Command line: /home/psgendb/BIRCHDEV/bin-linux-x86_64/spades.py -1 /local/genbank/workspace/reads.uncorr.spades1.corrected/20090202_7_R1.00.0_0.cor.fastq.gz -2 /local/genbank/workspace/reads.uncorr.spades1.corrected/20090202_7_R2.00.0_0.cor.fastq.gz -1 /local/genbank/workspace/reads.uncorr.spades1.corrected/20090202_8_R1.00.0_1.cor.fastq.gz -2 /local/genbank/workspace/reads.uncorr.spades1.corrected/20090202_8_R2.00.0_1.cor.fastq.gz -1 /local/genbank/workspace/reads.uncorr.spades1.corrected/AB2kb_R1.00.0_2.cor.fastq.gz -2 /local/genbank/workspace/reads.uncorr.spades1.corrected/AB2kb_R2.00.0_2.cor.fastq.gz -1 /local/genbank/workspace/reads.uncorr.spades1.corrected/AB4kb_R1.00.0_3.cor.fastq.gz -2 /local/genbank/workspace/reads.uncorr.spades1.corrected/AB4kb_R2.00.0_3.cor.fastq.gz -1 /local/genbank/workspace/reads.uncorr.spades1.corrected/Algae6.2GB_6_R1.00.0_4.cor.fastq.gz -2 /local/genbank/workspace/reads.uncorr.spades1.corrected/Algae6.2GB_6_R2.00.0_4.cor.fastq.gz -1 /local/genbank/workspace/reads.uncorr.spades1.corrected/Algae6.2GB_7_R1.00.0_5.cor.fastq.gz -2 /local/genbank/workspace/reads.uncorr.spades1.corrected/Algae6.2GB_7_R2.00.0_5.cor.fastq.gz -1 /local/genbank/workspace/reads.uncorr.spades1.corrected/Algae6.2GB_8_R1.00.0_6.cor.fastq.gz -2 /local/genbank/workspace/reads.uncorr.spades1.corrected/Algae6.2GB_8_R2.00.0_6.cor.fastq.gz -1 /local/genbank/workspace/reads.uncorr.spades1.corrected/Algae7.2GB_6_R1.00.0_7.cor.fastq.gz -2 /local/genbank/workspace/reads.uncorr.spades1.corrected/Algae7.2GB_6_R2.00.0_7.cor.fastq.gz -1 /local/genbank/workspace/reads.uncorr.spades1.corrected/Algae7.2GB_7_R1.00.0_8.cor.fastq.gz -2 /local/genbank/workspace/reads.uncorr.spades1.corrected/Algae7.2GB_7_R2.00.0_8.cor.fastq.gz -1 /local/genbank/workspace/reads.uncorr.spades1.corrected/Algae7.2GB_8_R1.00.0_9.cor.fastq.gz -2 /local/genbank/workspace/reads.uncorr.spades1.corrected/Algae7.2GB_8_R2.00.0_9.cor.fastq.gz -s /local/genbank/workspace/reads.uncorr.spades1.corrected/2008-09allspades.fq -s /local/genbank/workspace/reads.uncorr.spades1.corrected/3-6.2-7.2allspades.fq -s /local/genbank/workspace/reads.uncorr.spades1.corrected/AGRFallspades.fq -s /local/genbank/workspace/reads.uncorr.spades1.corrected/454all.00.0_13.cor.fastq.gz --only-assembler -k 77 -m 225 -t 32 -o /local/genbank/workspace/reads.spadescorr.k77 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.spadescorr.k77 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.uncorr.spades1.corrected/20090202_7_R1.00.0_0.cor.fastq.gz', '/local/genbank/workspace/reads.uncorr.spades1.corrected/20090202_8_R1.00.0_1.cor.fastq.gz', '/local/genbank/workspace/reads.uncorr.spades1.corrected/AB2kb_R1.00.0_2.cor.fastq.gz', '/local/genbank/workspace/reads.uncorr.spades1.corrected/AB4kb_R1.00.0_3.cor.fastq.gz', '/local/genbank/workspace/reads.uncorr.spades1.corrected/Algae6.2GB_6_R1.00.0_4.cor.fastq.gz', '/local/genbank/workspace/reads.uncorr.spades1.corrected/Algae6.2GB_7_R1.00.0_5.cor.fastq.gz', '/local/genbank/workspace/reads.uncorr.spades1.corrected/Algae6.2GB_8_R1.00.0_6.cor.fastq.gz', '/local/genbank/workspace/reads.uncorr.spades1.corrected/Algae7.2GB_6_R1.00.0_7.cor.fastq.gz', '/local/genbank/workspace/reads.uncorr.spades1.corrected/Algae7.2GB_7_R1.00.0_8.cor.fastq.gz', '/local/genbank/workspace/reads.uncorr.spades1.corrected/Algae7.2GB_8_R1.00.0_9.cor.fastq.gz'] right reads: ['/local/genbank/workspace/reads.uncorr.spades1.corrected/20090202_7_R2.00.0_0.cor.fastq.gz', '/local/genbank/workspace/reads.uncorr.spades1.corrected/20090202_8_R2.00.0_1.cor.fastq.gz', '/local/genbank/workspace/reads.uncorr.spades1.corrected/AB2kb_R2.00.0_2.cor.fastq.gz', '/local/genbank/workspace/reads.uncorr.spades1.corrected/AB4kb_R2.00.0_3.cor.fastq.gz', '/local/genbank/workspace/reads.uncorr.spades1.corrected/Algae6.2GB_6_R2.00.0_4.cor.fastq.gz', '/local/genbank/workspace/reads.uncorr.spades1.corrected/Algae6.2GB_7_R2.00.0_5.cor.fastq.gz', '/local/genbank/workspace/reads.uncorr.spades1.corrected/Algae6.2GB_8_R2.00.0_6.cor.fastq.gz', '/local/genbank/workspace/reads.uncorr.spades1.corrected/Algae7.2GB_6_R2.00.0_7.cor.fastq.gz', '/local/genbank/workspace/reads.uncorr.spades1.corrected/Algae7.2GB_7_R2.00.0_8.cor.fastq.gz', '/local/genbank/workspace/reads.uncorr.spades1.corrected/Algae7.2GB_8_R2.00.0_9.cor.fastq.gz'] interlaced reads: not specified single reads: ['/local/genbank/workspace/reads.uncorr.spades1.corrected/2008-09allspades.fq', '/local/genbank/workspace/reads.uncorr.spades1.corrected/3-6.2-7.2allspades.fq', '/local/genbank/workspace/reads.uncorr.spades1.corrected/AGRFallspades.fq', '/local/genbank/workspace/reads.uncorr.spades1.corrected/454all.00.0_13.cor.fastq.gz'] merged reads: not specified Assembly parameters: k: [77] 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.spadescorr.k77/tmp Threads: 32 Memory limit (in Gb): 225 ======= SPAdes pipeline started. Log can be found here: /local/genbank/workspace/reads.spadescorr.k77/spades.log ===== Assembling started. == Running assembler: K77 0:00:00.000 4M / 4M INFO General (main.cpp : 74) Loaded config from /local/genbank/workspace/reads.spadescorr.k77/K77/configs/config.info 0:00:00.001 4M / 4M INFO General (memory_limit.cpp : 49) Memory limit set to 225 Gb 0:00:00.001 4M / 4M INFO General (main.cpp : 87) Starting SPAdes, built from refs/heads/spades_3.13.0, git revision 8ea46659e9b2aca35444a808db550ac333006f8b 0:00:00.001 4M / 4M INFO General (main.cpp : 88) Maximum k-mer length: 128 0:00:00.001 4M / 4M INFO General (main.cpp : 89) Assembling dataset (/local/genbank/workspace/reads.spadescorr.k77/dataset.info) with K=77 0:00:00.001 4M / 4M INFO General (main.cpp : 90) Maximum # of threads to use (adjusted due to OMP capabilities): 32 0:00:00.001 4M / 4M INFO General (launch.hpp : 51) SPAdes started 0:00:00.001 4M / 4M INFO General (launch.hpp : 58) Starting from stage: construction 0:00:00.001 4M / 4M INFO General (launch.hpp : 65) Two-step RR enabled: 0 0:00:00.001 4M / 4M INFO General (launch.hpp : 76) Will need read mapping, kmer mapper will be attached 0:00:00.001 4M / 4M INFO StageManager (stage.cpp : 132) STAGE == de Bruijn graph construction 0:00:00.010 4M / 4M INFO General (read_converter.hpp : 77) Converting reads to binary format for library #0 (takes a while) 0:00:00.010 4M / 4M INFO General (read_converter.hpp : 78) Converting paired reads 0:00:00.585 76M / 76M INFO General (binary_converter.hpp : 93) 16384 reads processed 0:00:00.957 84M / 84M INFO General (binary_converter.hpp : 93) 32768 reads processed 0:00:01.701 104M / 104M INFO General (binary_converter.hpp : 93) 65536 reads processed 0:00:03.193 136M / 136M INFO General (binary_converter.hpp : 93) 131072 reads processed 0:00:06.184 208M / 208M INFO General (binary_converter.hpp : 93) 262144 reads processed 0:00:12.211 348M / 348M INFO General (binary_converter.hpp : 93) 524288 reads processed 0:00:28.198 564M / 564M INFO General (binary_converter.hpp : 93) 1048576 reads processed 0:00:56.883 616M / 616M INFO General (binary_converter.hpp : 93) 2097152 reads processed 0:01:53.794 620M / 620M INFO General (binary_converter.hpp : 93) 4194304 reads processed 0:04:04.003 872M / 876M INFO General (binary_converter.hpp : 93) 8388608 reads processed 0:07:27.876 956M / 956M INFO General (binary_converter.hpp : 93) 16777216 reads processed 0:16:48.457 916M / 956M INFO General (binary_converter.hpp : 93) 33554432 reads processed 0:33:53.396 696M / 956M INFO General (binary_converter.hpp : 93) 67108864 reads processed 0:53:47.540 636M / 956M INFO General (binary_converter.hpp : 117) 105822607 reads written 0:53:50.590 8M / 956M INFO General (read_converter.hpp : 87) Converting single reads 0:53:50.996 136M / 956M INFO General (binary_converter.hpp : 93) 16384 reads processed 0:53:51.125 140M / 956M INFO General (binary_converter.hpp : 93) 32768 reads processed 0:53:51.386 152M / 956M INFO General (binary_converter.hpp : 93) 65536 reads processed 0:53:51.906 168M / 956M INFO General (binary_converter.hpp : 93) 131072 reads processed 0:53:52.948 204M / 956M INFO General (binary_converter.hpp : 93) 262144 reads processed 0:53:55.048 276M / 956M INFO General (binary_converter.hpp : 93) 524288 reads processed 0:53:59.245 420M / 956M INFO General (binary_converter.hpp : 93) 1048576 reads processed 0:54:07.425 708M / 956M INFO General (binary_converter.hpp : 93) 2097152 reads processed 0:54:23.432 1G / 1G INFO General (binary_converter.hpp : 93) 4194304 reads processed 0:55:05.036 1G / 1G INFO General (binary_converter.hpp : 93) 8388608 reads processed 0:56:28.347 1G / 1G INFO General (binary_converter.hpp : 93) 16777216 reads processed 0:59:17.643 1G / 1G INFO General (binary_converter.hpp : 93) 33554432 reads processed 1:04:58.799 1G / 1G INFO General (binary_converter.hpp : 93) 67108864 reads processed 1:12:33.099 3G / 3G INFO General (binary_converter.hpp : 117) 99317237 reads written 1:12:41.258 16M / 3G INFO General (read_converter.hpp : 95) Converting merged reads 1:12:41.586 144M / 3G INFO General (binary_converter.hpp : 117) 0 reads written 1:12:41.886 12M / 3G INFO General (construction.cpp : 111) Max read length 700 1:12:41.887 12M / 3G INFO General (construction.cpp : 117) Average read length 77.5334 1:12:41.887 12M / 3G INFO General (stage.cpp : 101) PROCEDURE == k+1-mer counting 1:12:41.889 12M / 3G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 1024 files using 32 threads. This might take a while. 1:12:41.895 8M / 3G INFO General (file_limit.hpp : 32) Open file limit set to 4096 1:12:41.895 8M / 3G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.34367 Gb 1:12:41.895 8M / 3G INFO General (kmer_splitters.hpp : 97) Using cell size of 21845 1:14:01.274 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 197455616 reads 1:15:25.971 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 294850240 reads 1:16:50.016 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 381765461 reads 1:17:32.826 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 621924902 reads 1:17:32.827 17G / 18G INFO General (kmer_splitters.hpp : 295) Adding contigs from previous K 1:17:39.208 132M / 18G INFO General (kmer_splitters.hpp : 308) Used 621924902 reads 1:17:39.209 132M / 18G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 1:20:11.403 132M / 18G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 666559367 kmers in total. 1:20:11.403 132M / 18G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 1:23:19.672 128M / 18G INFO General (stage.cpp : 101) PROCEDURE == Extension index construction 1:23:19.674 128M / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 1:23:19.674 128M / 18G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 512 files using 32 threads. This might take a while. 