Command line: /home/psgendb/BIRCHDEV/bin-linux-x86_64/spades.py -1 /local/genbank/workspace/reads.all/AB2kb_R1.illumina-1.8+_valid_1P.fq.corrected.fq -2 /local/genbank/workspace/reads.all/AB2kb_R2.illumina-1.8+_valid_2P.fq.corrected.fq -1 /local/genbank/workspace/reads.all/AB4kb_R1.illumina-1.8+_valid_1P.fq.corrected.fq -2 /local/genbank/workspace/reads.all/AB4kb_R2.illumina-1.8+_valid_2P.fq.corrected.fq -1 /local/genbank/workspace/reads.all/20090202_7_1_1P.fastq.corrected.fq -2 /local/genbank/workspace/reads.all/20090202_7_2_2P.fastq.corrected.fq -1 /local/genbank/workspace/reads.all/20090202_8_1_valid_1P.fq.corrected.fq -2 /local/genbank/workspace/reads.all/20090202_8_2_valid_2P.fq.corrected.fq -1 /local/genbank/workspace/reads.all/Algae6.2GB_6_1_1P.fastq.corrected.fq -2 /local/genbank/workspace/reads.all/Algae6.2GB_6_2_2P.fastq.corrected.fq -1 /local/genbank/workspace/reads.all/Algae6.2GB_7_1_1P.fastq.corrected.fq -2 /local/genbank/workspace/reads.all/Algae6.2GB_7_2_2P.fastq.corrected.fq -1 /local/genbank/workspace/reads.all/Algae6.2GB_8_1_1P.fastq.corrected.fq -2 /local/genbank/workspace/reads.all/Algae6.2GB_8_2_2P.fastq.corrected.fq -1 /local/genbank/workspace/reads.all/Algae7.2GB_6_1_1P.fastq.corrected.fq -2 /local/genbank/workspace/reads.all/Algae7.2GB_6_2_2P.fastq.corrected.fq -1 /local/genbank/workspace/reads.all/Algae7.2GB_7_1_1P.fastq.corrected.fq -2 /local/genbank/workspace/reads.all/Algae7.2GB_7_2_2P.fastq.corrected.fq -1 /local/genbank/workspace/reads.all/Algae7.2GB_8_1_1P.fastq.corrected.fq -2 /local/genbank/workspace/reads.all/Algae7.2GB_8_2_2P.fastq.corrected.fq -s /local/genbank/workspace/reads.all/454.corrected.fq -s /local/genbank/workspace/reads.all/2008SE.fq -s /local/genbank/workspace/reads.all/20090202.pollux.unpaired.fq -s /local/genbank/workspace/reads.all/367GB.fq -s /local/genbank/workspace/reads.all/AB4kbUnpaired.fq --only-assembler -k 21,33,41 -m 63 -t 32 -o /local/genbank/workspace/reads.all/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.all/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.all/AB2kb_R1.illumina-1.8+_valid_1P.fq.corrected.fq', '/local/genbank/workspace/reads.all/AB4kb_R1.illumina-1.8+_valid_1P.fq.corrected.fq', '/local/genbank/workspace/reads.all/20090202_7_1_1P.fastq.corrected.fq', '/local/genbank/workspace/reads.all/20090202_8_1_valid_1P.fq.corrected.fq', '/local/genbank/workspace/reads.all/Algae6.2GB_6_1_1P.fastq.corrected.fq', '/local/genbank/workspace/reads.all/Algae6.2GB_7_1_1P.fastq.corrected.fq', '/local/genbank/workspace/reads.all/Algae6.2GB_8_1_1P.fastq.corrected.fq', '/local/genbank/workspace/reads.all/Algae7.2GB_6_1_1P.fastq.corrected.fq', '/local/genbank/workspace/reads.all/Algae7.2GB_7_1_1P.fastq.corrected.fq', '/local/genbank/workspace/reads.all/Algae7.2GB_8_1_1P.fastq.corrected.fq'] right reads: ['/local/genbank/workspace/reads.all/AB2kb_R2.illumina-1.8+_valid_2P.fq.corrected.fq', '/local/genbank/workspace/reads.all/AB4kb_R2.illumina-1.8+_valid_2P.fq.corrected.fq', '/local/genbank/workspace/reads.all/20090202_7_2_2P.fastq.corrected.fq', '/local/genbank/workspace/reads.all/20090202_8_2_valid_2P.fq.corrected.fq', '/local/genbank/workspace/reads.all/Algae6.2GB_6_2_2P.fastq.corrected.fq', '/local/genbank/workspace/reads.all/Algae6.2GB_7_2_2P.fastq.corrected.fq', '/local/genbank/workspace/reads.all/Algae6.2GB_8_2_2P.fastq.corrected.fq', '/local/genbank/workspace/reads.all/Algae7.2GB_6_2_2P.fastq.corrected.fq', '/local/genbank/workspace/reads.all/Algae7.2GB_7_2_2P.fastq.corrected.fq', '/local/genbank/workspace/reads.all/Algae7.2GB_8_2_2P.fastq.corrected.fq'] interlaced reads: not specified single reads: ['/local/genbank/workspace/reads.all/454.corrected.fq', '/local/genbank/workspace/reads.all/2008SE.fq', '/local/genbank/workspace/reads.all/20090202.pollux.unpaired.fq', '/local/genbank/workspace/reads.all/367GB.fq', '/local/genbank/workspace/reads.all/AB4kbUnpaired.fq'] merged reads: not specified Assembly parameters: k: [21, 33, 41] 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.all/spades1/tmp Threads: 32 Memory limit (in Gb): 63 ======= SPAdes pipeline started. Log can be found here: /local/genbank/workspace/reads.all/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.all/spades1/K21/configs/config.info 0:00:00.000 4M / 4M INFO General (memory_limit.cpp : 49) Memory limit set to 63 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.all/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 0:00:00.317 76M / 76M INFO General (binary_converter.hpp : 93) 16384 reads processed 0:00:00.509 88M / 88M INFO General (binary_converter.hpp : 93) 32768 reads processed 0:00:00.896 108M / 108M INFO General (binary_converter.hpp : 93) 65536 reads processed 0:00:01.681 148M / 148M INFO General (binary_converter.hpp : 93) 131072 reads processed 0:00:03.294 228M / 228M INFO General (binary_converter.hpp : 93) 262144 reads processed 0:00:06.417 388M / 388M INFO General (binary_converter.hpp : 93) 524288 reads processed 0:00:15.778 644M / 644M INFO General (binary_converter.hpp : 93) 1048576 reads processed 0:00:31.442 648M / 648M INFO General (binary_converter.hpp : 93) 2097152 reads processed 0:01:03.629 684M / 684M INFO General (binary_converter.hpp : 93) 4194304 reads processed 0:02:12.090 708M / 708M INFO General (binary_converter.hpp : 93) 8388608 reads processed 0:04:24.653 728M / 728M INFO General (binary_converter.hpp : 93) 16777216 reads processed 0:08:19.215 652M / 856M INFO General (binary_converter.hpp : 93) 33554432 reads processed 0:08:40.630 604M / 856M INFO General (binary_converter.hpp : 117) 35067264 reads written 0:08:42.374 4M / 856M INFO General (read_converter.hpp : 87) Converting single reads 0:08:42.763 144M / 856M INFO General (binary_converter.hpp : 93) 16384 reads processed 0:08:42.999 156M / 856M INFO General (binary_converter.hpp : 93) 32768 reads processed 0:08:43.490 184M / 856M INFO General (binary_converter.hpp : 93) 65536 reads processed 0:08:44.472 240M / 856M INFO General (binary_converter.hpp : 93) 131072 reads processed 0:08:46.299 340M / 856M INFO General (binary_converter.hpp : 93) 262144 reads processed 0:08:49.133 508M / 856M INFO General (binary_converter.hpp : 93) 524288 reads processed 0:08:55.856 904M / 904M INFO General (binary_converter.hpp : 93) 1048576 reads processed 0:09:02.923 1G / 1G INFO General (binary_converter.hpp : 93) 2097152 reads processed 0:09:11.799 1G / 1G INFO General (binary_converter.hpp : 93) 4194304 reads processed 0:09:38.862 1G / 1G INFO General (binary_converter.hpp : 93) 8388608 reads processed 0:10:24.881 1G / 1G INFO General (binary_converter.hpp : 93) 16777216 reads processed 0:11:08.667 956M / 1G INFO General (binary_converter.hpp : 117) 22655284 reads written 0:11:10.904 8M / 1G INFO General (read_converter.hpp : 95) Converting merged reads 0:11:11.123 136M / 1G INFO General (binary_converter.hpp : 117) 0 reads written 0:11:11.956 4M / 1G INFO General (construction.cpp : 111) Max read length 581 0:11:11.956 4M / 1G INFO General (construction.cpp : 117) Average read length 84.7984 0:11:11.956 4M / 1G INFO General (stage.cpp : 101) PROCEDURE == k+1-mer counting 0:11:11.959 4M / 1G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 1024 files using 32 threads. This might take a while. 0:11:11.961 4M / 1G INFO General (file_limit.hpp : 32) Open file limit set to 4096 0:11:11.961 4M / 1G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 0.656209 Gb 0:11:11.961 4M / 1G INFO General (kmer_splitters.hpp : 97) Using cell size of 65536 0:11:31.066 17G / 17G INFO General (kmer_splitters.hpp : 289) Processed 8318310 reads 0:11:39.749 17G / 17G INFO General (kmer_splitters.hpp : 289) Processed 16250767 reads 0:11:47.773 17G / 17G INFO General (kmer_splitters.hpp : 289) Processed 21868794 reads 0:11:55.672 17G / 17G INFO General (kmer_splitters.hpp : 289) Processed 26431605 reads 0:12:07.530 17G / 17G INFO General (kmer_splitters.hpp : 289) Processed 38812138 reads 0:12:17.482 17G / 17G INFO General (kmer_splitters.hpp : 289) Processed 43948018 reads 0:12:40.218 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 60665745 reads 0:13:05.676 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 81585029 reads 0:13:31.638 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 100411489 reads 0:13:49.476 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 112351063 reads 0:14:07.704 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 124502000 reads 0:14:22.910 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 142930962 reads 0:14:40.776 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 162952407 reads 0:15:07.486 17G / 18G INFO General (kmer_splitters.hpp : 295) Adding contigs from previous K 0:15:10.983 132M / 18G INFO General (kmer_splitters.hpp : 308) Used 185579624 reads 0:15:10.983 132M / 18G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:16:09.064 132M / 18G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 577961569 kmers in total. 0:16:09.064 132M / 18G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:16:59.939 128M / 18G INFO General (stage.cpp : 101) PROCEDURE == Extension index construction 0:16:59.941 128M / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:16:59.941 128M / 18G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 512 files using 32 threads. This might take a while. 0:16:59.943 128M / 18G INFO General (file_limit.hpp : 32) Open file limit set to 4096 0:16:59.943 128M / 18G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 0.654948 Gb 0:16:59.943 128M / 18G INFO General (kmer_splitters.hpp : 97) Using cell size of 131072 0:17:05.243 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 5812282 kmers 0:17:10.240 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 23761997 kmers 0:17:14.939 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 41821394 kmers 0:17:19.963 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 59871649 kmers 0:17:24.692 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 77950246 kmers 0:17:30.152 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 96003505 kmers 0:17:34.915 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 114058683 kmers 0:17:40.143 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 132117803 kmers 0:17:44.905 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 150179704 kmers 0:17:50.113 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 168234545 kmers 0:17:54.888 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 186295144 kmers 0:18:00.088 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 204353169 kmers 0:18:04.830 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 222419941 kmers 0:18:09.896 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 240469168 kmers 0:18:14.712 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 258536739 kmers 0:18:20.309 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 276605991 kmers 0:18:25.177 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 294659159 kmers 0:18:30.473 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 312722232 kmers 0:18:35.238 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 330791028 kmers 0:19:35.803 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 547543355 kmers 0:19:45.888 17G / 18G INFO General (kmer_splitters.hpp : 385) Used 577962593 kmers. 