InitialCleaning 0:59:10.347 12G / 18G INFO General (simplification.cpp : 68) Most init cleaning disabled since detected mean 0 was less than activation coverage 10 0:59:10.347 12G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Self conjugate edge remover 0:59:13.505 12G / 18G INFO Simplification (parallel_processing.hpp : 167) Self conjugate edge remover triggered 0 times 0:59:13.505 12G / 18G INFO StageManager (stage.cpp : 132) STAGE == Simplification 0:59:13.505 12G / 18G INFO General (simplification.cpp : 357) Graph simplification started 0:59:13.505 12G / 18G INFO General (graph_simplification.hpp : 634) Creating parallel br instance 0:59:13.505 12G / 18G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 1 0:59:13.505 12G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:59:43.482 12G / 18G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 730370 times 0:59:43.482 12G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 1:18:56.379 13G / 18G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 2530004 times 1:18:56.379 13G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 1:19:48.230 13G / 18G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 1:19:48.230 13G / 18G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 2 1:19:48.230 13G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 1:20:02.453 13G / 18G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 100963 times 1:20:02.453 13G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 1:20:07.927 13G / 18G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 1723 times 1:20:07.927 13G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 1:31:11.949 13G / 18G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 8383870 times 1:31:11.949 13G / 18G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 3 1:31:11.949 13G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 1:31:27.329 13G / 18G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 182665 times 1:31:27.329 13G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 1:35:12.889 13G / 18G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 190638 times 1:35:12.889 13G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 1:38:03.059 13G / 18G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 1852537 times 1:38:03.060 13G / 18G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 4 1:38:03.060 13G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 1:38:07.174 13G / 18G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 32701 times 1:38:07.174 13G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 1:39:24.981 13G / 18G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 78235 times 1:39:24.981 13G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 1:40:28.652 13G / 18G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 717442 times 1:40:28.652 13G / 18G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 5 1:40:28.652 13G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 1:40:30.628 13G / 18G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 13642 times 1:40:30.629 13G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 1:41:06.977 13G / 18G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 37867 times 1:41:06.978 13G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 1:41:40.131 13G / 18G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 376703 times 1:41:40.131 13G / 18G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 6 1:41:40.131 13G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 1:41:41.258 13G / 18G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 6959 times 1:41:41.258 13G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 1:42:02.482 13G / 18G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 21854 times 1:42:02.482 13G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 1:42:20.591 13G / 18G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 228165 times 1:42:20.591 13G / 18G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 7 1:42:20.591 13G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 1:42:21.190 13G / 18G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 3714 times 1:42:21.190 13G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 1:42:34.657 13G / 18G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 14382 times 1:42:34.657 13G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 1:42:48.545 13G / 18G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 160797 times 1:42:48.545 13G / 18G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 8 1:42:48.545 13G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 1:42:49.006 13G / 18G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 2206 times 1:42:49.006 13G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 1:42:58.499 13G / 18G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 10685 times 1:42:58.499 13G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 1:43:08.262 12G / 18G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 120826 times 1:43:08.262 12G / 18G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 9 1:43:08.262 12G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 1:43:08.580 12G / 18G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 1375 times 1:43:08.580 12G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 1:43:16.881 12G / 18G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 8373 times 1:43:16.881 12G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 1:43:26.534 12G / 18G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 96128 times 1:43:26.534 12G / 18G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 10 1:43:26.534 12G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 1:43:26.907 12G / 18G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 873 times 1:43:26.907 12G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 1:43:33.598 12G / 18G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 6719 times 1:43:33.598 12G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 1:43:40.211 12G / 18G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 82120 times 1:43:40.212 12G / 18G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 11 1:43:40.212 12G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 1:43:41.385 12G / 18G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 6248 times 1:43:41.385 12G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 1:44:17.316 12G / 18G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 11401 times 1:44:17.316 12G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 1:44:19.144 12G / 18G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 151 times 1:44:19.144 12G / 18G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 12 1:44:19.144 12G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 1:44:19.266 12G / 18G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 3 times 1:44:19.266 12G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 1:44:19.290 12G / 18G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 6 times 1:44:19.290 12G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 1:44:19.290 12G / 18G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 1:44:19.290 12G / 18G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 13 1:44:19.290 12G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 1:44:19.290 12G / 18G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 1:44:19.290 12G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 1:44:19.290 12G / 18G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 1:44:19.290 12G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 1:44:19.290 12G / 18G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 1:44:19.291 12G / 18G INFO StageManager (stage.cpp : 132) STAGE == Simplification Cleanup 1:44:19.291 12G / 18G INFO General (simplification.cpp : 196) PROCEDURE == Post simplification 1:44:19.291 12G / 18G INFO General (graph_simplification.hpp : 453) Disconnection of relatively low covered edges disabled 1:44:19.291 12G / 18G INFO General (graph_simplification.hpp : 489) Complex tip clipping disabled 1:44:19.291 12G / 18G INFO General (graph_simplification.hpp : 634) Creating parallel br instance 1:44:19.291 12G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 1:44:20.009 12G / 18G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 3 times 1:44:20.009 12G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 1:44:47.040 12G / 18G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 91 times 1:44:47.040 12G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 1:44:47.730 12G / 18G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 1:44:47.730 12G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 1:45:13.318 12G / 18G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 2 times 1:45:13.319 12G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 1:45:13.319 12G / 18G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 1:45:13.319 12G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 1:45:13.319 12G / 18G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 1:45:13.319 12G / 18G INFO General (simplification.cpp : 330) Disrupting self-conjugate edges 1:45:20.901 12G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Removing isolated edges 1:45:29.662 11G / 18G INFO Simplification (parallel_processing.hpp : 167) Removing isolated edges triggered 825380 times 1:45:29.662 11G / 18G INFO General (simplification.cpp : 470) Counting average coverage 1:45:31.740 11G / 18G INFO General (simplification.cpp : 476) Average coverage = 43.7079 1:45:31.740 11G / 18G INFO StageManager (stage.cpp : 132) STAGE == Contig Output 1:45:31.740 11G / 18G INFO General (contig_output_stage.cpp : 40) Writing GFA to /local/genbank/workspace/reads.all3.spades1//K21/assembly_graph_with_scaffolds.gfa 1:45:51.585 11G / 18G INFO General (contig_output.hpp : 22) Outputting contigs to /local/genbank/workspace/reads.all3.spades1//K21/before_rr.fasta 1:46:20.542 11G / 18G INFO General (contig_output_stage.cpp : 51) Outputting FastG graph to /local/genbank/workspace/reads.all3.spades1//K21/assembly_graph.fastg 1:47:42.456 11G / 18G INFO General (contig_output.hpp : 22) Outputting contigs to /local/genbank/workspace/reads.all3.spades1//K21/simplified_contigs.fasta 1:48:11.515 11G / 18G INFO General (contig_output.hpp : 22) Outputting contigs to /local/genbank/workspace/reads.all3.spades1//K21/final_contigs.fasta 1:48:39.986 11G / 18G INFO StageManager (stage.cpp : 132) STAGE == Contig Output 1:48:39.986 11G / 18G INFO General (contig_output_stage.cpp : 40) Writing GFA to /local/genbank/workspace/reads.all3.spades1//K21/assembly_graph_with_scaffolds.gfa 1:48:59.405 11G / 18G INFO General (contig_output.hpp : 22) Outputting contigs to /local/genbank/workspace/reads.all3.spades1//K21/before_rr.fasta 1:49:27.656 11G / 18G INFO General (contig_output_stage.cpp : 51) Outputting FastG graph to /local/genbank/workspace/reads.all3.spades1//K21/assembly_graph.fastg 1:50:51.150 11G / 18G INFO General (contig_output.hpp : 22) Outputting contigs to /local/genbank/workspace/reads.all3.spades1//K21/simplified_contigs.fasta 1:51:19.906 11G / 18G INFO General (contig_output.hpp : 22) Outputting contigs to /local/genbank/workspace/reads.all3.spades1//K21/final_contigs.fasta 1:51:48.307 11G / 18G INFO General (launch.hpp : 149) SPAdes finished 1:52:29.880 128M / 18G INFO General (main.cpp : 109) Assembling time: 1 hours 52 minutes 29 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.all3.spades1/K33/configs/config.info 0:00:00.000 4M / 4M INFO General (memory_limit.cpp : 49) Memory limit set to 130 Gb 0:00:00.000 4M / 4M INFO General (main.cpp : 87) Starting SPAdes, built from refs/heads/spades_3.13.0, git revision 8ea46659e9b2aca35444a808db550ac333006f8b 0:00:00.000 4M / 4M INFO General (main.cpp : 88) Maximum k-mer length: 128 0:00:00.000 4M / 4M INFO General (main.cpp : 89) Assembling dataset (/local/genbank/workspace/reads.all3.spades1/dataset.info) with K=33 0:00:00.000 4M / 4M INFO General (main.cpp : 90) Maximum # of threads to use (adjusted due to OMP capabilities): 32 0:00:00.000 4M / 4M INFO General (launch.hpp : 51) SPAdes started 0:00:00.000 4M / 4M INFO General (launch.hpp : 58) Starting from stage: construction 0:00:00.000 4M / 4M INFO General (launch.hpp : 65) Two-step RR enabled: 0 0:00:00.000 4M / 4M INFO StageManager (stage.cpp : 132) STAGE == de Bruijn graph construction 0:00:00.005 4M / 4M INFO General (read_converter.hpp : 59) Binary reads detected 0:00:00.072 4M / 4M INFO General (construction.cpp : 111) Max read length 700 0:00:00.072 4M / 4M INFO General (construction.cpp : 117) Average read length 80.6457 0:00:00.072 4M / 4M INFO General (stage.cpp : 101) PROCEDURE == k+1-mer counting 0:00:00.073 4M / 4M INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 1024 files using 32 threads. This might take a while. 0:00:00.076 4M / 4M INFO General (file_limit.hpp : 32) Open file limit set to 4096 0:00:00.076 4M / 4M INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 1.35413 Gb 0:00:00.076 4M / 4M INFO General (kmer_splitters.hpp : 97) Using cell size of 32768 0:00:19.428 17G / 17G INFO General (kmer_splitters.hpp : 289) Processed 6913334 reads 0:00:35.181 17G / 17G INFO General (kmer_splitters.hpp : 289) Processed 14462045 reads 0:00:50.825 17G / 17G INFO General (kmer_splitters.hpp : 289) Processed 21914479 reads 0:01:06.525 17G / 17G INFO General (kmer_splitters.hpp : 289) Processed 29632754 reads 0:01:18.342 17G / 17G INFO General (kmer_splitters.hpp : 289) Processed 35687494 reads 0:01:38.676 17G / 17G INFO General (kmer_splitters.hpp : 289) Processed 48162474 reads 0:01:59.819 17G / 17G INFO General (kmer_splitters.hpp : 289) Processed 61083538 reads 0:02:17.401 17G / 17G INFO General (kmer_splitters.hpp : 289) Processed 70825083 reads 0:02:26.744 17G / 17G INFO General (kmer_splitters.hpp : 289) Processed 74849838 reads 0:02:36.404 17G / 17G INFO General (kmer_splitters.hpp : 289) Processed 78691234 reads 0:02:46.009 17G / 17G INFO General (kmer_splitters.hpp : 289) Processed 82482228 reads 0:02:57.678 17G / 17G INFO General (kmer_splitters.hpp : 289) Processed 86763718 reads 0:05:09.035 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 134437096 reads 0:11:11.712 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 272726009 reads 0:15:56.297 17G / 18G INFO General (kmer_splitters.hpp : 295) Adding contigs from previous K 0:18:23.859 132M / 18G INFO General (kmer_splitters.hpp : 308) Used 419421056 reads 0:18:23.859 132M / 18G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:21:54.657 132M / 18G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 1003709495 kmers in total. 0:21:54.658 132M / 18G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:24:44.991 128M / 18G INFO General (stage.cpp : 101) PROCEDURE == Extension index construction 0:24:44.993 128M / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:24:44.993 128M / 18G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 512 files using 32 threads. This might take a while. 0:24:44.994 128M / 18G INFO General (file_limit.hpp : 32) Open file limit set to 4096 0:24:44.994 128M / 18G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 1.35286 Gb 0:24:44.994 128M / 18G INFO General (kmer_splitters.hpp : 97) Using cell size of 65536 0:24:50.929 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 7367412 kmers 0:24:55.663 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 15775115 kmers 0:25:00.189 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 24520978 kmers 0:25:07.024 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 38654562 kmers 0:25:11.659 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 47043247 kmers 0:25:16.488 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 55783740 kmers 0:25:23.159 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 70014607 kmers 0:25:27.709 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 78412293 kmers 0:25:32.512 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 87147716 kmers 0:25:39.422 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 101372667 kmers 0:25:43.982 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 109764291 kmers 0:25:48.688 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 118501212 kmers 0:25:55.377 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 132744117 kmers 0:26:00.238 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 141139391 kmers 0:26:04.882 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 149887757 kmers 0:26:11.544 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 164103189 kmers 0:26:16.073 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 172498581 kmers 0:26:20.802 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 181239818 kmers 0:27:08.846 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 275325236 kmers 0:29:23.606 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 540499892 kmers 0:33:21.736 17G / 18G INFO General (kmer_splitters.hpp : 385) Used 1003712567 kmers. 