Command line: /home/psgendb/BIRCHDEV/bin-linux-x86_64/spades.py -1 /local/genbank/workspace/reads.all3/20090202_7_R1.fq -2 /local/genbank/workspace/reads.all3/20090202_7_R2.fq -1 /local/genbank/workspace/reads.all3/20090202_8_R1.fq -2 /local/genbank/workspace/reads.all3/20090202_8_R2.fq -1 /local/genbank/workspace/reads.all3/AB2kb_R1.fq -2 /local/genbank/workspace/reads.all3/AB2kb_R2.fq -1 /local/genbank/workspace/reads.all3/AB4kb_R1.fq -2 /local/genbank/workspace/reads.all3/AB4kb_R2.fq -1 /local/genbank/workspace/reads.all3/Algae6.2_6_R1.fq -2 /local/genbank/workspace/reads.all3/Algae6.2_6_R2.fq -1 /local/genbank/workspace/reads.all3/Algae6.2_7_R1.fq -2 /local/genbank/workspace/reads.all3/Algae6.2_7_R2.fq -1 /local/genbank/workspace/reads.all3/Algae6.2_8_R1.fq -2 /local/genbank/workspace/reads.all3/Algae6.2_8_R2.fq -1 /local/genbank/workspace/reads.all3/Algae7.2GB_6_R1.fq -2 /local/genbank/workspace/reads.all3/Algae7.2GB_6_R2.fq -1 /local/genbank/workspace/reads.all3/Algae7.2GB_7_R1.fq -2 /local/genbank/workspace/reads.all3/Algae7.2GB_7_R2.fq -1 /local/genbank/workspace/reads.all3/Algae7.2GB_8_R1.fq -2 /local/genbank/workspace/reads.all3/Algae7.2GB_8_R2.fq -s /local/genbank/workspace/reads.all3/2008-09allU.fq -s /local/genbank/workspace/reads.all3/3-6.2-7.2GBallU.fq -s /local/genbank/workspace/reads.all3/AGRFUall.fq -s /local/genbank/workspace/reads.all3/454U.fq --only-assembler -k 55 -m 130 -t 32 -o /local/genbank/workspace/reads.all3.spades1.55 System information: SPAdes version: 3.13.0 Python version: 2.7.5 OS: Linux-3.10.0-1160.25.1.el7.x86_64-x86_64-with-redhat-7.9-Maipo Output dir: /local/genbank/workspace/reads.all3.spades1.55 Mode: ONLY assembling (without read error correction) Debug mode is turned OFF Dataset parameters: Multi-cell mode (you should set '--sc' flag if input data was obtained with MDA (single-cell) technology or --meta flag if processing metagenomic dataset) Reads: Library number: 1, library type: paired-end orientation: fr left reads: ['/local/genbank/workspace/reads.all3/20090202_7_R1.fq', '/local/genbank/workspace/reads.all3/20090202_8_R1.fq', '/local/genbank/workspace/reads.all3/AB2kb_R1.fq', '/local/genbank/workspace/reads.all3/AB4kb_R1.fq', '/local/genbank/workspace/reads.all3/Algae6.2_6_R1.fq', '/local/genbank/workspace/reads.all3/Algae6.2_7_R1.fq', '/local/genbank/workspace/reads.all3/Algae6.2_8_R1.fq', '/local/genbank/workspace/reads.all3/Algae7.2GB_6_R1.fq', '/local/genbank/workspace/reads.all3/Algae7.2GB_7_R1.fq', '/local/genbank/workspace/reads.all3/Algae7.2GB_8_R1.fq'] right reads: ['/local/genbank/workspace/reads.all3/20090202_7_R2.fq', '/local/genbank/workspace/reads.all3/20090202_8_R2.fq', '/local/genbank/workspace/reads.all3/AB2kb_R2.fq', '/local/genbank/workspace/reads.all3/AB4kb_R2.fq', '/local/genbank/workspace/reads.all3/Algae6.2_6_R2.fq', '/local/genbank/workspace/reads.all3/Algae6.2_7_R2.fq', '/local/genbank/workspace/reads.all3/Algae6.2_8_R2.fq', '/local/genbank/workspace/reads.all3/Algae7.2GB_6_R2.fq', '/local/genbank/workspace/reads.all3/Algae7.2GB_7_R2.fq', '/local/genbank/workspace/reads.all3/Algae7.2GB_8_R2.fq'] interlaced reads: not specified single reads: ['/local/genbank/workspace/reads.all3/2008-09allU.fq', '/local/genbank/workspace/reads.all3/3-6.2-7.2GBallU.fq', '/local/genbank/workspace/reads.all3/AGRFUall.fq', '/local/genbank/workspace/reads.all3/454U.fq'] merged reads: not specified Assembly parameters: k: [55] Repeat resolution is enabled Mismatch careful mode is turned OFF MismatchCorrector will be SKIPPED Coverage cutoff is turned OFF Other parameters: Dir for temp files: /local/genbank/workspace/reads.all3.spades1.55/tmp Threads: 32 Memory limit (in Gb): 130 ======= SPAdes pipeline started. Log can be found here: /local/genbank/workspace/reads.all3.spades1.55/spades.log ===== Assembling started. == Running assembler: K55 0:00:00.000 4M / 4M INFO General (main.cpp : 74) Loaded config from /local/genbank/workspace/reads.all3.spades1.55/K55/configs/config.info 0:00:00.000 4M / 4M INFO General (memory_limit.cpp : 49) Memory limit set to 130 Gb 0:00:00.000 4M / 4M INFO General (main.cpp : 87) Starting SPAdes, built from refs/heads/spades_3.13.0, git revision 8ea46659e9b2aca35444a808db550ac333006f8b 0:00:00.000 4M / 4M INFO General (main.cpp : 88) Maximum k-mer length: 128 0:00:00.000 4M / 4M INFO General (main.cpp : 89) Assembling dataset (/local/genbank/workspace/reads.all3.spades1.55/dataset.info) with K=55 0:00:00.000 4M / 4M INFO General (main.cpp : 90) Maximum # of threads to use (adjusted due to OMP capabilities): 32 0:00:00.000 4M / 4M INFO General (launch.hpp : 51) SPAdes started 0:00:00.000 4M / 4M INFO General (launch.hpp : 58) Starting from stage: construction 0:00:00.000 4M / 4M INFO General (launch.hpp : 65) Two-step RR enabled: 0 0:00:00.000 4M / 4M INFO General (launch.hpp : 76) Will need read mapping, kmer mapper will be attached 0:00:00.000 4M / 4M INFO StageManager (stage.cpp : 132) STAGE == de Bruijn graph construction 0:00:00.006 4M / 4M INFO General (read_converter.hpp : 77) Converting reads to binary format for library #0 (takes a while) 0:00:00.006 4M / 4M INFO General (read_converter.hpp : 78) Converting paired reads 0:00:00.277 76M / 76M INFO General (binary_converter.hpp : 93) 16384 reads processed 0:00:00.426 84M / 84M INFO General (binary_converter.hpp : 93) 32768 reads processed 0:00:00.724 104M / 104M INFO General (binary_converter.hpp : 93) 65536 reads processed 0:00:01.319 136M / 136M INFO General (binary_converter.hpp : 93) 131072 reads processed 0:00:02.519 208M / 208M INFO General (binary_converter.hpp : 93) 262144 reads processed 0:00:04.872 344M / 344M INFO General (binary_converter.hpp : 93) 524288 reads processed 0:00:12.307 564M / 564M INFO General (binary_converter.hpp : 93) 1048576 reads processed 0:00:24.385 596M / 596M INFO General (binary_converter.hpp : 93) 2097152 reads processed 0:00:51.825 844M / 848M INFO General (binary_converter.hpp : 93) 4194304 reads processed 0:01:53.020 868M / 880M INFO General (binary_converter.hpp : 93) 8388608 reads processed 0:03:55.289 940M / 952M INFO General (binary_converter.hpp : 93) 16777216 reads processed 0:08:05.696 864M / 952M INFO General (binary_converter.hpp : 93) 33554432 reads processed 0:16:02.218 668M / 952M INFO General (binary_converter.hpp : 93) 67108864 reads processed 0:19:04.249 516M / 952M INFO General (binary_converter.hpp : 117) 80455197 reads written 0:19:05.470 4M / 952M INFO General (read_converter.hpp : 87) Converting single reads 0:19:05.734 136M / 952M INFO General (binary_converter.hpp : 93) 16384 reads processed 0:19:05.807 140M / 952M INFO General (binary_converter.hpp : 93) 32768 reads processed 0:19:05.952 148M / 952M INFO General (binary_converter.hpp : 93) 65536 reads processed 0:19:06.244 168M / 952M INFO General (binary_converter.hpp : 93) 131072 reads processed 0:19:06.830 204M / 952M INFO General (binary_converter.hpp : 93) 262144 reads processed 0:19:08.008 272M / 952M INFO General (binary_converter.hpp : 93) 524288 reads processed 0:19:10.358 412M / 952M INFO General (binary_converter.hpp : 93) 1048576 reads processed 0:19:14.856 700M / 952M INFO General (binary_converter.hpp : 93) 2097152 reads processed 0:19:23.692 1G / 1G INFO General (binary_converter.hpp : 93) 4194304 reads processed 0:19:47.738 1G / 1G INFO General (binary_converter.hpp : 93) 8388608 reads processed 0:20:34.189 1G / 1G INFO General (binary_converter.hpp : 93) 16777216 reads processed 0:22:07.495 1G / 1G INFO General (binary_converter.hpp : 93) 33554432 reads processed 0:24:15.144 2G / 3G INFO General (binary_converter.hpp : 117) 48800134 reads written 0:24:19.249 12M / 3G INFO General (read_converter.hpp : 95) Converting merged reads 0:24:20.291 140M / 3G INFO General (binary_converter.hpp : 117) 0 reads written 0:24:20.434 8M / 3G INFO General (construction.cpp : 111) Max read length 700 0:24:20.434 8M / 3G INFO General (construction.cpp : 117) Average read length 80.6457 0:24:20.434 8M / 3G INFO General (stage.cpp : 101) PROCEDURE == k+1-mer counting 0:24:20.436 8M / 3G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 1024 files using 32 threads. This might take a while. 0:24:20.439 8M / 3G INFO General (file_limit.hpp : 32) Open file limit set to 4096 0:24:20.439 8M / 3G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 1.35409 Gb 0:24:20.439 8M / 3G INFO General (kmer_splitters.hpp : 97) Using cell size of 32768 0:24:41.063 17G / 17G INFO General (kmer_splitters.hpp : 289) Processed 18592329 reads 0:24:57.469 17G / 17G INFO General (kmer_splitters.hpp : 289) Processed 38794175 reads 0:25:19.151 17G / 17G INFO General (kmer_splitters.hpp : 289) Processed 71475773 reads 0:25:29.034 17G / 17G INFO General (kmer_splitters.hpp : 289) Processed 80913728 reads 0:25:44.970 17G / 17G INFO General (kmer_splitters.hpp : 289) Processed 92759119 reads 0:26:06.287 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 95596359 reads 0:26:42.294 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 114779835 reads 0:27:19.335 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 141389029 reads 0:27:56.162 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 168308637 reads 0:28:32.940 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 195786877 reads 0:29:09.936 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 223384313 reads 0:29:42.931 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 241099982 reads 0:30:06.145 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 252886349 reads 0:30:55.302 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 278903660 reads 0:32:51.283 17G / 18G INFO General (kmer_splitters.hpp : 295) Adding contigs from previous K 0:32:54.697 132M / 18G INFO General (kmer_splitters.hpp : 308) Used 419421056 reads 0:32:54.697 132M / 18G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:35:25.273 132M / 18G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 920009214 kmers in total. 0:35:25.273 132M / 18G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:38:03.302 128M / 18G INFO General (stage.cpp : 101) PROCEDURE == Extension index construction 0:38:03.303 128M / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:38:03.304 128M / 18G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 512 files using 32 threads. This might take a while. 0:38:03.305 128M / 18G INFO General (file_limit.hpp : 32) Open file limit set to 4096 0:38:03.305 128M / 18G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 1.35286 Gb 0:38:03.305 128M / 18G INFO General (kmer_splitters.hpp : 97) Using cell size of 65536 0:38:09.336 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 7802134 kmers 0:38:14.538 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 17218052 kmers 0:38:19.077 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 25953730 kmers 0:38:24.403 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 36507551 kmers 0:38:29.294 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 45908722 kmers 0:38:34.515 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 54650718 kmers 0:38:39.579 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 65251313 kmers 0:38:44.802 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 74655010 kmers 0:38:49.371 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 83404010 kmers 0:38:54.789 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 94007327 kmers 0:38:59.739 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 103410158 kmers 0:39:04.652 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 112159436 kmers 0:39:09.706 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 122753733 kmers 0:39:14.900 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 132151738 kmers 0:39:19.821 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 140884050 kmers 0:39:25.180 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 151516378 kmers 0:39:30.119 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 160922187 kmers 0:39:35.017 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 169666771 kmers 0:40:31.108 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 275899614 kmers 0:42:52.680 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 543389828 kmers 0:46:12.340 17G / 18G INFO General (kmer_splitters.hpp : 385) Used 920012286 kmers. 