1:23:19.676 128M / 18G INFO General (file_limit.hpp : 32) Open file limit set to 4096 1:23:19.677 128M / 18G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.34245 Gb 1:23:19.677 128M / 18G INFO General (kmer_splitters.hpp : 97) Using cell size of 43690 1:23:26.613 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 5512788 kmers 1:23:32.128 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 11453893 kmers 1:23:37.272 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 17303170 kmers 1:23:44.326 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 26283890 kmers 1:23:49.772 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 32238064 kmers 1:23:55.072 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 38085474 kmers 1:24:02.130 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 47130461 kmers 1:24:07.480 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 53084448 kmers 1:24:12.741 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 58934199 kmers 1:24:19.737 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 67944610 kmers 1:24:25.150 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 73901914 kmers 1:24:30.604 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 79757299 kmers 1:24:37.680 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 88783002 kmers 1:24:43.741 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 94742741 kmers 1:24:49.115 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 100582518 kmers 1:24:56.236 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 109608531 kmers 1:25:01.642 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 115556664 kmers 1:25:19.632 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 136376441 kmers 1:27:21.307 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 276230981 kmers 1:31:09.301 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 537994566 kmers 1:33:01.884 17G / 18G INFO General (kmer_splitters.hpp : 385) Used 666562439 kmers. 1:33:05.027 128M / 18G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 1:35:43.357 128M / 18G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 682465379 kmers in total. 1:35:43.357 128M / 18G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 1:38:56.940 128M / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 1:40:08.675 520M / 18G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 1:43:07.720 520M / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 316469606 bytes occupied (3.70972 bits per kmer). 1:43:08.838 1G / 18G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 99) Building k-mer extensions from k+1-mers 1:43:48.747 1G / 18G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 103) Building k-mer extensions from k+1-mers finished. 1:43:48.755 1G / 18G INFO General (stage.cpp : 101) PROCEDURE == Condensing graph 1:43:48.966 1G / 18G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 355) Extracting unbranching paths 1:44:50.154 3G / 18G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 374) Extracting unbranching paths finished. 30578449 sequences extracted 1:45:24.931 3G / 18G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 310) Collecting perfect loops 1:45:41.849 3G / 18G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 343) Collecting perfect loops finished. 35 loops collected 1:46:48.304 12G / 18G INFO General (stage.cpp : 101) PROCEDURE == Filling coverage indices (PHM) 1:46:48.305 12G / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 1:46:48.305 12G / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 1:47:22.319 12G / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 309108962 bytes occupied (3.7099 bits per kmer). 1:47:26.380 15G / 18G INFO General (construction.cpp : 388) Collecting k-mer coverage information from reads, this takes a while. 1:48:49.918 15G / 18G INFO General (construction.cpp : 508) Filling coverage and flanking coverage from PHM 1:49:20.860 15G / 18G INFO General (construction.cpp : 464) Processed 32000000 edges 1:49:41.216 15G / 18G INFO General (construction.cpp : 464) Processed 61156667 edges 1:49:52.030 11G / 18G INFO StageManager (stage.cpp : 132) STAGE == EC Threshold Finding 1:49:52.084 11G / 18G INFO General (kmer_coverage_model.cpp : 181) Kmer coverage valley at: 127 1:49:52.086 11G / 18G INFO General (kmer_coverage_model.cpp : 201) K-mer histogram maximum: 129 1:49:52.086 11G / 18G INFO General (kmer_coverage_model.cpp : 237) Estimated median coverage: 130. Coverage mad: 2.9652 1:49:52.088 11G / 18G INFO General (kmer_coverage_model.cpp : 259) Fitting coverage model 1:49:52.940 11G / 18G INFO General (kmer_coverage_model.cpp : 295) ... iteration 2 1:49:54.773 11G / 18G INFO General (kmer_coverage_model.cpp : 295) ... iteration 4 1:49:56.481 11G / 18G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 124.013. Fitted coverage std. dev: 7.64354 1:49:56.505 11G / 18G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 0.995756 1:49:56.505 11G / 18G WARN General (kmer_coverage_model.cpp : 366) Failed to determine erroneous kmer threshold. Threshold set to: 127 1:49:56.505 11G / 18G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 172541 1:49:56.506 11G / 18G INFO General (genomic_info_filler.cpp : 114) Failed to estimate mean coverage 1:49:56.506 11G / 18G INFO General (genomic_info_filler.cpp : 127) EC coverage threshold value was calculated as 127 1:49:56.506 11G / 18G INFO General (genomic_info_filler.cpp : 128) Trusted kmer low bound: 0 1:49:56.506 11G / 18G INFO StageManager (stage.cpp : 132) STAGE == Gap Closer 1:49:56.506 11G / 18G INFO General (graph_pack.hpp : 101) Index refill 1:49:56.510 11G / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 1:49:56.510 11G / 18G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 512 files using 32 threads. This might take a while. 1:49:56.512 11G / 18G INFO General (file_limit.hpp : 32) Open file limit set to 4096 1:49:56.512 11G / 18G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.22705 Gb 1:49:56.512 11G / 18G INFO General (kmer_splitters.hpp : 97) Using cell size of 43690 1:52:46.716 28G / 29G INFO General (edge_index_builders.hpp : 77) Processed 55536748 edges 1:53:06.072 28G / 29G INFO General (edge_index_builders.hpp : 77) Processed 61156699 edges 1:53:06.073 28G / 29G INFO General (edge_index_builders.hpp : 82) Used 61156699 sequences. 1:53:11.588 11G / 29G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 1:55:33.392 11G / 29G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 666559367 kmers in total. 