0:19:49.437 128M / 18G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:20:41.588 128M / 18G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 570306882 kmers in total. 0:20:41.589 128M / 18G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:21:32.627 128M / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:22:10.642 396M / 18G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 0:22:57.872 396M / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 264465336 bytes occupied (3.7098 bits per kmer). 0:22:58.582 940M / 18G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 99) Building k-mer extensions from k+1-mers 0:23:33.219 940M / 18G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 103) Building k-mer extensions from k+1-mers finished. 0:23:33.226 940M / 18G INFO General (stage.cpp : 101) PROCEDURE == Early tip clipping 0:23:33.226 940M / 18G INFO General (construction.cpp : 253) Early tip clipper length bound set as (RL - K) 0:23:33.226 940M / 18G INFO Early tip clipping (early_simplification.hpp : 181) Early tip clipping 0:24:46.976 992M / 18G INFO Early tip clipping (early_simplification.hpp : 184) 89555130 22-mers were removed by early tip clipper 0:24:46.976 992M / 18G INFO General (stage.cpp : 101) PROCEDURE == Condensing graph 0:24:47.248 992M / 18G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 355) Extracting unbranching paths 0:25:32.695 2G / 18G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 374) Extracting unbranching paths finished. 24395645 sequences extracted 0:25:52.632 2G / 18G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 310) Collecting perfect loops 0:26:04.301 2G / 18G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 343) Collecting perfect loops finished. 772 loops collected 0:26:22.561 7G / 18G INFO General (stage.cpp : 101) PROCEDURE == Filling coverage indices (PHM) 0:26:22.562 7G / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:26:22.564 7G / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:26:41.888 7G / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 268029100 bytes occupied (3.70999 bits per kmer). 0:26:42.870 10G / 18G INFO General (construction.cpp : 388) Collecting k-mer coverage information from reads, this takes a while. 0:29:13.596 10G / 18G INFO General (construction.cpp : 508) Filling coverage and flanking coverage from PHM 0:29:31.839 10G / 18G INFO General (construction.cpp : 464) Processed 32000000 edges 0:29:40.860 10G / 18G INFO General (construction.cpp : 464) Processed 48777661 edges 0:29:43.855 6G / 18G INFO StageManager (stage.cpp : 132) STAGE == EC Threshold Finding 0:29:46.730 7G / 18G INFO General (kmer_coverage_model.cpp : 181) Kmer coverage valley at: 207 0:29:46.775 6G / 18G INFO General (kmer_coverage_model.cpp : 201) K-mer histogram maximum: 208 0:29:46.775 6G / 18G WARN General (kmer_coverage_model.cpp : 218) Too many erroneous kmers, the estimates might be unreliable 0:29:46.775 6G / 18G INFO General (kmer_coverage_model.cpp : 237) Estimated median coverage: 208. Coverage mad: 47.8124 0:29:46.832 6G / 18G INFO General (kmer_coverage_model.cpp : 259) Fitting coverage model 0:29:47.732 7G / 18G INFO General (kmer_coverage_model.cpp : 295) ... iteration 2 0:29:49.851 7G / 18G INFO General (kmer_coverage_model.cpp : 295) ... iteration 4 0:29:56.404 7G / 18G INFO General (kmer_coverage_model.cpp : 295) ... iteration 8 0:30:09.940 7G / 18G INFO General (kmer_coverage_model.cpp : 295) ... iteration 16 0:30:37.468 7G / 18G INFO General (kmer_coverage_model.cpp : 295) ... iteration 32 0:31:20.276 7G / 18G INFO General (kmer_coverage_model.cpp : 295) ... iteration 64 0:32:39.147 7G / 18G INFO General (kmer_coverage_model.cpp : 295) ... iteration 128 0:32:49.963 7G / 18G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 12.2837. Fitted coverage std. dev: 5.20231 0:32:49.965 7G / 18G WARN General (kmer_coverage_model.cpp : 327) Valley value was estimated improperly, reset to 6 0:32:49.982 7G / 18G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 0.790539 0:32:49.982 7G / 18G WARN General (kmer_coverage_model.cpp : 366) Failed to determine erroneous kmer threshold. Threshold set to: 6 0:32:49.982 7G / 18G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 196643526 0:32:49.984 6G / 18G INFO General (genomic_info_filler.cpp : 114) Failed to estimate mean coverage 0:32:49.984 6G / 18G INFO General (genomic_info_filler.cpp : 127) EC coverage threshold value was calculated as 6 0:32:49.984 6G / 18G INFO General (genomic_info_filler.cpp : 128) Trusted kmer low bound: 0 0:32:49.984 6G / 18G INFO StageManager (stage.cpp : 132) STAGE == Raw Simplification 0:32:49.984 6G / 18G INFO General (simplification.cpp : 128) PROCEDURE == InitialCleaning 0:32:50.018 6G / 18G INFO General (simplification.cpp : 68) Most init cleaning disabled since detected mean 0 was less than activation coverage 10 0:32:50.018 6G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Self conjugate edge remover 0:32:51.951 6G / 18G INFO Simplification (parallel_processing.hpp : 167) Self conjugate edge remover triggered 0 times 0:32:51.951 6G / 18G INFO StageManager (stage.cpp : 132) STAGE == Simplification 0:32:51.952 6G / 18G INFO General (simplification.cpp : 357) Graph simplification started 0:32:51.952 6G / 18G INFO General (graph_simplification.hpp : 634) Creating parallel br instance 0:32:51.952 6G / 18G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 1 0:32:51.952 6G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:33:07.724 6G / 18G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 359835 times 0:33:07.724 6G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:41:00.728 7G / 18G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 937601 times 0:41:00.728 7G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:41:28.740 7G / 18G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:41:28.740 7G / 18G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 2 0:41:28.741 7G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:41:34.307 7G / 18G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 48900 times 0:41:34.307 7G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:41:38.237 7G / 18G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 749 times 0:41:38.237 7G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:47:28.731 7G / 18G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 4344337 times 0:47:28.731 7G / 18G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 3 0:47:28.731 7G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:47:37.846 7G / 18G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 109585 times 0:47:37.847 7G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:49:38.370 7G / 18G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 127022 times 0:49:38.370 7G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:50:05.538 7G / 18G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 314383 times 0:50:05.538 7G / 18G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 4 0:50:05.538 7G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:50:07.519 7G / 18G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 14098 times 0:50:07.519 7G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:50:27.250 7G / 18G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 19813 times 0:50:27.250 7G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:51:58.539 7G / 18G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 956747 times 0:51:58.539 7G / 18G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 5 0:51:58.539 7G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:52:01.299 7G / 18G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 33466 times 0:52:01.300 7G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:52:46.606 7G / 18G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 57094 times 0:52:46.606 7G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:53:14.908 7G / 18G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 331907 times 0:53:14.908 7G / 18G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 6 0:53:14.908 7G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:53:16.329 7G / 18G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 13085 times 0:53:16.329 7G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:53:37.065 7G / 18G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 26195 times 0:53:37.065 7G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:53:47.314 7G / 18G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 133895 times 0:53:47.314 7G / 18G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 7 0:53:47.314 7G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:53:47.908 7G / 18G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 5124 times 0:53:47.908 7G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:53:56.615 7G / 18G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 11008 times 0:53:56.615 7G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:54:09.427 7G / 18G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 164968 times 0:54:09.427 7G / 18G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 8 0:54:09.427 7G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:54:09.972 7G / 18G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 5534 times 0:54:09.972 7G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:54:19.868 7G / 18G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 13639 times 0:54:19.868 7G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:54:25.491 7G / 18G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 76044 times 0:54:25.491 7G / 18G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 9 0:54:25.491 7G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:54:25.780 7G / 18G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 2698 times 0:54:25.780 7G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:54:31.348 7G / 18G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 6754 times 0:54:31.348 7G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:54:39.041 7G / 18G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 102386 times 0:54:39.041 7G / 18G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 10 0:54:39.041 7G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:54:39.372 7G / 18G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 2962 times 0:54:39.372 7G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:54:45.865 7G / 18G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 8876 