0:46:14.718 128M / 18G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:50:03.274 128M / 18G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 929899292 kmers in total. 0:50:03.274 128M / 18G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:52:44.099 128M / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:53:57.426 588M / 18G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 0:56:14.690 588M / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 431221216 bytes occupied (3.70983 bits per kmer). 0:56:15.838 1G / 18G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 99) Building k-mer extensions from k+1-mers 0:57:05.479 1G / 18G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 103) Building k-mer extensions from k+1-mers finished. 0:57:05.483 1G / 18G INFO General (stage.cpp : 101) PROCEDURE == Condensing graph 0:57:05.662 1G / 18G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 355) Extracting unbranching paths 0:58:26.501 4G / 18G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 374) Extracting unbranching paths finished. 51087999 sequences extracted 0:59:07.467 4G / 18G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 310) Collecting perfect loops 0:59:26.694 4G / 18G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 343) Collecting perfect loops finished. 135 loops collected 1:00:14.828 18G / 22G INFO General (stage.cpp : 101) PROCEDURE == Filling coverage indices (PHM) 1:00:14.828 18G / 22G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 1:00:14.829 18G / 22G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 1:00:56.496 18G / 22G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 426636398 bytes occupied (3.70984 bits per kmer). 1:00:58.052 21G / 22G INFO General (construction.cpp : 388) Collecting k-mer coverage information from reads, this takes a while. 1:03:46.677 21G / 22G INFO General (construction.cpp : 508) Filling coverage and flanking coverage from PHM 1:04:08.290 21G / 22G INFO General (construction.cpp : 464) Processed 32000000 edges 1:04:24.783 21G / 22G INFO General (construction.cpp : 464) Processed 64000000 edges 1:04:41.260 21G / 22G INFO General (construction.cpp : 464) Processed 96000000 edges 1:04:44.508 21G / 22G INFO General (construction.cpp : 464) Processed 102174735 edges 1:04:51.390 16G / 22G INFO StageManager (stage.cpp : 132) STAGE == EC Threshold Finding 1:04:52.976 16G / 22G INFO General (kmer_coverage_model.cpp : 181) Kmer coverage valley at: 224 1:04:53.005 16G / 22G INFO General (kmer_coverage_model.cpp : 201) K-mer histogram maximum: 226 1:04:53.005 16G / 22G INFO General (kmer_coverage_model.cpp : 237) Estimated median coverage: 227. Coverage mad: 2.9652 1:04:53.041 16G / 22G INFO General (kmer_coverage_model.cpp : 259) Fitting coverage model 1:04:53.995 16G / 22G INFO General (kmer_coverage_model.cpp : 295) ... iteration 2 1:04:56.232 16G / 22G INFO General (kmer_coverage_model.cpp : 295) ... iteration 4 1:05:00.960 16G / 22G INFO General (kmer_coverage_model.cpp : 295) ... iteration 8 1:05:10.374 16G / 22G INFO General (kmer_coverage_model.cpp : 295) ... iteration 16 1:05:29.122 16G / 22G INFO General (kmer_coverage_model.cpp : 295) ... iteration 32 1:06:01.997 16G / 22G INFO General (kmer_coverage_model.cpp : 295) ... iteration 64 1:06:09.793 16G / 22G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 141.853. Fitted coverage std. dev: 7.95576 1:06:09.793 16G / 22G WARN General (kmer_coverage_model.cpp : 327) Valley value was estimated improperly, reset to 75 1:06:09.808 16G / 22G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 1 1:06:09.808 16G / 22G WARN General (kmer_coverage_model.cpp : 366) Failed to determine erroneous kmer threshold. Threshold set to: 75 1:06:09.808 16G / 22G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 4645116 1:06:09.809 16G / 22G INFO General (genomic_info_filler.cpp : 114) Failed to estimate mean coverage 1:06:09.809 16G / 22G INFO General (genomic_info_filler.cpp : 127) EC coverage threshold value was calculated as 75 1:06:09.809 16G / 22G INFO General (genomic_info_filler.cpp : 128) Trusted kmer low bound: 0 1:06:09.809 16G / 22G INFO StageManager (stage.cpp : 132) STAGE == Gap Closer 1:06:09.809 16G / 22G INFO General (graph_pack.hpp : 101) Index refill 1:06:09.814 16G / 22G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 1:06:09.814 16G / 22G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 512 files using 32 threads. This might take a while. 1:06:09.817 16G / 22G INFO General (file_limit.hpp : 32) Open file limit set to 4096 1:06:09.818 16G / 22G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 1.17839 Gb 1:06:09.818 16G / 22G INFO General (kmer_splitters.hpp : 97) Using cell size of 65536 1:08:47.108 34G / 35G INFO General (edge_index_builders.hpp : 77) Processed 97780868 edges 1:08:55.971 34G / 35G INFO General (edge_index_builders.hpp : 77) Processed 102174767 edges 1:08:55.971 34G / 35G INFO General (edge_index_builders.hpp : 82) Used 102174767 sequences. 1:09:00.259 16G / 35G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 1:11:11.736 16G / 35G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 920009214 kmers in total. 1:11:11.736 16G / 35G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 1:13:49.398 16G / 35G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 1:15:07.639 17G / 35G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 1:17:23.837 17G / 35G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 426619334 bytes occupied (3.7097 bits per kmer). 