1:55:33.392 11G / 29G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 1:58:42.707 11G / 29G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 1:59:59.108 11G / 29G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 2:02:26.987 11G / 29G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 309093064 bytes occupied (3.70971 bits per kmer). 2:02:41.907 26G / 29G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while. 2:03:16.021 26G / 29G INFO General (edge_index.hpp : 92) Index refilled 2:03:16.045 26G / 29G INFO General (gap_closer.cpp : 159) Preparing shift maps 2:05:53.028 32G / 32G INFO General (gap_closer.cpp : 119) Processing paired reads (takes a while) 2:06:18.163 35G / 35G INFO General (gap_closer.cpp : 138) Used 105822607 paired reads 2:06:18.163 35G / 35G INFO General (gap_closer.cpp : 140) Merging paired indices 2:08:19.677 27G / 35G INFO GapCloser (gap_closer.cpp : 346) Closing short gaps 2:17:16.600 28G / 35G INFO GapCloser (gap_closer.cpp : 380) Closing short gaps complete: filled 137613 gaps after checking 2249597 candidates 2:19:40.529 26G / 35G INFO StageManager (stage.cpp : 132) STAGE == Raw Simplification 2:19:47.537 11G / 35G INFO General (simplification.cpp : 128) PROCEDURE == InitialCleaning 2:19:47.538 11G / 35G INFO General (simplification.cpp : 68) Most init cleaning disabled since detected mean 0 was less than activation coverage 10 2:19:47.538 11G / 35G INFO Simplification (parallel_processing.hpp : 165) Running Self conjugate edge remover 2:19:55.706 11G / 35G INFO Simplification (parallel_processing.hpp : 167) Self conjugate edge remover triggered 1 times 2:19:55.706 11G / 35G INFO StageManager (stage.cpp : 132) STAGE == Simplification 2:19:55.706 11G / 35G INFO General (simplification.cpp : 357) Graph simplification started 2:19:55.706 11G / 35G INFO General (graph_simplification.hpp : 634) Creating parallel br instance 2:19:55.706 11G / 35G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 1 2:19:55.706 11G / 35G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 2:27:02.158 11G / 35G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 6534914 times 2:27:02.158 11G / 35G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 2:37:41.886 16G / 35G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 429176 times 2:37:41.887 16G / 35G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 2:38:02.396 16G / 35G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 74364 times 2:38:02.396 16G / 35G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 2 2:38:02.396 16G / 35G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 2:38:05.814 16G / 35G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 22582 times 2:38:05.814 16G / 35G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 2:38:17.698 16G / 35G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 3363 times 2:38:17.698 16G / 35G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 2:38:17.938 16G / 35G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 1471 times 2:38:17.938 16G / 35G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 3 2:38:17.938 16G / 35G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 2:38:17.953 16G / 35G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 83 times 2:38:17.953 16G / 35G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 2:38:19.279 16G / 35G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 302 times 2:38:19.280 16G / 35G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 2:38:19.345 16G / 35G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 472 times 2:38:19.345 16G / 35G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 4 2:38:19.345 16G / 35G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 2:38:19.349 16G / 35G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 30 times 2:38:19.349 16G / 35G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 2:38:19.660 16G / 35G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 93 times 2:38:19.660 16G / 35G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 2:38:19.702 16G / 35G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 254 times 2:38:19.702 16G / 35G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 5 2:38:19.702 16G / 35G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 2:38:19.704 16G / 35G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 18 times 2:38:19.704 16G / 35G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 2:38:19.998 16G / 35G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 36 times 2:38:19.999 16G / 35G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 2:38:20.017 16G / 35G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 144 times 2:38:20.017 16G / 35G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 6 2:38:20.017 16G / 35G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 2:38:20.018 16G / 35G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 14 times 2:38:20.018 16G / 35G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 2:38:20.099 16G / 35G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 25 times 2:38:20.099 16G / 35G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 2:38:20.109 16G / 35G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 78 times 2:38:20.109 16G / 35G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 7 2:38:20.109 16G / 35G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 2:38:20.110 16G / 35G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 7 times 2:38:20.110 16G / 35G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 2:38:20.145 16G / 35G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 14 times 2:38:20.146 16G / 35G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 