times 0:54:45.865 7G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:54:51.412 7G / 18G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 76876 times 0:54:51.412 7G / 18G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 11 0:54:51.412 7G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:54:52.330 7G / 18G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 5027 times 0:54:52.330 7G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:55:14.546 7G / 18G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 10180 times 0:55:14.547 7G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:55:15.733 7G / 18G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 166 times 0:55:15.733 7G / 18G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 12 0:55:15.733 7G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:55:15.802 7G / 18G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 15 times 0:55:15.802 7G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:55:15.848 7G / 18G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 3 times 0:55:15.848 7G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:55:15.848 7G / 18G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:55:15.848 7G / 18G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 13 0:55:15.848 7G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:55:15.848 7G / 18G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:55:15.848 7G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:55:15.848 7G / 18G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:55:15.848 7G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:55:15.848 7G / 18G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:55:15.848 7G / 18G INFO StageManager (stage.cpp : 132) STAGE == Simplification Cleanup 0:55:15.848 7G / 18G INFO General (simplification.cpp : 196) PROCEDURE == Post simplification 0:55:15.848 7G / 18G INFO General (graph_simplification.hpp : 453) Disconnection of relatively low covered edges disabled 0:55:15.848 7G / 18G INFO General (graph_simplification.hpp : 489) Complex tip clipping disabled 0:55:15.849 7G / 18G INFO General (graph_simplification.hpp : 634) Creating parallel br instance 0:55:15.849 7G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:55:16.446 7G / 18G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 2 times 0:55:16.447 7G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:55:33.493 7G / 18G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 76 times 0:55:33.493 7G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:55:34.079 7G / 18G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:55:34.080 7G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:55:51.473 7G / 18G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 3 times 0:55:51.474 7G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:55:51.474 7G / 18G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:55:51.474 7G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:55:51.474 7G / 18G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:55:51.474 7G / 18G INFO General (simplification.cpp : 330) Disrupting self-conjugate edges 0:55:59.295 7G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Removing isolated edges 0:56:08.963 6G / 18G INFO Simplification (parallel_processing.hpp : 167) Removing isolated edges triggered 722837 times 0:56:08.963 6G / 18G INFO General (simplification.cpp : 470) Counting average coverage 0:56:13.766 6G / 18G INFO General (simplification.cpp : 476) Average coverage = 26.3161 0:56:13.767 6G / 18G INFO StageManager (stage.cpp : 132) STAGE == Contig Output 0:56:13.767 6G / 18G INFO General (contig_output_stage.cpp : 40) Writing GFA to /local/genbank/workspace/reads.all/spades1//K21/assembly_graph_with_scaffolds.gfa 0:56:30.013 6G / 18G INFO General (contig_output.hpp : 22) Outputting contigs to /local/genbank/workspace/reads.all/spades1//K21/before_rr.fasta 0:56:50.760 6G / 18G INFO General (contig_output_stage.cpp : 51) Outputting FastG graph to /local/genbank/workspace/reads.all/spades1//K21/assembly_graph.fastg 0:57:49.956 6G / 18G INFO General (contig_output.hpp : 22) Outputting contigs to /local/genbank/workspace/reads.all/spades1//K21/simplified_contigs.fasta 0:58:10.072 6G / 18G INFO General (contig_output.hpp : 22) Outputting contigs to /local/genbank/workspace/reads.all/spades1//K21/final_contigs.fasta 0:58:29.689 6G / 18G INFO StageManager (stage.cpp : 132) STAGE == Contig Output 0:58:29.689 6G / 18G INFO General (contig_output_stage.cpp : 40) Writing GFA to /local/genbank/workspace/reads.all/spades1//K21/assembly_graph_with_scaffolds.gfa 0:58:42.266 6G / 18G INFO General (contig_output.hpp : 22) Outputting contigs to /local/genbank/workspace/reads.all/spades1//K21/before_rr.fasta 0:59:01.860 6G / 18G INFO General (contig_output_stage.cpp : 51) Outputting FastG graph to /local/genbank/workspace/reads.all/spades1//K21/assembly_graph.fastg 1:00:08.158 6G / 18G INFO General (contig_output.hpp : 22) Outputting contigs to /local/genbank/workspace/reads.all/spades1//K21/simplified_contigs.fasta 1:00:34.160 6G / 18G INFO General (contig_output.hpp : 22) Outputting contigs to /local/genbank/workspace/reads.all/spades1//K21/final_contigs.fasta 1:00:58.797 6G / 18G INFO General (launch.hpp : 149) SPAdes finished 1:01:31.266 128M / 18G INFO General (main.cpp : 109) Assembling time: 1 hours 1 minutes 31 seconds Max read length detected as 581 == Running assembler: K33 0:00:00.000 4M / 4M INFO General (main.cpp : 74) Loaded config from /local/genbank/workspace/reads.all/spades1/K33/configs/config.info 0:00:00.000 4M / 4M INFO General (memory_limit.cpp : 49) Memory limit set to 63 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.all/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 0:00:00.121 4M / 4M INFO General (construction.cpp : 111) Max read length 581 0:00:00.121 4M / 4M INFO General (construction.cpp : 117) Average read length 84.7984 0:00:00.121 4M / 4M INFO General (stage.cpp : 101) PROCEDURE == k+1-mer counting 0:00:00.124 4M / 4M INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 1024 files using 32 threads. This might take a while. 0:00:00.127 4M / 4M INFO General (file_limit.hpp : 32) Open file limit set to 4096 0:00:00.127 4M / 4M INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 0.656209 Gb 0:00:00.127 4M / 4M INFO General (kmer_splitters.hpp : 97) Using cell size of 32768 0:00:25.700 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 5348330 reads 0:00:37.139 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 11160655 reads 0:00:47.371 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 16163265 reads 0:00:56.794 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 20157154 reads 0:01:06.363 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 23504777 reads 0:01:15.273 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 26442095 reads 0:01:28.946 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 35305672 reads 0:01:42.058 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 41334747 reads 0:01:53.582 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 44369076 reads 0:02:23.206 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 55108017 reads 0:02:57.660 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 68913981 reads 0:03:32.338 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 82742955 reads 0:06:07.116 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 145823362 reads 0:07:22.517 17G / 18G INFO General (kmer_splitters.hpp : 295) Adding contigs from previous K 0:09:23.180 132M / 18G INFO General (kmer_splitters.hpp : 308) Used 185579624 reads 0:09:23.180 132M / 18G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:11:54.081 132M / 18G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 630736253 kmers in total. 0:11:54.081 132M / 18G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:14:06.746 128M / 18G INFO General (stage.cpp : 101) PROCEDURE == Extension index construction 0:14:06.752 128M / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:14:06.752 128M / 18G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 512 files using 32 threads. This might take a while. 0:14:06.754 128M / 18G INFO General (file_limit.hpp : 32) Open file limit set to 4096 0:14:06.754 128M / 18G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 0.654948 Gb 0:14:06.754 128M / 18G INFO General (kmer_splitters.hpp : 97) Using cell size of 65536 0:14:14.197 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 7292370 kmers 0:14:19.402 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 15623874 kmers 0:14:24.972 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 26935452 kmers 0:14:30.281 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 35268686 kmers 0:14:35.858 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 46644189 kmers 0:14:41.130 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 54985599 kmers 0:14:46.965 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 66353319 kmers 0:14:52.414 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 74695671 kmers 0:14:58.331 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 86062133 kmers 0:15:03.559 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 94406472 kmers 0:15:09.369 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 105780585 kmers 0:15:14.648 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 114130962 kmers 0:15:20.560 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 125490479 kmers 0:15:25.760 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 133830864 kmers 0:15:31.972 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 145207853 kmers 0:15:37.037 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 153550380 kmers 0:15:43.409 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 164914343 kmers 0:15:48.525 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 173258289 kmers 0:16:43.949 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 271822405 kmers 0:19:13.655 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 539408532 kmers 0:20:07.124 17G / 18G INFO General (kmer_splitters.hpp : 385) Used 630738301 kmers. 0:20:10.671 128M / 18G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:21:52.533 128M / 18G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 628343271 kmers in total. 0:21:52.533 128M / 18G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:23:39.675 128M / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:24:24.615 452M / 18G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 0:26:00.641 452M / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 291387772 bytes occupied (3.70992 bits per kmer). 0:26:01.420 1G / 18G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 99) Building k-mer extensions from k+1-mers 0:26:36.067 1G / 18G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 103) Building k-mer extensions from k+1-mers finished. 