1:17:47.989 37G / 37G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while. 1:18:29.692 37G / 37G INFO General (edge_index.hpp : 92) Index refilled 1:18:29.715 37G / 37G INFO General (gap_closer.cpp : 159) Preparing shift maps 1:21:23.729 44G / 44G INFO General (gap_closer.cpp : 119) Processing paired reads (takes a while) 1:22:36.443 46G / 46G INFO General (gap_closer.cpp : 138) Used 80455197 paired reads 1:22:36.443 46G / 46G INFO General (gap_closer.cpp : 140) Merging paired indices 1:24:02.688 38G / 46G INFO GapCloser (gap_closer.cpp : 346) Closing short gaps 1:33:08.828 38G / 46G INFO GapCloser (gap_closer.cpp : 380) Closing short gaps complete: filled 78812 gaps after checking 1350989 candidates 1:34:03.537 37G / 46G INFO StageManager (stage.cpp : 132) STAGE == Raw Simplification 1:34:09.698 16G / 46G INFO General (simplification.cpp : 128) PROCEDURE == InitialCleaning 1:34:09.698 16G / 46G INFO General (simplification.cpp : 68) Most init cleaning disabled since detected mean 0 was less than activation coverage 10 1:34:09.698 16G / 46G INFO Simplification (parallel_processing.hpp : 165) Running Self conjugate edge remover 1:34:16.496 16G / 46G INFO Simplification (parallel_processing.hpp : 167) Self conjugate edge remover triggered 0 times 1:34:16.497 16G / 46G INFO StageManager (stage.cpp : 132) STAGE == Simplification 1:34:16.497 16G / 46G INFO General (simplification.cpp : 357) Graph simplification started 1:34:16.497 16G / 46G INFO General (graph_simplification.hpp : 634) Creating parallel br instance 1:34:16.497 16G / 46G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 1 1:34:16.497 16G / 46G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 1:48:00.886 17G / 46G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 20498610 times 1:48:00.886 17G / 46G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 1:50:32.272 18G / 46G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 264924 times 1:50:32.272 18G / 46G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 1:50:55.093 18G / 46G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 188368 times 1:50:55.093 18G / 46G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 2 1:50:55.093 18G / 46G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 1:50:58.539 18G / 46G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 59484 times 1:50:58.539 18G / 46G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 1:51:08.880 18G / 46G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 12545 times 1:51:08.880 18G / 46G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 1:51:10.933 18G / 46G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 21934 times 1:51:10.934 18G / 46G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 3 1:51:10.934 18G / 46G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 1:51:11.104 18G / 46G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 2331 times 1:51:11.104 18G / 46G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 1:51:13.890 18G / 46G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 2767 times 1:51:13.890 18G / 46G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 1:51:14.459 18G / 46G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 6414 times 1:51:14.459 18G / 46G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 4 1:51:14.459 18G / 46G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 1:51:14.500 18G / 46G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 499 times 1:51:14.501 18G / 46G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 1:51:15.425 18G / 46G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 929 times 1:51:15.425 18G / 46G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 1:51:15.690 18G / 46G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 3133 times 1:51:15.690 18G / 46G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 5 1:51:15.690 18G / 46G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 1:51:15.707 18G / 46G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 194 times 1:51:15.707 18G / 46G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 1:51:16.232 18G / 46G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 550 times 1:51:16.232 18G / 46G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 1:51:16.396 18G / 46G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 1880 times 1:51:16.396 18G / 46G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 6 1:51:16.396 18G / 46G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 1:51:16.406 18G / 46G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 107 times 1:51:16.406 18G / 46G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 1:51:16.663 18G / 46G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 311 times 1:51:16.663 18G / 46G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 1:51:16.771 18G / 46G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 1249 times 1:51:16.771 18G / 46G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 7 1:51:16.771 18G / 46G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 1:51:16.776 18G / 46G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 57 times 1:51:16.776 18G / 46G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 1:51:16.972 18G / 46G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 251 times 1:51:16.972 18G / 46G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 1:51:17.034 18G / 46G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 765 times 1:51:17.034 18G / 46G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 8 1:51:17.034 18G / 46G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 1:51:17.037 18G / 46G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 37 times 1:51:17.037 18G / 46G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 1:51:17.166 18G / 46G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 157 times 1:51:17.166 18G / 46G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 