0:33:24.461 128M / 18G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:36:01.424 128M / 18G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 1000508482 kmers in total. 0:36:01.424 128M / 18G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:38:52.522 128M / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:40:12.204 584M / 18G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 0:42:38.216 584M / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 463947046 bytes occupied (3.70969 bits per kmer). 0:42:39.464 1G / 18G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 99) Building k-mer extensions from k+1-mers 0:43:32.381 1G / 18G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 103) Building k-mer extensions from k+1-mers finished. 0:43:32.385 1G / 18G INFO General (stage.cpp : 101) PROCEDURE == Early tip clipping 0:43:32.385 1G / 18G INFO General (construction.cpp : 253) Early tip clipper length bound set as (RL - K) 0:43:32.385 1G / 18G INFO Early tip clipping (early_simplification.hpp : 181) Early tip clipping 0:45:27.042 1G / 18G INFO Early tip clipping (early_simplification.hpp : 184) 310894237 34-mers were removed by early tip clipper 0:45:27.042 1G / 18G INFO General (stage.cpp : 101) PROCEDURE == Condensing graph 0:45:27.212 1G / 18G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 355) Extracting unbranching paths 0:46:32.557 2G / 18G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 374) Extracting unbranching paths finished. 22325803 sequences extracted 0:46:58.788 2G / 18G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 310) Collecting perfect loops 0:47:19.739 2G / 18G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 343) Collecting perfect loops finished. 1068 loops collected 0:47:39.637 8G / 18G INFO General (stage.cpp : 101) PROCEDURE == Filling coverage indices (PHM) 0:47:39.640 8G / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:47:39.641 8G / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:48:23.869 8G / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 465444124 bytes occupied (3.70979 bits per kmer). 0:48:25.545 12G / 18G INFO General (construction.cpp : 388) Collecting k-mer coverage information from reads, this takes a while. 0:52:55.633 12G / 18G INFO General (construction.cpp : 508) Filling coverage and flanking coverage from PHM 0:53:21.902 12G / 18G INFO General (construction.cpp : 464) Processed 32000000 edges 0:53:31.569 12G / 18G INFO General (construction.cpp : 464) Processed 44645043 edges 0:53:38.623 6G / 18G INFO StageManager (stage.cpp : 132) STAGE == EC Threshold Finding 0:53:42.486 7G / 18G INFO General (kmer_coverage_model.cpp : 181) Kmer coverage valley at: 188 0:53:42.565 6G / 18G INFO General (kmer_coverage_model.cpp : 201) K-mer histogram maximum: 189 0:53:42.566 6G / 18G WARN General (kmer_coverage_model.cpp : 218) Too many erroneous kmers, the estimates might be unreliable 0:53:42.566 6G / 18G INFO General (kmer_coverage_model.cpp : 237) Estimated median coverage: 189. Coverage mad: 45.5764 0:53:42.661 6G / 18G INFO General (kmer_coverage_model.cpp : 259) Fitting coverage model 0:53:43.521 7G / 18G INFO General (kmer_coverage_model.cpp : 295) ... iteration 2 0:53:45.263 7G / 18G INFO General (kmer_coverage_model.cpp : 295) ... iteration 4 0:53:50.599 7G / 18G INFO General (kmer_coverage_model.cpp : 295) ... iteration 8 0:54:03.822 7G / 18G INFO General (kmer_coverage_model.cpp : 295) ... iteration 16 0:54:25.598 7G / 18G INFO General (kmer_coverage_model.cpp : 295) ... iteration 32 0:54:56.450 7G / 18G INFO General (kmer_coverage_model.cpp : 295) ... iteration 64 0:55:46.646 7G / 18G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 22.26. Fitted coverage std. dev: 13.7956 0:55:46.646 7G / 18G WARN General (kmer_coverage_model.cpp : 327) Valley value was estimated improperly, reset to 2 0:55:46.656 7G / 18G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 1 0:55:46.656 7G / 18G WARN General (kmer_coverage_model.cpp : 366) Failed to determine erroneous kmer threshold. Threshold set to: 2 0:55:46.656 7G / 18G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 498768384 0:55:46.657 6G / 18G INFO General (genomic_info_filler.cpp : 114) Failed to estimate mean coverage 0:55:46.657 6G / 18G INFO General (genomic_info_filler.cpp : 127) EC coverage threshold value was calculated as 2 0:55:46.657 6G / 18G INFO General (genomic_info_filler.cpp : 128) Trusted kmer low bound: 0 0:55:46.657 6G / 18G INFO StageManager (stage.cpp : 132) STAGE == Raw Simplification 0:55:46.658 6G / 18G INFO General (simplification.cpp : 128) PROCEDURE == InitialCleaning 0:55:46.659 6G / 18G INFO General (simplification.cpp : 68) Most init cleaning disabled since detected mean 0 was less than activation coverage 10 0:55:46.659 6G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Self conjugate edge remover 0:55:48.677 6G / 18G INFO Simplification (parallel_processing.hpp : 167) Self conjugate edge remover triggered 1227 times 0:55:48.677 6G / 18G INFO StageManager (stage.cpp : 132) STAGE == Simplification 0:55:48.677 6G / 18G INFO General (simplification.cpp : 357) Graph simplification started 0:55:48.677 6G / 18G INFO General (graph_simplification.hpp : 634) Creating parallel br instance 0:55:48.678 6G / 18G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 1 0:55:48.678 6G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:56:27.130 7G / 18G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 1335503 times 0:56:27.130 7G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 1:01:23.946 7G / 18G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 768413 times 1:01:23.946 7G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 1:01:40.842 7G / 18G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 16965 times 1:01:40.842 7G / 18G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 2 1:01:40.842 7G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 1:01:46.484 7G / 18G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 39375 times 1:01:46.484 7G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 1:01:48.924 7G / 18G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 1138 times 1:01:48.924 7G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 1:01:48.948 7G / 18G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 281 times 1:01:48.948 7G / 18G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 3 1:01:48.948 7G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 1:01:48.958 7G / 18G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 124 times 1:01:48.958 7G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 1:01:49.118 7G / 18G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 16 times 1:01:49.118 7G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 1:01:49.153 7G / 18G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 441 times 1:01:49.153 7G / 18G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 4 1:01:49.153 7G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 1:01:49.156 7G / 18G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 41 times 1:01:49.156 7G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 1:01:49.352 7G / 18G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 30 times 1:01:49.352 7G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 1:01:49.461 7G / 18G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 1350 times 1:01:49.461 7G / 18G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 5 1:01:49.461 7G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 1:01:49.473 7G / 18G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 181 times 1:01:49.473 7G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 1:01:50.099 7G / 18G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 50 times 1:01:50.099 7G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 1:05:37.301 7G / 18G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 2584001 times 1:05:37.301 7G / 18G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 6 1:05:37.301 7G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 1:05:44.204 7G / 18G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 88674 times 1:05:44.204 7G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 1:06:49.096 7G / 18G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 58207 times 1:06:49.097 7G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 1:07:24.435 7G / 18G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 427012 times 1:07:24.436 7G / 18G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 7 1:07:24.436 7G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 1:07:25.866 7G / 18G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 11991 times 1:07:25.866 7G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 1:07:43.449 7G / 18G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 10713 times 1:07:43.449 7G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 1:07:51.280 7G / 18G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 110507 times 1:07:51.280 7G / 18G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 8 1:07:51.280 7G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 1:07:51.781 7G / 18G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 5777 times 1:07:51.781 7G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 1:07:57.870 7G / 18G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 4779 times 1:07:57.870 7G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 1:08:04.448 7G / 18G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 86574 times 1:08:04.448 7G / 18G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 9 1:08:04.448 7G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 1:08:04.837 7G / 18G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 4577 times 1:08:04.837 7G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 1:08:09.579 7G / 18G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 4110 times 1:08:09.579 7G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 1:08:17.863 7G / 18G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 86190 times 1:08:17.863 7G / 18G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 10 1:08:17.863 7G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 1:08:18.317 7G / 18G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 4223 times 1:08:18.317 7G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 1:08:24.345 7G / 18G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 3981 times 1:08:24.345 7G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 1:09:24.841 7G / 18G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 558805 times 1:09:24.841 7G / 18G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 11 1:09:24.841 7G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 1:09:28.264 7G / 18G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 23878 times 1:09:28.264 7G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 1:10:15.054 7G / 18G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 20433 times 1:10:15.054 7G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 1:10:17.325 7G / 18G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 10 times 1:10:17.325 7G / 18G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 12 1:10:17.325 7G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 1:10:17.460 7G / 18G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 248 times 1:10:17.460 7G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 1:10:17.541 7G / 18G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 6 times 1:10:17.541 7G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 1:10:17.541 7G / 18G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 1:10:17.541 7G / 18G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 13 1:10:17.541 7G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 1:10:17.541 7G / 18G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 1:10:17.541 7G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 1:10:17.541 7G / 18G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 1:10:17.541 7G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 1:10:17.541 7G / 18G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 1:10:17.541 7G / 18G INFO StageManager (stage.cpp : 132) STAGE == Simplification Cleanup 1:10:17.541 7G / 18G INFO General (simplification.cpp : 196) PROCEDURE == Post simplification 1:10:17.541 7G / 18G INFO General (graph_simplification.hpp : 453) Disconnection of relatively low covered edges disabled 1:10:17.541 7G / 18G INFO General (graph_simplification.hpp : 489) Complex tip clipping disabled 1:10:17.541 7G / 18G INFO General (graph_simplification.hpp : 634) Creating parallel br instance 1:10:17.541 7G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 1:10:18.800 7G / 18G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 112 times 1:10:18.800 7G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 1:10:53.539 7G / 18G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 172 times 1:10:53.539 7G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 1:10:54.647 7G / 18G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 2 times 1:10:54.647 7G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 1:11:28.688 7G / 18G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 5 times 1:11:28.688 7G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 1:11:28.688 7G / 18G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 1:11:28.688 7G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 1:11:28.688 7G / 18G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 1:11:28.688 7G / 18G INFO General (simplification.cpp : 330) Disrupting self-conjugate edges 1:11:45.363 7G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Removing isolated edges 1:12:16.774 7G / 18G INFO Simplification (parallel_processing.hpp : 167) Removing isolated edges triggered 2744600 times 1:12:16.774 7G / 18G INFO General (simplification.cpp : 470) Counting average coverage 1:12:20.789 7G / 18G INFO General (simplification.cpp : 476) Average coverage = 27.8646 1:12:20.789 7G / 18G INFO StageManager (stage.cpp : 132) STAGE == Contig Output 1:12:20.789 7G / 18G INFO General (contig_output_stage.cpp : 40) Writing GFA to /local/genbank/workspace/reads.all3.spades1//K33/assembly_graph_with_scaffolds.gfa 1:13:02.341 7G / 18G INFO General (contig_output.hpp : 22) Outputting contigs to /local/genbank/workspace/reads.all3.spades1//K33/before_rr.fasta 1:13:42.917 7G / 18G INFO General (contig_output_stage.cpp : 51) Outputting FastG graph to /local/genbank/workspace/reads.all3.spades1//K33/assembly_graph.fastg 1:15:29.894 7G / 18G INFO General (contig_output.hpp : 22) Outputting contigs to /local/genbank/workspace/reads.all3.spades1//K33/simplified_contigs.fasta 1:16:08.269 7G / 18G INFO General (contig_output.hpp : 22) Outputting contigs to /local/genbank/workspace/reads.all3.spades1//K33/final_contigs.fasta 1:16:46.664 7G / 18G INFO StageManager (stage.cpp : 132) STAGE == Contig Output 1:16:46.664 7G / 18G INFO General (contig_output_stage.cpp : 40) Writing GFA to /local/genbank/workspace/reads.all3.spades1//K33/assembly_graph_with_scaffolds.gfa 1:17:09.614 7G / 18G INFO General (contig_output.hpp : 22) Outputting contigs to /local/genbank/workspace/reads.all3.spades1//K33/before_rr.fasta 1:17:48.123 7G / 18G INFO General (contig_output_stage.cpp : 51) Outputting FastG graph to /local/genbank/workspace/reads.all3.spades1//K33/assembly_graph.fastg 1:19:34.090 7G / 18G INFO General (contig_output.hpp : 22) Outputting contigs to /local/genbank/workspace/reads.all3.spades1//K33/simplified_contigs.fasta 1:20:12.222 7G / 18G INFO General (contig_output.hpp : 22) Outputting contigs to /local/genbank/workspace/reads.all3.spades1//K33/final_contigs.fasta 1:20:50.184 7G / 18G INFO General (launch.hpp : 149) SPAdes finished 1:21:20.304 128M / 18G INFO General (main.cpp : 109) Assembling time: 1 hours 21 minutes 20 seconds == Running assembler: K55 0:00:00.000 4M / 4M INFO General (main.cpp : 74) Loaded config from /local/genbank/workspace/reads.all3.spades1/K55/configs/config.info 0:00:00.000 4M / 4M INFO General (memory_limit.cpp : 49) Memory limit set to 130 Gb 0:00:00.000 4M / 4M INFO General (main.cpp : 87) Starting SPAdes, built from refs/heads/spades_3.13.0, git revision 8ea46659e9b2aca35444a808db550ac333006f8b 0:00:00.000 4M / 4M INFO General (main.cpp : 88) Maximum k-mer length: 128 0:00:00.000 4M / 4M INFO General (main.cpp : 89) Assembling dataset (/local/genbank/workspace/reads.all3.spades1/dataset.info) with K=55 0:00:00.000 4M / 4M INFO General (main.cpp : 90) Maximum # of threads to use (adjusted due to OMP capabilities): 32 0:00:00.000 4M / 4M INFO General (launch.hpp : 51) SPAdes started 0:00:00.000 4M / 4M INFO General (launch.hpp : 58) Starting from stage: construction 0:00:00.000 4M / 4M INFO General (launch.hpp : 65) Two-step RR enabled: 0 0:00:00.000 4M / 4M INFO General (launch.hpp : 76) Will need read mapping, kmer mapper will be attached 0:00:00.000 4M / 4M INFO StageManager (stage.cpp : 132) STAGE == de Bruijn graph construction 0:00:00.009 4M / 4M INFO General (read_converter.hpp : 59) Binary reads detected 0:00:00.103 4M / 4M INFO General (construction.cpp : 111) Max read length 700 0:00:00.103 4M / 4M INFO General (construction.cpp : 117) Average read length 80.6457 0:00:00.103 4M / 4M INFO General (stage.cpp : 101) PROCEDURE == k+1-mer counting 0:00:00.105 4M / 4M INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 1024 files using 32 threads. This might take a while. 