0:26:36.071 1G / 18G INFO General (stage.cpp : 101) PROCEDURE == Early tip clipping 0:26:36.071 1G / 18G INFO General (construction.cpp : 253) Early tip clipper length bound set as (RL - K) 0:26:36.071 1G / 18G INFO Early tip clipping (early_simplification.hpp : 181) Early tip clipping 0:27:52.645 1G / 18G INFO Early tip clipping (early_simplification.hpp : 184) 150095228 34-mers were removed by early tip clipper 0:27:52.645 1G / 18G INFO General (stage.cpp : 101) PROCEDURE == Condensing graph 0:27:52.894 1G / 18G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 355) Extracting unbranching paths 0:28:36.901 1G / 18G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 374) Extracting unbranching paths finished. 13442217 sequences extracted 0:28:55.876 1G / 18G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 310) Collecting perfect loops 0:29:09.057 1G / 18G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 343) Collecting perfect loops finished. 1334 loops collected 0:29:20.557 4G / 18G INFO General (stage.cpp : 101) PROCEDURE == Filling coverage indices (PHM) 0:29:20.557 4G / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:29:20.557 4G / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:29:46.373 5G / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 292498776 bytes occupied (3.70993 bits per kmer). 0:29:47.430 7G / 18G INFO General (construction.cpp : 388) Collecting k-mer coverage information from reads, this takes a while. 0:31:52.639 7G / 18G INFO General (construction.cpp : 508) Filling coverage and flanking coverage from PHM 0:32:17.654 7G / 18G INFO General (construction.cpp : 464) Processed 26880088 edges 0:32:22.043 4G / 18G INFO StageManager (stage.cpp : 132) STAGE == EC Threshold Finding 0:32:23.669 4G / 18G INFO General (kmer_coverage_model.cpp : 181) Kmer coverage valley at: 174 0:32:23.720 4G / 18G INFO General (kmer_coverage_model.cpp : 201) K-mer histogram maximum: 175 0:32:23.720 4G / 18G WARN General (kmer_coverage_model.cpp : 218) Too many erroneous kmers, the estimates might be unreliable 0:32:23.720 4G / 18G INFO General (kmer_coverage_model.cpp : 237) Estimated median coverage: 175. Coverage mad: 43.8559 0:32:23.781 4G / 18G INFO General (kmer_coverage_model.cpp : 259) Fitting coverage model 0:32:24.461 4G / 18G INFO General (kmer_coverage_model.cpp : 295) ... iteration 2 0:32:26.007 4G / 18G INFO General (kmer_coverage_model.cpp : 295) ... iteration 4 0:32:30.797 4G / 18G INFO General (kmer_coverage_model.cpp : 295) ... iteration 8 0:32:41.579 4G / 18G INFO General (kmer_coverage_model.cpp : 295) ... iteration 16 0:33:03.528 4G / 18G INFO General (kmer_coverage_model.cpp : 295) ... iteration 32 0:33:41.435 4G / 18G INFO General (kmer_coverage_model.cpp : 295) ... iteration 64 0:34:48.501 4G / 18G INFO General (kmer_coverage_model.cpp : 295) ... iteration 128 0:35:22.977 4G / 18G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 10.6468. Fitted coverage std. dev: 4.44345 0:35:22.977 4G / 18G WARN General (kmer_coverage_model.cpp : 327) Valley value was estimated improperly, reset to 5 0:35:22.990 4G / 18G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 0.838632 0:35:22.990 4G / 18G WARN General (kmer_coverage_model.cpp : 366) Failed to determine erroneous kmer threshold. Threshold set to: 5 0:35:22.990 4G / 18G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 196943524 0:35:22.991 4G / 18G INFO General (genomic_info_filler.cpp : 114) Failed to estimate mean coverage 0:35:22.991 4G / 18G INFO General (genomic_info_filler.cpp : 127) EC coverage threshold value was calculated as 5 0:35:22.991 4G / 18G INFO General (genomic_info_filler.cpp : 128) Trusted kmer low bound: 0 0:35:22.991 4G / 18G INFO StageManager (stage.cpp : 132) STAGE == Raw Simplification 0:35:22.991 4G / 18G INFO General (simplification.cpp : 128) PROCEDURE == InitialCleaning 0:35:22.991 4G / 18G INFO General (simplification.cpp : 68) Most init cleaning disabled since detected mean 0 was less than activation coverage 10 0:35:22.991 4G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Self conjugate edge remover 0:35:24.253 4G / 18G INFO Simplification (parallel_processing.hpp : 167) Self conjugate edge remover triggered 1504 times 0:35:24.253 4G / 18G INFO StageManager (stage.cpp : 132) STAGE == Simplification 0:35:24.253 4G / 18G INFO General (simplification.cpp : 357) Graph simplification started 0:35:24.253 4G / 18G INFO General (graph_simplification.hpp : 634) Creating parallel br instance 0:35:24.253 4G / 18G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 1 0:35:24.253 4G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:35:42.345 4G / 18G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 659696 times 0:35:42.345 4G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:38:19.458 4G / 18G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 371784 times 0:38:19.458 4G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:38:30.553 4G / 18G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 11815 times 0:38:30.554 4G / 18G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 2 0:38:30.554 4G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:38:32.957 4G / 18G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 26903 times 0:38:32.957 4G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:38:34.581 4G / 18G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 1071 times 0:38:34.581 4G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:41:01.460 4G / 18G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 1734271 times 0:41:01.460 4G / 18G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 3 0:41:01.460 4G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:41:07.307 4G / 18G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 82963 times 0:41:07.307 4G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:41:46.436 4G / 18G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 51804 times 0:41:46.436 4G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:42:10.267 4G / 18G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 339917 times 0:42:10.267 4G / 18G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 4 0:42:10.267 4G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:42:11.718 4G / 18G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 17156 times 0:42:11.718 4G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:42:24.242 4G / 18G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 16485 times 0:42:24.242 4G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:43:07.573 4G / 18G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 421149 times 0:43:07.573 4G / 18G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 5 0:43:07.573 4G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:43:09.615 4G / 18G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 26683 times 0:43:09.615 4G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:43:23.956 4G / 18G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 25373 times 0:43:23.956 4G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:43:32.996 4G / 18G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 115972 times 0:43:32.996 4G / 18G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 6 0:43:32.996 4G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:43:33.607 4G / 18G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 7241 times 0:43:33.607 4G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:43:39.788 4G / 18G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 9562 times 0:43:39.788 4G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:43:51.827 4G / 18G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 137062 times 0:43:51.827 4G / 18G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 7 0:43:51.827 4G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:43:52.518 4G / 18G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 8573 times 0:43:52.518 4G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:43:58.417 4G / 18G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 11365 times 0:43:58.417 4G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:44:02.473 4G / 18G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 54843 times 0:44:02.473 4G / 18G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 8 0:44:02.473 4G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:44:02.764 4G / 18G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 3464 times 0:44:02.764 4G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:44:06.516 4G / 18G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 5341 times 0:44:06.516 4G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:44:11.687 4G / 18G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 59431 times 0:44:11.687 4G / 18G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 9 0:44:11.687 4G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:44:11.984 4G / 18G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 3540 times 0:44:11.985 4G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:44:14.880 4G / 18G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 5698 times 0:44:14.880 4G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:44:17.741 4G / 18G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 36836 times 0:44:17.741 4G / 18G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 10 0:44:17.741 4G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:44:17.926 4G / 18G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 2205 times 0:44:17.926 4G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:44:19.981 4G / 18G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 3696 times 0:44:19.981 4G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:44:23.060 4G / 18G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 38134 times 0:44:23.060 4G / 18G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 11 0:44:23.060 4G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:44:24.117 4G / 18G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 4888 times 0:44:24.117 4G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:44:30.716 4G / 18G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 5151 times 0:44:30.716 4G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:44:31.625 4G / 18G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 37 times 0:44:31.625 4G / 18G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 12 0:44:31.625 4G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:44:31.657 4G / 18G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 40 times 0:44:31.657 4G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:44:31.673 4G / 18G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 4 times 0:44:31.673 4G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:44:31.673 4G / 18G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:44:31.673 4G / 