1:51:17.211 18G / 46G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 605 times 1:51:17.211 18G / 46G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 9 1:51:17.211 18G / 46G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 1:51:17.214 18G / 46G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 47 times 1:51:17.215 18G / 46G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 1:51:17.305 18G / 46G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 110 times 1:51:17.305 18G / 46G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 1:51:17.339 18G / 46G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 453 times 1:51:17.340 18G / 46G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 10 1:51:17.340 18G / 46G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 1:51:17.342 18G / 46G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 27 times 1:51:17.342 18G / 46G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 1:51:17.408 18G / 46G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 78 times 1:51:17.408 18G / 46G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 1:51:17.433 18G / 46G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 343 times 1:51:17.433 18G / 46G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 11 1:51:17.434 18G / 46G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 1:51:21.771 18G / 46G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 2129 times 1:51:21.771 18G / 46G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 1:51:25.004 18G / 46G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 182 times 1:51:25.004 18G / 46G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 1:51:27.982 18G / 46G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 50 times 1:51:27.983 18G / 46G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 12 1:51:27.983 18G / 46G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 1:51:27.983 18G / 46G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 2 times 1:51:27.983 18G / 46G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 1:51:27.996 18G / 46G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 8 times 1:51:27.996 18G / 46G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 1:51:27.996 18G / 46G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 1:51:27.996 18G / 46G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 13 1:51:27.996 18G / 46G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 1:51:27.996 18G / 46G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 1 times 1:51:27.996 18G / 46G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 1:51:27.996 18G / 46G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 1:51:27.996 18G / 46G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 1:51:27.996 18G / 46G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 1:51:27.996 18G / 46G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 14 1:51:27.996 18G / 46G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 1:51:27.996 18G / 46G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 1:51:27.996 18G / 46G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 1:51:27.997 18G / 46G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 1:51:27.997 18G / 46G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 1:51:27.997 18G / 46G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 1:51:27.997 18G / 46G INFO StageManager (stage.cpp : 132) STAGE == Gap Closer 1:51:27.997 18G / 46G INFO General (graph_pack.hpp : 101) Index refill 1:51:28.002 18G / 46G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 1:51:28.002 18G / 46G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 512 files using 32 threads. This might take a while. 1:51:28.005 18G / 46G INFO General (file_limit.hpp : 32) Open file limit set to 4096 1:51:28.005 18G / 46G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 1.15678 Gb 1:51:28.005 18G / 46G INFO General (kmer_splitters.hpp : 97) Using cell size of 65536 1:53:01.681 36G / 46G INFO General (edge_index_builders.hpp : 77) Processed 20728555 edges 1:53:01.681 36G / 46G INFO General (edge_index_builders.hpp : 82) Used 20728555 sequences. 1:53:05.220 18G / 46G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 1:54:23.015 18G / 46G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 529805192 kmers in total. 1:54:23.016 18G / 46G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 1:55:55.699 18G / 46G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 1:56:35.078 19G / 46G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 1:58:04.423 19G / 46G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 245679784 bytes occupied (3.70974 bits per kmer). 1:58:21.968 31G / 46G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while. 1:58:45.395 31G / 46G INFO General (edge_index.hpp : 92) Index refilled 1:58:45.418 31G / 46G INFO General (gap_closer.cpp : 159) Preparing shift maps 1:59:35.151 34G / 46G INFO General (gap_closer.cpp : 119) Processing paired reads (takes a while) 2:01:23.899 38G / 46G INFO General (gap_closer.cpp : 138) Used 80455197 paired reads 2:01:23.900 38G / 46G INFO General (gap_closer.cpp : 140) Merging paired indices 2:03:35.808 31G / 46G INFO GapCloser (gap_closer.cpp : 346) Closing short gaps 2:06:07.537 31G / 46G INFO GapCloser (gap_closer.cpp : 380) Closing short gaps complete: filled 104210 gaps after checking 1949544 candidates 2:09:29.121 31G / 46G INFO StageManager (stage.cpp : 132) STAGE == Simplification Cleanup 2:09:29.122 31G / 46G INFO General (simplification.cpp : 196) PROCEDURE == Post simplification 2:09:29.122 31G / 46G INFO General (graph_simplification.hpp : 453) Disconnection of relatively low covered edges disabled 2:09:29.122 31G / 46G INFO General (graph_simplification.hpp : 489) Complex tip clipping disabled 2:09:29.122 31G / 46G INFO General (graph_simplification.hpp : 634) Creating parallel br instance 2:09:29.122 