0:00:00.108 4M / 4M INFO General (file_limit.hpp : 32) Open file limit set to 4096 0:00:00.108 4M / 4M INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 1.35413 Gb 0:00:00.108 4M / 4M INFO General (kmer_splitters.hpp : 97) Using cell size of 32768 0:00:21.159 17G / 17G INFO General (kmer_splitters.hpp : 289) Processed 18592329 reads 0:00:37.412 17G / 17G INFO General (kmer_splitters.hpp : 289) Processed 38794175 reads 0:00:59.021 17G / 17G INFO General (kmer_splitters.hpp : 289) Processed 71475773 reads 0:01:09.001 17G / 17G INFO General (kmer_splitters.hpp : 289) Processed 80913728 reads 0:01:24.843 17G / 17G INFO General (kmer_splitters.hpp : 289) Processed 92759119 reads 0:01:45.904 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 95596359 reads 0:02:21.494 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 114779835 reads 0:02:57.903 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 141389029 reads 0:03:34.303 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 168308637 reads 0:04:10.760 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 195786877 reads 0:04:47.199 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 223384313 reads 0:05:19.737 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 241099982 reads 0:05:42.537 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 252886349 reads 0:06:31.346 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 278903660 reads 0:08:26.779 17G / 18G INFO General (kmer_splitters.hpp : 295) Adding contigs from previous K 0:11:17.288 132M / 18G INFO General (kmer_splitters.hpp : 308) Used 419421056 reads 0:11:17.288 132M / 18G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:13:48.068 132M / 18G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 928229700 kmers in total. 0:13:48.068 132M / 18G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:16:25.139 128M / 18G INFO General (stage.cpp : 101) PROCEDURE == Extension index construction 0:16:25.141 128M / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:16:25.141 128M / 18G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 512 files using 32 threads. This might take a while. 0:16:25.143 128M / 18G INFO General (file_limit.hpp : 32) Open file limit set to 4096 0:16:25.143 128M / 18G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 1.35286 Gb 0:16:25.143 128M / 18G INFO General (kmer_splitters.hpp : 97) Using cell size of 65536 0:16:31.705 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 7790569 kmers 0:16:36.928 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 17198275 kmers 0:16:41.558 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 25976073 kmers 0:16:46.948 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 36741868 kmers 0:16:51.810 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 46135084 kmers 0:16:56.755 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 54930651 kmers 0:17:01.806 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 65741744 kmers 0:17:07.043 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 75140901 kmers 0:17:11.632 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 83940889 kmers 0:17:16.971 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 94755350 kmers 0:17:21.768 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 104149270 kmers 0:17:26.663 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 112954007 kmers 0:17:31.797 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 123757020 kmers 0:17:36.956 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 133148186 kmers 0:17:41.801 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 141935256 kmers 0:17:47.178 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 152780144 kmers 0:17:52.151 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 162181486 kmers 0:17:57.161 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 170975721 kmers 0:18:47.582 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 268784285 kmers 0:21:08.951 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 539254815 kmers 0:24:32.695 17G / 18G INFO General (kmer_splitters.hpp : 385) Used 928232772 kmers. 0:24:35.575 128M / 18G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:28:06.063 128M / 18G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 937366471 kmers in total. 0:28:06.063 128M / 18G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:30:47.146 128M / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:32:00.173 584M / 18G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 0:34:16.948 584M / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 434671882 bytes occupied (3.70973 bits per kmer). 0:34:18.105 1G / 18G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 99) Building k-mer extensions from k+1-mers 0:35:06.503 1G / 18G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 103) Building k-mer extensions from k+1-mers finished. 0:35:06.508 1G / 18G INFO General (stage.cpp : 101) PROCEDURE == Condensing graph 0:35:06.690 1G / 18G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 355) Extracting unbranching paths 0:36:24.967 4G / 18G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 374) Extracting unbranching paths finished. 50894396 sequences extracted 0:37:03.985 4G / 18G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 310) Collecting perfect loops 0:37:23.388 4G / 18G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 343) Collecting perfect loops finished. 145 loops collected 0:38:10.497 18G / 22G INFO General (stage.cpp : 101) PROCEDURE == Filling coverage indices (PHM) 0:38:10.497 18G / 22G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:38:10.497 18G / 22G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:38:50.220 18G / 22G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 430454138 bytes occupied (3.70989 bits per kmer). 0:38:51.759 21G / 22G INFO General (construction.cpp : 388) Collecting k-mer coverage information from reads, this takes a while. 0:41:29.884 21G / 22G INFO General (construction.cpp : 508) Filling coverage and flanking coverage from PHM 0:41:49.737 21G / 22G INFO General (construction.cpp : 464) Processed 32000000 edges 0:42:04.259 21G / 22G INFO General (construction.cpp : 464) Processed 64000000 edges 0:42:19.626 21G / 22G INFO General (construction.cpp : 464) Processed 96000000 edges 0:42:22.271 21G / 22G INFO General (construction.cpp : 464) Processed 101786234 edges 0:42:28.830 16G / 22G INFO StageManager (stage.cpp : 132) STAGE == EC Threshold Finding 0:42:30.422 16G / 22G INFO General (kmer_coverage_model.cpp : 181) Kmer coverage valley at: 224 0:42:30.467 16G / 22G INFO General (kmer_coverage_model.cpp : 201) K-mer histogram maximum: 226 0:42:30.468 16G / 22G INFO General (kmer_coverage_model.cpp : 237) Estimated median coverage: 227. Coverage mad: 2.9652 0:42:30.519 16G / 22G INFO General (kmer_coverage_model.cpp : 259) Fitting coverage model 0:42:31.471 16G / 22G INFO General (kmer_coverage_model.cpp : 295) ... iteration 2 0:42:33.684 16G / 22G INFO General (kmer_coverage_model.cpp : 295) ... iteration 4 0:42:38.363 16G / 22G INFO General (kmer_coverage_model.cpp : 295) ... iteration 8 0:42:47.644 16G / 22G INFO General (kmer_coverage_model.cpp : 295) ... iteration 16 0:43:06.124 16G / 22G INFO General (kmer_coverage_model.cpp : 295) ... iteration 32 0:43:38.724 16G / 22G INFO General (kmer_coverage_model.cpp : 295) ... iteration 64 0:43:46.445 16G / 22G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 141.853. Fitted coverage std. dev: 7.95576 0:43:46.445 16G / 22G WARN General (kmer_coverage_model.cpp : 327) Valley value was estimated improperly, reset to 75 0:43:46.460 16G / 22G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 1 0:43:46.460 16G / 22G WARN General (kmer_coverage_model.cpp : 366) Failed to determine erroneous kmer threshold. Threshold set to: 75 0:43:46.460 16G / 22G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 4645116 0:43:46.461 16G / 22G INFO General (genomic_info_filler.cpp : 114) Failed to estimate mean coverage 0:43:46.461 16G / 22G INFO General (genomic_info_filler.cpp : 127) EC coverage threshold value was calculated as 75 0:43:46.461 16G / 22G INFO General (genomic_info_filler.cpp : 128) Trusted kmer low bound: 0 0:43:46.461 16G / 22G INFO StageManager (stage.cpp : 132) STAGE == Gap Closer 0:43:46.461 16G / 22G INFO General (graph_pack.hpp : 101) Index refill 0:43:46.466 16G / 22G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:43:46.466 16G / 22G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 512 files using 32 threads. This might take a while. 0:43:46.472 16G / 22G INFO General (file_limit.hpp : 32) Open file limit set to 4096 0:43:46.472 16G / 22G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 1.17981 Gb 0:43:46.472 16G / 22G INFO General (kmer_splitters.hpp : 97) Using cell size of 65536 0:46:20.976 34G / 35G INFO General (edge_index_builders.hpp : 77) Processed 96734643 edges 0:46:30.507 34G / 35G INFO General (edge_index_builders.hpp : 77) Processed 101786266 edges 0:46:30.507 34G / 35G INFO General (edge_index_builders.hpp : 82) Used 101786266 sequences. 0:46:34.634 16G / 35G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:48:46.506 16G / 35G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 928229700 kmers in total. 0:48:46.506 16G / 35G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:51:22.963 16G / 35G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:52:34.886 17G / 35G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 0:54:50.469 17G / 35G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 430431448 bytes occupied (3.7097 bits per kmer). 0:55:07.122 37G / 37G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while. 0:55:41.546 37G / 37G INFO General (edge_index.hpp : 92) Index refilled 0:55:41.574 37G / 37G INFO General (gap_closer.cpp : 159) Preparing shift maps 0:58:34.368 44G / 44G INFO General (gap_closer.cpp : 119) Processing paired reads (takes a while) 0:59:37.026 45G / 45G INFO General (gap_closer.cpp : 138) Used 80455197 paired reads 0:59:37.026 45G / 45G INFO General (gap_closer.cpp : 140) Merging paired indices 1:00:52.555 38G / 45G INFO GapCloser (gap_closer.cpp : 346) Closing short gaps 1:08:27.546 38G / 45G INFO GapCloser (gap_closer.cpp : 380) Closing short gaps complete: filled 39998 gaps after checking 869179 candidates 1:08:55.235 38G / 45G INFO StageManager (stage.cpp : 132) STAGE == Raw Simplification 1:08:58.455 16G / 45G INFO General (simplification.cpp : 128) PROCEDURE == InitialCleaning 1:08:58.455 16G / 45G INFO General (simplification.cpp : 68) Most init cleaning disabled since detected mean 0 was less than activation coverage 10 1:08:58.455 16G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Self conjugate edge remover 1:09:03.944 16G / 45G INFO Simplification (parallel_processing.hpp : 167) Self conjugate edge remover triggered 1003 times 1:09:03.944 16G / 45G INFO StageManager (stage.cpp : 132) STAGE == Simplification 1:09:03.944 16G / 45G INFO General (simplification.cpp : 357) Graph simplification started 1:09:03.944 16G / 45G INFO General (graph_simplification.hpp : 634) Creating parallel br instance 1:09:03.944 16G / 45G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 1 1:09:03.944 16G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 1:20:38.718 17G / 45G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 20695595 times 1:20:38.718 17G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 1:23:33.046 18G / 45G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 276060 times 1:23:33.046 18G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 1:24:11.277 18G / 45G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 209995 times 1:24:11.277 18G / 45G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 2 1:24:11.277 18G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 1:24:15.416 18G / 45G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 57259 times 1:24:15.416 18G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 1:24:28.415 18G / 45G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 12576 times 1:24:28.415 18G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 1:24:30.847 18G / 45G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 23940 times 1:24:30.847 18G / 45G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 3 1:24:30.847 18G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 1:24:31.020 18G / 45G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 2186 times 1:24:31.020 18G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 1:24:33.958 18G / 45G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 2745 times 1:24:33.958 18G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 1:24:34.594 18G / 45G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 6676 times 1:24:34.594 18G / 45G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 4 1:24:34.594 18G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 1:24:34.636 18G / 45G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 467 times 1:24:34.636 18G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 1:24:35.565 18G / 45G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 916 times 1:24:35.566 18G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 1:24:35.869 18G / 45G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 3246 times 1:24:35.869 18G / 45G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 5 1:24:35.869 18G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 1:24:35.889 18G / 45G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 199 times 1:24:35.889 18G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 1:24:36.383 18G / 45G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 541 times 1:24:36.383 18G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 1:24:36.573 18G / 45G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 1921 times 1:24:36.573 18G / 45G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 6 1:24:36.573 18G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 1:24:36.582 18G / 45G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 97 times 1:24:36.582 18G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 1:24:36.864 18G / 45G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 296 times 1:24:36.864 18G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 1:24:36.981 18G / 45G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 1299 times 1:24:36.981 18G / 45G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 7 1:24:36.981 18G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 1:24:36.987 18G / 45G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 61 times 1:24:36.987 18G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 1:24:37.225 18G / 45G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 242 times 1:24:37.225 18G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 1:24:37.293 18G / 45G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 812 times 1:24:37.293 18G / 45G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 8 1:24:37.293 18G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 1:24:37.297 18G / 45G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 40 times 1:24:37.297 18G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 1:24:37.480 18G / 45G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 161 times 1:24:37.480 18G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 1:24:37.530 18G / 45G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 621 times 1:24:37.530 18G / 45G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 9 1:24:37.530 18G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 1:24:37.533 18G / 45G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 42 times 1:24:37.533 18G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 1:24:37.625 18G / 45G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 110 times 1:24:37.625 18G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 1:24:37.662 18G / 45G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 474 times 1:24:37.662 18G / 45G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 10 1:24:37.662 18G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 1:24:37.664 18G / 45G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 22 times 1:24:37.664 18G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 1:24:37.739 18G / 45G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 72 times 1:24:37.739 18G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 1:24:37.768 18G / 45G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 369 times 1:24:37.768 18G / 45G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 11 1:24:37.768 18G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 1:24:41.805 18G / 45G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 2400 times 1:24:41.805 18G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 1:24:45.034 18G / 45G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 175 times 1:24:45.034 18G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 1:24:47.883 18G / 45G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 41 times 1:24:47.883 18G / 45G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 12 1:24:47.883 18G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 1:24:47.884 18G / 45G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 2 times 1:24:47.884 18G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 1:24:47.891 18G / 45G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 7 times 1:24:47.891 18G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 1:24:47.891 18G / 45G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 1:24:47.891 18G / 45G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 13 1:24:47.891 18G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 1:24:47.891 18G / 45G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 1 times 1:24:47.891 18G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 1:24:47.891 18G / 45G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 1:24:47.891 18G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 1:24:47.891 18G / 45G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 1:24:47.891 18G / 45G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 14 1:24:47.892 18G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 1:24:47.892 18G / 45G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 1:24:47.892 18G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 1:24:47.892 18G / 45G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 1:24:47.892 18G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 1:24:47.892 18G / 45G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 1:24:47.892 18G / 45G INFO StageManager (stage.cpp : 132) STAGE == Gap Closer 1:24:47.892 18G / 45G INFO General (graph_pack.hpp : 101) Index refill 1:24:47.898 18G / 45G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 1:24:47.898 18G / 45G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 512 files using 32 threads. This might take a while. 