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 99 -m 225 -t 32 -o /local/genbank/workspace/reads.spadescorr.k99 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.k99 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: [99] 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.k99/tmp Threads: 32 Memory limit (in Gb): 225 ======= SPAdes pipeline started. Log can be found here: /local/genbank/workspace/reads.spadescorr.k99/spades.log ===== Assembling started. == Running assembler: K99 0:00:00.000 4M / 4M INFO General (main.cpp : 74) Loaded config from /local/genbank/workspace/reads.spadescorr.k99/K99/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.k99/dataset.info) with K=99 0:00:00.001 4M / 4M INFO General (main.cpp : 90) Maximum # of threads to use (adjusted due to OMP capabilities): 32 0:00:00.001 4M / 4M INFO General (launch.hpp : 51) SPAdes started 0:00:00.001 4M / 4M INFO General (launch.hpp : 58) Starting from stage: construction 0:00:00.001 4M / 4M INFO General (launch.hpp : 65) Two-step RR enabled: 0 0:00:00.001 4M / 4M INFO General (launch.hpp : 76) Will need read mapping, kmer mapper will be attached 0:00:00.001 4M / 4M INFO StageManager (stage.cpp : 132) STAGE == de Bruijn graph construction 0:00:00.006 4M / 4M INFO General (read_converter.hpp : 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 0:00:00.565 76M / 76M INFO General (binary_converter.hpp : 93) 16384 reads processed 0:00:00.941 84M / 84M INFO General (binary_converter.hpp : 93) 32768 reads processed 0:00:01.702 104M / 104M INFO General (binary_converter.hpp : 93) 65536 reads processed 0:00:03.282 136M / 136M INFO General (binary_converter.hpp : 93) 131072 reads processed 0:00:06.323 208M / 208M INFO General (binary_converter.hpp : 93) 262144 reads processed 0:00:12.434 348M / 348M INFO General (binary_converter.hpp : 93) 524288 reads processed 0:00:28.435 564M / 564M INFO General (binary_converter.hpp : 93) 1048576 reads processed 0:00:57.293 616M / 616M INFO General (binary_converter.hpp : 93) 2097152 reads processed 0:01:54.982 620M / 620M INFO General (binary_converter.hpp : 93) 4194304 reads processed 0:04:04.590 872M / 876M INFO General (binary_converter.hpp : 93) 8388608 reads processed 0:08:44.652 956M / 956M INFO General (binary_converter.hpp : 93) 16777216 reads processed 0:18:05.179 916M / 956M INFO General (binary_converter.hpp : 93) 33554432 reads processed 0:36:21.406 696M / 956M INFO General (binary_converter.hpp : 93) 67108864 reads processed 0:56:19.373 636M / 956M INFO General (binary_converter.hpp : 117) 105822607 reads written 0:56:22.366 8M / 956M INFO General (read_converter.hpp : 87) Converting single reads 0:56:22.788 136M / 956M INFO General (binary_converter.hpp : 93) 16384 reads processed 0:56:22.917 140M / 956M INFO General (binary_converter.hpp : 93) 32768 reads processed 0:56:23.176 152M / 956M INFO General (binary_converter.hpp : 93) 65536 reads processed 0:56:23.699 168M / 956M INFO General (binary_converter.hpp : 93) 131072 reads processed 0:56:24.749 204M / 956M INFO General (binary_converter.hpp : 93) 262144 reads processed 0:56:26.856 276M / 956M INFO General (binary_converter.hpp : 93) 524288 reads processed 0:56:31.024 420M / 956M INFO General (binary_converter.hpp : 93) 1048576 reads processed 0:56:39.398 708M / 956M INFO General (binary_converter.hpp : 93) 2097152 reads processed 0:56:56.283 1G / 1G INFO General (binary_converter.hpp : 93) 4194304 reads processed 0:57:38.520 1G / 1G INFO General (binary_converter.hpp : 93) 8388608 reads processed 0:59:02.905 1G / 1G INFO General (binary_converter.hpp : 93) 16777216 reads processed 1:01:55.457 1G / 1G INFO General (binary_converter.hpp : 93) 33554432 reads processed 1:07:44.014 1G / 1G INFO General (binary_converter.hpp : 93) 67108864 reads processed 1:15:25.327 3G / 3G INFO General (binary_converter.hpp : 117) 99317237 reads written 1:15:33.565 16M / 3G INFO General (read_converter.hpp : 95) Converting merged reads 1:15:33.910 144M / 3G INFO General (binary_converter.hpp : 117) 0 reads written 1:15:35.963 12M / 3G INFO General (construction.cpp : 111) Max read length 700 1:15:35.963 12M / 3G INFO General (construction.cpp : 117) Average read length 77.5334 1:15:35.963 12M / 3G INFO General (stage.cpp : 101) PROCEDURE == k+1-mer counting 1:15:35.966 12M / 3G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 1024 files using 32 threads. This might take a while. 1:15:35.972 8M / 3G INFO General (file_limit.hpp : 32) Open file limit set to 4096 1:15:35.972 8M / 3G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.34367 Gb 1:15:35.972 8M / 3G INFO General (kmer_splitters.hpp : 97) Using cell size of 16384 1:17:01.198 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 197448570 reads 1:18:01.053 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 621924902 reads 1:18:01.054 17G / 18G INFO General (kmer_splitters.hpp : 295) Adding contigs from previous K 1:18:07.543 132M / 18G INFO General (kmer_splitters.hpp : 308) Used 621924902 reads 1:18:07.543 132M / 18G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 1:19:32.900 132M / 18G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 275712644 kmers in total. 