18G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 13 0:44:31.673 4G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:44:31.673 4G / 18G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:44:31.673 4G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:44:31.673 4G / 18G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:44:31.673 4G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:44:31.673 4G / 18G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:44:31.673 4G / 18G INFO StageManager (stage.cpp : 132) STAGE == Simplification Cleanup 0:44:31.673 4G / 18G INFO General (simplification.cpp : 196) PROCEDURE == Post simplification 0:44:31.673 4G / 18G INFO General (graph_simplification.hpp : 453) Disconnection of relatively low covered edges disabled 0:44:31.673 4G / 18G INFO General (graph_simplification.hpp : 489) Complex tip clipping disabled 0:44:31.673 4G / 18G INFO General (graph_simplification.hpp : 634) Creating parallel br instance 0:44:31.673 4G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:44:32.506 4G / 18G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 9 times 0:44:32.506 4G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:44:37.364 4G / 18G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 36 times 0:44:37.364 4G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:44:38.112 4G / 18G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:44:38.112 4G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:44:42.990 4G / 18G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 1 times 0:44:42.990 4G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:44:42.990 4G / 18G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:44:42.990 4G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:44:42.990 4G / 18G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:44:42.990 4G / 18G INFO General (simplification.cpp : 330) Disrupting self-conjugate edges 0:44:47.237 4G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Removing isolated edges 0:44:58.710 3G / 18G INFO Simplification (parallel_processing.hpp : 167) Removing isolated edges triggered 1340738 times 0:44:58.710 3G / 18G INFO General (simplification.cpp : 470) Counting average coverage 0:44:59.473 3G / 18G INFO General (simplification.cpp : 476) Average coverage = 19.9519 0:44:59.473 3G / 18G INFO StageManager (stage.cpp : 132) STAGE == Contig Output 0:44:59.473 3G / 18G INFO General (contig_output_stage.cpp : 40) Writing GFA to /local/genbank/workspace/reads.all/spades1//K33/assembly_graph_with_scaffolds.gfa 0:45:07.731 3G / 18G INFO General (contig_output.hpp : 22) Outputting contigs to /local/genbank/workspace/reads.all/spades1//K33/before_rr.fasta 0:45:20.875 3G / 18G INFO General (contig_output_stage.cpp : 51) Outputting FastG graph to /local/genbank/workspace/reads.all/spades1//K33/assembly_graph.fastg 0:46:05.866 3G / 18G INFO General (contig_output.hpp : 22) Outputting contigs to /local/genbank/workspace/reads.all/spades1//K33/simplified_contigs.fasta 0:46:19.504 3G / 18G INFO General (contig_output.hpp : 22) Outputting contigs to /local/genbank/workspace/reads.all/spades1//K33/final_contigs.fasta 0:46:32.773 3G / 18G INFO StageManager (stage.cpp : 132) STAGE == Contig Output 0:46:32.773 3G / 18G INFO General (contig_output_stage.cpp : 40) Writing GFA to /local/genbank/workspace/reads.all/spades1//K33/assembly_graph_with_scaffolds.gfa 0:46:42.219 3G / 18G INFO General (contig_output.hpp : 22) Outputting contigs to /local/genbank/workspace/reads.all/spades1//K33/before_rr.fasta 0:46:55.411 3G / 18G INFO General (contig_output_stage.cpp : 51) Outputting FastG graph to /local/genbank/workspace/reads.all/spades1//K33/assembly_graph.fastg 0:47:35.632 3G / 18G INFO General (contig_output.hpp : 22) Outputting contigs to /local/genbank/workspace/reads.all/spades1//K33/simplified_contigs.fasta 0:47:49.017 3G / 18G INFO General (contig_output.hpp : 22) Outputting contigs to /local/genbank/workspace/reads.all/spades1//K33/final_contigs.fasta 0:48:03.837 3G / 18G INFO General (launch.hpp : 149) SPAdes finished 0:48:15.742 132M / 18G INFO General (main.cpp : 109) Assembling time: 0 hours 48 minutes 15 seconds == Running assembler: K41 0:00:00.000 4M / 4M INFO General (main.cpp : 74) Loaded config from /local/genbank/workspace/reads.all/spades1/K41/configs/config.info 0:00:00.000 4M / 4M INFO General (memory_limit.cpp : 49) Memory limit set to 63 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.all/spades1/dataset.info) with K=41 0:00:00.000 4M / 4M INFO General (main.cpp : 90) Maximum # of threads to use (adjusted due to OMP capabilities): 32 0:00:00.000 4M / 4M INFO General (launch.hpp : 51) SPAdes started 0:00:00.000 4M / 4M INFO General (launch.hpp : 58) Starting from stage: construction 0:00:00.000 4M / 4M INFO General (launch.hpp : 65) Two-step RR enabled: 0 0:00:00.000 4M / 4M INFO General (launch.hpp : 76) Will need read mapping, kmer mapper will be attached 0:00:00.000 4M / 4M INFO StageManager (stage.cpp : 132) STAGE == de Bruijn graph construction 0:00:00.010 4M / 4M INFO General (read_converter.hpp : 59) Binary reads detected 0:00:00.109 4M / 4M INFO General (construction.cpp : 111) Max read length 581 0:00:00.109 4M / 4M INFO General (construction.cpp : 117) Average read length 84.7984 0:00:00.109 4M / 4M INFO General (stage.cpp : 101) PROCEDURE == k+1-mer counting 0:00:00.111 4M / 4M INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 1024 files using 32 threads. This might take a while. 0:00:00.114 4M / 4M INFO General (file_limit.hpp : 32) Open file limit set to 4096 0:00:00.114 4M / 4M INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 0.656209 Gb 0:00:00.114 4M / 4M INFO General (kmer_splitters.hpp : 97) Using cell size of 32768 0:00:26.943 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 6388366 reads 0:00:39.791 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 13773704 reads 0:00:50.844 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 19439977 reads 0:01:01.881 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 23718418 reads 0:01:13.325 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 28497435 reads 0:01:30.218 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 40548683 reads 0:01:43.255 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 44059570 reads 0:02:15.917 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 56728508 reads 0:02:55.134 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 73497553 reads 0:03:32.934 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 90197356 reads 0:04:09.865 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 102938024 reads 0:04:36.827 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 112863670 reads 0:05:29.101 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 138395922 reads 0:06:44.105 17G / 18G INFO General (kmer_splitters.hpp : 295) Adding contigs from previous K 0:08:48.627 132M / 18G INFO General (kmer_splitters.hpp : 308) Used 185579624 reads 0:08:48.627 132M / 18G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:11:01.675 132M / 18G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 638177543 kmers in total. 0:11:01.675 132M / 18G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:12:57.476 128M / 18G INFO General (stage.cpp : 101) PROCEDURE == Extension index construction 0:12:57.479 128M / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:12:57.479 128M / 18G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 512 files using 32 threads. This might take a while. 0:12:57.481 128M / 18G INFO General (file_limit.hpp : 32) Open file limit set to 4096 0:12:57.482 128M / 18G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 0.654948 Gb 0:12:57.482 128M / 18G INFO General (kmer_splitters.hpp : 97) Using cell size of 65536 0:13:05.131 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 8129079 kmers 0:13:10.543 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 16548057 kmers 0:13:16.597 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 28025352 kmers 0:13:22.088 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 36458982 kmers 0:13:28.555 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 47959588 kmers 0:13:44.092 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 56394608 kmers 0:13:50.601 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 67905401 kmers 0:13:55.568 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 76336520 kmers 0:14:02.249 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 87853289 kmers 0:14:07.851 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 96287204 kmers 0:14:14.382 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 107800868 kmers 0:14:19.752 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 116229886 kmers 0:14:25.992 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 127736947 kmers 0:14:32.130 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 136167163 kmers 0:14:38.331 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 147680473 kmers 0:14:43.581 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 156118054 kmers 0:14:50.087 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 167625834 kmers 0:14:55.552 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 176057388 kmers 0:15:54.297 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 275776007 kmers 0:18:35.409 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 546549531 kmers 0:19:31.837 17G / 18G INFO General (kmer_splitters.hpp : 385) Used 638179591 kmers. 0:19:34.900 128M / 18G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:21:16.636 128M / 18G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 638269684 kmers in total. 0:21:16.636 128M / 18G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:23:11.015 128M / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:24:00.726 448M / 18G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 0:25:39.254 448M / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 295975112 bytes occupied (3.70972 bits per kmer). 0:25:40.056 1G / 18G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 99) Building k-mer extensions from k+1-mers 0:26:15.018 1G / 18G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 103) Building k-mer extensions from k+1-mers finished. 0:26:15.022 1G / 18G INFO General (stage.cpp : 101) PROCEDURE == Condensing graph 0:26:15.296 1G / 18G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 355) Extracting unbranching paths 0:27:09.651 2G / 18G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 374) Extracting unbranching paths finished. 29298176 sequences extracted 0:27:36.657 2G / 18G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 310) Collecting perfect loops 0:27:50.419 2G / 18G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 343) Collecting perfect loops finished. 