1:24:47.900 18G / 45G INFO General (file_limit.hpp : 32) Open file limit set to 4096 1:24:47.900 18G / 45G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 1.15837 Gb 1:24:47.900 18G / 45G INFO General (kmer_splitters.hpp : 97) Using cell size of 65536 1:26:19.527 36G / 45G INFO General (edge_index_builders.hpp : 77) Processed 19428297 edges 1:26:19.528 36G / 45G INFO General (edge_index_builders.hpp : 82) Used 19428297 sequences. 1:26:23.421 18G / 45G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 1:27:40.230 18G / 45G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 524866658 kmers in total. 1:27:40.231 18G / 45G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 1:29:11.285 18G / 45G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 1:29:50.172 19G / 45G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 1:31:11.181 19G / 45G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 243389784 bytes occupied (3.70974 bits per kmer). 1:31:29.549 30G / 45G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while. 1:31:49.303 30G / 45G INFO General (edge_index.hpp : 92) Index refilled 1:31:49.325 30G / 45G INFO General (gap_closer.cpp : 159) Preparing shift maps 1:32:40.607 33G / 45G INFO General (gap_closer.cpp : 119) Processing paired reads (takes a while) 1:34:26.560 36G / 45G INFO General (gap_closer.cpp : 138) Used 80455197 paired reads 1:34:26.560 36G / 45G INFO General (gap_closer.cpp : 140) Merging paired indices 1:35:47.395 31G / 45G INFO GapCloser (gap_closer.cpp : 346) Closing short gaps 1:37:30.811 31G / 45G INFO GapCloser (gap_closer.cpp : 380) Closing short gaps complete: filled 24855 gaps after checking 1243096 candidates 1:39:07.300 30G / 45G INFO StageManager (stage.cpp : 132) STAGE == Simplification Cleanup 1:39:07.300 30G / 45G INFO General (simplification.cpp : 196) PROCEDURE == Post simplification 1:39:07.300 30G / 45G INFO General (graph_simplification.hpp : 453) Disconnection of relatively low covered edges disabled 1:39:07.300 30G / 45G INFO General (graph_simplification.hpp : 489) Complex tip clipping disabled 1:39:07.300 30G / 45G INFO General (graph_simplification.hpp : 634) Creating parallel br instance 1:39:07.300 30G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 1:39:10.470 30G / 45G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 1 times 1:39:10.470 30G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 1:39:13.318 30G / 45G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 1 times 1:39:13.318 30G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 1:39:16.313 30G / 45G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 1:39:16.313 30G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 1:39:19.059 30G / 45G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 1:39:19.059 30G / 45G INFO General (simplification.cpp : 330) Disrupting self-conjugate edges 1:39:53.095 30G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Removing isolated edges 1:52:21.005 18G / 45G INFO Simplification (parallel_processing.hpp : 167) Removing isolated edges triggered 9561215 times 1:52:21.007 18G / 45G INFO General (simplification.cpp : 470) Counting average coverage 1:52:21.998 18G / 45G INFO General (simplification.cpp : 476) Average coverage = 16.3769 1:52:21.998 18G / 45G WARN General (simplification.cpp : 479) The determined erroneous connection coverage threshold may be determined improperly 1:52:21.998 18G / 45G INFO StageManager (stage.cpp : 132) STAGE == Contig Output 1:52:21.998 18G / 45G INFO General (contig_output_stage.cpp : 40) Writing GFA to /local/genbank/workspace/reads.all3.spades1//K55/assembly_graph_with_scaffolds.gfa 1:52:27.514 18G / 45G INFO General (contig_output.hpp : 22) Outputting contigs to /local/genbank/workspace/reads.all3.spades1//K55/before_rr.fasta 1:52:35.749 18G / 45G INFO General (contig_output_stage.cpp : 51) Outputting FastG graph to /local/genbank/workspace/reads.all3.spades1//K55/assembly_graph.fastg 1:52:58.588 18G / 45G INFO General (contig_output.hpp : 22) Outputting contigs to /local/genbank/workspace/reads.all3.spades1//K55/simplified_contigs.fasta 1:53:06.861 18G / 45G INFO General (contig_output.hpp : 22) Outputting contigs to /local/genbank/workspace/reads.all3.spades1//K55/final_contigs.fasta 1:53:16.687 18G / 45G INFO StageManager (stage.cpp : 132) STAGE == Contig Output 1:53:16.687 18G / 45G INFO General (contig_output_stage.cpp : 40) Writing GFA to /local/genbank/workspace/reads.all3.spades1//K55/assembly_graph_with_scaffolds.gfa 1:53:21.909 18G / 45G INFO General (contig_output.hpp : 22) Outputting contigs to /local/genbank/workspace/reads.all3.spades1//K55/before_rr.fasta 1:53:30.080 18G / 45G INFO General (contig_output_stage.cpp : 51) Outputting FastG graph to /local/genbank/workspace/reads.all3.spades1//K55/assembly_graph.fastg 1:53:56.239 18G / 45G INFO General (contig_output.hpp : 22) Outputting contigs to /local/genbank/workspace/reads.all3.spades1//K55/simplified_contigs.fasta 1:54:04.796 18G / 45G INFO General (contig_output.hpp : 22) Outputting contigs to /local/genbank/workspace/reads.all3.spades1//K55/final_contigs.fasta 1:54:12.952 18G / 45G INFO General (launch.hpp : 149) SPAdes finished 1:55:17.512 136M / 45G INFO General (main.cpp : 109) Assembling time: 1 hours 55 minutes 17 seconds == Running assembler: K77 0:00:00.000 4M / 4M INFO General (main.cpp : 74) Loaded config from /local/genbank/workspace/reads.all3.spades1/K77/configs/config.info 0:00:00.000 4M / 4M INFO General (memory_limit.cpp : 49) Memory limit set to 130 Gb 0:00:00.000 4M / 4M INFO General (main.cpp : 87) Starting SPAdes, built from refs/heads/spades_3.13.0, git revision 8ea46659e9b2aca35444a808db550ac333006f8b 0:00:00.000 4M / 4M INFO General (main.cpp : 88) Maximum k-mer length: 128 0:00:00.000 4M / 4M INFO General (main.cpp : 89) Assembling dataset (/local/genbank/workspace/reads.all3.spades1/dataset.info) with K=77 0:00:00.000 4M / 4M INFO General (main.cpp : 90) Maximum # of threads to use (adjusted due to OMP capabilities): 32 0:00:00.000 4M / 4M INFO General (launch.hpp : 51) SPAdes started 0:00:00.000 4M / 4M INFO General (launch.hpp : 58) Starting from stage: construction 0:00:00.000 4M / 4M INFO General (launch.hpp : 65) Two-step RR enabled: 0 0:00:00.000 4M / 4M INFO General (launch.hpp : 76) Will need read mapping, kmer mapper will be attached 0:00:00.000 4M / 4M INFO StageManager (stage.cpp : 132) STAGE == de Bruijn graph construction 0:00:00.004 4M / 4M INFO General (read_converter.hpp : 59) Binary reads detected 0:00:00.066 4M / 4M INFO General (construction.cpp : 111) Max read length 700 0:00:00.066 4M / 4M INFO General (construction.cpp : 117) Average read length 80.6457 0:00:00.066 4M / 4M INFO General (stage.cpp : 101) PROCEDURE == k+1-mer counting 0:00:00.068 4M / 4M INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 1024 files using 32 threads. This might take a while. 0:00:00.070 4M / 4M INFO General (file_limit.hpp : 32) Open file limit set to 4096 0:00:00.070 4M / 4M INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 1.35413 Gb 0:00:00.070 4M / 4M INFO General (kmer_splitters.hpp : 97) Using cell size of 21845 0:00:43.141 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 96281910 reads 0:01:33.141 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 142705150 reads 0:02:20.471 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 198715923 reads 0:03:07.299 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 244424917 reads 0:03:39.510 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 274400132 reads 0:04:01.621 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 419421056 reads 0:04:01.621 17G / 18G INFO General (kmer_splitters.hpp : 295) Adding contigs from previous K 0:06:56.129 132M / 18G INFO General (kmer_splitters.hpp : 308) Used 419421056 reads 0:06:56.129 132M / 18G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:09:15.018 132M / 18G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 593470145 kmers in total. 0:09:15.018 132M / 18G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:11:46.552 128M / 18G INFO General (stage.cpp : 101) PROCEDURE == Extension index construction 0:11:46.554 128M / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:11:46.554 128M / 18G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 512 files using 32 threads. This might take a while. 0:11:46.556 128M / 18G INFO General (file_limit.hpp : 32) Open file limit set to 4096 0:11:46.556 128M / 18G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 1.35286 Gb 0:11:46.556 128M / 18G INFO General (kmer_splitters.hpp : 97) Using cell size of 43690 0:11:52.632 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 5512022 kmers 0:11:57.485 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 11436251 kmers 0:12:01.892 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 17219870 kmers 0:12:07.042 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 24041738 kmers 0:12:11.684 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 29957976 kmers 0:12:16.615 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 35741307 kmers 0:12:21.418 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 42592732 kmers 0:12:26.419 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 48514052 kmers 0:12:30.858 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 54302999 kmers 0:12:36.052 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 61138046 kmers 0:12:40.615 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 67060854 kmers 0:12:45.397 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 72847329 kmers 0:12:50.305 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 79684116 kmers 0:12:55.220 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 85605932 kmers 0:12:59.916 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 91384168 kmers 0:13:05.034 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 98236241 kmers 0:13:09.565 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 104156045 kmers 0:13:33.824 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 135314647 kmers 0:15:20.247 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 271067291 kmers 0:18:52.445 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 543327481 kmers 0:19:32.766 17G / 18G INFO General (kmer_splitters.hpp : 385) Used 593473217 kmers. 0:19:35.243 132M / 18G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:23:31.322 132M / 18G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 605613702 kmers in total. 0:23:31.322 132M / 18G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:26:06.694 132M / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:26:54.295 452M / 18G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 0:29:07.213 452M / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 280832680 bytes occupied (3.70973 bits per kmer). 0:29:07.959 1G / 18G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 99) Building k-mer extensions from k+1-mers 0:29:40.159 1G / 18G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 103) Building k-mer extensions from k+1-mers finished. 0:29:40.164 1G / 18G INFO General (stage.cpp : 101) PROCEDURE == Condensing graph 0:29:40.343 1G / 18G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 355) Extracting unbranching paths 0:30:31.408 2G / 18G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 374) Extracting unbranching paths finished. 25588050 sequences extracted 0:30:57.999 2G / 18G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 310) Collecting perfect loops 0:31:10.632 2G / 18G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 343) Collecting perfect loops finished. 98 loops collected 0:31:41.975 10G / 18G INFO General (stage.cpp : 101) PROCEDURE == Filling coverage indices (PHM) 0:31:41.975 10G / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:31:41.975 10G / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:32:07.498 10G / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 275209360 bytes occupied (3.70983 bits per kmer). 0:32:08.486 12G / 18G INFO General (construction.cpp : 388) Collecting k-mer coverage information from reads, this takes a while. 0:33:05.113 12G / 18G INFO General (construction.cpp : 508) Filling coverage and flanking coverage from PHM 0:33:27.106 12G / 18G INFO General (construction.cpp : 464) Processed 32000000 edges 0:33:38.492 12G / 18G INFO General (construction.cpp : 464) Processed 51175877 edges 0:33:44.144 9G / 18G INFO StageManager (stage.cpp : 132) STAGE == EC Threshold Finding 0:33:44.332 9G / 18G INFO General (kmer_coverage_model.cpp : 181) Kmer coverage valley at: 125 0:33:44.336 9G / 18G INFO General (kmer_coverage_model.cpp : 201) K-mer histogram maximum: 127 0:33:44.336 9G / 18G INFO General (kmer_coverage_model.cpp : 237) Estimated median coverage: 128. Coverage mad: 2.9652 0:33:44.341 9G / 18G INFO General (kmer_coverage_model.cpp : 259) Fitting coverage model 0:33:44.810 9G / 18G INFO General (kmer_coverage_model.cpp : 295) ... iteration 2 0:33:45.991 9G / 18G INFO General (kmer_coverage_model.cpp : 295) ... iteration 4 0:33:48.332 9G / 18G INFO General (kmer_coverage_model.cpp : 295) ... iteration 8 0:33:52.738 9G / 18G INFO General (kmer_coverage_model.cpp : 295) ... iteration 16 0:34:05.660 9G / 18G INFO General (kmer_coverage_model.cpp : 295) ... iteration 32 0:34:37.992 9G / 18G INFO General (kmer_coverage_model.cpp : 295) ... iteration 64 0:34:59.973 9G / 18G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 16.5162. Fitted coverage std. dev: 6.84749 0:34:59.973 9G / 18G WARN General (kmer_coverage_model.cpp : 327) Valley value was estimated improperly, reset to 8 0:34:59.982 9G / 18G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 0.866934 0:34:59.982 9G / 18G WARN General (kmer_coverage_model.cpp : 366) Failed to determine erroneous kmer threshold. Threshold set to: 8 0:34:59.982 9G / 18G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 49509452 0:34:59.983 9G / 18G INFO General (genomic_info_filler.cpp : 114) Failed to estimate mean coverage 0:34:59.983 9G / 18G INFO General (genomic_info_filler.cpp : 127) EC coverage threshold value was calculated as 8 0:34:59.983 9G / 18G INFO General (genomic_info_filler.cpp : 128) Trusted kmer low bound: 0 0:34:59.983 9G / 18G INFO StageManager (stage.cpp : 132) STAGE == Gap Closer 0:34:59.983 9G / 18G INFO General (graph_pack.hpp : 101) Index refill 0:34:59.988 9G / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:34:59.988 9G / 18G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 512 files using 32 threads. This might take a while. 