1:19:32.901 132M / 18G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 1:21:16.756 128M / 18G INFO General (stage.cpp : 101) PROCEDURE == Extension index construction 1:21:16.758 128M / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 1:21:16.758 128M / 18G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 512 files using 32 threads. This might take a while. 1:21:16.760 128M / 18G INFO General (file_limit.hpp : 32) Open file limit set to 4096 1:21:16.760 128M / 18G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.34245 Gb 1:21:16.760 128M / 18G INFO General (kmer_splitters.hpp : 97) Using cell size of 32768 1:21:23.954 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 4420039 kmers 1:21:32.029 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 12979412 kmers 1:21:40.290 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 21589915 kmers 1:21:48.533 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 30202256 kmers 1:21:56.786 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 38826548 kmers 1:22:05.070 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 47432679 kmers 1:22:13.424 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 56052983 kmers 1:22:21.696 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 64669995 kmers 1:22:30.398 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 73283907 kmers 1:22:38.599 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 81895095 kmers 1:22:47.070 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 90514324 kmers 1:22:55.384 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 99136282 kmers 1:23:03.442 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 107739635 kmers 1:23:11.683 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 116350772 kmers 1:23:19.846 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 124964286 kmers 1:23:27.956 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 133586887 kmers 1:23:36.640 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 142205629 kmers 1:23:44.837 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 150827450 kmers 1:25:39.782 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 271460122 kmers 1:25:44.836 17G / 18G INFO General (kmer_splitters.hpp : 385) Used 275713668 kmers. 1:25:48.094 128M / 18G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 1:27:20.405 128M / 18G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 292774939 kmers in total. 1:27:20.405 128M / 18G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 1:29:10.045 128M / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 1:29:45.522 320M / 18G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 1:31:18.625 320M / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 135768520 bytes occupied (3.70984 bits per kmer). 1:31:19.168 600M / 18G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 99) Building k-mer extensions from k+1-mers 1:31:36.718 600M / 18G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 103) Building k-mer extensions from k+1-mers finished. 1:31:36.726 600M / 18G INFO General (stage.cpp : 101) PROCEDURE == Condensing graph 1:31:36.921 600M / 18G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 355) Extracting unbranching paths 1:32:02.955 2G / 18G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 374) Extracting unbranching paths finished. 20369477 sequences extracted 1:32:17.894 2G / 18G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 310) Collecting perfect loops 1:32:24.165 2G / 18G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 343) Collecting perfect loops finished. 4 loops collected 1:33:05.357 8G / 18G INFO General (stage.cpp : 101) PROCEDURE == Filling coverage indices (PHM) 1:33:05.358 8G / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 1:33:05.358 8G / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 1:33:18.900 8G / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 127864472 bytes occupied (3.71008 bits per kmer). 1:33:20.373 9G / 18G INFO General (construction.cpp : 388) Collecting k-mer coverage information from reads, this takes a while. 1:33:55.144 9G / 18G INFO General (construction.cpp : 508) Filling coverage and flanking coverage from PHM 1:34:17.553 9G / 18G INFO General (construction.cpp : 464) Processed 32000000 edges 1:34:21.566 9G / 18G INFO General (construction.cpp : 464) Processed 40738947 edges 1:34:27.291 8G / 18G INFO StageManager (stage.cpp : 132) STAGE == EC Threshold Finding 1:34:27.301 8G / 18G INFO General (kmer_coverage_model.cpp : 181) Kmer coverage valley at: 78 1:34:27.301 8G / 18G INFO General (kmer_coverage_model.cpp : 201) K-mer histogram maximum: 80 1:34:27.301 8G / 18G INFO General (kmer_coverage_model.cpp : 237) Estimated median coverage: 81. Coverage mad: 2.9652 1:34:27.301 8G / 18G INFO General (kmer_coverage_model.cpp : 259) Fitting coverage model 1:34:27.559 8G / 18G INFO General (kmer_coverage_model.cpp : 295) ... iteration 2 1:34:28.035 8G / 18G INFO General (kmer_coverage_model.cpp : 295) ... iteration 4 1:34:28.897 8G / 18G INFO General (kmer_coverage_model.cpp : 295) ... iteration 8 1:34:30.554 8G / 18G INFO General (kmer_coverage_model.cpp : 295) ... iteration 16 1:34:34.609 8G / 18G INFO General (kmer_coverage_model.cpp : 295) ... iteration 32 1:34:47.098 8G / 18G INFO General (kmer_coverage_model.cpp : 295) ... iteration 64 1:34:50.928 8G / 18G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 17.1808. Fitted coverage std. dev: 2.40312 1:34:50.929 8G / 18G WARN General (kmer_coverage_model.cpp : 327) Valley value was estimated improperly, reset to 7 1:34:50.936 8G / 18G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 1 1:34:50.936 8G / 18G WARN General (kmer_coverage_model.cpp : 366) Failed to determine erroneous kmer threshold. Threshold set to: 7 1:34:50.936 8G / 18G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 19873661 1:34:50.936 8G / 18G INFO General (genomic_info_filler.cpp : 114) Failed to estimate mean coverage 1:34:50.936 8G / 18G INFO General (genomic_info_filler.cpp : 127) EC coverage threshold value was calculated as 7 1:34:50.936 8G / 18G INFO General (genomic_info_filler.cpp : 128) Trusted kmer low bound: 0 1:34:50.936 8G / 18G INFO StageManager (stage.cpp : 132) STAGE == Gap Closer 1:34:50.936 8G / 18G INFO General (graph_pack.hpp : 101) Index refill 1:34:50.943 8G / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 1:34:50.943 8G / 18G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 512 files using 32 threads. This might take a while. 1:34:50.946 8G / 18G INFO General (file_limit.hpp : 32) Open file limit set to 4096 1:34:50.946 8G / 18G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.25753 Gb 1:34:50.946 8G / 18G INFO General (kmer_splitters.hpp : 97) Using cell size of 32768 1:36:38.270 25G / 26G INFO General (edge_index_builders.hpp : 77) Processed 40738947 edges 1:36:38.271 25G / 26G INFO General (edge_index_builders.hpp : 82) Used 40738947 sequences. 1:36:44.015 8G / 26G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 1:38:04.203 8G / 26G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 275712644 kmers in total. 1:38:04.203 8G / 26G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 1:39:46.521 8G / 26G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 1:40:17.051 8G / 26G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 1:41:41.669 8G / 26G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 127856528 bytes occupied (3.70985 bits per kmer). 1:41:48.938 14G / 26G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while. 1:42:04.948 14G / 26G INFO General (edge_index.hpp : 92) Index refilled 1:42:04.970 14G / 26G INFO General (gap_closer.cpp : 159) Preparing shift maps 1:44:31.555 19G / 26G INFO General (gap_closer.cpp : 119) Processing paired reads (takes a while) 1:44:43.295 21G / 26G INFO General (gap_closer.cpp : 138) Used 105822607 paired reads 1:44:43.295 21G / 26G INFO General (gap_closer.cpp : 140) Merging paired indices 1:46:38.380 15G / 26G INFO GapCloser (gap_closer.cpp : 346) Closing short gaps 1:52:34.935 15G / 26G INFO GapCloser (gap_closer.cpp : 380) Closing short gaps complete: filled 52591 gaps after checking 799890 candidates 1:53:26.174 14G / 26G INFO StageManager (stage.cpp : 132) STAGE == Raw Simplification 1:53:27.897 8G / 26G INFO General (simplification.cpp : 128) PROCEDURE == InitialCleaning 1:53:27.898 8G / 26G INFO General (simplification.cpp : 68) Most init cleaning disabled since detected mean 0 was less than activation coverage 10 1:53:27.898 8G / 26G INFO Simplification (parallel_processing.hpp : 165) Running Self conjugate edge remover 1:53:33.917 8G / 26G INFO Simplification (parallel_processing.hpp : 167) Self conjugate edge remover triggered 0 times 1:53:33.917 8G / 26G INFO StageManager (stage.cpp : 132) STAGE == Simplification 1:53:33.917 8G / 26G INFO General (simplification.cpp : 357) Graph simplification started 1:53:33.917 8G / 26G INFO General (graph_simplification.hpp : 634) Creating parallel br instance 1:53:33.917 8G / 26G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 1 1:53:33.917 8G / 26G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 1:54:45.510 8G / 26G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 1088154 times 1:54:45.510 8G / 26G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 2:02:37.630 12G / 26G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 270573 times 2:02:37.630 12G / 26G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 2:02:44.602 12G / 26G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 2:02:44.602 12G / 26G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 2 2:02:44.602 12G / 26G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 2:02:45.417 12G / 26G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 5802 times 2:02:45.418 12G / 26G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 2:02:45.968 12G / 26G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 283 times 2:02:45.968 12G / 26G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 2:02:47.184 12G / 26G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 11389 times 2:02:47.184 12G / 26G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 