175 loops collected 0:28:17.749 10G / 18G INFO General (stage.cpp : 101) PROCEDURE == Filling coverage indices (PHM) 0:28:17.749 10G / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:28:17.749 10G / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:28:41.875 10G / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 295958962 bytes occupied (3.71005 bits per kmer). 0:28:42.991 12G / 18G INFO General (construction.cpp : 388) Collecting k-mer coverage information from reads, this takes a while. 0:30:41.621 12G / 18G INFO General (construction.cpp : 508) Filling coverage and flanking coverage from PHM 0:31:02.757 12G / 18G INFO General (construction.cpp : 464) Processed 32000000 edges 0:31:18.021 12G / 18G INFO General (construction.cpp : 464) Processed 58593223 edges 0:31:22.334 9G / 18G INFO StageManager (stage.cpp : 132) STAGE == EC Threshold Finding 0:31:23.572 9G / 18G INFO General (kmer_coverage_model.cpp : 181) Kmer coverage valley at: 185 0:31:23.597 9G / 18G INFO General (kmer_coverage_model.cpp : 201) K-mer histogram maximum: 186 0:31:23.597 9G / 18G WARN General (kmer_coverage_model.cpp : 218) Too many erroneous kmers, the estimates might be unreliable 0:31:23.597 9G / 18G INFO General (kmer_coverage_model.cpp : 237) Estimated median coverage: 186. Coverage mad: 45.2132 0:31:23.627 9G / 18G INFO General (kmer_coverage_model.cpp : 259) Fitting coverage model 0:31:24.298 9G / 18G INFO General (kmer_coverage_model.cpp : 295) ... iteration 2 0:31:25.905 9G / 18G INFO General (kmer_coverage_model.cpp : 295) ... iteration 4 0:31:31.049 9G / 18G INFO General (kmer_coverage_model.cpp : 295) ... iteration 8 0:31:42.653 9G / 18G INFO General (kmer_coverage_model.cpp : 295) ... iteration 16 0:32:03.443 9G / 18G INFO General (kmer_coverage_model.cpp : 295) ... iteration 32 0:32:25.846 9G / 18G INFO General (kmer_coverage_model.cpp : 295) ... iteration 64 0:33:06.300 9G / 18G INFO General (kmer_coverage_model.cpp : 295) ... iteration 128 0:34:08.775 9G / 18G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 10.143. Fitted coverage std. dev: 4.23898 0:34:08.775 9G / 18G WARN General (kmer_coverage_model.cpp : 327) Valley value was estimated improperly, reset to 5 0:34:08.785 9G / 18G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 0.852343 0:34:08.785 9G / 18G WARN General (kmer_coverage_model.cpp : 366) Failed to determine erroneous kmer threshold. Threshold set to: 5 0:34:08.785 9G / 18G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 174700803 0:34:08.786 9G / 18G INFO General (genomic_info_filler.cpp : 114) Failed to estimate mean coverage 0:34:08.786 9G / 18G INFO General (genomic_info_filler.cpp : 127) EC coverage threshold value was calculated as 5 0:34:08.786 9G / 18G INFO General (genomic_info_filler.cpp : 128) Trusted kmer low bound: 0 0:34:08.786 9G / 18G INFO StageManager (stage.cpp : 132) STAGE == Gap Closer 0:34:08.786 9G / 18G INFO General (graph_pack.hpp : 101) Index refill 0:34:08.794 9G / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:34:08.794 9G / 18G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 512 files using 32 threads. This might take a while. 0:34:08.800 9G / 18G INFO General (file_limit.hpp : 32) Open file limit set to 4096 0:34:08.800 9G / 18G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 0.560425 Gb 0:34:08.800 9G / 18G INFO General (kmer_splitters.hpp : 97) Using cell size of 65536 0:36:05.735 26G / 27G INFO General (edge_index_builders.hpp : 77) Processed 58593223 edges 0:36:05.736 26G / 27G INFO General (edge_index_builders.hpp : 82) Used 58593223 sequences. 0:36:10.130 9G / 27G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:37:46.089 9G / 27G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 638177543 kmers in total. 0:37:46.089 9G / 27G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:39:39.810 9G / 27G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:40:28.096 9G / 27G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 0:42:15.612 9G / 27G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 295943658 bytes occupied (3.70986 bits per kmer). 0:42:21.140 23G / 27G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while. 0:42:42.394 23G / 27G INFO General (edge_index.hpp : 92) Index refilled 0:42:42.426 23G / 27G INFO General (gap_closer.cpp : 159) Preparing shift maps 0:43:46.705 26G / 27G INFO General (gap_closer.cpp : 119) Processing paired reads (takes a while) 0:44:52.190 26G / 27G INFO General (gap_closer.cpp : 138) Used 35067264 paired reads 0:44:52.190 26G / 27G INFO General (gap_closer.cpp : 140) Merging paired indices 0:45:18.184 24G / 27G INFO GapCloser (gap_closer.cpp : 346) Closing short gaps 0:49:00.153 24G / 27G INFO GapCloser (gap_closer.cpp : 380) Closing short gaps complete: filled 45361 gaps after checking 745461 candidates 0:49:18.048 23G / 27G INFO StageManager (stage.cpp : 132) STAGE == Raw Simplification 0:49:18.167 9G / 27G INFO General (simplification.cpp : 128) PROCEDURE == InitialCleaning 0:49:18.167 9G / 27G INFO General (simplification.cpp : 68) Most init cleaning disabled since detected mean 0 was less than activation coverage 10 0:49:18.167 9G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Self conjugate edge remover 0:49:21.825 9G / 27G INFO Simplification (parallel_processing.hpp : 167) Self conjugate edge remover triggered 689 times 0:49:21.826 9G / 27G INFO StageManager (stage.cpp : 132) STAGE == Simplification 0:49:21.826 9G / 27G INFO General (simplification.cpp : 357) Graph simplification started 0:49:21.826 9G / 27G INFO General (graph_simplification.hpp : 634) Creating parallel br instance 0:49:21.826 9G / 27G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 1 0:49:21.826 9G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:55:26.347 9G / 27G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 11403612 times 0:55:26.347 9G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:57:44.820 10G / 27G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 196870 times 0:57:44.820 10G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:57:52.108 10G / 27G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 3257 times 0:57:52.108 10G / 27G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 2 0:57:52.108 10G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:57:53.880 10G / 27G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 15156 times 0:57:53.880 10G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:57:55.604 10G / 27G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 536 times 0:57:55.604 10G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:59:26.431 10G / 27G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 808445 times 0:59:26.431 10G / 27G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 3 0:59:26.431 10G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:59:31.228 10G / 27G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 63493 times 0:59:31.228 10G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:59:58.064 10G / 27G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 26402 times 0:59:58.064 10G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 1:00:15.358 10G / 27G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 196974 times 1:00:15.358 10G / 27G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 4 1:00:15.358 10G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 1:00:16.799 10G / 27G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 16429 times 1:00:16.799 10G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 1:00:27.095 10G / 27G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 10583 times 1:00:27.095 10G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 1:00:50.784 10G / 27G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 224172 times 1:00:50.785 10G / 27G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 5 1:00:50.785 10G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 1:00:52.394 10G / 27G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 20078 times 1:00:52.394 10G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 1:01:04.845 10G / 27G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 13876 times 1:01:04.845 10G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 1:01:11.140 10G / 27G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 64011 times 1:01:11.141 10G / 27G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 6 1:01:11.141 10G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 1:01:11.753 10G / 27G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 6331 times 1:01:11.753 10G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 1:01:17.605 10G / 27G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 5746 times 1:01:17.606 10G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 1:01:27.405 10G / 27G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 76465 times 1:01:27.406 10G / 27G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 7 1:01:27.406 10G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 1:01:28.128 10G / 27G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 6659 times 1:01:28.128 10G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 1:01:34.994 10G / 27G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 6617 times 1:01:34.994 10G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 1:01:39.056 10G / 27G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 31872 times 1:01:39.056 10G / 27G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 8 1:01:39.056 10G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 1:01:39.442 10G / 27G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 3002 times 1:01:39.442 10G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 1:01:44.347 10G / 27G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 3427 times 1:01:44.347 10G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 1:01:50.595 10G / 27G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 35520 times 1:01:50.595 10G / 27G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 9 1:01:50.595 10G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 1:01:51.326 10G / 27G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 2873 times 1:01:51.326 10G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 1:01:57.850 10G / 27G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 3419 times 1:01:57.850 10G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 1:02:01.910 10G / 27G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 23204 times 1:02:01.911 10G / 27G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 10 1:02:01.911 10G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 1:02:02.130 10G / 27G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 1909 times 1:02:02.130 10G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 1:02:06.629 10G / 27G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 2284 times 1:02:06.629 10G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 1:02:09.817 10G / 27G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 