2:38:20.156 16G / 35G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 81 times 2:38:20.156 16G / 35G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 8 2:38:20.156 16G / 35G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 2:38:20.157 16G / 35G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 8 times 2:38:20.157 16G / 35G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 2:38:20.229 16G / 35G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 11 times 2:38:20.230 16G / 35G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 2:38:20.237 16G / 35G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 57 times 2:38:20.237 16G / 35G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 9 2:38:20.237 16G / 35G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 2:38:20.238 16G / 35G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 9 times 2:38:20.238 16G / 35G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 2:38:20.263 16G / 35G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 7 times 2:38:20.263 16G / 35G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 2:38:20.268 16G / 35G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 38 times 2:38:20.268 16G / 35G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 10 2:38:20.268 16G / 35G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 2:38:20.269 16G / 35G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 9 times 2:38:20.269 16G / 35G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 2:38:20.292 16G / 35G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 8 times 2:38:20.292 16G / 35G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 2:38:20.295 16G / 35G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 29 times 2:38:20.295 16G / 35G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 11 2:38:20.295 16G / 35G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 2:38:28.070 16G / 35G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 646 times 2:38:28.070 16G / 35G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 2:38:33.435 16G / 35G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 30 times 2:38:33.435 16G / 35G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 2:38:38.909 16G / 35G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 3 times 2:38:38.909 16G / 35G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 12 2:38:38.909 16G / 35G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 2:38:38.910 16G / 35G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 2:38:38.910 16G / 35G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 2:38:38.911 16G / 35G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 2:38:38.911 16G / 35G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 2:38:38.911 16G / 35G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 2:38:38.911 16G / 35G INFO StageManager (stage.cpp : 132) STAGE == Gap Closer 2:38:38.911 16G / 35G INFO General (graph_pack.hpp : 101) Index refill 2:38:38.921 16G / 35G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 2:38:38.921 16G / 35G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 512 files using 32 threads. This might take a while. 2:38:38.925 16G / 35G INFO General (file_limit.hpp : 32) Open file limit set to 4096 2:38:38.925 16G / 35G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.17501 Gb 2:38:38.925 16G / 35G INFO General (kmer_splitters.hpp : 97) Using cell size of 43690 2:41:02.388 33G / 35G INFO General (edge_index_builders.hpp : 77) Processed 32567946 edges 2:41:02.388 33G / 35G INFO General (edge_index_builders.hpp : 82) Used 32567946 sequences. 2:41:09.035 16G / 35G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 2:43:03.319 16G / 35G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 515908787 kmers in total. 2:43:03.319 16G / 35G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 2:45:29.378 16G / 35G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 2:46:26.472 16G / 35G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 2:48:28.483 16G / 35G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 239236024 bytes occupied (3.70974 bits per kmer). 2:48:49.714 27G / 35G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while. 2:49:20.201 27G / 35G INFO General (edge_index.hpp : 92) Index refilled 2:49:20.225 27G / 35G INFO General (gap_closer.cpp : 159) Preparing shift maps 2:50:55.978 32G / 35G INFO General (gap_closer.cpp : 119) Processing paired reads (takes a while) 2:51:36.402 36G / 36G INFO General (gap_closer.cpp : 138) Used 105822607 paired reads 2:51:36.402 36G / 36G INFO General (gap_closer.cpp : 140) Merging paired indices 2:54:42.075 29G / 36G INFO GapCloser (gap_closer.cpp : 346) Closing short gaps 3:01:01.446 29G / 36G INFO GapCloser (gap_closer.cpp : 380) Closing short gaps complete: filled 24349 gaps after checking 2230743 candidates 3:03:01.498 27G / 36G INFO StageManager (stage.cpp : 132) STAGE == Simplification Cleanup 3:03:01.498 27G / 36G INFO General (simplification.cpp : 196) PROCEDURE == Post simplification 3:03:01.498 27G / 36G INFO General (graph_simplification.hpp : 453) Disconnection of relatively low covered edges disabled 3:03:01.498 27G / 36G INFO General (graph_simplification.hpp : 489) Complex tip clipping disabled 3:03:01.498 27G / 36G INFO General (graph_simplification.hpp : 634) Creating parallel br instance 3:03:01.498 27G / 36G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 3:03:09.736 27G / 36G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 3:03:09.736 27G / 36G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 3:03:13.629 27G / 36G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 3:03:13.629 27G / 