31G / 46G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 2:09:34.672 31G / 46G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 2:09:34.672 31G / 46G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 2:09:38.099 31G / 46G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 1 times 2:09:38.099 31G / 46G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 2:09:42.182 31G / 46G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 2:09:42.182 31G / 46G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 2:09:45.436 31G / 46G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 2:09:45.436 31G / 46G INFO General (simplification.cpp : 330) Disrupting self-conjugate edges 2:10:31.883 31G / 46G INFO Simplification (parallel_processing.hpp : 165) Running Removing isolated edges 2:24:17.392 18G / 46G INFO Simplification (parallel_processing.hpp : 167) Removing isolated edges triggered 10139508 times 2:24:17.393 18G / 46G INFO General (simplification.cpp : 470) Counting average coverage 2:24:17.629 18G / 46G INFO General (simplification.cpp : 476) Average coverage = 19.5279 2:24:17.629 18G / 46G WARN General (simplification.cpp : 479) The determined erroneous connection coverage threshold may be determined improperly 2:24:17.629 18G / 46G INFO StageManager (stage.cpp : 132) STAGE == Mismatch Correction 2:24:17.629 18G / 46G INFO General (graph_pack.hpp : 109) Normalizing k-mer map. Total 35231600 kmers to process 2:25:08.800 18G / 46G INFO General (graph_pack.hpp : 111) Normalizing done 2:35:50.836 36G / 46G INFO General (mismatch_shall_not_pass.hp: 189) Finished collecting potential mismatches positions 2:37:44.369 18G / 46G INFO General (mismatch_shall_not_pass.hp: 290) All edges processed 2:37:48.456 18G / 46G INFO General (mismatch_correction.cpp : 27) Corrected 552 nucleotides 2:37:48.457 18G / 46G INFO StageManager (stage.cpp : 132) STAGE == Contig Output 2:37:48.457 18G / 46G INFO General (contig_output_stage.cpp : 40) Writing GFA to /local/genbank/workspace/reads.all3.spades1.55//K55/assembly_graph_with_scaffolds.gfa 2:37:56.529 18G / 46G INFO General (contig_output.hpp : 22) Outputting contigs to /local/genbank/workspace/reads.all3.spades1.55//K55/before_rr.fasta 2:38:03.066 18G / 46G INFO General (contig_output_stage.cpp : 51) Outputting FastG graph to /local/genbank/workspace/reads.all3.spades1.55//K55/assembly_graph.fastg 2:38:23.182 18G / 46G INFO General (contig_output.hpp : 22) Outputting contigs to /local/genbank/workspace/reads.all3.spades1.55//K55/simplified_contigs.fasta 2:38:30.403 18G / 46G INFO General (contig_output.hpp : 22) Outputting contigs to /local/genbank/workspace/reads.all3.spades1.55//K55/intermediate_contigs.fasta 2:38:37.078 18G / 46G INFO StageManager (stage.cpp : 132) STAGE == Paired Information Counting 2:38:38.272 18G / 46G INFO General (graph_pack.hpp : 109) Normalizing k-mer map. Total 35275990 kmers to process 2:39:32.323 18G / 46G INFO General (graph_pack.hpp : 111) Normalizing done 2:39:33.126 18G / 46G INFO General (pair_info_count.cpp : 320) Min edge length for estimation: 2356 2:39:33.126 18G / 46G INFO General (pair_info_count.cpp : 331) Estimating insert size for library #0 2:39:33.126 18G / 46G INFO General (pair_info_count.cpp : 190) Estimating insert size (takes a while) 2:39:34.410 18G / 46G INFO General (pair_info_count.cpp : 39) Selecting usual mapper 2:39:44.644 19G / 46G INFO General (sequence_mapper_notifier.h: 80) Processed 200000 reads 2:39:44.806 19G / 46G INFO General (sequence_mapper_notifier.h: 80) Processed 400000 reads 2:39:45.096 19G / 46G INFO General (sequence_mapper_notifier.h: 80) Processed 600000 reads 2:39:45.158 19G / 46G INFO General (sequence_mapper_notifier.h: 80) Processed 800000 reads 2:39:45.523 19G / 46G INFO General (sequence_mapper_notifier.h: 80) Processed 1000000 reads 2:39:45.608 19G / 46G INFO General (sequence_mapper_notifier.h: 80) Processed 1200000 reads 2:39:45.935 19G / 46G INFO General (sequence_mapper_notifier.h: 80) Processed 2200000 reads 2:39:47.008 19G / 46G INFO General (sequence_mapper_notifier.h: 80) Processed 4200000 reads 2:39:59.308 19G / 46G INFO General (sequence_mapper_notifier.h: 80) Processed 8400000 reads 2:40:14.294 19G / 46G INFO General (sequence_mapper_notifier.h: 80) Processed 16800000 reads 2:40:51.906 19G / 46G INFO General (sequence_mapper_notifier.h: 80) Processed 33600000 reads 2:41:41.069 19G / 46G INFO General (sequence_mapper_notifier.h: 80) Processed 67200000 reads 2:42:01.442 18G / 46G INFO General (sequence_mapper_notifier.h: 98) Total 80455197 reads processed 2:42:02.132 18G / 46G INFO General (pair_info_count.cpp : 209) Edge pairs: 67108864 (rough upper limit) 2:42:02.132 18G / 46G INFO General (pair_info_count.cpp : 213) 10903281 paired reads (13.552% of all) aligned to long edges 2:42:02.284 18G / 46G INFO General (pair_info_count.cpp : 354) Insert size = 255.853, deviation = 71.0407, left quantile = 165, right quantile = 328, read length = 700 2:42:02.284 18G / 46G WARN General (pair_info_count.cpp : 358) Estimated mean insert size 255.853 is very small compared to read length 700 2:42:02.473 18G / 46G INFO General (pair_info_count.cpp : 371) Filtering data for library #0 2:42:02.516 18G / 46G INFO General (pair_info_count.cpp : 39) Selecting usual mapper 2:42:11.936 18G / 46G INFO General (sequence_mapper_notifier.h: 80) Processed 200000 reads 2:42:11.937 18G / 46G INFO General (sequence_mapper_notifier.h: 80) Processed 400000 reads 2:42:12.002 18G / 46G INFO General (sequence_mapper_notifier.h: 80) Processed 600000 reads 2:42:12.067 18G / 46G INFO General (sequence_mapper_notifier.h: 80) Processed 800000 reads 2:42:12.148 18G / 46G INFO General (sequence_mapper_notifier.h: 80) Processed 1000000 reads 2:42:12.197 18G / 46G INFO General (sequence_mapper_notifier.h: 80) Processed 1200000 reads 2:42:12.333 18G / 46G INFO General (sequence_mapper_notifier.h: 80) Processed 2200000 reads 