24542 times 1:02:09.817 10G / 27G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 11 1:02:09.817 10G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 1:02:11.578 10G / 27G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 8096 times 1:02:11.578 10G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 1:02:16.761 10G / 27G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 3152 times 1:02:16.761 10G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 1:02:17.830 10G / 27G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 47 times 1:02:17.830 10G / 27G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 12 1:02:17.830 10G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 1:02:17.847 10G / 27G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 34 times 1:02:17.847 10G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 1:02:17.854 10G / 27G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 3 times 1:02:17.854 10G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 1:02:17.854 10G / 27G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 1:02:17.854 10G / 27G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 13 1:02:17.854 10G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 1:02:17.854 10G / 27G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 1:02:17.854 10G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 1:02:17.854 10G / 27G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 1:02:17.854 10G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 1:02:17.854 10G / 27G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 1:02:17.854 10G / 27G INFO StageManager (stage.cpp : 132) STAGE == Gap Closer 1:02:17.854 10G / 27G INFO General (graph_pack.hpp : 101) Index refill 1:02:17.863 10G / 27G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 1:02:17.863 10G / 27G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 512 files using 32 threads. This might take a while. 1:02:17.866 10G / 27G INFO General (file_limit.hpp : 32) Open file limit set to 4096 1:02:17.866 10G / 27G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 0.549642 Gb 1:02:17.866 10G / 27G INFO General (kmer_splitters.hpp : 97) Using cell size of 65536 1:03:20.172 27G / 28G INFO General (edge_index_builders.hpp : 77) Processed 5103732 edges 1:03:20.172 27G / 28G INFO General (edge_index_builders.hpp : 82) Used 5103732 sequences. 1:03:23.556 10G / 28G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 1:04:12.265 10G / 28G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 318059376 kmers in total. 1:04:12.265 10G / 28G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 1:05:08.063 10G / 28G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 1:05:26.474 10G / 28G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 1:06:20.948 10G / 28G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 147492832 bytes occupied (3.70982 bits per kmer). 1:06:30.146 17G / 28G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while. 1:06:44.066 17G / 28G INFO General (edge_index.hpp : 92) Index refilled 1:06:44.102 17G / 28G INFO General (gap_closer.cpp : 159) Preparing shift maps 1:06:52.960 18G / 28G INFO General (gap_closer.cpp : 119) Processing paired reads (takes a while) 1:08:18.139 18G / 28G INFO General (gap_closer.cpp : 138) Used 35067264 paired reads 1:08:18.139 18G / 28G INFO General (gap_closer.cpp : 140) Merging paired indices 1:08:32.714 17G / 28G INFO GapCloser (gap_closer.cpp : 346) Closing short gaps 1:09:02.520 17G / 28G INFO GapCloser (gap_closer.cpp : 380) Closing short gaps complete: filled 11960 gaps after checking 501549 candidates 1:09:33.838 17G / 28G INFO StageManager (stage.cpp : 132) STAGE == Simplification Cleanup 1:09:33.839 17G / 28G INFO General (simplification.cpp : 196) PROCEDURE == Post simplification 1:09:33.839 17G / 28G INFO General (graph_simplification.hpp : 453) Disconnection of relatively low covered edges disabled 1:09:33.839 17G / 28G INFO General (graph_simplification.hpp : 489) Complex tip clipping disabled 1:09:33.839 17G / 28G INFO General (graph_simplification.hpp : 634) Creating parallel br instance 1:09:33.839 17G / 28G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 1:09:35.067 17G / 28G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 58 times 1:09:35.067 17G / 28G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 1:09:37.922 17G / 28G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 16 times 1:09:37.922 17G / 28G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 1:09:38.811 17G / 28G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 1:09:38.811 17G / 28G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 1:09:41.787 17G / 28G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 1:09:41.787 17G / 28G INFO General (simplification.cpp : 330) Disrupting self-conjugate edges 1:09:51.620 17G / 28G INFO Simplification (parallel_processing.hpp : 165) Running Removing isolated edges 1:14:21.624 14G / 28G INFO Simplification (parallel_processing.hpp : 167) Removing isolated edges triggered 1946251 times 1:14:21.625 14G / 28G INFO General (simplification.cpp : 470) Counting average coverage 1:14:23.104 14G / 28G INFO General (simplification.cpp : 476) Average coverage = 16.8493 1:14:23.104 14G / 28G INFO StageManager (stage.cpp : 132) STAGE == Mismatch Correction 1:14:23.104 14G / 28G INFO General (graph_pack.hpp : 109) Normalizing k-mer map. Total 25775321 kmers to process 1:14:55.546 14G / 28G INFO General (graph_pack.hpp : 111) Normalizing done 1:21:27.112 27G / 28G INFO General (mismatch_shall_not_pass.hp: 189) Finished collecting potential mismatches positions 1:22:51.531 15G / 28G INFO General (mismatch_shall_not_pass.hp: 290) All edges processed 1:22:53.795 14G / 28G INFO General (mismatch_correction.cpp : 27) Corrected 1104 nucleotides 1:22:53.798 14G / 28G INFO StageManager (stage.cpp : 132) STAGE == Contig Output 1:22:53.798 14G / 28G INFO General (contig_output_stage.cpp : 40) Writing GFA to /local/genbank/workspace/reads.all/spades1//K41/assembly_graph_with_scaffolds.gfa 1:23:10.575 14G / 28G INFO General (contig_output.hpp : 22) Outputting contigs to /local/genbank/workspace/reads.all/spades1//K41/before_rr.fasta 1:23:24.905 14G / 28G INFO General (contig_output_stage.cpp : 51) Outputting FastG graph to /local/genbank/workspace/reads.all/spades1//K41/assembly_graph.fastg 1:23:59.804 14G / 28G INFO General (contig_output.hpp : 22) Outputting contigs to /local/genbank/workspace/reads.all/spades1//K41/simplified_contigs.fasta 1:24:12.665 14G / 28G INFO General (contig_output.hpp : 22) Outputting contigs to /local/genbank/workspace/reads.all/spades1//K41/intermediate_contigs.fasta 1:24:23.788 14G / 28G INFO StageManager (stage.cpp : 132) STAGE == Paired Information Counting 1:24:30.535 14G / 28G INFO General (graph_pack.hpp : 109) Normalizing k-mer map. Total 25837689 kmers to process 1:25:03.119 14G / 28G INFO General (graph_pack.hpp : 111) Normalizing done 1:25:05.439 14G / 28G INFO General (pair_info_count.cpp : 320) Min edge length for estimation: 1382 1:25:05.440 14G / 28G INFO General (pair_info_count.cpp : 331) Estimating insert size for library #0 1:25:05.440 14G / 28G INFO General (pair_info_count.cpp : 190) Estimating insert size (takes a while) 1:25:05.832 15G / 28G INFO General (pair_info_count.cpp : 39) Selecting usual mapper 1:25:24.826 15G / 28G INFO General (sequence_mapper_notifier.h: 80) Processed 200000 reads 1:25:25.060 15G / 28G INFO General (sequence_mapper_notifier.h: 80) Processed 400000 reads 1:25:25.496 15G / 28G INFO General (sequence_mapper_notifier.h: 80) Processed 600000 reads 1:25:25.986 15G / 28G INFO General (sequence_mapper_notifier.h: 80) Processed 800000 reads 1:25:26.698 15G / 28G INFO General (sequence_mapper_notifier.h: 80) Processed 1000000 reads 1:25:26.766 15G / 28G INFO General (sequence_mapper_notifier.h: 80) Processed 1200000 reads 1:25:27.129 15G / 28G INFO General (sequence_mapper_notifier.h: 80) Processed 2200000 reads 1:25:28.576 15G / 28G INFO General (sequence_mapper_notifier.h: 80) Processed 4200000 reads 1:25:46.785 15G / 28G INFO General (sequence_mapper_notifier.h: 80) Processed 8400000 reads 1:26:14.893 15G / 28G INFO General (sequence_mapper_notifier.h: 80) Processed 16800000 reads 1:26:51.934 15G / 28G INFO General (sequence_mapper_notifier.h: 98) Total 35067264 reads processed 1:26:52.644 15G / 28G INFO General (pair_info_count.cpp : 209) Edge pairs: 151750816 1:26:52.644 15G / 28G INFO General (pair_info_count.cpp : 213) 3689925 paired reads (10.5224% of all) aligned to long edges 1:26:52.652 14G / 28G INFO General (pair_info_count.cpp : 354) Insert size = 253.751, deviation = 72.3511, left quantile = 164, right quantile = 328, read length = 581 1:26:52.652 14G / 28G WARN General (pair_info_count.cpp : 358) Estimated mean insert size 253.751 is very small compared to read length 581 1:26:52.820 15G / 28G INFO General (pair_info_count.cpp : 371) Filtering data for library #0 1:26:52.903 15G / 28G INFO General (pair_info_count.cpp : 39) Selecting usual mapper 1:27:13.828 15G / 28G INFO General (sequence_mapper_notifier.h: 80) Processed 200000 reads 1:27:13.979 15G / 28G INFO General (sequence_mapper_notifier.h: 80) Processed 400000 reads 1:27:14.565 15G / 28G INFO General (sequence_mapper_notifier.h: 80) Processed 600000 reads 1:27:14.746 15G / 28G INFO General (sequence_mapper_notifier.h: 80) Processed 800000 reads 1:27:14.850 15G / 28G INFO General (sequence_mapper_notifier.h: 80) Processed 1000000 reads 1:27:14.934 15G / 28G INFO General (sequence_mapper_notifier.h: 80) Processed 1200000 reads 1:27:15.047 15G / 28G INFO General (sequence_mapper_notifier.h: 80) Processed 2200000 reads 1:27:16.267 15G / 28G INFO General (sequence_mapper_notifier.h: 80) Processed 4200000 reads 1:27:33.596 15G / 28G INFO General (sequence_mapper_notifier.h: 80) Processed 8400000 reads 1:28:16.158 15G / 28G INFO General (sequence_mapper_notifier.h: 80) Processed 16800000 reads 1:29:14.813 15G / 28G INFO General (sequence_mapper_notifier.h: 80) Processed 33725336 reads 1:29:26.723 15G / 28G INFO General (sequence_mapper_notifier.h: 98) Total 35067264 reads processed 1:29:26.724 15G / 28G INFO General (pair_info_count.cpp : 383) Mapping library #0 1:29:26.724 15G / 28G INFO General (pair_info_count.cpp : 385) Mapping paired reads (takes a while) 1:29:26.724 15G / 28G INFO General (pair_info_count.cpp : 289) Left insert size quantile 164, right insert size quantile 328, filtering threshold 2, rounding threshold 0 1:29:26.796 15G / 28G INFO General (pair_info_count.cpp : 39) Selecting usual mapper 1:30:10.821 16G / 28G INFO General (sequence_mapper_notifier.h: 80) Processed 200000 reads 1:30:11.202 16G / 28G INFO General (sequence_mapper_notifier.h: 80) Processed 400000 reads 1:30:11.229 16G / 28G INFO General (sequence_mapper_notifier.h: 80) Processed 600000 reads 