36G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 3:03:19.963 27G / 36G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 3:03:19.964 27G / 36G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 3:03:25.397 27G / 36G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 3:03:25.397 27G / 36G INFO General (simplification.cpp : 330) Disrupting self-conjugate edges 3:04:51.438 27G / 36G INFO Simplification (parallel_processing.hpp : 165) Running Removing isolated edges 3:31:36.406 21G / 36G INFO Simplification (parallel_processing.hpp : 167) Removing isolated edges triggered 16218731 times 3:31:36.406 21G / 36G INFO General (simplification.cpp : 470) Counting average coverage 3:31:36.927 21G / 36G INFO General (simplification.cpp : 476) Average coverage = 10.9268 3:31:36.927 21G / 36G WARN General (simplification.cpp : 479) The determined erroneous connection coverage threshold may be determined improperly 3:31:36.927 21G / 36G INFO StageManager (stage.cpp : 132) STAGE == Mismatch Correction 3:31:36.927 21G / 36G INFO General (graph_pack.hpp : 109) Normalizing k-mer map. Total 71993423 kmers to process 3:35:05.363 21G / 36G INFO General (graph_pack.hpp : 111) Normalizing done 4:06:37.983 71G / 71G INFO General (mismatch_shall_not_pass.hp: 189) Finished collecting potential mismatches positions 4:15:23.524 22G / 71G INFO General (mismatch_shall_not_pass.hp: 290) All edges processed 4:15:42.091 21G / 71G INFO General (mismatch_correction.cpp : 27) Corrected 331 nucleotides 4:15:42.094 21G / 71G INFO StageManager (stage.cpp : 132) STAGE == Contig Output 4:15:42.094 21G / 71G INFO General (contig_output_stage.cpp : 40) Writing GFA to /local/genbank/workspace/reads.spadescorr.k77//K77/assembly_graph_with_scaffolds.gfa 4:15:47.400 21G / 71G INFO General (contig_output.hpp : 22) Outputting contigs to /local/genbank/workspace/reads.spadescorr.k77//K77/before_rr.fasta 4:15:51.793 21G / 71G INFO General (contig_output_stage.cpp : 51) Outputting FastG graph to /local/genbank/workspace/reads.spadescorr.k77//K77/assembly_graph.fastg 4:16:04.601 21G / 71G INFO General (contig_output.hpp : 22) Outputting contigs to /local/genbank/workspace/reads.spadescorr.k77//K77/simplified_contigs.fasta 4:16:08.986 21G / 71G INFO General (contig_output.hpp : 22) Outputting contigs to /local/genbank/workspace/reads.spadescorr.k77//K77/intermediate_contigs.fasta 4:16:13.500 21G / 71G INFO StageManager (stage.cpp : 132) STAGE == Paired Information Counting 4:16:14.231 21G / 71G INFO General (graph_pack.hpp : 109) Normalizing k-mer map. Total 72033153 kmers to process 4:19:36.166 21G / 71G INFO General (graph_pack.hpp : 111) Normalizing done 4:19:36.656 21G / 71G INFO General (pair_info_count.cpp : 320) Min edge length for estimation: 4402 4:19:36.656 21G / 71G INFO General (pair_info_count.cpp : 331) Estimating insert size for library #0 4:19:36.656 21G / 71G INFO General (pair_info_count.cpp : 190) Estimating insert size (takes a while) 4:19:38.497 21G / 71G INFO General (pair_info_count.cpp : 39) Selecting usual mapper 4:19:44.930 21G / 71G INFO General (sequence_mapper_notifier.h: 80) Processed 200000 reads 4:19:45.009 21G / 71G INFO General (sequence_mapper_notifier.h: 80) Processed 400000 reads 4:19:45.078 21G / 71G INFO General (sequence_mapper_notifier.h: 80) Processed 600000 reads 4:19:45.219 21G / 71G INFO General (sequence_mapper_notifier.h: 80) Processed 800000 reads 4:19:45.336 21G / 71G INFO General (sequence_mapper_notifier.h: 80) Processed 1000000 reads 4:19:45.460 21G / 71G INFO General (sequence_mapper_notifier.h: 80) Processed 1200000 reads 4:19:46.340 21G / 71G INFO General (sequence_mapper_notifier.h: 80) Processed 2200000 reads 4:19:48.280 21G / 71G INFO General (sequence_mapper_notifier.h: 80) Processed 4200000 reads 4:19:57.312 21G / 71G INFO General (sequence_mapper_notifier.h: 80) Processed 8400000 reads 4:20:08.989 21G / 71G INFO General (sequence_mapper_notifier.h: 80) Processed 16800000 reads 4:20:33.221 21G / 71G INFO General (sequence_mapper_notifier.h: 80) Processed 33600000 reads 4:21:14.671 21G / 71G INFO General (sequence_mapper_notifier.h: 80) Processed 67227826 reads 4:21:58.863 21G / 71G INFO General (sequence_mapper_notifier.h: 98) Total 105822607 reads processed 4:22:00.029 21G / 71G INFO General (pair_info_count.cpp : 209) Edge pairs: 67108864 (rough upper limit) 4:22:00.029 21G / 71G INFO General (pair_info_count.cpp : 213) 467271 paired reads (0.441561% of all) aligned to long edges 4:22:00.243 21G / 71G INFO General (pair_info_count.cpp : 354) Insert size = 293.009, deviation = 78.9957, left quantile = 196, right quantile = 402, read length = 700 4:22:00.243 21G / 71G WARN General (pair_info_count.cpp : 358) Estimated mean insert size 293.009 is very small compared to read length 700 4:22:00.356 21G / 71G INFO General (pair_info_count.cpp : 371) Filtering data for library #0 4:22:00.405 21G / 71G INFO General (pair_info_count.cpp : 39) Selecting usual mapper 4:22:06.979 21G / 71G INFO General (sequence_mapper_notifier.h: 80) Processed 200000 reads 4:22:07.155 21G / 71G INFO General (sequence_mapper_notifier.h: 80) Processed 400000 reads 4:22:07.165 21G / 71G INFO General (sequence_mapper_notifier.h: 80) Processed 600000 reads 4:22:07.363 21G / 71G INFO General (sequence_mapper_notifier.h: 80) Processed 800000 reads 4:22:07.378 21G / 71G INFO General (sequence_mapper_notifier.h: 80) Processed 1000000 reads 4:22:07.402 21G / 71G INFO General (sequence_mapper_notifier.h: 80) Processed 1200000 reads 4:22:07.463 21G / 71G INFO General (sequence_mapper_notifier.h: 80) Processed 2200000 reads 4:22:07.603 21G / 71G INFO General (sequence_mapper_notifier.h: 80) Processed 4200000 reads 4:22:17.249 21G / 71G INFO General (sequence_mapper_notifier.h: 