3 2:02:47.184 12G / 26G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 2:02:47.328 12G / 26G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 1800 times 2:02:47.328 12G / 26G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 2:02:53.733 12G / 26G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 4896 times 2:02:53.733 12G / 26G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 2:02:53.921 12G / 26G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 1316 times 2:02:53.921 12G / 26G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 4 2:02:53.921 12G / 26G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 2:02:53.952 12G / 26G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 175 times 2:02:53.952 12G / 26G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 2:02:54.666 12G / 26G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 630 times 2:02:54.666 12G / 26G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 2:02:54.734 12G / 26G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 604 times 2:02:54.734 12G / 26G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 5 2:02:54.734 12G / 26G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 2:02:54.740 12G / 26G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 34 times 2:02:54.740 12G / 26G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 2:02:55.052 12G / 26G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 231 times 2:02:55.052 12G / 26G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 2:02:55.119 12G / 26G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 443 times 2:02:55.119 12G / 26G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 6 2:02:55.119 12G / 26G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 2:02:55.123 12G / 26G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 28 times 2:02:55.123 12G / 26G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 2:02:55.358 12G / 26G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 186 times 2:02:55.358 12G / 26G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 2:02:55.384 12G / 26G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 222 times 2:02:55.384 12G / 26G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 7 2:02:55.384 12G / 26G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 2:02:55.385 12G / 26G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 6 times 2:02:55.385 12G / 26G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 2:02:55.473 12G / 26G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 71 times 2:02:55.473 12G / 26G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 2:02:55.490 12G / 26G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 144 times 2:02:55.490 12G / 26G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 8 2:02:55.490 12G / 26G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 2:02:55.490 12G / 26G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 3 times 2:02:55.490 12G / 26G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 2:02:55.541 12G / 26G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 54 times 2:02:55.542 12G / 26G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 2:02:55.553 12G / 26G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 100 times 2:02:55.553 12G / 26G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 9 2:02:55.553 12G / 26G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 2:02:55.553 12G / 26G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 3 times 2:02:55.553 12G / 26G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 2:02:55.574 12G / 26G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 20 times 2:02:55.574 12G / 26G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 2:02:55.584 12G / 26G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 91 times 2:02:55.584 12G / 26G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 10 2:02:55.584 12G / 26G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 2:02:55.585 12G / 26G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 3 times 2:02:55.585 12G / 26G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 2:02:55.625 12G / 26G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 23 times 2:02:55.625 12G / 26G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 2:02:55.631 12G / 26G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 56 times 2:02:55.631 12G / 26G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 11 2:02:55.631 12G / 26G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 2:03:01.479 12G / 26G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 85 times 2:03:01.479 12G / 26G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 2:03:05.471 12G / 26G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 32 times 2:03:05.471 12G / 26G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 2:03:09.010 12G / 26G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 1 times 2:03:09.010 12G / 26G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 12 2:03:09.010 12G / 26G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 2:03:09.010 12G / 26G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 2:03:09.010 12G / 26G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 2:03:09.010 12G / 26G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 2:03:09.010 12G / 26G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 2:03:09.010 12G / 26G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 2:03:09.011 12G / 26G INFO StageManager (stage.cpp : 132) STAGE == Gap Closer 2:03:09.011 12G / 26G INFO General (graph_pack.hpp : 101) Index refill 2:03:09.023 12G / 26G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 2:03:09.023 12G / 26G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 512 files using 32 threads. This might take a while. 