1:30:11.283 16G / 28G INFO General (sequence_mapper_notifier.h: 80) Processed 800000 reads 1:30:11.794 16G / 28G INFO General (sequence_mapper_notifier.h: 80) Processed 1000000 reads 1:30:11.854 16G / 28G INFO General (sequence_mapper_notifier.h: 80) Processed 1200000 reads 1:30:12.301 16G / 28G INFO General (sequence_mapper_notifier.h: 80) Processed 2200000 reads 1:30:13.464 16G / 28G INFO General (sequence_mapper_notifier.h: 80) Processed 4200000 reads 1:30:30.860 16G / 28G INFO General (sequence_mapper_notifier.h: 80) Processed 8400000 reads 1:33:18.278 18G / 28G INFO General (sequence_mapper_notifier.h: 80) Processed 16800000 reads 1:39:25.858 20G / 28G INFO General (sequence_mapper_notifier.h: 98) Total 35067264 reads processed 1:39:26.398 20G / 28G INFO StageManager (stage.cpp : 132) STAGE == Distance Estimation 1:39:26.398 20G / 28G INFO General (distance_estimation.cpp : 173) Processing library #0 1:39:26.398 20G / 28G INFO General (distance_estimation.cpp : 149) Weight Filter Done 1:39:26.398 20G / 28G INFO DistanceEstimator (distance_estimation.hpp : 116) Using SIMPLE distance estimator 2:15:37.531 27G / 28G INFO General (distance_estimation.cpp : 34) Filtering info 2:15:37.532 27G / 28G INFO General (pair_info_filters.hpp : 242) Start filtering; index size: 602403790 2:22:40.242 24G / 28G INFO General (pair_info_filters.hpp : 263) Done filtering 2:22:40.248 23G / 28G INFO General (distance_estimation.cpp : 156) Refining clustered pair information 2:23:07.983 23G / 28G INFO General (distance_estimation.cpp : 158) The refining of clustered pair information has been finished 2:23:07.983 23G / 28G INFO General (distance_estimation.cpp : 160) Improving paired information 2:40:20.266 25G / 28G INFO PairInfoImprover (pair_info_improver.hpp : 103) Paired info stats: missing = 29860335; contradictional = 76 3:22:07.608 26G / 32G INFO PairInfoImprover (pair_info_improver.hpp : 103) Paired info stats: missing = 15211259; contradictional = 2 3:22:07.608 26G / 32G INFO General (distance_estimation.cpp : 103) Filling scaffolding index 3:22:07.608 26G / 32G INFO DistanceEstimator (distance_estimation.hpp : 116) Using SMOOTHING distance estimator 3:56:45.894 28G / 32G INFO General (distance_estimation.cpp : 34) Filtering info 3:56:45.894 28G / 32G INFO General (pair_info_filters.hpp : 242) Start filtering; index size: 29526063 3:57:07.034 29G / 32G INFO General (pair_info_filters.hpp : 263) Done filtering 3:57:07.207 28G / 32G INFO General (distance_estimation.cpp : 182) Clearing raw paired index 3:58:15.982 22G / 32G INFO StageManager (stage.cpp : 132) STAGE == Repeat Resolving 3:58:15.982 22G / 32G INFO General (repeat_resolving.cpp : 69) Using Path-Extend repeat resolving 3:58:15.982 22G / 32G INFO General (launcher.cpp : 477) ExSPAnder repeat resolving tool started 3:58:22.400 24G / 32G INFO General (launcher.cpp : 392) Creating main extenders, unique edge length = 2000 3:58:22.400 24G / 32G INFO General (extenders_logic.cpp : 275) Estimated coverage of library #0 is 16.8493 3:58:22.569 24G / 32G INFO General (extenders_logic.cpp : 275) Estimated coverage of library #0 is 16.8493 3:58:23.613 24G / 32G INFO General (extenders_logic.cpp : 472) Using 1 paired-end library 3:58:23.613 24G / 32G INFO General (extenders_logic.cpp : 473) Using 1 paired-end scaffolding library 3:58:23.613 24G / 32G INFO General (extenders_logic.cpp : 474) Using 0 single read libraries 3:58:23.613 24G / 32G INFO General (launcher.cpp : 420) Total number of extenders is 3 3:58:23.613 24G / 32G INFO General (path_extender.hpp : 885) Processed 0 paths from 571361 (0%) 3:58:23.902 24G / 32G INFO General (path_extender.hpp : 883) Processed 128 paths from 571361 (0%) 3:58:24.108 24G / 32G INFO General (path_extender.hpp : 883) Processed 256 paths from 571361 (0%) 3:58:24.502 24G / 32G INFO General (path_extender.hpp : 883) Processed 512 paths from 571361 (0%) 3:58:25.103 24G / 32G INFO General (path_extender.hpp : 883) Processed 1024 paths from 571361 (0%) 3:58:26.071 24G / 32G INFO General (path_extender.hpp : 883) Processed 2048 paths from 571361 (0%) 3:58:28.304 24G / 32G INFO General (path_extender.hpp : 883) Processed 4096 paths from 571361 (0%) 3:58:32.368 24G / 32G INFO General (path_extender.hpp : 883) Processed 8192 paths from 571361 (1%) 3:58:39.933 24G / 32G INFO General (path_extender.hpp : 883) Processed 16384 paths from 571361 (2%) 3:58:55.389 25G / 32G INFO General (path_extender.hpp : 883) Processed 32768 paths from 571361 (5%) 3:59:17.575 25G / 32G INFO General (path_extender.hpp : 885) Processed 57137 paths from 571361 (10%) 3:59:24.602 25G / 32G INFO General (path_extender.hpp : 883) Processed 65536 paths from 571361 (11%) 4:00:07.398 25G / 32G INFO General (path_extender.hpp : 885) Processed 114274 paths from 571361 (20%) 4:00:26.817 26G / 32G INFO General (path_extender.hpp : 883) Processed 131072 paths from 571361 (22%) 4:01:23.058 26G / 32G INFO General (path_extender.hpp : 885) Processed 171411 paths from 571361 (30%) 4:03:21.348 26G / 32G INFO General (path_extender.hpp : 885) Processed 228548 paths from 571361 (40%) 4:05:12.537 27G / 32G INFO General (path_extender.hpp : 883) Processed 262144 paths from 571361 (45%) 4:06:25.043 27G / 32G INFO General (path_extender.hpp : 885) Processed 285685 paths from 571361 (50%) 4:07:52.819 27G / 32G INFO General (path_extender.hpp : 885) Processed 342822 paths from 571361 (60%) 4:08:47.220 27G / 32G INFO General (path_extender.hpp : 885) Processed 399959 paths from 571361 (70%) 4:09:19.652 28G / 32G INFO General (path_extender.hpp : 885) Processed 457096 paths from 571361 (80%) 4:09:41.105 28G / 32G INFO General (path_extender.hpp : 885) Processed 514233 paths from 571361 (90%) 4:09:44.742 28G / 32G INFO General (path_extender.hpp : 883) Processed 524288 paths from 571361 (91%) 4:09:52.749 28G / 32G INFO General (launcher.cpp : 234) Finalizing paths 4:09:52.749 28G / 32G INFO General (launcher.cpp : 236) Deduplicating paths 4:12:21.548 28G / 32G INFO General (launcher.cpp : 240) Paths deduplicated 4:12:21.548 28G / 32G INFO PEResolver (pe_resolver.hpp : 295) Removing overlaps 4:12:21.548 28G / 32G INFO PEResolver (pe_resolver.hpp : 298) Sorting paths 4:12:22.533 28G / 32G INFO PEResolver (pe_resolver.hpp : 305) Marking overlaps 4:12:22.533 28G / 32G INFO OverlapRemover (pe_resolver.hpp : 130) Marking start/end overlaps 4:14:54.349 28G / 32G INFO OverlapRemover (pe_resolver.hpp : 133) Marking remaining overlaps 4:17:30.739 28G / 32G INFO PEResolver (pe_resolver.hpp : 308) Splitting paths 4:17:32.910 28G / 32G INFO PEResolver (pe_resolver.hpp : 313) Deduplicating paths 4:17:50.838 28G / 32G INFO PEResolver (pe_resolver.hpp : 315) Overlaps removed 4:17:56.835 28G / 32G INFO General (launcher.cpp : 257) Paths finalized 4:17:56.835 28G / 32G INFO General (launcher.cpp : 427) Closing gaps in paths 4:18:01.355 28G / 32G INFO General (launcher.cpp : 455) Gap closing completed 4:18:02.483 28G / 32G INFO General (launcher.cpp : 286) Traversing tandem repeats 4:18:15.498 28G / 32G INFO General (launcher.cpp : 296) Traversed 71 loops 4:18:15.498 28G / 32G INFO General (launcher.cpp : 234) Finalizing paths 4:18:15.498 28G / 32G INFO General (launcher.cpp : 236) Deduplicating paths 4:18:16.247 28G / 32G INFO General (launcher.cpp : 240) Paths deduplicated 4:18:16.247 28G / 32G INFO PEResolver (pe_resolver.hpp : 295) Removing overlaps 4:18:16.247 28G / 32G INFO PEResolver (pe_resolver.hpp : 298) Sorting paths 4:18:17.626 28G / 32G INFO PEResolver (pe_resolver.hpp : 305) Marking overlaps 4:18:17.627 28G / 32G INFO OverlapRemover (pe_resolver.hpp : 130) Marking start/end overlaps 4:18:18.997 28G / 32G INFO OverlapRemover (pe_resolver.hpp : 133) Marking remaining overlaps 4:18:20.520 28G / 32G INFO PEResolver (pe_resolver.hpp : 308) Splitting paths 4:18:20.643 28G / 32G INFO PEResolver (pe_resolver.hpp : 313) Deduplicating paths 4:18:21.396 28G / 32G INFO PEResolver (pe_resolver.hpp : 315) Overlaps removed 4:18:24.874 28G / 32G INFO General (launcher.cpp : 257) Paths finalized 4:18:26.582 28G / 32G INFO General (launcher.cpp : 529) ExSPAnder repeat resolving tool finished 4:18:40.754 24G / 32G INFO StageManager (stage.cpp : 132) STAGE == Contig Output 4:18:40.754 24G / 32G INFO General (contig_output_stage.cpp : 40) Writing GFA to /local/genbank/workspace/reads.all/spades1//K41/assembly_graph_with_scaffolds.gfa 4:18:49.853 24G / 32G INFO General (contig_output.hpp : 22) Outputting contigs to /local/genbank/workspace/reads.all/spades1//K41/before_rr.fasta 4:19:00.740 24G / 32G INFO General (contig_output_stage.cpp : 51) Outputting FastG graph to /local/genbank/workspace/reads.all/spades1//K41/assembly_graph.fastg 4:19:40.407 25G / 32G INFO General (contig_output_stage.cpp : 20) Outputting FastG paths to /local/genbank/workspace/reads.all/spades1//K41/final_contigs.paths 4:19:56.581 24G / 32G INFO General (contig_output_stage.cpp : 20) Outputting FastG paths to /local/genbank/workspace/reads.all/spades1//K41/scaffolds.paths 4:20:11.992 24G / 32G INFO General (launch.hpp : 149) SPAdes finished 4:21:30.036 412M / 32G INFO General (main.cpp : 109) Assembling time: 4 hours 21 minutes 30 seconds ===== Assembling finished. Used k-mer sizes: 21, 33, 41 * Assembled contigs are in /local/genbank/workspace/reads.all/spades1/contigs.fasta * Assembled scaffolds are in /local/genbank/workspace/reads.all/spades1/scaffolds.fasta * Assembly graph is in /local/genbank/workspace/reads.all/spades1/assembly_graph.fastg * Assembly graph in GFA format is in /local/genbank/workspace/reads.all/spades1/assembly_graph_with_scaffolds.gfa * Paths in the assembly graph corresponding to the contigs are in /local/genbank/workspace/reads.all/spades1/contigs.paths * Paths in the assembly graph corresponding to the scaffolds are in /local/genbank/workspace/reads.all/spades1/scaffolds.paths ======= SPAdes pipeline finished WITH WARNINGS! === Error correction and assembling warnings: * 0:29:46.775 6G / 18G WARN General (kmer_coverage_model.cpp : 218) Too many erroneous kmers, the estimates might be unreliable * 0:32:49.965 7G / 18G WARN General (kmer_coverage_model.cpp : 327) Valley value was estimated improperly, reset to 6 * 0:32:49.982 7G / 18G WARN General (kmer_coverage_model.cpp : 366) Failed to determine erroneous kmer threshold. Threshold set to: 6 * 0:35:22.977 4G / 18G WARN General (kmer_coverage_model.cpp : 327) Valley value was estimated improperly, reset to 5 * 0:35:22.990 4G / 18G WARN General (kmer_coverage_model.cpp : 366) Failed to determine erroneous kmer threshold. Threshold set to: 5 * 1:26:52.652 14G / 28G WARN General (pair_info_count.cpp : 358) Estimated mean insert size 253.751 is very small compared to read length 581 ======= Warnings saved to /local/genbank/workspace/reads.all/spades1/warnings.log SPAdes log can be found here: /local/genbank/workspace/reads.all/spades1/spades.log Thank you for using SPAdes!