0:34:59.990 9G / 18G INFO General (file_limit.hpp : 32) Open file limit set to 4096 0:34:59.990 9G / 18G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 1.25753 Gb 0:34:59.990 9G / 18G INFO General (kmer_splitters.hpp : 97) Using cell size of 43690 0:37:32.301 26G / 27G INFO General (edge_index_builders.hpp : 77) Processed 51175877 edges 0:37:32.301 26G / 27G INFO General (edge_index_builders.hpp : 82) Used 51175877 sequences. 0:37:36.594 9G / 27G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:39:45.644 9G / 27G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 593470145 kmers in total. 0:39:45.645 9G / 27G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:42:17.006 9G / 27G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:43:12.562 9G / 27G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 0:45:23.086 9G / 27G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 275201472 bytes occupied (3.70973 bits per kmer). 0:45:39.532 22G / 27G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while. 0:46:05.576 22G / 27G INFO General (edge_index.hpp : 92) Index refilled 0:46:05.598 22G / 27G INFO General (gap_closer.cpp : 159) Preparing shift maps 0:47:22.169 27G / 27G INFO General (gap_closer.cpp : 119) Processing paired reads (takes a while) 0:47:45.132 28G / 28G INFO General (gap_closer.cpp : 138) Used 80455197 paired reads 0:47:45.132 28G / 28G INFO General (gap_closer.cpp : 140) Merging paired indices 0:48:24.425 23G / 28G INFO GapCloser (gap_closer.cpp : 346) Closing short gaps 0:51:53.709 23G / 28G INFO GapCloser (gap_closer.cpp : 380) Closing short gaps complete: filled 34299 gaps after checking 686130 candidates 0:52:16.793 22G / 28G INFO StageManager (stage.cpp : 132) STAGE == Raw Simplification 0:52:19.708 9G / 28G INFO General (simplification.cpp : 128) PROCEDURE == InitialCleaning 0:52:19.709 9G / 28G INFO General (simplification.cpp : 68) Most init cleaning disabled since detected mean 0 was less than activation coverage 10 0:52:19.709 9G / 28G INFO Simplification (parallel_processing.hpp : 165) Running Self conjugate edge remover 0:52:23.559 9G / 28G INFO Simplification (parallel_processing.hpp : 167) Self conjugate edge remover triggered 45 times 0:52:23.559 9G / 28G INFO StageManager (stage.cpp : 132) STAGE == Simplification 0:52:23.559 9G / 28G INFO General (simplification.cpp : 357) Graph simplification started 0:52:23.559 9G / 28G INFO General (graph_simplification.hpp : 634) Creating parallel br instance 0:52:23.559 9G / 28G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 1 0:52:23.559 9G / 28G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:56:40.354 9G / 28G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 6529189 times 0:56:40.354 9G / 28G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:58:24.751 11G / 28G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 152242 times 0:58:24.752 11G / 28G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:58:28.128 11G / 28G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 1791 times 0:58:28.128 11G / 28G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 2 0:58:28.128 11G / 28G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:58:28.471 11G / 28G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 3983 times 0:58:28.471 11G / 28G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:58:29.114 11G / 28G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 531 times 0:58:29.114 11G / 28G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:58:30.978 11G / 28G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 17112 times 0:58:30.978 11G / 28G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 3 0:58:30.978 11G / 28G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:58:31.243 11G / 28G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 5793 times 0:58:31.243 11G / 28G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:58:33.467 11G / 28G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 2009 times 0:58:33.467 11G / 28G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:58:34.093 11G / 28G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 5332 times 0:58:34.093 11G / 28G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 4 0:58:34.093 11G / 28G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:58:34.164 11G / 28G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 1403 times 0:58:34.164 11G / 28G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:58:34.898 11G / 28G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 692 times 0:58:34.898 11G / 28G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:58:35.256 11G / 28G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 3024 times 0:58:35.256 11G / 28G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 5 0:58:35.256 11G / 28G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:58:35.291 11G / 28G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 708 times 0:58:35.291 11G / 28G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:58:35.765 11G / 28G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 392 times 0:58:35.765 11G / 28G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:58:35.968 11G / 28G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 1967 times 0:58:35.968 11G / 28G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 6 0:58:35.968 11G / 28G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:58:35.989 11G / 28G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 421 times 0:58:35.989 11G / 28G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:58:36.235 11G / 28G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 259 times 0:58:36.235 11G / 28G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:58:36.347 11G / 28G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 1086 times 0:58:36.347 11G / 28G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 7 0:58:36.347 11G / 28G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:58:36.358 11G / 28G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 220 times 0:58:36.358 11G / 28G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:58:36.574 11G / 28G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 210 times 0:58:36.574 11G / 28G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:58:36.665 11G / 28G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 901 times 0:58:36.665 11G / 28G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 8 0:58:36.665 11G / 28G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:58:36.673 11G / 28G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 155 times 0:58:36.673 11G / 28G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:58:36.849 11G / 28G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 165 times 0:58:36.849 11G / 28G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:58:36.925 11G / 28G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 679 times 0:58:36.925 11G / 28G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 9 0:58:36.925 11G / 28G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:58:36.931 11G / 28G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 126 times 0:58:36.931 11G / 28G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:58:37.033 11G / 28G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 110 times 0:58:37.033 11G / 28G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:58:37.080 11G / 28G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 476 times 0:58:37.080 11G / 28G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 10 0:58:37.080 11G / 28G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:58:37.084 11G / 28G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 75 times 0:58:37.084 11G / 28G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:58:37.182 11G / 28G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 108 times 0:58:37.182 11G / 28G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:58:37.221 11G / 28G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 417 times 0:58:37.221 11G / 28G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 11 0:58:37.221 11G / 28G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:58:40.996 11G / 28G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 1633 times 0:58:40.996 11G / 28G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:58:44.200 11G / 28G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 158 times 0:58:44.200 11G / 28G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:58:47.187 11G / 28G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 10 times 0:58:47.187 11G / 28G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 12 0:58:47.187 11G / 28G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:58:47.188 11G / 28G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 1 times 0:58:47.188 11G / 28G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:58:47.192 11G / 28G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 2 times 0:58:47.192 11G / 28G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:58:47.192 11G / 28G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:58:47.192 11G / 28G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 13 0:58:47.192 11G / 28G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:58:47.192 11G / 28G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:58:47.192 11G / 28G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:58:47.192 11G / 28G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:58:47.192 11G / 28G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:58:47.192 11G / 28G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:58:47.192 11G / 28G INFO StageManager (stage.cpp : 132) STAGE == Gap Closer 0:58:47.192 11G / 28G INFO General (graph_pack.hpp : 101) Index refill 0:58:47.198 11G / 28G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:58:47.198 11G / 28G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 512 files using 32 threads. This might take a while. 0:58:47.200 11G / 28G INFO General (file_limit.hpp : 32) Open file limit set to 4096 0:58:47.200 11G / 28G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 1.23592 Gb 0:58:47.200 11G / 28G INFO General (kmer_splitters.hpp : 97) Using cell size of 43690 1:00:50.810 28G / 29G INFO General (edge_index_builders.hpp : 77) Processed 24693349 edges 1:00:50.810 28G / 29G INFO General (edge_index_builders.hpp : 82) Used 24693349 sequences. 1:00:55.092 11G / 29G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 1:02:40.226 11G / 29G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 489553068 kmers in total. 1:02:40.227 11G / 29G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 1:04:45.778 11G / 29G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 1:05:30.263 11G / 29G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 1:07:19.928 11G / 29G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 227015088 bytes occupied (3.70975 bits per kmer). 1:07:33.368 22G / 29G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while. 1:07:53.250 22G / 29G INFO General (edge_index.hpp : 92) Index refilled 1:07:53.271 22G / 29G INFO General (gap_closer.cpp : 159) Preparing shift maps 1:08:53.153 26G / 29G INFO General (gap_closer.cpp : 119) Processing paired reads (takes a while) 1:09:23.089 28G / 29G INFO General (gap_closer.cpp : 138) Used 80455197 paired reads 1:09:23.089 28G / 29G INFO General (gap_closer.cpp : 140) Merging paired indices 1:10:41.551 23G / 29G INFO GapCloser (gap_closer.cpp : 346) Closing short gaps 1:13:15.278 23G / 29G INFO GapCloser (gap_closer.cpp : 380) Closing short gaps complete: filled 5852 gaps after checking 1274043 candidates 1:13:48.910 22G / 29G INFO StageManager (stage.cpp : 132) STAGE == Simplification Cleanup 1:13:48.910 22G / 29G INFO General (simplification.cpp : 196) PROCEDURE == Post simplification 1:13:48.910 22G / 29G INFO General (graph_simplification.hpp : 453) Disconnection of relatively low covered edges disabled 1:13:48.910 22G / 29G INFO General (graph_simplification.hpp : 489) Complex tip clipping disabled 1:13:48.910 22G / 29G INFO General (graph_simplification.hpp : 634) Creating parallel br instance 1:13:48.910 22G / 29G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 1:13:54.458 22G / 29G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 27 times 1:13:54.458 22G / 29G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 1:13:57.368 22G / 29G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 1:13:57.368 22G / 29G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 1:14:01.169 22G / 29G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 1:14:01.169 22G / 29G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 1:14:03.958 22G / 29G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 1:14:03.958 22G / 29G INFO General (simplification.cpp : 330) Disrupting self-conjugate edges 1:14:37.980 22G / 29G INFO Simplification (parallel_processing.hpp : 165) Running Removing isolated edges 1:25:28.449 16G / 29G INFO Simplification (parallel_processing.hpp : 167) Removing isolated edges triggered 12218533 times 1:25:28.450 16G / 29G INFO General (simplification.cpp : 470) Counting average coverage 1:25:30.999 16G / 29G INFO General (simplification.cpp : 476) Average coverage = 5.17639 1:25:30.999 16G / 29G WARN General (simplification.cpp : 479) The determined erroneous connection coverage threshold may be determined improperly 1:25:30.999 16G / 29G INFO StageManager (stage.cpp : 132) STAGE == Contig Output 1:25:30.999 16G / 29G INFO General (contig_output_stage.cpp : 40) Writing GFA to /local/genbank/workspace/reads.all3.spades1//K77/assembly_graph_with_scaffolds.gfa 1:25:35.926 16G / 29G INFO General (contig_output.hpp : 22) Outputting contigs to /local/genbank/workspace/reads.all3.spades1//K77/before_rr.fasta 1:25:43.932 16G / 29G INFO General (contig_output_stage.cpp : 51) Outputting FastG graph to /local/genbank/workspace/reads.all3.spades1//K77/assembly_graph.fastg 1:26:07.846 16G / 29G INFO General (contig_output.hpp : 22) Outputting contigs to /local/genbank/workspace/reads.all3.spades1//K77/simplified_contigs.fasta 1:26:16.504 16G / 29G INFO General (contig_output.hpp : 22) Outputting contigs to /local/genbank/workspace/reads.all3.spades1//K77/final_contigs.fasta 1:26:24.839 16G / 29G INFO StageManager (stage.cpp : 132) STAGE == Contig Output 1:26:24.839 16G / 29G INFO General (contig_output_stage.cpp : 40) Writing GFA to /local/genbank/workspace/reads.all3.spades1//K77/assembly_graph_with_scaffolds.gfa 1:26:29.765 16G / 29G INFO General (contig_output.hpp : 22) Outputting contigs to /local/genbank/workspace/reads.all3.spades1//K77/before_rr.fasta 1:26:38.100 16G / 29G INFO General (contig_output_stage.cpp : 51) Outputting FastG graph to /local/genbank/workspace/reads.all3.spades1//K77/assembly_graph.fastg 1:27:02.441 16G / 29G INFO General (contig_output.hpp : 22) Outputting contigs to /local/genbank/workspace/reads.all3.spades1//K77/simplified_contigs.fasta 1:27:11.182 16G / 29G INFO General (contig_output.hpp : 22) Outputting contigs to /local/genbank/workspace/reads.all3.spades1//K77/final_contigs.fasta 1:27:19.276 16G / 29G INFO General (launch.hpp : 149) SPAdes finished 1:28:08.828 136M / 29G INFO General (main.cpp : 109) Assembling time: 1 hours 28 minutes 8 seconds == Running assembler: K99 0:00:00.000 4M / 4M INFO General (main.cpp : 74) Loaded config from /local/genbank/workspace/reads.all3.spades1/K99/configs/config.info 0:00:00.001 4M / 4M INFO General (memory_limit.cpp : 49) Memory limit set to 130 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.all3.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 0:00:00.005 4M / 4M INFO General (read_converter.hpp : 59) Binary reads detected 0:00:00.068 4M / 4M INFO General (construction.cpp : 111) Max read length 700 0:00:00.068 4M / 4M INFO General (construction.cpp : 117) Average read length 80.6457 0:00:00.068 4M / 4M INFO General (stage.cpp : 101) PROCEDURE == k+1-mer counting 0:00:00.070 4M / 4M INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 1024 files using 32 threads. This might take a while. 0:00:00.072 4M / 4M INFO General (file_limit.hpp : 32) Open file limit set to 4096 0:00:00.072 4M / 4M INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 1.35413 Gb 0:00:00.072 4M / 4M INFO General (kmer_splitters.hpp : 97) Using cell size of 16384 0:00:47.659 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 96736117 reads 0:01:27.131 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 419421056 reads 0:01:27.131 17G / 18G INFO General (kmer_splitters.hpp : 295) Adding contigs from previous K 0:05:00.349 132M / 18G INFO General (kmer_splitters.hpp : 308) Used 419421056 reads 0:05:00.349 132M / 18G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:06:35.980 132M / 18G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 306803868 kmers in total. 