2:03:09.025 12G / 26G INFO General (file_limit.hpp : 32) Open file limit set to 4096 2:03:09.025 12G / 26G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.21147 Gb 2:03:09.025 12G / 26G INFO General (kmer_splitters.hpp : 97) Using cell size of 32768 2:04:23.492 30G / 30G INFO General (edge_index_builders.hpp : 77) Processed 34610685 edges 2:04:23.492 30G / 30G INFO General (edge_index_builders.hpp : 82) Used 34610685 sequences. 2:04:28.506 12G / 30G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 2:05:25.488 12G / 30G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 190651371 kmers in total. 2:05:25.488 12G / 30G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 2:06:36.271 12G / 30G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 2:06:57.492 12G / 30G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 2:08:04.768 12G / 30G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 88413568 bytes occupied (3.70996 bits per kmer). 2:08:09.830 17G / 30G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while. 2:08:22.148 17G / 30G INFO General (edge_index.hpp : 92) Index refilled 2:08:22.171 17G / 30G INFO General (gap_closer.cpp : 159) Preparing shift maps 2:09:53.218 21G / 30G INFO General (gap_closer.cpp : 119) Processing paired reads (takes a while) 2:10:07.772 23G / 30G INFO General (gap_closer.cpp : 138) Used 105822607 paired reads 2:10:07.773 23G / 30G INFO General (gap_closer.cpp : 140) Merging paired indices 2:11:44.097 18G / 30G INFO GapCloser (gap_closer.cpp : 346) Closing short gaps 2:16:28.240 18G / 30G INFO GapCloser (gap_closer.cpp : 380) Closing short gaps complete: filled 931 gaps after checking 882254 candidates 2:16:52.915 17G / 30G INFO StageManager (stage.cpp : 132) STAGE == Simplification Cleanup 2:16:52.915 17G / 30G INFO General (simplification.cpp : 196) PROCEDURE == Post simplification 2:16:52.915 17G / 30G INFO General (graph_simplification.hpp : 453) Disconnection of relatively low covered edges disabled 2:16:52.915 17G / 30G INFO General (graph_simplification.hpp : 489) Complex tip clipping disabled 2:16:52.915 17G / 30G INFO General (graph_simplification.hpp : 634) Creating parallel br instance 2:16:52.915 17G / 30G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 2:17:00.080 17G / 30G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 2:17:00.080 17G / 30G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 2:17:04.151 17G / 30G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 2:17:04.151 17G / 30G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 2:17:09.094 17G / 30G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 2:17:09.094 17G / 30G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 2:17:14.696 17G / 30G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 2:17:14.696 17G / 30G INFO General (simplification.cpp : 330) Disrupting self-conjugate edges 2:18:36.911 17G / 30G INFO Simplification (parallel_processing.hpp : 165) Running Removing isolated edges 2:29:29.733 11G / 30G INFO Simplification (parallel_processing.hpp : 167) Removing isolated edges triggered 17267619 times 2:29:29.733 11G / 30G INFO General (simplification.cpp : 470) Counting average coverage 2:29:30.040 11G / 30G INFO General (simplification.cpp : 476) Average coverage = 5.76238 2:29:30.041 11G / 30G WARN General (simplification.cpp : 479) The determined erroneous connection coverage threshold may be determined improperly 2:29:30.041 11G / 30G INFO StageManager (stage.cpp : 132) STAGE == Mismatch Correction 2:29:30.041 11G / 30G INFO General (graph_pack.hpp : 109) Normalizing k-mer map. Total 58751180 kmers to process 2:31:10.742 11G / 30G INFO General (graph_pack.hpp : 111) Normalizing done 2:45:46.368 49G / 49G INFO General (mismatch_shall_not_pass.hp: 189) Finished collecting potential mismatches positions 2:52:30.573 12G / 49G INFO General (mismatch_shall_not_pass.hp: 290) All edges processed 2:52:39.472 11G / 49G INFO General (mismatch_correction.cpp : 27) Corrected 732 nucleotides 2:52:39.474 11G / 49G INFO StageManager (stage.cpp : 132) STAGE == Contig Output 2:52:39.474 11G / 49G INFO General (contig_output_stage.cpp : 40) Writing GFA to /local/genbank/workspace/reads.spadescorr.k99//K99/assembly_graph_with_scaffolds.gfa 2:52:42.630 11G / 49G INFO General (contig_output.hpp : 22) Outputting contigs to /local/genbank/workspace/reads.spadescorr.k99//K99/before_rr.fasta 2:52:46.730 11G / 49G INFO General (contig_output_stage.cpp : 51) Outputting FastG graph to /local/genbank/workspace/reads.spadescorr.k99//K99/assembly_graph.fastg 2:52:57.569 11G / 49G INFO General (contig_output.hpp : 22) Outputting contigs to /local/genbank/workspace/reads.spadescorr.k99//K99/simplified_contigs.fasta 2:53:01.345 11G / 49G INFO General (contig_output.hpp : 22) Outputting contigs to /local/genbank/workspace/reads.spadescorr.k99//K99/intermediate_contigs.fasta 2:53:04.974 11G / 49G INFO StageManager (stage.cpp : 132) STAGE == Paired Information Counting 2:53:05.509 11G / 49G INFO General (graph_pack.hpp : 109) Normalizing k-mer map. Total 58865224 kmers to process 2:55:20.718 11G / 49G INFO General (graph_pack.hpp : 111) Normalizing done 2:55:21.198 11G / 49G INFO General (pair_info_count.cpp : 320) Min edge length for estimation: 3057 2:55:21.198 11G / 49G INFO General (pair_info_count.cpp : 331) Estimating insert size for library #0 2:55:21.198 11G / 49G INFO General (pair_info_count.cpp : 190) Estimating insert size (takes a while) 2:55:23.136 12G / 49G INFO General (pair_info_count.cpp : 39) Selecting usual mapper 2:55:30.132 12G / 49G INFO General (sequence_mapper_notifier.h: 80) Processed 200000 reads 2:55:30.211 12G / 49G INFO General (sequence_mapper_notifier.h: 80) Processed 400000 reads 2:55:30.296 12G / 49G INFO General (sequence_mapper_notifier.h: 80) Processed 600000 reads 2:55:30.381 12G / 49G INFO General (sequence_mapper_notifier.h: 80) Processed 800000 reads 2:55:30.567 12G / 49G INFO General (sequence_mapper_notifier.h: 80) Processed 1000000 reads 2:55:30.716 12G / 49G INFO General (sequence_mapper_notifier.h: 80) Processed 1200000 reads 2:55:31.681 12G / 49G INFO General (sequence_mapper_notifier.h: 80) Processed 2200000 reads 2:55:33.647 12G / 49G INFO General (sequence_mapper_notifier.h: 80) Processed 4200000 reads 2:55:36.564 12G / 49G INFO General (sequence_mapper_notifier.h: 80) Processed 8400000 reads 2:55:47.959 12G / 49G INFO General (sequence_mapper_notifier.h: 80) Processed 16800000 reads 2:56:05.819 12G / 49G INFO General (sequence_mapper_notifier.h: 80) Processed 33600000 reads 2:56:47.819 12G / 49G INFO General (sequence_mapper_notifier.h: 80) Processed 67200000 reads 2:57:38.653 12G / 49G INFO General (sequence_mapper_notifier.h: 98) Total 105822607 reads processed 2:57:39.825 12G / 49G INFO General (pair_info_count.cpp : 209) Edge pairs: 67108864 (rough upper limit) 2:57:39.825 12G / 49G INFO General (pair_info_count.cpp : 213) 68058 paired reads (0.0643133% of all) aligned to long edges 2:57:40.034 11G / 49G INFO General (pair_info_count.cpp : 354) Insert size = 286.59, deviation = 74.8264, left quantile = 193, right quantile = 389, read length = 700 2:57:40.034 11G / 49G WARN General (pair_info_count.cpp : 358) Estimated mean insert size 286.59 is very small compared to read length 700 2:57:40.328 12G / 49G INFO General (pair_info_count.cpp : 371) Filtering data for library #0 2:57:40.386 12G / 49G INFO General (pair_info_count.cpp : 39) Selecting usual mapper 2:57:48.081 12G / 49G INFO General (sequence_mapper_notifier.h: 80) Processed 200000 reads 2:57:48.102 12G / 49G INFO General (sequence_mapper_notifier.h: 80) Processed 400000 reads 2:57:48.117 12G / 49G INFO General (sequence_mapper_notifier.h: 80) Processed 600000 reads 2:57:48.132 12G / 49G INFO General (sequence_mapper_notifier.h: 80) Processed 800000 reads 2:57:48.170 12G / 49G INFO General (sequence_mapper_notifier.h: 80) Processed 1000000 reads 2:57:48.173 12G / 49G INFO General (sequence_mapper_notifier.h: 80) Processed 1200000 reads 2:57:48.229 12G / 49G INFO General (sequence_mapper_notifier.h: 80) Processed 2200000 reads 2:57:48.329 12G / 49G INFO General (sequence_mapper_notifier.h: 80) Processed 4200000 reads 2:57:57.696 12G / 49G INFO General (sequence_mapper_notifier.h: 80) Processed 8400000 reads 2:58:06.350 12G / 49G INFO General (sequence_mapper_notifier.h: 80) Processed 16800000 reads 2:58:31.645 12G / 49G INFO General (sequence_mapper_notifier.h: 80) Processed 33600000 reads 2:59:14.299 12G / 49G INFO General (sequence_mapper_notifier.h: 80) Processed 67200000 reads 3:00:00.835 12G / 49G INFO General (sequence_mapper_notifier.h: 98) Total 105822607 reads processed 3:00:00.837 12G / 49G INFO General (pair_info_count.cpp : 383) Mapping library #0 3:00:00.837 12G / 49G INFO General (pair_info_count.cpp : 385) Mapping paired reads (takes a while) 3:00:00.837 12G / 49G INFO General (pair_info_count.cpp : 289) Left insert size quantile 193, right insert size quantile 389, filtering threshold 2, rounding threshold 0 3:00:00.915 12G / 49G INFO General (pair_info_count.cpp : 39) Selecting usual mapper 3:00:08.761 12G / 49G INFO General (sequence_mapper_notifier.h: 80) Processed 200000 reads 3:00:08.804 12G / 49G INFO General (sequence_mapper_notifier.h: 80) Processed 400000 reads 3:00:08.808 12G / 49G INFO General (sequence_mapper_notifier.h: 80) Processed 600000 reads 3:00:08.818 12G / 49G INFO General (sequence_mapper_notifier.h: 80) Processed 800000 reads 3:00:08.824 12G / 49G INFO General (sequence_mapper_notifier.h: 80) Processed 1000000 reads 3:00:08.849 