2:42:12.504 18G / 46G INFO General (sequence_mapper_notifier.h: 80) Processed 4200000 reads 2:42:24.279 18G / 46G INFO General (sequence_mapper_notifier.h: 80) Processed 8400000 reads 2:42:36.761 18G / 46G INFO General (sequence_mapper_notifier.h: 80) Processed 16800000 reads 2:43:14.495 18G / 46G INFO General (sequence_mapper_notifier.h: 80) Processed 33600000 reads 2:44:04.019 18G / 46G INFO General (sequence_mapper_notifier.h: 80) Processed 67200000 reads 2:44:18.850 18G / 46G INFO General (sequence_mapper_notifier.h: 98) Total 80455197 reads processed 2:44:18.851 18G / 46G INFO General (pair_info_count.cpp : 383) Mapping library #0 2:44:18.851 18G / 46G INFO General (pair_info_count.cpp : 385) Mapping paired reads (takes a while) 2:44:18.851 18G / 46G INFO General (pair_info_count.cpp : 289) Left insert size quantile 165, right insert size quantile 328, filtering threshold 2, rounding threshold 0 2:44:18.919 18G / 46G INFO General (pair_info_count.cpp : 39) Selecting usual mapper 2:44:42.871 18G / 46G INFO General (sequence_mapper_notifier.h: 80) Processed 200000 reads 2:44:43.518 18G / 46G INFO General (sequence_mapper_notifier.h: 80) Processed 400000 reads 2:44:44.185 18G / 46G INFO General (sequence_mapper_notifier.h: 80) Processed 600000 reads 2:44:44.196 18G / 46G INFO General (sequence_mapper_notifier.h: 80) Processed 800000 reads 2:44:44.454 18G / 46G INFO General (sequence_mapper_notifier.h: 80) Processed 1000000 reads 2:44:44.487 18G / 46G INFO General (sequence_mapper_notifier.h: 80) Processed 1200000 reads 2:44:46.827 18G / 46G INFO General (sequence_mapper_notifier.h: 80) Processed 2200000 reads 2:44:47.439 18G / 46G INFO General (sequence_mapper_notifier.h: 80) Processed 4200000 reads 2:44:59.085 18G / 46G INFO General (sequence_mapper_notifier.h: 80) Processed 8400000 reads 2:45:11.832 18G / 46G INFO General (sequence_mapper_notifier.h: 80) Processed 16800000 reads 2:46:28.196 18G / 46G INFO General (sequence_mapper_notifier.h: 80) Processed 33600000 reads 2:48:56.675 19G / 46G INFO General (sequence_mapper_notifier.h: 80) Processed 67142674 reads 2:49:32.679 19G / 46G INFO General (sequence_mapper_notifier.h: 98) Total 80455197 reads processed 2:49:32.848 18G / 46G INFO StageManager (stage.cpp : 132) STAGE == Distance Estimation 2:49:32.848 18G / 46G INFO General (distance_estimation.cpp : 173) Processing library #0 2:49:32.848 18G / 46G INFO General (distance_estimation.cpp : 149) Weight Filter Done 2:49:32.848 18G / 46G INFO DistanceEstimator (distance_estimation.hpp : 116) Using SIMPLE distance estimator 2:50:25.077 19G / 46G INFO General (distance_estimation.cpp : 34) Filtering info 2:50:25.077 19G / 46G INFO General (pair_info_filters.hpp : 242) Start filtering; index size: 11715595 2:50:32.887 19G / 46G INFO General (pair_info_filters.hpp : 263) Done filtering 2:50:32.893 19G / 46G INFO General (distance_estimation.cpp : 156) Refining clustered pair information 2:50:33.985 19G / 46G INFO General (distance_estimation.cpp : 158) The refining of clustered pair information has been finished 2:50:33.985 19G / 46G INFO General (distance_estimation.cpp : 160) Improving paired information 2:51:29.599 19G / 46G INFO PairInfoImprover (pair_info_improver.hpp : 103) Paired info stats: missing = 718326; contradictional = 202 2:55:41.487 19G / 46G INFO PairInfoImprover (pair_info_improver.hpp : 103) Paired info stats: missing = 172854; contradictional = 0 2:55:41.488 19G / 46G INFO General (distance_estimation.cpp : 103) Filling scaffolding index 2:55:41.488 19G / 46G INFO DistanceEstimator (distance_estimation.hpp : 116) Using SMOOTHING distance estimator 2:56:49.871 19G / 46G INFO General (distance_estimation.cpp : 34) Filtering info 2:56:49.871 19G / 46G INFO General (pair_info_filters.hpp : 242) Start filtering; index size: 1412730 2:56:50.904 19G / 46G INFO General (pair_info_filters.hpp : 263) Done filtering 2:56:50.904 19G / 46G INFO General (distance_estimation.cpp : 182) Clearing raw paired index 2:56:56.608 18G / 46G INFO StageManager (stage.cpp : 132) STAGE == Repeat Resolving 2:56:56.608 18G / 46G INFO General (repeat_resolving.cpp : 69) Using Path-Extend repeat resolving 2:56:56.608 18G / 46G INFO General (launcher.cpp : 477) ExSPAnder repeat resolving tool started 2:56:58.587 19G / 46G INFO General (launcher.cpp : 392) Creating main extenders, unique edge length = 2000 2:56:58.588 19G / 46G INFO General (extenders_logic.cpp : 275) Estimated coverage of library #0 is 19.5279 2:56:58.678 19G / 46G INFO General (extenders_logic.cpp : 275) Estimated coverage of library #0 is 19.5279 2:56:59.119 19G / 46G INFO General (extenders_logic.cpp : 472) Using 1 paired-end library 2:56:59.119 19G / 46G INFO General (extenders_logic.cpp : 473) Using 1 paired-end scaffolding library 2:56:59.119 19G / 46G INFO General (extenders_logic.cpp : 474) Using 0 single read libraries 2:56:59.119 19G / 46G INFO General (launcher.cpp : 420) Total number of extenders is 3 2:56:59.119 19G / 46G INFO General (path_extender.hpp : 885) Processed 0 paths from 112946 (0%) 2:56:59.386 19G / 46G INFO General (path_extender.hpp : 883) Processed 128 paths from 112946 (0%) 2:56:59.587 19G / 46G INFO General (path_extender.hpp : 883) Processed 256 paths from 112946 (0%) 2:57:00.079 19G / 46G INFO General (path_extender.hpp : 883) Processed 512 paths from 112946 (0%) 2:57:00.974 19G / 46G INFO General (path_extender.hpp : 883) Processed 1024 paths from 112946 (0%) 2:57:02.224 19G / 46G INFO General (path_extender.hpp : 883) Processed 2048 paths from 112946 (1%) 2:57:04.550 19G / 46G INFO General (path_extender.hpp : 883) Processed 4096 paths from 112946 (3%) 2:57:08.096 19G / 46G INFO General (path_extender.hpp : 883) Processed 8192 paths from 112946 (7%) 2:57:10.475 19G / 46G INFO General (path_extender.hpp : 885) Processed 11295 paths from 112946 (10%) 2:57:14.038 19G / 46G INFO General (path_extender.hpp : 883) Processed 16384 paths from 