0:06:35.980 132M / 18G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:08:21.701 128M / 18G INFO General (stage.cpp : 101) PROCEDURE == Extension index construction 0:08:21.703 128M / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:08:21.703 128M / 18G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 512 files using 32 threads. This might take a while. 0:08:21.705 128M / 18G INFO General (file_limit.hpp : 32) Open file limit set to 4096 0:08:21.705 128M / 18G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 1.35286 Gb 0:08:21.705 128M / 18G INFO General (kmer_splitters.hpp : 97) Using cell size of 32768 0:08:29.065 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 4290009 kmers 0:08:33.860 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 8675132 kmers 0:08:38.693 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 13859324 kmers 0:08:43.540 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 18245729 kmers 0:08:48.433 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 23444869 kmers 0:08:53.295 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 27822189 kmers 0:08:58.197 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 33029583 kmers 0:09:03.117 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 37407641 kmers 0:09:08.057 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 42621278 kmers 0:09:12.932 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 47004178 kmers 0:09:17.836 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 52209394 kmers 0:09:22.798 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 56587064 kmers 0:09:27.757 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 61802049 kmers 0:09:32.618 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 66181608 kmers 0:09:37.754 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 71395091 kmers 0:09:42.752 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 75779563 kmers 0:09:47.742 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 80980594 kmers 0:10:47.297 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 138491586 kmers 0:13:05.650 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 272733125 kmers 0:13:42.153 17G / 18G INFO General (kmer_splitters.hpp : 385) Used 306805916 kmers. 0:13:45.471 128M / 18G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:16:00.150 128M / 18G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 317430788 kmers in total. 0:16:00.150 128M / 18G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:17:48.484 128M / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:18:16.627 324M / 18G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 0:19:52.502 324M / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 147201592 bytes occupied (3.70983 bits per kmer). 0:19:52.901 628M / 18G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 99) Building k-mer extensions from k+1-mers 0:20:09.486 628M / 18G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 103) Building k-mer extensions from k+1-mers finished. 0:20:09.491 624M / 18G INFO General (stage.cpp : 101) PROCEDURE == Condensing graph 0:20:09.670 624M / 18G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 355) Extracting unbranching paths 0:20:36.071 1G / 18G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 374) Extracting unbranching paths finished. 12552463 sequences extracted 0:20:50.032 1G / 18G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 310) Collecting perfect loops 0:20:56.574 1G / 18G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 343) Collecting perfect loops finished. 13 loops collected 0:21:13.722 5G / 18G INFO General (stage.cpp : 101) PROCEDURE == Filling coverage indices (PHM) 0:21:13.722 5G / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:21:13.722 5G / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:21:27.367 5G / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 142282024 bytes occupied (3.71005 bits per kmer). 0:21:27.893 6G / 18G INFO General (construction.cpp : 388) Collecting k-mer coverage information from reads, this takes a while. 0:21:52.718 6G / 18G INFO General (construction.cpp : 508) Filling coverage and flanking coverage from PHM 0:22:10.519 6G / 18G INFO General (construction.cpp : 464) Processed 25104900 edges 0:22:15.123 5G / 18G INFO StageManager (stage.cpp : 132) STAGE == EC Threshold Finding 0:22:15.134 5G / 18G INFO General (kmer_coverage_model.cpp : 181) Kmer coverage valley at: 48 0:22:15.135 5G / 18G INFO General (kmer_coverage_model.cpp : 201) K-mer histogram maximum: 50 0:22:15.135 5G / 18G INFO General (kmer_coverage_model.cpp : 237) Estimated median coverage: 51. Coverage mad: 2.9652 0:22:15.135 5G / 18G INFO General (kmer_coverage_model.cpp : 259) Fitting coverage model 0:22:15.319 5G / 18G INFO General (kmer_coverage_model.cpp : 295) ... iteration 2 0:22:15.728 5G / 18G INFO General (kmer_coverage_model.cpp : 295) ... iteration 4 0:22:16.589 5G / 18G INFO General (kmer_coverage_model.cpp : 295) ... iteration 8 0:22:19.007 5G / 18G INFO General (kmer_coverage_model.cpp : 295) ... iteration 16 0:22:26.511 5G / 18G INFO General (kmer_coverage_model.cpp : 295) ... iteration 32 0:22:37.436 5G / 18G INFO General (kmer_coverage_model.cpp : 295) ... iteration 64 0:22:40.817 5G / 18G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 12.3628. Fitted coverage std. dev: 5.56269 0:22:40.818 5G / 18G WARN General (kmer_coverage_model.cpp : 327) Valley value was estimated improperly, reset to 2 0:22:40.820 5G / 18G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 1 0:22:40.820 5G / 18G WARN General (kmer_coverage_model.cpp : 366) Failed to determine erroneous kmer threshold. Threshold set to: 2 0:22:40.820 5G / 18G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 81584070 0:22:40.823 5G / 18G INFO General (genomic_info_filler.cpp : 114) Failed to estimate mean coverage 0:22:40.823 5G / 18G INFO General (genomic_info_filler.cpp : 127) EC coverage threshold value was calculated as 2 0:22:40.823 5G / 18G INFO General (genomic_info_filler.cpp : 128) Trusted kmer low bound: 0 0:22:40.823 5G / 18G INFO StageManager (stage.cpp : 132) STAGE == Gap Closer 0:22:40.825 5G / 18G INFO General (graph_pack.hpp : 101) Index refill 0:22:40.828 5G / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:22:40.828 5G / 18G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 512 files using 32 threads. This might take a while. 0:22:40.839 5G / 18G INFO General (file_limit.hpp : 32) Open file limit set to 4096 0:22:40.840 5G / 18G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 1.30013 Gb 0:22:40.840 5G / 18G INFO General (kmer_splitters.hpp : 97) Using cell size of 32768 0:24:25.271 22G / 23G INFO General (edge_index_builders.hpp : 77) Processed 25104900 edges 0:24:25.271 22G / 23G INFO General (edge_index_builders.hpp : 82) Used 25104900 sequences. 0:24:29.159 5G / 23G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:25:58.332 5G / 23G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 306803868 kmers in total. 0:25:58.332 5G / 23G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:27:43.585 5G / 23G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:28:08.659 5G / 23G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 0:29:51.858 5G / 23G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 142283904 bytes occupied (3.71009 bits per kmer). 0:29:54.881 12G / 23G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while. 0:30:05.618 12G / 23G INFO General (edge_index.hpp : 92) Index refilled 0:30:05.640 12G / 23G INFO General (gap_closer.cpp : 159) Preparing shift maps 0:30:40.883 15G / 23G INFO General (gap_closer.cpp : 119) Processing paired reads (takes a while) 0:30:48.033 16G / 23G INFO General (gap_closer.cpp : 138) Used 80455197 paired reads 0:30:48.033 16G / 23G INFO General (gap_closer.cpp : 140) Merging paired indices 0:31:07.960 12G / 23G INFO GapCloser (gap_closer.cpp : 346) Closing short gaps 0:32:55.666 12G / 23G INFO GapCloser (gap_closer.cpp : 380) Closing short gaps complete: filled 18933 gaps after checking 451451 candidates 0:33:12.596 12G / 23G INFO StageManager (stage.cpp : 132) STAGE == Raw Simplification 0:33:12.874 5G / 23G INFO General (simplification.cpp : 128) PROCEDURE == InitialCleaning 0:33:12.874 5G / 23G INFO General (simplification.cpp : 68) Most init cleaning disabled since detected mean 0 was less than activation coverage 10 0:33:12.874 5G / 23G INFO Simplification (parallel_processing.hpp : 165) Running Self conjugate edge remover 0:33:15.122 5G / 23G INFO Simplification (parallel_processing.hpp : 167) Self conjugate edge remover triggered 17 times 0:33:15.122 5G / 23G INFO StageManager (stage.cpp : 132) STAGE == Simplification 0:33:15.122 5G / 23G INFO General (simplification.cpp : 357) Graph simplification started 0:33:15.123 5G / 23G INFO General (graph_simplification.hpp : 634) Creating parallel br instance 0:33:15.123 5G / 23G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 1 0:33:15.123 5G / 23G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:33:49.275 5G / 23G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 753360 times 0:33:49.275 5G / 23G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:35:09.737 6G / 23G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 95792 times 0:35:09.737 6G / 23G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:35:12.168 6G / 23G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 1051 times 0:35:12.169 6G / 23G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 2 0:35:12.169 6G / 23G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:35:12.381 6G / 23G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 2327 times 0:35:12.381 6G / 23G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:35:13.283 6G / 23G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 811 times 0:35:13.283 6G / 23G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:35:13.300 6G / 23G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 213 times 0:35:13.300 6G / 23G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 3 0:35:13.300 6G / 23G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:35:13.306 6G / 23G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 56 times 0:35:13.306 6G / 23G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:35:13.453 6G / 23G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 140 times 0:35:13.453 6G / 23G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:35:13.465 6G / 23G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 153 times 0:35:13.465 6G / 23G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 4 0:35:13.465 6G / 23G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:35:13.466 6G / 23G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 19 times 0:35:13.467 6G / 23G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:35:13.558 6G / 23G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 109 times 0:35:13.558 6G / 23G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:35:13.570 6G / 23G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 136 times 0:35:13.570 6G / 23G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 5 0:35:13.570 6G / 23G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:35:13.572 6G / 23G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 18 times 0:35:13.572 6G / 23G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:35:13.647 6G / 23G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 70 times 0:35:13.647 6G / 23G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:35:14.459 6G / 23G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 4312 times 0:35:14.459 6G / 23G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 6 0:35:14.459 6G / 23G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:35:14.489 6G / 23G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 449 times 0:35:14.489 6G / 23G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:35:15.450 6G / 23G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 851 times 0:35:15.450 6G / 23G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:35:15.575 6G / 23G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 1440 times 0:35:15.575 6G / 23G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 7 0:35:15.575 6G / 23G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:35:15.585 6G / 23G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 139 times 0:35:15.585 6G / 23G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:35:15.860 6G / 23G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 244 times 0:35:15.861 6G / 23G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:35:15.896 6G / 23G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 380 times 0:35:15.896 6G / 23G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 8 0:35:15.896 6G / 23G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:35:15.900 6G / 23G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 32 times 0:35:15.900 6G / 23G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:35:16.002 6G / 23G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 95 times 0:35:16.002 6G / 23G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:35:16.031 6G / 23G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 278 times 0:35:16.031 6G / 23G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 9 0:35:16.031 6G / 23G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:35:16.032 6G / 23G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 23 times 0:35:16.032 6G / 23G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:35:16.099 6G / 23G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 65 times 0:35:16.099 6G / 23G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:35:16.128 6G / 23G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 229 times 0:35:16.128 6G / 23G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 10 0:35:16.128 6G / 23G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:35:16.130 6G / 23G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 21 times 0:35:16.130 6G / 23G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:35:16.168 6G / 23G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 37 times 0:35:16.168 6G / 23G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:35:16.323 6G / 23G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 702 times 0:35:16.323 6G / 23G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 11 0:35:16.323 6G / 23G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:35:19.323 6G / 23G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 1157 times 0:35:19.323 6G / 23G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:35:21.810 6G / 23G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 161 times 0:35:21.810 6G / 23G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:35:24.068 6G / 23G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 2 times 0:35:24.068 6G / 23G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 12 0:35:24.068 6G / 23G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:35:24.069 6G / 23G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 4 times 0:35:24.069 6G / 23G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:35:24.071 6G / 23G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 1 times 0:35:24.071 6G / 23G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:35:24.071 6G / 23G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:35:24.071 6G / 23G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 13 0:35:24.071 6G / 23G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:35:24.071 6G / 23G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:35:24.071 6G / 23G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:35:24.071 6G / 23G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:35:24.071 6G / 23G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:35:24.071 6G / 23G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:35:24.071 6G / 23G INFO StageManager (stage.cpp : 132) STAGE == Gap Closer 0:35:24.071 6G / 23G INFO General (graph_pack.hpp : 101) Index refill 0:35:24.077 6G / 23G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:35:24.077 6G / 23G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 512 files using 32 threads. This might take a while. 0:35:24.079 6G / 23G INFO General (file_limit.hpp : 32) Open file limit set to 4096 0:35:24.079 6G / 23G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 1.28316 Gb 0:35:24.079 6G / 23G INFO General (kmer_splitters.hpp : 97) Using cell size of 32768 0:36:56.526 24G / 25G INFO General (edge_index_builders.hpp : 77) Processed 21481686 edges 0:36:56.526 24G / 25G INFO General (edge_index_builders.hpp : 82) Used 21481686 sequences. 0:36:59.968 6G / 25G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:38:18.886 6G / 25G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 271343901 kmers in total. 0:38:18.886 6G / 25G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:39:51.771 6G / 25G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:40:13.958 6G / 25G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 0:41:33.375 6G / 25G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 125830920 bytes occupied (3.70986 bits per kmer). 