12G / 49G INFO General (sequence_mapper_notifier.h: 80) Processed 1200000 reads 3:00:08.901 12G / 49G INFO General (sequence_mapper_notifier.h: 80) Processed 2200000 reads 3:00:08.986 12G / 49G INFO General (sequence_mapper_notifier.h: 80) Processed 4200000 reads 3:00:16.130 12G / 49G INFO General (sequence_mapper_notifier.h: 80) Processed 8400000 reads 3:00:24.139 12G / 49G INFO General (sequence_mapper_notifier.h: 80) Processed 16800000 reads 3:00:50.531 12G / 49G INFO General (sequence_mapper_notifier.h: 80) Processed 33600000 reads 3:01:27.518 12G / 49G INFO General (sequence_mapper_notifier.h: 80) Processed 67200000 reads 3:02:05.383 12G / 49G INFO General (sequence_mapper_notifier.h: 98) Total 105822607 reads processed 3:02:05.478 11G / 49G INFO StageManager (stage.cpp : 132) STAGE == Distance Estimation 3:02:05.479 11G / 49G INFO General (distance_estimation.cpp : 173) Processing library #0 3:02:05.479 11G / 49G INFO General (distance_estimation.cpp : 149) Weight Filter Done 3:02:05.479 11G / 49G INFO DistanceEstimator (distance_estimation.hpp : 116) Using SIMPLE distance estimator 3:02:05.933 11G / 49G INFO General (distance_estimation.cpp : 34) Filtering info 3:02:05.934 11G / 49G INFO General (pair_info_filters.hpp : 242) Start filtering; index size: 79632 3:02:06.136 11G / 49G INFO General (pair_info_filters.hpp : 263) Done filtering 3:02:06.137 11G / 49G INFO General (distance_estimation.cpp : 156) Refining clustered pair information 3:02:06.149 11G / 49G INFO General (distance_estimation.cpp : 158) The refining of clustered pair information has been finished 3:02:06.149 11G / 49G INFO General (distance_estimation.cpp : 160) Improving paired information 3:02:06.549 11G / 49G INFO PairInfoImprover (pair_info_improver.hpp : 103) Paired info stats: missing = 2169; contradictional = 0 3:02:06.966 11G / 49G INFO PairInfoImprover (pair_info_improver.hpp : 103) Paired info stats: missing = 1251; contradictional = 0 3:02:06.966 11G / 49G INFO General (distance_estimation.cpp : 103) Filling scaffolding index 3:02:06.967 11G / 49G INFO DistanceEstimator (distance_estimation.hpp : 116) Using SMOOTHING distance estimator 3:02:07.216 11G / 49G INFO General (distance_estimation.cpp : 34) Filtering info 3:02:07.216 11G / 49G INFO General (pair_info_filters.hpp : 242) Start filtering; index size: 76382 3:02:07.334 11G / 49G INFO General (pair_info_filters.hpp : 263) Done filtering 3:02:07.335 11G / 49G INFO General (distance_estimation.cpp : 182) Clearing raw paired index 3:02:07.377 11G / 49G INFO StageManager (stage.cpp : 132) STAGE == Repeat Resolving 3:02:07.377 11G / 49G INFO General (repeat_resolving.cpp : 69) Using Path-Extend repeat resolving 3:02:07.377 11G / 49G INFO General (launcher.cpp : 477) ExSPAnder repeat resolving tool started 3:02:07.977 12G / 49G INFO General (launcher.cpp : 392) Creating main extenders, unique edge length = 2000 3:02:07.978 12G / 49G INFO General (extenders_logic.cpp : 275) Estimated coverage of library #0 is 5.76238 3:02:08.012 12G / 49G INFO General (extenders_logic.cpp : 275) Estimated coverage of library #0 is 5.76238 3:02:08.173 12G / 49G INFO General (extenders_logic.cpp : 472) Using 1 paired-end library 3:02:08.173 12G / 49G INFO General (extenders_logic.cpp : 473) Using 1 paired-end scaffolding library 3:02:08.173 12G / 49G INFO General (extenders_logic.cpp : 474) Using 0 single read libraries 3:02:08.173 12G / 49G INFO General (launcher.cpp : 420) Total number of extenders is 3 3:02:08.173 12G / 49G INFO General (path_extender.hpp : 885) Processed 0 paths from 36614 (0%) 3:02:08.202 12G / 49G INFO General (path_extender.hpp : 883) Processed 128 paths from 36614 (0%) 3:02:08.228 12G / 49G INFO General (path_extender.hpp : 883) Processed 256 paths from 36614 (0%) 3:02:08.270 12G / 49G INFO General (path_extender.hpp : 883) Processed 512 paths from 36614 (1%) 3:02:08.336 12G / 49G INFO General (path_extender.hpp : 883) Processed 1024 paths from 36614 (2%) 3:02:08.455 12G / 49G INFO General (path_extender.hpp : 883) Processed 2048 paths from 36614 (5%) 3:02:08.625 12G / 49G INFO General (path_extender.hpp : 885) Processed 3662 paths from 36614 (10%) 3:02:08.676 12G / 49G INFO General (path_extender.hpp : 883) Processed 4096 paths from 36614 (11%) 3:02:09.007 12G / 49G INFO General (path_extender.hpp : 885) Processed 7324 paths from 36614 (20%) 3:02:09.097 12G / 49G INFO General (path_extender.hpp : 883) Processed 8192 paths from 36614 (22%) 3:02:09.391 12G / 49G INFO General (path_extender.hpp : 885) Processed 10986 paths from 36614 (30%) 3:02:09.801 12G / 49G INFO General (path_extender.hpp : 885) Processed 14648 paths from 36614 (40%) 3:02:09.985 12G / 49G INFO General (path_extender.hpp : 883) Processed 16384 paths from 36614 (44%) 3:02:10.191 12G / 49G INFO General (path_extender.hpp : 885) Processed 18310 paths from 36614 (50%) 3:02:10.578 12G / 49G INFO General (path_extender.hpp : 885) Processed 21972 paths from 36614 (60%) 3:02:10.959 12G / 49G INFO General (path_extender.hpp : 885) Processed 25634 paths from 36614 (70%) 3:02:11.335 12G / 49G INFO General (path_extender.hpp : 885) Processed 