80) Processed 8400000 reads 4:22:27.247 21G / 71G INFO General (sequence_mapper_notifier.h: 80) Processed 16800000 reads 4:22:50.634 21G / 71G INFO General (sequence_mapper_notifier.h: 80) Processed 33600000 reads 4:23:33.562 21G / 71G INFO General (sequence_mapper_notifier.h: 80) Processed 67200000 reads 4:24:12.049 21G / 71G INFO General (sequence_mapper_notifier.h: 98) Total 105822607 reads processed 4:24:12.051 21G / 71G INFO General (pair_info_count.cpp : 383) Mapping library #0 4:24:12.051 21G / 71G INFO General (pair_info_count.cpp : 385) Mapping paired reads (takes a while) 4:24:12.051 21G / 71G INFO General (pair_info_count.cpp : 289) Left insert size quantile 196, right insert size quantile 402, filtering threshold 2, rounding threshold 0 4:24:12.124 21G / 71G INFO General (pair_info_count.cpp : 39) Selecting usual mapper 4:24:18.677 21G / 71G INFO General (sequence_mapper_notifier.h: 80) Processed 200000 reads 4:24:18.752 21G / 71G INFO General (sequence_mapper_notifier.h: 80) Processed 400000 reads 4:24:18.901 21G / 71G INFO General (sequence_mapper_notifier.h: 80) Processed 600000 reads 4:24:18.902 21G / 71G INFO General (sequence_mapper_notifier.h: 80) Processed 800000 reads 4:24:18.920 21G / 71G INFO General (sequence_mapper_notifier.h: 80) Processed 1000000 reads 4:24:18.932 21G / 71G INFO General (sequence_mapper_notifier.h: 80) Processed 1200000 reads 4:24:18.993 21G / 71G INFO General (sequence_mapper_notifier.h: 80) Processed 2200000 reads 4:24:19.181 21G / 71G INFO General (sequence_mapper_notifier.h: 80) Processed 4200000 reads 4:24:28.932 21G / 71G INFO General (sequence_mapper_notifier.h: 80) Processed 8400000 reads 4:24:38.059 21G / 71G INFO General (sequence_mapper_notifier.h: 80) Processed 16800000 reads 4:25:02.979 21G / 71G INFO General (sequence_mapper_notifier.h: 80) Processed 33600000 reads 4:25:53.583 21G / 71G INFO General (sequence_mapper_notifier.h: 80) Processed 67200000 reads 4:26:36.658 21G / 71G INFO General (sequence_mapper_notifier.h: 98) Total 105822607 reads processed 4:26:36.709 21G / 71G INFO StageManager (stage.cpp : 132) STAGE == Distance Estimation 4:26:36.709 21G / 71G INFO General (distance_estimation.cpp : 173) Processing library #0 4:26:36.709 21G / 71G INFO General (distance_estimation.cpp : 149) Weight Filter Done 4:26:36.709 21G / 71G INFO DistanceEstimator (distance_estimation.hpp : 116) Using SIMPLE distance estimator 4:26:39.684 21G / 71G INFO General (distance_estimation.cpp : 34) Filtering info 4:26:39.684 21G / 71G INFO General (pair_info_filters.hpp : 242) Start filtering; index size: 477400 4:26:40.208 21G / 71G INFO General (pair_info_filters.hpp : 263) Done filtering 4:26:40.208 21G / 71G INFO General (distance_estimation.cpp : 156) Refining clustered pair information 4:26:40.267 21G / 71G INFO General (distance_estimation.cpp : 158) The refining of clustered pair information has been finished 4:26:40.267 21G / 71G INFO General (distance_estimation.cpp : 160) Improving paired information 4:26:41.550 21G / 71G INFO PairInfoImprover (pair_info_improver.hpp : 103) Paired info stats: missing = 17749; contradictional = 10 4:26:43.023 21G / 71G INFO PairInfoImprover (pair_info_improver.hpp : 103) Paired info stats: missing = 3556; contradictional = 0 4:26:43.023 21G / 71G INFO General (distance_estimation.cpp : 103) Filling scaffolding index 4:26:43.023 21G / 71G INFO DistanceEstimator (distance_estimation.hpp : 116) Using SMOOTHING distance estimator 4:26:45.845 21G / 71G INFO General (distance_estimation.cpp : 34) Filtering info 4:26:45.845 21G / 71G INFO General (pair_info_filters.hpp : 242) Start filtering; index size: 111383 4:26:46.002 21G / 71G INFO General (pair_info_filters.hpp : 263) Done filtering 4:26:46.002 21G / 71G INFO General (distance_estimation.cpp : 182) Clearing raw paired index 4:26:46.560 21G / 71G INFO StageManager (stage.cpp : 132) STAGE == Repeat Resolving 4:26:46.560 21G / 71G INFO General (repeat_resolving.cpp : 69) Using Path-Extend repeat resolving 4:26:46.560 21G / 71G INFO General (launcher.cpp : 477) ExSPAnder repeat resolving tool started 4:26:47.152 21G / 71G INFO General (launcher.cpp : 392) Creating main extenders, unique edge length = 2000 4:26:47.152 21G / 71G INFO General (extenders_logic.cpp : 275) Estimated coverage of library #0 is 10.9268 4:26:47.190 21G / 71G INFO General (extenders_logic.cpp : 275) Estimated coverage of library #0 is 10.9268 4:26:47.366 21G / 71G INFO General (extenders_logic.cpp : 472) Using 1 paired-end library 4:26:47.366 21G / 71G INFO General (extenders_logic.cpp : 473) Using 1 paired-end scaffolding library 4:26:47.366 21G / 71G INFO General (extenders_logic.cpp : 474) Using 0 single read libraries 4:26:47.366 21G / 71G INFO General (launcher.cpp : 420) Total number of extenders is 3 4:26:47.366 21G / 71G INFO General (path_extender.hpp : 885) Processed 0 paths from 39952 (0%) 4:26:47.407 21G / 71G INFO General (path_extender.hpp : 883) Processed 128 paths from 39952 (0%) 4:26:47.458 21G / 71G INFO General (path_extender.hpp : 883) Processed 256 paths from 39952 (0%) 4:26:47.529 21G / 71G INFO General (path_extender.hpp : 883) Processed 512 paths from 39952 (1%) 4:26:47.631 21G / 71G INFO General (path_extender.hpp : 883) Processed 1024 paths from 39952 (2%) 4:26:47.814 21G / 71G INFO General (path_extender.hpp : 883) Processed 2048 paths from 39952 (5%) 4:26:48.097 21G / 71G INFO General (path_extender.hpp : 885) Processed 3996 paths from 39952 (10%) 4:26:48.108 21G / 71G INFO General (path_extender.hpp : 883) Processed 4096 paths from 39952 (10%) 4:26:48.758 21G / 71G INFO General (path_extender.hpp : 885) Processed 7992 paths from 39952 (20%) 4:26:48.784 21G / 71G INFO General (path_extender.hpp : 883) Processed 8192 paths from 39952 (20%) 4:26:49.422 21G / 71G INFO General (path_extender.hpp : 885) Processed 11988 paths from 39952 (30%) 4:26:50.019 21G / 71G INFO General (path_extender.hpp : 885) Processed 15984 paths from 39952 (40%) 4:26:50.067 21G / 71G INFO General (path_extender.hpp : 883) Processed 16384 paths from 39952 (41%) 4:26:50.632 21G / 71G INFO General (path_extender.hpp : 885) Processed 19980 paths from 39952 (50%) 4:26:51.648 21G / 71G INFO General (path_extender.hpp : 885) Processed 23976 paths from 39952 (60%) 4:26:52.468 21G / 71G INFO General (path_extender.hpp : 885) Processed 27972 paths from 39952 (70%) 4:26:53.306 21G / 71G INFO General (path_extender.hpp : 885) Processed 31968 paths from 39952 (80%) 4:26:53.460 21G / 71G INFO General (path_extender.hpp : 883) Processed 32768 paths from 39952 (82%) 4:26:54.076 21G / 71G INFO General (path_extender.hpp : 885) Processed 35964 paths from 39952 (90%) 4:26:55.821 21G / 71G INFO General (launcher.cpp : 234) Finalizing paths 4:26:55.821 21G / 71G INFO General (launcher.cpp : 236) Deduplicating paths 4:26:56.112 21G / 71G INFO General (launcher.cpp : 240) Paths deduplicated 4:26:56.112 21G / 71G INFO PEResolver (pe_resolver.hpp : 295) Removing overlaps 4:26:56.112 21G / 71G INFO PEResolver (pe_resolver.hpp : 298) Sorting paths 4:26:56.276 21G / 71G INFO PEResolver (pe_resolver.hpp : 305) Marking overlaps 4:26:56.276 21G / 71G INFO OverlapRemover (pe_resolver.hpp : 130) Marking start/end overlaps 4:26:56.418 21G / 71G INFO OverlapRemover (pe_resolver.hpp : 133) Marking remaining overlaps 4:26:56.578 21G / 71G INFO PEResolver (pe_resolver.hpp : 308) Splitting paths 4:26:56.600 21G / 71G INFO PEResolver (pe_resolver.hpp : 313) Deduplicating paths 4:26:56.696 21G / 71G INFO PEResolver (pe_resolver.hpp : 315) Overlaps removed 4:26:57.084 21G / 71G INFO General (launcher.cpp : 257) Paths finalized 4:26:57.085 21G / 71G INFO General (launcher.cpp : 427) Closing gaps in paths 4:26:57.842 21G / 71G INFO General (launcher.cpp : 455) Gap closing completed 4:26:58.051 21G / 71G INFO General (launcher.cpp : 286) Traversing tandem repeats 4:26:59.087 21G / 71G INFO General (launcher.cpp : 296) Traversed 1 loops 4:26:59.087 21G / 71G INFO General (launcher.cpp : 234) Finalizing paths 4:26:59.087 21G / 71G INFO General (launcher.cpp : 236) Deduplicating paths 4:26:59.156 21G / 71G INFO General (launcher.cpp : 240) Paths deduplicated 4:26:59.156 21G / 71G INFO PEResolver (pe_resolver.hpp : 295) Removing overlaps 4:26:59.156 21G / 71G INFO PEResolver (pe_resolver.hpp : 298) Sorting paths 4:26:59.258 21G / 71G INFO PEResolver (pe_resolver.hpp : 305) Marking overlaps 4:26:59.258 21G / 71G INFO OverlapRemover (pe_resolver.hpp : 130) Marking start/end overlaps 4:26:59.392 21G / 71G INFO OverlapRemover (pe_resolver.hpp : 133) Marking remaining overlaps 4:26:59.529 21G / 71G INFO PEResolver (pe_resolver.hpp : 308) Splitting paths 4:26:59.541 21G / 71G INFO PEResolver (pe_resolver.hpp : 313) Deduplicating paths 4:26:59.608 21G / 71G INFO PEResolver (pe_resolver.hpp : 315) Overlaps removed 4:26:59.920 21G / 71G INFO General (launcher.cpp : 257) Paths finalized 4:27:00.438 21G / 71G INFO General (launcher.cpp : 529) ExSPAnder repeat resolving tool finished 4:27:01.047 21G / 71G INFO StageManager (stage.cpp : 132) STAGE == Contig Output 4:27:01.047 21G / 71G INFO General (contig_output_stage.cpp : 40) Writing GFA to /local/genbank/workspace/reads.spadescorr.k77//K77/assembly_graph_with_scaffolds.gfa 4:27:03.933 21G / 71G INFO General (contig_output.hpp : 22) Outputting contigs to /local/genbank/workspace/reads.spadescorr.k77//K77/before_rr.fasta 4:27:08.902 21G / 71G INFO General (contig_output_stage.cpp : 51) Outputting FastG graph to /local/genbank/workspace/reads.spadescorr.k77//K77/assembly_graph.fastg 4:27:20.865 21G / 71G INFO General (contig_output_stage.cpp : 20) Outputting FastG paths to /local/genbank/workspace/reads.spadescorr.k77//K77/final_contigs.paths 4:27:27.254 21G / 71G INFO General (contig_output_stage.cpp : 20) Outputting FastG paths to /local/genbank/workspace/reads.spadescorr.k77//K77/scaffolds.paths 4:27:32.564 21G / 71G INFO General (launch.hpp : 149) SPAdes finished 4:30:36.884 140M / 71G INFO General (main.cpp : 109) Assembling time: 4 hours 30 minutes 36 seconds ===== Assembling finished. Used k-mer sizes: 77 * Assembled contigs are in /local/genbank/workspace/reads.spadescorr.k77/contigs.fasta * Assembled scaffolds are in /local/genbank/workspace/reads.spadescorr.k77/scaffolds.fasta * Assembly graph is in /local/genbank/workspace/reads.spadescorr.k77/assembly_graph.fastg * Assembly graph in GFA format is in /local/genbank/workspace/reads.spadescorr.k77/assembly_graph_with_scaffolds.gfa * Paths in the assembly graph corresponding to the contigs are in /local/genbank/workspace/reads.spadescorr.k77/contigs.paths * Paths in the assembly graph corresponding to the scaffolds are in /local/genbank/workspace/reads.spadescorr.k77/scaffolds.paths ======= SPAdes pipeline finished WITH WARNINGS! === Error correction and assembling warnings: * 1:49:56.505 11G / 18G WARN General (kmer_coverage_model.cpp : 366) Failed to determine erroneous kmer threshold. Threshold set to: 127 * 3:31:36.927 21G / 36G WARN General (simplification.cpp : 479) The determined erroneous connection coverage threshold may be determined improperly * 4:22:00.243 21G / 71G WARN General (pair_info_count.cpp : 358) Estimated mean insert size 293.009 is very small compared to read length 700 ======= Warnings saved to /local/genbank/workspace/reads.spadescorr.k77/warnings.log SPAdes log can be found here: /local/genbank/workspace/reads.spadescorr.k77/spades.log Thank you for using SPAdes!