0:41:38.171 13G / 25G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while. 0:41:48.102 13G / 25G INFO General (edge_index.hpp : 92) Index refilled 0:41:48.123 13G / 25G INFO General (gap_closer.cpp : 159) Preparing shift maps 0:42:26.548 16G / 25G INFO General (gap_closer.cpp : 119) Processing paired reads (takes a while) 0:42:34.425 17G / 25G INFO General (gap_closer.cpp : 138) Used 80455197 paired reads 0:42:34.426 17G / 25G INFO General (gap_closer.cpp : 140) Merging paired indices 0:43:04.369 13G / 25G INFO GapCloser (gap_closer.cpp : 346) Closing short gaps 0:44:52.784 13G / 25G INFO GapCloser (gap_closer.cpp : 380) Closing short gaps complete: filled 443 gaps after checking 633188 candidates 0:45:00.842 13G / 25G INFO StageManager (stage.cpp : 132) STAGE == Simplification Cleanup 0:45:00.842 13G / 25G INFO General (simplification.cpp : 196) PROCEDURE == Post simplification 0:45:00.842 13G / 25G INFO General (graph_simplification.hpp : 453) Disconnection of relatively low covered edges disabled 0:45:00.842 13G / 25G INFO General (graph_simplification.hpp : 489) Complex tip clipping disabled 0:45:00.842 13G / 25G INFO General (graph_simplification.hpp : 634) Creating parallel br instance 0:45:00.842 13G / 25G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:45:05.467 13G / 25G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 25 times 0:45:05.467 13G / 25G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:45:07.893 13G / 25G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 1 times 0:45:07.893 13G / 25G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:45:10.950 13G / 25G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 2 times 0:45:10.950 13G / 25G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:45:13.290 13G / 25G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:45:13.290 13G / 25G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:45:13.290 13G / 25G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:45:13.290 13G / 25G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:45:13.293 13G / 25G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:45:13.293 13G / 25G INFO General (simplification.cpp : 330) Disrupting self-conjugate edges 0:45:36.731 13G / 25G INFO Simplification (parallel_processing.hpp : 165) Running Removing isolated edges 0:48:52.929 10G / 25G INFO Simplification (parallel_processing.hpp : 167) Removing isolated edges triggered 10633413 times 0:48:52.930 10G / 25G INFO General (simplification.cpp : 470) Counting average coverage 0:48:53.974 10G / 25G INFO General (simplification.cpp : 476) Average coverage = 2.03362 0:48:53.974 10G / 25G INFO StageManager (stage.cpp : 132) STAGE == Contig Output 0:48:53.974 10G / 25G INFO General (contig_output_stage.cpp : 40) Writing GFA to /local/genbank/workspace/reads.all3.spades1//K99/assembly_graph_with_scaffolds.gfa 0:48:59.236 10G / 25G INFO General (contig_output.hpp : 22) Outputting contigs to /local/genbank/workspace/reads.all3.spades1//K99/before_rr.fasta 0:49:07.143 10G / 25G INFO General (contig_output_stage.cpp : 51) Outputting FastG graph to /local/genbank/workspace/reads.all3.spades1//K99/assembly_graph.fastg 0:49:30.773 10G / 25G INFO General (contig_output.hpp : 22) Outputting contigs to /local/genbank/workspace/reads.all3.spades1//K99/simplified_contigs.fasta 0:49:40.673 10G / 25G INFO General (contig_output.hpp : 22) Outputting contigs to /local/genbank/workspace/reads.all3.spades1//K99/final_contigs.fasta 0:49:49.860 10G / 25G INFO StageManager (stage.cpp : 132) STAGE == Contig Output 0:49:49.861 10G / 25G INFO General (contig_output_stage.cpp : 40) Writing GFA to /local/genbank/workspace/reads.all3.spades1//K99/assembly_graph_with_scaffolds.gfa 0:49:56.109 10G / 25G INFO General (contig_output.hpp : 22) Outputting contigs to /local/genbank/workspace/reads.all3.spades1//K99/before_rr.fasta 0:50:04.243 10G / 25G INFO General (contig_output_stage.cpp : 51) Outputting FastG graph to /local/genbank/workspace/reads.all3.spades1//K99/assembly_graph.fastg 0:50:29.835 10G / 25G INFO General (contig_output.hpp : 22) Outputting contigs to /local/genbank/workspace/reads.all3.spades1//K99/simplified_contigs.fasta 0:50:39.727 10G / 25G INFO General (contig_output.hpp : 22) Outputting contigs to /local/genbank/workspace/reads.all3.spades1//K99/final_contigs.fasta 0:50:47.976 10G / 25G INFO General (launch.hpp : 149) SPAdes finished 0:51:14.302 132M / 25G INFO General (main.cpp : 109) Assembling time: 0 hours 51 minutes 14 seconds == Running assembler: K127 0:00:00.000 4M / 4M INFO General (main.cpp : 74) Loaded config from /local/genbank/workspace/reads.all3.spades1/K127/configs/config.info 0:00:00.000 4M / 4M INFO General (memory_limit.cpp : 49) Memory limit set to 130 Gb 0:00:00.000 4M / 4M INFO General (main.cpp : 87) Starting SPAdes, built from refs/heads/spades_3.13.0, git revision 8ea46659e9b2aca35444a808db550ac333006f8b 0:00:00.000 4M / 4M INFO General (main.cpp : 88) Maximum k-mer length: 128 0:00:00.000 4M / 4M INFO General (main.cpp : 89) Assembling dataset (/local/genbank/workspace/reads.all3.spades1/dataset.info) with K=127 0:00:00.000 4M / 4M INFO General (main.cpp : 90) Maximum # of threads to use (adjusted due to OMP capabilities): 32 0:00:00.000 4M / 4M INFO General (launch.hpp : 51) SPAdes started 0:00:00.000 4M / 4M INFO General (launch.hpp : 58) Starting from stage: construction 0:00:00.000 4M / 4M INFO General (launch.hpp : 65) Two-step RR enabled: 0 0:00:00.000 4M / 4M INFO General (launch.hpp : 76) Will need read mapping, kmer mapper will be attached 0:00:00.000 4M / 4M INFO StageManager (stage.cpp : 132) STAGE == de Bruijn graph construction 0:00:00.005 4M / 4M INFO General (read_converter.hpp : 59) Binary reads detected 0:00:00.070 4M / 4M INFO General (construction.cpp : 111) Max read length 700 0:00:00.070 4M / 4M INFO General (construction.cpp : 117) Average read length 80.6457 0:00:00.070 4M / 4M INFO General (stage.cpp : 101) PROCEDURE == k+1-mer counting 0:00:00.072 4M / 4M INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 1024 files using 32 threads. This might take a while. 0:00:00.075 4M / 4M INFO General (file_limit.hpp : 32) Open file limit set to 4096 0:00:00.075 4M / 4M INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 1.35413 Gb 0:00:00.075 4M / 4M INFO General (kmer_splitters.hpp : 97) Using cell size of 16384 0:00:51.385 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 97156922 reads 0:01:13.749 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 419421056 reads 0:01:13.749 17G / 18G INFO General (kmer_splitters.hpp : 295) Adding contigs from previous K 0:04:39.655 132M / 18G INFO General (kmer_splitters.hpp : 308) Used 419421056 reads 0:04:39.655 132M / 18G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:06:08.606 132M / 18G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 288621279 kmers in total. 0:06:08.606 132M / 18G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:07:48.002 128M / 18G INFO General (stage.cpp : 101) PROCEDURE == Extension index construction 0:07:48.003 128M / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:07:48.003 128M / 18G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 512 files using 32 threads. This might take a while. 0:07:48.005 128M / 18G INFO General (file_limit.hpp : 32) Open file limit set to 4096 0:07:48.005 128M / 18G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 1.35286 Gb 0:07:48.005 128M / 18G INFO General (kmer_splitters.hpp : 97) Using cell size of 32768 0:07:54.794 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 4293766 kmers 0:07:59.684 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 8706816 kmers 0:08:04.315 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 13314325 kmers 0:08:09.223 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 17734344 kmers 0:08:13.913 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 22328180 kmers 0:08:18.855 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 26743715 kmers 0:08:23.566 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 31347579 kmers 0:08:28.513 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 35760347 kmers 0:08:33.326 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 40366305 kmers 0:08:38.450 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 44778084 kmers 0:08:43.219 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 49383452 kmers 0:08:48.081 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 53791612 kmers 0:08:52.732 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 58399557 kmers 0:08:57.652 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 62808012 kmers 0:09:02.654 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 67417715 kmers 0:09:07.548 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 71838221 kmers 0:09:12.248 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 76442356 kmers 0:10:15.140 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 134958414 kmers 0:12:37.799 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 270273654 kmers 0:12:58.361 17G / 18G INFO General (kmer_splitters.hpp : 385) Used 288623327 kmers. 0:13:01.499 132M / 18G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:14:31.746 128M / 18G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 288714787 kmers in total. 0:14:31.746 128M / 18G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:16:10.316 128M / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:16:36.967 320M / 18G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 0:18:11.519 320M / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 133885832 bytes occupied (3.70984 bits per kmer). 0:18:11.875 596M / 18G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 99) Building k-mer extensions from k+1-mers 0:18:28.547 596M / 18G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 103) Building k-mer extensions from k+1-mers finished. 0:18:28.551 596M / 18G INFO General (stage.cpp : 101) PROCEDURE == Condensing graph 0:18:28.725 596M / 18G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 355) Extracting unbranching paths 0:18:50.980 764M / 18G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 374) Extracting unbranching paths finished. 1231854 sequences extracted 0:19:02.483 764M / 18G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 310) Collecting perfect loops 0:19:08.671 764M / 18G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 343) Collecting perfect loops finished. 13 loops collected 0:19:10.715 1G / 18G INFO General (stage.cpp : 101) PROCEDURE == Filling coverage indices (PHM) 0:19:10.715 1G / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:19:10.715 1G / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:19:24.389 1G / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 133850732 bytes occupied (3.71007 bits per kmer). 0:19:24.876 2G / 18G INFO General (construction.cpp : 388) Collecting k-mer coverage information from reads, this takes a while. 0:19:46.936 2G / 18G INFO General (construction.cpp : 508) Filling coverage and flanking coverage from PHM 0:20:02.078 2G / 18G INFO General (construction.cpp : 464) Processed 2463722 edges 0:20:06.479 560M / 18G INFO StageManager (stage.cpp : 132) STAGE == EC Threshold Finding 0:20:06.485 560M / 18G INFO General (kmer_coverage_model.cpp : 181) Kmer coverage valley at: 60 0:20:06.486 560M / 18G INFO General (kmer_coverage_model.cpp : 201) K-mer histogram maximum: 61 0:20:06.486 560M / 18G WARN General (kmer_coverage_model.cpp : 218) Too many erroneous kmers, the estimates might be unreliable 0:20:06.486 560M / 18G INFO General (kmer_coverage_model.cpp : 237) Estimated median coverage: 61. Coverage mad: 25.8925 0:20:06.486 560M / 18G INFO General (kmer_coverage_model.cpp : 259) Fitting coverage model 0:20:06.609 560M / 18G INFO General (kmer_coverage_model.cpp : 295) ... iteration 2 0:20:06.890 560M / 18G INFO General (kmer_coverage_model.cpp : 295) ... iteration 4 0:20:07.733 560M / 18G INFO General (kmer_coverage_model.cpp : 295) ... iteration 8 0:20:09.700 560M / 18G INFO General (kmer_coverage_model.cpp : 295) ... iteration 16 0:20:15.439 560M / 18G INFO General (kmer_coverage_model.cpp : 295) ... iteration 32 0:20:23.637 560M / 18G INFO General (kmer_coverage_model.cpp : 295) ... iteration 64 0:20:40.826 560M / 18G INFO General (kmer_coverage_model.cpp : 295) ... iteration 128 0:20:41.129 560M / 18G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 10.9539. Fitted coverage std. dev: 5.25376 0:20:41.129 560M / 18G WARN General (kmer_coverage_model.cpp : 327) Valley value was estimated improperly, reset to 2 0:20:41.132 560M / 18G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 1 0:20:41.132 560M / 18G WARN General (kmer_coverage_model.cpp : 366) Failed to determine erroneous kmer threshold. Threshold set to: 2 0:20:41.132 560M / 18G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 71572654 0:20:41.133 560M / 18G INFO General (genomic_info_filler.cpp : 114) Failed to estimate mean coverage 0:20:41.133 560M / 18G INFO General (genomic_info_filler.cpp : 127) EC coverage threshold value was calculated as 2 0:20:41.133 560M / 18G INFO General (genomic_info_filler.cpp : 128) Trusted kmer low bound: 0 0:20:41.133 560M / 18G INFO StageManager (stage.cpp : 132) STAGE == Gap Closer 0:20:41.133 560M / 18G INFO General (graph_pack.hpp : 101) Index refill 0:20:41.137 560M / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:20:41.137 560M / 18G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 512 files using 32 threads. This might take a while. 0:20:41.139 560M / 18G INFO General (file_limit.hpp : 32) Open file limit set to 4096 0:20:41.139 560M / 18G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 1.34847 Gb 0:20:41.139 560M / 18G INFO General (kmer_splitters.hpp : 97) Using cell size of 32768 0:22:16.163 18G / 18G INFO General (edge_index_builders.hpp : 77) Processed 2463722 edges 0:22:16.163 18G / 18G INFO General (edge_index_builders.hpp : 82) Used 2463722 sequences. 0:22:20.074 560M / 18G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:23:43.609 560M / 18G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 288621279 kmers in total. 0:23:43.609 560M / 18G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:25:21.820 560M / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:25:48.179 752M / 18G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 0:27:24.780 752M / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 133842416 bytes occupied (3.70984 bits per kmer). 0:27:28.947 7G / 18G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while. 