29296 paths from 36614 (80%) 3:02:11.688 12G / 49G INFO General (path_extender.hpp : 883) Processed 32768 paths from 36614 (89%) 3:02:11.709 12G / 49G INFO General (path_extender.hpp : 885) Processed 32958 paths from 36614 (90%) 3:02:12.534 12G / 49G INFO General (launcher.cpp : 234) Finalizing paths 3:02:12.534 12G / 49G INFO General (launcher.cpp : 236) Deduplicating paths 3:02:12.700 12G / 49G INFO General (launcher.cpp : 240) Paths deduplicated 3:02:12.700 12G / 49G INFO PEResolver (pe_resolver.hpp : 295) Removing overlaps 3:02:12.700 12G / 49G INFO PEResolver (pe_resolver.hpp : 298) Sorting paths 3:02:12.779 12G / 49G INFO PEResolver (pe_resolver.hpp : 305) Marking overlaps 3:02:12.780 12G / 49G INFO OverlapRemover (pe_resolver.hpp : 130) Marking start/end overlaps 3:02:12.858 12G / 49G INFO OverlapRemover (pe_resolver.hpp : 133) Marking remaining overlaps 3:02:12.947 12G / 49G INFO PEResolver (pe_resolver.hpp : 308) Splitting paths 3:02:12.956 12G / 49G INFO PEResolver (pe_resolver.hpp : 313) Deduplicating paths 3:02:13.002 12G / 49G INFO PEResolver (pe_resolver.hpp : 315) Overlaps removed 3:02:13.401 12G / 49G INFO General (launcher.cpp : 257) Paths finalized 3:02:13.401 12G / 49G INFO General (launcher.cpp : 427) Closing gaps in paths 3:02:13.735 12G / 49G INFO General (launcher.cpp : 455) Gap closing completed 3:02:13.877 12G / 49G INFO General (launcher.cpp : 286) Traversing tandem repeats 3:02:14.467 12G / 49G INFO General (launcher.cpp : 296) Traversed 7 loops 3:02:14.467 12G / 49G INFO General (launcher.cpp : 234) Finalizing paths 3:02:14.467 12G / 49G INFO General (launcher.cpp : 236) Deduplicating paths 3:02:14.511 12G / 49G INFO General (launcher.cpp : 240) Paths deduplicated 3:02:14.511 12G / 49G INFO PEResolver (pe_resolver.hpp : 295) Removing overlaps 3:02:14.511 12G / 49G INFO PEResolver (pe_resolver.hpp : 298) Sorting paths 3:02:14.571 12G / 49G INFO PEResolver (pe_resolver.hpp : 305) Marking overlaps 3:02:14.571 12G / 49G INFO OverlapRemover (pe_resolver.hpp : 130) Marking start/end overlaps 3:02:14.649 12G / 49G INFO OverlapRemover (pe_resolver.hpp : 133) Marking remaining overlaps 3:02:14.731 12G / 49G INFO PEResolver (pe_resolver.hpp : 308) Splitting paths 3:02:14.736 12G / 49G INFO PEResolver (pe_resolver.hpp : 313) Deduplicating paths 3:02:14.786 12G / 49G INFO PEResolver (pe_resolver.hpp : 315) Overlaps removed 3:02:15.061 12G / 49G INFO General (launcher.cpp : 257) Paths finalized 3:02:15.335 12G / 49G INFO General (launcher.cpp : 529) ExSPAnder repeat resolving tool finished 3:02:15.622 12G / 49G INFO StageManager (stage.cpp : 132) STAGE == Contig Output 3:02:15.623 12G / 49G INFO General (contig_output_stage.cpp : 40) Writing GFA to /local/genbank/workspace/reads.spadescorr.k99//K99/assembly_graph_with_scaffolds.gfa 3:02:17.230 12G / 49G INFO General (contig_output.hpp : 22) Outputting contigs to /local/genbank/workspace/reads.spadescorr.k99//K99/before_rr.fasta 3:02:19.770 12G / 49G INFO General (contig_output_stage.cpp : 51) Outputting FastG graph to /local/genbank/workspace/reads.spadescorr.k99//K99/assembly_graph.fastg 3:02:27.658 12G / 49G INFO General (contig_output_stage.cpp : 20) Outputting FastG paths to /local/genbank/workspace/reads.spadescorr.k99//K99/final_contigs.paths 3:02:31.297 12G / 49G INFO General (contig_output_stage.cpp : 20) Outputting FastG paths to /local/genbank/workspace/reads.spadescorr.k99//K99/scaffolds.paths 3:02:36.190 12G / 49G INFO General (launch.hpp : 149) SPAdes finished 3:03:57.358 140M / 49G INFO General (main.cpp : 109) Assembling time: 3 hours 3 minutes 57 seconds ===== Assembling finished. Used k-mer sizes: 99 * Assembled contigs are in /local/genbank/workspace/reads.spadescorr.k99/contigs.fasta * Assembled scaffolds are in /local/genbank/workspace/reads.spadescorr.k99/scaffolds.fasta * Assembly graph is in /local/genbank/workspace/reads.spadescorr.k99/assembly_graph.fastg * Assembly graph in GFA format is in /local/genbank/workspace/reads.spadescorr.k99/assembly_graph_with_scaffolds.gfa * Paths in the assembly graph corresponding to the contigs are in /local/genbank/workspace/reads.spadescorr.k99/contigs.paths * Paths in the assembly graph corresponding to the scaffolds are in /local/genbank/workspace/reads.spadescorr.k99/scaffolds.paths ======= SPAdes pipeline finished WITH WARNINGS! === Error correction and assembling warnings: * 1:34:50.929 8G / 18G WARN General (kmer_coverage_model.cpp : 327) Valley value was estimated improperly, reset to 7 * 1:34:50.936 8G / 18G WARN General (kmer_coverage_model.cpp : 366) Failed to determine erroneous kmer threshold. Threshold set to: 7 * 2:29:30.041 11G / 30G WARN General (simplification.cpp : 479) The determined erroneous connection coverage threshold may be determined improperly * 2:57:40.034 11G / 49G WARN General (pair_info_count.cpp : 358) Estimated mean insert size 286.59 is very small compared to read length 700 ======= Warnings saved to /local/genbank/workspace/reads.spadescorr.k99/warnings.log SPAdes log can be found here: /local/genbank/workspace/reads.spadescorr.k99/spades.log Thank you for using SPAdes!