112946 (14%) 2:57:18.017 19G / 46G INFO General (path_extender.hpp : 885) Processed 22590 paths from 112946 (20%) 2:57:24.019 19G / 46G INFO General (path_extender.hpp : 883) Processed 32768 paths from 112946 (29%) 2:57:24.688 19G / 46G INFO General (path_extender.hpp : 885) Processed 33885 paths from 112946 (30%) 2:57:30.275 19G / 46G INFO General (path_extender.hpp : 885) Processed 45180 paths from 112946 (40%) 2:57:34.884 19G / 46G INFO General (path_extender.hpp : 885) Processed 56475 paths from 112946 (50%) 2:57:37.737 19G / 46G INFO General (path_extender.hpp : 883) Processed 65536 paths from 112946 (58%) 2:57:38.425 19G / 46G INFO General (path_extender.hpp : 885) Processed 67770 paths from 112946 (60%) 2:57:41.634 19G / 46G INFO General (path_extender.hpp : 885) Processed 79065 paths from 112946 (70%) 2:57:44.289 19G / 46G INFO General (path_extender.hpp : 885) Processed 90360 paths from 112946 (80%) 2:57:51.144 19G / 46G INFO General (path_extender.hpp : 885) Processed 101655 paths from 112946 (90%) 2:57:58.767 19G / 46G INFO General (launcher.cpp : 234) Finalizing paths 2:57:58.767 19G / 46G INFO General (launcher.cpp : 236) Deduplicating paths 2:58:03.153 19G / 46G INFO General (launcher.cpp : 240) Paths deduplicated 2:58:03.153 19G / 46G INFO PEResolver (pe_resolver.hpp : 295) Removing overlaps 2:58:03.153 19G / 46G INFO PEResolver (pe_resolver.hpp : 298) Sorting paths 2:58:03.720 19G / 46G INFO PEResolver (pe_resolver.hpp : 305) Marking overlaps 2:58:03.720 19G / 46G INFO OverlapRemover (pe_resolver.hpp : 130) Marking start/end overlaps 2:58:10.025 19G / 46G INFO OverlapRemover (pe_resolver.hpp : 133) Marking remaining overlaps 2:58:15.613 19G / 46G INFO PEResolver (pe_resolver.hpp : 308) Splitting paths 2:58:15.907 19G / 46G INFO PEResolver (pe_resolver.hpp : 313) Deduplicating paths 2:58:16.779 19G / 46G INFO PEResolver (pe_resolver.hpp : 315) Overlaps removed 2:58:19.145 19G / 46G INFO General (launcher.cpp : 257) Paths finalized 2:58:19.145 19G / 46G INFO General (launcher.cpp : 427) Closing gaps in paths 2:58:20.486 19G / 46G INFO General (launcher.cpp : 455) Gap closing completed 2:58:20.803 19G / 46G INFO General (launcher.cpp : 286) Traversing tandem repeats 2:58:22.739 19G / 46G INFO General (launcher.cpp : 296) Traversed 11 loops 2:58:22.740 19G / 46G INFO General (launcher.cpp : 234) Finalizing paths 2:58:22.740 19G / 46G INFO General (launcher.cpp : 236) Deduplicating paths 2:58:22.869 19G / 46G INFO General (launcher.cpp : 240) Paths deduplicated 2:58:22.870 19G / 46G INFO PEResolver (pe_resolver.hpp : 295) Removing overlaps 2:58:22.870 19G / 46G INFO PEResolver (pe_resolver.hpp : 298) Sorting paths 2:58:23.124 19G / 46G INFO PEResolver (pe_resolver.hpp : 305) Marking overlaps 2:58:23.124 19G / 46G INFO OverlapRemover (pe_resolver.hpp : 130) Marking start/end overlaps 2:58:23.369 19G / 46G INFO OverlapRemover (pe_resolver.hpp : 133) Marking remaining overlaps 2:58:23.638 19G / 46G INFO PEResolver (pe_resolver.hpp : 308) Splitting paths 2:58:23.664 19G / 46G INFO PEResolver (pe_resolver.hpp : 313) Deduplicating paths 2:58:23.794 19G / 46G INFO PEResolver (pe_resolver.hpp : 315) Overlaps removed 2:58:24.527 19G / 46G INFO General (launcher.cpp : 257) Paths finalized 2:58:25.208 19G / 46G INFO General (launcher.cpp : 529) ExSPAnder repeat resolving tool finished 2:58:27.529 19G / 46G INFO StageManager (stage.cpp : 132) STAGE == Contig Output 2:58:27.529 19G / 46G INFO General (contig_output_stage.cpp : 40) Writing GFA to /local/genbank/workspace/reads.all3.spades1.55//K55/assembly_graph_with_scaffolds.gfa 2:58:31.968 19G / 46G INFO General (contig_output.hpp : 22) Outputting contigs to /local/genbank/workspace/reads.all3.spades1.55//K55/before_rr.fasta 2:58:40.470 19G / 46G INFO General (contig_output_stage.cpp : 51) Outputting FastG graph to /local/genbank/workspace/reads.all3.spades1.55//K55/assembly_graph.fastg 2:59:02.852 19G / 46G INFO General (contig_output_stage.cpp : 20) Outputting FastG paths to /local/genbank/workspace/reads.all3.spades1.55//K55/final_contigs.paths 2:59:13.374 19G / 46G INFO General (contig_output_stage.cpp : 20) Outputting FastG paths to /local/genbank/workspace/reads.all3.spades1.55//K55/scaffolds.paths 2:59:23.477 19G / 46G INFO General (launch.hpp : 149) SPAdes finished 3:00:23.646 168M / 46G INFO General (main.cpp : 109) Assembling time: 3 hours 0 minutes 23 seconds ===== Assembling finished. Used k-mer sizes: 55 * Assembled contigs are in /local/genbank/workspace/reads.all3.spades1.55/contigs.fasta * Assembled scaffolds are in /local/genbank/workspace/reads.all3.spades1.55/scaffolds.fasta * Assembly graph is in /local/genbank/workspace/reads.all3.spades1.55/assembly_graph.fastg * Assembly graph in GFA format is in /local/genbank/workspace/reads.all3.spades1.55/assembly_graph_with_scaffolds.gfa * Paths in the assembly graph corresponding to the contigs are in /local/genbank/workspace/reads.all3.spades1.55/contigs.paths * Paths in the assembly graph corresponding to the scaffolds are in /local/genbank/workspace/reads.all3.spades1.55/scaffolds.paths ======= SPAdes pipeline finished WITH WARNINGS! === Error correction and assembling warnings: * 1:06:09.793 16G / 22G WARN General (kmer_coverage_model.cpp : 327) Valley value was estimated improperly, reset to 75 * 1:06:09.808 16G / 22G WARN General (kmer_coverage_model.cpp : 366) Failed to determine erroneous kmer threshold. Threshold set to: 75 * 2:24:17.629 18G / 46G WARN General (simplification.cpp : 479) The determined erroneous connection coverage threshold may be determined improperly * 2:42:02.284 18G / 46G WARN General (pair_info_count.cpp : 358) Estimated mean insert size 255.853 is very small compared to read length 700 ======= Warnings saved to /local/genbank/workspace/reads.all3.spades1.55/warnings.log SPAdes log can be found here: /local/genbank/workspace/reads.all3.spades1.55/spades.log Thank you for using SPAdes!