0:27:38.314 7G / 18G INFO General (edge_index.hpp : 92) Index refilled 0:27:38.336 7G / 18G INFO General (gap_closer.cpp : 159) Preparing shift maps 0:27:40.487 7G / 18G INFO General (gap_closer.cpp : 119) Processing paired reads (takes a while) 0:27:44.008 7G / 18G INFO General (gap_closer.cpp : 138) Used 80455197 paired reads 0:27:44.008 7G / 18G INFO General (gap_closer.cpp : 140) Merging paired indices 0:27:44.595 7G / 18G INFO GapCloser (gap_closer.cpp : 346) Closing short gaps 0:27:48.624 7G / 18G INFO GapCloser (gap_closer.cpp : 380) Closing short gaps complete: filled 0 gaps after checking 0 candidates 0:27:48.759 7G / 18G INFO StageManager (stage.cpp : 132) STAGE == Raw Simplification 0:27:49.546 560M / 18G INFO General (simplification.cpp : 128) PROCEDURE == InitialCleaning 0:27:49.546 560M / 18G INFO General (simplification.cpp : 68) Most init cleaning disabled since detected mean 0 was less than activation coverage 10 0:27:49.546 560M / 18G INFO Simplification (parallel_processing.hpp : 165) Running Self conjugate edge remover 0:27:49.677 560M / 18G INFO Simplification (parallel_processing.hpp : 167) Self conjugate edge remover triggered 1 times 0:27:49.677 560M / 18G INFO StageManager (stage.cpp : 132) STAGE == Simplification 0:27:49.677 560M / 18G INFO General (simplification.cpp : 357) Graph simplification started 0:27:49.677 560M / 18G INFO General (graph_simplification.hpp : 634) Creating parallel br instance 0:27:49.677 560M / 18G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 1 0:27:49.677 560M / 18G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:28:07.312 596M / 18G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 451240 times 0:28:07.312 596M / 18G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:28:56.568 1G / 18G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 51393 times 0:28:56.568 1G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:28:56.638 1G / 18G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 175 times 0:28:56.638 1G / 18G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 2 0:28:56.638 1G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:28:56.766 1G / 18G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 1237 times 0:28:56.766 1G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:28:57.048 1G / 18G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 201 times 0:28:57.048 1G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:28:57.051 1G / 18G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 36 times 0:28:57.051 1G / 18G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 3 0:28:57.051 1G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:28:57.051 1G / 18G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 2 times 0:28:57.051 1G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:28:57.099 1G / 18G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 32 times 0:28:57.099 1G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:28:57.102 1G / 18G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 41 times 0:28:57.102 1G / 18G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 4 0:28:57.102 1G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:28:57.102 1G / 18G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:28:57.102 1G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:28:57.146 1G / 18G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 38 times 0:28:57.147 1G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:28:57.151 1G / 18G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 56 times 0:28:57.151 1G / 18G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 5 0:28:57.151 1G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:28:57.152 1G / 18G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 2 times 0:28:57.152 1G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:28:57.196 1G / 18G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 42 times 0:28:57.196 1G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:28:57.896 1G / 18G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 2807 times 0:28:57.896 1G / 18G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 6 0:28:57.896 1G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:28:57.915 1G / 18G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 283 times 0:28:57.915 1G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:28:58.606 1G / 18G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 523 times 0:28:58.606 1G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:28:58.655 1G / 18G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 379 times 0:28:58.655 1G / 18G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 7 0:28:58.655 1G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:28:58.660 1G / 18G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 47 times 0:28:58.660 1G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:28:58.772 1G / 18G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 79 times 0:28:58.772 1G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:28:58.792 1G / 18G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 171 times 0:28:58.792 1G / 18G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 8 0:28:58.792 1G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:28:58.793 1G / 18G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 8 times 0:28:58.793 1G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:28:58.859 1G / 18G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 40 times 0:28:58.859 1G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:28:58.882 1G / 18G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 160 times 0:28:58.882 1G / 18G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 9 0:28:58.882 1G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:28:58.883 1G / 18G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 12 times 0:28:58.883 1G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:28:58.920 1G / 18G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 31 times 0:28:58.920 1G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:28:58.941 1G / 18G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 136 times 0:28:58.941 1G / 18G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 10 0:28:58.941 1G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:28:58.941 1G / 18G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 10 times 0:28:58.941 1G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:28:58.989 1G / 18G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 33 times 0:28:58.989 1G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:28:59.140 1G / 18G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 486 times 0:28:59.140 1G / 18G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 11 0:28:59.140 1G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:28:59.224 1G / 18G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 175 times 0:28:59.224 1G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:28:59.436 1G / 18G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 103 times 0:28:59.437 1G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:28:59.486 1G / 18G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:28:59.486 1G / 18G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 12 0:28:59.486 1G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:28:59.487 1G / 18G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 3 times 0:28:59.487 1G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:28:59.490 1G / 18G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 2 times 0:28:59.490 1G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:28:59.490 1G / 18G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:28:59.490 1G / 18G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 13 0:28:59.490 1G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:28:59.490 1G / 18G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:28:59.490 1G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:28:59.490 1G / 18G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:28:59.490 1G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:28:59.490 1G / 18G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:28:59.490 1G / 18G INFO StageManager (stage.cpp : 132) STAGE == Gap Closer 0:28:59.490 1G / 18G INFO General (graph_pack.hpp : 101) Index refill 0:28:59.496 1G / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:28:59.496 1G / 18G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 512 files using 32 threads. This might take a while. 0:28:59.498 1G / 18G INFO General (file_limit.hpp : 32) Open file limit set to 4096 0:28:59.498 1G / 18G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 1.33728 Gb 0:28:59.498 1G / 18G INFO General (kmer_splitters.hpp : 97) Using cell size of 32768 0:30:24.964 19G / 19G INFO General (edge_index_builders.hpp : 77) Processed 323539 edges 0:30:24.964 19G / 19G INFO General (edge_index_builders.hpp : 82) Used 323539 sequences. 0:30:28.450 1G / 19G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:31:42.305 1G / 19G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 254608231 kmers in total. 0:31:42.305 1G / 19G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:33:09.881 1G / 19G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:33:31.012 1G / 19G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 0:34:54.665 1G / 19G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 118070344 bytes occupied (3.70987 bits per kmer). 0:35:00.336 7G / 19G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while. 0:35:08.860 7G / 19G INFO General (edge_index.hpp : 92) Index refilled 0:35:08.882 7G / 19G INFO General (gap_closer.cpp : 159) Preparing shift maps 0:35:09.691 7G / 19G INFO General (gap_closer.cpp : 119) Processing paired reads (takes a while) 0:35:13.043 7G / 19G INFO General (gap_closer.cpp : 138) Used 80455197 paired reads 0:35:13.043 7G / 19G INFO General (gap_closer.cpp : 140) Merging paired indices 0:35:13.247 7G / 19G INFO GapCloser (gap_closer.cpp : 346) Closing short gaps 0:35:13.931 7G / 19G INFO GapCloser (gap_closer.cpp : 380) Closing short gaps complete: filled 0 gaps after checking 0 candidates 0:35:14.006 7G / 19G INFO StageManager (stage.cpp : 132) STAGE == Simplification Cleanup 0:35:14.006 7G / 19G INFO General (simplification.cpp : 196) PROCEDURE == Post simplification 0:35:14.006 7G / 19G INFO General (graph_simplification.hpp : 453) Disconnection of relatively low covered edges disabled 0:35:14.006 7G / 19G INFO General (graph_simplification.hpp : 489) Complex tip clipping disabled 0:35:14.006 7G / 19G INFO General (graph_simplification.hpp : 634) Creating parallel br instance 0:35:14.006 7G / 19G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:35:14.082 7G / 19G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:35:14.082 7G / 19G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:35:14.181 7G / 19G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 1 times 0:35:14.181 7G / 19G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:35:14.232 7G / 19G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:35:14.232 7G / 19G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:35:14.301 7G / 19G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:35:14.301 7G / 19G INFO General (simplification.cpp : 330) Disrupting self-conjugate edges 0:35:14.674 7G / 19G INFO Simplification (parallel_processing.hpp : 165) Running Removing isolated edges 0:35:57.524 7G / 19G INFO Simplification (parallel_processing.hpp : 167) Removing isolated edges triggered 66872 times 0:35:57.524 7G / 19G INFO General (simplification.cpp : 470) Counting average coverage 0:35:57.765 7G / 19G INFO General (simplification.cpp : 476) Average coverage = 1.78218 0:35:57.765 7G / 19G WARN General (simplification.cpp : 479) The determined erroneous connection coverage threshold may be determined improperly 0:35:57.765 7G / 19G INFO StageManager (stage.cpp : 132) STAGE == Mismatch Correction 0:35:57.765 7G / 19G INFO General (graph_pack.hpp : 109) Normalizing k-mer map. Total 14277686 kmers to process 0:36:17.405 7G / 19G INFO General (graph_pack.hpp : 111) Normalizing done 0:40:42.436 16G / 19G INFO General (mismatch_shall_not_pass.hp: 189) Finished collecting potential mismatches positions 0:41:37.488 7G / 19G INFO General (mismatch_shall_not_pass.hp: 290) All edges processed 0:41:38.340 7G / 19G INFO General (mismatch_correction.cpp : 27) Corrected 102 nucleotides 0:41:38.341 7G / 19G INFO StageManager (stage.cpp : 132) STAGE == Contig Output 0:41:38.341 7G / 19G INFO General (contig_output_stage.cpp : 40) Writing GFA to /local/genbank/workspace/reads.all3.spades1//K127/assembly_graph_with_scaffolds.gfa 0:41:43.028 7G / 19G INFO General (contig_output.hpp : 22) Outputting contigs to /local/genbank/workspace/reads.all3.spades1//K127/before_rr.fasta 0:41:51.344 7G / 19G INFO General (contig_output_stage.cpp : 51) Outputting FastG graph to /local/genbank/workspace/reads.all3.spades1//K127/assembly_graph.fastg 0:42:12.529 7G / 19G INFO General (contig_output.hpp : 22) Outputting contigs to /local/genbank/workspace/reads.all3.spades1//K127/simplified_contigs.fasta 0:42:19.961 7G / 19G INFO General (contig_output.hpp : 22) Outputting contigs to /local/genbank/workspace/reads.all3.spades1//K127/intermediate_contigs.fasta 0:42:27.394 7G / 19G INFO StageManager (stage.cpp : 132) STAGE == Paired Information Counting 0:42:28.146 7G / 19G INFO General (graph_pack.hpp : 109) Normalizing k-mer map. Total 14296800 kmers to process 0:42:44.643 7G / 19G INFO General (graph_pack.hpp : 111) Normalizing done 0:42:44.784 7G / 19G INFO General (pair_info_count.cpp : 320) Min edge length for estimation: 3522 0:42:44.785 7G / 19G INFO General (pair_info_count.cpp : 331) Estimating insert size for library #0 0:42:44.785 7G / 19G INFO General (pair_info_count.cpp : 190) Estimating insert size (takes a while) 0:42:46.038 7G / 19G INFO General (pair_info_count.cpp : 39) Selecting usual mapper 0:42:51.714 7G / 19G INFO General (sequence_mapper_notifier.h: 80) Processed 200000 reads 0:42:51.989 7G / 19G INFO General (sequence_mapper_notifier.h: 80) Processed 400000 reads 0:42:52.100 7G / 19G INFO General (sequence_mapper_notifier.h: 80) Processed 600000 reads 0:42:52.204 7G / 19G INFO General (sequence_mapper_notifier.h: 80) Processed 800000 reads 0:42:52.317 7G / 19G INFO General (sequence_mapper_notifier.h: 80) Processed 1000000 reads 0:42:52.431 7G / 19G INFO General (sequence_mapper_notifier.h: 80) Processed 1200000 reads 0:42:53.061 7G / 19G INFO General (sequence_mapper_notifier.h: 80) Processed 2200000 reads 0:42:54.020 7G / 19G INFO General (sequence_mapper_notifier.h: 80) Processed 4200000 reads 0:42:55.918 7G / 19G INFO General (sequence_mapper_notifier.h: 80) Processed 8400000 reads 0:43:03.710 7G / 19G INFO General (sequence_mapper_notifier.h: 80) Processed 16800000 reads 0:43:19.703 7G / 19G INFO General (sequence_mapper_notifier.h: 80) Processed 33600000 reads 0:43:51.358 7G / 19G INFO General (sequence_mapper_notifier.h: 80) Processed 67200000 reads 0:44:02.908 7G / 19G INFO General (sequence_mapper_notifier.h: 98) Total 80455197 reads processed 0:44:03.601 7G / 19G INFO General (pair_info_count.cpp : 209) Edge pairs: 67108864 (rough upper limit) 0:44:03.601 7G / 19G INFO General (pair_info_count.cpp : 213) 0 paired reads (0% of all) aligned to long edges 0:44:03.726 7G / 19G WARN General (pair_info_count.cpp : 339) Unable to estimate insert size for paired library #0 0:44:03.726 7G / 19G WARN General (pair_info_count.cpp : 345) None of paired reads aligned properly. Please, check orientation of your read pairs. 0:44:03.727 7G / 19G INFO StageManager (stage.cpp : 132) STAGE == Distance Estimation 0:44:03.727 7G / 19G INFO General (distance_estimation.cpp : 182) Clearing raw paired index 0:44:03.727 7G / 19G INFO StageManager (stage.cpp : 132) STAGE == Repeat Resolving 0:44:03.727 7G / 19G WARN General (repeat_resolving.cpp : 63) Insert size was not estimated for any of the paired libraries, repeat resolution module will not run. 0:44:03.727 7G / 19G INFO StageManager (stage.cpp : 132) STAGE == Contig Output 0:44:03.727 7G / 19G INFO General (contig_output_stage.cpp : 40) Writing GFA to /local/genbank/workspace/reads.all3.spades1//K127/assembly_graph_with_scaffolds.gfa 0:44:09.549 7G / 19G INFO General (contig_output.hpp : 22) Outputting contigs to /local/genbank/workspace/reads.all3.spades1//K127/before_rr.fasta 0:44:17.542 7G / 19G INFO General (contig_output_stage.cpp : 51) Outputting FastG graph to /local/genbank/workspace/reads.all3.spades1//K127/assembly_graph.fastg 0:44:42.984 7G / 19G INFO General (contig_output.hpp : 22) Outputting contigs to /local/genbank/workspace/reads.all3.spades1//K127/simplified_contigs.fasta 0:44:50.841 7G / 19G INFO General (contig_output.hpp : 22) Outputting contigs to /local/genbank/workspace/reads.all3.spades1//K127/final_contigs.fasta 0:44:58.442 7G / 19G INFO General (launch.hpp : 149) SPAdes finished 0:45:11.316 132M / 19G INFO General (main.cpp : 109) Assembling time: 0 hours 45 minutes 11 seconds ===== Assembling finished. Used k-mer sizes: 21, 33, 55, 77, 99, 127 * Assembled contigs are in /local/genbank/workspace/reads.all3.spades1/contigs.fasta * Assembly graph is in /local/genbank/workspace/reads.all3.spades1/assembly_graph.fastg * Assembly graph in GFA format is in /local/genbank/workspace/reads.all3.spades1/assembly_graph_with_scaffolds.gfa ======= SPAdes pipeline finished WITH WARNINGS! === Error correction and assembling warnings: * 0:59:09.918 12G / 18G WARN General (kmer_coverage_model.cpp : 327) Valley value was estimated improperly, reset to 9 * 0:59:09.934 12G / 18G WARN General (kmer_coverage_model.cpp : 366) Failed to determine erroneous kmer threshold. Threshold set to: 9 * 0:53:42.566 6G / 18G WARN General (kmer_coverage_model.cpp : 218) Too many erroneous kmers, the estimates might be unreliable * 0:55:46.646 7G / 18G WARN General (kmer_coverage_model.cpp : 327) Valley value was estimated improperly, reset to 2 * 0:55:46.656 7G / 18G WARN General (kmer_coverage_model.cpp : 366) Failed to determine erroneous kmer threshold. Threshold set to: 2 * 0:43:46.445 16G / 22G WARN General (kmer_coverage_model.cpp : 327) Valley value was estimated improperly, reset to 75 * 0:43:46.460 16G / 22G WARN General (kmer_coverage_model.cpp : 366) Failed to determine erroneous kmer threshold. Threshold set to: 75 * 1:52:21.998 18G / 45G WARN General (simplification.cpp : 479) The determined erroneous connection coverage threshold may be determined improperly * 0:34:59.973 9G / 18G WARN General (kmer_coverage_model.cpp : 327) Valley value was estimated improperly, reset to 8 * 0:34:59.982 9G / 18G WARN General (kmer_coverage_model.cpp : 366) Failed to determine erroneous kmer threshold. Threshold set to: 8 * 0:44:03.726 7G / 19G WARN General (pair_info_count.cpp : 339) Unable to estimate insert size for paired library #0 * 0:44:03.726 7G / 19G WARN General (pair_info_count.cpp : 345) None of paired reads aligned properly. Please, check orientation of your read pairs. * 0:44:03.727 7G / 19G 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.all3.spades1/warnings.log SPAdes log can be found here: /local/genbank/workspace/reads.all3.spades1/spades.log Thank you for using SPAdes!